Revision: 1054 Author: kuprov Date: 06 February 2012 15:00:36 Message: Some corrections from Alexander. ---- Modified : /examples/dnp/dnp_solid_kb_third_order.m Revision: 1053 Author: kuprov Date: 06 February 2012 12:30:12 Message: Final set of examples for KB-averaged solid effect DNP simulation in reduced state spaces. ---- Modified : /examples/dnp/dnp_solid_kb_third_order.m Added : /examples/dnp/dnp_solid_kb_fourth_order.m Modified : /examples/dnp/dnp_solid_kb_second_order.m Revision: 1052 Author: kuprov Date: 06 February 2012 12:03:16 Message: Further work on bringing DNP examples up to the Spinach standard of readability. ---- Added : /examples/dnp/dnp_solid_kb_third_order.m Modified : /examples/dnp/dnp_solid_kb_second_order.m Revision: 1051 Author: kuprov Date: 06 February 2012 11:15:36 Message: Slowly going through Alexander's example files for solid effect DNP and documenting every step. ---- Added : /examples/dnp/dnp_solid_kb_second_order.m Modified : /examples/dnp/dnp_solid_bruteforce.m Revision: 1050 Author: luke Date: 27 January 2012 16:21:06 Message: Accidentally left the debug flag on. ---- Modified : /kernel/utilities/dec.m Revision: 1049 Author: luke Date: 27 January 2012 15:52:32 Message: Forgot to add in the parfor before committing last time. Also added some comments. ---- Modified : /kernel/utilities/dec.m Revision: 1048 Author: luke Date: 26 January 2012 17:09:56 Message: Minor improvements to dec(). ---- Modified : /kernel/utilities/dec.m Revision: 1046 Author: luke Date: 26 January 2012 10:09:46 Message: Minor changes to dec(). ---- Modified : /kernel/utilities/dec.m Revision: 1045 Author: kuprov Date: 25 January 2012 16:35:41 Message: Removed an old and ugly construction around the orientation arrays -- the orientation function no longer needs the spin system structure and no longer returns a cell when called with a single set of Euler angles. ---- Modified : /examples/dnp/dnp_solid_bruteforce.m Modified : /docs/3. Kernel functions.docx Modified : /examples/dmrg/dmrg_test_3.m Modified : /examples/nmr_solids/cross_polarization_test_1.m Modified : /examples/nmr_solids/cross_polarization_test_2.m Modified : /examples/nmr_solids/oc_quadrupole.m Modified : /exp/clip_hsqc.m Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/hsqc.m Modified : /exp/maryan.m Modified : /exp/pulse_acquire.m Modified : /kernel/analytics.m Modified : /kernel/equilibrium.m Modified : /kernel/hilbert_space/hs_equilibrium.m Modified : /kernel/orientation.m Revision: 1043 Author: luke Date: 25 January 2012 15:42:23 Message: Moving dec to main project repository. ---- Added : /kernel/utilities/dec.m Modified : /kernel/evolution.m Revision: 1042 Author: kuprov Date: 25 January 2012 15:11:06 Message: Updates to the documentation. I really really should sit down and write the bloody thing... :( ---- Modified : /docs/3. Kernel functions.docx Added : /docs/6. Internal tolerances.docx (Copy from path: /docs/internal_tolerances.docx, Revision, 1040) Deleted : /docs/internal_tolerances.docx Added : /docs/7. Pulse sequence parameters.docx (Copy from path: /docs/pulse sequence parameters.docx, Revision, 1040) Deleted : /docs/pulse sequence parameters.docx Revision: 1041 Author: kuprov Date: 25 January 2012 11:58:43 Message: A slight modification to the pulse shape reader -- it now checks for the downsampling accuracy. Also, some more installation notes. ---- Modified : /examples/dnp/dnp_solid_bruteforce.m Modified : /etc/read_wave.m Modified : /installation.txt Revision: 1040 Author: kuprov Date: 23 January 2012 09:28:10 Message: The first example of a solid effect DNP simulation using proper Spinach syntax - with T1/T2 relaxation theory option, coordinate specification for the dipole-dipole interactions, etc. ---- Added : /examples/dnp/dnp_solid_bruteforce.m Modified : /kernel/evolution.m Deleted : /examples/relaxation_theory/dnp_test_1.m Deleted : /examples/relaxation_theory/dnp_test_2.m Deleted : /examples/relaxation_theory/dnp_test_3.m Revision: 1039 Author: kuprov Date: 23 January 2012 07:48:13 Message: Cleaned up the liquid state DNP examples. Now moving Walter's solid effect algorithms from the top secret location into the main repository example set... ---- Added : /examples/dnp Added : /examples/dnp/dnp_liquid_1.m Added : /examples/dnp/dnp_liquid_2.m Added : /examples/dnp/dnp_liquid_3.m Deleted : /examples/long_lived_states Added : /examples/singlets (Copy from path: /examples/long_lived_states, Revision, 1033) Modified : /kernel/sle.m Revision: 1038 Author: kuprov Date: 23 January 2012 07:23:53 Message: Beta version of the PCS module -- adds pseudocontact shifts to nuclear Zeeman interactions on request. ---- Deleted : /kernel/pcs.m Added : /kernel/pseudocon.m (Copy from path: /kernel/pcs.m, Revision, 1037) Revision: 1037 Author: kuprov Date: 18 January 2012 17:36:32 Message: Very basic PCS function -- currently assumes the metal is at the origin. ---- Added : /kernel/pcs.m Revision: 1036 Author: kuprov Date: 17 January 2012 13:27:24 Message: Minor acceleration. The CG function now passes all tests to machine precision. ---- Modified : /kernel/utilities/clebsch_gordan.m Revision: 1035 Author: kuprov Date: 17 January 2012 13:20:12 Message: Another testing table for the CG coefficients. ---- Modified : /kernel/utilities/clebsch_gordan.m Modified : /examples/kernel_tests/clebsch_gordan/cg_test.m Deleted : /examples/kernel_tests/clebsch_gordan/cg_test_table.mat Added : /examples/kernel_tests/clebsch_gordan/cg_test_table_large.mat Added : /examples/kernel_tests/clebsch_gordan/cg_test_table_small.mat Revision: 1034 Author: kuprov Date: 17 January 2012 10:03:27 Message: Improved the accuracy of high-rank CG coefficients to machine precision and absorbed the special case function. ---- Modified : /kernel/utilities/clebsch_gordan.m Modified : /examples/kernel_tests/clebsch_gordan/cg_test.m Deleted : /kernel/utilities/clebsch_gordan_sle.m Revision: 1033 Author: kuprov Date: 07 January 2012 09:15:16 Message: A testing set for the CG coefficients. Removed the logfactorial path from the generic CG function -- numerical accuracy too low. ---- Modified : /kernel/utilities/clebsch_gordan.m Added : /examples/kernel_tests (Copy from path: /examples/kernel, Revision, 1032) Added : /examples/kernel_tests/clebsch_gordan Added : /examples/kernel_tests/clebsch_gordan/cg_test.m Added : /examples/kernel_tests/clebsch_gordan/cg_test_table.mat Deleted : /examples/kernel Added : /examples/kernel_tests/clebsch_gordan/cg_test_gen.m Added : /examples/kernel_tests/clebsch_gordan/cg_test_gen.nb Revision: 1032 Author: kuprov Date: 23 December 2011 19:32:11 Message: Slightly better printing for the Hamiltonian superoperator and the beginnings of an SLE test set. Plenty of disconnected subspaces detected by path tracing, actually... ---- Modified : /kernel/utilities/clebsch_gordan.m Added : /examples/sle Added : /examples/sle/test_case.m Modified : /kernel/h_superop.m Modified : /kernel/utilities/validate.m Revision: 1031 Author: kuprov Date: 23 December 2011 15:56:38 Message: A rewrite of the symbolic branch of the Clebsh-Gordan function -- makes use of a faster kind of exact arithmetic now. ---- Modified : /kernel/utilities/clebsch_gordan.m Revision: 1030 Author: kuprov Date: 22 December 2011 17:53:54 Message: A lot of further work on the SLE module. ---- Modified : /kernel/sle.m Modified : /kernel/utilities/clebsch_gordan.m Added : /kernel/utilities/clebsch_gordan_sle.m Deleted : /kernel/utilities/logfactorial.m Revision: 1029 Author: kuprov Date: 22 December 2011 15:21:09 Message: Hopefully, the final CG function -- runs gammaln() numerics for as long as double precision allows, switches to exact integer algebra otherwise. ---- Modified : /kernel/utilities/clebsch_gordan.m Revision: 1028 Author: kuprov Date: 22 December 2011 12:55:44 Message: A fix to the CG function using symbolic algebra. ---- Modified : /kernel/utilities/clebsch_gordan.m Revision: 1027 Author: kuprov Date: 21 December 2011 16:57:50 Message: Some more work on the SLE module. ---- Modified : /kernel/sle.m Modified : /kernel/utilities/logfactorial.m Revision: 1026 Author: kuprov Date: 20 December 2011 17:53:43 Message: State-of-the-art Clebsch-Gordan function using log-factorials to work around the double precision overflows for large values of indices. Pretty spectacular precision, if you ever computed CGCs for a living. ---- Modified : /kernel/utilities/clebsch_gordan.m Added : /kernel/utilities/logfactorial.m Revision: 1025 Author: kuprov Date: 20 December 2011 16:43:28 Message: Fast enough Clebsch-Gordan coefficient calculator using a factorial look-up table. ---- Modified : /kernel/sle.m Modified : /kernel/utilities/clebsch_gordan.m Revision: 1024 Author: kuprov Date: 20 December 2011 14:52:55 Message: Somewhat faster Wigner action generation. Still not fast enough, though... ---- Modified : /kernel/sle.m Modified : /kernel/utilities/lmn2lin.m Revision: 1023 Author: kuprov Date: 19 December 2011 17:26:09 Message: On second thought, reverted the Wigner function indexing to base one. What was appropriate for state enumeration (zero was "default" unit state) is not a good idea here. ---- Modified : /kernel/utilities/lmn2lin.m Modified : /kernel/utilities/lin2lmn.m Revision: 1022 Author: kuprov Date: 19 December 2011 16:54:02 Message: Switched the Wigner function enumerators to zero base indexing to match the conventions in the functions that deal with irreducible spherical tensors. ---- Modified : /kernel/utilities/lmn2lin.m Modified : /kernel/utilities/lin2lmn.m Revision: 1021 Author: kuprov Date: 19 December 2011 16:41:56 Message: Translator from linear indexing into L,M,N indexing for Wigner functions. Quite an exercise in array indexing, it must be said... :) ---- Added : /kernel/utilities/lin2lmn.m Revision: 1020 Author: kuprov Date: 19 December 2011 14:59:34 Message: Some bullet-proofing for the index translators -- internal double-checking is now performed and some more explanation was added to the header. ---- Modified : /kernel/utilities/lin2lm.m Modified : /kernel/utilities/lm2lin.m Revision: 1019 Author: kuprov Date: 19 December 2011 11:47:45 Message: Some auxiliary index transformation functions for the SLE module. ---- Modified : /kernel/sle.m Added : /kernel/utilities/lmn2lin.m Modified : /kernel/utilities/lm2lin.m Modified : /etc/axis_1d.m Revision: 1018 Author: kuprov Date: 17 December 2011 16:04:02 Message: A bit more efficient Wigner action generator... might have to pre-compute the bloody things and ship them with Spinach -- they are really slow to build. ---- Modified : /kernel/sle.m Revision: 1017 Author: kuprov Date: 08 December 2011 16:20:27 Message: Some more work on the SLE module. Veeeeeeeery slow -- various screens not implemented yet. ---- Modified : /kernel/sle.m Modified : /kernel/utilities/clebsch_gordan.m Modified : /kernel/utilities/krondelta.m Revision: 1016 Author: kuprov Date: 08 December 2011 14:50:01 Message: Clebsch-Gordan coefficients in the minimally expensive and minimally fussy (all factorials of negative numbers quietly flush the coefficient to zero) configuration. ---- Modified : /kernel/sle.m Added : /kernel/utilities/clebsch_gordan.m Revision: 1015 Author: kuprov Date: 06 December 2011 16:18:41 Message: Getting started with the SLE module... ---- Added : /kernel/sle.m Modified : /kernel/correlation.m Revision: 1014 Author: kuprov Date: 29 November 2011 10:47:08 Message: Minor checks and fixes on the DMRG module. ---- Modified : / Modified : /examples/dmrg/dmrg_test_1.m Modified : /kernel/dmrg/cito2mpo.m Modified : /kernel/dmrg/cits2mps.m Modified : /kernel/dmrg/mpo_compress.m Modified : /kernel/dmrg/mps2cits.m Modified : /kernel/dmrg/mps_compress.m Revision: 1013 Author: kuprov Date: 29 November 2011 10:33:18 Message: Some polishing for the DMRG examples. All attempts to get TEBD trajectories have run aground because of two problems: (a) Dimension explosion at the MPO-MPS product stage, (b) catastrophic loss of accuracy at long range even with very tight singular value cut-off. It does not appear that time-dependent DMRG/MPS is any good beyond a few initial time steps in general. ---- Modified : /examples/dmrg/dmrg_test_3.m Modified : /examples/dmrg/dmrg_test_1.m Modified : /examples/dmrg/dmrg_test_2.m Modified : /examples/dmrg/dmrg_test_4.m Modified : /examples/dmrg/dmrg_test_5.m Modified : /examples/dmrg/dmrg_test_6.m Revision: 1012 Author: kuprov Date: 24 November 2011 17:05:01 Message: A minor fix to diagnostic output of h_superop.m function. ---- Modified : /kernel/h_superop.m Revision: 1011 Author: kuprov Date: 23 November 2011 09:43:29 Message: Minor updates to the DMRG module. ---- Modified : /kernel/dmrg/cito2mpo.m Added : /kernel/dmrg/cits2mps.m (Copy from path: /kernel/dmrg/cist2mps.m, Revision, 1010) Modified : /kernel/dmrg/mps_compress.m Deleted : /kernel/dmrg/cist2mps.m Deleted : /kernel/dmrg/cist2spinach.m Added : /kernel/dmrg/cits2spinach.m (Copy from path: /kernel/dmrg/cist2spinach.m, Revision, 1010) Revision: 1010 Author: kuprov Date: 18 November 2011 11:00:43 Message: Some polishing for the DMRG module. ---- Modified : /kernel/dmrg/cito2mpo.m Added : /kernel/dmrg/mpo_compress.m (Copy from path: /kernel/dmrg/mpo_comp.m, Revision, 1009) Added : /kernel/dmrg/mps2cits.m (Copy from path: /kernel/dmrg/mps2cist.m, Revision, 1009) Added : /kernel/dmrg/mps_compress.m (Copy from path: /kernel/dmrg/mps_comp.m, Revision, 1009) Modified : /kernel/dmrg/cist2mps.m Modified : /kernel/dmrg/cist2spinach.m Modified : /kernel/create.m Modified : /kernel/dmrg/cito2spinach.m Modified : /kernel/dmrg/mpo2cito.m Deleted : /kernel/dmrg/mpo_comp.m Modified : /kernel/dmrg/mpo_x_mps.m Deleted : /kernel/dmrg/mps2cist.m Deleted : /kernel/dmrg/mps_comp.m Added : /kernel/dmrg/mps_scalar.m (Copy from path: /kernel/dmrg/mps_scp.m, Revision, 1009) Deleted : /kernel/dmrg/mps_scp.m Deleted : /kernel/dmrg/spinach2cist.m Modified : /kernel/dmrg/spinach2cito.m Added : /kernel/dmrg/spinach2cits.m (Copy from path: /kernel/dmrg/spinach2cist.m, Revision, 1009) Revision: 1009 Author: kuprov Date: 17 November 2011 21:41:41 Message: A bug fix to the MPS compression utility and the beginnings of an MPO-MPS product function. ---- Added : /kernel/dmrg/mpo_x_mps.m Modified : /kernel/dmrg/mps_comp.m Revision: 1008 Author: kuprov Date: 08 November 2011 22:47:35 Message: Compression utility for the matrix product operators. ---- Modified : /examples/dmrg/dmrg_test_6.m Added : /kernel/dmrg/mpo_comp.m Revision: 1007 Author: kuprov Date: 08 November 2011 22:33:51 Message: Full forward and backward translation with the new MPO indexing. ---- Added : /kernel/dmrg/mpo2cito.m Modified : /kernel/dmrg/mps2cist.m Revision: 1006 Author: kuprov Date: 08 November 2011 21:56:57 Message: Changed the indexing of matrix product operators. ---- Modified : /kernel/dmrg/cito2mpo.m Added : /kernel/dmrg/mps2cist.m (Copy from path: /kernel/dmrg/mp2ci.m, Revision, 1005) Added : /kernel/dmrg/mps_comp.m (Copy from path: /kernel/dmrg/compress_mps.m, Revision, 1005) Added : /kernel/dmrg/mps_scp.m (Copy from path: /kernel/dmrg/mp_scp.m, Revision, 1004) Deleted : /kernel/dmrg/compress_mps.m Deleted : /kernel/dmrg/mp2ci.m Deleted : /kernel/dmrg/mp_scp.m Revision: 1005 Author: kuprov Date: 08 November 2011 21:42:25 Message: Bug fixes and MPS compression utility. ---- Modified : /kernel/dmrg/cist2mps.m Added : /kernel/dmrg/compress_mps.m Modified : /kernel/dmrg/mp2ci.m Revision: 1004 Author: kuprov Date: 08 November 2011 19:19:14 Message: Scalar product and the generalized MP2CI transformation. ---- Deleted : /kernel/dmrg/mpo2cito.m Deleted : /kernel/dmrg/mps2cist.m Added : /kernel/dmrg/mp2ci.m (Copy from path: /kernel/dmrg/mpo2cito.m, Revision, 1002) Added : /kernel/dmrg/mp_scp.m Revision: 1003 Author: kuprov Date: 08 November 2011 18:18:53 Message: DMRG bug fix for spins higher than 1/2 and updates to examples to reflect new syntax. ---- Modified : /examples/dmrg/dmrg_test_3.m Modified : /examples/dmrg/dmrg_test_1.m Modified : /kernel/dmrg/cito2mpo.m Modified : /examples/dmrg/dmrg_test_2.m Modified : /examples/dmrg/dmrg_test_4.m Modified : /examples/dmrg/dmrg_test_5.m Added : /examples/dmrg/dmrg_test_6.m Modified : /kernel/dmrg/cist2mps.m Revision: 1002 Author: kuprov Date: 08 November 2011 18:00:48 Message: More infrastructure operations for the DMRG module. ---- Added : /kernel/dmrg/cito2mpo.m Added : /kernel/dmrg/cist2mps.m (Copy from path: /kernel/dmrg/cit2mps.m, Revision, 1000) Added : /kernel/dmrg/mpo2cito.m Added : /kernel/dmrg/mps2cist.m (Copy from path: /kernel/dmrg/mps2cit.m, Revision, 1000) Deleted : /kernel/dmrg/cit2mps.m Deleted : /kernel/dmrg/mps2cit.m Revision: 1001 Author: kuprov Date: 08 November 2011 16:29:55 Message: More infrastructure operations for the DMRG module. The Tensor Toolbox really made a difference. ---- Added : /kernel/dmrg/cist2spinach.m (Copy from path: /kernel/dmrg/cit2spinach.m, Revision, 1000) Added : /kernel/dmrg/cito2spinach.m Added : /kernel/dmrg/spinach2cist.m (Copy from path: /kernel/dmrg/spinach2cit.m, Revision, 1000) Added : /kernel/dmrg/spinach2cito.m Deleted : /kernel/dmrg/cit2spinach.m Deleted : /kernel/dmrg/spinach2cit.m Revision: 1000 Author: kuprov Date: 07 November 2011 22:30:25 Message: Some polishing to the new DMRG infrastructure. ---- Modified : /examples/dmrg/dmrg_test_3.m Modified : /examples/dmrg/dmrg_test_1.m Modified : /examples/dmrg/dmrg_test_2.m Modified : /examples/dmrg/dmrg_test_4.m Modified : /examples/dmrg/dmrg_test_5.m Deleted : /examples/dmrg/dmrg_test_6.m Modified : /kernel/create.m Modified : /kernel/dmrg/cit2mps.m Modified : /kernel/dmrg/mps2cit.m Modified : /kernel/dmrg/cit2spinach.m Modified : /kernel/dmrg/spinach2cit.m Deleted : /examples/dmrg/dmrg_test_7.m Deleted : /examples/dmrg/dmrg_test_8.m Deleted : /kernel/dmrg/exact_diag.m Deleted : /kernel/dmrg/random_mps.m Revision: 999 Author: kuprov Date: 07 November 2011 21:21:51 Message: A re-write of the DMRG module using Tensor Toolbox from Sandia Labs. Much cleaner indexing now. ---- Deleted : /kernel/dmrg/mps_compress.m Added : /kernel/dmrg/cit2mps.m Added : /kernel/dmrg/mps2cit.m Added : /kernel/dmrg/cit2spinach.m Added : /kernel/dmrg/spinach2cit.m Added : /kernel/dmrg/random_mps.m Deleted : /kernel/dmrg/ci2mpo.m Deleted : /kernel/dmrg/ci2mps.m Deleted : /kernel/dmrg/mps2ci.m Deleted : /kernel/dmrg/mps_add.m Deleted : /kernel/dmrg/pauli2mpo.m Revision: 998 Author: kuprov Date: 07 November 2011 15:34:34 Message: Further updates to the documentation. ---- Added : /docs/3. Kernel functions.docx (Copy from path: /docs/3. Kernel functionality.docx, Revision, 994) Modified : /docs/1. Input preparation.docx Modified : /docs/2. Basis set selection.docx Deleted : /docs/3. Kernel functionality.docx Revision: 997 Author: kuprov Date: 06 November 2011 23:26:32 Message: Some improvements to the documentation. ---- Modified : /docs/1. Input preparation.docx Modified : /etc/g03_parse.m Modified : /kernel/r_superop.m Revision: 996 Author: kuprov Date: 03 November 2011 21:45:28 Message: Final clean-up for the DMRG functions. They might not be of much use, but kernel is kernel. ---- Modified : /examples/dmrg/dmrg_test_3.m Modified : /kernel/dmrg/mps_compress.m Modified : /examples/dmrg/dmrg_test_2.m Modified : /examples/dmrg/dmrg_test_4.m Modified : /examples/dmrg/dmrg_test_5.m Modified : /examples/dmrg/dmrg_test_6.m Added : /examples/dmrg/dmrg_test_7.m Added : /examples/dmrg/dmrg_test_8.m Added : /kernel/dmrg/ci2mpo.m Modified : /kernel/dmrg/ci2mps.m Modified : /kernel/dmrg/mps2ci.m Modified : /kernel/dmrg/mps_add.m Added : /kernel/dmrg/pauli2mpo.m Revision: 995 Author: kuprov Date: 03 November 2011 19:06:11 Message: Some MPS examples for systems with relaxation where the high spin orders are kept down. The nnz for MPS goes down, but still remains of the same order as nnz of the Spinach state vector. It also became clear that adopting MPS would require me to re-write the entire history of magnetic resonance theory in mind-twisting tensor product notation. Whosoever is interested is at liberty to do this, but it will not be me. DMRG matter closed. ---- Modified : /examples/dmrg/dmrg_test_3.m Modified : /examples/dmrg/dmrg_test_2.m Modified : /examples/dmrg/dmrg_test_4.m Added : /examples/dmrg/dmrg_test_5.m Added : /examples/dmrg/dmrg_test_6.m Revision: 994 Author: kuprov Date: 01 November 2011 21:47:56 Message: Two more functions for the DMRG/MPS module. Turns out that the set of MPS states of a given structure is not closed under addition and addition itself has cubic scaling, because recompression is necessary. ---- Added : /kernel/dmrg/mps_compress.m Modified : /kernel/dmrg/ci2mps.m Added : /kernel/dmrg/mps_add.m Revision: 993 Author: kuprov Date: 01 November 2011 20:24:01 Message: Clean-up in the DMRG directory plus some extra statistics printed by ci2mps. ---- Modified : /kernel/dmrg/ci2mps.m Deleted : /kernel/dmrg/create_mps.m Deleted : /kernel/dmrg/mps2statevec.m Deleted : /kernel/dmrg/mps_bfgs.m Deleted : /kernel/dmrg/state_err.m Deleted : /kernel/dmrg/stretch_mps.m Revision: 992 Author: kuprov Date: 01 November 2011 16:32:10 Message: The anisotropic diffusion model for the relaxation module is fully tested and cleared for production calculations. ---- Modified : /docs/1. Input preparation.docx Modified : /kernel/r_superop.m Modified : /kernel/utilities/significant.m Revision: 991 Author: kuprov Date: 30 October 2011 23:16:36 Message: All Monte-Carlo tests check out -- the correlation function module is cleared for production calculations. ---- Modified : /examples/kernel/correlation_test_1.m Modified : /examples/kernel/correlation_test_2.m Added : /examples/kernel/correlation_test_3.m Revision: 990 Author: kuprov Date: 30 October 2011 22:47:56 Message: Bug found and quashed in the correlation function -- JHF was right about body-centered reference frame. An extra test function for the axial diffusion correlation function, that one is now fully tested. ---- Modified : /examples/kernel/correlation_test_1.m Added : /examples/kernel/correlation_test_2.m Modified : /kernel/utilities/correlation_function.m Revision: 989 Author: kuprov Date: 30 October 2011 20:54:30 Message: A very reassuring Monte-Carlo test for the isotropic rotational correlation function. Thinking about making this the default way to compute correlation functions, actually, this would avoid trusting a great deal of very dubious-looking literature... ---- Added : /examples/kernel/correlation_test_1.m Revision: 988 Author: kuprov Date: 28 October 2011 22:51:12 Message: A bug fix in the correlation function. ---- Modified : /kernel/utilities/correlation_function.m Revision: 987 Author: kuprov Date: 28 October 2011 22:39:16 Message: Some polishing for the new functionality in the relaxation theory module. ---- Modified : /kernel/create.m Modified : /kernel/r_superop.m Modified : /kernel/utilities/correlation_function.m Revision: 986 Author: kuprov Date: 28 October 2011 20:19:22 Message: Axial and anisotropic diffusion options implemented for the Redfield superoperator. Not tested yet, treat with extreme caution. ---- Modified : /kernel/utilities/validate.m Modified : /kernel/create.m Modified : /kernel/r_superop.m Modified : /kernel/utilities/correlation_function.m Revision: 985 Author: kuprov Date: 28 October 2011 17:59:22 Message: Kronecker's delta symbol. Shame on Matlab for not having it. ---- Added : /kernel/utilities/krondelta.m Revision: 984 Author: kuprov Date: 27 October 2011 21:43:41 Message: An extra DMRG test and some array clean-up elsewhere. DMRG still does not live up to the marketing. ---- Added : /examples/dmrg/dmrg_test_4.m Modified : /kernel/dmrg/ci2mps.m Revision: 983 Author: kuprov Date: 27 October 2011 20:40:33 Message: Two test case calculations on a typical NMR system, comparing Spinach state vector representation with MPS. So far, epic fail for MPS. ---- Added : /examples/dmrg/dmrg_test_3.m Modified : /examples/dmrg/dmrg_test_2.m Modified : /kernel/dmrg/ci2mps.m Added : /examples/molecules/wtphene.log Revision: 982 Author: kuprov Date: 27 October 2011 17:52:24 Message: Forward and backward translators between Spinach state vector space and MPS representations using SVD. ---- Modified : /kernel/dmrg/ci2mps.m Added : /kernel/dmrg/mps2ci.m Revision: 981 Author: kuprov Date: 27 October 2011 17:17:01 Message: Making progress with the DMRG/MPS module. Man, what a monstrously complicated formalism... ---- Added : /kernel/dmrg/ci2mps.m Added : /kernel/dmrg/mps_bfgs.m (Copy from path: /kernel/dmrg/mps.m, Revision, 980) Deleted : /kernel/dmrg/mps.m Revision: 980 Author: kuprov Date: 26 October 2011 19:56:00 Message: Some improvements to the DMRG module. ---- Modified : /examples/dmrg/dmrg_test_2.m Modified : /kernel/dmrg/mps.m Revision: 979 Author: kuprov Date: 26 October 2011 16:45:47 Message: Alternative indexing for the MPS tensor -- quite a bit faster now. ---- Added : /kernel/dmrg/create_mps.m Modified : /kernel/dmrg/mps2statevec.m Modified : /kernel/dmrg/state_err.m Modified : /kernel/dmrg/stretch_mps.m Modified : /kernel/dmrg/mps.m Deleted : /kernel/dmrg/cplx2reim.m Deleted : /kernel/dmrg/reim2cplx.m Deleted : /kernel/dmrg/stuff_mps.m Revision: 978 Author: kuprov Date: 25 October 2011 22:18:50 Message: BFGS optimization works. Big difference, dammit. :) ---- Modified : /kernel/dmrg/mps.m Revision: 977 Author: kuprov Date: 25 October 2011 22:12:23 Message: Sort of got the DMRG2CI transformation derivatives to work. There's likely some capacity for data re-use and acceleration, but that's future work. ---- Modified : /examples/dmrg/dmrg_test_2.m Modified : /kernel/dmrg/state_err.m Modified : /kernel/dmrg/mps.m Revision: 976 Author: kuprov Date: 25 October 2011 20:19:12 Message: A painfully slow, but working MPS transformation. ---- Added : /examples/dmrg/dmrg_test_2.m Added : /kernel/dmrg/state_err.m Added : /kernel/dmrg/mps.m Added : /kernel/dmrg/cplx2reim.m Added : /kernel/dmrg/reim2cplx.m Revision: 975 Author: kuprov Date: 25 October 2011 18:34:12 Message: Some infrastructure functions for MPS manipulation. ---- Added : /kernel/dmrg/mps2statevec.m Added : /kernel/dmrg/stretch_mps.m Added : /kernel/dmrg/stuff_mps.m Deleted : /kernel/dmrg/contract.m Revision: 974 Author: kuprov Date: 25 October 2011 15:12:03 Message: Minor fix. ---- Modified : /kernel/utilities/stepsize.m Revision: 973 Author: kuprov Date: 25 October 2011 15:09:52 Message: Switched the step size estimator to use the infinity-norm -- much faster now and probably more reliable. ---- Modified : /kernel/utilities/stepsize.m Revision: 972 Author: kuprov Date: 24 October 2011 22:38:58 Message: MPS contractor for the DMRG module. ---- Added : /kernel/dmrg/contract.m Revision: 971 Author: kuprov Date: 24 October 2011 22:02:08 Message: Minor fix to the contour plotter. ---- Modified : /etc/contour_plot.m Revision: 970 Author: kuprov Date: 17 October 2011 11:07:54 Message: Added the intermolecular / intramolecular switch to the kinetics options -- this controls the fate of multi-spin orders. ---- Modified : / Modified : /kernel/create.m Modified : /docs/1. Input preparation.docx Revision: 969 Author: kuprov Date: 17 October 2011 10:44:13 Message: Minor commits in preparation to expanding the relaxation and kinetics modules. ---- Modified : /examples/dmrg/dmrg_test_1.m Modified : /kernel/dmrg/exact_diag.m Modified : /examples/nmr/cosy45_rotanone.m Modified : /kernel/k_superop.m Modified : /kernel/optimal_control/wave_basis.m Revision: 968 Author: kuprov Date: 04 October 2011 12:13:02 Message: Slightly more informative messages in ZTE. ---- Modified : /kernel/zte.m Revision: 967 Author: kuprov Date: 04 October 2011 12:08:58 Message: Moved the ZTE disable switch inside the ZTE function -- it returns a unit projector if it finds itself disabled. ---- Modified : /kernel/zte.m Modified : /kernel/reduce.m Revision: 966 Author: kuprov Date: 04 October 2011 12:01:53 Message: A slightly more informative ZTE module -- makes it clear to the user what is being done. ---- Modified : /kernel/zte.m Revision: 965 Author: kuprov Date: 27 September 2011 11:30:53 Message: Starting to read up on DMRG and experiment with spin chains. So far, the good old Arnoldi method crunches just fine through a 20-spin chain in mere seconds. ---- Added : /examples/dmrg Added : /examples/dmrg/dmrg_test_1.m Added : /kernel/dmrg Added : /kernel/dmrg/exact_diag.m Revision: 964 Author: kuprov Date: 25 September 2011 14:25:28 Message: Minor fix to the examples - this version goes online. ---- Modified : /examples/nmr_solids/oc_quadrupole.m Modified : /etc/shift_iso.m Revision: 963 Author: kuprov Date: 24 September 2011 16:06:51 Message: Added an extra option to the contour plotter (user can choose to ignore positive or negative contours now). Removed DSS from HSQC until further testing is done. Removed explicit dilution and CLIP-HSQC example until such time as we find a neat isotope dilution algorithm. Tidied up the plotting in the two HSQC examples. ---- Modified : /exp/hsqc.m Modified : /installation.txt Modified : /etc/contour_plot.m Deleted : /examples/nmr/clip_hsqc_sucrose.m Modified : /examples/nmr/hsqc_strychnine.m Modified : /examples/nmr/hsqc_sucrose.m Revision: 962 Author: kuprov Date: 22 September 2011 15:50:09 Message: Assorted refinements in preparation for posting the new version online. ---- Modified : /etc/read_wave.m Modified : /kernel/r_superop.m Modified : /etc/data_processing/baseline.m Modified : /examples/kernel/symmetry_test_3.m Modified : /examples/long_lived_states/decoherence_bicyclopropylidene.m Added : /examples/molecules/benzoquinone.log (Copy from path: /examples/molecules/pbenzoquinone.log, Revision, 960) Deleted : /examples/molecules/pbenzoquinone.log Modified : /kernel/path_trace.m Modified : /kernel/utilities/tolerances.m Revision: 961 Author: kuprov Date: 22 September 2011 15:41:29 Message: Update to the correction utility for the isotropic couplings. ---- Added : /etc/shift_iso.m (Copy from path: /etc/fix_iso.m, Revision, 960) Modified : /examples/nmr/clip_hsqc_sucrose.m Deleted : /etc/fix_iso.m Revision: 960 Author: kuprov Date: 06 September 2011 16:17:56 Message: Updates to the Hilbert space module test files to reflect the calculations reported in the paper. ---- Modified : /installation.txt Modified : /examples/kernel/hilbert_space_test_2.m Modified : /examples/kernel/hilbert_space_test_3.m Modified : /kernel/hilbert_space/hs_evolution.m Modified : /kernel/utilities/hadm.m Revision: 959 Author: luke Date: 06 September 2011 15:37:32 Message: Minor change to hs_evolution to disable the obnoxious warning about parallel mtimes. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 958 Author: kuprov Date: 05 September 2011 16:06:08 Message: Returned the double-transpose algorithm as an option for the parallel evaluation of final states in the Hilbert space module. ---- Modified : /kernel/hilbert_space/hs_evolution.m Modified : /kernel/utilities/hadm.m Revision: 957 Author: luke Date: 05 September 2011 14:48:07 Message: Corrections to the isotropic chemical shifts of the sucrose HSQC-spectra based upon values given in Duker and Serianni, /Carbohydrate Research/, 1993. ---- Modified : /exp/hsqc.m Modified : /examples/nmr/clip_hsqc_sucrose.m Modified : /examples/nmr/hsqc_sucrose.m Added : /etc/fix_iso.m Revision: 956 Author: kuprov Date: 05 September 2011 10:49:05 Message: Replaced PDFs of published papers with DOI links. Much slimmer distribution now. ---- Deleted : /docs/published_papers/Paper 1 - state space restriction.pdf Added : /docs/published_papers/Paper 1 - state space restriction.url Deleted : /docs/published_papers/Paper 10 - accuracy analysis.pdf Added : /docs/published_papers/Paper 10 - accuracy analysis.url Added : /docs/published_papers/Paper 11 - optimal control.url Deleted : /docs/published_papers/Paper 2 - zero track elimination.pdf Added : /docs/published_papers/Paper 2 - zero track elimination.url Deleted : /docs/published_papers/Paper 3 - sequence benchmarking.pdf Added : /docs/published_papers/Paper 3 - sequence benchmarking.url Deleted : /docs/published_papers/Paper 4 - analytical gradients.pdf Added : /docs/published_papers/Paper 4 - analytical gradients.url Deleted : /docs/published_papers/Paper 5 - basis screening techniques.pdf Added : /docs/published_papers/Paper 5 - basis screening techniques.url Deleted : /docs/published_papers/Paper 6 - spinach program.pdf Added : /docs/published_papers/Paper 6 - spinach program.url Deleted : /docs/published_papers/Paper 7 - relaxation theory.pdf Added : /docs/published_papers/Paper 7 - relaxation theory.url Deleted : /docs/published_papers/Paper 8 - destination state screening.pdf Added : /docs/published_papers/Paper 8 - destination state screening.url Deleted : /docs/published_papers/Paper 9 - long-lived states.pdf Added : /docs/published_papers/Paper 9 - long-lived states.url Revision: 955 Author: kuprov Date: 04 September 2011 16:52:41 Message: Added Hadamard product function, added serial propagation options to the Hilbert space module, updated the installation instructions. ---- Modified : /installation.txt Modified : /kernel/hilbert_space/hs_evolution.m Added : /kernel/utilities/hadm.m Revision: 954 Author: kuprov Date: 02 September 2011 18:01:34 Message: Final version of the parallel Hilbert space propagation module. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 953 Author: luke Date: 02 September 2011 15:24:12 Message: A small function that removes spins from sys and inter has been added called kill_spins(), and clip_hsqc_sucrose() has been modified to take advantage of it. dilute() has been modified such that it no longer breaks when given symmetry input. ---- Modified : /etc/dilute.m Added : /etc/kill_spins.m Modified : /examples/nmr/clip_hsqc_sucrose.m Revision: 952 Author: kuprov Date: 01 September 2011 20:38:00 Message: Updates to Spinach documentation and cosmetic changes to reflect those updates in the code. ---- Modified : /docs/1. Input preparation.docx Deleted : /docs/internal tolerances.docx Added : /docs/internal_tolerances.docx (Copy from path: /docs/internal tolerances.docx, Revision, 950) Modified : /installation.txt Modified : /kernel/create.m Modified : /kernel/utilities/validate.m Revision: 951 Author: luke Date: 01 September 2011 15:44:30 Message: clip_hsqc() now propagates backwards from the detection state to the first gradient. This avoids having to propagate 4 rho_stacks through half the simulation and leads to a large acceleration in simulation time. Thanks go to Martin Koos for the idea. ---- Modified : /exp/clip_hsqc.m Revision: 950 Author: kuprov Date: 30 August 2011 10:50:09 Message: Added accuracy analysis paper to the doc stash. ---- Modified : /docs/published_papers/Paper 1 - state space restriction.pdf Added : /docs/published_papers/Paper 10 - accuracy analysis.pdf Modified : /docs/published_papers/Paper 7 - relaxation theory.pdf Revision: 949 Author: kuprov Date: 27 August 2011 22:35:12 Message: A bit more documentation for the Veshtort-Griffin pulses. ---- Modified : /kernel/pulse_shapes/vg_pulse.m Revision: 948 Author: kuprov Date: 23 August 2011 14:43:11 Message: An example of a Veshtort-Griffin selective pulse. ---- Added : /examples/nmr/shaped_pulse_vg.m Modified : /kernel/pulse_shapes/vg_pulse.m Revision: 947 Author: kuprov Date: 23 August 2011 14:22:37 Message: Veshtort-Griffin shaped pulses. ---- Added : /kernel/pulse_shapes Added : /kernel/pulse_shapes/vg_pulse.m Revision: 946 Author: kuprov Date: 20 August 2011 14:53:01 Message: Added a correlation order selection function working in a manner similar to the coherence order selection function. ---- Modified : /kernel/coherence.m Added : /kernel/correlation.m Revision: 945 Author: kuprov Date: 20 August 2011 14:44:37 Message: Cosmetic refinements to the relaxation superoperator module. ---- Modified : /kernel/r_superop.m Revision: 944 Author: kuprov Date: 14 August 2011 17:45:22 Message: Made benzoquinone a pulse-acquire example as well. ---- Added : /examples/esr/pulse_acquire_benzoquinone.m Revision: 943 Author: kuprov Date: 14 August 2011 16:40:31 Message: Final version of the selective pulse example. ---- Modified : /examples/optimal_control/selective_pulse_template.m Revision: 942 Author: kuprov Date: 14 August 2011 16:02:12 Message: Further refinements to the GRAPE module. ---- Deleted : /examples/optimal_control/basis_pulse_template.m Added : /examples/optimal_control/broadband_pulse_template.m (Copy from path: /examples/optimal_control/custom_pulse_template.m, Revision, 941) Deleted : /examples/optimal_control/custom_pulse_template.m Modified : /examples/optimal_control/magic_pulse_template.m Added : /examples/optimal_control/selective_pulse_template.m (Copy from path: /examples/optimal_control/basis_pulse_template.m, Revision, 941) Modified : /kernel/optimal_control/grape.m Modified : /kernel/optimal_control/weighted_target.m Revision: 941 Author: kuprov Date: 14 August 2011 14:28:26 Message: Major improvements to the GRAPE module. Better and more general examples. ---- Added : /examples/optimal_control/basis_pulse_template.m Deleted : /examples/optimal_control/broadband_pulse_template.m Deleted : /examples/optimal_control/broadband_pulse_template_ap.m Added : /examples/optimal_control/custom_pulse_template.m Modified : /examples/optimal_control/magic_pulse_template.m Deleted : /examples/optimal_control/state_transfer_example_1.m Deleted : /examples/optimal_control/state_transfer_example_2.m Deleted : /examples/optimal_control/universal_rotation_template.m Deleted : /examples/optimal_control/universal_rotation_xy_controls.m Modified : /kernel/optimal_control/grape.m Modified : /kernel/optimal_control/wave_basis.m Revision: 940 Author: kuprov Date: 14 August 2011 11:06:56 Message: A decent function returning an orthogonalized waveform basis for the optimal control module. ---- Added : /kernel/optimal_control/wave_basis.m Revision: 939 Author: kuprov Date: 14 August 2011 10:13:43 Message: Some improvements to the GRAPE function. ---- Modified : /etc/sim_pulse.m Deleted : /kernel/optimal_control/Grifin-like pulses.pdf Modified : /kernel/optimal_control/grape.m Modified : /kernel/optimal_control/weighted_target.m Revision: 938 Author: naum Date: 12 August 2011 10:39:19 Message: preliminary results "design of selective pulses" ---- Added : /kernel/optimal_control/Grifin-like pulses.pdf Revision: 937 Author: kuprov Date: 05 August 2011 10:37:39 Message: Final version of the SABRE parahydrogenation example. ---- Added : /examples/parahydrogen/sabre_pyridine.m (Copy from path: /examples/parahydrogen/singlet_transfer.m, Revision, 935) Deleted : /examples/parahydrogen/singlet_transfer.m Revision: 936 Author: kuprov Date: 04 August 2011 17:26:52 Message: Some improvements. ---- Modified : /etc/decouple.m Modified : /exp/pulse_acquire.m Revision: 935 Author: kuprov Date: 04 August 2011 17:25:04 Message: A neat little example of parahydrogen-induced polarization transfer -- matched the literature on the first try. I have a theory about the whole thing and about why the pattern is so resilient to a change in J-couplings. ---- Added : /examples/parahydrogen Added : /examples/parahydrogen/singlet_transfer.m Revision: 934 Author: kuprov Date: 04 August 2011 15:48:30 Message: Minor convenience update for the decoupler. ---- Modified : /etc/decouple.m Revision: 933 Author: kuprov Date: 03 August 2011 16:51:29 Message: Removed parallelization from Hilbert space trajectory calculation option -- could not find any way of implementing it that would not be terminally ugly. The interleaved propagation with compression may well have its day eventually, but we are not that desperate yet. ---- Deleted : /examples/kernel/hilbert_space_test_4.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 932 Author: kuprov Date: 03 August 2011 16:06:58 Message: Final state statistics done. ---- Modified : /examples/kernel/hilbert_space_test_2.m Revision: 931 Author: kuprov Date: 03 August 2011 15:40:21 Message: Observables statistics. ---- Modified : /examples/kernel/hilbert_space_test_3.m Revision: 930 Author: kuprov Date: 03 August 2011 11:49:42 Message: Test file for the trajectory type benchmark. ---- Modified : /examples/kernel/hilbert_space_test_4.m Revision: 929 Author: kuprov Date: 03 August 2011 11:30:57 Message: A slightly easier version of the trajectory type propagation in Hilbert space. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 928 Author: kuprov Date: 03 August 2011 10:38:09 Message: Final version of the observable type propagation in Hilbert space. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 927 Author: kuprov Date: 02 August 2011 17:56:45 Message: A cosmetic reshuffle of the final-state evolution function using spmd instead of parfor. ---- Modified : /examples/kernel/hilbert_space_test_2.m Modified : /kernel/hilbert_space/hs_evolution.m Modified : /kernel/utilities/clean_up.m Revision: 926 Author: kuprov Date: 02 August 2011 16:22:42 Message: Well, I don't know what one is supposed to smoke before coding parallel Matlab functions, but they do not sell it around here. Anyway, here's a less memory-hungry implementation of observable type propagation in Hilbert space. You will have to manually kill a silly warning in @codistributed/mtimes, see the installation notes. ---- Modified : /installation.txt Modified : /kernel/hilbert_space/hs_evolution.m Revision: 925 Author: kuprov Date: 02 August 2011 11:32:46 Message: Took the bandwidth reduction out of the Hilbert space propagation module -- doesn't seem to do much. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 924 Author: kuprov Date: 02 August 2011 10:27:36 Message: A weighted target function for the optimal control module. ---- Modified : /examples/esr/relaxation_fremy.m Modified : /examples/long_lived_states/decoherence_diacetylene.m Added : /kernel/optimal_control/weighted_target.m Revision: 923 Author: kuprov Date: 01 August 2011 17:37:31 Message: Some directory structure improvement. ---- Modified : /examples/kernel/equilibrium_state_test.m Modified : /installation.txt Deleted : /kernel/grape.m Added : /kernel/optimal_control Added : /kernel/optimal_control/cartesian2polar.m (Copy from path: /kernel/utils/cartesian2polar.m, Revision, 921) Added : /kernel/optimal_control/grape.m (Copy from path: /kernel/grape.m, Revision, 921) Added : /kernel/optimal_control/polar2cartesian.m (Copy from path: /kernel/utils/polar2cartesian.m, Revision, 921) Added : /kernel/utilities (Copy from path: /kernel/utils, Revision, 921) Deleted : /kernel/utilities/cartesian2polar.m Deleted : /kernel/utilities/polar2cartesian.m Deleted : /kernel/utils Revision: 922 Author: kuprov Date: 01 August 2011 17:27:35 Message: Updated the thermal equilibrium test file -- it now demonstrates full sync between state normalization in Hilbert and Liouville space. ---- Added : /examples/kernel/equilibrium_state_test.m (Copy from path: /examples/kernel/hilbert_space_test_5.m, Revision, 921) Deleted : /examples/kernel/hilbert_space_test_5.m Deleted : /examples/relaxation_theory/equilibrium_test_1.m Revision: 921 Author: kuprov Date: 01 August 2011 17:09:22 Message: Statistics on the observables run. ---- Modified : /examples/kernel/hilbert_space_test_3.m Revision: 920 Author: kuprov Date: 31 July 2011 20:06:23 Message: Following some false alarm complaints, removed the Hermitian property validation from the Hamiltonian superoperator function. ---- Modified : /kernel/h_superop.m Revision: 919 Author: kuprov Date: 31 July 2011 19:20:20 Message: Removed some scaffolding -- coherence flow is handled by analytics.m so a separate directory is not necessary. Removed the expv mex option, it seems to always be slower than the Matlab code. ---- Deleted : /etc/coherence_visualisation Modified : /kernel/hilbert_space/hs_evolution.m Deleted : /kernel/mex_files Modified : /kernel/utils/expv.m Revision: 918 Author: kuprov Date: 29 July 2011 15:45:25 Message: Preparing for the observable evolution test. ---- Modified : /examples/kernel/hilbert_space_test_2.m Modified : /examples/kernel/hilbert_space_test_3.m Revision: 917 Author: kuprov Date: 29 July 2011 15:35:11 Message: Final version of the final state parallelization benchmark, with statistics. ---- Modified : /examples/kernel/hilbert_space_test_2.m Revision: 916 Author: kuprov Date: 29 July 2011 13:31:55 Message: Some statistics update for the final state evaluation test. Still running... ---- Modified : /examples/kernel/hilbert_space_test_2.m Revision: 915 Author: kuprov Date: 28 July 2011 20:52:39 Message: A bug fix in one of the examples. ---- Modified : /examples/kernel/hilbert_space_test_2.m Revision: 914 Author: luke Date: 27 July 2011 12:33:13 Message: Bugfixes to dilute(). It's use means that many of the carbon peaks may be run and fitted separately in the CLIP-HSQC experiment. ---- Modified : /etc/dilute.m Modified : /examples/nmr/clip_hsqc_sucrose.m Revision: 913 Author: luke Date: 26 July 2011 13:42:16 Message: clip_hsqc() modified to make use of destination state screening at intermediate steps of the calculation. As only certain coherences are allowed through the coherence filters, only subspaces containing these certain coherences need be propagated in the prior propagation steps. ---- Modified : /etc/dilute.m Modified : /exp/clip_hsqc.m Modified : /kernel/coherence.m Revision: 912 Author: luke Date: 22 July 2011 17:37:49 Message: CLIP-HSQC added as an experiment type, along with an example demonstrating residual dipolar couplings. ---- Added : /examples/nmr/clip_hsqc_sucrose.m Added : /exp/clip_hsqc.m Modified : /exp/hsqc.m Modified : /kernel/utils/sphten2mat.m Revision: 911 Author: luke Date: 19 July 2011 16:03:57 Message: Or alternatively it was right the other way around. Sorry. ---- Modified : /examples/nmr/hsqc_strychnine.m Modified : /examples/nmr/hsqc_sucrose.m Revision: 910 Author: luke Date: 19 July 2011 14:33:26 Message: Avoid HSQC being reflected into the right quadrant. ---- Modified : /examples/nmr/hsqc_strychnine.m Modified : /examples/nmr/hsqc_sucrose.m Revision: 909 Author: luke Date: 19 July 2011 10:05:36 Message: Or rather, the strong coupling artefacts disappeared when I accidentally divided all the couplings by 3... ---- Modified : /etc/dilute.m Revision: 908 Author: luke Date: 18 July 2011 19:47:18 Message: The small antiphase components in the HSQC spectra turn out to be due to non-physical magnetization transfer between dilute 13C nuclei. A short script has been written to split the input into separate simulations, one for each 13C. It is very rough at the moment (it doesn't even take account of coordinates yet). ---- Added : /etc/dilute.m Modified : /examples/nmr/hsqc_strychnine.m Modified : /examples/nmr/hsqc_sucrose.m Revision: 907 Author: luke Date: 18 July 2011 16:10:36 Message: Echo-anti echo HSQC implemented. The real part of the signal now has an absorptive lineshape meaning narrower lines as compared to the previous code that used abs(). ---- Modified : /examples/nmr/hsqc_strychnine.m Modified : /examples/nmr/hsqc_sucrose.m Modified : /exp/hsqc.m Revision: 906 Author: luke Date: 18 July 2011 15:10:56 Message: DQF-COSY and NOESY are for some reason upside down (peaks are emissive rather than absorptive). The spectra have been given explicit negations to reflect this. ---- Modified : /examples/nmr/dqf_cosy_strychnine.m Modified : /examples/nmr/dqf_cosy_sucrose.m Modified : /examples/nmr/noesy_strychnine.m Modified : /examples/nmr/noesy_sucrose.m Revision: 905 Author: luke Date: 18 July 2011 14:38:52 Message: DQF-COSY spectra now in the correct quadrant. ---- Modified : /examples/nmr/dqf_cosy_strychnine.m Modified : /examples/nmr/dqf_cosy_sucrose.m Modified : /exp/dqf_cosy.m Revision: 904 Author: luke Date: 18 July 2011 11:10:12 Message: Forgot to add the slightly modified version of coherence(). One can now select specific coherences on specific spins. ---- Modified : /kernel/coherence.m Revision: 903 Author: luke Date: 18 July 2011 10:59:18 Message: Updated DQF_COSY. States hypercomplex detection added in order to give correctly phased lineshapes. Thanks to members of the Burkhard Luy group for pointing out the phasing problem and helping to find their cause. ---- Modified : /etc/axis_1d.m Modified : /examples/nmr/dqf_cosy_strychnine.m Modified : /examples/nmr/dqf_cosy_sucrose.m Modified : /exp/dqf_cosy.m Revision: 902 Author: kuprov Date: 17 July 2011 16:41:04 Message: An interesting experiment of trying to offload a tight inner loop into a Fortran MEX file. It looks like my dislike of compiled languages pays off - Fortran code (linked against Intel's MKL sparse BLAS) is marginally slower and takes twice as much memory. And, importantly, it takes the whole bloody weekend (instead of 15 minutes) to write. No more experiments with compiled languages. ---- Added : /kernel/mex_files Added : /kernel/mex_files/expv_core.f Added : /kernel/mex_files/expv_core.mexw64 Modified : /kernel/utils/expv.m Revision: 901 Author: kuprov Date: 15 July 2011 12:11:56 Message: A normalization test for the kernel and assorted improvements to the GRAPE module and optimal control templates. ---- Added : /examples/kernel/normalization_test_1.m Modified : /examples/optimal_control/magic_pulse_template.m Modified : /examples/optimal_control/universal_rotation_xy_controls.m Modified : /kernel/grape.m Revision: 900 Author: kuprov Date: 14 July 2011 13:43:06 Message: Improved the universal rotations example and removed the small matrix bypass from the step function -- expv is now always faster than expm. ---- Modified : /examples/optimal_control/universal_rotation_xy_controls.m Modified : /kernel/step.m Revision: 899 Author: kuprov Date: 14 July 2011 10:59:03 Message: Update to the magic pulse template to reflect the new normalization conventions. ---- Modified : /examples/optimal_control/magic_pulse_template.m Revision: 898 Author: kuprov Date: 14 July 2011 10:13:33 Message: This whole Krylov/Chebyshev business seems to be hot air -- just as with matrix exponentiation, the scaled-and-squared Taylor series is five times faster on the wall clock and just as accurate. Anyway, meet the shiny new expv function - ten lines of code. ---- Modified : /examples/optimal_control/magic_pulse_template.m Modified : /exp/dqf_cosy.m Modified : /kernel/equilibrium.m Modified : /kernel/step.m Modified : /kernel/utils/expv.m Revision: 897 Author: kuprov Date: 13 July 2011 21:18:11 Message: Minor fix. ---- Modified : /examples/esr/pulse_acquire_perfluoropyrene.m Revision: 896 Author: kuprov Date: 13 July 2011 21:13:19 Message: Some safety catches inside the new expv function. ---- Modified : /kernel/equilibrium.m Modified : /kernel/step.m Modified : /kernel/utils/expv.m Revision: 895 Author: kuprov Date: 13 July 2011 20:55:08 Message: Some finishing touches on and around the new expv function. ---- Modified : /kernel/equilibrium.m Modified : /kernel/utils/expv.m Modified : /kernel/utils/tolerances.m Revision: 894 Author: kuprov Date: 13 July 2011 20:19:57 Message: A much improved version of expv, now as fast and as accurate as Sidje's. Took some doing. :) ---- Modified : /etc/sim_pulse.m Modified : /kernel/step.m Modified : /kernel/utils/expv.m Modified : /kernel/zte.m Revision: 893 Author: kuprov Date: 13 July 2011 17:28:56 Message: Returned to the original expv -- the new one was very considerably slower. ---- Modified : /etc/sim_pulse.m Modified : /kernel/equilibrium.m Modified : /kernel/step.m Modified : /kernel/utils/expv.m Modified : /kernel/zte.m Revision: 892 Author: kuprov Date: 13 July 2011 17:18:28 Message: Streamlined Luke's DQF-COSY. ---- Modified : /exp/dqf_cosy.m Revision: 891 Author: kuprov Date: 13 July 2011 15:58:34 Message: Minor refinements to the new expv. ---- Modified : /kernel/utils/expv.m Revision: 890 Author: kuprov Date: 13 July 2011 15:52:10 Message: Killed the G-S procedure and used svd instead in expv. Much more accurate now. ---- Modified : /kernel/utils/expv.m Revision: 889 Author: kuprov Date: 13 July 2011 15:29:24 Message: Our own version of expv -- a lot clearer, but a bit slower at the moment. Working on it. ---- Modified : /etc/sim_pulse.m Modified : /kernel/equilibrium.m Modified : /kernel/step.m Modified : /kernel/utils/expv.m Modified : /kernel/zte.m Revision: 888 Author: luke Date: 13 July 2011 15:07:13 Message: DQF-COSY now uses an explicit double-quantum filter instead of phase-cycling. ---- Modified : /exp/dqf_cosy.m Revision: 887 Author: kuprov Date: 13 July 2011 09:51:03 Message: Documentation for the GRAPE module and Hannah's paper. ---- Added : /docs/published_papers/Paper 9 - long-lived states.pdf Modified : /kernel/grape.m Revision: 886 Author: kuprov Date: 12 July 2011 17:32:10 Message: Moved the two-spin singlet example into the long-lived states directory. ---- Added : /examples/long_lived_states/levitt_singlet.m (Copy from path: /examples/relaxation_theory/dd_test_2.m, Revision, 884) Modified : /examples/relaxation_theory/dd_test_2.m Deleted : /examples/relaxation_theory/dd_test_3.m Revision: 885 Author: kuprov Date: 12 July 2011 17:03:57 Message: State generation changed completely. Instead of trawling the state list, Spinach now multiplies a unit state by the corresponding left side product superoperator. This guarantees that the normalization of states always stays in sync with the normalization of operators. ---- Modified : /etc/singlet.m Modified : /exp/dqf_cosy.m Modified : /kernel/p_superop.m Modified : /kernel/statevec.m Modified : /kernel/utils/state.m Revision: 884 Author: hannah Date: 07 July 2011 10:21:39 Message: Changing gaussian files of molecule examples so consistent with SI of paper. ---- Deleted : /examples/molecules/benzoquinone.log Added : /examples/molecules/d4bicyclopropylidene.log Modified : /examples/molecules/napthalenetetrone.log Added : /examples/molecules/pbenzoquinone.log Revision: 883 Author: luke Date: 06 July 2011 11:07:33 Message: Made a change to residual() to avoid the matrix diagonalizations. The change assumes that the coupling matrices are symmetric. Also some minor changes in other functions. ---- Modified : /etc/residual.m Modified : /kernel/a_superop.m Modified : /kernel/utils/euler2wigner.m Modified : /kernel/utils/mat2sphten.m Revision: 882 Author: kuprov Date: 01 July 2011 16:14:07 Message: Minor fixes. ---- Modified : /etc/residual.m Modified : /kernel/create.m Revision: 881 Author: kuprov Date: 01 July 2011 15:55:05 Message: A function to compute residual interactions in liquid crystals (this one is pretty strongly limited to high-field NMR), an extension of HSQC to deal with partially ordered systems and an example of a two-spin system with an RDC. ---- Added : /etc/residual.m Added : /examples/rdc Added : /examples/rdc/rdc_test_1.m Modified : /exp/hsqc.m Modified : /kernel/utils/validate.m Revision: 880 Author: kuprov Date: 01 July 2011 14:30:23 Message: A loud warning to the effect that relaxing the system to thermal equilibrium overwrites unit state populations at the propagation stage. ---- Modified : /kernel/create.m Revision: 879 Author: kuprov Date: 01 July 2011 14:12:42 Message: Refinements to the path tracer and zero tracker -- orphan states are now treated more carefully in the path tracer and ZTE takes care to never drop the unit state track, even when it is not populated. ---- Modified : /kernel/path_trace.m Modified : /kernel/zte.m Revision: 878 Author: kuprov Date: 28 June 2011 23:33:21 Message: The create function would absorb the order matrix, if supplied, and print the RDC scaling factors on dipolar interactions, but would not take any action -- this RDC business is a muddy pool of special cases that probably needs to be isolated into a separate function until we finally find decent equations for full residual tensors. ---- Modified : /kernel/create.m Revision: 877 Author: kuprov Date: 28 June 2011 19:52:32 Message: A family of uniform triple-angle grids for RDC calculations. God bless Malcolm Levitt. ---- Added : /exp/grids/zcw_100.txt Added : /exp/grids/zcw_1154.txt Added : /exp/grids/zcw_144.txt Added : /exp/grids/zcw_200.txt Added : /exp/grids/zcw_300.txt Added : /exp/grids/zcw_3722.txt Added : /exp/grids/zcw_50.txt Added : /exp/grids/zcw_538.txt Added : /exp/grids/zcw_6044.txt Revision: 876 Author: kuprov Date: 27 June 2011 21:01:12 Message: Slightly more careful memory allocation in p_superop and a lot of disclaimers for the example simulations, making it clear that the DFT calculations were preformed in vacuum. ---- Modified : /examples/esr/endor_methyl.m Modified : /examples/esr/endor_nitroxide.m Modified : /examples/esr/endor_phenyl.m Modified : /examples/esr/eseem_methyl.m Modified : /examples/esr/eseem_nitroxide_15n.m Modified : /examples/esr/eseem_phenyl.m Modified : /examples/esr/pulse_acquire_chrysene.m Modified : /examples/esr/pulse_acquire_methyl.m Modified : /examples/esr/pulse_acquire_nitroxide.m Modified : /examples/esr/pulse_acquire_perfluoropyrene.m Modified : /examples/esr/pulse_acquire_phenyl.m Modified : /examples/esr/relaxation_nitroxide.m Modified : /examples/esr/relaxation_parafluorotoluene.m Modified : /examples/long_lived_states/decoherence_benzoquinone.m Modified : /examples/long_lived_states/decoherence_bicyclopropylidene.m Modified : /examples/long_lived_states/decoherence_diacetylene.m Modified : /examples/long_lived_states/decoherence_napthalenetetrone.m Modified : /examples/nmr/cosy90_strychnine.m Modified : /examples/nmr/cosy90_sucrose.m Modified : /examples/nmr/dqf_cosy_strychnine.m Modified : /examples/nmr/dqf_cosy_sucrose.m Modified : /examples/nmr/hetcor_strychnine.m Modified : /examples/nmr/hetcor_sucrose.m Modified : /examples/nmr/hmqc_strychnine.m Modified : /examples/nmr/hmqc_sucrose.m Modified : /examples/nmr/hsqc_strychnine.m Modified : /examples/nmr/hsqc_sucrose.m Modified : /examples/nmr/noesy_strychnine.m Modified : /examples/nmr/noesy_sucrose.m Modified : /examples/nmr/pulse_acquire_strychnine.m Modified : /examples/nmr/pulse_acquire_sucrose.m Modified : /examples/relaxation_theory/cross_relaxation.m Modified : /examples/relaxation_theory/dd_csa_test_2.m Modified : /exp/cosy.m Modified : /kernel/p_superop.m Revision: 875 Author: naum Date: 22 June 2011 14:37:43 Message: Some refinements to a GRAPE example. ---- Modified : /examples/optimal_control/broadband_pulse_template_ap.m Revision: 874 Author: kuprov Date: 21 June 2011 22:37:53 Message: Minor improvements to GRAPE related functions. ---- Modified : /kernel/grape.m Modified : /kernel/utils/cartesian2polar.m Modified : /kernel/utils/polar2cartesian.m Revision: 873 Author: naum Date: 21 June 2011 15:57:29 Message: A general function translating XY values and gradients into amplitude-phase values and gradients, and an example of waveform optimization with amplitude-phase variation including a hard amplitude ceiling and an average amplitude restraint. ---- Added : /examples/optimal_control/broadband_pulse_template_ap.m Added : /kernel/utils/cartesian2polar.m Added : /kernel/utils/polar2cartesian.m Revision: 872 Author: kuprov Date: 17 June 2011 17:58:00 Message: Modifications to the experiment files to reflect the passive rotation conventions. ---- Modified : /examples/kernel/rotations_test.m Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/maryan.m Modified : /exp/pulse_acquire.m Revision: 871 Author: kuprov Date: 16 June 2011 18:04:12 Message: On Stefan's advice, added warning messages to dcm2euler -- now prints a warning at 1e-6 tolerance violation and bombs out at 1e-2 tolerance violation. Also, unified the rotational conventions with EasySpin. ---- Modified : /examples/kernel/rotations_test.m Modified : /kernel/utils/dcm2euler.m Modified : /kernel/utils/dcm2wigner.m Modified : /kernel/utils/euler2dcm.m Modified : /kernel/utils/euler2wigner.m Revision: 870 Author: naum Date: 16 June 2011 16:14:42 Message: Added an example with XY control modulation, square restraints on the maximum amplitude and a non-linear restraint on the RMS RF power. A few bugs are fixed (guess of both signs needs to be provided and upper/lower bounds must be vectors of the same length as guess and never scalars). ---- Modified : /examples/optimal_control/broadband_pulse_template.m Modified : /examples/optimal_control/magic_pulse_template.m Modified : /examples/optimal_control/state_transfer_example_1.m Modified : /examples/optimal_control/state_transfer_example_2.m Modified : /examples/optimal_control/universal_rotation_template.m Added : /examples/optimal_control/universal_rotation_xy_controls.m Revision: 869 Author: naum Date: 16 June 2011 11:46:39 Message: Added fourth order central finite difference derivatives to the GRAPE module. No apparent difference from the second order -- the step is, it seems, well chosen. ---- Modified : /kernel/grape.m Revision: 868 Author: luke Date: 16 June 2011 11:28:35 Message: Altered hs_operator() to use kron-products of ISTs instead of calling hs_generators(). This means that a) only the operators that are needed are formed, which is better memorywise, and b) all T_{l,m} can now be generated in H-space using the same syntax as to operator() (obviously without the option of 'right' or 'left' sided operator). hs_hamiltonian() has been modified to take this greater simplicity into account. Need to implement some sort of caching to disc in order to prevent recomputation of already generated matrices though. ---- Modified : /kernel/hilbert_space/hs_hamiltonian.m Modified : /kernel/hilbert_space/hs_operator.m Revision: 867 Author: kuprov Date: 15 June 2011 16:50:18 Message: Modifications to the diagnostics utility to make it less ambiguous. ---- Modified : /etc/state_diagnostics.m Modified : /examples/long_lived_states/decoherence_diacetylene.m Revision: 866 Author: kuprov Date: 15 June 2011 16:29:45 Message: Added another long-lived state example file - on request from the Warren group. ---- Modified : /etc/state_diagnostics.m Added : /examples/long_lived_states/decoherence_diacetylene.m Added : /examples/molecules/diacetylene.log Revision: 865 Author: luke Date: 15 June 2011 10:38:19 Message: Small bug in hs_step(). ---- Modified : /kernel/hilbert_space/hs_step.m Revision: 864 Author: kuprov Date: 10 June 2011 13:49:12 Message: Moved dcm2euler and dcm2wigner into the kernel (now fully tested) and updated the rotations test file. ---- Deleted : /etc/dcm2euler.m Deleted : /etc/dcm2wigner.m Modified : /examples/kernel/rotations_test.m Added : /kernel/utils/dcm2euler.m (Copy from path: /etc/dcm2euler.m, Revision, 863) Added : /kernel/utils/dcm2wigner.m (Copy from path: /etc/dcm2wigner.m, Revision, 862) Revision: 863 Author: kuprov Date: 10 June 2011 12:18:08 Message: Clarified rotation conventions throughout the kernel and made it dead certain that the kernel rotation functions are all internally and mutually consistent. ---- Modified : /etc/dcm2euler.m Added : /examples/kernel/rotations_test.m Modified : /kernel/utils/euler2dcm.m Modified : /kernel/utils/euler2wigner.m Revision: 862 Author: kuprov Date: 09 June 2011 21:52:22 Message: Updated the Hamiltonians to use the new spherical tensor transformation function. All rotation and relaxation theory tests check out. Things are now considerably more systematic so far as rotations go. ---- Modified : /etc/quat2euler.m Modified : /kernel/h_superop.m Modified : /kernel/hilbert_space/hs_evolution.m Modified : /kernel/hilbert_space/hs_hamiltonian.m Modified : /kernel/spin.m Revision: 861 Author: kuprov Date: 09 June 2011 17:00:23 Message: Made some signs consistent as well. All literature results seen so far are self-contradictory, i.e. the result of the forward-backward transformation does not match the original matrix. ---- Modified : /kernel/utils/mat2sphten.m Modified : /kernel/utils/sphten2mat.m Revision: 860 Author: kuprov Date: 09 June 2011 16:22:46 Message: A self-consistent pair of transformations from 3x3 Cartesian notation into spherical tensor notation. ---- Modified : /kernel/utils/mat2sphten.m Added : /kernel/utils/sphten2mat.m Revision: 859 Author: naum Date: 09 June 2011 11:48:15 Message: Enabled multi-target optimization in the GRAPE module and added an example of a universal rotation pulse optimization. ---- Added : /examples/optimal_control/universal_rotation_template.m Modified : /kernel/grape.m Revision: 858 Author: kuprov Date: 08 June 2011 21:32:05 Message: Reverted all changes related to the dilution switch. Mixtures are a user-land problem -- the kernel only simulates well-defined spin systems. ---- Modified : /kernel/create.m Deleted : /kernel/utils/dilute.m Modified : /kernel/utils/validate.m Revision: 857 Author: kuprov Date: 08 June 2011 21:25:49 Message: It looks like we'll have to do the full-whack Wigner function treatments with RDC -- the available literature only reports special cases. In this spirit, starting off with a general Cartesian-to-Wigner transformation function. ---- Added : /kernel/utils/mat2sphten.m Revision: 856 Author: kuprov Date: 08 June 2011 15:59:38 Message: Refinements to the Optimal Control example set. ---- Modified : /examples/optimal_control/broadband_pulse_template.m Deleted : /examples/optimal_control/oc4_waveform.mat Deleted : /examples/optimal_control/oc5_waveform.mat Deleted : /examples/optimal_control/optimal_control_1.m Deleted : /examples/optimal_control/optimal_control_2.m Deleted : /examples/optimal_control/optimal_control_3.m Deleted : /examples/optimal_control/optimal_control_4.m Deleted : /examples/optimal_control/optimal_control_5.m Deleted : /examples/optimal_control/optimal_control_6.m Deleted : /examples/optimal_control/optimal_control_7.m Added : /examples/optimal_control/state_transfer_example_1.m (Copy from path: /examples/optimal_control/optimal_control_6.m, Revision, 855) Added : /examples/optimal_control/state_transfer_example_2.m (Copy from path: /examples/optimal_control/optimal_control_7.m, Revision, 855) Deleted : /examples/optimal_control/waveform.mat Revision: 855 Author: naum Date: 08 June 2011 15:31:40 Message: An extra optimal control example -- phase profile modulation under a user-specified amplitude profile. ---- Added : /examples/optimal_control/broadband_pulse_template.m Revision: 854 Author: kuprov Date: 07 June 2011 15:30:11 Message: Added a 'liquid_crystal' regime to the kernel. Not doing anything much yet, just there for future reference by secondary functions. ---- Modified : /kernel/create.m Modified : /kernel/utils/validate.m Revision: 853 Author: kuprov Date: 07 June 2011 14:45:52 Message: Got the kernel to respect the sys.dilute switch. ---- Modified : /kernel/create.m Modified : /kernel/utils/dilute.m Revision: 852 Author: kuprov Date: 07 June 2011 12:19:43 Message: Introduced a function to remove all couplings between spins that the user has declared as belonging to a dilute isotope, such as 13C. ---- Added : /kernel/utils/dilute.m Modified : /kernel/utils/validate.m Revision: 851 Author: kuprov Date: 06 June 2011 21:03:02 Message: A more serious go at the residual dipolar couplings. Stuff should now work out of the box if the order matrix is supplied. Now need to create switches for HSQC and such to disable decoupling in the indirect dimension, and we are all set so far as dipolar couplings are concerned. ---- Modified : /etc/axis_2d.m Modified : /kernel/create.m Deleted : /kernel/rdc.m Modified : /kernel/utils/summary.m Modified : /kernel/utils/validate.m Revision: 850 Author: kuprov Date: 05 June 2011 15:43:25 Message: Modified both CP examples to use absorptive state space boundary -- much better convergence with respect to the basis set size, although it is not clear how to set the damping rate (currently ad hoc). ---- Modified : /examples/nmr_solids/cross_polarization_test_1.m Modified : /examples/nmr_solids/cross_polarization_test_2.m Revision: 849 Author: kuprov Date: 05 June 2011 15:16:45 Message: Implemented boundary damping -- the highest spin orders in the basis are uniformly damped at the user-specified rate to simulate the "irreversible" loss of magnetization in the depths of (presumably very large) product space. This will likely improve the description of solid state systems where a lot of stuff gets populated, but barely anything ever gets back. ---- Modified : /kernel/r_superop.m Revision: 848 Author: kuprov Date: 05 June 2011 14:17:09 Message: Final commit before posting the new version online. ---- Modified : /examples/nmr_solids/cross_polarization_test_1.m Modified : /installation.txt Revision: 847 Author: kuprov Date: 04 June 2011 15:13:21 Message: Much nicer implementation of the singlet state examples -- actually avoids relaxation superoperator diagonalization this time, using preconditioned 'eigs' instead. ---- Modified : /examples/long_lived_states/decoherence_benzoquinone.m Added : /examples/long_lived_states/decoherence_bicyclopropylidene.m Modified : /examples/long_lived_states/decoherence_napthalenetetrone.m Deleted : /examples/long_lived_states/quantum_memory_test_3.m Deleted : /examples/long_lived_states/quantum_memory_test_4.m Added : /examples/molecules/bicyclopropylidene.log Revision: 846 Author: kuprov Date: 02 June 2011 22:06:21 Message: Final versions of the cross-polarization examples. Another case, unfortunately, of systems requiring huge basis sets and ridiculous amounts of memory -- more or less converged only with state space dimensions way over 1M in both systems. ---- Modified : /examples/nmr_solids/cross_polarization_test_1.m Modified : /examples/nmr_solids/cross_polarization_test_2.m Revision: 845 Author: kuprov Date: 02 June 2011 22:01:42 Message: Typo fix. ---- Deleted : /examples/long_lived_states/decoherence_naphthalentetrone.m Added : /examples/long_lived_states/decoherence_napthalenetetrone.m Deleted : /examples/molecules/naphthalenetetrone.log Added : /examples/molecules/napthalenetetrone.log Revision: 844 Author: kuprov Date: 02 June 2011 18:05:33 Message: Naphthalentetrone long-lived states example file. ---- Added : /examples/long_lived_states/decoherence_naphthalentetrone.m Deleted : /examples/long_lived_states/quantum_memory_test_2.m Added : /examples/molecules/naphthalenetetrone.log Revision: 843 Author: kuprov Date: 02 June 2011 17:57:36 Message: Some accuracy tweaking for the CP examples. ---- Modified : /examples/nmr_solids/cross_polarization_test_1.m Modified : /examples/nmr_solids/cross_polarization_test_2.m Revision: 842 Author: kuprov Date: 02 June 2011 16:26:15 Message: Another CP example with polyalanine proton bath supplied by Alex Nevzorov. Takes a pretty long time to run, even with 4-spin orders and the opportunities for reduction seem to be rather slim, unless we crank the drop level up for ZTE in the hope of dumping the body angle band around the magic angle isolines. ---- Added : /examples/nmr_solids/cross_polarization_test_2.m Revision: 841 Author: kuprov Date: 02 June 2011 16:06:21 Message: Fixed the cross-polarization example file. The result makes sense now. ---- Modified : /examples/nmr_solids/cross_polarization_test_1.m Revision: 840 Author: luke Date: 01 June 2011 11:48:02 Message: Correction of a minor typo. ---- Modified : /exp/endor.m Revision: 839 Author: kuprov Date: 31 May 2011 21:08:14 Message: Replaced one of the singlets examples with the actual real benzoquinone -- I guess people will come looking for it when Hannah's paper is published. ---- Added : /examples/long_lived_states (Copy from path: /examples/quantum_computing, Revision, 838) Added : /examples/long_lived_states/decoherence_benzoquinone.m (Copy from path: /examples/quantum_computing/quantum_memory_test_1.m, Revision, 838) Deleted : /examples/long_lived_states/quantum_memory_test_1.m Added : /examples/molecules/benzoquinone.log Deleted : /examples/quantum_computing Revision: 838 Author: kuprov Date: 31 May 2011 18:14:55 Message: Extensive clean-up of NMR examples. ---- Added : /examples/kernel/high_spin_test_1.m (Copy from path: /examples/nmr/high_spin_test_1.m, Revision, 835) Deleted : /examples/nmr/chem_test_1.m Deleted : /examples/nmr/chem_test_2.m Added : /examples/nmr/cosy45_rotanone.m (Copy from path: /examples/nmr/cosy_test_5.m, Revision, 835) Added : /examples/nmr/cosy90_derome.m (Copy from path: /examples/nmr/cosy_test_3.m, Revision, 835) Added : /examples/nmr/cosy90_rotanone.m (Copy from path: /examples/nmr/cosy_test_4.m, Revision, 835) Added : /examples/nmr/cosy90_strychnine.m (Copy from path: /examples/nmr/cosy_test_1.m, Revision, 835) Added : /examples/nmr/cosy90_sucrose.m (Copy from path: /examples/nmr/cosy_test_2.m, Revision, 835) Deleted : /examples/nmr/cosy_test_1.m Deleted : /examples/nmr/cosy_test_2.m Deleted : /examples/nmr/cosy_test_3.m Deleted : /examples/nmr/cosy_test_4.m Deleted : /examples/nmr/cosy_test_5.m Added : /examples/nmr/dqf_cosy_strychnine.m (Copy from path: /examples/nmr/dqf_cosy_test_1.m, Revision, 835) Added : /examples/nmr/dqf_cosy_sucrose.m (Copy from path: /examples/nmr/dqf_cosy_test_2.m, Revision, 835) Deleted : /examples/nmr/dqf_cosy_test_1.m Deleted : /examples/nmr/dqf_cosy_test_2.m Added : /examples/nmr/exchange_asymmetric.m (Copy from path: /examples/nmr/chem_test_2.m, Revision, 835) Added : /examples/nmr/exchange_symmetric.m (Copy from path: /examples/nmr/chem_test_1.m, Revision, 835) Added : /examples/nmr/hetcor_strychnine.m (Copy from path: /examples/nmr/hetcor_test_2.m, Revision, 835) Added : /examples/nmr/hetcor_sucrose.m (Copy from path: /examples/nmr/hetcor_test_1.m, Revision, 835) Deleted : /examples/nmr/hetcor_test_1.m Deleted : /examples/nmr/hetcor_test_2.m Deleted : /examples/nmr/high_spin_test_1.m Added : /examples/nmr/hmqc_strychnine.m (Copy from path: /examples/nmr/hmqc_test_2.m, Revision, 835) Added : /examples/nmr/hmqc_sucrose.m (Copy from path: /examples/nmr/hmqc_test_1.m, Revision, 835) Deleted : /examples/nmr/hmqc_test_1.m Deleted : /examples/nmr/hmqc_test_2.m Added : /examples/nmr/hsqc_strychnine.m (Copy from path: /examples/nmr/hsqc_test_2.m, Revision, 835) Added : /examples/nmr/hsqc_sucrose.m (Copy from path: /examples/nmr/hsqc_test_1.m, Revision, 835) Deleted : /examples/nmr/hsqc_test_1.m Deleted : /examples/nmr/hsqc_test_2.m Added : /examples/nmr/noesy_strychnine.m (Copy from path: /examples/nmr/noesy_test_1.m, Revision, 835) Added : /examples/nmr/noesy_sucrose.m (Copy from path: /examples/nmr/noesy_test_2.m, Revision, 835) Deleted : /examples/nmr/noesy_test_1.m Deleted : /examples/nmr/noesy_test_2.m Modified : /examples/nmr/pulse_acquire_rotanone.m Added : /examples/nmr/pulse_acquire_strychnine.m (Copy from path: /examples/nmr/pulse_acquire_test_1.m, Revision, 835) Added : /examples/nmr/pulse_acquire_sucrose.m (Copy from path: /examples/nmr/pulse_acquire_test_2.m, Revision, 835) Deleted : /examples/nmr/pulse_acquire_test_1.m Deleted : /examples/nmr/pulse_acquire_test_2.m Added : /examples/nmr/shaped_pulse_gaussian.m (Copy from path: /examples/nmr/shaped_pulse_test_1.m, Revision, 835) Added : /examples/nmr/shaped_pulse_q5.m (Copy from path: /examples/nmr/shaped_pulse_test_2.m, Revision, 835) Deleted : /examples/nmr/shaped_pulse_test_1.m Deleted : /examples/nmr/shaped_pulse_test_2.m Deleted : /examples/nmr/zero_field_1.m Deleted : /examples/nmr/zero_field_2.m Added : /examples/nmr/zero_field_methanol.m (Copy from path: /examples/nmr/zero_field_1.m, Revision, 835) Added : /examples/nmr/zero_field_pyridine.m (Copy from path: /examples/nmr/zero_field_2.m, Revision, 835) Revision: 837 Author: luke Date: 31 May 2011 16:54:08 Message: Attempt at the Hilbert space documentation. Probably relies too heavily on knowledge of previous sections in the documentation at the moment. ---- Modified : /docs/4. Hilbert space module.docx Revision: 836 Author: kuprov Date: 31 May 2011 16:51:54 Message: Final clean-up of the ESR examples. ---- Deleted : /examples/esr/eseem_14N.m Deleted : /examples/esr/eseem_15N.m Added : /examples/esr/eseem_nitroxide_14n.m (Copy from path: /examples/esr/eseem_14N.m, Revision, 835) Added : /examples/esr/eseem_nitroxide_15n.m (Copy from path: /examples/esr/eseem_15N.m, Revision, 835) Modified : /examples/esr/pulse_acquire_biaryl.m Added : /examples/esr/pulse_acquire_nitroxide.m (Copy from path: /examples/esr/solids_test_1.m, Revision, 835) Added : /examples/esr/relaxation_fremy.m (Copy from path: /examples/esr/relaxation_test_3.m, Revision, 835) Added : /examples/esr/relaxation_nitroxide.m (Copy from path: /examples/esr/relaxation_test_2.m, Revision, 835) Added : /examples/esr/relaxation_parafluoronitrobenzene.m (Copy from path: /examples/esr/relaxation_test_1.m, Revision, 835) Added : /examples/esr/relaxation_parafluorotoluene.m (Copy from path: /examples/esr/relaxation_test_4.m, Revision, 835) Deleted : /examples/esr/relaxation_test_1.m Deleted : /examples/esr/relaxation_test_2.m Deleted : /examples/esr/relaxation_test_3.m Deleted : /examples/esr/relaxation_test_4.m Deleted : /examples/esr/solids_test_1.m Revision: 835 Author: luke Date: 31 May 2011 16:11:31 Message: Phase cycling of the time-domain Mims ENDOR. ---- Modified : /exp/endor.m Revision: 834 Author: kuprov Date: 31 May 2011 16:09:52 Message: Merged the CW and Mims ENDOR versions. ---- Modified : /examples/esr/endor_benzoquinone.m Modified : /examples/esr/endor_methyl.m Modified : /examples/esr/endor_nitroxide.m Modified : /examples/esr/endor_phenyl.m Modified : /exp/endor.m Revision: 833 Author: kuprov Date: 31 May 2011 13:43:45 Message: A minor fix. ---- Modified : /examples/esr/endor_benzoquinone.m Revision: 832 Author: kuprov Date: 31 May 2011 12:17:02 Message: Some polishing for ENDOR. ---- Added : /examples/esr/endor_benzoquinone.m Modified : /examples/esr/endor_methyl.m Modified : /examples/esr/endor_nitroxide.m Modified : /examples/esr/endor_phenyl.m Modified : /exp/endor.m Revision: 831 Author: kuprov Date: 29 May 2011 17:53:38 Message: Some speed-up for the Gaussian log parser -- becomes important when you have to parse 10,000 logs in a DSF run. Decided also to leave Hilbert space sequences to the users: those who are smart enough to know the difference between Hilbert and Liouville space won't have any trouble writing Hilbert space pulse sequences for themselves. ---- Modified : /etc/g03_parse.m Deleted : /exp/hs_pulse_acquire.m Revision: 830 Author: kuprov Date: 29 May 2011 17:10:56 Message: Assorted improvements and fixes to the Hilbert space module. ---- Added : /exp/hs_pulse_acquire.m Modified : /kernel/a_superop.m Modified : /kernel/analytics.m Modified : /kernel/evolution.m Modified : /kernel/hilbert_space/hs_equilibrium.m Modified : /kernel/hilbert_space/hs_evolution.m Modified : /kernel/hilbert_space/hs_operator.m Modified : /kernel/hilbert_space/hs_step.m Revision: 829 Author: kuprov Date: 29 May 2011 10:58:04 Message: On request from the Weizmann Institute, reinstated the multicoil detection in the evolution function. ---- Modified : /kernel/evolution.m Revision: 828 Author: kuprov Date: 28 May 2011 18:41:06 Message: Another go at the documentation. Luke, could you please document the Hilbert space module? ---- Deleted : /docs/1. Input preparation manual.docx Added : /docs/1. Input preparation.docx (Copy from path: /docs/1. Input preparation manual.docx, Revision, 825) Modified : /docs/2. Basis set selection.docx Added : /docs/3. Kernel functionality.docx Added : /docs/4. Hilbert space module.docx Modified : /docs/developer_notes/architecture_overview.pdf Added : /docs/internal tolerances.docx (Copy from path: /docs/table_3 - tolerances.docx, Revision, 825) Added : /docs/pulse sequence parameters.docx (Copy from path: /docs/table_5 - sequence parameters.docx, Revision, 825) Deleted : /docs/table_3 - tolerances.docx Deleted : /docs/table_5 - sequence parameters.docx Modified : /installation.txt Revision: 827 Author: kuprov Date: 28 May 2011 17:33:49 Message: Added bandwidth reduction transformation to the Hilbert space evolution function. ---- Modified : /examples/kernel/hilbert_space_test_3.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 826 Author: kuprov Date: 28 May 2011 16:41:02 Message: A minor change to Gaussian parser to make it compatible with DSF code. A step function for the Hilbert space module. ---- Modified : /etc/g03_parse.m Modified : /kernel/hilbert_space/hs_equilibrium.m Added : /kernel/hilbert_space/hs_step.m (Copy from path: /kernel/step.m, Revision, 825) Revision: 825 Author: kuprov Date: 25 May 2011 15:44:21 Message: Ported Luke's equilibrium function. Note the upside-down magnetic field -- this is because E=-mu*B (note the minus), which spinach kernel has (through IK's omission) so far ignored. This will have to be ordered up at some point. ---- Added : /examples/kernel/hilbert_space_test_5.m Added : /kernel/hilbert_space/hs_equilibrium.m Revision: 824 Author: kuprov Date: 25 May 2011 14:30:14 Message: Used difference coding to reduce the thread communication overhead in the trajectory type call to hs_evolution. It looks like we are done with the parallelization here. It remains to be seen what the appropriate value is for the difference drop tolerance, the current value seems about right. ---- Modified : /examples/kernel/hilbert_space_test_4.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 823 Author: kuprov Date: 24 May 2011 21:36:49 Message: Implemented time-interleaved propagation for the trajectory type call to the evolution function -- since there are matrix multiplications all over the place anyway, we might just as well afford a longer propagator. Dumped the 3D sparse arrays (too slow + no longer necessary). Did not test the function (getting late), so needs some testing/debugging. ---- Modified : /kernel/hilbert_space/hs_evolution.m Deleted : /kernel/hilbert_space/ndSparse.m Revision: 822 Author: kuprov Date: 21 May 2011 19:56:53 Message: Bad news -- couldn't find any parallel implementation of the trajectory mode that would be even marginally faster than the serial calculation. Good news -- sparse 3D arrays are not that hard after all. ---- Modified : /kernel/hilbert_space/hs_evolution.m Added : /kernel/hilbert_space/ndSparse.m Revision: 821 Author: kuprov Date: 21 May 2011 18:43:03 Message: Parallel calculation of trajectories implemented to a first approximation. Not particularly good -- too much inter-thread communication in the recomposition stage. Needs some thinking about how to slice the arrays. ---- Modified : /etc/shaped_pulse.m Added : /examples/kernel/hilbert_space_test_4.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 820 Author: kuprov Date: 19 May 2011 17:46:04 Message: Enforced the latest version of Matlab in the parallel propagation module - even the 2010b does not appear to stomach our parallelization crusade. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 819 Author: kuprov Date: 19 May 2011 16:36:35 Message: Minor refinements. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 818 Author: luke Date: 19 May 2011 16:23:40 Message: Slice matrices to get rid of the MatLab warnings. ---- Modified : /kernel/hilbert_space/hs_evolution.m Revision: 817 Author: kuprov Date: 19 May 2011 16:11:35 Message: Got the observable type calculation to run marginally faster on 4 cores than the serial job... some memory-related polishing remains. ---- Added : /examples/kernel/hilbert_space_test_3.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 816 Author: kuprov Date: 19 May 2011 12:25:07 Message: Minimalist version of final-state Hilbert space propagation done. An attempt to implement path tracing has led to a horrifying 200-line monster, need to think about ways of putting it neatly. Krylov propagation probably pointless in Hilbert space -- density matrix has the same dimension as the propagator, so quadratic vs. cubic scaling argument does not apply. ---- Modified : /examples/kernel/hilbert_space_test_2.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 815 Author: kuprov Date: 19 May 2011 11:53:05 Message: Plain old parfor seems to be doing the same job faster. :( ---- Modified : /examples/kernel/hilbert_space_test_2.m Deleted : /examples/kernel/hs_gather.m Deleted : /kernel/hilbert_space/hs_distribute.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 814 Author: kuprov Date: 19 May 2011 11:17:35 Message: Got the parallel propagation on a 4-core box to be twice as fast as the serial propagation, at the cost of some very explicit parallel allocation routines (4 cores currently hard-wired). ---- Modified : /examples/kernel/hilbert_space_test_2.m Added : /examples/kernel/hs_gather.m Added : /kernel/hilbert_space/hs_distribute.m Modified : /kernel/hilbert_space/hs_evolution.m Revision: 813 Author: kuprov Date: 18 May 2011 17:49:06 Message: Parallel propagation to final state sort of works, but it is not clear what the benefits are... ---- Added : /examples/kernel/hilbert_space_test_2.m Modified : /kernel/hilbert_space/hs_evolution.m Modified : /kernel/hilbert_space/hs_hamiltonian.m Revision: 812 Author: kuprov Date: 18 May 2011 15:39:59 Message: Updated the generator caching module to also stockpile the raising and lowering operators, made the module quieter. Realized that "state" and "operator" are the same in Hilbert space, and so one needs just one function there. Got the first test (commutation) to pass. ---- Added : /examples/kernel/hilbert_space_test_1.m Modified : /kernel/h_superop.m Modified : /kernel/hilbert_space/hs_generators.m Added : /kernel/hilbert_space/hs_operator.m (Copy from path: /kernel/hilbert_space/hs_state.m, Revision, 811) Deleted : /kernel/hilbert_space/hs_state.m Revision: 811 Author: kuprov Date: 17 May 2011 20:50:13 Message: Beginnings of a properly systematic Hilbert space module with (courtesy of Luke) parallel time propagation. Probably won't work just yet -- lots of testing and expansion needed. ---- Modified : /examples/nmr/pulse_acquire_rotanone.m Deleted : /kernel/cache/generators_2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /kernel/h_operator.m Added : /kernel/hilbert_space Added : /kernel/hilbert_space/hs_evolution.m Added : /kernel/hilbert_space/hs_generators.m (Copy from path: /kernel/utils/generators.m, Revision, 810) Added : /kernel/hilbert_space/hs_hamiltonian.m (Copy from path: /kernel/h_operator.m, Revision, 810) Added : /kernel/hilbert_space/hs_state.m Deleted : /kernel/utils/generators.m Revision: 810 Author: kuprov Date: 16 May 2011 17:56:36 Message: Added the detection of non-interaction subsystems to the create script. From the kernel perspective, this is a user-land problem -- the user ought to be smart enough to simulate independent subsystems separately. ---- Modified : /examples/nmr/cosy_test_1.m Modified : /examples/nmr/cosy_test_2.m Modified : /examples/nmr/dqf_cosy_test_1.m Modified : /examples/nmr/dqf_cosy_test_2.m Modified : /kernel/create.m Revision: 809 Author: kuprov Date: 16 May 2011 17:04:45 Message: Miscellaneous commits before shifting the Hilbert space module over from dev. ---- Modified : /etc/ascii_export.m Modified : /etc/fftdiff.m Modified : /etc/g03_parse.m Modified : /etc/g03_to_spinach.m Modified : /etc/metric.m Deleted : /examples/esr/endor_15N.m Added : /examples/esr/endor_nitroxide.m (Copy from path: /examples/esr/endor_15N.m, Revision, 808) Modified : /exp/noesy.m Revision: 808 Author: luke Date: 09 May 2011 15:31:18 Message: Small bugfix. ---- Modified : /kernel/h_operator.m Revision: 807 Author: kuprov Date: 05 May 2011 15:53:37 Message: A cross-polarization example file for Alex Nevzorov. ---- Added : /examples/nmr_solids/cross_polarization_test_1.m Revision: 806 Author: luke Date: 04 May 2011 11:52:56 Message: Small bugfix to the stepsize() function. ---- Modified : /kernel/utils/stepsize.m Revision: 805 Author: kuprov Date: 04 May 2011 10:52:03 Message: Lots of clean-up and resilience improvements. ---- Modified : /examples/esr/eseem_14N.m Modified : /examples/esr/pulse_acquire_methyl.m Modified : /examples/esr/pulse_acquire_phenyl.m Deleted : /examples/nmr/large_scale_test_2.m Deleted : /examples/nmr/simpson_test_1.m Deleted : /examples/nmr/simpson_test_2.m Deleted : /examples/nmr/solids_test_1.m Deleted : /examples/nmr/solids_test_2.m Deleted : /examples/nmr/solids_test_3.m Deleted : /examples/nmr/solids_test_4.m Added : /examples/nmr_solids/simpson_test_1.m Added : /examples/nmr_solids/simpson_test_2.m Added : /examples/nmr_solids/solids_test_1.m Added : /examples/nmr_solids/solids_test_2.m Added : /examples/nmr_solids/solids_test_3.m Added : /examples/nmr_solids/solids_test_4.m Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/r_superop.m Modified : /kernel/utils/banner.m Modified : /kernel/utils/clean_up.m Modified : /kernel/utils/click.m Modified : /kernel/utils/combnk.m Modified : /kernel/utils/euler2dcm.m Modified : /kernel/utils/human2opspec.m Modified : /kernel/utils/irr_sph_ten.m Modified : /kernel/utils/ist_product_table.m Modified : /kernel/utils/lin2lm.m Modified : /kernel/utils/lm2lin.m Modified : /kernel/utils/negligible.m Modified : /kernel/utils/operator.m Modified : /kernel/utils/pad.m Modified : /kernel/utils/pauli.m Modified : /kernel/utils/scomponents.m Modified : /kernel/utils/significant.m Modified : /kernel/utils/simps.m Modified : /kernel/utils/sparse_to_csr.m Modified : /kernel/utils/stepsize.m Modified : /kernel/utils/symmetry_group.m Modified : /kernel/utils/tensor_analysis.m Modified : /kernel/utils/tolerances.m Modified : /kernel/utils/validate.m Revision: 804 Author: kuprov Date: 03 May 2011 11:07:38 Message: As per Luke's suggestion, a more memory-friendly sparse matrix construction in the T1,T2 option of the relaxation superoperator. ---- Modified : /kernel/r_superop.m Revision: 803 Author: kuprov Date: 01 May 2011 19:43:18 Message: Included all our published papers into the Spinach documentation folder -- this will save the users some looking up. ---- Deleted : /docs/published_papers/Paper 0 - zero track elimination.pdf Deleted : /docs/published_papers/Paper 1 - analytical gradients.pdf Added : /docs/published_papers/Paper 1 - state space restriction.pdf Deleted : /docs/published_papers/Paper 2 - sequence benchmarking.pdf Added : /docs/published_papers/Paper 2 - zero track elimination.pdf Deleted : /docs/published_papers/Paper 3 - densely coupled spin systems.pdf Added : /docs/published_papers/Paper 3 - sequence benchmarking.pdf Added : /docs/published_papers/Paper 4 - analytical gradients.pdf Deleted : /docs/published_papers/Paper 4 - spinach program.pdf Added : /docs/published_papers/Paper 5 - basis screening techniques.pdf Deleted : /docs/published_papers/Paper 5 - relaxation theory.pdf Deleted : /docs/published_papers/Paper 6 - destination state screening.pdf Added : /docs/published_papers/Paper 6 - spinach program.pdf Added : /docs/published_papers/Paper 7 - relaxation theory.pdf Added : /docs/published_papers/Paper 8 - destination state screening.pdf Revision: 802 Author: kuprov Date: 01 May 2011 19:39:25 Message: Another go at the documentation. ---- Modified : /docs/1. Input preparation manual.docx Modified : /docs/2. Basis set selection.docx Added : /docs/published_papers Added : /docs/published_papers/Paper 0 - zero track elimination.pdf Added : /docs/published_papers/Paper 1 - analytical gradients.pdf Added : /docs/published_papers/Paper 2 - sequence benchmarking.pdf Added : /docs/published_papers/Paper 3 - densely coupled spin systems.pdf Added : /docs/published_papers/Paper 4 - spinach program.pdf Added : /docs/published_papers/Paper 5 - relaxation theory.pdf Added : /docs/published_papers/Paper 6 - destination state screening.pdf Deleted : /docs/table_1 - spin system specification.docx Deleted : /docs/table_4 - state indexing.docx Revision: 801 Author: kuprov Date: 01 May 2011 17:40:10 Message: Another go at the documentation. ---- Modified : /docs/2. Basis set selection.docx Modified : /kernel/utils/generators.m Revision: 800 Author: kuprov Date: 30 April 2011 20:09:15 Message: Another go at the documentation. ---- Added : /docs/2. Basis set selection.docx Deleted : /docs/architecture_overview.pdf Added : /docs/developer_notes Added : /docs/developer_notes/architecture_overview.pdf Added : /docs/developer_notes/spin_system.pdf Added : /docs/developer_notes/spin_system_bas.pdf Added : /docs/developer_notes/spin_system_comp.pdf Added : /docs/developer_notes/spin_system_inter.pdf Added : /docs/developer_notes/spin_system_rlx.pdf Added : /docs/developer_notes/spin_system_sys.pdf Deleted : /docs/spin_system.pdf Deleted : /docs/spin_system_bas.pdf Deleted : /docs/spin_system_comp.pdf Deleted : /docs/spin_system_inter.pdf Deleted : /docs/spin_system_rlx.pdf Deleted : /docs/spin_system_sys.pdf Deleted : /docs/table_2 - basis specification.docx Revision: 799 Author: kuprov Date: 30 April 2011 17:19:35 Message: Added the empirical T1,T2 relaxation mode to the relaxation superoperator. Created a banner to be printed at the start of the pre-coded pulse sequences. ---- Modified : /docs/1. Input preparation manual.docx Modified : /examples/nmr/cosy_test_5.m Modified : /exp/cosy.m Modified : /exp/dqf_cosy.m Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /exp/mfe.m Modified : /exp/noesy.m Modified : /exp/pulse_acquire.m Modified : /exp/zerofield.m Modified : /kernel/create.m Modified : /kernel/r_superop.m Modified : /kernel/utils/banner.m Modified : /kernel/utils/summary.m Modified : /kernel/utils/validate.m Revision: 798 Author: kuprov Date: 26 April 2011 15:33:08 Message: Minor changes. ---- Modified : /kernel/coherence.m Modified : /kernel/utils/correlation_function.m Modified : /kernel/utils/symmetrize.m Revision: 797 Author: kuprov Date: 18 April 2011 17:11:57 Message: A minor fix to the Simpson input filter. ---- Modified : /etc/simpson2spinach.m Revision: 796 Author: kuprov Date: 18 April 2011 14:17:43 Message: A bug fix in the GRAPE module and a quadrupole optimal control example. ---- Added : /examples/nmr_solids Added : /examples/nmr_solids/oc_quadrupole.m Modified : /kernel/analytics.m Modified : /kernel/grape.m Revision: 795 Author: kuprov Date: 13 April 2011 23:52:10 Message: Enabled the symmetry treatment in the shaped pulse function. ---- Modified : /etc/shaped_pulse.m Modified : /kernel/utils/dfpt.m Revision: 794 Author: kuprov Date: 06 April 2011 18:50:13 Message: Fixed a potential bug in the basis function and updated one test. ---- Modified : /examples/kernel/symmetry_test_1.m Modified : /kernel/basis.m Revision: 793 Author: kuprov Date: 02 April 2011 10:56:54 Message: Fixed a minor bug in the projection selector for the basis and introduced a new function performing algebraic coherence selection -- this will get rid of a lot of phase cycles, gradients and such. ---- Modified : /kernel/basis.m Added : /kernel/coherence.m Modified : /kernel/rdc.m Revision: 792 Author: kuprov Date: 01 April 2011 22:06:09 Message: Updated the operator caching -- it is no longer the default, but switches on if the user supplies an identifier. ---- Modified : /kernel/create.m Modified : /kernel/p_superop.m Revision: 791 Author: kuprov Date: 01 April 2011 14:11:52 Message: Final fix to the basis function. ---- Modified : /kernel/basis.m Revision: 790 Author: kuprov Date: 01 April 2011 14:05:21 Message: Fixed a bug that Luke spotted in the basis generation policy. Also, made the basis descriptor array single-precision, this saves some memory. ---- Modified : /kernel/basis.m Revision: 789 Author: kuprov Date: 31 March 2011 17:01:28 Message: Two minor fixes. The ESR module is in a good shape. Further development subject to user demand. ---- Modified : /examples/esr/endor_15N.m Modified : /examples/esr/pulse_acquire_perfluoropyrene.m Revision: 788 Author: luke Date: 31 March 2011 15:46:44 Message: Minor corrections to the plotting in the ESEEM files. ---- Modified : /examples/esr/eseem_15N.m Modified : /examples/esr/eseem_methyl.m Modified : /examples/esr/eseem_phenyl.m Revision: 787 Author: luke Date: 31 March 2011 15:35:56 Message: Tidied up the ENDOR test files and renamed the pulse acquire files. ---- Added : /examples/esr/endor_15N.m (Copy from path: /examples/esr/endor_test_1.m, Revision, 785) Added : /examples/esr/endor_methyl.m (Copy from path: /examples/esr/endor_test_3.m, Revision, 785) Added : /examples/esr/endor_phenyl.m (Copy from path: /examples/esr/endor_test_2.m, Revision, 785) Deleted : /examples/esr/endor_test_1.m Deleted : /examples/esr/endor_test_2.m Deleted : /examples/esr/endor_test_3.m Added : /examples/esr/pulse_acquire_biaryl.m (Copy from path: /examples/esr/pulse_acquire_test_3.m, Revision, 785) Added : /examples/esr/pulse_acquire_chrysene.m (Copy from path: /examples/esr/pulse_acquire_test_4.m, Revision, 785) Added : /examples/esr/pulse_acquire_methyl.m (Copy from path: /examples/esr/pulse_acquire_test_1.m, Revision, 785) Added : /examples/esr/pulse_acquire_phenyl.m (Copy from path: /examples/esr/pulse_acquire_test_2.m, Revision, 785) Deleted : /examples/esr/pulse_acquire_test_1.m Deleted : /examples/esr/pulse_acquire_test_2.m Deleted : /examples/esr/pulse_acquire_test_3.m Deleted : /examples/esr/pulse_acquire_test_4.m Revision: 786 Author: luke Date: 31 March 2011 15:09:20 Message: Tidied up the ESEEM examples. ---- Added : /examples/esr/eseem_14N.m (Copy from path: /examples/esr/eseem_test_4.m, Revision, 785) Added : /examples/esr/eseem_15N.m (Copy from path: /examples/esr/eseem_test_1.m, Revision, 785) Added : /examples/esr/eseem_methyl.m (Copy from path: /examples/esr/eseem_test_3.m, Revision, 785) Added : /examples/esr/eseem_phenyl.m (Copy from path: /examples/esr/eseem_test_2.m, Revision, 785) Deleted : /examples/esr/eseem_test_1.m Deleted : /examples/esr/eseem_test_2.m Deleted : /examples/esr/eseem_test_3.m Deleted : /examples/esr/eseem_test_4.m Revision: 785 Author: kuprov Date: 28 March 2011 15:26:14 Message: A somewhat more SSR-friendly Spin Chemistry system. ---- Added : /examples/molecules/anthraquinone_disulphonate_anion.log Added : /examples/molecules/tryptophan_neutral_radical.log Revision: 784 Author: luke Date: 28 March 2011 14:19:22 Message: Fixed a small bug... ---- Modified : /kernel/utils/human2opspec.m Revision: 783 Author: luke Date: 28 March 2011 12:37:48 Message: Tightened up the regexp in human2opspec, removing the need for some of the numeric checks, etc. ---- Modified : /kernel/utils/human2opspec.m Revision: 782 Author: kuprov Date: 24 March 2011 17:40:45 Message: A correction to the IK-0 basis policy for certain special cases. ---- Modified : /kernel/basis.m Revision: 781 Author: kuprov Date: 24 March 2011 17:05:31 Message: Much faster basis generation for IK-0. ---- Modified : /kernel/basis.m Revision: 780 Author: kuprov Date: 22 March 2011 10:54:49 Message: Added the HFC and g-tensor calculation for 1,3-DCB anion. It seems, the only way to get the Spin Chemistry crowd to pay attention is to publish the calculations -- reality is harder to ignore. ---- Added : /examples/molecules/1,3-dcb_anion.log Deleted : /examples/molecules/perfluoropyrene.log Added : /examples/molecules/perfluoropyrene_cation.log (Copy from path: /examples/molecules/perfluoropyrene_cation_radical.log, Revision, 779) Deleted : /examples/molecules/perfluoropyrene_cation_radical.log Added : /examples/molecules/perfluoropyrene_neutral.log (Copy from path: /examples/molecules/perfluoropyrene.log, Revision, 779) Deleted : /examples/molecules/pyrene.log Deleted : /examples/molecules/pyrene_cation_radical.log Added : /examples/molecules/pyrene_neutral.log (Copy from path: /examples/molecules/pyrene.log, Revision, 779) Revision: 779 Author: kuprov Date: 21 March 2011 18:20:00 Message: Beginnings of the Residual Dipolar Coupling and Residual CSA module. The operator caching feature rocks. :) ---- Added : /kernel/rdc.m Revision: 778 Author: kuprov Date: 21 March 2011 16:35:01 Message: A good go at a systematic manual. ---- Modified : /docs/1. Input preparation manual.docx Deleted : /docs/table_6 - gaussian import parameters.docx Revision: 777 Author: luke Date: 21 March 2011 16:08:13 Message: Small bug in k_superop(). ---- Modified : /kernel/k_superop.m Revision: 776 Author: luke Date: 21 March 2011 14:33:05 Message: Added a switch to disable superoperator caching ( sys.disable={...,'caching',...}; ), and a few minor bug fixes. ---- Modified : /kernel/create.m Modified : /kernel/k_superop.m Modified : /kernel/p_superop.m Modified : /kernel/utils/validate.m Revision: 775 Author: kuprov Date: 19 March 2011 18:30:15 Message: You must be joking. ---- Modified : /kernel/h_superop.m Modified : /kernel/k_superop.m Revision: 774 Author: hannah Date: 18 March 2011 17:29:05 Message: Third time lucky. Sorry!! ---- Modified : /kernel/k_superop.m Revision: 773 Author: hannah Date: 18 March 2011 17:27:56 Message: k_superop spin chem bit actually fixed this time I think ---- Modified : /kernel/h_superop.m Revision: 772 Author: hannah Date: 18 March 2011 16:56:55 Message: Quick fix for the new identifier thing in k_superop for the spin chemistry kinetics. ---- Modified : /kernel/k_superop.m Revision: 771 Author: kuprov Date: 18 March 2011 15:58:09 Message: Added pyrene cation radical. ---- Added : /examples/molecules/pyrene_cation_radical.log Revision: 770 Author: luke Date: 18 March 2011 11:40:27 Message: Added a few lines such that the reseeding doesn't affect any other instances of random number generation that the user may be running. ---- Modified : /kernel/create.m Revision: 769 Author: luke Date: 17 March 2011 17:12:09 Message: Changed RNG seed from MatLab default when creating a new job identifier. ---- Modified : /kernel/create.m Revision: 768 Author: kuprov Date: 17 March 2011 16:45:43 Message: Starting the tedious job of writing a full Spinach manual -- a few tolerances have been brought in line with what is actually necessary. ---- Added : /docs/1. Input preparation manual.docx Modified : /docs/table_3 - tolerances.docx Modified : /kernel/utils/tolerances.m Modified : /scratch Revision: 767 Author: kuprov Date: 17 March 2011 14:41:09 Message: Minor fix to the relaxation superoperator. ---- Modified : /kernel/r_superop.m Revision: 766 Author: kuprov Date: 17 March 2011 12:18:06 Message: Added a cursory check to the disk caching capability. ---- Modified : /kernel/p_superop.m Revision: 765 Author: kuprov Date: 17 March 2011 12:04:25 Message: Experimental support of disk caching and restarts. ---- Modified : /kernel/create.m Modified : /kernel/p_superop.m Added : /scratch Revision: 764 Author: kuprov Date: 16 March 2011 18:15:34 Message: Some cosmetic improvements. ---- Modified : /examples/nmr/noesy_test_1.m Modified : /examples/nmr/noesy_test_2.m Modified : /kernel/r_superop.m Revision: 763 Author: kuprov Date: 16 March 2011 15:33:39 Message: Polished Luke's implementation of the thermal equilibrium function and moved it to the kernel to replace the previous one. All very nice and general now. ---- Modified : /kernel/equilibrium.m Modified : /kernel/h_superop.m Modified : /kernel/utils/operator.m Revision: 762 Author: kuprov Date: 14 March 2011 17:31:28 Message: Some more molecules for the example set. ---- Added : /examples/molecules/perfluoropyrene.log Added : /examples/molecules/pyrene.log Modified : /kernel/h_superop.m Revision: 761 Author: kuprov Date: 12 March 2011 17:20:37 Message: Better memory recycling in the relaxation superoperator. ---- Modified : /kernel/r_superop.m Revision: 760 Author: kuprov Date: 12 March 2011 16:25:59 Message: A pretty dramatic example of a brute-force 11-spin ESR simulation in a complete 4,194,304-dimensional basis set, which gets chopped down to 1024 by ZTE at the propagation stage, but not before the Liouvillian actually gets computed. ---- Added : /examples/esr/pulse_acquire_perfluoropyrene.m Added : /examples/molecules/perfluoropyrene_cation_radical.log Revision: 759 Author: kuprov Date: 11 March 2011 14:36:35 Message: Reduced the memory footprint of the relaxation superoperator module. ---- Modified : /kernel/r_superop.m Revision: 758 Author: kuprov Date: 11 March 2011 12:05:08 Message: MARYAN has been parallelized, another example was added. Some functions from the Spinach development directory have been moved across. ---- Modified : / Added : /etc/data_processing Added : /etc/data_processing/baseline.m Added : /etc/metric.m Modified : /examples/spin_chemistry/maryan_test_1.m Added : /examples/spin_chemistry/maryan_test_2.m Modified : /exp/maryan.m Revision: 757 Author: kuprov Date: 10 March 2011 12:13:07 Message: Some refinement to NMR examples. ---- Deleted : /examples/nmr/large_scale_test_1.m Added : /examples/nmr/pulse_acquire_naphtopyranone.m Added : /examples/nmr/pulse_acquire_peptide.m (Copy from path: /examples/nmr/large_scale_test_1.m, Revision, 756) Added : /examples/nmr/pulse_acquire_rotanone.m (Copy from path: /examples/nmr/pulse_acquire_test_3.m, Revision, 756) Deleted : /examples/nmr/pulse_acquire_test_3.m Revision: 756 Author: kuprov Date: 09 March 2011 16:29:04 Message: Matlab version 2010a or later is now explicitly enforced. We do not officially support earlier versions -- they are slow and much of the parallel functionality is missing from them. ---- Modified : /kernel/basis.m Modified : /kernel/create.m Modified : /kernel/r_superop.m Revision: 755 Author: kuprov Date: 09 March 2011 16:05:21 Message: A slightly more logical form for Hannah's singlet state fix. ---- Modified : /etc/singlet.m Revision: 754 Author: hannah Date: 09 March 2011 10:15:00 Message: Corrected error in singlet code arising from inconsistency with new state function (the single spin vs multi spin thing inside is quite confusing!) spin chemistry tests now work again. Also changed [~.var]=op in basis and r_superop to [rubbish,var] because otherwise it crashes older versions of matlab, hope no one minds. ---- Modified : /etc/singlet.m Modified : /kernel/basis.m Modified : /kernel/r_superop.m Revision: 753 Author: kuprov Date: 08 March 2011 15:16:15 Message: Norm dynamics analysis function added to the kernel. ---- Added : /kernel/analytics.m Revision: 752 Author: kuprov Date: 08 March 2011 11:44:03 Message: A template for a large class of Optimal Control problems and a minor safety catch for the relaxation theory module. ---- Added : /examples/optimal_control/magic_pulse_template.m Deleted : /examples/optimal_control/optimal_control_8.m Modified : /kernel/r_superop.m Revision: 751 Author: kuprov Date: 27 February 2011 16:52:28 Message: Another optimal control example. ---- Added : /examples/optimal_control/optimal_control_8.m Revision: 750 Author: kuprov Date: 13 February 2011 21:06:24 Message: Updated some tolerance settings. ---- Modified : /kernel/utils/tolerances.m Revision: 749 Author: kuprov Date: 13 February 2011 21:01:48 Message: Added the central finite-difference option to the GRAPE gradient algorithm selection. ---- Modified : /examples/optimal_control/optimal_control_1.m Modified : /examples/optimal_control/optimal_control_2.m Modified : /examples/optimal_control/optimal_control_3.m Modified : /examples/optimal_control/optimal_control_5.m Modified : /examples/optimal_control/optimal_control_6.m Modified : /examples/optimal_control/optimal_control_7.m Modified : /kernel/grape.m Modified : /kernel/utils/pauli.m Modified : /kernel/utils/tolerances.m Revision: 748 Author: kuprov Date: 11 February 2011 16:56:12 Message: Made the coherence level filtering an option for all basis sets. ---- Modified : /examples/spin_chemistry/mary_test_1.m Modified : /examples/spin_chemistry/mary_test_2.m Modified : /examples/spin_chemistry/mary_test_3.m Modified : /examples/spin_chemistry/mary_test_4.m Modified : /examples/spin_chemistry/mary_test_5.m Modified : /examples/spin_chemistry/mary_test_6.m Modified : /kernel/basis.m Revision: 747 Author: kuprov Date: 08 February 2011 21:16:31 Message: Generalized the GRAPE module somewhat and updated the examples. ---- Modified : /examples/optimal_control/optimal_control_1.m Modified : /examples/optimal_control/optimal_control_2.m Modified : /examples/optimal_control/optimal_control_3.m Modified : /examples/optimal_control/optimal_control_5.m Modified : /examples/optimal_control/optimal_control_6.m Modified : /examples/optimal_control/optimal_control_7.m Modified : /kernel/grape.m Modified : /kernel/utils/tolerances.m Revision: 746 Author: gareth Date: 07 February 2011 15:01:07 Message: Visualiser has now been ported to use the spinach kernel evolution function. Visualiser has now been ported to use the spinach kernel evolution function. ---- Modified : /etc/coherence_visualisation/visualiser.m Revision: 745 Author: luke Date: 07 February 2011 14:35:58 Message: Pulse acquire sequence for residual norm analysis. ---- Added : /etc/coherence_visualisation/visualiser_test_1.m Revision: 744 Author: gareth Date: 07 February 2011 13:36:24 Message: Gaussian input files for the molecule described in SpectrochimicaArtaA559-565 suitable for geometry optimisation and calculation of the NMR parameters. ---- Added : /etc/coherence_visualisation/spectrochimica_arta_A78_559_565-mdopt.gjf Added : /etc/coherence_visualisation/spectrochimica_arta_A78_559_565-mdopt.mol Added : /etc/coherence_visualisation/spectrochimica_arta_A78_559_565.gjf Added : /etc/coherence_visualisation/spectrochimica_arta_A78_559_565.mol Revision: 743 Author: gareth Date: 02 February 2011 12:02:57 Message: First round of cleaning up the coherence visualiser. Begun using the spinach kernel evolution function. ---- Modified : /etc/coherence_visualisation/visualiser.m Revision: 742 Author: gareth Date: 02 February 2011 11:23:22 Message: Some tools for visualising the movement of coherence though the spin orders. In a very rough state Some tools for visualising the movement of coherence though the spin orders. In a very rough state ---- Added : /etc/coherence_visualisation Added : /etc/coherence_visualisation/visualiser.m Revision: 741 Author: kuprov Date: 30 January 2011 21:19:33 Message: Final touches before putting the new release online. ---- Deleted : /examples/nmr/solids_test_5.m Modified : /examples/optimal_control/optimal_control_6.m Modified : /examples/optimal_control/optimal_control_7.m Revision: 740 Author: kuprov Date: 30 January 2011 21:06:40 Message: Some cosmetic improvements here and there. ---- Modified : /examples/kernel/commutation_test_1.m Modified : /examples/kernel/commutation_test_2.m Modified : /examples/kernel/commutation_test_3.m Modified : /kernel/equilibrium.m Modified : /kernel/utils/tolerances.m Revision: 739 Author: kuprov Date: 30 January 2011 20:34:23 Message: Major clean-up of Luke's implementation of the user-friendly operator and state specification syntax. It is getting increasingly difficult to modify kernel parts because of all the dependencies downstream. ---- Deleted : /etc/state.m Added : /kernel/utils/human2opspec.m (Copy from path: /kernel/utils/operator_specification.m, Revision, 732) Modified : /kernel/utils/operator.m Deleted : /kernel/utils/operator_specification.m Modified : /kernel/utils/pad.m Modified : /kernel/utils/pauli.m Modified : /kernel/utils/report.m Added : /kernel/utils/state.m (Copy from path: /etc/state.m, Revision, 732) Revision: 738 Author: kuprov Date: 30 January 2011 17:51:26 Message: Removed the 'refocused_trajectory' option from the evolution function -- it seems to be unnecessarily messy. Did lots of clean-up work in the kernel. ---- Deleted : /examples/nmr/crazed_test_1.m Deleted : /exp/crazed.m Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /exp/noesy.m Modified : /kernel/basis.m Modified : /kernel/c_superop.m Modified : /kernel/create.m Modified : /kernel/equilibrium.m Modified : /kernel/evolution.m Revision: 737 Author: kuprov Date: 30 January 2011 14:28:01 Message: More clean-up and polishing in the kernel. ---- Modified : /examples/esr Modified : /examples/nmr/chem_test_1.m Modified : /examples/nmr/chem_test_2.m Modified : /kernel/k_superop.m Modified : /kernel/orientation.m Modified : /kernel/p_superop.m Modified : /kernel/path_trace.m Modified : /kernel/propagator.m Modified : /kernel/r_superop.m Modified : /kernel/reduce.m Modified : /kernel/spin.m Revision: 736 Author: kuprov Date: 29 January 2011 19:16:12 Message: Fixed a previously latent bug in the create function. ---- Modified : /kernel/create.m Revision: 735 Author: kuprov Date: 29 January 2011 19:14:25 Message: Some polishing in places. ---- Modified : /kernel/a_superop.m Added : /kernel/cache/generators_2__2__2.mat Modified : /kernel/create.m Modified : /kernel/secularity.m Modified : /kernel/spin.m Modified : /kernel/statevec.m Modified : /kernel/step.m Modified : /kernel/zte.m Revision: 734 Author: kuprov Date: 29 January 2011 17:22:06 Message: Fixed a self-consistent pair of bugs in Luke's ESEEM example and made create slightly more resilient to user specification. ---- Modified : /examples/esr/eseem_test_4.m Modified : /kernel/create.m Revision: 733 Author: kuprov Date: 29 January 2011 16:50:42 Message: Some refinements to Luke's new ESEEM example. ---- Modified : /examples/esr/eseem_test_4.m Revision: 732 Author: luke Date: 27 January 2011 15:10:32 Message: Added a quadrupolar 14N ESEEM example. ---- Added : /examples/esr/eseem_test_4.m Revision: 731 Author: hannah Date: 25 January 2011 15:28:58 Message: Corrected small bug in Hore Jones operator ---- Modified : /kernel/k_superop.m Revision: 730 Author: kuprov Date: 15 January 2011 16:12:52 Message: Revert an accidental commit. ---- Modified : /examples/kernel/symmetry_test_1.m Modified : /examples/kernel/symmetry_test_2.m Revision: 729 Author: kuprov Date: 15 January 2011 16:11:29 Message: Some docs renamed plus made sure that the propagator function plays well with the Hilbert space simulations. ---- Deleted : /docs/Figure 1.pdf Deleted : /docs/Figure 2.pdf Deleted : /docs/Figure 3.pdf Deleted : /docs/Figure 4.pdf Deleted : /docs/Figure 5.pdf Deleted : /docs/Figure 6.pdf Deleted : /docs/Figure 7.pdf Deleted : /docs/Figure 8.pdf Added : /docs/architecture_overview.pdf (Copy from path: /docs/Figure 2.pdf, Revision, 726) Added : /docs/spin_system.pdf (Copy from path: /docs/Figure 3.pdf, Revision, 726) Added : /docs/spin_system_bas.pdf (Copy from path: /docs/Figure 4.pdf, Revision, 726) Added : /docs/spin_system_comp.pdf (Copy from path: /docs/Figure 6.pdf, Revision, 726) Added : /docs/spin_system_inter.pdf (Copy from path: /docs/Figure 5.pdf, Revision, 726) Added : /docs/spin_system_rlx.pdf (Copy from path: /docs/Figure 7.pdf, Revision, 726) Added : /docs/spin_system_sys.pdf (Copy from path: /docs/Figure 8.pdf, Revision, 726) Modified : /examples/kernel/symmetry_test_1.m Modified : /examples/kernel/symmetry_test_2.m Added : /kernel/cache/generators_2__2__2__2__2__2__2__2__2__2__2__2__2.mat Revision: 728 Author: kuprov Date: 15 January 2011 16:01:50 Message: [DNP/Nottingham] Integrating the Hilbert space module from Rev 360: Hamiltonian generator done... ---- Added : /kernel/h_operator.m Modified : /kernel/h_superop.m Revision: 727 Author: kuprov Date: 15 January 2011 14:49:21 Message: [DNP/Nottingham] Integrating the Hilbert space module from Rev 360: generator caching utility done... ---- Added : /kernel/cache/generators_2__2__2__2__2__2.mat Modified : /kernel/utils/banner.m Added : /kernel/utils/generators.m (Copy from path: /Spinach/Spinach core/hilb_statelist_gen.m, Revision, 360) Revision: 726 Author: luke Date: 12 January 2011 08:38:22 Message: Changes to h_superop() and some experiments to make them more human readable through the use of the new operator_specification(). As they are called by the kernel, operator() and operator_specification() have now both been promoted into kernel/utils/. Added a bit of documentation for evolution() (though reading the source code of some pre-built exp/* files is still recommended for any first time users). ---- Deleted : /etc/operator.m Deleted : /etc/operator_specification.m Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /exp/mfe.m Modified : /exp/zerofield.m Modified : /kernel/evolution.m Modified : /kernel/h_superop.m Added : /kernel/utils/operator.m Added : /kernel/utils/operator_specification.m Revision: 725 Author: kuprov Date: 10 January 2011 21:20:40 Message: Switched the GRAPE module completely to Hausdorff series. ---- Modified : /kernel/grape.m Revision: 724 Author: luke Date: 07 January 2011 17:48:16 Message: Version of the changes to operator_specification that works in a way consistent with its previous incarnation but allows much greater flexibility. ---- Modified : /etc/operator.m Modified : /etc/operator_specification.m Modified : /etc/singlet.m Modified : /etc/state.m Revision: 723 Author: kuprov Date: 07 January 2011 09:53:21 Message: Documentation and comment updates on a few functions. ---- Modified : /etc/operator_specification.m Modified : /etc/state.m Modified : /kernel/a_superop.m Modified : /kernel/c_superop.m Revision: 722 Author: kuprov Date: 06 January 2011 13:52:40 Message: Some minor changes. ---- Modified : /examples/esr/relaxation_test_1.m Modified : /kernel/c_superop.m Revision: 721 Author: luke Date: 05 January 2011 18:53:18 Message: Rolled back the previous 2 commits until such time as the functions are working consistently. ---- Modified : /etc/operator.m Modified : /etc/operator_specification.m Modified : /etc/singlet.m Modified : /etc/state.m Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /exp/mfe.m Modified : /exp/zerofield.m Revision: 720 Author: luke Date: 05 January 2011 16:02:50 Message: Edited the installation instructions to reflect Spinach's memory requirements. ---- Modified : /installation.txt Revision: 719 Author: luke Date: 05 January 2011 11:50:47 Message: Changes to operator_specification that allow for the specification of more complicated operators and states without having to call c_superop or statevec directly. This gives much greater human readability to such specifications. ---- Modified : /etc/operator.m Modified : /etc/operator_specification.m Modified : /etc/singlet.m Modified : /etc/state.m Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /exp/mfe.m Modified : /exp/zerofield.m Modified : /kernel/c_superop.m Revision: 718 Author: kuprov Date: 28 December 2010 18:26:22 Message: Minor axis fix for the DD-CSA example, plus lots of comments added. ---- Modified : /examples/relaxation_theory/dd_csa_test_2.m Revision: 717 Author: luke Date: 27 December 2010 16:56:42 Message: Tidied up a few functions by removing repetition. ---- Modified : /etc/operator.m Added : /etc/operator_specification.m Modified : /etc/state.m Modified : /kernel/evolution.m Revision: 716 Author: kuprov Date: 15 December 2010 17:30:26 Message: Another symmetry test. ---- Added : /examples/kernel/symmetry_test_3.m Revision: 715 Author: kuprov Date: 15 December 2010 16:30:38 Message: Tightened up some tolerances. ---- Modified : /kernel/utils/tolerances.m Revision: 714 Author: kuprov Date: 15 December 2010 12:31:10 Message: Fixed the time arrow direction bug in spinach kernel (source and destination were swapped in p_superop) and fixed all the resulting frequency flips downstream. Phase cycles make more sense now. ---- Modified : /examples/kernel/commutation_test_1.m Modified : /examples/kernel/commutation_test_2.m Modified : /examples/kernel/commutation_test_3.m Modified : /examples/nmr/noesy_test_1.m Modified : /examples/nmr/noesy_test_2.m Modified : /examples/nmr/solids_test_1.m Modified : /examples/relaxation_theory/dd_csa_test_2.m Modified : /exp/dqf_cosy.m Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /exp/pulse_acquire.m Modified : /exp/zerofield.m Modified : /kernel/cache/ist_product_table_2.mat Modified : /kernel/cache/ist_product_table_3.mat Modified : /kernel/cache/ist_product_table_4.mat Modified : /kernel/cache/ist_product_table_5.mat Modified : /kernel/cache/ist_product_table_6.mat Modified : /kernel/cache/ist_product_table_7.mat Modified : /kernel/cache/ist_product_table_8.mat Deleted : /kernel/cache/ist_product_table_9.mat Modified : /kernel/p_superop.m Revision: 713 Author: kuprov Date: 13 December 2010 18:40:02 Message: Documentation update. ---- Modified : /docs/table_1 - spin system specification.docx Modified : /docs/table_2 - basis specification.docx Revision: 712 Author: kuprov Date: 13 December 2010 17:53:06 Message: The lowfield switch is gone from the kernel -- all the procedures associated with correctly configuring the kernel to run high field (NMR etc), low field (SpinChem etc) and pseudosecular (ESEEM etc) simulations is now handled by secularity() and understood by h_superop.m(). ---- Modified : /docs/table_1 - spin system specification.docx Modified : /etc/plot_1d.m Modified : /examples/esr/endor_test_1.m Modified : /examples/esr/endor_test_2.m Modified : /examples/esr/endor_test_3.m Modified : /examples/esr/eseem_test_1.m Modified : /examples/esr/eseem_test_2.m Modified : /examples/esr/eseem_test_3.m Modified : /examples/spin_chemistry/mary_test_6.m Modified : /exp/noesy.m Modified : /kernel/create.m Modified : /kernel/equilibrium.m Modified : /kernel/h_superop.m Modified : /kernel/utils/validate.m Revision: 711 Author: luke Date: 13 December 2010 17:43:45 Message: Rolled back the previous revision. ---- Deleted : /examples/esr/comparison Deleted : /examples/esr/endor_test_simple.m Deleted : /examples/esr/eseem_test_quadrupole.m Revision: 710 Author: luke Date: 13 December 2010 17:43:11 Message: Comparison of eseem and endor with known test cases. ---- Added : /examples/esr/comparison Added : /examples/esr/comparison/eseem_test_1_ES.m Added : /examples/esr/comparison/eseem_test_2_ES.m Added : /examples/esr/comparison/eseem_test_3_ES.m Added : /examples/esr/endor_test_simple.m Added : /examples/esr/eseem_test_quadrupole.m Revision: 709 Author: luke Date: 13 December 2010 17:01:51 Message: A few more ESEEM and ENDOR examples. ---- Modified : /examples/esr/endor_test_1.m Added : /examples/esr/endor_test_2.m Added : /examples/esr/endor_test_3.m Modified : /examples/esr/eseem_test_1.m Added : /examples/esr/eseem_test_2.m Added : /examples/esr/eseem_test_3.m Revision: 708 Author: luke Date: 13 December 2010 16:46:12 Message: Changes to a couple of experiment files. noesy has been changed to reflect that the hypercomplex parts likely evolve in separate sets of subspaces. Minor bugfixes to the other two experiments. ---- Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/noesy.m Revision: 707 Author: luke Date: 03 December 2010 11:06:59 Message: Some small changes to the noesy experiment in order to make it faster. ---- Modified : /exp/noesy.m Revision: 706 Author: luke Date: 02 December 2010 10:26:10 Message: Updated several exp/* files such that they no longer rely on scaling and squaring for the 'final' evolutions but instead generate an appropriate timestep and number of steps. ---- Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /exp/noesy.m Revision: 705 Author: luke Date: 01 December 2010 12:22:31 Message: Added informative error messages to these two functions. ---- Modified : /kernel/h_superop.m Modified : /kernel/secularity.m Revision: 704 Author: luke Date: 01 December 2010 11:12:53 Message: Fixed a bug in endor() whereby the 'final' evolutions would just take one big step. ---- Modified : /exp/endor.m Revision: 703 Author: kuprov Date: 30 November 2010 18:05:28 Message: Reworked secularity control in the kernel. No assumptions about the rotating frame situation are made by the kernel anymore -- it is the responsibility of the user to call secularity.m before calling h_superop.m now. ---- Modified : /examples/kernel/symmetry_test_1.m Added : /examples/nmr/crazed_test_1.m (Copy from path: /examples/nmr/intermol_mqcs_test_1.m, Revision, 702) Deleted : /examples/nmr/intermol_mqcs_test_1.m Modified : /examples/nmr/shaped_pulse_test_1.m Modified : /examples/nmr/shaped_pulse_test_2.m Deleted : /examples/nmr/solids_lineshape_test_1.m Added : /examples/nmr/solids_test_5.m (Copy from path: /examples/nmr/solids_lineshape_test_1.m, Revision, 702) Modified : /examples/optimal_control/optimal_control_1.m Modified : /examples/optimal_control/optimal_control_2.m Modified : /examples/optimal_control/optimal_control_3.m Modified : /examples/optimal_control/optimal_control_4.m Modified : /examples/optimal_control/optimal_control_5.m Modified : /examples/optimal_control/optimal_control_6.m Modified : /examples/optimal_control/optimal_control_7.m Added : /examples/optimal_control/waveform.mat Modified : /examples/relaxation_theory/cross_relaxation.m Modified : /examples/relaxation_theory/dd_csa_test_2.m Modified : /examples/relaxation_theory/dnp_test_1.m Modified : /examples/relaxation_theory/dnp_test_2.m Modified : /examples/relaxation_theory/dnp_test_3.m Modified : /exp/cosy.m Modified : /exp/crazed.m Modified : /exp/dqf_cosy.m Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /exp/mfe.m Modified : /exp/noesy.m Modified : /exp/pulse_acquire.m Modified : /exp/zerofield.m Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/r_superop.m Added : /kernel/secularity.m Modified : /kernel/step.m Revision: 702 Author: luke Date: 23 November 2010 17:09:26 Message: Edits to ESEEM and ENDOR experiments, as well as the example files. Note that sys.regime must now be specified for ESEEM (ENDOR defaults to 'liquid'); only 'powder' and 'crystal' are valid ESEEM regimes. ESEEM now also take twice the time-step it did previously. ---- Modified : /etc/apodization.m Modified : /examples/esr/endor_test_1.m Modified : /examples/esr/eseem_test_1.m Modified : /exp/endor.m Modified : /exp/eseem.m Revision: 701 Author: kuprov Date: 23 November 2010 13:50:47 Message: Hushed up the clean-up function -- too loud when clean-up is disabled and in some other cases. Added two more optimal control examples. ---- Added : /examples/optimal_control/optimal_control_6.m Added : /examples/optimal_control/optimal_control_7.m Modified : /kernel/evolution.m Modified : /kernel/k_superop.m Modified : /kernel/utils/clean_up.m Revision: 700 Author: kuprov Date: 22 November 2010 15:33:56 Message: Another optimal control example. ---- Added : /examples/optimal_control/oc5_waveform.mat Added : /examples/optimal_control/optimal_control_5.m Revision: 699 Author: kuprov Date: 22 November 2010 15:28:51 Message: Basic parallelization in the GRAPE module, quick and dirty. ---- Modified : /kernel/grape.m Revision: 698 Author: kuprov Date: 22 November 2010 12:20:16 Message: Minor alterations to GRAPE examples. ---- Modified : /examples/optimal_control/oc4_waveform.mat Modified : /examples/optimal_control/optimal_control_4.m Revision: 697 Author: kuprov Date: 22 November 2010 10:53:35 Message: Some more optimal control examples. Switched the old ones back to the exact gradient -- much faster now. ---- Added : /examples/optimal_control/oc4_waveform.mat Modified : /examples/optimal_control/optimal_control_1.m Modified : /examples/optimal_control/optimal_control_2.m Modified : /examples/optimal_control/optimal_control_3.m Added : /examples/optimal_control/optimal_control_4.m Revision: 696 Author: kuprov Date: 21 November 2010 18:50:49 Message: A considerably faster exact gradient option for GRAPE and a thermal relaxation patch to the shaped pulse function. ---- Modified : /etc/shaped_pulse.m Modified : /kernel/grape.m Revision: 695 Author: kuprov Date: 21 November 2010 13:39:56 Message: Another optimal control example. ---- Added : /examples/optimal_control/optimal_control_3.m Modified : /kernel/reduce.m Revision: 694 Author: kuprov Date: 16 November 2010 12:41:48 Message: Some more convenience and consistency improvements around the rotation functions in etc directory. ---- Modified : /etc/aa2quat.m Modified : /etc/apodization.m Modified : /etc/dcm2euler.m Modified : /etc/dcm2wigner.m Modified : /kernel/utils/euler2dcm.m Modified : /kernel/utils/euler2wigner.m Revision: 693 Author: kuprov Date: 16 November 2010 11:51:10 Message: Made euler2dcm recognize vector and scalar input styles. Changed dcm2euler to ensure self-consistency and transparency. ---- Modified : /etc/dcm2euler.m Modified : /kernel/utils/euler2dcm.m Revision: 692 Author: kuprov Date: 16 November 2010 11:11:07 Message: Extracted GTPC's angle-axis to quaternion converter function into a separate file in etc. ---- Added : /etc/aa2quat.m Modified : /etc/quat2euler.m Revision: 691 Author: kuprov Date: 15 November 2010 15:35:11 Message: A streamlined NOESY sequence, in response to Hannah's bug fix. Much faster now and makes much more sense. ---- Modified : /examples/nmr/noesy_test_1.m Modified : /examples/nmr/noesy_test_2.m Modified : /exp/noesy.m Revision: 690 Author: kuprov Date: 15 November 2010 15:21:43 Message: Added a safety feature to the propagator module -- if the uses abuse the matrix exponentials (by taking outrageously long time steps), all accuracy parameters are tightened automatically. Added some comments to the cleanup function. ---- Modified : /kernel/propagator.m Modified : /kernel/utils/clean_up.m Revision: 689 Author: kuprov Date: 15 November 2010 15:03:35 Message: Clean-up and comments in the evolution module. Multi-coil detection abandoned -- not much need. Step control override in the 'final' section removed -- would slow down the simulation if the users take very large time steps (e.g. in DNP simulations). ---- Modified : /examples/relaxation_theory/dnp_test_3.m Modified : /kernel/evolution.m Revision: 688 Author: luke Date: 15 November 2010 12:45:27 Message: Fixed a minor bug. ---- Modified : /kernel/evolution.m Revision: 687 Author: luke Date: 15 November 2010 10:30:21 Message: Vectorized the inner loop of the 'focus' case in evolution. ---- Modified : /kernel/evolution.m Revision: 686 Author: luke Date: 12 November 2010 17:50:09 Message: Time domain ENDOR as of Schweiger and Jeschke (2001, OUP) pg 390ff. Note that the change requires the addition of parameters.tau to any ENDOR example. Also modified the 'final' option in evolution to apply DSS. ---- Modified : /examples/esr/endor_test_1.m Modified : /exp/endor.m Modified : /kernel/evolution.m Revision: 685 Author: kuprov Date: 09 November 2010 18:08:31 Message: Much richer gradient accuracy control in the GRAPE module. ---- Modified : /examples/optimal_control/optimal_control_1.m Modified : /examples/optimal_control/optimal_control_2.m Modified : /kernel/grape.m Revision: 684 Author: kuprov Date: 09 November 2010 16:30:11 Message: A minor improvement to Gaussian parser -- only relevant for crashed logs. ---- Modified : /etc/g03_parse.m Revision: 683 Author: kuprov Date: 09 November 2010 16:07:11 Message: A minor improvement to Gaussian parser -- only relevant for crashed logs. ---- Modified : /etc/g03_parse.m Revision: 682 Author: luke Date: 08 November 2010 16:37:15 Message: Have updated evolution() to be slightly more flexible with regard to the 'refocused_trajectory' case; evolution given this option now recursively calls itself twice: once for 'trajectory' and then for 'refocus'. This adds greater flexibility to what one can do with evolution(). Have also updated eseem() to take advantage of it (there is an endor() equivalent, but I need to test it). ---- Modified : /exp/eseem.m Modified : /kernel/evolution.m Revision: 681 Author: hannah Date: 04 November 2010 14:58:03 Message: Sorry, transferred wrong version. This is the correct example file. ---- Modified : /examples/nmr/intermol_mqcs_test_1.m Revision: 680 Author: hannah Date: 04 November 2010 14:47:32 Message: Added a new example code and pulse sequence (crazed) which predicts long range intermolecular coherences as seen by Warren et al. ---- Added : /examples/nmr/intermol_mqcs_test_1.m Added : /exp/crazed.m Revision: 679 Author: hannah Date: 01 November 2010 17:52:10 Message: Corrected minor typo in noesy.m ---- Modified : /exp/noesy.m Revision: 678 Author: luke Date: 01 November 2010 17:04:08 Message: Implemented disabling sparse-matrix clean up (sys.disable={'clean-up'};) as it is in the documentation but was not implemented. The warnings if one does disable it can get rather obnoxious however (as clean_up() is called for every subspace by propagator() ). ---- Modified : /kernel/utils/clean_up.m Revision: 677 Author: hannah Date: 29 October 2010 13:40:03 Message: Corrected previous example. Liouvillian now supplied to pulse acquire. ---- Modified : /examples/nmr/solids_lineshape_test_1.m Revision: 676 Author: hannah Date: 29 October 2010 12:50:40 Message: Added new example solid state nmr file which reproduces the lineshapes from Anderson statistical theory - specifically figure 2 from his 1954 paper (full ref in code). ---- Added : /examples/nmr/solids_lineshape_test_1.m Revision: 675 Author: luke Date: 29 October 2010 11:31:40 Message: Added in the option of disabling destination state screening and updated docs appropriately. Also removed 'sparse' as an option to disable as it is not implemented in /Spinach/. ---- Modified : /docs/table_1 - spin system specification.docx Modified : /kernel/evolution.m Modified : /kernel/utils/validate.m Revision: 674 Author: kuprov Date: 28 October 2010 22:11:21 Message: Rolled back the previous commit. ---- Deleted : /examples/relaxation_theory/dnp_test_4.m Revision: 673 Author: kuprov Date: 28 October 2010 20:44:25 Message: An extra DNP example. ---- Added : /examples/relaxation_theory/dnp_test_4.m Revision: 672 Author: kuprov Date: 28 October 2010 20:40:03 Message: Tightened up very considerably the tolerances associated with state dropping in path tracing and symmetry factorization. Will sleep much better now. State vector scaling in ZTE is no longer necessary. ---- Modified : /kernel/utils/tolerances.m Modified : /kernel/zte.m Revision: 671 Author: kuprov Date: 28 October 2010 19:48:52 Message: A minor path fix. ---- Modified : /examples/relaxation_theory/cross_relaxation.m Revision: 670 Author: kuprov Date: 28 October 2010 18:49:41 Message: Slightly more robust norm estimator in the relaxation superoperator module and a n example of a cross-relaxation NMR experiment. ---- Added : /examples/molecules/tma.log Added : /examples/relaxation_theory/cross_relaxation.m Modified : /kernel/r_superop.m Revision: 669 Author: kuprov Date: 27 October 2010 11:17:14 Message: A fairly neat symmetry test. ---- Added : /examples/kernel/symmetry_test_2.m Revision: 668 Author: kuprov Date: 27 October 2010 11:06:12 Message: Considerably faster symmetry module. ---- Modified : /kernel/basis.m Revision: 667 Author: luke Date: 25 October 2010 15:50:27 Message: Added Ilya's relaxation correction to the 'refocused_trajectory' case in evolution.m, and made a few minor clarifications elsewhere. ---- Modified : /kernel/evolution.m Modified : /kernel/utils/significant.m Revision: 666 Author: kuprov Date: 23 October 2010 15:32:50 Message: Fixed a relaxation bug in the destination screening procedure. ---- Modified : /kernel/evolution.m Revision: 665 Author: luke Date: 20 October 2010 14:14:36 Message: Added option of supplying destination to 'refocused_trajectory' in evolution, and have modified endor and eseem experiments to take advantage of it. ---- Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /kernel/evolution.m Revision: 664 Author: luke Date: 20 October 2010 11:33:11 Message: Different implementation of Matthew's idea to implement detection state screening. The 'observable' case now runs reduce on the coil state instead of rho. ---- Modified : /kernel/evolution.m Revision: 663 Author: kuprov Date: 19 October 2010 18:29:42 Message: A pilot implementation of MK's idea of a detection state screen -- all subspaces not containing the detection state are being dropped. Massive speed-ups in NMR tests... :) ---- Modified : /kernel/evolution.m Revision: 662 Author: hannah Date: 19 October 2010 10:55:35 Message: Corrected small factor in RP kinetics bit. ---- Modified : /kernel/k_superop.m Revision: 661 Author: kuprov Date: 16 October 2010 18:18:05 Message: Correct carotene and pyrene cations HFC/g-tensor calculations added. ---- Modified : /examples/molecules/chrysene_cation.log Added : /examples/molecules/pyrene_cation.log Revision: 660 Author: kuprov Date: 15 October 2010 17:33:31 Message: Fixed the title line of the chrysene DFT calculation. ---- Modified : /examples/molecules/chrysene_cation.log Revision: 659 Author: kuprov Date: 15 October 2010 17:29:39 Message: MK's chrysene and pyrene files deleted chrysene already there, pyrene is wrong. ---- Deleted : /examples/molecules/chrysene_nmr.log Deleted : /examples/molecules/pyrene_nmr.log Revision: 658 Author: matthew Date: 14 October 2010 12:35:54 Message: Pyrene and chrysene NMR GIAO Gaussian log files added for the ESR calculations for the sake of the ESR state space restriction paper (Paper 10 in the repository) ---- Added : /examples/molecules/chrysene_nmr.log Added : /examples/molecules/pyrene_nmr.log Revision: 657 Author: hannah Date: 13 October 2010 17:40:11 Message: Found mistake in signs of anisotropic interaction expansion. Don't think it was affecting anything, but corrected now anyway I think. ---- Modified : /kernel/h_superop.m Revision: 656 Author: luke Date: 13 October 2010 16:42:27 Message: Fixed a small bug if one attempted to write to a logfile. ---- Modified : /kernel/utils/report.m Revision: 655 Author: kuprov Date: 09 October 2010 20:31:17 Message: Finally got the hypercomplex detection to work in the NOESY sequence. Beautiful stuff... :) ---- Modified : /etc/apodization.m Modified : /examples/nmr/noesy_test_1.m Modified : /examples/nmr/noesy_test_2.m Modified : /exp/noesy.m Revision: 654 Author: kuprov Date: 09 October 2010 15:21:31 Message: Slightly better reporting for ESR-2 basis set. An extra relaxation theory example. ---- Added : /examples/esr/relaxation_test_4.m Added : /examples/molecules/parafluorotoluene.log Modified : /kernel/basis.m Revision: 653 Author: kuprov Date: 08 October 2010 17:33:55 Message: Added a neat example of chrysene cation radical. ---- Added : /examples/esr/pulse_acquire_test_4.m Added : /examples/molecules/chrysene_cation.log Revision: 652 Author: kuprov Date: 04 October 2010 13:30:41 Message: Added Chebyshev series as an option for the calculation of exponential propagators. Appears to be slower than Taylor for sparse matrices that require the clean-up of stray non-zeros. Taken together with finite convergence radius (compared to Taylor's infinite), Chebyshev seems to be in all respects an inferior choice. ---- Modified : /docs/table_1 - spin system specification.docx Modified : /docs/table_2 - basis specification.docx Modified : /docs/table_3 - tolerances.docx Modified : /docs/table_4 - state indexing.docx Modified : /docs/table_5 - sequence parameters.docx Modified : /kernel/propagator.m Modified : /kernel/utils/tolerances.m Revision: 651 Author: kuprov Date: 03 October 2010 18:33:10 Message: Cosmetic improvement for ZTE - it will skip the reduction if the state vector norm is so small that everything gets dropped. This usually means that the user got something wrong. ---- Modified : /kernel/step.m Modified : /kernel/zte.m Revision: 650 Author: kuprov Date: 03 October 2010 17:55:17 Message: Simpson input filter fixed and tested. Need to run some powder patterns to make sure we are on the same page with Simpson on various rotational conventions. ---- Modified : /etc/simpson2spinach.m Added : /examples/molecules/simpson_input_3.in Added : /examples/molecules/simpson_input_4.in Modified : /installation.txt Modified : /kernel/create.m Modified : /kernel/utils/summary.m Modified : /kernel/utils/tensor_analysis.m Revision: 649 Author: kuprov Date: 30 September 2010 18:15:11 Message: An update to the equilibrium state generator -- traces of multi-spin states, which only become significant at millikelvin temperatures, have been included. The remaining sequences modified to request the equilibrium state from the kernel rather than stipulate their own. ---- Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /kernel/equilibrium.m Modified : /kernel/r_superop.m Revision: 648 Author: kuprov Date: 26 September 2010 00:33:07 Message: Minor. ---- Modified : /kernel/equilibrium.m Revision: 647 Author: kuprov Date: 22 September 2010 16:47:32 Message: Minor changes in response to Peter's comments. ---- Modified : /examples/esr/pulse_acquire_test_1.m Modified : /examples/esr/pulse_acquire_test_2.m Modified : /examples/esr/pulse_acquire_test_3.m Modified : /examples/esr/relaxation_test_1.m Modified : /examples/esr/relaxation_test_2.m Modified : /examples/esr/relaxation_test_3.m Modified : /examples/esr/solids_test_1.m Deleted : /examples/spin_chemistry/phosph_rad_pair_relax_and_ref.fig Modified : /installation.txt Modified : /kernel/create.m Modified : /kernel/utils/summary.m Revision: 646 Author: kuprov Date: 22 September 2010 09:27:48 Message: Unified some paths in the evolution function and updated docs and installation instructions. ---- Modified : /docs/Figure 1.pdf Added : /docs/table_1 - spin system specification.docx Deleted : /docs/table_1.docx Added : /docs/table_2 - basis specification.docx Deleted : /docs/table_2.docx Added : /docs/table_3 - tolerances.docx Deleted : /docs/table_3.docx Added : /docs/table_4 - state indexing.docx Deleted : /docs/table_4.docx Added : /docs/table_5 - sequence parameters.docx Deleted : /docs/table_5.docx Added : /docs/table_6 - gaussian import parameters.docx Deleted : /docs/table_6.docx Modified : /exp/endor.m Modified : /exp/eseem.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /installation.txt Modified : /kernel/evolution.m Modified : /kernel/utils/banner.m Revision: 645 Author: hannah Date: 22 September 2010 09:15:57 Message: MARY test with relaxation and reference. Don't expect answer to be exactly on the "reference" because both calculated with slightly different approximations but should probably be close? ---- Added : /examples/spin_chemistry/mary_test_6.m Added : /examples/spin_chemistry/phosph_rad_pair_relax_and_ref.fig Revision: 644 Author: kuprov Date: 21 September 2010 18:39:04 Message: Added Mims ENDOR with an example. ESR subsystem shaping up... :) ---- Added : /examples/esr/endor_test_1.m Added : /exp/endor.m Modified : /kernel/evolution.m Revision: 643 Author: kuprov Date: 21 September 2010 16:52:30 Message: Polished the ESEEM sequence and added an example. ---- Added : /examples/esr/eseem_test_1.m Modified : /exp/eseem.m Revision: 642 Author: kuprov Date: 21 September 2010 16:10:01 Message: Added Kaiser window and ESEEM sequence. ---- Modified : /etc/apodization.m Modified : /examples/nmr/zero_field_1.m Modified : /examples/nmr/zero_field_2.m Modified : /examples/relaxation_theory/dd_csa_test_1.m Added : /exp/eseem.m Modified : /exp/hmqc.m Modified : /kernel/h_superop.m Revision: 641 Author: hannah Date: 20 September 2010 17:06:50 Message: Relaxation input allowed by validate for full operator was 'full' but r_superop only recognised 'all'. Now option is 'full' in r_superop. ---- Modified : /kernel/r_superop.m Revision: 640 Author: kuprov Date: 20 September 2010 11:56:28 Message: A minor bug fix in 2D NMR examples. ---- Modified : /examples/nmr/cosy_test_1.m Modified : /examples/nmr/cosy_test_2.m Modified : /examples/nmr/cosy_test_3.m Modified : /examples/nmr/cosy_test_4.m Modified : /examples/nmr/cosy_test_5.m Modified : /examples/nmr/dqf_cosy_test_1.m Modified : /examples/nmr/dqf_cosy_test_2.m Modified : /examples/nmr/hetcor_test_1.m Modified : /examples/nmr/hetcor_test_2.m Modified : /examples/nmr/hmqc_test_1.m Modified : /examples/nmr/hmqc_test_2.m Modified : /examples/nmr/hsqc_test_1.m Modified : /examples/nmr/hsqc_test_2.m Modified : /examples/nmr/noesy_test_1.m Modified : /examples/nmr/noesy_test_2.m Revision: 639 Author: kuprov Date: 19 September 2010 16:26:27 Message: The necessary acknowledgements. ---- Added : /etc/wave/acknowledgements.txt Added : /exp/grids/acknowldegements.txt Deleted : /exp/grids/lebedev.c Deleted : /exp/grids/sphere.c Revision: 638 Author: kuprov Date: 19 September 2010 16:22:25 Message: Minor filesystem tweaks. ---- Added : /docs/Figure 1.pdf (Copy from path: /docs/syntax/Figure 1.pdf, Revision, 637) Added : /docs/Figure 2.pdf (Copy from path: /docs/syntax/Figure 2.pdf, Revision, 637) Added : /docs/Figure 3.pdf (Copy from path: /docs/syntax/Figure 3.pdf, Revision, 637) Added : /docs/Figure 4.pdf (Copy from path: /docs/syntax/Figure 4.pdf, Revision, 637) Added : /docs/Figure 5.pdf (Copy from path: /docs/syntax/Figure 5.pdf, Revision, 637) Added : /docs/Figure 6.pdf (Copy from path: /docs/syntax/Figure 6.pdf, Revision, 637) Added : /docs/Figure 7.pdf (Copy from path: /docs/syntax/Figure 7.pdf, Revision, 637) Added : /docs/Figure 8.pdf (Copy from path: /docs/syntax/Figure 8.pdf, Revision, 637) Deleted : /docs/architecture Deleted : /docs/data structures Deleted : /docs/syntax Added : /docs/table_1.docx (Copy from path: /docs/syntax/table_1.docx, Revision, 637) Added : /docs/table_2.docx (Copy from path: /docs/syntax/table_2.docx, Revision, 637) Added : /docs/table_3.docx (Copy from path: /docs/syntax/table_3.docx, Revision, 637) Added : /docs/table_4.docx (Copy from path: /docs/syntax/table_4.docx, Revision, 637) Added : /docs/table_5.docx (Copy from path: /docs/syntax/table_5.docx, Revision, 637) Added : /docs/table_6.docx (Copy from path: /docs/syntax/table_6.docx, Revision, 637) Modified : /installation.txt Revision: 637 Author: kuprov Date: 17 September 2010 16:44:46 Message: Flags and documentation. ---- Added : /docs/syntax/Figure 1.pdf Added : /docs/syntax/Figure 2.pdf Added : /docs/syntax/Figure 3.pdf Added : /docs/syntax/Figure 4.pdf Added : /docs/syntax/Figure 5.pdf Added : /docs/syntax/Figure 6.pdf Added : /docs/syntax/Figure 7.pdf Added : /docs/syntax/Figure 8.pdf Modified : /docs/syntax/table_1.docx Modified : /docs/syntax/table_2.docx Modified : /docs/syntax/table_3.docx Added : /docs/syntax/table_4.docx Added : /docs/syntax/table_5.docx Added : /docs/syntax/table_6.docx Modified : /examples/kernel/commutation_test_1.m Modified : /examples/kernel/commutation_test_2.m Modified : /examples/kernel/commutation_test_3.m Modified : /examples/kernel/symmetry_test_1.m Modified : /examples/nmr/high_spin_test_1.m Modified : /examples/nmr/large_scale_test_1.m Modified : /examples/nmr/large_scale_test_2.m Modified : /examples/nmr/shaped_pulse_test_1.m Modified : /examples/nmr/shaped_pulse_test_2.m Modified : /examples/nmr/simpson_test_1.m Modified : /examples/nmr/simpson_test_2.m Modified : /examples/nmr/zero_field_1.m Modified : /examples/nmr/zero_field_2.m Modified : /examples/optimal_control/optimal_control_1.m Modified : /examples/optimal_control/optimal_control_2.m Modified : /examples/quantum_computing/quantum_memory_test_1.m Modified : /examples/quantum_computing/quantum_memory_test_2.m Modified : /examples/quantum_computing/quantum_memory_test_3.m Modified : /examples/quantum_computing/quantum_memory_test_4.m Modified : /examples/relaxation_theory/csa_test_1.m Deleted : /examples/relaxation_theory/csa_test_1.nb Modified : /examples/relaxation_theory/dd_csa_test_1.m Deleted : /examples/relaxation_theory/dd_csa_test_1.nb Modified : /examples/relaxation_theory/dd_csa_test_2.m Modified : /examples/relaxation_theory/dd_quad_test_1.m Modified : /examples/relaxation_theory/dd_test_1.m Deleted : /examples/relaxation_theory/dd_test_1.nb Modified : /examples/relaxation_theory/dd_test_2.m Modified : /examples/relaxation_theory/dd_test_3.m Modified : /examples/relaxation_theory/dnp_test_1.m Modified : /examples/relaxation_theory/dnp_test_2.m Modified : /examples/relaxation_theory/dnp_test_3.m Modified : /examples/relaxation_theory/equilibrium_test_1.m Modified : /examples/relaxation_theory/hfc_test_1.m Deleted : /examples/relaxation_theory/hfc_test_1.nb Modified : /examples/relaxation_theory/quad_test_1.m Modified : /examples/spin_chemistry/mfe_test_1.m Modified : /exp/mfe.m Modified : /exp/sequence_report.m Modified : /exp/zerofield.m Revision: 636 Author: kuprov Date: 17 September 2010 16:27:49 Message: An epic polish for all the example files -- I am mostly satisfied by it at this point. ---- Modified : /etc/apodization.m Modified : /etc/axis_1d.m Modified : /etc/axis_2d.m Modified : /etc/contour_plot.m Added : /etc/fftdiff.m Modified : /etc/plot_1d.m Deleted : /examples/dnp Modified : /examples/esr/pulse_acquire_test_1.m Modified : /examples/esr/pulse_acquire_test_2.m Modified : /examples/esr/pulse_acquire_test_3.m Modified : /examples/esr/relaxation_test_1.m Modified : /examples/esr/relaxation_test_2.m Modified : /examples/esr/relaxation_test_3.m Deleted : /examples/esr/relaxation_test_4.m Modified : /examples/esr/solids_test_1.m Added : /examples/kernel/commutation_test_1.m (Copy from path: /examples/kernel/single_spin_test_1.m, Revision, 634) Added : /examples/kernel/commutation_test_2.m (Copy from path: /examples/kernel/single_spin_test_2.m, Revision, 634) Added : /examples/kernel/commutation_test_3.m (Copy from path: /examples/kernel/three_spin_test_1.m, Revision, 634) Deleted : /examples/kernel/equilibrium_test_1.m Deleted : /examples/kernel/four_spin_test_1.m Deleted : /examples/kernel/large_scale_test_1.m Deleted : /examples/kernel/large_scale_test_2.m Deleted : /examples/kernel/large_scale_test_3.m Deleted : /examples/kernel/shaped_pulse_test_1.m Deleted : /examples/kernel/simpson_test_1.m Deleted : /examples/kernel/simpson_test_2.m Deleted : /examples/kernel/single_spin_test_1.m Deleted : /examples/kernel/single_spin_test_2.m Modified : /examples/kernel/symmetry_test_1.m Deleted : /examples/kernel/three_spin_test_1.m Deleted : /examples/kernel/two_spin_test_1.m Modified : /examples/nmr/chem_test_1.m Modified : /examples/nmr/chem_test_2.m Modified : /examples/nmr/cosy_test_1.m Modified : /examples/nmr/cosy_test_2.m Modified : /examples/nmr/cosy_test_3.m Modified : /examples/nmr/cosy_test_4.m Modified : /examples/nmr/cosy_test_5.m Modified : /examples/nmr/dqf_cosy_test_1.m Modified : /examples/nmr/dqf_cosy_test_2.m Modified : /examples/nmr/hetcor_test_1.m Modified : /examples/nmr/hetcor_test_2.m Added : /examples/nmr/high_spin_test_1.m (Copy from path: /examples/kernel/four_spin_test_1.m, Revision, 634) Modified : /examples/nmr/hmqc_test_1.m Modified : /examples/nmr/hmqc_test_2.m Modified : /examples/nmr/hsqc_test_1.m Modified : /examples/nmr/hsqc_test_2.m Added : /examples/nmr/large_scale_test_1.m (Copy from path: /examples/kernel/large_scale_test_1.m, Revision, 634) Added : /examples/nmr/large_scale_test_2.m (Copy from path: /examples/kernel/large_scale_test_3.m, Revision, 634) Modified : /examples/nmr/noesy_test_1.m Modified : /examples/nmr/noesy_test_2.m Modified : /examples/nmr/pulse_acquire_test_1.m Modified : /examples/nmr/pulse_acquire_test_2.m Modified : /examples/nmr/pulse_acquire_test_3.m Added : /examples/nmr/shaped_pulse_test_1.m (Copy from path: /examples/kernel/shaped_pulse_test_1.m, Revision, 634) Added : /examples/nmr/shaped_pulse_test_2.m Added : /examples/nmr/simpson_test_1.m (Copy from path: /examples/kernel/simpson_test_1.m, Revision, 634) Added : /examples/nmr/simpson_test_2.m (Copy from path: /examples/kernel/simpson_test_2.m, Revision, 634) Modified : /examples/nmr/solids_test_1.m Modified : /examples/nmr/solids_test_2.m Modified : /examples/nmr/solids_test_3.m Modified : /examples/nmr/solids_test_4.m Added : /examples/nmr/zero_field_1.m (Copy from path: /examples/optical_magnetometry/zero_field_1.m, Revision, 634) Added : /examples/nmr/zero_field_2.m (Copy from path: /examples/optical_magnetometry/zero_field_2.m, Revision, 634) Deleted : /examples/optical_magnetometry Modified : /examples/relaxation_theory/dd_quad_test_1.m Added : /examples/relaxation_theory/dnp_test_1.m (Copy from path: /examples/dnp/dnp_test_1.m, Revision, 634) Added : /examples/relaxation_theory/dnp_test_2.m (Copy from path: /examples/dnp/dnp_test_2.m, Revision, 634) Added : /examples/relaxation_theory/dnp_test_3.m (Copy from path: /examples/dnp/dnp_test_3.m, Revision, 634) Added : /examples/relaxation_theory/equilibrium_test_1.m (Copy from path: /examples/kernel/equilibrium_test_1.m, Revision, 634) Modified : /exp/cosy.m Modified : /exp/dqf_cosy.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /exp/noesy.m Modified : /exp/pulse_acquire.m Modified : /exp/sequence_report.m Modified : /exp/zerofield.m Modified : /kernel/create.m Modified : /kernel/path_trace.m Modified : /kernel/spin.m Deleted : /kernel/utils/fourdif.m Modified : /kernel/utils/tolerances.m Revision: 635 Author: kuprov Date: 16 September 2010 11:39:31 Message: Removed a restriction that enforced no Redfield theory in solid state -- there seem to be enough desperate people that want to commit that particular sin. Also removed Kominis superoperator: out of the box it produces a load of garbage. ---- Modified : /kernel/create.m Modified : /kernel/k_superop.m Revision: 634 Author: kuprov Date: 15 September 2010 18:39:43 Message: Some modifications to the MFE experiment. ---- Deleted : /examples/spin_chemistry/kinetics_test_1.m Added : /examples/spin_chemistry/mfe_test_1.m (Copy from path: /examples/spin_chemistry/kinetics_test_1.m, Revision, 630) Added : /exp/mfe.m (Copy from path: /exp/singlet_dynamics.m, Revision, 630) Modified : /exp/sequence_report.m Deleted : /exp/singlet_dynamics.m Revision: 633 Author: kuprov Date: 15 September 2010 12:13:22 Message: Fixed a bug in the orientation function. Ordered up the Spin Chemistry examples and finalized MARY/MARYAN experiment files. ---- Modified : /examples/spin_chemistry/mary_test_1.m Modified : /examples/spin_chemistry/mary_test_2.m Added : /examples/spin_chemistry/mary_test_3.m (Copy from path: /examples/spin_chemistry/timmel_cpl_fig_3.m, Revision, 628) Added : /examples/spin_chemistry/mary_test_4.m (Copy from path: /examples/spin_chemistry/timmel_molphys_fig_1.m, Revision, 628) Added : /examples/spin_chemistry/mary_test_5.m (Copy from path: /examples/spin_chemistry/timmel_molphys_fig_5.m, Revision, 628) Added : /examples/spin_chemistry/maryan_test_1.m (Copy from path: /examples/spin_chemistry/rodgers_thesis_fig_7_10.m, Revision, 628) Deleted : /examples/spin_chemistry/rodgers_thesis_fig_7_10.m Deleted : /examples/spin_chemistry/rodgers_thesis_fig_7_8.m Deleted : /examples/spin_chemistry/timmel_cpl_fig_3.m Deleted : /examples/spin_chemistry/timmel_molphys_fig_1.m Deleted : /examples/spin_chemistry/timmel_molphys_fig_5.m Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /kernel/orientation.m Deleted : /kernel/rotations Revision: 632 Author: kuprov Date: 14 September 2010 20:48:05 Message: Minor file shifting. ---- Deleted : /kernel/rotations/euler2dcm.m Deleted : /kernel/rotations/euler2wigner.m Added : /kernel/utils/euler2dcm.m (Copy from path: /kernel/rotations/euler2dcm.m, Revision, 628) Added : /kernel/utils/euler2wigner.m (Copy from path: /kernel/rotations/euler2wigner.m, Revision, 628) Revision: 631 Author: kuprov Date: 14 September 2010 19:01:50 Message: A considerably richer apodization function. ---- Modified : /etc/apodization.m Revision: 630 Author: kuprov Date: 14 September 2010 17:14:15 Message: Added recombination kinetics superoperators with a few examples. ---- Modified : /examples/kernel/two_spin_test_1.m Added : /examples/spin_chemistry/kinetics_test_1.m Added : /exp/singlet_dynamics.m Modified : /kernel/create.m Modified : /kernel/k_superop.m Modified : /kernel/p_superop.m Revision: 629 Author: kuprov Date: 13 September 2010 11:12:14 Message: Demoted dcm2wigner to the userland and eliminated its use from the kernel. Put some extra comments to the grape function. ---- Modified : /etc/dcm2euler.m Added : /etc/dcm2wigner.m (Copy from path: /kernel/rotations/dcm2wigner.m, Revision, 628) Modified : /etc/quat2euler.m Modified : /kernel/grape.m Deleted : /kernel/rotations/dcm2wigner.m Modified : /kernel/utils/scomponents.m Modified : /kernel/utils/sparse_to_csr.m Modified : /kernel/utils/summary.m Modified : /kernel/utils/tensor_analysis.m Revision: 628 Author: kuprov Date: 12 September 2010 19:37:21 Message: Minor tweaks to the evolution and the propagator modules. ---- Modified : /examples/esr/relaxation_test_4.m Modified : /kernel/evolution.m Modified : /kernel/path_trace.m Modified : /kernel/propagator.m Revision: 627 Author: kuprov Date: 11 September 2010 16:59:32 Message: Cleaned up the orientation function. ---- Modified : /examples/spin_chemistry/rodgers_thesis_fig_7_8.m Modified : /exp/maryan.m Modified : /exp/pulse_acquire.m Modified : /kernel/orientation.m Revision: 626 Author: kuprov Date: 11 September 2010 12:22:05 Message: Modified the secularity masking in the relaxation module - it no longer requires an outrageous amount of memory for large systems. Added a large-scale ESR relaxation theory test. ---- Added : /examples/esr/relaxation_test_4.m Deleted : /examples/molecules/biaryl.gjf Deleted : /examples/molecules/biaryl.log Deleted : /examples/molecules/biaryl_nmr.gjf Deleted : /examples/molecules/biaryl_nmr.log Modified : /kernel/r_superop.m Revision: 625 Author: kuprov Date: 10 September 2010 12:39:59 Message: Introduced ESR-2 basis set -- complete on electrons and anisotropically coupled nuclei, {E,Lz} on isotropically coupled nuclei. This is much more accurate for relaxation theory. ---- Modified : /examples/esr/relaxation_test_1.m Modified : /examples/esr/relaxation_test_2.m Modified : /examples/esr/relaxation_test_3.m Modified : /examples/esr/solids_test_1.m Modified : /kernel/basis.m Modified : /kernel/utils/validate.m Revision: 624 Author: matthew Date: 09 September 2010 20:13:47 Message: New calculations on biaryl radicals, this time with charge=1 and multiplicity=2 and EPR II basis set ---- Added : /examples/molecules/biaryl.gjf (Copy from path: /examples/molecules/biaryl.gjf, Revision, 622) Added : /examples/molecules/biaryl.log (Copy from path: /examples/molecules/biaryl.log, Revision, 622) Added : /examples/molecules/biaryl_nmr.gjf (Copy from path: /examples/molecules/biaryl_nmr.gjf, Revision, 622) Added : /examples/molecules/biaryl_nmr.log (Copy from path: /examples/molecules/biaryl_nmr.log, Revision, 622) Revision: 623 Author: kuprov Date: 09 September 2010 12:10:33 Message: A bug needs fixing in biaryl example. ---- Deleted : /examples/molecules/biaryl.gjf Deleted : /examples/molecules/biaryl.log Deleted : /examples/molecules/biaryl_nmr.gjf Deleted : /examples/molecules/biaryl_nmr.log Revision: 622 Author: matthew Date: 09 September 2010 11:59:13 Message: New Gaussian jobs on biaryl cation radical and on camphor for the sake of benchmarking against literature magnetic resonance spectra ---- Added : /examples/molecules/biaryl.gjf Added : /examples/molecules/biaryl.log Added : /examples/molecules/biaryl_nmr.gjf Added : /examples/molecules/biaryl_nmr.log Added : /examples/molecules/camphor.log Revision: 621 Author: kuprov Date: 09 September 2010 09:48:51 Message: Added anticommutation superoperators -- will be useful in the kinetics module. ---- Added : /kernel/a_superop.m Revision: 620 Author: kuprov Date: 08 September 2010 18:18:26 Message: Minor refinements in the examples section. ---- Modified : /examples/esr/pulse_acquire_test_2.m Modified : /examples/esr/relaxation_test_1.m Modified : /examples/esr/relaxation_test_3.m Modified : /examples/esr/solids_test_1.m Modified : /examples/nmr/pulse_acquire_test_1.m Modified : /examples/nmr/pulse_acquire_test_2.m Modified : /examples/nmr/pulse_acquire_test_3.m Revision: 619 Author: kuprov Date: 08 September 2010 18:00:21 Message: A very dramatic ESR example - 13 spins, including two 14N nuclei. ---- Modified : /examples/esr/pulse_acquire_test_1.m Modified : /examples/esr/pulse_acquire_test_2.m Modified : /examples/esr/pulse_acquire_test_3.m Added : /examples/esr/solids_test_1.m Modified : /kernel/r_superop.m Modified : /kernel/utils/stepsize.m Modified : /kernel/utils/tolerances.m Revision: 618 Author: kuprov Date: 08 September 2010 17:19:15 Message: Quite a breakthrough -- introduced a conservation-filtered ESR-1 basis set: complete on electrons and z-only on nuclei, to match the conservation laws of high-field ESR. Massive speed-up across the spectrum of ESR calculations. Relaxation seems to work in ESR-1 too, but this needs double-checking. ---- Modified : /examples/esr/pulse_acquire_test_1.m Modified : /examples/esr/pulse_acquire_test_2.m Modified : /examples/esr/pulse_acquire_test_3.m Modified : /examples/esr/relaxation_test_1.m Modified : /examples/esr/relaxation_test_2.m Modified : /kernel/basis.m Modified : /kernel/utils/validate.m Revision: 617 Author: kuprov Date: 08 September 2010 15:30:50 Message: Added the Fremy salt example (adapted from EasySpin example set). ---- Added : /examples/esr/pulse_acquire_test_2.m (Copy from path: /examples/esr/pulse_acquire_test_4.m, Revision, 613) Deleted : /examples/esr/pulse_acquire_test_4.m Modified : /examples/esr/relaxation_test_1.m Modified : /examples/esr/relaxation_test_2.m Added : /examples/esr/relaxation_test_3.m Revision: 616 Author: kuprov Date: 08 September 2010 15:00:32 Message: Considerable speed-up in h_superop.m -- it now aggressively avoids doing the work it does not have to do. ---- Modified : /kernel/h_superop.m Revision: 615 Author: kuprov Date: 08 September 2010 14:54:14 Message: Fixed the EPR axis scale. ---- Modified : /etc/axis_1d.m Revision: 614 Author: kuprov Date: 08 September 2010 14:18:06 Message: A massive speed-up in the relaxation theory module and two new relaxation theory tests for EPR. ---- Deleted : /examples/esr/pulse_acquire_test_2.m Added : /examples/esr/relaxation_test_1.m Added : /examples/esr/relaxation_test_2.m (Copy from path: /examples/esr/pulse_acquire_test_2.m, Revision, 613) Modified : /kernel/create.m Modified : /kernel/r_superop.m Revision: 613 Author: kuprov Date: 05 September 2010 17:54:16 Message: Introduced phenomenological damping as an option for the relaxation theory. Removed all the spurious garbage from the sequence reporting utility. Improved diagnostic reporting from the Hamiltonian superoperator. ---- Modified : /exp/sequence_report.m Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/r_superop.m Modified : /kernel/utils/validate.m Revision: 612 Author: kuprov Date: 05 September 2010 15:08:58 Message: Decided against printing the secularity status during create script. This is really for the user land to decide. The default decisions are still made, just not printed. ---- Modified : /kernel/utils/summary.m Revision: 611 Author: kuprov Date: 05 September 2010 14:18:29 Message: Made ZTE normalize the state vector before processing, cleaned up a few sequences. ---- Modified : /exp/dqf_cosy.m Modified : /exp/noesy.m Modified : /kernel/zte.m Revision: 610 Author: kuprov Date: 05 September 2010 13:35:16 Message: Allowed high-spin electrons. For example, 'E3' specifies a spin-1 electron shell. 'E2' is the same as 'E'. ---- Modified : /etc/plot_1d.m Modified : /kernel/create.m Modified : /kernel/spin.m Revision: 609 Author: kuprov Date: 03 September 2010 10:57:09 Message: A slight alteration to the validation tolerances. ---- Modified : /kernel/utils/validate.m Revision: 608 Author: kuprov Date: 31 August 2010 18:26:55 Message: Documentation update and cleaning up of tolerances. ---- Modified : /docs/syntax/table_1.docx Added : /docs/syntax/table_2.docx Added : /docs/syntax/table_3.docx Modified : /kernel/utils/tolerances.m Revision: 607 Author: kuprov Date: 31 August 2010 17:09:50 Message: Updated the docs. ---- Added : /docs/architecture Added : /docs/architecture/Figure 2.pdf Deleted : /docs/basis_parameters.docx Deleted : /docs/c_superop_parameters.docx Deleted : /docs/click_parameters.docx Deleted : /docs/create_parameters.docx Added : /docs/data structures Added : /docs/data structures/Figure 3.pdf Added : /docs/data structures/Figure 4.pdf Added : /docs/data structures/Figure 5.pdf Added : /docs/data structures/Figure 6.pdf Added : /docs/data structures/Figure 7.pdf Added : /docs/data structures/Figure 8.pdf Deleted : /docs/equilibrium_parameters.docx Deleted : /docs/evolution_parameters.docx Deleted : /docs/expv_parameters.docx Deleted : /docs/grape_parameters.docx Deleted : /docs/h_superop_parameters.docx Deleted : /docs/k_superop_parameters.docx Deleted : /docs/lin2lm_parameters.docx Deleted : /docs/lm2lin_parameters.docx Deleted : /docs/orientation_parameters.docx Deleted : /docs/p_superop_parameters.docx Deleted : /docs/path_trace_parameters.docx Deleted : /docs/propagator_parameters.docx Deleted : /docs/r_superop_parameters.docx Deleted : /docs/reduce_parameters.docx Deleted : /docs/report_parameters.docx Deleted : /docs/spin_parameters.docx Deleted : /docs/statevec_parameters.docx Deleted : /docs/step_parameters.docx Added : /docs/syntax Added : /docs/syntax/table_1.docx Deleted : /docs/zte_parameters.docx Revision: 606 Author: kuprov Date: 31 August 2010 09:50:11 Message: Removed the Bioinformatics Toolbox components from the kernel and replaced them with an open-source function. Should produce a lot fewer licensing errors from now on. ---- Modified : /kernel/path_trace.m Deleted : /kernel/utils/graphalgs.mexa64 Deleted : /kernel/utils/graphalgs.mexglx Deleted : /kernel/utils/graphalgs.mexmaci Deleted : /kernel/utils/graphalgs.mexs64 Deleted : /kernel/utils/graphalgs.mexw32 Deleted : /kernel/utils/graphalgs.mexw64 Deleted : /kernel/utils/graphconncomp.m Added : /kernel/utils/scomponents.m Added : /kernel/utils/sparse_to_csr.m Revision: 605 Author: kuprov Date: 27 August 2010 20:45:00 Message: Found and fixed a very stealthy kernel bug - many thanks to MK for spotting. ---- Modified : /etc/g03_to_spinach.m Modified : /examples/nmr/chem_test_1.m Modified : /examples/nmr/chem_test_2.m Modified : /examples/nmr/cosy_test_4.m Modified : /examples/nmr/cosy_test_5.m Modified : /kernel/basis.m Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/p_superop.m Modified : /kernel/utils/summary.m Modified : /kernel/utils/validate.m Revision: 604 Author: kuprov Date: 24 August 2010 17:49:17 Message: Added a COSY-45 example and updated the contouring in one of the existing files. ---- Modified : /examples/nmr/cosy_test_2.m Added : /examples/nmr/cosy_test_5.m Revision: 603 Author: kuprov Date: 24 August 2010 17:29:38 Message: A modification to COSY to allow COSY45 and COSY60. A cosmetic contouring change to one of the examples. ---- Modified : /examples/nmr/cosy_test_3.m Modified : /examples/nmr/cosy_test_4.m Modified : /exp/cosy.m Revision: 602 Author: kuprov Date: 24 August 2010 16:50:43 Message: Cosy-45 stuff deleted until such time as it starts working. Rotanone examples introduced. ---- Deleted : /examples/nmr/cosy_45_test_1.m Deleted : /examples/nmr/cosy_45_test_2.m Deleted : /examples/nmr/cosy_45_test_3.m Deleted : /examples/nmr/cosy_45_test_rotanone.m Added : /examples/nmr/cosy_test_4.m (Copy from path: /examples/nmr/cosy_test_rotanone.m, Revision, 600) Deleted : /examples/nmr/cosy_test_rotanone.m Added : /examples/nmr/pulse_acquire_test_3.m (Copy from path: /examples/nmr/pulse_acquire_test_rotanone.m, Revision, 600) Deleted : /examples/nmr/pulse_acquire_test_rotanone.m Deleted : /exp/cosy_45.m Revision: 601 Author: kuprov Date: 24 August 2010 16:34:47 Message: A bug fix to the kinetics superoperator. Deleted the enormous fig files from the previous commit. ---- Deleted : /examples/nmr/cosy_45_test_1.fig Deleted : /examples/nmr/cosy_45_test_2.fig Deleted : /examples/nmr/cosy_45_test_3.fig Deleted : /examples/nmr/cosy_45_test_rotanone.fig Deleted : /examples/nmr/cosy_test_rotanone.fig Deleted : /examples/nmr/pulse_acquire_test_rotanone.fig Modified : /kernel/k_superop.m Revision: 600 Author: matthew Date: 24 August 2010 16:06:34 Message: Cosy_45 pulse sequence added together with suitable tests. The problem with cosy_45 still persisting that the off-diagonal peaks appear too weak and not too many of them are there. Most probably, the phase cycle must be fixed for cosy_45.m Also, different pulse sequences and tests for rotanone. Rotanone has got 3 different methyl group where the symmetry module in basis can be nicely tested. Attached are pulse acquire (artificially too much of resolution due to lack of the relaxation module), cosy and cosy_45 pulse sequences. ---- Added : /examples/nmr/cosy_45_test_1.fig Added : /examples/nmr/cosy_45_test_1.m Added : /examples/nmr/cosy_45_test_2.fig Added : /examples/nmr/cosy_45_test_2.m Added : /examples/nmr/cosy_45_test_3.fig Added : /examples/nmr/cosy_45_test_3.m Added : /examples/nmr/cosy_45_test_rotanone.fig Added : /examples/nmr/cosy_45_test_rotanone.m Added : /examples/nmr/cosy_test_rotanone.fig Added : /examples/nmr/cosy_test_rotanone.m Added : /examples/nmr/pulse_acquire_test_rotanone.fig Added : /examples/nmr/pulse_acquire_test_rotanone.m Added : /exp/cosy_45.m Revision: 599 Author: kuprov Date: 24 August 2010 15:58:58 Message: Two chemical exchange examples. ---- Deleted : /examples/internal_consistency Added : /examples/kernel (Copy from path: /examples/internal_consistency, Revision, 598) Added : /examples/nmr/chem_test_1.m Added : /examples/nmr/chem_test_2.m Revision: 598 Author: kuprov Date: 24 August 2010 11:55:55 Message: Added basis validation, renamed tests into examples. ---- Added : /examples (Copy from path: /tests, Revision, 595) Replacing : /examples/optimal_control/optimal_control_1.m (Copy from path: /tests/optimal_control/optimal_control_1.m, Revision, 597) Modified : /kernel/basis.m Modified : /kernel/utils/validate.m Deleted : /tests Revision: 597 Author: kuprov Date: 23 August 2010 20:38:29 Message: Full validation checks up and running for the create module. It is now significantly harder for the user to do something silly. :) ---- Modified : /kernel/create.m Modified : /kernel/utils/validate.m Modified : /tests/optimal_control/optimal_control_1.m Revision: 596 Author: kuprov Date: 23 August 2010 12:19:22 Message: Slowly and carefully putting the input validation checks back into the kernel... ---- Modified : /kernel/create.m Modified : /kernel/utils/validate.m Revision: 595 Author: kuprov Date: 19 August 2010 18:47:53 Message: Brought the MARYAN tests to new syntax. ---- Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_10.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_8.m Revision: 594 Author: kuprov Date: 19 August 2010 18:16:12 Message: Abandoned the contents of the validation module for the time being. It will be filled in response to the errors that the users are actually making. ---- Modified : /kernel/basis.m Modified : /kernel/create.m Modified : /kernel/utils/fourdif.m Modified : /kernel/utils/validate.m Revision: 593 Author: kuprov Date: 19 August 2010 15:02:29 Message: Quadrupolar and dipole-quadrupolar relaxation tests likely of interest to Alex Jerschow. ---- Modified : /etc/plot_1d.m Added : /tests/relaxation_theory/dd_quad_test_1.m Added : /tests/relaxation_theory/quad_test_1.m Revision: 592 Author: kuprov Date: 19 August 2010 12:17:12 Message: Added DQF-COSY sequence with examples. ---- Modified : /exp/cosy.m Added : /exp/dqf_cosy.m Added : /tests/nmr/dqf_cosy_test_1.m Added : /tests/nmr/dqf_cosy_test_2.m Revision: 591 Author: kuprov Date: 16 August 2010 18:45:46 Message: Allowed space clusterization in IK-2 basis sets. ---- Modified : /kernel/basis.m Revision: 590 Author: kuprov Date: 16 August 2010 18:44:59 Message: Modified noesy tests so that they actually run in reasonable time. ---- Modified : /tests/nmr/noesy_test_1.m Modified : /tests/nmr/noesy_test_2.m Revision: 589 Author: kuprov Date: 16 August 2010 17:23:53 Message: Solid-state EPR added, optimal control examples modified to be more convincing, fixes and tightening up all over the place. Three regimes are now available: liquid, crystal and powder; pulse_acquire behaves accordingly. ---- Modified : /etc/plot_1d.m Modified : /exp/pulse_acquire.m Deleted : /exp/pulse_acquire_powder.m Deleted : /exp/pulse_acquire_zerofield.m Added : /exp/zerofield.m (Copy from path: /exp/pulse_acquire_zerofield.m, Revision, 569) Modified : /kernel/create.m Added : /kernel/utils/fourdif.m Modified : /tests/esr/pulse_acquire_test_1.m Modified : /tests/esr/pulse_acquire_test_2.m Modified : /tests/esr/pulse_acquire_test_3.m Added : /tests/esr/pulse_acquire_test_4.m Modified : /tests/internal_consistency/four_spin_test_1.m Modified : /tests/internal_consistency/large_scale_test_1.m Modified : /tests/internal_consistency/large_scale_test_2.m Modified : /tests/internal_consistency/large_scale_test_3.m Added : /tests/internal_consistency/shaped_pulse_test_1.m (Copy from path: /tests/nmr/shaped_pulse_test_1.m, Revision, 569) Modified : /tests/internal_consistency/simpson_test_1.m Modified : /tests/internal_consistency/simpson_test_2.m Modified : /tests/internal_consistency/three_spin_test_1.m Modified : /tests/nmr/noesy_test_1.m Modified : /tests/nmr/noesy_test_2.m Deleted : /tests/nmr/shaped_pulse_test_1.m Modified : /tests/nmr/solids_test_1.m Modified : /tests/nmr/solids_test_2.m Modified : /tests/nmr/solids_test_3.m Modified : /tests/nmr/solids_test_4.m Modified : /tests/optical_magnetometry/zero_field_1.m Modified : /tests/optical_magnetometry/zero_field_2.m Modified : /tests/optimal_control/optimal_control_1.m Modified : /tests/optimal_control/optimal_control_2.m Deleted : /tests/optimal_control/optimal_control_3.m Deleted : /tests/optimal_control/spin_chain_1.m Deleted : /tests/optimal_control/spin_chain_2.m Deleted : /tests/optimal_control/spin_chain_3.m Deleted : /tests/optimal_control/spin_chain_4.m Deleted : /tests/optimal_control/spin_chain_5.m Deleted : /tests/optimal_control/spin_chain_6.m Modified : /tests/relaxation_theory/dd_csa_test_2.m Revision: 588 Author: kuprov Date: 15 August 2010 18:55:37 Message: Cleaned up and tested the quadrupole examples. Massive speed-up due to edits made in the previous commit. Default Lebedev rank back to 131 -- needed for quadrupole systems. ---- Modified : /kernel/utils/tolerances.m Deleted : /tests/nmr/quadrupole_test_1.m Deleted : /tests/nmr/quadrupole_test_2.m Added : /tests/nmr/solids_test_3.m (Copy from path: /tests/nmr/quadrupole_test_1.m, Revision, 569) Added : /tests/nmr/solids_test_4.m (Copy from path: /tests/nmr/quadrupole_test_2.m, Revision, 569) Revision: 587 Author: kuprov Date: 15 August 2010 18:38:31 Message: Complete rewrite of the solids version of pulse-acquire -- about 50 times faster now. Introduced a Krylov disable switch into the evolution module. Massively accelerated the orientation module when many orientations need to be computed at once. ---- Modified : /exp/pulse_acquire_powder.m Modified : /kernel/evolution.m Modified : /kernel/orientation.m Modified : /kernel/utils/clean_up.m Modified : /kernel/utils/tolerances.m Modified : /tests/nmr/solids_test_1.m Modified : /tests/nmr/solids_test_2.m Revision: 586 Author: kuprov Date: 15 August 2010 16:04:58 Message: Three ESR examples -- nitroxide, phenyl and methyl. Beautiful g-hfc cross-correlation pattern on nitroxide... :) ---- Deleted : /exp/inversion_recovery.m Added : /tests/esr/pulse_acquire_test_1.m Added : /tests/esr/pulse_acquire_test_2.m Added : /tests/esr/pulse_acquire_test_3.m Modified : /tests/nmr/pulse_acquire_test_1.m Modified : /tests/nmr/pulse_acquire_test_2.m Revision: 585 Author: kuprov Date: 15 August 2010 15:33:42 Message: Got the pulse_acquire sequence to report back and use the central plotting facilities. Updated the examples. ---- Modified : /etc/axis_1d.m Modified : /etc/contour_plot.m Added : /etc/plot_1d.m Modified : /exp/pulse_acquire.m Modified : /exp/sequence_report.m Modified : /tests/nmr/noesy_test_1.m Modified : /tests/nmr/noesy_test_2.m Modified : /tests/nmr/pulse_acquire_test_1.m Modified : /tests/nmr/pulse_acquire_test_2.m Revision: 584 Author: kuprov Date: 15 August 2010 14:41:31 Message: More directory reshuffling for the tests. ---- Added : /tests/dnp Added : /tests/dnp/dnp_test_1.m Added : /tests/dnp/dnp_test_2.m Added : /tests/dnp/dnp_test_3.m Added : /tests/nmr/cosy_test_3.m (Copy from path: /tests/nmr/derome_fig_8_26.m, Revision, 580) Deleted : /tests/nmr/derome_fig_8_26.m Deleted : /tests/nmr/noe_test_1.m Deleted : /tests/nmr/offset_test_1.m Deleted : /tests/nmr/zero_field_1.m Deleted : /tests/nmr/zero_field_2.m Added : /tests/optical_magnetometry Added : /tests/optical_magnetometry/zero_field_1.m Added : /tests/optical_magnetometry/zero_field_2.m Deleted : /tests/relaxation_theory/dnp_test_1.m Deleted : /tests/relaxation_theory/dnp_test_2.m Deleted : /tests/relaxation_theory/dnp_test_3.m Revision: 583 Author: kuprov Date: 15 August 2010 14:33:48 Message: Some more renaming. ---- Added : /tests/internal_consistency (Copy from path: /tests/kernel, Revision, 569) Deleted : /tests/internal_consistency/relaxation Added : /tests/internal_consistency/simpson_test_1.m (Copy from path: /tests/kernel/simpson_test_1.m, Revision, 582) Added : /tests/internal_consistency/simpson_test_2.m (Copy from path: /tests/kernel/simpson_test_2.m, Revision, 582) Deleted : /tests/io Deleted : /tests/kernel Deleted : /tests/relaxation Added : /tests/relaxation_theory (Copy from path: /tests/relaxation, Revision, 582) Revision: 582 Author: kuprov Date: 15 August 2010 14:28:03 Message: A bit of moving things around in preparation for adding ESR and CIDNP functionality. ---- Modified : /etc/axis_1d.m Modified : /exp/noesy.m Added : /tests/esr Deleted : /tests/io/simpson_test_1.m Deleted : /tests/io/simpson_test_2.m Deleted : /tests/kernel/relaxation Added : /tests/kernel/simpson_test_1.m (Copy from path: /tests/io/simpson_test_1.m, Revision, 569) Added : /tests/kernel/simpson_test_2.m (Copy from path: /tests/io/simpson_test_2.m, Revision, 569) Added : /tests/molecules/cyclopentyl.log Added : /tests/molecules/methyl.log Added : /tests/molecules/phenyl.log Modified : /tests/nmr/noesy_test_1.m Modified : /tests/nmr/noesy_test_2.m Added : /tests/relaxation (Copy from path: /tests/kernel/relaxation, Revision, 569) Replacing : /tests/relaxation/csa_test_1.m (Copy from path: /tests/kernel/relaxation/csa_test_1.m, Revision, 570) Replacing : /tests/relaxation/csa_test_1.nb (Copy from path: /tests/kernel/relaxation/csa_test_1.nb, Revision, 570) Replacing : /tests/relaxation/dd_test_3.m (Copy from path: /tests/kernel/relaxation/dd_test_3.m, Revision, 570) Revision: 581 Author: kuprov Date: 14 August 2010 18:48:07 Message: Coloc abandoned, NOESY tested to production level. Should find out why the diagonal peaks are still phase-twist rather than pure absorption. ---- Deleted : /exp/coloc.m Modified : /exp/cosy.m Modified : /exp/hetcor.m Modified : /exp/noesy.m Modified : /exp/sequence_report.m Modified : /tests/nmr/noesy_test_1.m Modified : /tests/nmr/noesy_test_2.m Revision: 580 Author: kuprov Date: 14 August 2010 16:41:06 Message: A significant rewrite in the propagator module. COSY sequence and examples are tested against literature and cleared for release. ---- Modified : /etc/axis_2d.m Modified : /exp/cosy.m Modified : /exp/hsqc.m Modified : /kernel/propagator.m Added : /kernel/utils/clean_up.m Modified : /kernel/utils/tolerances.m Modified : /tests/nmr/cosy_test_1.m Modified : /tests/nmr/cosy_test_2.m Modified : /tests/nmr/derome_fig_8_26.m Revision: 579 Author: kuprov Date: 14 August 2010 12:36:55 Message: HMBC abandoned as an ill-defined sequence - not a good example simulation. ---- Modified : /exp/hetcor.m Deleted : /exp/hmbc.m Modified : /tests/nmr/hetcor_test_1.m Modified : /tests/nmr/hetcor_test_2.m Deleted : /tests/nmr/hmbc_test_1.m Deleted : /tests/nmr/hmbc_test_2.m Modified : /tests/nmr/hmqc_test_1.m Modified : /tests/nmr/hmqc_test_2.m Modified : /tests/nmr/hsqc_test_1.m Modified : /tests/nmr/hsqc_test_2.m Revision: 578 Author: kuprov Date: 14 August 2010 12:26:09 Message: HSQC, HMQC, HETCOR are done and tested against the literature data. ---- Modified : /etc/contour_plot.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /tests/nmr/hetcor_test_1.m Modified : /tests/nmr/hetcor_test_2.m Modified : /tests/nmr/hmqc_test_1.m Modified : /tests/nmr/hsqc_test_1.m Modified : /tests/nmr/hsqc_test_2.m Revision: 577 Author: kuprov Date: 13 August 2010 18:26:25 Message: HSQC and HMQC are done and tested. Beautiful. :) ---- Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /tests/nmr/hsqc_test_1.m Modified : /tests/nmr/hsqc_test_2.m Revision: 576 Author: kuprov Date: 13 August 2010 18:21:14 Message: Starting to move across MK's updated sequences. HMBC is suspect. ---- Modified : /etc/axis_2d.m Modified : /etc/contour_plot.m Added : /exp/coloc.m Modified : /exp/cosy.m Modified : /exp/hmbc.m Modified : /exp/hmqc.m Modified : /exp/sequence_report.m Modified : /tests/nmr/hmbc_test_1.m Modified : /tests/nmr/hmbc_test_2.m Modified : /tests/nmr/hmqc_test_1.m Modified : /tests/nmr/hmqc_test_2.m Revision: 575 Author: kuprov Date: 13 August 2010 16:59:40 Message: A minor bugfix in the evolution function. ---- Modified : /kernel/evolution.m Revision: 574 Author: kuprov Date: 13 August 2010 13:06:20 Message: Some more quantum memory stuff. ---- Modified : /tests/quantum_computing/quantum_memory_test_1.m Modified : /tests/quantum_computing/quantum_memory_test_2.m Modified : /tests/quantum_computing/quantum_memory_test_3.m Added : /tests/quantum_computing/quantum_memory_test_4.m Revision: 573 Author: kuprov Date: 13 August 2010 12:47:20 Message: Some examples of non-trivial quantum memories beyond Levitt singlet. Not as rich as originally anticipated, but there are some. ---- Added : /tests/quantum_computing Added : /tests/quantum_computing/quantum_memory_test_1.m Added : /tests/quantum_computing/quantum_memory_test_2.m Added : /tests/quantum_computing/quantum_memory_test_3.m Revision: 572 Author: kuprov Date: 13 August 2010 11:42:43 Message: Another forgotten file plus locks. ---- Modified : /kernel/cache/ist_product_table_2.mat Modified : /kernel/cache/ist_product_table_3.mat Modified : /kernel/cache/ist_product_table_4.mat Modified : /kernel/cache/ist_product_table_5.mat Modified : /kernel/cache/ist_product_table_6.mat Modified : /kernel/cache/ist_product_table_7.mat Modified : /kernel/cache/ist_product_table_8.mat Modified : /kernel/cache/ist_product_table_9.mat Added : /kernel/rotations/dcm2wigner.m Modified : /kernel/rotations/euler2wigner.m Modified : /kernel/utils/banner.m Modified : /kernel/utils/click.m Modified : /kernel/utils/combnk.m Modified : /kernel/utils/correlation_function.m Modified : /kernel/utils/dfpt.m Modified : /kernel/utils/expv.m Modified : /kernel/utils/graphalgs.mexa64 Modified : /kernel/utils/graphalgs.mexglx Modified : /kernel/utils/graphalgs.mexmaci Modified : /kernel/utils/graphalgs.mexs64 Modified : /kernel/utils/graphalgs.mexw32 Modified : /kernel/utils/graphalgs.mexw64 Modified : /kernel/utils/graphconncomp.m Modified : /kernel/utils/irr_sph_ten.m Modified : /kernel/utils/ist_product_table.m Modified : /kernel/utils/lin2lm.m Modified : /kernel/utils/lm2lin.m Modified : /kernel/utils/negligible.m Modified : /kernel/utils/pad.m Modified : /kernel/utils/pauli.m Modified : /kernel/utils/report.m Modified : /kernel/utils/significant.m Modified : /kernel/utils/simps.m Modified : /kernel/utils/stepsize.m Modified : /kernel/utils/summary.m Modified : /kernel/utils/symmetrize.m Modified : /kernel/utils/symmetry_group.m Modified : /kernel/utils/tensor_analysis.m Modified : /kernel/utils/tolerances.m Modified : /kernel/utils/validate.m Revision: 571 Author: kuprov Date: 12 August 2010 17:32:50 Message: Reinstated an accidentally deleted file. ---- Added : /kernel/rotations/euler2wigner.m Revision: 570 Author: kuprov Date: 12 August 2010 17:21:48 Message: An epic fix to the relaxation module -- all analytical results are now matched, all relaxation matrices are rotation-invariant and all relaxation parameters behave smoothly as a function of everything else in the system. ---- Modified : /kernel/create.m Modified : /kernel/h_superop.m Deleted : /kernel/rotations/dcm2wigner.m Modified : /kernel/rotations/euler2dcm.m Deleted : /kernel/rotations/euler2wigner.m Deleted : /kernel/rotations/sph2xyz.m Modified : /tests/kernel/relaxation/csa_test_1.m Modified : /tests/kernel/relaxation/csa_test_1.nb Modified : /tests/kernel/relaxation/dd_test_3.m Revision: 569 Author: hannah Date: 12 August 2010 11:44:39 Message: h_superop: Using H written in terms of all interaction tensor values rather than just principle values. (Avoids having to rotate it back) ---- Modified : /kernel/h_superop.m Revision: 568 Author: kuprov Date: 10 August 2010 16:25:55 Message: Another necessary file. ---- Added : /kernel/rotations/sph2xyz.m Revision: 567 Author: kuprov Date: 10 August 2010 16:24:04 Message: Dipolar self-consistency test added - currently failing. ---- Added : /tests/kernel/relaxation/dd_test_3.m Revision: 566 Author: kuprov Date: 10 August 2010 16:00:35 Message: Two more files. ---- Added : /tests/kernel/relaxation/hfc_test_1.m Added : /tests/kernel/relaxation/hfc_test_1.nb Revision: 565 Author: kuprov Date: 10 August 2010 15:59:48 Message: Starting to move MK's axis + reporting contribution across. Added a hyperfine coupling relaxation theory test. ---- Modified : /etc/apodization.m Modified : /etc/axis_1d.m Added : /etc/axis_2d.m Modified : /etc/decouple.m Modified : /etc/gauss2mhz.m Modified : /etc/homospoil.m Modified : /etc/mt2hz.m Modified : /etc/offset.m Modified : /etc/operator.m Modified : /etc/singlet.m Modified : /etc/state.m Added : /exp/sequence_report.m Modified : /kernel/h_superop.m Revision: 564 Author: kuprov Date: 08 August 2010 18:06:54 Message: A major kernel rewrite to enforce our beautiful specifications in the actual code. Quite a few bugs found and quashed, particularly in the relaxation theory module. The code has undergone very, very rigorous testing. ---- Modified : /etc/axis_1d.m Modified : /etc/decouple.m Modified : /etc/g03_to_spinach.m Modified : /etc/homospoil.m Modified : /etc/operator.m Modified : /etc/singlet.m Modified : /etc/state.m Modified : /etc/state_diagnostics.m Modified : /exp/cosy.m Modified : /exp/hetcor.m Modified : /exp/hmbc.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /exp/inversion_recovery.m Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /exp/noesy.m Modified : /exp/pulse_acquire.m Modified : /exp/pulse_acquire_powder.m Modified : /exp/pulse_acquire_zerofield.m Modified : /installation.txt Modified : /kernel/basis.m Modified : /kernel/c_superop.m Deleted : /kernel/click.m Modified : /kernel/create.m Modified : /kernel/equilibrium.m Modified : /kernel/evolution.m Deleted : /kernel/expv.m Modified : /kernel/grape.m Modified : /kernel/h_superop.m Modified : /kernel/k_superop.m Deleted : /kernel/lin2lm.m Deleted : /kernel/lm2lin.m Modified : /kernel/orientation.m Modified : /kernel/p_superop.m Deleted : /kernel/pad.m Modified : /kernel/path_trace.m Deleted : /kernel/private Modified : /kernel/propagator.m Modified : /kernel/r_superop.m Modified : /kernel/reduce.m Deleted : /kernel/report.m Modified : /kernel/rotations/dcm2wigner.m Modified : /kernel/rotations/euler2dcm.m Modified : /kernel/rotations/euler2wigner.m Deleted : /kernel/simps.m Modified : /kernel/spin.m Modified : /kernel/statevec.m Modified : /kernel/step.m Added : /kernel/utils Added : /kernel/utils/banner.m Added : /kernel/utils/click.m Added : /kernel/utils/combnk.m Added : /kernel/utils/correlation_function.m Added : /kernel/utils/dfpt.m Added : /kernel/utils/expv.m Added : /kernel/utils/graphalgs.mexa64 Added : /kernel/utils/graphalgs.mexglx Added : /kernel/utils/graphalgs.mexmaci Added : /kernel/utils/graphalgs.mexs64 Added : /kernel/utils/graphalgs.mexw32 Added : /kernel/utils/graphalgs.mexw64 Added : /kernel/utils/graphconncomp.m Added : /kernel/utils/irr_sph_ten.m Added : /kernel/utils/ist_product_table.m Added : /kernel/utils/lin2lm.m Added : /kernel/utils/lm2lin.m Added : /kernel/utils/negligible.m Added : /kernel/utils/pad.m Added : /kernel/utils/pauli.m Added : /kernel/utils/report.m Added : /kernel/utils/significant.m Added : /kernel/utils/simps.m Added : /kernel/utils/stepsize.m Added : /kernel/utils/summary.m Added : /kernel/utils/symmetrize.m Added : /kernel/utils/symmetry_group.m Added : /kernel/utils/tensor_analysis.m Added : /kernel/utils/tolerances.m Added : /kernel/utils/validate.m Modified : /kernel/zte.m Deleted : /tests/io/simpson_input_1.in Deleted : /tests/io/simpson_input_2.in Modified : /tests/io/simpson_test_1.m Modified : /tests/io/simpson_test_2.m Modified : /tests/kernel/equilibrium_test_1.m Modified : /tests/kernel/four_spin_test_1.m Modified : /tests/kernel/large_scale_test_1.m Modified : /tests/kernel/large_scale_test_2.m Added : /tests/kernel/large_scale_test_3.m (Copy from path: /tests/io/simpson_test_1.m, Revision, 559) Modified : /tests/kernel/relaxation/csa_test_1.m Added : /tests/kernel/relaxation/csa_test_1.nb Modified : /tests/kernel/relaxation/dd_csa_test_1.m Added : /tests/kernel/relaxation/dd_csa_test_1.nb Modified : /tests/kernel/relaxation/dd_csa_test_2.m Modified : /tests/kernel/relaxation/dd_test_1.m Added : /tests/kernel/relaxation/dd_test_1.nb Modified : /tests/kernel/relaxation/dd_test_2.m Modified : /tests/kernel/relaxation/dnp_test_1.m Modified : /tests/kernel/relaxation/dnp_test_2.m Modified : /tests/kernel/relaxation/dnp_test_3.m Modified : /tests/kernel/single_spin_test_1.m Modified : /tests/kernel/single_spin_test_2.m Modified : /tests/kernel/symmetry_test_1.m Modified : /tests/kernel/three_spin_test_1.m Modified : /tests/kernel/two_spin_test_1.m Added : /tests/molecules/simpson_input_1.in (Copy from path: /tests/io/simpson_input_1.in, Revision, 559) Added : /tests/molecules/simpson_input_2.in (Copy from path: /tests/io/simpson_input_2.in, Revision, 559) Modified : /tests/nmr/derome_fig_8_26.m Modified : /tests/nmr/noe_test_1.m Modified : /tests/nmr/noesy_test_1.m Modified : /tests/nmr/noesy_test_2.m Modified : /tests/nmr/offset_test_1.m Modified : /tests/nmr/pulse_acquire_test_1.m Modified : /tests/nmr/pulse_acquire_test_2.m Modified : /tests/nmr/shaped_pulse_test_1.m Modified : /tests/nmr/solids_test_1.m Modified : /tests/nmr/zero_field_1.m Modified : /tests/nmr/zero_field_2.m Modified : /tests/optimal_control/optimal_control_1.m Modified : /tests/optimal_control/optimal_control_2.m Modified : /tests/optimal_control/optimal_control_3.m Modified : /tests/optimal_control/spin_chain_1.m Modified : /tests/optimal_control/spin_chain_2.m Modified : /tests/optimal_control/spin_chain_3.m Modified : /tests/optimal_control/spin_chain_4.m Modified : /tests/optimal_control/spin_chain_5.m Modified : /tests/optimal_control/spin_chain_6.m Modified : /tests/spin_chemistry/mary_test_1.m Modified : /tests/spin_chemistry/mary_test_2.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_10.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_8.m Modified : /tests/spin_chemistry/timmel_cpl_fig_3.m Modified : /tests/spin_chemistry/timmel_molphys_fig_1.m Modified : /tests/spin_chemistry/timmel_molphys_fig_5.m Revision: 563 Author: kuprov Date: 16 July 2010 16:52:19 Message: Data structure clean-up: new sys subfield created in spin_system for system parameters. The rest of the code modified accordingly. ---- Modified : /exp/mary.m Modified : /exp/maryan.m Modified : /exp/pulse_acquire_powder.m Modified : /kernel/create.m Modified : /kernel/grape.m Modified : /kernel/private/ist_product_table.m Modified : /kernel/reduce.m Modified : /kernel/report.m Modified : /tests/kernel/relaxation/dd_csa_test_2.m Modified : /tests/nmr/shaped_pulse_test_1.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_10.m Revision: 562 Author: kuprov Date: 16 July 2010 16:47:09 Message: Reinstated the Simpson integrator. ---- Added : /kernel/simps.m Revision: 561 Author: kuprov Date: 16 July 2010 16:39:55 Message: Promote pad to the kernel. ---- Added : /kernel/pad.m (Copy from path: /kernel/private/pad.m, Revision, 560) Deleted : /kernel/private/pad.m Revision: 560 Author: kuprov Date: 16 July 2010 16:31:37 Message: Reinstated the pad function. ---- Added : /kernel/private/pad.m Revision: 559 Author: kuprov Date: 14 July 2010 17:02:18 Message: Further clean-up and moving things around between the development directories and master repository. ---- Added : /etc/ascii_export.m Added : /etc/dcm2euler.m (Copy from path: /kernel/rotations/dcm2euler.m, Revision, 557) Added : /etc/quat2euler.m (Copy from path: /kernel/rotations/quat2euler.m, Revision, 557) Added : /etc/simpson2spinach.m Deleted : /kernel/rotations/dcm2euler.m Deleted : /kernel/rotations/quat2euler.m Added : /tests/io Added : /tests/io/simpson_input_1.in Added : /tests/io/simpson_input_2.in Added : /tests/io/simpson_test_1.m Added : /tests/io/simpson_test_2.m Deleted : /tests/kernel/relaxation/csa_relaxation.m Deleted : /tests/kernel/relaxation/csa_relaxation.nb Added : /tests/kernel/relaxation/csa_test_1.m (Copy from path: /tests/kernel/relaxation/csa_relaxation.m, Revision, 557) Deleted : /tests/kernel/relaxation/dd-csa_cross-correlation.nb Deleted : /tests/kernel/relaxation/dd_csa_cross_correlation.m Added : /tests/kernel/relaxation/dd_csa_test_1.m (Copy from path: /tests/kernel/relaxation/dd_csa_cross_correlation.m, Revision, 557) Added : /tests/kernel/relaxation/dd_csa_test_2.m (Copy from path: /tests/kernel/relaxation/kumar_jmr.m, Revision, 557) Deleted : /tests/kernel/relaxation/dd_relaxation.m Deleted : /tests/kernel/relaxation/dd_relaxation.nb Added : /tests/kernel/relaxation/dd_test_1.m (Copy from path: /tests/kernel/relaxation/dd_relaxation.m, Revision, 557) Added : /tests/kernel/relaxation/dd_test_2.m (Copy from path: /tests/kernel/relaxation/levitt_singlet.m, Revision, 557) Deleted : /tests/kernel/relaxation/dorai.pdf Deleted : /tests/kernel/relaxation/epr_relaxation.nb Deleted : /tests/kernel/relaxation/kumar_jmr.log Deleted : /tests/kernel/relaxation/kumar_jmr.m Deleted : /tests/kernel/relaxation/levitt_singlet.m Deleted : /tests/molecules/3-fluorotyrosine.log Deleted : /tests/molecules/NACL.LOG Deleted : /tests/molecules/alpha0beta45gamma0.dip Deleted : /tests/molecules/alpha0beta45gamma90.dip Deleted : /tests/molecules/chlorofluoroethylene.log Deleted : /tests/molecules/chloroform.log Added : /tests/molecules/fdnb.log (Copy from path: /tests/kernel/relaxation/kumar_jmr.log, Revision, 557) Deleted : /tests/molecules/formyl-mlf.log Deleted : /tests/molecules/ja100625p.pdf Deleted : /tests/molecules/ja909656w.pdf Revision: 558 Author: kuprov Date: 14 July 2010 16:49:14 Message: Directory structure clean-up -- preparing to make the repository public and minimizing the checkout size. ---- Deleted : /docs/dcm2wigner.pdf Deleted : /docs/lebedev_quadratures_1.pdf Deleted : /docs/lebedev_quadratures_2.pdf Deleted : /docs/levante_ernst_cpl_1995.pdf Added : /etc/axis_1d.m (Copy from path: /exp/axis_1d.m, Revision, 557) Deleted : /etc/baseline.m Deleted : /etc/g03_to_easyspin.m Deleted : /etc/metric.m Deleted : /etc/pad.m Deleted : /etc/simps.m Deleted : /etc/wave/acknowledgements.txt Deleted : /exp/axis_1d.m Deleted : /exp/derivative_pulse_acquire.m Deleted : /tests/references Revision: 557 Author: kuprov Date: 13 July 2010 16:51:39 Message: MK's HMBC with phase cycle eliminated. A bug fixed in the contouring function. ---- Modified : /etc/contour_plot.m Added : /exp/hmbc.m Added : /tests/nmr/hmbc_test_1.m Added : /tests/nmr/hmbc_test_2.m Revision: 556 Author: kuprov Date: 13 July 2010 15:33:37 Message: Cleaned up -- shifted the history and development away from what would soon become a public repository. Fixed a bug in Gaussian parser. Made the waveform reader check for system architecture before reading a file. Made the state diagnostics output a bit broader. Eliminated explicit phase cycling in HSQC and HMQC. Made the equilibrium function bomb out in low field. Renamed and updated some tests. ---- Deleted : /TODO.txt Deleted : /dev Modified : /etc/g03_to_spinach.m Modified : /etc/read_wave.m Modified : /etc/state_diagnostics.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /installation.txt Modified : /kernel/equilibrium.m Deleted : /previous_version Added : /tests/kernel/large_scale_test_1.m (Copy from path: /tests/kernel/scaling_test_1.m, Revision, 555) Added : /tests/kernel/large_scale_test_2.m (Copy from path: /tests/kernel/scaling_test_2.m, Revision, 555) Deleted : /tests/kernel/scaling_test_1.m Deleted : /tests/kernel/scaling_test_2.m Modified : /tests/kernel/single_spin_test_1.m Modified : /tests/kernel/single_spin_test_2.m Modified : /tests/kernel/symmetry_test_1.m Modified : /tests/kernel/two_spin_test_1.m Deleted : /tests/molecules/hetcor_test_1.fig Deleted : /tests/molecules/hetcor_test_2.fig Deleted : /tests/molecules/hmqc_test_1.fig Deleted : /tests/molecules/hmqc_test_2.fig Deleted : /tests/molecules/hsqc_test_1.fig Deleted : /tests/molecules/hsqc_test_2.fig Deleted : /tests/nmr/pulse_test_1.m Added : /tests/nmr/shaped_pulse_test_1.m (Copy from path: /tests/nmr/pulse_test_1.m, Revision, 555) Modified : /tests/optimal_control/optimal_control_1.m Revision: 555 Author: kuprov Date: 09 July 2010 12:29:02 Message: Zero-field optically-detected NMR simulations for Dima Budker and a dedicated pulse sequence to perform them.. Essentially the same mathematics as MARY, hence could literally be done in five minutes. ---- Modified : /TODO.txt Added : /exp/pulse_acquire_zerofield.m Added : /tests/nmr/zero_field_1.m Added : /tests/nmr/zero_field_2.m Added : /tests/references/zero_field_literature Added : /tests/references/zero_field_literature/pyridine_couplings_1.pdf Added : /tests/references/zero_field_literature/pyridine_couplings_2.pdf Revision: 554 Author: kuprov Date: 06 July 2010 21:19:15 Message: Removed the display threshold from state diagnostics, added fundamental constants and temperature field to the create function, generalized the equilibrium function to respect the temperature field, updated the dnp tests to use the temperature field, added a test function for the equilibrium module. ---- Modified : /etc/state_diagnostics.m Modified : /kernel/create.m Modified : /kernel/equilibrium.m Added : /tests/kernel/equilibrium_test_1.m Modified : /tests/kernel/relaxation/dnp_test_1.m Modified : /tests/kernel/relaxation/dnp_test_2.m Modified : /tests/kernel/relaxation/dnp_test_3.m Revision: 553 Author: kuprov Date: 06 July 2010 17:02:52 Message: Deleted some garbage, updated the Gaussian parser to adapt to the slash styles of different platforms, updated some tests to respect the stricter syntax rules. ---- Deleted : /dev/EXPH test.docx Deleted : /dev/exph.asv Deleted : /dev/exph2.asv Deleted : /dev/exph2_speedup_1.fig Deleted : /dev/exph2_speedup_1.png Deleted : /dev/exph2_speedup_2.fig Deleted : /dev/exph2_speedup_2.png Deleted : /dev/exph3.asv Deleted : /dev/exph4.asv Deleted : /dev/exph4_speedup_1.fig Deleted : /dev/exph5.asv Deleted : /dev/exph5_speedup_1.fig Deleted : /dev/exph5_speedup_2.fig Deleted : /dev/exph5_test_plus.asv Deleted : /dev/exph6.asv Deleted : /dev/exph6_speedup_1.fig Deleted : /dev/exph7_speedup_1.fig Deleted : /dev/exph_5steps_speedup_1.fig Deleted : /dev/exph_5steps_speedup_2.fig Deleted : /dev/exph_speedup_1.fig Deleted : /dev/exph_speedup_1.png Deleted : /dev/exph_speedup_2.fig Deleted : /dev/exph_speedup_2.png Deleted : /dev/exph_test.asv Deleted : /dev/exph_test2.asv Deleted : /dev/exph_test_plus.asv Deleted : /dev/expv_test.asv Deleted : /dev/kron_min.asv Deleted : /dev/pulse seq dev/hmqc_t1_ramp_test_1.png Deleted : /dev/pulse seq dev/hmqc_t1_ramp_test_2.fig Deleted : /dev/pulse seq dev/hmqc_t1_ramp_test_2.png Deleted : /dev/pulse seq dev/hsqc_t1_ramp_test_1.fig Deleted : /dev/pulse seq dev/hsqc_t1_ramp_test_1.png Deleted : /dev/pulse seq dev/hsqc_t1_ramp_test_2.fig Deleted : /dev/pulse seq dev/hsqc_t1_ramp_test_2.png Deleted : /dev/pulse seq dev/hsqc_test_2.fig Deleted : /dev/pulse seq dev/hsqc_test_2.png Modified : /etc/g03_parse.m Modified : /tests/optimal_control/optimal_control_1.m Modified : /tests/optimal_control/optimal_control_3.m Revision: 552 Author: kuprov Date: 05 July 2010 15:04:55 Message: Another DNP test for Walter. ---- Added : /tests/kernel/relaxation/dnp_test_3.m Revision: 551 Author: kuprov Date: 05 July 2010 14:48:50 Message: DNP test functions for Walter Kockenberger. ---- Modified : /TODO.txt Added : /tests/kernel/relaxation/dnp_test_1.m Added : /tests/kernel/relaxation/dnp_test_2.m Deleted : /tests/kernel/relaxation/epr_relaxation.m Revision: 550 Author: matthew Date: 28 June 2010 15:30:17 Message: Tests of newly added sequences. Test_1 means test spectra on sucrose, test_2 means test spectra on strychnine. (Test_3 and Test_4 were identical to Test_1 and Test_2, respectively and were thus deleted.) ---- Added : /tests/molecules/hetcor_test_1.fig Added : /tests/molecules/hetcor_test_2.fig Modified : /tests/molecules/hmqc_test_1.fig Modified : /tests/molecules/hmqc_test_2.fig Deleted : /tests/molecules/hmqc_test_3.fig Deleted : /tests/molecules/hmqc_test_4.fig Added : /tests/molecules/hsqc_test_1.fig Added : /tests/molecules/hsqc_test_2.fig Revision: 549 Author: kuprov Date: 27 June 2010 16:28:29 Message: Updated MK's sequences to use the decoupler. Shifted the basis printing tolerance. Introduced a dilute nucleus option into Gaussian importer (now allows dumping e.g. 13C-13C couplings), made all example files use it. Massive speed-up and more realistic spectra as a result. ---- Added : /etc/decouple.m Modified : /etc/g03_to_spinach.m Modified : /exp/hetcor.m Modified : /exp/hmqc.m Modified : /exp/hsqc.m Modified : /kernel/private/tolerances.m Modified : /tests/nmr/hetcor_test_1.m Modified : /tests/nmr/hetcor_test_2.m Modified : /tests/nmr/hmqc_test_1.m Modified : /tests/nmr/hmqc_test_2.m Modified : /tests/nmr/hsqc_test_1.m Modified : /tests/nmr/hsqc_test_2.m Revision: 548 Author: kuprov Date: 24 June 2010 11:16:08 Message: MK's newly implemented HETCOR with a channel swap error fixed. Slightly increased level of description in all heteronuclear examples -- can afford that with IK-2 basis set. ---- Added : /exp/hetcor.m Added : /tests/nmr/hetcor_test_1.m Added : /tests/nmr/hetcor_test_2.m Modified : /tests/nmr/hmqc_test_1.m Modified : /tests/nmr/hmqc_test_2.m Deleted : /tests/nmr/hmqc_test_3.m Deleted : /tests/nmr/hmqc_test_4.m Modified : /tests/nmr/hsqc_test_1.m Modified : /tests/nmr/hsqc_test_2.m Revision: 547 Author: kuprov Date: 23 June 2010 10:16:17 Message: Added example files for EPR systems. ---- Added : /tests/kernel/relaxation/epr_relaxation.m Added : /tests/kernel/relaxation/epr_relaxation.nb Revision: 546 Author: kuprov Date: 22 June 2010 22:37:36 Message: Fixed MK's sloppy programming -- paranoia.m is meant to catch errors, not cause them! ---- Modified : /kernel/private/paranoia.m Revision: 545 Author: kuprov Date: 21 June 2010 10:15:48 Message: Some more docs from Hannah. ---- Added : /docs/c_superop_parameters.docx Added : /docs/click_parameters.docx Added : /docs/equilibrium_parameters.docx Added : /docs/evolution_parameters.docx Added : /docs/expv_parameters.docx Added : /docs/grape_parameters.docx Added : /docs/h_superop_parameters.docx Added : /docs/k_superop_parameters.docx Added : /docs/lin2lm_parameters.docx Added : /docs/lm2lin_parameters.docx Added : /docs/orientation_parameters.docx Added : /docs/p_superop_parameters.docx Added : /docs/path_trace_parameters.docx Added : /docs/propagator_parameters.docx Added : /docs/r_superop_parameters.docx Added : /docs/reduce_parameters.docx Added : /docs/report_parameters.docx Added : /docs/spin_parameters.docx Added : /docs/statevec_parameters.docx Added : /docs/step_parameters.docx Added : /docs/zte_parameters.docx Revision: 544 Author: kuprov Date: 21 June 2010 09:54:21 Message: MK's HSQC sequence and examples plus some documentation. ---- Added : /docs/basis_parameters.docx Added : /docs/create_parameters.docx Deleted : /docs/relaxation_superoperator.docx Added : /exp/hsqc.m Added : /tests/nmr/hsqc_test_1.m Added : /tests/nmr/hsqc_test_2.m Revision: 543 Author: kuprov Date: 19 June 2010 10:43:35 Message: Adopted MK's version of HMQC as the primary version, added an example for the relaxation module recovering the Levitt singlet directly from the Redfield superoperator. ---- Modified : /exp/hmqc.m Deleted : /exp/hmqc_simple.m Added : /tests/kernel/relaxation/levitt_singlet.m Modified : /tests/nmr/noesy_test_1.m Added : /tests/nmr/noesy_test_2.m (Copy from path: /tests/nmr/noesy_test_3.m, Revision, 542) Deleted : /tests/nmr/noesy_test_3.m Revision: 542 Author: matthew Date: 17 June 2010 12:58:04 Message: The version of paranoia.m with a debugged segment testing create output. The short version of HMQC with only 2 phases in the phase cycle. The tests for short and long versions of HMQC on sucrose and strychnine. ---- Modified : /exp/hmqc.m Added : /exp/hmqc_simple.m Modified : /kernel/private/paranoia.m Added : /tests/molecules/NACL.LOG Added : /tests/molecules/hmqc_test_1.fig Added : /tests/molecules/hmqc_test_2.fig Added : /tests/molecules/hmqc_test_3.fig Added : /tests/molecules/hmqc_test_4.fig Added : /tests/nmr/hmqc_test_3.m Added : /tests/nmr/hmqc_test_4.m Revision: 541 Author: kuprov Date: 11 June 2010 10:55:17 Message: Merged MK's latest additions to the syntax checker into paranoia.m. ---- Modified : /kernel/private/paranoia.m Revision: 540 Author: kuprov Date: 10 June 2010 16:58:44 Message: Some polishing of the standard pulse sequences and the associated example files. ---- Modified : /exp/cosy.m Added : /exp/noesy.m Deleted : /tests/molecules/CHLOROFORM.LOG Deleted : /tests/molecules/chloroform.GJF Deleted : /tests/molecules/chloroform.chk Added : /tests/molecules/chloroform.log (Copy from path: /tests/molecules/chloroform_nmr.out, Revision, 536) Deleted : /tests/molecules/chloroform.out Deleted : /tests/molecules/chloroform_nmr.GJF Deleted : /tests/molecules/chloroform_nmr.out Deleted : /tests/molecules/menthol.GJF Deleted : /tests/molecules/menthol.log Deleted : /tests/molecules/menthol_nmr.gjf Deleted : /tests/molecules/menthol_nmr.log Modified : /tests/nmr/cosy_test_1.m Modified : /tests/nmr/cosy_test_2.m Modified : /tests/nmr/derome_fig_8_26.m Modified : /tests/nmr/noesy_test_1.m Deleted : /tests/nmr/noesy_test_2.m Modified : /tests/nmr/noesy_test_3.m Modified : /tests/nmr/pulse_acquire_test_1.m Revision: 539 Author: kuprov Date: 09 June 2010 18:39:31 Message: Unix and PC paths have been unified in much of the code. Slightly updated installation instructions. Undid Hannah's fix to basis.m -- the type of symmetry treatment is decided based in the number of irreps the code finds, whatever is found is looped over ad added up, so there's no need for an extra switch. Integrated paranoia into create.m, made a few cosmetic changes, permitted coordinated to be supplied as cell array with omissions -- spins with empty coordinate cells are ignored for the purposes of dipolar interactions. Rearranged regime switches for relaxation. Made cosmetic changes to evolution.m Significantly accelerated h_superop.m by not computing operators unless absolutely necessary. Added a Redfield superoperator accuracy tolerance and made r_superop.m obey it. Updated all tests to respect the current syntax and not trip over the newly introduced checks. ---- Modified : /exp/maryan.m Modified : /exp/pulse_acquire_powder.m Modified : /installation.txt Modified : /kernel/basis.m Modified : /kernel/create.m Modified : /kernel/evolution.m Modified : /kernel/h_superop.m Modified : /kernel/private/summary.m Modified : /kernel/private/tolerances.m Modified : /kernel/r_superop.m Modified : /kernel/reduce.m Modified : /kernel/step.m Modified : /kernel/zte.m Modified : /tests/kernel/relaxation/csa_relaxation.m Modified : /tests/kernel/relaxation/dd_relaxation.m Modified : /tests/kernel/relaxation/kumar_jmr.m Modified : /tests/kernel/scaling_test_1.m Modified : /tests/kernel/scaling_test_2.m Added : /tests/molecules/ja100625p.pdf (Copy from path: /tests/nmr/ja100625p.pdf, Revision, 532) Added : /tests/molecules/ja909656w.pdf (Copy from path: /tests/nmr/ja909656w.pdf, Revision, 532) Modified : /tests/nmr/cosy_test_2.m Deleted : /tests/nmr/ja100625p.pdf Deleted : /tests/nmr/ja909656w.pdf Modified : /tests/nmr/noe_test_1.m Modified : /tests/nmr/noesy_test_2.m Deleted : /tests/nmr/pulse sequence editing by symbolic computation.pdf Modified : /tests/nmr/pulse_test_1.m Modified : /tests/nmr/solids_test_2.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_10.m Revision: 538 Author: kuprov Date: 09 June 2010 18:07:10 Message: More fixes. That function is meant to catch errors, not cause them! ---- Modified : /kernel/private/paranoia.m Revision: 537 Author: kuprov Date: 09 June 2010 18:05:00 Message: Fixed MK's additions to paranoia.m. Untested code should never be committed. ---- Modified : /kernel/private/paranoia.m Revision: 536 Author: matthew Date: 09 June 2010 15:11:45 Message: Some additional sanity checks on the output filed structure of spin_system ---- Modified : /kernel/private/paranoia.m Revision: 535 Author: kuprov Date: 08 June 2010 18:39:32 Message: An update to the input checker. ---- Modified : /kernel/private/paranoia.m Revision: 534 Author: hannah Date: 08 June 2010 17:22:27 Message: Just swapped round the ordering tolerance description in the tolerances.m function description so that it matches the order of tolerances in the code. ---- Modified : /kernel/private/tolerances.m Revision: 533 Author: kuprov Date: 08 June 2010 16:09:24 Message: Modifications to MK's segment of the syntax checker. Use as template. ---- Modified : /kernel/private/paranoia.m Revision: 532 Author: matthew Date: 08 June 2010 12:59:12 Message: Segment of paranoia written checking that the output of create.m (the spin_system structure) meets reasonable self-consistency expectations. Philosophy adapted that the user is responsible for inputting interaction strength parameters by hand, so inconsistencies of the 'weak - strong' are not reported as errors as they are still grammatically allowed. All the rest of the spin_system structure is being checked for grammatical errors. ---- Modified : /kernel/private/paranoia.m Revision: 531 Author: kuprov Date: 07 June 2010 18:17:50 Message: An update to the syntax checker and a minor bug fixed. ---- Modified : /kernel/private/paranoia.m Modified : /kernel/private/symmetrize.m Revision: 530 Author: kuprov Date: 07 June 2010 11:23:40 Message: An update to the input checker. ---- Modified : /kernel/private/paranoia.m Revision: 529 Author: hannah Date: 07 June 2010 10:50:58 Message: update to paranoia.m checking output from basis. ---- Modified : /kernel/basis.m Modified : /kernel/private/paranoia.m Revision: 528 Author: kuprov Date: 05 June 2010 16:48:26 Message: An update to the consistency checker. ---- Modified : /kernel/private/paranoia.m Modified : /kernel/reduce.m Revision: 527 Author: kuprov Date: 05 June 2010 16:04:34 Message: Minor alterations to the spin database and the beginnings of a comprehensive input and self-consistency checker. ---- Added : /kernel/private/paranoia.m Deleted : /kernel/private/sanity_check.m Modified : /kernel/spin.m Revision: 526 Author: matthew Date: 04 June 2010 17:53:39 Message: Amended spin.m function with NMR properties of all available nuclei. Data taken from: % NMR Periodic Table % Rider University NMR Facility, Department of Chemistry % http://arrhenius.rider.edu/nmr/NMR_tutor/periodic_table/nmr_pt_frameset.html ---- Modified : /kernel/spin.m Revision: 525 Author: kuprov Date: 02 June 2010 11:10:32 Message: Made HMQC magnitude-mode, added a few cosmetic improvements and a couple of tests. ---- Modified : /exp/hmqc.m Modified : /kernel/evolution.m Modified : /tests/nmr/hmqc_test_1.m Added : /tests/nmr/hmqc_test_2.m Revision: 524 Author: kuprov Date: 01 June 2010 17:49:11 Message: Removed untested code from production Spinach directories. ---- Added : /dev/pulse seq dev/hmqc_t1_ramp.m (Copy from path: /exp/hmqc_t1_ramp.m, Revision, 522) Added : /dev/pulse seq dev/hsqc.m (Copy from path: /exp/hsqc.m, Revision, 522) Added : /dev/pulse seq dev/hsqc_t1_ramp.m (Copy from path: /exp/hsqc_t1_ramp.m, Revision, 522) Deleted : /exp/hmqc_t1_ramp.m Deleted : /exp/hsqc.m Deleted : /exp/hsqc_t1_ramp.m Revision: 523 Author: kuprov Date: 01 June 2010 17:43:31 Message: Made the contouring function independent of the calling context. Removed the decoupler (far too buggy, need something new). Outsourced the dimension reduction into a separate kernel function. Added a refocused trajectory option to the evolution function -- to deal with those nasty sliding pulses in the middle of F1 times. Wrote the HMQC function. ---- Modified : /etc/contour_plot.m Deleted : /etc/decouple.m Modified : /exp/cosy.m Added : /exp/hmqc.m Deleted : /format Modified : /kernel/evolution.m Added : /kernel/reduce.m Deleted : /tests/APSEQ Added : /tests/nmr/hmqc_test_1.m Added : /tests/nmr/noesy_test_3.m Revision: 522 Author: kuprov Date: 30 May 2010 15:27:21 Message: Looks like KP accidentally committed a repository database... fixed. ---- Deleted : /README.txt Deleted : /conf Deleted : /db Deleted : /hooks Deleted : /locks Modified : /tests/nmr/cosy_test_2.m Revision: 521 Author: pervushin Date: 30 May 2010 12:23:31 Message: ---- Added : /README.txt Added : /conf Added : /conf/authz Added : /conf/passwd Added : /conf/svnserve.conf Added : /db Added : /db/current Added : /db/format Added : /db/fs-type Added : /db/revprops Added : /db/revprops/0 Added : /db/revprops/0/0 Added : /db/revs Added : /db/revs/0 Added : /db/revs/0/0 Added : /db/transactions Added : /db/txn-current Added : /db/txn-current-lock Added : /db/txn-protorevs Added : /db/uuid Added : /db/write-lock Added : /format Added : /hooks Added : /hooks/post-commit.tmpl Added : /hooks/post-lock.tmpl Added : /hooks/post-revprop-change.tmpl Added : /hooks/post-unlock.tmpl Added : /hooks/pre-commit.tmpl Added : /hooks/pre-lock.tmpl Added : /hooks/pre-revprop-change.tmpl Added : /hooks/pre-unlock.tmpl Added : /hooks/start-commit.tmpl Added : /locks Added : /locks/db-logs.lock Added : /locks/db.lock Revision: 520 Author: matthew Date: 28 May 2010 13:32:19 Message: File location modified. The pulse sequences under development were put into the dev subdirectory. ---- Added : /dev/pulse seq dev Added : /dev/pulse seq dev/hmqc_t1_ramp_test_1.m Added : /dev/pulse seq dev/hmqc_t1_ramp_test_1.png Added : /dev/pulse seq dev/hmqc_t1_ramp_test_2.fig Added : /dev/pulse seq dev/hmqc_t1_ramp_test_2.m Added : /dev/pulse seq dev/hmqc_t1_ramp_test_2.png Added : /dev/pulse seq dev/hsqc_t1_ramp_test_1.fig Added : /dev/pulse seq dev/hsqc_t1_ramp_test_1.m Added : /dev/pulse seq dev/hsqc_t1_ramp_test_1.png Added : /dev/pulse seq dev/hsqc_t1_ramp_test_2.fig Added : /dev/pulse seq dev/hsqc_t1_ramp_test_2.m Added : /dev/pulse seq dev/hsqc_t1_ramp_test_2.png Added : /dev/pulse seq dev/hsqc_test_1.m Added : /dev/pulse seq dev/hsqc_test_2.fig Added : /dev/pulse seq dev/hsqc_test_2.m Added : /dev/pulse seq dev/hsqc_test_2.png Modified : /exp/hsqc_t1_ramp.m Deleted : /tests/nmr/hmqc_t1_ramp_test_1.m Deleted : /tests/nmr/hmqc_t1_ramp_test_1.png Deleted : /tests/nmr/hmqc_t1_ramp_test_2.fig Deleted : /tests/nmr/hmqc_t1_ramp_test_2.m Deleted : /tests/nmr/hmqc_t1_ramp_test_2.png Deleted : /tests/nmr/hsqc_t1_ramp_test_1.fig Deleted : /tests/nmr/hsqc_t1_ramp_test_1.m Deleted : /tests/nmr/hsqc_t1_ramp_test_1.png Deleted : /tests/nmr/hsqc_t1_ramp_test_2.fig Deleted : /tests/nmr/hsqc_t1_ramp_test_2.m Deleted : /tests/nmr/hsqc_t1_ramp_test_2.png Deleted : /tests/nmr/hsqc_test_1.m Revision: 519 Author: matthew Date: 28 May 2010 09:45:46 Message: First attempt to write HSQC and HMQC sequences as implemented from J. Cavanagh et al, Protein NMR spectroscopy, Chapter 7, pp 535 - 550. Some additional entries into molecule database of Gaussian NMR GIAO output files. APSEQ Mathematica package for pulse sequence editing by symbolic calculation. ---- Added : /exp/hmqc_t1_ramp.m Modified : /exp/hsqc.m Added : /exp/hsqc_t1_ramp.m Added : /tests/APSEQ Added : /tests/APSEQ/apsDistribution Added : /tests/APSEQ/apsDistribution/zip.feb15 Added : /tests/APSEQ/apsDistribution/zip.feb15/README Added : /tests/APSEQ/apsDistribution/zip.feb15/all.mscp Added : /tests/APSEQ/apsDistribution/zip.feb15/apsExamples.pdf Added : /tests/APSEQ/apsDistribution/zip.feb15/apsExamples.tex Added : /tests/APSEQ/apsDistribution/zip.feb15/apsExamplesForComparison.pdf Added : /tests/APSEQ/apsDistribution/zip.feb15/apsImplementation.pdf Added : /tests/APSEQ/apsDistribution/zip.feb15/apsParameters.pdf Added : /tests/APSEQ/apsDistribution/zip.feb15/apseq.m Added : /tests/APSEQ/apsDistribution/zip.feb15/apseqValidationReport.10.02.09.22.16.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/diff.out Added : /tests/APSEQ/apsDistribution/zip.feb15/isOK.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/nmr.auto Added : /tests/APSEQ/apsDistribution/zip.feb15/nmr.dta Added : /tests/APSEQ/apsDistribution/zip.feb15/nmr.extra Added : /tests/APSEQ/apsDistribution/zip.feb15/part01.mscp Added : /tests/APSEQ/apsDistribution/zip.feb15/part02.mscp Added : /tests/APSEQ/apsDistribution/zip.feb15/part03.mscp Added : /tests/APSEQ/apsDistribution/zip.feb15/part04.mscp Added : /tests/APSEQ/apsDistribution/zip.feb15/reference Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_basic.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_basic_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_editedGradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_editedGradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_gradientEnhanced.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_gradientEnhanced_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_gradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_HSQC_gradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_TOCSY_HSQC_basic.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_TOCSY_HSQC_editedGradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_TOCSY_HSQC_gradientEnhanced.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/2D_TOCSY_HSQC_gradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_HSQC_basic_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_HSQC_editedGradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_HSQC_gradientEnhanced_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_HSQC_gradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_TOCSY_HSQC_basic.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_TOCSY_HSQC_editedGradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_TOCSY_HSQC_gradientEnhanced.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/3D_TOCSY_HSQC_gradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/HETCOR_refocused.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/INEPT_gradientAssisted.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/pulseLabelTest01.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/pulseLabelTest02.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/temporaryName.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/reference/twoFlips.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/tex.out Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16 Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_basic.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_basic_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_editedGradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_editedGradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_gradientEnhanced.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_gradientEnhanced_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_gradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_HSQC_gradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_TOCSY_HSQC_basic.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_TOCSY_HSQC_editedGradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_TOCSY_HSQC_gradientEnhanced.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/2D_TOCSY_HSQC_gradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_HSQC_basic_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_HSQC_editedGradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_HSQC_gradientEnhanced_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_HSQC_gradientSelected_TOCSY.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_TOCSY_HSQC_basic.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_TOCSY_HSQC_editedGradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_TOCSY_HSQC_gradientEnhanced.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/3D_TOCSY_HSQC_gradientSelected.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/HETCOR_refocused.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/INEPT_gradientAssisted.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/pulseLabelTest01.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/pulseLabelTest02.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/temporaryName.txt Added : /tests/APSEQ/apsDistribution/zip.feb15/validation.10.02.09.22.16/twoFlips.txt Added : /tests/APSEQ/apsImplementation.pdf Added : /tests/APSEQ/apsParameters.pdf Added : /tests/APSEQ/pulse sequence editing by symbolic calculation.pdf Added : /tests/APSEQ/pulse sequences.pdf Added : /tests/molecules/CHLOROFORM.LOG Added : /tests/molecules/chloroform.GJF Added : /tests/molecules/chloroform.chk Added : /tests/molecules/chloroform.out Added : /tests/molecules/chloroform_nmr.GJF Added : /tests/molecules/chloroform_nmr.out Added : /tests/molecules/menthol.GJF Added : /tests/molecules/menthol.log Added : /tests/molecules/menthol_nmr.gjf Added : /tests/molecules/menthol_nmr.log Added : /tests/nmr/hmqc_t1_ramp_test_1.m Added : /tests/nmr/hmqc_t1_ramp_test_1.png Added : /tests/nmr/hmqc_t1_ramp_test_2.fig Added : /tests/nmr/hmqc_t1_ramp_test_2.m Added : /tests/nmr/hmqc_t1_ramp_test_2.png Added : /tests/nmr/hsqc_t1_ramp_test_1.fig Added : /tests/nmr/hsqc_t1_ramp_test_1.m Added : /tests/nmr/hsqc_t1_ramp_test_1.png Added : /tests/nmr/hsqc_t1_ramp_test_2.fig Added : /tests/nmr/hsqc_t1_ramp_test_2.m Added : /tests/nmr/hsqc_t1_ramp_test_2.png Added : /tests/nmr/pulse sequence editing by symbolic computation.pdf Revision: 518 Author: kuprov Date: 26 May 2010 11:05:54 Message: Added sucrose to the standard molecule set. ---- Added : /tests/molecules/sucrose.log Added : /tests/nmr/cosy_test_2.m Revision: 517 Author: matthew Date: 20 May 2010 18:39:43 Message: A very crude initial HSQC and a bug fix in the decouple function (decoupler needs to be double-checked - IK). Plotter needs to be adapted to heteronuclear data -- currently fudging. ---- Modified : /etc/decouple.m Added : /exp/hsqc.m Added : /tests/nmr/hsqc_test_1.m Revision: 516 Author: kuprov Date: 19 May 2010 18:24:39 Message: Fixed a bug in the path function. Kudos to MK for getting me to do it. ---- Modified : /kernel/create.m Revision: 515 Author: kuprov Date: 17 May 2010 10:11:01 Message: A minor update to the apodization function and a test function to reproduce Kumar's paper. ---- Modified : /etc/apodization.m Modified : /tests/kernel/relaxation/kumar_jmr.log Modified : /tests/kernel/relaxation/kumar_jmr.m Revision: 514 Author: kuprov Date: 04 May 2010 18:40:34 Message: Updated the contouring in COSY, fixed the thermal equilibrium relaxation treatment in the evolution function. ---- Modified : /exp/cosy.m Modified : /kernel/evolution.m Modified : /tests/nmr/noesy_test_1.m Revision: 513 Author: kuprov Date: 04 May 2010 10:38:20 Message: A bug fix in the apodization function -- the first (1d) and the corner (2d) points of the FID are now divided by 2. A new iterative thresholding baseline estimator. A contouring fix for the COSY/NOESY function. A fix for the pulse-acquire function -- it no longer fudges the pulse. An update to ZTE function to include thermal relaxation. An extra DD-CSA cross-correlation test. ---- Modified : /etc/apodization.m Added : /etc/baseline.m Modified : /exp/cosy.m Modified : /exp/pulse_acquire.m Modified : /kernel/zte.m Added : /tests/kernel/relaxation/dorai.pdf Added : /tests/kernel/relaxation/kumar_jmr.log Added : /tests/kernel/relaxation/kumar_jmr.m Modified : /tests/nmr/cosy_test_1.m Revision: 512 Author: kuprov Date: 27 April 2010 16:57:20 Message: Much improved contour plotter, better reporting in the path tracer. ---- Modified : /etc/contour_plot.m Modified : /exp/cosy.m Modified : /kernel/path_trace.m Revision: 511 Author: kuprov Date: 26 April 2010 11:00:48 Message: Made bottom contours grey instead of white for visibility, made the homospoil function destroy zero-quantum coherences by default, added offset to the axis builder, added a COSY test function (the one used in the Redfield paper), changed a couple of tests to lower field to emphasize multiplicity. ---- Modified : /etc/contour_plot.m Modified : /etc/homospoil.m Modified : /exp/axis_1d.m Modified : /exp/cosy.m Added : /tests/nmr/cosy_test_1.m Modified : /tests/nmr/noesy_test_1.m Modified : /tests/nmr/pulse_acquire_test_1.m Revision: 510 Author: kuprov Date: 19 April 2010 18:41:55 Message: An updated Gaussian parser and halfway through to a simple EasySpin interface. ---- Modified : /etc/g03_parse.m Added : /etc/g03_to_easyspin.m Revision: 509 Author: kuprov Date: 17 April 2010 21:50:44 Message: Minor bugs fixed in GRAPE and exponential modules, two NMR papers with nice simulation targets added. ---- Modified : /kernel/grape.m Modified : /kernel/propagator.m Added : /tests/nmr/ja100625p.pdf Added : /tests/nmr/ja909656w.pdf Modified : /tests/optimal_control/optimal_control_1.m Modified : /tests/optimal_control/optimal_control_2.m Modified : /tests/optimal_control/optimal_control_3.m Revision: 508 Author: kuprov Date: 17 April 2010 20:26:42 Message: Much faster version of the derivative propagator module. ---- Modified : /kernel/grape.m Modified : /kernel/private/tolerances.m Modified : /kernel/propagator.m Revision: 507 Author: kuprov Date: 14 April 2010 17:10:23 Message: Minor fix. ---- Modified : /tests/optimal_control/optimal_control_3.m Revision: 506 Author: kuprov Date: 13 April 2010 00:32:51 Message: Added the exact gradient option to the GRAPE module. Quite a bit slower at the moment, but I'll figure out a way to speed it up sooner or later... ---- Modified : /kernel/create.m Modified : /kernel/grape.m Modified : /tests/optimal_control/optimal_control_1.m Modified : /tests/optimal_control/optimal_control_2.m Added : /tests/optimal_control/optimal_control_3.m Revision: 505 Author: kuprov Date: 11 April 2010 00:44:47 Message: A couple of examples for the optimal control module. ---- Modified : /tests/optimal_control/optimal_control_1.m Added : /tests/optimal_control/optimal_control_2.m Revision: 504 Author: kuprov Date: 11 April 2010 00:23:15 Message: Another minor bug in GRAPE. Works like a dream -- see the example. ---- Modified : /kernel/grape.m Revision: 503 Author: kuprov Date: 11 April 2010 00:20:35 Message: Fixed a show-stopper bug in the grape procedure. Should work now. ---- Modified : /kernel/grape.m Revision: 502 Author: matthew Date: 10 April 2010 21:55:03 Message: Two updated Hilbert space propagation routines: exph6 [Hadamard propagator with clean up] and exph7 [Taylor propagator with clean up]. In the Hadamard routine the commutator has built-in clean up passes. Also, in both routines the subroutine finding the biggest eigenvalue was modified. Now, the subroutine uses the normest Matlab built-in function as opposed to the eigs routine used earlier. This, seems to improve the overall speed of both routines. Benchmarking of exph6 and exph7 with sparse random matrices H and rho shows that, when the matrices are constructed by adding the unit matrix and then symmetrized, the Hadamard routine exph6 seems to outperform the Taylor routine. This happens at least for H and rho matrices of sparsity 0.0001 in the size range between 2^8 and 2^12. ---- Added : /dev/exph6.asv Added : /dev/exph6.m Added : /dev/exph6_speedup_1.fig Added : /dev/exph6_test_plus.m Added : /dev/exph7.m Added : /dev/exph7_speedup_1.fig Added : /dev/exph7_test_plus.m Revision: 501 Author: kuprov Date: 08 April 2010 16:47:44 Message: Final parser for SIMPSON input, another example of its usage, an algorithm force switch added to the create script (not respected elsewhere in the code yet), aluminium and silicon added to the spin list. ---- Modified : /TODO.txt Deleted : /dev/simpson/N1C2H7.in Modified : /dev/simpson/simpson2spinach.m Added : /dev/simpson/simpson_input_1.in (Copy from path: /dev/simpson/N1C2H7.in, Revision, 496) Added : /dev/simpson/simpson_input_2.in Deleted : /dev/simpson/simpson_test.m Added : /dev/simpson/simpson_test_1.m (Copy from path: /dev/simpson/simpson_test.m, Revision, 499) Added : /dev/simpson/simpson_test_2.m Modified : /kernel/create.m Modified : /kernel/spin.m Revision: 500 Author: kuprov Date: 08 April 2010 13:10:57 Message: Made the pulse_acquire_powder.m function respect the grid choice, added grid selection to the create script, set a few needs_lock flags. ---- Modified : /exp/pulse_acquire_powder.m Modified : /kernel/create.m Modified : /kernel/grape.m Modified : /kernel/private/symmetrize.m Revision: 499 Author: kuprov Date: 08 April 2010 10:52:56 Message: Fixed a bug in the create script, a few Krylov-related bugs in the evolution script and added an ascii export function dumping the essential simulation infrastructure into text files. ---- Added : /dev/simpson/ascii_export.m Modified : /dev/simpson/simpson_test.m Modified : /kernel/create.m Modified : /kernel/evolution.m Revision: 498 Author: kuprov Date: 08 April 2010 09:18:47 Message: Fixed a bug in pulse-acquire, added a symmetrization statement to the hamiltonian superoperator, told the propagator function to return a dense matrix if a matrix turns out to be dense. ---- Modified : /exp/pulse_acquire.m Modified : /kernel/h_superop.m Modified : /kernel/propagator.m Revision: 497 Author: kuprov Date: 08 April 2010 09:08:48 Message: Made the pulse-acquire sequence aware of the regime switch, outsourced tensor symmetrization function into a separate private kernel file, fixed a couple of bugs in the create script. ---- Modified : /dev/simpson/simpson2spinach.m Modified : /dev/simpson/simpson_test.m Modified : /exp/pulse_acquire.m Modified : /kernel/create.m Modified : /kernel/private/summary.m Added : /kernel/private/symmetrize.m Modified : /kernel/private/tensor_analysis.m Revision: 496 Author: kuprov Date: 07 April 2010 16:52:19 Message: Pilot version of the SIMPSON parser. Strange bug in Matlab diagonalization routine. ---- Added : /dev/simpson Added : /dev/simpson/N1C2H7.in Added : /dev/simpson/simpson2spinach.m Added : /dev/simpson/simpson_test.m Modified : /kernel/create.m Revision: 495 Author: kuprov Date: 04 April 2010 18:52:02 Message: A pilot version of the GRAPE gradient module. A lot of debugging is in order. ---- Added : /dev/optimal_control Added : /dev/optimal_control/grape_on_steroids.m Added : /kernel/grape.m Modified : /kernel/step.m Deleted : /tests/optimal_control/nitroxide.m Added : /tests/optimal_control/optimal_control_1.m Modified : /tests/optimal_control/spin_chain_6.m Revision: 494 Author: kuprov Date: 03 April 2010 17:04:00 Message: The evolution function now skips the unpopulated subspaces, some minor bugs fixed here and there, the optimal control examples cleaned up and rewritten to take advantage of the new technology. ---- Modified : /kernel/evolution.m Modified : /kernel/step.m Modified : /tests/nmr/pulse_acquire_test_1.m Modified : /tests/nmr/pulse_acquire_test_2.m Deleted : /tests/optimal_control/five_spin_test_1.m Deleted : /tests/optimal_control/five_spin_test_2.m Deleted : /tests/optimal_control/five_spin_test_3.m Deleted : /tests/optimal_control/five_spin_test_4.m Deleted : /tests/optimal_control/five_spin_test_5.m Deleted : /tests/optimal_control/five_spin_test_6.m Deleted : /tests/optimal_control/five_spin_test_7.m Added : /tests/optimal_control/spin_chain_1.m (Copy from path: /tests/optimal_control/five_spin_test_2.m, Revision, 486) Added : /tests/optimal_control/spin_chain_2.m (Copy from path: /tests/optimal_control/five_spin_test_3.m, Revision, 486) Added : /tests/optimal_control/spin_chain_3.m (Copy from path: /tests/optimal_control/five_spin_test_4.m, Revision, 486) Added : /tests/optimal_control/spin_chain_4.m (Copy from path: /tests/optimal_control/five_spin_test_5.m, Revision, 486) Added : /tests/optimal_control/spin_chain_5.m (Copy from path: /tests/optimal_control/five_spin_test_6.m, Revision, 486) Added : /tests/optimal_control/spin_chain_6.m (Copy from path: /tests/optimal_control/five_spin_test_7.m, Revision, 486) Revision: 493 Author: kuprov Date: 02 April 2010 20:43:05 Message: Large number of small fixes highlighted by a run through the testing set. ---- Modified : /etc/apodization.m Modified : /exp/cosy.m Modified : /exp/pulse_acquire_powder.m Modified : /kernel/evolution.m Modified : /kernel/private/stepsize.m Modified : /kernel/private/tolerances.m Modified : /kernel/propagator.m Modified : /tests/nmr/noe_test_1.m Deleted : /tests/spin_chemistry/mary_test_3.m Revision: 492 Author: kuprov Date: 02 April 2010 19:35:30 Message: Fixed a bug in the axis generator, rewrote pulse-acquire to take advantage of the new technology, fixed a couple of bugs in the evolution and stepsize functions, and caught a very transient bug in ZTE module. Deleted a whole load of redundant tests and ported the offset test across. ---- Modified : /exp/axis_1d.m Modified : /exp/pulse_acquire.m Modified : /exp/pulse_acquire_powder.m Modified : /kernel/evolution.m Modified : /kernel/private/stepsize.m Modified : /kernel/zte.m Deleted : /previous_version/Spinach tests/bath_test_2.m Deleted : /previous_version/Spinach tests/lie_algebra_test_1.m Deleted : /previous_version/Spinach tests/molecules Deleted : /previous_version/Spinach tests/offset_test_1.m Deleted : /previous_version/Spinach tests/operator_test_1.m Deleted : /previous_version/Spinach tests/solids_test_1.m Deleted : /previous_version/Spinach tests/solids_test_2.m Deleted : /previous_version/Spinach tests/spin_chain_1.m Deleted : /previous_version/Spinach tests/spin_chain_2.m Added : /tests/nmr/offset_test_1.m (Copy from path: /previous_version/Spinach tests/offset_test_1.m, Revision, 486) Modified : /tests/nmr/pulse_test_1.m Revision: 491 Author: kuprov Date: 02 April 2010 18:15:07 Message: Moved across the shaped pulse tests and made sure that they execute as expected. Fixed a bug in the basis function. Changed the summary output a bit. ---- Modified : /TODO.txt Modified : /etc/shaped_pulse.m Modified : /kernel/basis.m Modified : /kernel/private/summary.m Deleted : /previous_version/Spinach tests/pulse_test_1.m Deleted : /previous_version/Spinach tests/pulse_test_2.m Added : /tests/nmr/pulse_test_1.m (Copy from path: /previous_version/Spinach tests/pulse_test_1.m, Revision, 486) Revision: 490 Author: kuprov Date: 02 April 2010 16:39:11 Message: Added an inversion-recovery experiment, introduced an option to relax to the thermal equilibrium state as well as the infinite-temperature state and added a paper on the subject to the docs section. ---- Added : /docs/levante_ernst_cpl_1995.pdf Deleted : /etc/thermal_dm.m Added : /exp/inversion_recovery.m Modified : /kernel/create.m Added : /kernel/equilibrium.m (Copy from path: /etc/thermal_dm.m, Revision, 486) Modified : /kernel/evolution.m Modified : /kernel/private/banner.m Modified : /kernel/r_superop.m Modified : /tests/kernel/relaxation/csa_relaxation.m Revision: 489 Author: kuprov Date: 02 April 2010 14:55:55 Message: Another basis set and the graph theory binaries for the three platforms not covered so far. ---- Modified : /kernel/basis.m Added : /kernel/private/graphalgs.mexglx Added : /kernel/private/graphalgs.mexmaci Added : /kernel/private/graphalgs.mexs64 Revision: 488 Author: kuprov Date: 01 April 2010 18:20:37 Message: Modified create.m to stack up multiple specifications, introduced a small function to estimate propagation step size and the number of steps required, shifted all reporting from the create script into a separate summary function, introduced a function performing group-theoretical analysis of interaction tensors. ---- Modified : /TODO.txt Modified : /kernel/create.m Modified : /kernel/private/significant.m Modified : /kernel/private/stepsize.m Added : /kernel/private/summary.m Added : /kernel/private/tensor_analysis.m Modified : /tests/nmr/noe_test_1.m Revision: 487 Author: kuprov Date: 31 March 2010 15:36:43 Message: Completed the generic evolution function, introduced a step function as a wrapper to expv and deleted a few redundant things. ---- Deleted : /etc/delay.m Deleted : /etc/hard_pulse.m Modified : /exp/cosy.m Modified : /kernel/evolution.m Added : /kernel/step.m Revision: 486 Author: kuprov Date: 30 March 2010 20:07:30 Message: First draft of the evolution function that will be capable of transparently using all our state space reduction technology. Also a neat little function to compute evolution step sizes. ---- Added : /kernel/evolution.m (Copy from path: /previous_version/Spinach core/propagate.m, Revision, 479) Added : /kernel/private/sanity_check.m (Copy from path: /previous_version/Spinach core/sanity_check.m, Revision, 479) Added : /kernel/private/stepsize.m Modified : /tests/nmr/noe_test_1.m Added : /tests/references/mary_literature (Copy from path: /previous_version/Spinach experiments/mary_literature, Revision, 479) Revision: 485 Author: kuprov Date: 30 March 2010 11:49:29 Message: Migrated the metric function and the development directories. ---- Added : /dev/derivatives Added : /dev/derivatives/derivativeCOSY.m (Copy from path: /previous_version/Spinach experiments/derivativeCOSY.m, Revision, 479) Added : /dev/derivatives/derivative_shaped_pulse.m (Copy from path: /previous_version/Spinach aux/derivative_shaped_pulse.m, Revision, 479) Added : /dev/hilbert_space Added : /dev/hilbert_space/hilb_statelist_gen.m (Copy from path: /previous_version/Spinach core/hilb_statelist_gen.m, Revision, 479) Added : /dev/symmetry Added : /dev/symmetry/@permutation (Copy from path: /previous_version/Spinach core/symmetry_groups/@permutation, Revision, 479) Added : /dev/symmetry/permutation_group_class_list.m (Copy from path: /previous_version/Spinach core/symmetry_groups/permutation_group_class_list.m, Revision, 479) Added : /etc/metric.m (Copy from path: /previous_version/Spinach core/metric.m, Revision, 479) Deleted : /previous_version/Spinach aux Deleted : /previous_version/Spinach core Deleted : /previous_version/Spinach experiments Revision: 484 Author: kuprov Date: 29 March 2010 18:25:30 Message: Ported the shaped pulse functions and waveforms, cleaned up the old version directory. ---- Added : /etc/read_wave.m (Copy from path: /previous_version/Spinach aux/read_wave.m, Revision, 479) Added : /etc/shaped_pulse.m (Copy from path: /previous_version/Spinach aux/shaped_pulse.m, Revision, 479) Added : /etc/sim_pulse.m (Copy from path: /previous_version/Spinach aux/sim_pulse.m, Revision, 479) Added : /etc/simps.m (Copy from path: /previous_version/Spinach aux/simps.m, Revision, 479) Added : /etc/wave (Copy from path: /previous_version/Spinach aux/wave, Revision, 479) Deleted : /previous_version/Spinach aux/apodization.m Deleted : /previous_version/Spinach aux/delay.m Deleted : /previous_version/Spinach aux/g03_parse.m Deleted : /previous_version/Spinach aux/g03_to_spinach.m Deleted : /previous_version/Spinach aux/gauss2mhz.m Deleted : /previous_version/Spinach aux/hard_pulse.m Deleted : /previous_version/Spinach aux/offset.m Deleted : /previous_version/Spinach aux/pad.m Deleted : /previous_version/Spinach aux/preSSR_hfi_pm.m Deleted : /previous_version/Spinach aux/preSSR_hfi_zz_op.m Deleted : /previous_version/Spinach aux/preSSR_state_finder.m Deleted : /previous_version/Spinach aux/preSSR_zeeman.m Deleted : /previous_version/Spinach aux/protein.m Deleted : /previous_version/Spinach aux/read_wave.m Deleted : /previous_version/Spinach aux/shaped_pulse.m Deleted : /previous_version/Spinach aux/sim_pulse.m Deleted : /previous_version/Spinach aux/simps.m Deleted : /previous_version/Spinach aux/wave Revision: 483 Author: kuprov Date: 29 March 2010 18:02:07 Message: Ported the homospoil function, added NOESY functionality to the cosy function (should rename at some point), fixed a couple of bugs in the create script, a couple of bugs in the Hamiltonian superoperator, shifted the state indexing functions into the main kernel, deleted the buggy Lin23 graph theory binary, ported (to a first approximation) a couple of NOESY tests, added relaxation to one of the pulse-acquire tests. ---- Modified : /TODO.txt Added : /etc/homospoil.m (Copy from path: /previous_version/Spinach aux/homospoil.m, Revision, 479) Modified : /exp/cosy.m Modified : /kernel/create.m Modified : /kernel/h_superop.m Added : /kernel/lin2lm.m (Copy from path: /kernel/private/lin2lm.m, Revision, 479) Added : /kernel/lm2lin.m (Copy from path: /kernel/private/lm2lin.m, Revision, 479) Deleted : /kernel/private/graphalgs.mexglx Deleted : /kernel/private/lin2lm.m Deleted : /kernel/private/lm2lin.m Modified : /kernel/private/negligible.m Modified : /kernel/private/significant.m Deleted : /previous_version/Spinach aux/homospoil.m Deleted : /previous_version/Spinach tests/noesy_test_1.m Deleted : /previous_version/Spinach tests/noesy_test_2.m Added : /tests/nmr/noesy_test_1.m (Copy from path: /previous_version/Spinach tests/noesy_test_1.m, Revision, 479) Added : /tests/nmr/noesy_test_2.m (Copy from path: /previous_version/Spinach tests/noesy_test_2.m, Revision, 479) Modified : /tests/nmr/pulse_acquire_test_1.m Revision: 482 Author: matthew Date: 29 March 2010 16:25:03 Message: The Hilbert space propagation routine EXPH5 along with the testing routine exph5_test_plus.m % EXPH5 computes an approximation of: % % rho_t = exp(t*H)*rho*exp(-t*H) % % for a general matrix A using the Hadamard lemma: % % exp(itH)rho exp(-itH) = rho + it/1! [H,rho] + (it)^2/2! [H,[H,rho]] + % (it)^3/3! [H,[H,[H,rho]]] + .... % % The above equation is computed in an iterative way Benchmarking has been done against EXPM (Fig1) and EXPH4 (Fig4). rho and H matrices were constructed by adding unity matrices to them and symmetrizing. The relative speedup of the EXPH5 routine to the EXPM is the same as for EXPH4 (both routines are very similar in speed for matrices of size up to 2^12 ---- Added : /dev/exph5.asv Added : /dev/exph5.m Added : /dev/exph5_speedup_1.fig Added : /dev/exph5_speedup_2.fig Added : /dev/exph5_test_plus.asv Added : /dev/exph5_test_plus.m Revision: 481 Author: kuprov Date: 29 March 2010 16:03:06 Message: Moved the diagnostics function across from the previous version of Spinach, updated the delay function to respect the output stream, moved across the thermal equilibrium density matrix function, renamed Gareth's function, added an NOE test. ---- Modified : /etc/delay.m Added : /etc/pad.m (Copy from path: /previous_version/Spinach kope/pad.m, Revision, 479) Added : /etc/state_diagnostics.m (Copy from path: /previous_version/Spinach aux/diagnostics.m, Revision, 479) Added : /etc/thermal_dm.m (Copy from path: /previous_version/Spinach core/thermal_dm.m, Revision, 479) Added : /kernel/rotations/quat2euler.m (Copy from path: /kernel/rotations/quaternion2euler.m, Revision, 479) Deleted : /kernel/rotations/quaternion.m Deleted : /kernel/rotations/quaternion2euler.m Deleted : /previous_version/Spinach aux/diagnostics.m Deleted : /previous_version/Spinach core/thermal_dm.m Deleted : /previous_version/Spinach kope/pad.m Deleted : /previous_version/Spinach tests/noe_test_1.m Added : /tests/nmr/noe_test_1.m (Copy from path: /previous_version/Spinach tests/noe_test_1.m, Revision, 479) Revision: 480 Author: kuprov Date: 29 March 2010 14:52:19 Message: Added extra relaxation theory parameters to the create script. Modified the relaxation superoperator to respect those options. ---- Added : /exp/derivative_pulse_acquire.m (Copy from path: /previous_version/Spinach experiments/derivative_pulse_acquire.m, Revision, 474) Modified : /kernel/create.m Modified : /kernel/r_superop.m Deleted : /previous_version/Spinach experiments/derivative_pulse_acquire.m Revision: 479 Author: gareth Date: 29 March 2010 14:29:59 Message: Highly experimental quaternion to euler angle converter added. From the file: % Converts Quaternion into Euler angles (Varshalovich B convention). % %Quaternion is defined as a structure with the following fields: %q.w,q.x,q.y,q.z %Such a structure can be constructed with the quaternion(w,x,y,z) function % %This method appears to be numerically stable but should be considered %experimental ---- Added : /kernel/rotations/quaternion.m Added : /kernel/rotations/quaternion2euler.m Revision: 478 Author: kuprov Date: 18 March 2010 19:29:12 Message: Fixed the projection ordering throughout the code, achieved full match to DD and CSA-CSA cross-correlation and a near-complete match to DD-CSA-CSA system. ---- Modified : /kernel/h_superop.m Modified : /tests/kernel/relaxation/csa_relaxation.nb Modified : /tests/kernel/relaxation/dd-csa_cross-correlation.nb Modified : /tests/kernel/relaxation/dd_csa_cross_correlation.m Modified : /tests/kernel/relaxation/dd_relaxation.nb Revision: 477 Author: kuprov Date: 18 March 2010 16:06:06 Message: Fixed a state indexing bug (ISTs are sorted by descending projection inside each rank). Got the CSA-CSA cross-correlation test to match the analytical result exactly. This is a major win -- that clears a lot of Spinach for production calculations. ---- Deleted : /etc/euler2dcm.m Modified : /etc/operator.m Modified : /etc/state.m Modified : /kernel/basis.m Modified : /kernel/h_superop.m Modified : /kernel/rotations/euler2dcm.m Modified : /tests/kernel/relaxation/csa_relaxation.m Modified : /tests/kernel/relaxation/csa_relaxation.nb Revision: 476 Author: kuprov Date: 17 March 2010 18:43:49 Message: Added a DD-CSA test and fixed a couple of minor bugs here and there. The diagonal of the relaxation superoperator is definitely correct at the moment, the rotational conventions are being hunted down. ---- Modified : /kernel/propagator.m Modified : /kernel/r_superop.m Modified : /tests/kernel/relaxation/csa_relaxation.nb Modified : /tests/kernel/relaxation/dd-csa_cross-correlation.nb Added : /tests/kernel/relaxation/dd_csa_cross_correlation.m Modified : /tests/kernel/relaxation/dd_relaxation.m Modified : /tests/kernel/relaxation/dd_relaxation.nb Revision: 475 Author: kuprov Date: 17 March 2010 18:01:38 Message: A major refinement to exph4. ---- Modified : /dev/exph4.m Revision: 474 Author: kuprov Date: 17 March 2010 17:54:34 Message: A bug fixed in the relaxation superoperator, almost perfect match achieved to analytical results for CSA-CSA cross-correlation (some cross-correlation signs are currently off, suggesting a rotational convention misalignment, but all amplitudes are correct). ---- Modified : /kernel/r_superop.m Modified : /tests/kernel/relaxation/csa_relaxation.m Modified : /tests/kernel/relaxation/csa_relaxation.nb Revision: 473 Author: matthew Date: 17 March 2010 15:08:00 Message: Some new literature and tests of exph4 ---- Added : /dev/017_brancik.pdf Added : /dev/19ways+.pdf Added : /dev/2250matrixexponential.pdf Added : /dev/A useful expansion of the exponential of the sum of two non commuting matrices one of which is diagonal.pdf Added : /dev/ExponentialExplicitSoTAC1993.pdf Added : /dev/MatrixEponenential.pdf Added : /dev/Variational Hilbert-space-truncation.pdf Modified : /dev/exph.m Added : /dev/exph4_speedup_1.fig Modified : /dev/exph4_test_plus.m Added : /dev/exph_5steps_speedup_1.fig Added : /dev/exph_5steps_speedup_2.fig Added : /dev/matrix.pdf Added : /dev/rome08_talk.pdf Added : /dev/spectral theorem.pdf Revision: 472 Author: matthew Date: 17 March 2010 12:43:13 Message: A new routine exph4 added. This routine makes use of the Taylor expansion technique used in Spinach function propagator.m ---- Added : /dev/exph4.asv Added : /dev/exph4.m Added : /dev/exph4_test_plus.m Added : /dev/matthew_test.m Revision: 471 Author: kuprov Date: 17 March 2010 11:53:55 Message: Moved across some relaxation theory tests. Obscure rotational invariance bugs... investigating. ---- Deleted : /previous_version/Spinach tests/etalons Added : /tests/kernel/relaxation Added : /tests/kernel/relaxation/csa_relaxation.m (Copy from path: /tests/kernel/relaxation_csa.m, Revision, 467) Added : /tests/kernel/relaxation/csa_relaxation.nb (Copy from path: /previous_version/Spinach tests/etalons/csa_relaxation.nb, Revision, 466) Added : /tests/kernel/relaxation/dd-csa_cross-correlation.nb (Copy from path: /previous_version/Spinach tests/etalons/dd-csa_cross-correlation.nb, Revision, 466) Added : /tests/kernel/relaxation/dd_relaxation.m Added : /tests/kernel/relaxation/dd_relaxation.nb (Copy from path: /previous_version/Spinach tests/etalons/dd_relaxation.nb, Revision, 466) Deleted : /tests/kernel/relaxation_csa.m Revision: 470 Author: kuprov Date: 16 March 2010 18:34:27 Message: Introduced secular interactions in a systematic. The Hamiltonian commutation superoperator no longer needs to know our assumptions about the working field -- it only needs to know the interaction "strength" (strong, secular, week) that it needs to return. ---- Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/private/mat2RxRyRz.m Added : /kernel/private/negligible.m Modified : /kernel/r_superop.m Modified : /tests/kernel/single_spin_test_1.m Modified : /tests/kernel/single_spin_test_2.m Modified : /tests/kernel/two_spin_test_1.m Modified : /tests/nmr/solids_test_1.m Revision: 469 Author: kuprov Date: 16 March 2010 14:37:24 Message: Replaced Simpson's rule with O(h^7) Boole's quadrature in the relaxation superoperator. This is as high-tech as we can reasonably go in a situation where we are forced to work on a uniform time grid. ---- Modified : /TODO.txt Modified : /kernel/r_superop.m Revision: 468 Author: kuprov Date: 16 March 2010 12:37:20 Message: Simpson quadrature instead of rectangles in relaxation superoperator. ---- Modified : /kernel/r_superop.m Revision: 467 Author: kuprov Date: 15 March 2010 12:22:27 Message: Fixed a minor bug in the relaxation superoperator and added two new tests. ---- Modified : /TODO.txt Modified : /kernel/r_superop.m Added : /tests/kernel/relaxation_csa.m Added : /tests/nmr/solids_test_2.m Revision: 466 Author: kuprov Date: 14 March 2010 15:45:23 Message: Deleted the Gaussian files -- this is the wrong repository. ---- Deleted : /dev/Gaussian Long Output Revision: 465 Author: kuprov Date: 14 March 2010 15:07:54 Message: Minor speed-related update. ---- Modified : /kernel/rotations/dcm2euler.m Revision: 464 Author: kuprov Date: 13 March 2010 16:08:56 Message: A very clunky but very reliable DCM to Euler converter for Gareth. ---- Added : /kernel/rotations/dcm2euler.m Modified : /kernel/rotations/dcm2wigner.m Modified : /kernel/rotations/euler2dcm.m Revision: 463 Author: matthew Date: 12 March 2010 16:03:26 Message: The changes made to the G03 code to try to force it to output more accurate magnetic observables ---- Added : /dev/Gaussian Long Output Added : /dev/Gaussian Long Output/l9999.F Added : /dev/Gaussian Long Output/l9999.F_gareth_charnock Added : /dev/Gaussian Long Output/utilam.F Added : /dev/Gaussian Long Output/utilam.F_maciej Revision: 462 Author: matthew Date: 09 March 2010 21:35:59 Message: the tolerance and number of terms in expv routine used in a loop of exph turned down to try to speed up the exph routine ---- Modified : /dev/exph.m Revision: 461 Author: kuprov Date: 08 March 2010 10:20:48 Message: A quick test of exph against the simple Taylor expansion for a real-world spin system. ---- Added : /dev/ilya_test.m Revision: 460 Author: matthew Date: 07 March 2010 21:37:11 Message: The benchmarking of EXPH and EXPH2 together with a docx file report. ---- Added : /dev/EXPH test.docx Added : /dev/exph2.asv Modified : /dev/exph2.m Added : /dev/exph2_speedup_1.fig Added : /dev/exph2_speedup_1.png Added : /dev/exph2_speedup_2.fig Added : /dev/exph2_speedup_2.png Added : /dev/exph2_test_plus.m Added : /dev/exph_speedup_1.fig Added : /dev/exph_speedup_1.png Added : /dev/exph_speedup_2.fig Added : /dev/exph_speedup_2.png Added : /dev/exph_test.asv Modified : /dev/exph_test.m Modified : /dev/exph_test2.asv Modified : /dev/exph_test2.m Modified : /dev/exph_test3.m Added : /dev/exph_test_plus.asv Added : /dev/exph_test_plus.m Added : /dev/expv.pdf Added : /dev/expvh.m Revision: 459 Author: kuprov Date: 06 March 2010 15:20:45 Message: A reworked Hamiltonian superoperator generator -- all bugs have been fixed and calls to expensive functions have been reduced to absolute minimum. ---- Modified : /TODO.txt Modified : /kernel/h_superop.m Added : /kernel/private/significant.m Revision: 458 Author: kuprov Date: 05 March 2010 12:36:50 Message: Testing set for optimal control. ---- Added : /TODO.txt (Copy from path: /previous_version/TODO.txt, Revision, 457) Added : /installation.txt (Copy from path: /previous_version/installation.txt, Revision, 457) Deleted : /previous_version/TODO.txt Deleted : /previous_version/installation.txt Added : /tests/molecules/nitroxide.log Added : /tests/optimal_control Added : /tests/optimal_control/five_spin_test_1.m Added : /tests/optimal_control/five_spin_test_2.m Added : /tests/optimal_control/five_spin_test_3.m Added : /tests/optimal_control/five_spin_test_4.m Added : /tests/optimal_control/five_spin_test_5.m Added : /tests/optimal_control/five_spin_test_6.m Added : /tests/optimal_control/five_spin_test_7.m Added : /tests/optimal_control/nitroxide.m Revision: 457 Author: kuprov Date: 02 March 2010 13:19:05 Message: Added the graph theory binary for 32-bit Linux systems. ---- Added : /kernel/private/graphalgs.mexglx Modified : /kernel/rotations/euler2dcm.m Revision: 456 Author: kuprov Date: 02 March 2010 12:10:05 Message: Tightened up the tolerance on ZTE - to prevent it from dropping the slowly accumulating states. ---- Modified : /kernel/private/tolerances.m Revision: 455 Author: kuprov Date: 24 February 2010 15:51:13 Message: 64-bit Linux binary for path tracer. ---- Added : /kernel/private/graphalgs.mexa64 Revision: 454 Author: kuprov Date: 24 February 2010 15:07:12 Message: Lebedev integrator coded for powder averages -- for a given number of points, this is probably the most accurate spherical integrator in existence. The project of getting an infinite-order extrapolation on this is left for grabs by any interested party. ---- Added : /docs/lebedev_quadratures_1.pdf Added : /docs/lebedev_quadratures_2.pdf Added : /exp/grids/lebedev.c Added : /exp/grids/lebedev_rank_101.dat Added : /exp/grids/lebedev_rank_107.dat Added : /exp/grids/lebedev_rank_11.dat Added : /exp/grids/lebedev_rank_113.dat Added : /exp/grids/lebedev_rank_119.dat Added : /exp/grids/lebedev_rank_125.dat Added : /exp/grids/lebedev_rank_13.dat Added : /exp/grids/lebedev_rank_131.dat Added : /exp/grids/lebedev_rank_15.dat Added : /exp/grids/lebedev_rank_17.dat Added : /exp/grids/lebedev_rank_19.dat Added : /exp/grids/lebedev_rank_21.dat Added : /exp/grids/lebedev_rank_23.dat Added : /exp/grids/lebedev_rank_25.dat Added : /exp/grids/lebedev_rank_27.dat Added : /exp/grids/lebedev_rank_29.dat Added : /exp/grids/lebedev_rank_3.dat Added : /exp/grids/lebedev_rank_31.dat Added : /exp/grids/lebedev_rank_35.dat Added : /exp/grids/lebedev_rank_41.dat Added : /exp/grids/lebedev_rank_47.dat Added : /exp/grids/lebedev_rank_5.dat Added : /exp/grids/lebedev_rank_53.dat Added : /exp/grids/lebedev_rank_59.dat Added : /exp/grids/lebedev_rank_65.dat Added : /exp/grids/lebedev_rank_7.dat Added : /exp/grids/lebedev_rank_71.dat Added : /exp/grids/lebedev_rank_77.dat Added : /exp/grids/lebedev_rank_83.dat Added : /exp/grids/lebedev_rank_89.dat Added : /exp/grids/lebedev_rank_9.dat Added : /exp/grids/lebedev_rank_95.dat Modified : /exp/pulse_acquire_powder.m Added : /tests/nmr/quadrupole_test_2.m Revision: 453 Author: kuprov Date: 24 February 2010 10:30:17 Message: Quadrupole interaction test added -- works beautifully. :) ---- Modified : /kernel/create.m Added : /tests/nmr/quadrupole_test_1.m (Copy from path: /tests/nmr/solids_test_1.m, Revision, 451) Revision: 452 Author: kuprov Date: 24 February 2010 10:15:57 Message: Re-introduced the (accidentally omitted) strong and weak coupling specification into the Hamiltonian superoperator. ---- Modified : /kernel/h_superop.m Revision: 451 Author: matthew Date: 23 February 2010 15:41:58 Message: A group of 3 Hilbert space propagators: (i) exph uses the idea of Kronecker decomposition plus Krylov technique based matrix exponentiation via expv (ii) exph2 uses the idea of efficient (N steps only Kronecker decomposition) plus expv; (iii) exph3 uses the ides of so called nearest Kronecker decomposition in one step only in the least squares sense [the least squares are performed via kron_min function] plus expv. Testing routines are provided for the exph, exph2 and exph3 ---- Added : /dev/exph.asv Added : /dev/exph2.m Added : /dev/exph3.asv Added : /dev/exph3.m Modified : /dev/exph_test.m Added : /dev/exph_test2.asv Added : /dev/exph_test2.m Added : /dev/exph_test3.m Added : /dev/expv.m Added : /dev/expv_test.asv Added : /dev/expv_test.m Added : /dev/kron_min.asv Added : /dev/kron_min.m Revision: 450 Author: kuprov Date: 23 February 2010 12:27:38 Message: A major unification of all Liouvillian-related structures. Rotations are now naturally incorporated into the function that returns the main Hamiltonian superoperator. ---- Deleted : /dev/new_h_superop.m Modified : /exp/maryan.m Modified : /exp/pulse_acquire_powder.m Modified : /kernel/h_superop.m Modified : /kernel/orientation.m Deleted : /kernel/private/dcm2wigner.m Deleted : /kernel/private/wigner_d.m Modified : /kernel/r_superop.m Deleted : /kernel/rotation_basis.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_8.m Revision: 449 Author: kuprov Date: 23 February 2010 11:05:49 Message: Three auxiliary rotation functions dealing with transformations between Euler angles, DCM and Wigner functions. Self-consistency checked. ---- Added : /kernel/rotations Added : /kernel/rotations/dcm2wigner.m (Copy from path: /kernel/private/dcm2wigner.m, Revision, 447) Added : /kernel/rotations/euler2dcm.m Added : /kernel/rotations/euler2wigner.m (Copy from path: /kernel/private/wigner_d.m, Revision, 447) Revision: 448 Author: kuprov Date: 22 February 2010 18:35:58 Message: A piece of visualization code from Chris Rodgers and a piece of the new hamiltonian superoperator function -- halfway to a major unification with the rotation basis generator. ---- Added : /dev/new_h_superop.m Added : /dev/visualization Added : /dev/visualization/Add3DAxes.m Added : /dev/visualization/Arrow3.m Added : /dev/visualization/AxisAtOrigin.m Added : /dev/visualization/MakeRegularThPhGrid.m Added : /dev/visualization/MakeSopheGrid.m Added : /dev/visualization/MakeSopheSolidAngles.m Added : /dev/visualization/PlotRegularThPhSurf.m Added : /dev/visualization/PlotSopheSurf.m Added : /dev/visualization/mycart2sph.m Added : /dev/visualization/myshading.m Added : /dev/visualization/mysph2cart.m Added : /dev/visualization/perp3.m Revision: 447 Author: kuprov Date: 22 February 2010 10:16:46 Message: Added tesselation information to the pre-computed icosahedral grids, modified the MARYAN demo to take advantage of that when plotting the answer. ---- Deleted : /exp/grids/icosahedral_10242.txt Added : /exp/grids/icosahedral_10242_triangles.txt Added : /exp/grids/icosahedral_10242_vertices.txt (Copy from path: /exp/grids/icosahedral_10242.txt, Revision, 446) Deleted : /exp/grids/icosahedral_12.txt Added : /exp/grids/icosahedral_12_triangles.txt Added : /exp/grids/icosahedral_12_vertices.txt (Copy from path: /exp/grids/icosahedral_12.txt, Revision, 446) Deleted : /exp/grids/icosahedral_162.txt Added : /exp/grids/icosahedral_162_triangles.txt Added : /exp/grids/icosahedral_162_vertices.txt (Copy from path: /exp/grids/icosahedral_162.txt, Revision, 446) Deleted : /exp/grids/icosahedral_2562.txt Added : /exp/grids/icosahedral_2562_triangles.txt Added : /exp/grids/icosahedral_2562_vertices.txt (Copy from path: /exp/grids/icosahedral_2562.txt, Revision, 446) Deleted : /exp/grids/icosahedral_42.txt Added : /exp/grids/icosahedral_42_triangles.txt Added : /exp/grids/icosahedral_42_vertices.txt (Copy from path: /exp/grids/icosahedral_42.txt, Revision, 446) Deleted : /exp/grids/icosahedral_642.txt Added : /exp/grids/icosahedral_642_triangles.txt Added : /exp/grids/icosahedral_642_vertices.txt (Copy from path: /exp/grids/icosahedral_642.txt, Revision, 446) Modified : /exp/maryan.m Added : /tests/spin_chemistry/rodgers_thesis_fig_7_10.m Revision: 446 Author: kuprov Date: 17 February 2010 22:12:55 Message: Cosmetic speed-ups in the propagator module, a powder-averaged pulse-acquire function and a test for it. ---- Added : /exp/pulse_acquire_powder.m Modified : /kernel/propagator.m Modified : /tests/nmr/solids_test_1.m Revision: 445 Author: kuprov Date: 17 February 2010 21:34:55 Message: MARYAN sequence and a few icosahedral grids. ---- Added : /exp/grids Added : /exp/grids/icosahedral_10242.txt Added : /exp/grids/icosahedral_12.txt Added : /exp/grids/icosahedral_162.txt Added : /exp/grids/icosahedral_2562.txt Added : /exp/grids/icosahedral_42.txt Added : /exp/grids/icosahedral_642.txt Added : /exp/grids/sphere.c Added : /exp/maryan.m (Copy from path: /exp/mary.m, Revision, 444) Revision: 444 Author: kuprov Date: 16 February 2010 22:33:56 Message: Fixed an ancient bug in the basis generator, added a 32-bit mex for the path tracer. ---- Modified : /kernel/private/cluster_gen.m Added : /kernel/private/graphalgs.mexw32 Modified : /kernel/private/graphalgs.mexw64 Modified : /kernel/private/graphconncomp.m Modified : /tests/nmr/pulse_acquire_test_1.m Revision: 443 Author: kuprov Date: 16 February 2010 15:51:02 Message: Introduced ZTE and path tracing into NMR sequences, massive speed-ups as a result. ---- Modified : /exp/cosy.m Modified : /exp/mary.m Modified : /exp/pulse_acquire.m Modified : /kernel/propagator.m Modified : /kernel/zte.m Revision: 442 Author: kuprov Date: 16 February 2010 11:06:20 Message: All path tracing bugs are well and truly sorted -- a nice implementation of Tarjan's algorithm was hooked up from the bioinformatics toolbox. Linear scaling with the number of non-zeros in the Liouvillian. ---- Modified : /kernel/path_trace.m Added : /kernel/private/graphalgs.mexw64 Added : /kernel/private/graphconncomp.m Modified : /kernel/private/tolerances.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_8.m Revision: 441 Author: kuprov Date: 15 February 2010 15:51:00 Message: Fixed a bug in the rotation basis and reproduced Figure 7.8 from CTR's thesis. ---- Modified : /kernel/rotation_basis.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_8.m Revision: 440 Author: matthew Date: 13 February 2010 00:28:04 Message: My routines to propagate a density matrix in Hilbert space. Benchmarked and tested perform better than expv for spares (<0.01 precent sparsity) matrices... ---- Added : /dev/exph.m Added : /dev/exph_test.m Revision: 439 Author: kuprov Date: 10 February 2010 18:23:53 Message: Another bug in the rotation basis. ---- Modified : /kernel/rotation_basis.m Revision: 438 Author: kuprov Date: 10 February 2010 18:09:01 Message: Two out of four pictures from CTR's thesis reporduced. Others are a matter of investigation... ---- Modified : /exp/pulse_acquire.m Modified : /tests/nmr/solids_test_1.m Modified : /tests/spin_chemistry/rodgers_thesis_fig_7_8.m Revision: 437 Author: kuprov Date: 10 February 2010 17:18:11 Message: Fixed some obvious bugs within the rotation basis generator and polished up the mary function. ---- Modified : /exp/mary.m Modified : /kernel/rotation_basis.m Revision: 436 Author: kuprov Date: 10 February 2010 17:11:49 Message: Made the MARY function respect the debugging switches. ---- Modified : /exp/mary.m Revision: 435 Author: kuprov Date: 10 February 2010 15:24:38 Message: Allowed user-supplied Liouvillians in MARY, fixed a couple of minor bugs in the rotation basis function and introduced a direction-dependent MARY test. ---- Modified : /exp/mary.m Modified : /kernel/create.m Modified : /kernel/rotation_basis.m Added : /tests/references/timmel_cpl_2001.pdf Added : /tests/spin_chemistry/rodgers_thesis_fig_7_8.m Revision: 434 Author: kuprov Date: 10 February 2010 10:50:58 Message: Two more simulation, with references, of literature MARY data. ---- Added : /tests/references Added : /tests/references/timmel_cpl_1998.pdf Added : /tests/references/timmel_molphys_1998.pdf Deleted : /tests/spin_chemistry/mary_test_4.m Added : /tests/spin_chemistry/timmel_cpl_fig_3.m (Copy from path: /tests/spin_chemistry/mary_test_4.m, Revision, 427) Added : /tests/spin_chemistry/timmel_molphys_fig_5.m Revision: 433 Author: kuprov Date: 10 February 2010 10:31:05 Message: Some clean-up and a new MARY test - a perfect reproduction of one of the figures in CRT's 1998 MolPhys paper. ---- Modified : /exp/mary.m Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/path_trace.m Modified : /tests/nmr/derome_fig_8_26.m Added : /tests/spin_chemistry/timmel_molphys_fig_1.m Revision: 432 Author: kuprov Date: 09 February 2010 18:40:53 Message: An extra apodization function, axes added to 2D contour plotter, the axis shifted correct way around in the axis function, cosmetic modification to the COSY function and a textbook example of a COSY spectrum from the Derome book -- the first textbook example to be reproduced down to the finest detail. ---- Modified : /etc/apodization.m Modified : /etc/contour_plot.m Modified : /exp/axis_1d.m Modified : /exp/cosy.m Deleted : /tests/nmr/cosy_test_1.m Deleted : /tests/nmr/cosy_test_2.m Added : /tests/nmr/derome_fig_8_26.m Revision: 431 Author: kuprov Date: 09 February 2010 11:19:23 Message: Started to code the Hilbert-space clone of expv. Nothing new, just copying Sidje's apprach for double-sided propagation. ---- Added : /dev Added : /dev/expvds.m Added : /dev/p130-sidje.pdf Revision: 430 Author: kuprov Date: 08 February 2010 12:19:46 Message: Added nifty offset clicks for the output of the various auxiliary functions. Spinach output became much more readable and interpretable -- it is now clear what is calling what. ---- Added : /kernel/click.m Modified : /kernel/h_superop.m Modified : /kernel/path_trace.m Modified : /kernel/private/cluster_gen.m Modified : /kernel/propagator.m Modified : /kernel/r_superop.m Modified : /kernel/report.m Modified : /kernel/rotation_basis.m Modified : /kernel/zte.m Revision: 429 Author: kuprov Date: 08 February 2010 11:51:36 Message: Basic coding and testing finished for a posteriori rotational averaging and diagonalization-free Liouville-space Redfield superoperator. Strict testing against known code and data remains. ---- Modified : /kernel/r_superop.m Modified : /kernel/rotation_basis.m Revision: 428 Author: kuprov Date: 08 February 2010 11:19:59 Message: minor clean-up in the create script. ---- Modified : /kernel/create.m Modified : /tests/nmr/pulse_acquire_test_1.m Revision: 427 Author: kuprov Date: 31 January 2010 19:27:45 Message: A cleaned-up version of the create.m script. Needs another pass and lots of testing. ---- Modified : /kernel/create.m Revision: 426 Author: kuprov Date: 30 January 2010 18:34:40 Message: Managed to reproduce Pake patterns for dipolar interaction and CSA. Not sure the amplitudes and roofs a right, that will need checking, but the basic idea seems to be working. ---- Modified : /kernel/create.m Modified : /kernel/rotation_basis.m Modified : /tests/nmr/solids_test_1.m Revision: 425 Author: kuprov Date: 29 January 2010 20:19:46 Message: Slight reordering in the create.m to treat correctly the case when the user did not supply any interaction information. Added the isotropic part of the Zeeman interaction to the rotation_basis.m function. ---- Modified : /kernel/create.m Modified : /kernel/rotation_basis.m Revision: 424 Author: kuprov Date: 27 January 2010 17:10:31 Message: Major changes all over the place. Fixed the Zeeman frequency signs (might need returning to at some point), switched pulse_acquire.m to central reporting system, disentangled Zeeman interaction and couplings on h_superop.m, fixed a bug in orientation.m, made rotation_basis.m aware of the rotating frame situation, removed obsolete lines from a few tests, migrated the euler2dcm.m function from the old kernel, added the new test function for CSA powder averaging. ---- Added : /etc/euler2dcm.m Modified : /etc/offset.m Modified : /exp/axis_1d.m Modified : /exp/pulse_acquire.m Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/orientation.m Modified : /kernel/rotation_basis.m Deleted : /previous_version/Spinach core/rotate_system.m Modified : /tests/kernel/four_spin_test_1.m Modified : /tests/kernel/single_spin_test_1.m Modified : /tests/kernel/single_spin_test_2.m Modified : /tests/nmr/cosy_test_2.m Modified : /tests/nmr/pulse_acquire_test_1.m Modified : /tests/nmr/pulse_acquire_test_2.m Modified : /tests/nmr/solids_test_1.m Revision: 423 Author: kuprov Date: 27 January 2010 14:58:22 Message: Significant bug fixes in solid state part of the Hamiltonian commutation superoperator -- now treating the rotating frame correctly. ---- Modified : /kernel/h_superop.m Revision: 422 Author: kuprov Date: 26 January 2010 18:47:12 Message: Disentangled the Zeeman interaction from couplings -- needed for the case where the system only has one spin. ---- Modified : /kernel/create.m Modified : /kernel/orientation.m Modified : /kernel/rotation_basis.m Deleted : /previous_version/Spinach core/clusters Modified : /tests/nmr/solids_test_1.m Revision: 421 Author: kuprov Date: 26 January 2010 17:47:13 Message: Moving towards full rotational factorization as the default modus operandi -- this would make MARYAN and solid-state NMR/EPR simulations fast and natural in Spinach. ---- Added : /kernel/orientation.m Added : /kernel/private/wigner_d.m (Copy from path: /previous_version/Spinach core/wigner_d.m, Revision, 418) Added : /kernel/rotation_basis.m Deleted : /previous_version/Spinach core/add_clusters.m Deleted : /previous_version/Spinach core/analytical_zte.m Deleted : /previous_version/Spinach core/axis_1d.m Deleted : /previous_version/Spinach core/cluster_cleanup.m Deleted : /previous_version/Spinach core/cluster_gen.m Deleted : /previous_version/Spinach core/cluster_ham.m Deleted : /previous_version/Spinach core/create.m Deleted : /previous_version/Spinach core/custom_operator.m Deleted : /previous_version/Spinach core/custom_state.m Deleted : /previous_version/Spinach core/decouple.m Deleted : /previous_version/Spinach core/exchange_superop.m Deleted : /previous_version/Spinach core/expv.m Deleted : /previous_version/Spinach core/irr_sph_ten.m Deleted : /previous_version/Spinach core/liouv_gen.m Deleted : /previous_version/Spinach core/nucleus.m Deleted : /previous_version/Spinach core/numerical_zte.m Deleted : /previous_version/Spinach core/path_trace.m Deleted : /previous_version/Spinach core/pauli.m Deleted : /previous_version/Spinach core/progmeter.m Deleted : /previous_version/Spinach core/prop_gen.m Deleted : /previous_version/Spinach core/report.m Deleted : /previous_version/Spinach core/singlet.m Deleted : /previous_version/Spinach core/spectral_density.m Deleted : /previous_version/Spinach core/state_pregen.m Deleted : /previous_version/Spinach core/statelist_gen.m Deleted : /previous_version/Spinach core/symmetry.m Deleted : /previous_version/Spinach core/symmetry_group.m Deleted : /previous_version/Spinach core/tolerances.m Deleted : /previous_version/Spinach core/warnings.m Deleted : /previous_version/Spinach core/wigner_d.m Revision: 420 Author: kuprov Date: 26 January 2010 12:27:54 Message: An update to the solids Hamiltonian. ---- Modified : /kernel/h_superop.m Modified : /tests/nmr/solids_test_1.m Revision: 419 Author: kuprov Date: 26 January 2010 10:39:38 Message: First attempt at migrating the solids Hamiltonian. ---- Modified : /kernel/create.m Modified : /kernel/h_superop.m Modified : /kernel/private/cluster_gen.m Modified : /kernel/private/correlation_function.m Added : /tests/nmr/solids_test_1.m Revision: 418 Author: kuprov Date: 19 January 2010 12:08:47 Message: Rough initial coding of the diagonalization-free generalized Redfield superoperator. Much debugging remains, please do not expect it to work! ---- Modified : /kernel/create.m Modified : /kernel/h_superop.m Added : /kernel/private/correlation_function.m Modified : /kernel/propagator.m Modified : /kernel/r_superop.m Revision: 417 Author: kuprov Date: 13 January 2010 12:23:12 Message: DCM2Wigner transformation fixed and tested. ---- Modified : /kernel/private/dcm2wigner.m Revision: 416 Author: kuprov Date: 11 January 2010 12:23:32 Message: Added tensor symmetry warning. If any interaction tensor in the system has significant anti-symmetric components, a warning is printed and the tensor is symmetrized. This is to ensure that the result plays well with the rotations module. ---- Modified : /etc/g03_parse.m Modified : /kernel/create.m Modified : /kernel/private/tolerances.m Revision: 415 Author: kuprov Date: 09 January 2010 15:15:24 Message: Two scaling tests and a minor mod to the propagator function -- the eigenvalue estimator was previously getting unstable if non-Hermitian round-off errors were present in the Liouvillian. ---- Modified : /kernel/propagator.m Added : /tests/kernel/scaling_test_1.m (Copy from path: /previous_version/Spinach tests/scaling_test_1.m, Revision, 410) Added : /tests/kernel/scaling_test_2.m (Copy from path: /previous_version/Spinach tests/scaling_test_2.m, Revision, 410) Revision: 414 Author: kuprov Date: 08 January 2010 17:07:24 Message: Fixed a minor omission in the state function, got the Hamiltonian superoperator to respect strong and weak coupling specification, added kernel test functions for two-, three-, and four-spin systems involving high spin. ---- Modified : /etc/state.m Modified : /kernel/h_superop.m Deleted : /previous_version/Spinach tests/high_spin_test_1.m Deleted : /previous_version/Spinach tests/scaling_test_1.m Deleted : /previous_version/Spinach tests/scaling_test_2.m Added : /tests/kernel/four_spin_test_1.m (Copy from path: /previous_version/Spinach tests/high_spin_test_1.m, Revision, 410) Deleted : /tests/kernel/single_spin.m Added : /tests/kernel/three_spin_test_1.m Modified : /tests/kernel/two_spin_test_1.m Revision: 413 Author: kuprov Date: 08 January 2010 16:29:23 Message: Some test scripts for the kernel, demonstrating perfect obedience of the commutation laws by one- and two-spin operators involving high spin. ---- Added : /tests/kernel/single_spin_test_1.m (Copy from path: /tests/kernel/single_spin.m, Revision, 410) Added : /tests/kernel/single_spin_test_2.m Added : /tests/kernel/two_spin_test_1.m Revision: 412 Author: kuprov Date: 08 January 2010 12:15:16 Message: Minor refinements to the symmetry function, plus ported the symmetry test across from the previous version of Spinach. ---- Modified : /kernel/basis.m Modified : /kernel/private/symmetry.m Deleted : /previous_version/Spinach tests/symmetry_test_1.m Added : /tests/kernel/symmetry_test_1.m (Copy from path: /previous_version/Spinach tests/symmetry_test_1.m, Revision, 410) Modified : /tests/spin_chemistry/mary_test_3.m Revision: 411 Author: kuprov Date: 08 January 2010 11:39:57 Message: Considerable speed-up in the symmetry factorization function, particularly with A1g calculations. ---- Modified : /kernel/private/symmetry.m Revision: 410 Author: kuprov Date: 04 January 2010 20:21:09 Message: Minor bug fixed in the Hamiltonian superoperator and a new function converting the directional cosine matrix into second-rank Wigner function matrix. A monumentally important function, that one. ---- Modified : /kernel/h_superop.m Added : /kernel/private/dcm2wigner.m Revision: 409 Author: kuprov Date: 02 January 2010 18:27:05 Message: Shifted the relaxation documents into the docs directory. Found a paper giving Wigner functions in terms of DCM elements - God bless the authors. :) ---- Deleted : /TODO.txt Deleted : /XML markup Added : /docs Added : /docs/dcm2wigner.pdf Added : /docs/relaxation_superoperator.docx (Copy from path: /previous_version/Documentation/relaxation_superoperator.docx, Revision, 401) Deleted : /previous_version/Documentation/relaxation_superoperator.docx Added : /previous_version/TODO.txt (Copy from path: /TODO.txt, Revision, 401) Added : /previous_version/XML markup (Copy from path: /XML markup, Revision, 401) Revision: 408 Author: kuprov Date: 02 January 2010 17:54:45 Message: Frequency sign flipped in the create script to match the convention for NMR parameters. ---- Modified : /kernel/create.m Revision: 407 Author: kuprov Date: 02 January 2010 17:40:18 Message: Fixed a normalization bug in the user-end operator and state function. Added a shortcut for a two-spin singlet. Migrated the COSY function of the associated tests. Fixed a crash in the basis function when coordinates are not supplied. Did some rewording in cluster generator, mostly for marketing reasons. Fixed a crash in the propagator function when the spin system is small. Migrated the contour plot function. ---- Added : /etc/contour_plot.m (Copy from path: /previous_version/Spinach aux/contour_plot.m, Revision, 401) Modified : /etc/operator.m Added : /etc/singlet.m Modified : /etc/state.m Replacing : /exp/axis_1d.m Added : /exp/cosy.m (Copy from path: /previous_version/Spinach experiments/expCOSY.m, Revision, 401) Modified : /kernel/basis.m Modified : /kernel/private/cluster_gen.m Modified : /kernel/propagator.m Deleted : /previous_version/Spinach aux/contour_plot.m Deleted : /previous_version/Spinach experiments/expCOSY.m Deleted : /previous_version/Spinach experiments/expMARY.m Deleted : /previous_version/Spinach experiments/expNOESY.m Deleted : /previous_version/Spinach experiments/pulse_acquire.m Deleted : /previous_version/Spinach tests/cosy_test_1.m Deleted : /previous_version/Spinach tests/cosy_test_2.m Added : /tests/kernel Added : /tests/kernel/single_spin.m (Copy from path: /tests/mary/mary_test_1.m, Revision, 403) Deleted : /tests/mary Added : /tests/nmr (Copy from path: /tests/pulse_acquire, Revision, 405) Added : /tests/nmr/cosy_test_1.m (Copy from path: /previous_version/Spinach tests/cosy_test_1.m, Revision, 401) Added : /tests/nmr/cosy_test_2.m (Copy from path: /previous_version/Spinach tests/cosy_test_2.m, Revision, 401) Modified : /tests/nmr/pulse_acquire_test_2.m Deleted : /tests/pulse_acquire Added : /tests/spin_chemistry (Copy from path: /tests/mary, Revision, 403) Revision: 406 Author: kuprov Date: 01 January 2010 18:31:42 Message: Found and fixed the frequency inversion bug. ---- Modified : /kernel/create.m Revision: 405 Author: kuprov Date: 01 January 2010 18:07:47 Message: Migrated the pulse-acquire tests. The axis is inverted for some reason. Investigating. ---- Deleted : /previous_version/Spinach tests/pulse_acquire_test_1.m Deleted : /previous_version/Spinach tests/pulse_acquire_test_2.m Added : /tests/pulse_acquire Added : /tests/pulse_acquire/pulse_acquire_test_1.m (Copy from path: /tests/pulse_acquire_test_1.m, Revision, 401) Added : /tests/pulse_acquire/pulse_acquire_test_2.m (Copy from path: /previous_version/Spinach tests/pulse_acquire_test_2.m, Revision, 401) Deleted : /tests/pulse_acquire_test_1.m Revision: 404 Author: kuprov Date: 01 January 2010 17:16:37 Message: Fixed a bizarre bug in the symmetry function. ---- Replacing : /kernel/private/symmetry.m (Copy from path: /previous_version/Spinach core/symmetry.m, Revision, 401) Revision: 403 Author: kuprov Date: 01 January 2010 16:25:28 Message: Shifted all MARY tests across and modified the MARY function somewhat. ---- Modified : /exp/mary.m Deleted : /previous_version/Spinach tests/mary_test_1.m Deleted : /previous_version/Spinach tests/mary_test_2.m Deleted : /previous_version/Spinach tests/mary_test_3.m Deleted : /previous_version/Spinach tests/mary_test_4.m Added : /tests/mary Added : /tests/mary/mary_test_1.m (Copy from path: /tests/mary_test_1.m, Revision, 401) Added : /tests/mary/mary_test_2.m (Copy from path: /previous_version/Spinach tests/mary_test_2.m, Revision, 401) Added : /tests/mary/mary_test_3.m (Copy from path: /previous_version/Spinach tests/mary_test_3.m, Revision, 401) Added : /tests/mary/mary_test_4.m (Copy from path: /previous_version/Spinach tests/mary_test_4.m, Revision, 401) Deleted : /tests/mary_test_1.m Revision: 402 Author: kuprov Date: 01 January 2010 11:15:48 Message: More intelligent product superoperator and finalized liquids Hamiltonian superoperator. ---- Modified : /kernel/h_superop.m Modified : /kernel/p_superop.m Revision: 401 Author: kuprov Date: 31 December 2009 21:20:11 Message: Deleted the cache files from the old Spinach core. Those are no longer used and their removal would ease the checkouts. ---- Deleted : /previous_version/Spinach core/clusters/generators_2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__2__3.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__3.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__2__3__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__3.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__3__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__3__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__3__3__3.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__4__4.mat Deleted : /previous_version/Spinach core/clusters/generators_2__2__8__8.mat Deleted : /previous_version/Spinach core/clusters/generators_2__3.mat Deleted : /previous_version/Spinach core/clusters/generators_2__3__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__3__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_2__8.mat Deleted : /previous_version/Spinach core/clusters/generators_3.mat Deleted : /previous_version/Spinach core/clusters/generators_3__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/generators_3__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__2__2__2__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__2__3.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__3.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__2__3__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__3.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__3__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__3__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__3__3__3.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__4__4.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__2__8__8.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__3.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__3__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__3__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_2__8.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_3.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_3__2__2__2.mat Deleted : /previous_version/Spinach core/clusters/state_vectors_3__2__2__2__2.mat Deleted : /previous_version/Spinach core/grids Deleted : /previous_version/Spinach core/tensor_toolbox Revision: 400 Author: kuprov Date: 31 December 2009 21:17:57 Message: Marked the previous version of Spinach as such. The functionality and code is currently being migrated to the new core. ---- Deleted : /Spinach Revision: 399 Author: kuprov Date: 31 December 2009 21:10:53 Message: Marked the previous version of Spinach as such. The functionality and code is currently being migrated to the new core. ---- Added : /previous_version (Copy from path: /Spinach, Revision, 398) Revision: 398 Author: kuprov Date: 31 December 2009 21:03:44 Message: Fixed the multi-spin Hamiltonian superoperators. ---- Modified : /kernel/h_superop.m Modified : /tests/mary_test_1.m Revision: 397 Author: kuprov Date: 31 December 2009 13:52:53 Message: Significantly more intelligent product superoperator code. ---- Modified : /kernel/p_superop.m Revision: 396 Author: kuprov Date: 30 December 2009 14:13:49 Message: Migrated the MARY experiment, the path tracing soubroutine in the kernel and one of the MARY tests. Because of the above mentioned issue with the operator generation, MARY only currently works in complete basis sets. Updating the superoperator generation is in progress. ---- Modified : /exp/mary.m Added : /kernel/path_trace.m (Copy from path: /Spinach/Spinach core/path_trace.m, Revision, 394) Modified : /tests/mary_test_1.m Revision: 395 Author: kuprov Date: 29 December 2009 15:02:38 Message: First go at porting MARY to the new Spinach architecture. The task of adapting Hannah's superoperator generation to the reduced basis sets turned out to be non-trivial. Some basis states that are thrown outside by one component of the superoperator could be returned by another, and this has to be taken into account, otherwise we have some bizarre invariances. ---- Added : /etc/mt2hz.m Modified : /exp/axis_1d.m Added : /exp/mary.m (Copy from path: /Spinach/Spinach experiments/expMARY.m, Revision, 394) Modified : /kernel/create.m Modified : /kernel/p_superop.m Added : /tests/mary_test_1.m (Copy from path: /Spinach/Spinach tests/mary_test_1.m, Revision, 394) Revision: 394 Author: kuprov Date: 21 December 2009 15:52:49 Message: pulse-acquire sequence and all the associated infrastructure, plus some fixes throughout the kernel that the migration has highlighted. ---- Modified : /etc/g03_to_spinach.m Modified : /etc/offset.m Added : /exp Added : /exp/axis_1d.m (Copy from path: /Spinach/Spinach core/axis_1d.m, Revision, 383) Added : /exp/pulse_acquire.m (Copy from path: /Spinach/Spinach experiments/pulse_acquire.m, Revision, 383) Modified : /kernel/create.m Deleted : /kernel/private/report.m Deleted : /kernel/private/spin.m Modified : /kernel/private/tolerances.m Modified : /kernel/r_superop.m Added : /kernel/report.m (Copy from path: /kernel/private/report.m, Revision, 383) Added : /kernel/spin.m (Copy from path: /kernel/private/spin.m, Revision, 383) Deleted : /tests/basis_test_1.m Deleted : /tests/create_test_1.m Deleted : /tests/g03_driver_test_1.m Deleted : /tests/kinetics_test_1.m Deleted : /tests/liouvillian_test_1.m Added : /tests/molecules/chlorofluoroethylene.log Deleted : /tests/operator_test_1.m Added : /tests/pulse_acquire_test_1.m Deleted : /tests/symmetry_test_1.m Revision: 393 Author: kuprov Date: 20 December 2009 14:53:39 Message: Migrated the offset function (removed the unnecessary ppm offset specification). ---- Added : /etc/offset.m (Copy from path: /Spinach/Spinach aux/offset.m, Revision, 383) Modified : /etc/state.m Revision: 392 Author: kuprov Date: 20 December 2009 14:46:07 Message: Cleaned up the user-friendly specification handling -- all 'L+' style specifications are moved to userland, the kernel only knows about opspecs. ---- Modified : /etc/operator.m Added : /etc/state.m (Copy from path: /kernel/state.m, Revision, 385) Modified : /kernel/c_superop.m Modified : /kernel/r_superop.m Deleted : /kernel/state.m Added : /kernel/statevec.m Revision: 391 Author: kuprov Date: 20 December 2009 14:03:26 Message: Cleaned up the kinetics superoperator and added the dummy relaxation superoperator. ---- Modified : /kernel/create.m Modified : /kernel/k_superop.m Added : /kernel/r_superop.m Modified : /tests/kinetics_test_1.m Revision: 390 Author: kuprov Date: 19 December 2009 17:26:40 Message: Added chemical kinetics ingestion to the create function and moved the decoupling function to the userland. ---- Added : /etc/decouple.m (Copy from path: /kernel/decouple.m, Revision, 386) Modified : /kernel/create.m Deleted : /kernel/decouple.m Modified : /tests/create_test_1.m Revision: 389 Author: kuprov Date: 19 December 2009 16:35:46 Message: Migrated the delay, hard_pulse and operator functions to the new userland. Updated commutation and product superoperators to accept multi-line opspecs and return the sum of the corresponding superoperators. ---- Added : /etc/delay.m (Copy from path: /Spinach/Spinach aux/delay.m, Revision, 383) Modified : /etc/g03_parse.m Modified : /etc/g03_to_spinach.m Added : /etc/gauss2mhz.m (Copy from path: /Spinach/Spinach aux/gauss2mhz.m, Revision, 383) Added : /etc/hard_pulse.m (Copy from path: /Spinach/Spinach aux/hard_pulse.m, Revision, 383) Added : /etc/operator.m Deleted : /etc/private Modified : /kernel/c_superop.m Modified : /kernel/p_superop.m Revision: 388 Author: kuprov Date: 19 December 2009 12:06:18 Message: Completed the Hamiltonian superoperator for the next generation of Spinach. Should now do solids as well. ---- Modified : /kernel/h_superop.m Revision: 387 Author: kuprov Date: 18 December 2009 18:17:21 Message: Finished the kinetics superoperator. Some fool-proofing might need to be done at some point. ---- Modified : /kernel/k_superop.m Modified : /tests/kinetics_test_1.m Revision: 386 Author: kuprov Date: 18 December 2009 16:18:08 Message: Migrated the analytical decoupler and started with the generalized kinetics superoperator. ---- Added : /kernel/decouple.m (Copy from path: /Spinach/Spinach core/decouple.m, Revision, 383) Added : /kernel/k_superop.m (Copy from path: /Spinach/Spinach core/exchange_superop.m, Revision, 383) Added : /tests/kinetics_test_1.m Modified : /tests/liouvillian_test_1.m Revision: 385 Author: kuprov Date: 14 December 2009 12:29:29 Message: Migrated the numerical zero track elimination subroutine. Analytical one is now built-in. ---- Added : /kernel/expv.m (Copy from path: /Spinach/Spinach core/expv.m, Revision, 383) Modified : /kernel/propagator.m Added : /kernel/zte.m (Copy from path: /Spinach/Spinach core/numerical_zte.m, Revision, 383) Revision: 384 Author: kuprov Date: 14 December 2009 12:15:59 Message: The new generation of Spinach is in the basic working order. Will now transfer all the infrastructure across. ---- Added : /etc/apodization.m (Copy from path: /Spinach/Spinach aux/apodization.m, Revision, 383) Added : /kernel/c_superop.m (Copy from path: /kernel/commutation_superoperator.m, Revision, 383) Deleted : /kernel/commutation_superoperator.m Added : /kernel/h_superop.m (Copy from path: /kernel/hamiltonian_superoperator.m, Revision, 383) Deleted : /kernel/hamiltonian_superoperator.m Added : /kernel/p_superop.m (Copy from path: /kernel/product_superoperator.m, Revision, 383) Deleted : /kernel/product_superoperator.m Added : /kernel/propagator.m (Copy from path: /Spinach/Spinach core/prop_gen.m, Revision, 383) Modified : /kernel/state.m Modified : /tests/liouvillian_test_1.m Revision: 383 Author: kuprov Date: 08 December 2009 13:49:11 Message: Some cosmetic changes to the new kernel. ---- Added : /kernel/hamiltonian_superoperator.m (Copy from path: /kernel/liouvillian.m, Revision, 381) Deleted : /kernel/liouvillian.m Modified : /kernel/product_superoperator.m Revision: 382 Author: kuprov Date: 07 December 2009 11:12:41 Message: Some directory tree updates. ---- Deleted : /Spinach/TODO.txt Deleted : /Spinach/XML markup Added : /TODO.txt (Copy from path: /Spinach/TODO.txt, Revision, 374) Added : /XML markup (Copy from path: /Spinach/XML markup, Revision, 381) Revision: 381 Author: kuprov Date: 23 November 2009 12:19:35 Message: Additions to the SpinXML schema (symmetry and chemical kinetics) following the discussion at the recent meeting. ---- Modified : /Spinach/XML markup/SpinXML/spinxml_schema.xsd Revision: 380 Author: kuprov Date: 11 November 2009 17:44:37 Message: Put the sided product superoperators into a separate kernel function. It seems the beasties are a lot more useful than I had originally thought. ---- Added : /kernel/commutation_superoperator.m (Copy from path: /kernel/superoperator.m, Revision, 379) Added : /kernel/product_superoperator.m Deleted : /kernel/superoperator.m Revision: 379 Author: kuprov Date: 11 November 2009 17:26:49 Message: Slightly more intelligent superoperator generator -- screens the spaces before matching them, resulting in some speed-ups. ---- Modified : /kernel/superoperator.m Revision: 378 Author: kuprov Date: 09 November 2009 16:42:35 Message: Fixed a bug with Hannah-style superoperator generator -- the identity state did sometimes cause trouble. ---- Modified : /kernel/superoperator.m Revision: 377 Author: kuprov Date: 04 November 2009 11:15:28 Message: Some intelligent defaults for the basis set generator, a pilot Liouvillian generator (currently stumbles in incomplete basis sets), a minor modification to the state generator, a few extra tests. ---- Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach tests/isoleucine.m Modified : /kernel/basis.m Added : /kernel/liouvillian.m (Copy from path: /Spinach/Spinach core/liouv_gen.m, Revision, 373) Added : /kernel/private/warnings.m (Copy from path: /Spinach/Spinach core/warnings.m, Revision, 373) Modified : /kernel/state.m Modified : /tests/basis_test_1.m Added : /tests/liouvillian_test_1.m Modified : /tests/operator_test_1.m Revision: 376 Author: hannah Date: 15 October 2009 14:34:45 Message: reduced relaxation matrix (for MARY) generator improved so will no take more advantage of symmetry groups and only produce one of a kind the long way. ---- Modified : /Spinach/Spinach core/ad hoc/red_relax_mat_gen.m Revision: 375 Author: hannah Date: 13 October 2009 09:47:28 Message: Chemical exchange now included for MARY simulations, operator is produced directly into the reduced state space, including a symmetry factorisation (so long as nuclei are exchanging equivalently within a group). Also added precomputed Liouvillians, exchange operators and relaxation matrices. ---- Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a2_11b0__sym_34_EEpairs_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a2_11b0__sym_34_EEpairs_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a4_1111b0__sym_3456_C2C2all_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a4_1111b0__sym_3456_C2C2all_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a4_1111b0__sym_3456_C2C2quads_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a4_1111b0__sym_3456_C2C2quads_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a8_11111111b0__sym_345678910_C4C4quads_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/chemex/Chemex_system_a8_11111111b0__sym_345678910_C4C4quads_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a0_b1_5_sym_3_E_0qc_total.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a1_1b0__sym_3_E_0qc_total.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a1_1b1_5_sym_34_EE_0qc_total.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a2_11b0__sym_34_EE_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a2_11b0__sym_34_EE_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a2_12b0__sym_34_EE_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a2_12b0__sym_34_EE_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a2_15b0__sym_34_EE_0qc_total.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_C3_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_C3_0qc_total.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_C3_0qc_total_ex.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_C3_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_EC2_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_EC2_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_EEE_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_EEE_0qc_total.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_345_EEE_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b0__sym_34_C2_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b1_2_sym_3456_C3E_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_111b1_2_sym_3456_C3E_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_122b0__sym_345_EC2_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_122b0__sym_345_EC2_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_122b0__sym_345_EEE_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a3_122b0__sym_345_EEE_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_C2C2_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_C2C2_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_C4_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_C4_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_EC3_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_EC3_0qc_total.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_EC3_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_EEEE_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1111b0__sym_3456_EEEE_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1112b0__sym_3456_EC2E_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a4_1112b0__sym_3456_EC2E_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a6_111111b0__sym_345678_C2C2C2_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a6_111111b0__sym_345678_C2C2C2_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a6_111111b0__sym_345678_C3C3_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a6_111111b0__sym_345678_C3C3_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a6_111111b0__sym_345678_EEEEEE_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a6_111111b0__sym_345678_EEEEEE_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a7_1111111b0__sym_3456789_C2C2C2E_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a7_1111111b0__sym_3456789_C2C2C2E_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a8_11111111b0__sym_345678910_C4C4_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a8_11111111b0__sym_345678910_C4C4_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a8_11111111b0__sym_345678910_C8_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/gen/system_a8_11111111b0__sym_345678910_C8_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relax_refs.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_a1_1b0_R_a3R_b_sym_3_E_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_a1_1b0_R_a3R_b_sym_3_E_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_a4_1111b0_R_a3456R_b_sym_3456_EC3_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_a4_1111b0_R_a3456R_b_sym_3456_EC3_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_a4_1111b0_R_a3456R_b_sym_3456_EEEE_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_a4_1111b0_R_a3456R_b_sym_3456_EEEE_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_alleq_a8_11111111b0_R_a345678910R_b_sym_345678910_C8_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/relax/relaxmat_alleq_a8_11111111b0_R_a345678910R_b_sym_345678910_C8_0qc_zz.mat Deleted : /Spinach/Incoming/Pre_computed_liouvillians/sym Added : /Spinach/Spinach core/ad hoc/MARY_chemex.m Added : /Spinach/Spinach core/ad hoc/MARY_relax_chemex.m Added : /Spinach/Spinach core/ad hoc/red_chem_ex_gen.m Modified : /Spinach/Spinach tests/oxford/MARY_generalised.m Revision: 374 Author: kuprov Date: 11 September 2009 17:22:57 Message: Allowed Gaussian parser to throw away orphan spins if the user so requests. Coded the Lz=0 MARY basis as an option for basis.m function. Added a couple of symmetrizer tests. ---- Modified : /etc/g03_to_spinach.m Modified : /kernel/basis.m Modified : /kernel/private/symmetry.m Modified : /tests/symmetry_test_1.m Revision: 373 Author: kuprov Date: 10 September 2009 17:58:07 Message: Speed improvement by a factor of 2-3 in the general-purpose a posteriori symmetrizer (still thinking about how to implement the a priori one cleanly). Added the symmetry options to the basis.m function. Vectorized the index transformation functions. ---- Modified : /kernel/basis.m Modified : /kernel/private/lin2lm.m Modified : /kernel/private/lm2lin.m Modified : /kernel/private/symmetry.m Added : /tests/symmetry_test_1.m (Copy from path: /Spinach/Spinach tests/symmetry_test_1.m, Revision, 364) Revision: 372 Author: kuprov Date: 09 September 2009 17:33:43 Message: Major architectural changes to the way symmetry is treated. Symmetry options are now the part of basis specification. Symmetrization can be applied to a pre-existing basis (restricted basis sets) or a complete basis can be generated directly in a symmetrized form. ---- Added : /kernel/basis.m (Copy from path: /kernel/basis_gen.m, Revision, 365) Deleted : /kernel/basis_gen.m Added : /kernel/private/symmetry.m (Copy from path: /Spinach/Spinach core/symmetry.m, Revision, 364) Added : /kernel/private/symmetry_group.m (Copy from path: /Spinach/Spinach core/symmetry_group.m, Revision, 364) Added : /kernel/state.m (Copy from path: /Spinach/Spinach core/custom_state.m, Revision, 364) Deleted : /tests/basis_gen_test_1.m Added : /tests/basis_test_1.m (Copy from path: /tests/basis_gen_test_1.m, Revision, 365) Modified : /tests/operator_test_1.m Revision: 371 Author: kuprov Date: 09 September 2009 12:28:01 Message: Fixed the bug in the superoperator generator. The thing can now quickly (frighteningly so) produce commutation superoperators for any state in the state space, and likely for some states outside as well, assuming the basis is closed with respect to the transformation in question. Cluster recoupling is officially obsolete. ---- Deleted : /kernel/cache/generators_2.mat Deleted : /kernel/cache/generators_2__2.mat Deleted : /kernel/cache/generators_2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2__2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2__2__2__2__2.mat Deleted : /kernel/cache/generators_2__2__2__2__3.mat Deleted : /kernel/cache/generators_2__2__2__3.mat Deleted : /kernel/cache/generators_2__2__2__3__2.mat Deleted : /kernel/cache/generators_2__2__3.mat Deleted : /kernel/cache/generators_2__2__3__2.mat Deleted : /kernel/cache/generators_2__2__3__2__2.mat Deleted : /kernel/cache/generators_2__2__3__3__3.mat Deleted : /kernel/cache/generators_2__2__4__4.mat Deleted : /kernel/cache/generators_2__2__8__8.mat Deleted : /kernel/cache/generators_2__3.mat Deleted : /kernel/cache/generators_2__3__2.mat Deleted : /kernel/cache/generators_2__3__2__2.mat Deleted : /kernel/cache/generators_2__8.mat Deleted : /kernel/cache/generators_3.mat Deleted : /kernel/cache/generators_3__2__2__2.mat Deleted : /kernel/cache/generators_3__2__2__2__2.mat Modified : /kernel/cache/ist_product_table_2.mat Modified : /kernel/cache/ist_product_table_3.mat Modified : /kernel/cache/ist_product_table_4.mat Modified : /kernel/cache/ist_product_table_5.mat Modified : /kernel/cache/ist_product_table_6.mat Modified : /kernel/cache/ist_product_table_7.mat Modified : /kernel/cache/ist_product_table_8.mat Modified : /kernel/cache/ist_product_table_9.mat Deleted : /kernel/cache/state_vectors_2.mat Deleted : /kernel/cache/state_vectors_2__2.mat Deleted : /kernel/cache/state_vectors_2__2__2.mat Deleted : /kernel/cache/state_vectors_2__2__2__2.mat Deleted : /kernel/cache/state_vectors_2__2__2__2__2.mat Deleted : /kernel/cache/state_vectors_2__2__2__2__2__2.mat Deleted : /kernel/cache/state_vectors_2__2__2__2__2__2__2.mat Deleted : /kernel/cache/state_vectors_2__2__2__2__2__2__2__2.mat Deleted : /kernel/cache/state_vectors_2__2__2__2__3.mat Deleted : /kernel/cache/state_vectors_2__2__2__3.mat Deleted : /kernel/cache/state_vectors_2__2__2__3__2.mat Deleted : /kernel/cache/state_vectors_2__2__3.mat Deleted : /kernel/cache/state_vectors_2__2__3__2.mat Deleted : /kernel/cache/state_vectors_2__2__3__2__2.mat Deleted : /kernel/cache/state_vectors_2__2__3__3__3.mat Deleted : /kernel/cache/state_vectors_2__2__4__4.mat Deleted : /kernel/cache/state_vectors_2__2__8__8.mat Deleted : /kernel/cache/state_vectors_2__3.mat Deleted : /kernel/cache/state_vectors_2__3__2.mat Deleted : /kernel/cache/state_vectors_2__3__2__2.mat Deleted : /kernel/cache/state_vectors_2__8.mat Deleted : /kernel/cache/state_vectors_3.mat Deleted : /kernel/cache/state_vectors_3__2__2__2.mat Deleted : /kernel/cache/state_vectors_3__2__2__2__2.mat Modified : /kernel/private/ist_product_table.m Modified : /kernel/superoperator.m Modified : /tests/operator_test_1.m Revision: 370 Author: kuprov Date: 09 September 2009 10:30:25 Message: Improved memory efficiency in the superoperator generator. An obscure bug currently crops up in the generation of three-spin operators -- all patterns are completely correct except for a tiny number of incorrect values. Investigating. ---- Added : /kernel/cache/ist_product_table_9.mat Modified : /kernel/superoperator.m Modified : /tests/operator_test_1.m Revision: 369 Author: kuprov Date: 08 September 2009 15:59:24 Message: The first stab at the fully general commutation superoperator generator, building on the fact that the sided product superoperators, unlike the commutation, can be stacked directly. ---- Modified : /kernel/superoperator.m Modified : /tests/operator_test_1.m Revision: 368 Author: kuprov Date: 08 September 2009 12:08:10 Message: Replaced the pre-computed commutator table with pre-computed left and right product table (the commutator table turned out to be insufficient to generate two-spin superoperators). Shifted some files around. ---- Added : /kernel/cache (Copy from path: /kernel/structure_constants, Revision, 364) Added : /kernel/cache/generators_2.mat (Copy from path: /kernel/clusters/generators_2.mat, Revision, 364) Added : /kernel/cache/generators_2__2.mat (Copy from path: /kernel/clusters/generators_2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2.mat (Copy from path: /kernel/clusters/generators_2__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__2.mat (Copy from path: /kernel/clusters/generators_2__2__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__2__2.mat (Copy from path: /kernel/clusters/generators_2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__2__2__2.mat (Copy from path: /kernel/clusters/generators_2__2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__2__2__2__2.mat (Copy from path: /kernel/clusters/generators_2__2__2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__2__2__2__2__2.mat (Copy from path: /kernel/clusters/generators_2__2__2__2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__2__3.mat (Copy from path: /kernel/clusters/generators_2__2__2__2__3.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__3.mat (Copy from path: /kernel/clusters/generators_2__2__2__3.mat, Revision, 364) Added : /kernel/cache/generators_2__2__2__3__2.mat (Copy from path: /kernel/clusters/generators_2__2__2__3__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__3.mat (Copy from path: /kernel/clusters/generators_2__2__3.mat, Revision, 364) Added : /kernel/cache/generators_2__2__3__2.mat (Copy from path: /kernel/clusters/generators_2__2__3__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__3__2__2.mat (Copy from path: /kernel/clusters/generators_2__2__3__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__2__3__3__3.mat (Copy from path: /kernel/clusters/generators_2__2__3__3__3.mat, Revision, 364) Added : /kernel/cache/generators_2__2__4__4.mat (Copy from path: /kernel/clusters/generators_2__2__4__4.mat, Revision, 364) Added : /kernel/cache/generators_2__2__8__8.mat (Copy from path: /kernel/clusters/generators_2__2__8__8.mat, Revision, 364) Added : /kernel/cache/generators_2__3.mat (Copy from path: /kernel/clusters/generators_2__3.mat, Revision, 364) Added : /kernel/cache/generators_2__3__2.mat (Copy from path: /kernel/clusters/generators_2__3__2.mat, Revision, 364) Added : /kernel/cache/generators_2__3__2__2.mat (Copy from path: /kernel/clusters/generators_2__3__2__2.mat, Revision, 364) Added : /kernel/cache/generators_2__8.mat (Copy from path: /kernel/clusters/generators_2__8.mat, Revision, 364) Added : /kernel/cache/generators_3.mat (Copy from path: /kernel/clusters/generators_3.mat, Revision, 364) Added : /kernel/cache/generators_3__2__2__2.mat (Copy from path: /kernel/clusters/generators_3__2__2__2.mat, Revision, 364) Added : /kernel/cache/generators_3__2__2__2__2.mat (Copy from path: /kernel/clusters/generators_3__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/ist_product_table_2.mat Added : /kernel/cache/ist_product_table_3.mat Added : /kernel/cache/ist_product_table_4.mat Added : /kernel/cache/ist_product_table_5.mat Added : /kernel/cache/ist_product_table_6.mat Added : /kernel/cache/ist_product_table_7.mat Added : /kernel/cache/ist_product_table_8.mat Added : /kernel/cache/state_vectors_2.mat (Copy from path: /kernel/clusters/state_vectors_2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__2__2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__2__2__2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__2__2__2__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__2__3.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__2__3.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__3.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__3.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__2__3__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__2__3__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__3.mat (Copy from path: /kernel/clusters/state_vectors_2__2__3.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__3__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__3__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__3__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__2__3__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__3__3__3.mat (Copy from path: /kernel/clusters/state_vectors_2__2__3__3__3.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__4__4.mat (Copy from path: /kernel/clusters/state_vectors_2__2__4__4.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__2__8__8.mat (Copy from path: /kernel/clusters/state_vectors_2__2__8__8.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__3.mat (Copy from path: /kernel/clusters/state_vectors_2__3.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__3__2.mat (Copy from path: /kernel/clusters/state_vectors_2__3__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__3__2__2.mat (Copy from path: /kernel/clusters/state_vectors_2__3__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_2__8.mat (Copy from path: /kernel/clusters/state_vectors_2__8.mat, Revision, 364) Added : /kernel/cache/state_vectors_3.mat (Copy from path: /kernel/clusters/state_vectors_3.mat, Revision, 364) Added : /kernel/cache/state_vectors_3__2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_3__2__2__2.mat, Revision, 364) Added : /kernel/cache/state_vectors_3__2__2__2__2.mat (Copy from path: /kernel/clusters/state_vectors_3__2__2__2__2.mat, Revision, 364) Deleted : /kernel/cache/structure_constants_2.mat Deleted : /kernel/cache/structure_constants_3.mat Deleted : /kernel/cache/structure_constants_4.mat Deleted : /kernel/cache/structure_constants_5.mat Deleted : /kernel/cache/structure_constants_6.mat Deleted : /kernel/cache/structure_constants_7.mat Deleted : /kernel/cache/structure_constants_8.mat Deleted : /kernel/cache/structure_constants_9.mat Deleted : /kernel/clusters Added : /kernel/private/ist_product_table.m (Copy from path: /kernel/private/struc_gen.m, Revision, 364) Deleted : /kernel/private/struc_gen.m Deleted : /kernel/structure_constants Modified : /kernel/superoperator.m Modified : /tests/operator_test_1.m Revision: 367 Author: kuprov Date: 08 September 2009 09:52:56 Message: After a bit of polishing, Hannah’s implementation of operator generator produced Lx,Ly,Lz operators in a 331,776-dimensional state space in about 10 seconds. The commutation relations are observed by the resulting 331k X 331k matrices to within 1e-16. Memory footprint of the entire calculation: around 50MB. ---- Modified : /kernel/superoperator.m Modified : /tests/operator_test_1.m Revision: 366 Author: kuprov Date: 07 September 2009 16:53:16 Message: Clean implementation of single-spin superoperators Hannah-style. Much faster than cluster recoupling, works quickly and memory-efficiently for state spaces in excess of 65k. The entire recoupling business is now likely obsolete -- clusterization would only be retained as a basis generation technique. ---- Deleted : /kernel/clusters/generators_2__2__2__2__2__2__2__2__2__2.mat Deleted : /kernel/clusters/generators_2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /kernel/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /kernel/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /kernel/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /kernel/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /kernel/operator.m Modified : /kernel/private/lin2lm.m Modified : /kernel/private/lm2lin.m Modified : /kernel/structure_constants/structure_constants_2.mat Modified : /kernel/structure_constants/structure_constants_3.mat Modified : /kernel/structure_constants/structure_constants_4.mat Modified : /kernel/structure_constants/structure_constants_5.mat Modified : /kernel/structure_constants/structure_constants_6.mat Modified : /kernel/structure_constants/structure_constants_7.mat Modified : /kernel/structure_constants/structure_constants_8.mat Modified : /kernel/structure_constants/structure_constants_9.mat Added : /kernel/superoperator.m (Copy from path: /kernel/operator.m, Revision, 364) Added : /tests/operator_test_1.m Revision: 365 Author: kuprov Date: 07 September 2009 11:55:11 Message: Reverted the basis set generator to the linear indexing of states in the order of appearance inthe list generated by irr_sph_ten.m function. ---- Modified : /kernel/basis_gen.m Modified : /kernel/private/lin2lm.m Modified : /kernel/private/lm2lin.m Modified : /tests/basis_gen_test_1.m Revision: 364 Author: kuprov Date: 06 September 2009 17:25:39 Message: Two new functions translating between linear and L,M indexing. Will move the basis set back to linear indexing, which seems to be a better idea for the time being. Re-generated complete normalized structure tables. They are not compatible with Hannah's code, but are compatible with its polished version (coming soon). ---- Deleted : /Spinach/Spinach core/hogben_tensor.m Added : /kernel/private/lin2lm.m Added : /kernel/private/lm2lin.m Modified : /kernel/private/struc_gen.m Modified : /kernel/structure_constants/structure_constants_2.mat Modified : /kernel/structure_constants/structure_constants_3.mat Modified : /kernel/structure_constants/structure_constants_4.mat Modified : /kernel/structure_constants/structure_constants_5.mat Modified : /kernel/structure_constants/structure_constants_6.mat Modified : /kernel/structure_constants/structure_constants_7.mat Modified : /kernel/structure_constants/structure_constants_8.mat Modified : /kernel/structure_constants/structure_constants_9.mat Revision: 363 Author: kuprov Date: 04 September 2009 17:44:44 Message: First go at cosmetic clean-up of Hannah's code. The ordered tensor list subroutine is now a part of irr_sph_ten.m function, missing database tables are now present. ---- Modified : /kernel/operator.m Modified : /kernel/private/angle2dcm.m Modified : /kernel/private/dcm2angle.m Modified : /kernel/private/irr_sph_ten.m Added : /kernel/private/pauli.m (Copy from path: /Spinach/Spinach core/pauli.m, Revision, 358) Added : /kernel/private/struc_gen.m Added : /kernel/structure_constants/structure_constants_2.mat (Copy from path: /kernel/structure_constants/table_of_product_coefficients_for_mult2.mat, Revision, 361) Added : /kernel/structure_constants/structure_constants_3.mat (Copy from path: /kernel/structure_constants/table_of_product_coefficients_for_mult3.mat, Revision, 361) Added : /kernel/structure_constants/structure_constants_4.mat (Copy from path: /kernel/structure_constants/table_of_product_coefficients_for_mult4.mat, Revision, 361) Added : /kernel/structure_constants/structure_constants_5.mat (Copy from path: /kernel/structure_constants/table_of_product_coefficients_for_mult5.mat, Revision, 361) Added : /kernel/structure_constants/structure_constants_6.mat Added : /kernel/structure_constants/structure_constants_7.mat Added : /kernel/structure_constants/structure_constants_8.mat Added : /kernel/structure_constants/structure_constants_9.mat (Copy from path: /kernel/structure_constants/table_of_product_coefficients_for_mult9.mat, Revision, 361) Deleted : /kernel/structure_constants/table_of_product_coefficients_for_mult2.mat Deleted : /kernel/structure_constants/table_of_product_coefficients_for_mult3.mat Deleted : /kernel/structure_constants/table_of_product_coefficients_for_mult4.mat Deleted : /kernel/structure_constants/table_of_product_coefficients_for_mult5.mat Deleted : /kernel/structure_constants/table_of_product_coefficients_for_mult9.mat Revision: 362 Author: hannah Date: 04 September 2009 17:05:23 Message: It is possible to symmetry factorise relaxing spins if they have the same relaxation-coefficients with all other spins, (even though not strictly equivalent).red_relax_mat_gen has been updated to allow for a pre-symmetry-factorisation of relaxing spins. ---- Modified : /Spinach/Spinach core/ad hoc/MARY_relax.m Modified : /Spinach/Spinach core/ad hoc/red_relax_mat_gen.m Modified : /Spinach/Spinach tests/oxford/MARY_generalised.m Revision: 361 Author: kuprov Date: 04 September 2009 16:32:07 Message: Starting to fit in Hannah's implementation of the custom operator function. The symmetry information would eventually be inherited through the data structure, so the third argument to operator.m will be deprecated at some point. ---- Added : /kernel/operator.m Added : /kernel/structure_constants Added : /kernel/structure_constants/table_of_product_coefficients_for_mult2.mat (Copy from path: /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult2.mat, Revision, 358) Added : /kernel/structure_constants/table_of_product_coefficients_for_mult3.mat (Copy from path: /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult3.mat, Revision, 358) Added : /kernel/structure_constants/table_of_product_coefficients_for_mult4.mat (Copy from path: /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult4.mat, Revision, 358) Added : /kernel/structure_constants/table_of_product_coefficients_for_mult5.mat (Copy from path: /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult5.mat, Revision, 358) Added : /kernel/structure_constants/table_of_product_coefficients_for_mult9.mat (Copy from path: /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult9.mat, Revision, 358) Revision: 360 Author: kuprov Date: 04 September 2009 15:09:12 Message: Updated the basis generator to print back diagnostic information and the resulting basis set. Fixed and double-checked the point dipolar interactions. Added the basis printing tolerance. ---- Modified : /kernel/basis_gen.m Modified : /kernel/create.m Modified : /kernel/private/tolerances.m Modified : /tests/basis_gen_test_1.m Modified : /tests/create_test_1.m Revision: 359 Author: kuprov Date: 02 September 2009 15:49:21 Message: Disabled coordinate return if a Gaussian log is read in the EPR mode -- positioning the electron is problematic because the electron-nuclear dipolar interactions interactions are already present in the HFC tensors. The user can specify coordinates by hand if need be. Made the printing of the distance matrix a bit neater in create.m ---- Modified : /etc/g03_to_spinach.m Modified : /kernel/create.m Modified : /tests/create_test_1.m Revision: 358 Author: hannah Date: 02 September 2009 14:05:36 Message: Added code to produce any operator (based upon Sz, Sp, Sm and E) immediately into a reduced state space. General for any spin, I, and any symmetry groups. ---- Added : /Spinach/Incoming/general_reduced_operator_generation Added : /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants Added : /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult2.mat Added : /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult3.mat Added : /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult4.mat Added : /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult5.mat Added : /Spinach/Incoming/general_reduced_operator_generation/irr_sph_ten_structure_constants/table_of_product_coefficients_for_mult9.mat Added : /Spinach/Incoming/general_reduced_operator_generation/reduced_op_gen.m Revision: 357 Author: kuprov Date: 02 September 2009 13:06:45 Message: Dipolar interactions are properly tested. All angles and magnitudes check out. ---- Modified : /kernel/create.m Modified : /tests/create_test_1.m Revision: 356 Author: kuprov Date: 01 September 2009 21:00:03 Message: The angles in the dipole operators are now computed correctly in all cases. Amplitudes and user-supplied tensors need testing. ---- Deleted : /etc/private/angle2dcm.m Deleted : /etc/private/dcm2angle.m Modified : /kernel/create.m Added : /kernel/private/angle2dcm.m (Copy from path: /etc/private/angle2dcm.m, Revision, 346) Added : /kernel/private/dcm2angle.m (Copy from path: /etc/private/dcm2angle.m, Revision, 345) Modified : /kernel/private/mat2RxRyRz.m Modified : /tests/create_test_1.m Revision: 355 Author: kuprov Date: 01 September 2009 13:18:56 Message: Good Lord, Euler angles are a mess... Siminovich's prophesy about recurrent bizarre troubles caused by them not being a correct parameterization of so(3) are coming true in full force. Anyway, Euler angles have been purged from the kernel and replaced by R(X), R(Y), R(Z) three-axis rotation convention from Matlab's Aerospace Toolbox. Will need to code Wigner functions for that convention, but that's a technicality. ---- Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__3__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__3__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__3__2__2__2__2__2__2__2__2__2__2__2.mat Modified : /kernel/create.m Added : /kernel/private/RxRyRz2mat.m (Copy from path: /kernel/private/eabg2mat.m, Revision, 350) Deleted : /kernel/private/eabg2mat.m Added : /kernel/private/mat2RxRyRz.m (Copy from path: /kernel/private/mat2eabg.m, Revision, 352) Deleted : /kernel/private/mat2eabg.m Revision: 354 Author: hannah Date: 01 September 2009 12:18:56 Message: MARY simulations now extended to product the SSR relaxation matrix for any number of relaxing spin-1/2 and spin-1 nuclei (is in theory general for any spin but need to move large tables from mathematica which is slightly pointless unless a particular nucleus is required). ---- Modified : /Spinach/Spinach core/ad hoc/MARY_exchange.m Modified : /Spinach/Spinach core/ad hoc/MARY_kinetics.m Modified : /Spinach/Spinach core/ad hoc/MARY_relax.m Modified : /Spinach/Spinach core/ad hoc/MARY_simple.m Modified : /Spinach/Spinach core/ad hoc/coeff_table_gen.m Modified : /Spinach/Spinach core/ad hoc/irr_sph_ten_product_coefficients/table_of_product_coefficients_for_mult2.mat Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_kinetics_sym.m Modified : /Spinach/Spinach core/ad hoc/red_liouv_gen.m Deleted : /Spinach/Spinach core/ad hoc/red_relax_gen.m Added : /Spinach/Spinach core/ad hoc/red_relax_mat_gen.m Modified : /Spinach/Spinach core/ad hoc/sph_ten_qc.m Modified : /Spinach/Spinach tests/oxford/MARY_general_old.m Modified : /Spinach/Spinach tests/oxford/MARY_generalised.m Revision: 353 Author: kuprov Date: 30 August 2009 17:40:25 Message: Completed the epic 500-line parameter processing function with full user feedback. Unless major bugs are found, create.m is now on freeze for a fairly long time. ---- Modified : /kernel/create.m Modified : /tests/create_test_1.m Revision: 352 Author: kuprov Date: 29 August 2009 18:23:44 Message: Cosmetic changes related to the ingestion of Cartesian coordinates. Electron is now assumed to be non-local and the coordinates are printed to the log. ---- Modified : /etc/g03_to_spinach.m Modified : /kernel/create.m Modified : /tests/create_test_1.m Revision: 351 Author: kuprov Date: 28 August 2009 17:11:41 Message: Alpha version of the updated create.m routine. Lots of testing required in various modes. ---- Modified : /etc/g03_to_spinach.m Modified : /kernel/create.m Modified : /kernel/private/tolerances.m Revision: 350 Author: kuprov Date: 27 August 2009 18:09:29 Message: An update to Gaussian driver to make it produce dense structures. Too much trouble handling sparse interaction structures at this stage. ---- Modified : /etc/g03_to_spinach.m Modified : /kernel/create.m Modified : /kernel/private/eabg2mat.m Modified : /kernel/private/mat2eabg.m Modified : /tests/g03_driver_test_1.m Revision: 349 Author: kuprov Date: 27 August 2009 14:24:54 Message: Zeeman tensor absorption / reporting is well and truly sorted. might need some double-checking to ensure that the Euler angles conform to Varshalovich B convention. ---- Modified : /kernel/create.m Modified : /tests/create_test_1.m Revision: 348 Author: kuprov Date: 26 August 2009 18:06:27 Message: Some private functions dealing with Euler angle transformations. Simplifications to Gaussian driver and major improvements to the create.m routine. ---- Modified : /etc/g03_parse.m Modified : /etc/g03_to_spinach.m Modified : /kernel/create.m Added : /kernel/private/eabg2mat.m Added : /kernel/private/mat2eabg.m Revision: 347 Author: kuprov Date: 26 August 2009 12:43:40 Message: Made create.m print the diagnostic information to the console and the logs. A summary of all interactions, distances and proximities is now provided. Introduced an options field to the Gaussian driver. ---- Modified : /etc/g03_to_spinach.m Modified : /kernel/create.m Modified : /tests/create_test_1.m Revision: 346 Author: kuprov Date: 25 August 2009 17:33:56 Message: Major architectural changes to the create.m routine. A neat table is now printed to the screen, summarizing Zeeman interactions. ---- Modified : /etc/g03_to_spinach.m Added : /etc/private/angle2dcm.m Modified : /kernel/create.m Modified : /kernel/private/spin.m Added : /tests/create_test_1.m Revision: 345 Author: kuprov Date: 24 August 2009 15:14:36 Message: Major architectural changes to the Gaussian driver, which has now been generalized to EPR properties as well. ---- Modified : /etc/g03_parse.m Modified : /etc/g03_to_spinach.m Added : /etc/private Added : /etc/private/dcm2angle.m Added : /etc/private/gauss2mhz.m (Copy from path: /Spinach/Spinach aux/gauss2mhz.m, Revision, 337) Added : /tests/g03_driver_test_1.m Added : /tests/molecules/3-fluorotyrosine.log Revision: 344 Author: kuprov Date: 23 August 2009 15:02:07 Message: Major architectural changes throughout the kernel. Basis set module has been generalized to have clusterization as merely in option in a list of possible basis set generation algorithms (an empty slot was left for Hannah's pre-elimination code). ---- Deleted : /kernel/banner.m Modified : /kernel/basis_gen.m Deleted : /kernel/cluster_gen.m Deleted : /kernel/irr_sph_ten.m Added : /kernel/private Added : /kernel/private/banner.m (Copy from path: /kernel/banner.m, Revision, 343) Added : /kernel/private/cluster_gen.m (Copy from path: /kernel/cluster_gen.m, Revision, 343) Added : /kernel/private/combnk.m Added : /kernel/private/irr_sph_ten.m (Copy from path: /kernel/irr_sph_ten.m, Revision, 343) Added : /kernel/private/report.m (Copy from path: /kernel/report.m, Revision, 343) Added : /kernel/private/spin.m (Copy from path: /kernel/spin.m, Revision, 343) Added : /kernel/private/tolerances.m (Copy from path: /kernel/tolerances.m, Revision, 343) Deleted : /kernel/report.m Deleted : /kernel/spin.m Deleted : /kernel/tolerances.m Added : /tests/basis_gen_test_1.m Deleted : /tests/pulse_acquire_test_1.m Deleted : /tests/pulse_acquire_test_2.m Revision: 343 Author: kuprov Date: 22 August 2009 18:08:51 Message: Massive speed-ups in the housekeeping. 10^5 dimensional basis sets across hundreds of clusters are now generated in seconds. Full parallelization in cluster_gen.m and basis_gen.m achieved. ---- Modified : /kernel/banner.m Modified : /kernel/basis_gen.m Modified : /kernel/cluster_gen.m Modified : /kernel/create.m Modified : /kernel/irr_sph_ten.m Modified : /kernel/spin.m Modified : /tests/pulse_acquire_test_2.m Revision: 342 Author: kuprov Date: 22 August 2009 17:38:21 Message: Massive (and disruptive) architectural changes in the clusterization and basis generation routines. End users are advised to use Revision 327 for the time being. ---- Modified : /kernel/banner.m Added : /kernel/basis_gen.m (Copy from path: /Spinach/Spinach core/statelist_gen.m, Revision, 337) Added : /kernel/cluster_gen.m (Copy from path: /kernel/clusters.m, Revision, 340) Deleted : /kernel/clusters.m Added : /kernel/irr_sph_ten.m (Copy from path: /Spinach/Spinach core/irr_sph_ten.m, Revision, 337) Modified : /tests/pulse_acquire_test_2.m Revision: 341 Author: kuprov Date: 21 August 2009 15:42:52 Message: Major cleanup of the repository. Please refer to the previous revisions of you require the files that had been deleted. Most have been moved to the main project repository. ---- Deleted : /Clipart Deleted : /Illustrations Deleted : /Miscellaneous Added : /etc Added : /etc/g03_parse.m (Copy from path: /Spinach/Spinach aux/g03_parse.m, Revision, 337) Added : /etc/g03_to_spinach.m (Copy from path: /Spinach/Spinach aux/g03_to_spinach.m, Revision, 337) Added : /tests Added : /tests/molecules (Copy from path: /Spinach/Spinach tests/molecules, Revision, 337) Added : /tests/pulse_acquire_test_1.m (Copy from path: /Spinach/Spinach tests/pulse_acquire_test_1.m, Revision, 337) Added : /tests/pulse_acquire_test_2.m (Copy from path: /Spinach/Spinach tests/pulse_acquire_test_2.m, Revision, 337) Revision: 340 Author: kuprov Date: 21 August 2009 15:41:49 Message: Completed the changes to the clusterizer and introduced a helper function holding the log banners for the various kernel functions. ---- Added : /kernel/banner.m Modified : /kernel/clusters.m Revision: 339 Author: kuprov Date: 21 August 2009 15:20:52 Message: Fundamental architecture change in clusterizer. Now supports all methods simultaneously and is driven by a data structure rather than by arguments passed. ---- Deleted : /kernel/cluster_gen.m Added : /kernel/clusters.m (Copy from path: /kernel/cluster_gen.m, Revision, 338) Modified : /kernel/create.m Deleted : /kernel/nucleus.m Added : /kernel/report.m (Copy from path: /Spinach/Spinach core/report.m, Revision, 337) Added : /kernel/spin.m (Copy from path: /kernel/nucleus.m, Revision, 338) Added : /kernel/tolerances.m (Copy from path: /Spinach/Spinach core/tolerances.m, Revision, 337) Revision: 338 Author: kuprov Date: 21 August 2009 12:42:09 Message: Forked the Spinach kernel in an attempt to sanitize it from ad hoc code and introduce better state lists. ---- Added : /kernel Added : /kernel/cluster_gen.m (Copy from path: /Spinach/Spinach core/cluster_gen.m, Revision, 337) Added : /kernel/clusters (Copy from path: /Spinach/Spinach core/clusters, Revision, 337) Added : /kernel/create.m (Copy from path: /Spinach/Spinach core/create.m, Revision, 337) Added : /kernel/nucleus.m (Copy from path: /Spinach/Spinach core/nucleus.m, Revision, 337) Revision: 337 Author: gareth Date: 20 August 2009 16:30:23 Message: Updated the spinxml_schema. Many scalar child notes have been changed to attributes which tends to result in smaller xml files that are easier to read. ---- Modified : /Spinach/XML markup/SpinXML/spinxml_schema.xsd Revision: 336 Author: kuprov Date: 19 August 2009 17:15:11 Message: Documentation updates and cosmetic improvements for the analytical decouple and Liouvillian generator. ---- Modified : /Spinach/Spinach core/decouple.m Modified : /Spinach/Spinach core/liouv_gen.m Revision: 335 Author: kuprov Date: 19 August 2009 16:15:53 Message: More documentation updates for Spinach core functions. ---- Modified : /Spinach/Spinach core/cluster_ham.m Modified : /Spinach/Spinach core/custom_state.m Revision: 334 Author: kuprov Date: 19 August 2009 15:48:29 Message: Some additional documentation to the clusterizer function moved across from the main documentation file. ---- Modified : /Spinach/Spinach core/cluster_gen.m Revision: 333 Author: kuprov Date: 19 August 2009 15:20:47 Message: Additional documentation and clean-up inside analytical and numerical zero track elimination subroutines. ---- Modified : /Spinach/Spinach core/analytical_zte.m Modified : /Spinach/Spinach core/numerical_zte.m Revision: 332 Author: kuprov Date: 19 August 2009 15:00:14 Message: A documentation update and some elimination of repeated code in the clusterization subroutine and the function that adds custom clusters to the spin system. ---- Modified : /Spinach/Spinach core/add_clusters.m Added : /Spinach/Spinach core/cluster_cleanup.m Modified : /Spinach/Spinach core/cluster_gen.m Revision: 331 Author: kuprov Date: 18 August 2009 17:11:29 Message: Fixed a couple of bugs with the new versions of create and tolerances. Made the report.m require lock for editing. ---- Modified : /Spinach/Spinach core/create.m Modified : /Spinach/Spinach core/report.m Modified : /Spinach/Spinach core/tolerances.m Revision: 330 Author: kuprov Date: 18 August 2009 16:50:20 Message: Create module is fully documented and prepared for m2html documenting procedure. The corresponding data has been removed from the Word documentation file. Also added an output routine that directs the output to the console or a file or hushes it altogether if the user so requests. ---- Modified : /Spinach/Spinach core/create.m Added : /Spinach/Spinach core/report.m Revision: 329 Author: kuprov Date: 18 August 2009 15:21:21 Message: Tolerances module is fully documented and prepared for m2html documenting procedure. The corresponding data has been removed from the Word documentation file. ---- Modified : /Spinach/Spinach core/tolerances.m Revision: 328 Author: kuprov Date: 15 August 2009 11:53:52 Message: Pilot implementation of Hogben tensors (very slow and spin 1/2 only at the moment) plus some clean-up in examples directories. Added a tensor manipulation toolbox (Sandia Labs) which supports sparse multidimensional arrays. Should switch over to native Matlab implementation if and when it appears. ---- Added : /Spinach/Spinach core/hogben_tensor.m Added : /Spinach/Spinach core/tensor_toolbox Added : /Spinach/Spinach core/tensor_toolbox/@ktensor Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/Contents.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/arrange.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/datadisp.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/disp.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/display.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/double.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/end.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/fixsigns.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/full.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/innerprod.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/ktensor.m Added : /Spinach/Spinach core/tensor_toolbox/@ktensor/minus.m Added : 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core/tensor_toolbox/met/ttm_me.m Added : /Spinach/Spinach core/tensor_toolbox/met/ttm_me_mem.m Added : /Spinach/Spinach core/tensor_toolbox/met/ttm_me_partition.m Added : /Spinach/Spinach core/tensor_toolbox/met/tucker_me.m Added : /Spinach/Spinach core/tensor_toolbox/met/tucker_me_test.m Added : /Spinach/Spinach core/tensor_toolbox/sptendiag.m Added : /Spinach/Spinach core/tensor_toolbox/sptenrand.m Added : /Spinach/Spinach core/tensor_toolbox/tendiag.m Added : /Spinach/Spinach core/tensor_toolbox/tenones.m Added : /Spinach/Spinach core/tensor_toolbox/tenrand.m Added : /Spinach/Spinach core/tensor_toolbox/tensor_toolbox_product_page.html Added : /Spinach/Spinach core/tensor_toolbox/tenzeros.m Added : /Spinach/Spinach core/tensor_toolbox/tt_assignment_type.m Added : /Spinach/Spinach core/tensor_toolbox/tt_dimscheck.m Added : /Spinach/Spinach core/tensor_toolbox/tt_ind2sub.m Added : /Spinach/Spinach core/tensor_toolbox/tt_intvec2str.m Added : /Spinach/Spinach core/tensor_toolbox/tt_matrix2cellstr.m Added : /Spinach/Spinach core/tensor_toolbox/tt_size2str.m Added : /Spinach/Spinach core/tensor_toolbox/tt_sizecheck.m Added : /Spinach/Spinach core/tensor_toolbox/tt_sub2ind.m Added : /Spinach/Spinach core/tensor_toolbox/tt_subscheck.m Added : /Spinach/Spinach core/tensor_toolbox/tt_subsubsref.m Added : /Spinach/Spinach core/tensor_toolbox/tt_valscheck.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/generate_spinsys.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/hnca_wC/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/generate_spinsys.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/tst.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/generate_spinsys.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/compute_all.m Modified : /Spinach/Spinach kope/build_graph_table.m Modified : /Spinach/Spinach kope/centered_pulses_kope.m Modified : /Spinach/Spinach kope/chop_kope.m Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope.m Modified : /Spinach/Spinach kope/delay_kope_dig.m Modified : /Spinach/Spinach kope/event_table_kope.m Modified : /Spinach/Spinach kope/example.m Modified : /Spinach/Spinach kope/example_sp.m Modified : /Spinach/Spinach kope/execute_pulse_sequence.m Modified : /Spinach/Spinach kope/fetch_single_transition_kope.m Modified : /Spinach/Spinach kope/fetch_state_kope.m Modified : /Spinach/Spinach kope/pulse_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_dec_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Modified : /Spinach/Spinach kope/purge.m Modified : /Spinach/Spinach kope/receiver_kope.m Modified : /Spinach/Spinach kope/reset_pp.m Modified : /Spinach/Spinach kope/select_state_kope.m Modified : /Spinach/Spinach kope/trajectory_kope.m Modified : /Spinach/Spinach tests/bath_test_2.m Modified : /Spinach/Spinach tests/cosy_test_1.m Modified : /Spinach/Spinach tests/cosy_test_2.m Modified : /Spinach/Spinach tests/decoupling_test_1.m Modified : /Spinach/Spinach tests/derivative_test_1.m Modified : /Spinach/Spinach tests/derivative_test_2.m Modified : /Spinach/Spinach tests/derivative_test_3.m Modified : /Spinach/Spinach tests/derivative_test_4.m Modified : /Spinach/Spinach tests/derivative_test_5.m Modified : /Spinach/Spinach tests/exchange_test_1.m Modified : /Spinach/Spinach tests/high_spin_test_1.m Modified : /Spinach/Spinach tests/homospoil_test_1.m Added : /Spinach/Spinach tests/lie_algebra_test_1.m Modified : /Spinach/Spinach tests/noe_test_1.m Modified : /Spinach/Spinach tests/noesy_test_1.m Modified : /Spinach/Spinach tests/noesy_test_2.m Modified : /Spinach/Spinach tests/offset_test_1.m Modified : /Spinach/Spinach tests/operator_test_1.m Modified : /Spinach/Spinach tests/pulse_acquire_test_1.m Modified : /Spinach/Spinach tests/pulse_acquire_test_2.m Modified : /Spinach/Spinach tests/pulse_test_1.m Modified : /Spinach/Spinach tests/pulse_test_2.m Modified : /Spinach/Spinach tests/scaling_test_1.m Modified : /Spinach/Spinach tests/scaling_test_2.m Modified : /Spinach/Spinach tests/solids_test_1.m Modified : /Spinach/Spinach tests/spin_chain_1.m Modified : /Spinach/Spinach tests/spin_chain_2.m Revision: 327 Author: kuprov Date: 14 August 2009 14:40:00 Message: A lot of minor modifications. Clean-up in create.m in preparation for making the relaxation superoperator universal across NMR and EPR simulations. ---- Modified : /Spinach/Spinach core/ad hoc/MARY_exchange.m Modified : /Spinach/Spinach core/ad hoc/MARY_kinetics.m Modified : /Spinach/Spinach core/ad hoc/MARY_relax.m Modified : /Spinach/Spinach core/ad hoc/MARY_simple.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_exchange.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_exchange_sym.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_kinetics.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_kinetics_sym.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_relax.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_relax_sym.m Modified : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_sym.m Added : /Spinach/Spinach core/create.m (Copy from path: /Spinach/Spinach core/create_ss.m, Revision, 325) Deleted : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/sanity_check.m Modified : /Spinach/Spinach core/tolerances.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/generate_spinsys.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/generate_spinsys.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/tst.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/generate_spinsys.m Modified : /Spinach/Spinach kope/HH_pdb.m Modified : /Spinach/Spinach kope/example.m Modified : /Spinach/Spinach kope/example_sp.m Modified : /Spinach/Spinach kope/rlx_gen_kope.m Modified : /Spinach/Spinach kope/trajectory_kope.m Modified : /Spinach/Spinach tests/bath_test_2.m Modified : /Spinach/Spinach tests/cosy_test_1.m Modified : /Spinach/Spinach tests/cosy_test_2.m Modified : /Spinach/Spinach tests/decoupling_test_1.m Modified : /Spinach/Spinach tests/derivative_test_1.m Modified : /Spinach/Spinach tests/derivative_test_2.m Modified : /Spinach/Spinach tests/derivative_test_3.m Modified : /Spinach/Spinach tests/derivative_test_4.m Modified : /Spinach/Spinach tests/derivative_test_5.m Modified : /Spinach/Spinach tests/exchange_test_1.m Modified : /Spinach/Spinach tests/high_spin_test_1.m Modified : /Spinach/Spinach tests/hilbert_space_test_1.m Modified : /Spinach/Spinach tests/hilbert_space_test_2.m Modified : /Spinach/Spinach tests/homospoil_test_1.m Modified : /Spinach/Spinach tests/mary_test_1.m Modified : /Spinach/Spinach tests/mary_test_2.m Modified : /Spinach/Spinach tests/mary_test_3.m Modified : /Spinach/Spinach tests/mary_test_4.m Modified : /Spinach/Spinach tests/metric_test_1.m Modified : /Spinach/Spinach tests/noe_test_1.m Modified : /Spinach/Spinach tests/noesy_test_1.m Modified : /Spinach/Spinach tests/noesy_test_2.m Modified : /Spinach/Spinach tests/offset_test_1.m Modified : /Spinach/Spinach tests/operator_test_1.m Modified : /Spinach/Spinach tests/oxford/ANISOTROPY_test.m Modified : /Spinach/Spinach tests/oxford/MARY_full_test.m Modified : /Spinach/Spinach tests/pulse_acquire_test_1.m Modified : /Spinach/Spinach tests/pulse_acquire_test_2.m Modified : /Spinach/Spinach tests/pulse_test_1.m Modified : /Spinach/Spinach tests/pulse_test_2.m Modified : /Spinach/Spinach tests/scaling_test_1.m Modified : /Spinach/Spinach tests/scaling_test_2.m Modified : /Spinach/Spinach tests/solids_test_1.m Modified : /Spinach/Spinach tests/solids_test_2.m Modified : /Spinach/Spinach tests/spin_chain_1.m Modified : /Spinach/Spinach tests/spin_chain_2.m Modified : /Spinach/Spinach tests/symmetry_test_1.m Revision: 326 Author: kuprov Date: 12 August 2009 12:20:29 Message: Added a test for the derivative with respect to the waveform truncation. Added a derivative shaped pulse function. ---- Added : /Spinach/Spinach aux/derivative_shaped_pulse.m Added : /Spinach/Spinach tests/derivative_test_5.m Modified : /Spinach/Spinach tests/exchange_test_1.m Revision: 325 Author: kuprov Date: 07 August 2009 12:29:46 Message: Fixed a bug with parameter differentiation of chemical exchange simulations. The analytical result now matches the numerics. ---- Modified : /Spinach/Spinach tests/exchange_test_1.m Revision: 324 Author: kuprov Date: 06 August 2009 17:53:57 Message: Four new functions for the core, mostly dealing with time propagation under various scenarios. Importantly, the are now aware of relaxation and would use non-uniform LvN equation if appropriate. ---- Added : /Spinach/Spinach core/observe.m Added : /Spinach/Spinach core/propagate.m Added : /Spinach/Spinach core/trajectory.m Added : /Spinach/Spinach core/warnings.m Revision: 323 Author: kuprov Date: 06 August 2009 15:49:24 Message: Updated the NOE example to use full non-uniform LvN equation. This also needs to be implemented across Spinach at some point. ---- Modified : /Spinach/Spinach aux/delay.m Modified : /Spinach/Spinach tests/noe_test_1.m Modified : /Spinach/TODO.txt Revision: 322 Author: kuprov Date: 06 August 2009 12:43:19 Message: Introduced the offset function into all pre-programmed pulse sequences and the axis generator. Updated all relevant examples to use the new functionality. ---- Modified : /Spinach/Spinach core/axis_1d.m Modified : /Spinach/Spinach core/tolerances.m Modified : /Spinach/Spinach experiments/derivativeCOSY.m Modified : /Spinach/Spinach experiments/derivative_pulse_acquire.m Modified : /Spinach/Spinach experiments/expCOSY.m Modified : /Spinach/Spinach experiments/expNOESY.m Modified : /Spinach/Spinach experiments/pulse_acquire.m Modified : /Spinach/Spinach tests/bath_test_2.m Modified : /Spinach/Spinach tests/cosy_test_1.m Modified : /Spinach/Spinach tests/cosy_test_2.m Modified : /Spinach/Spinach tests/decoupling_test_1.m Modified : /Spinach/Spinach tests/derivative_test_1.m Modified : /Spinach/Spinach tests/derivative_test_2.m Modified : /Spinach/Spinach tests/derivative_test_3.m Modified : /Spinach/Spinach tests/derivative_test_4.m Modified : /Spinach/Spinach tests/noesy_test_1.m Modified : /Spinach/Spinach tests/pulse_acquire_test_1.m Modified : /Spinach/Spinach tests/pulse_acquire_test_2.m Modified : /Spinach/Spinach tests/scaling_test_1.m Modified : /Spinach/Spinach tests/scaling_test_2.m Modified : /Spinach/Spinach tests/solids_test_1.m Revision: 321 Author: kuprov Date: 04 August 2009 21:42:33 Message: A large number of small fixes and alterations. Cleaned up the messaging and introduced progress indicators into liouv_gen.m, put an additional message into prop_gen.m, same for rlx_gen.m Introduced a Krylov method switchover tolerance -- when nnz(L) becomes larger than that number, the pre-programmed sequences ought to switch to Krylov propagation. Fixed the timestep calculation bug throughout the pre-programmed pulse sequences. Re-wrote pulse_acquire.m to perform an automatic method switchover at the above mentioned tolerance. Cleaned up apodization. Various related fixes to many example files to make them aware of / work with the new features. Fixed a bug in the chemical exchange differentiation example. Removed explicit parallelization from all examples. Updated the TODO list. ---- Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach core/prop_gen.m Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/tolerances.m Modified : /Spinach/Spinach experiments/derivativeCOSY.m Modified : /Spinach/Spinach experiments/derivative_pulse_acquire.m Modified : /Spinach/Spinach experiments/expCOSY.m Modified : /Spinach/Spinach experiments/expNOESY.m Modified : /Spinach/Spinach experiments/pulse_acquire.m Modified : /Spinach/Spinach tests/bath_test_2.m Modified : /Spinach/Spinach tests/cosy_test_1.m Modified : /Spinach/Spinach tests/cosy_test_2.m Modified : /Spinach/Spinach tests/decoupling_test_1.m Modified : /Spinach/Spinach tests/derivative_test_1.m Modified : /Spinach/Spinach tests/derivative_test_2.m Modified : /Spinach/Spinach tests/derivative_test_3.m Modified : /Spinach/Spinach tests/derivative_test_4.m Modified : /Spinach/Spinach tests/exchange_test_1.m Modified : /Spinach/Spinach tests/high_spin_test_1.m Modified : /Spinach/Spinach tests/hilbert_space_test_2.m Modified : /Spinach/Spinach tests/noesy_test_1.m Modified : /Spinach/Spinach tests/noesy_test_2.m Modified : /Spinach/Spinach tests/offset_test_1.m Added : /Spinach/Spinach tests/pulse_acquire_test_1.m Added : /Spinach/Spinach tests/pulse_acquire_test_2.m Modified : /Spinach/Spinach tests/scaling_test_1.m Modified : /Spinach/Spinach tests/scaling_test_2.m Modified : /Spinach/Spinach tests/solids_test_1.m Modified : /Spinach/Spinach tests/solids_test_2.m Modified : /Spinach/TODO.txt Added : /Spinach/XML markup/Prior Art Added : /Spinach/XML markup/Prior Art/phase cycles.pdf Revision: 320 Author: kuprov Date: 04 August 2009 11:47:46 Message: Added a referencing capability to the Gaussian log parser. Introduced a bootstrap apodization function -- apodization no longer needs to be carried out on a case-by-case basis. ---- Added : /Spinach/Spinach aux/apodization.m Modified : /Spinach/Spinach aux/g03_to_spinach.m Revision: 319 Author: kuprov Date: 04 August 2009 11:42:17 Message: Added the spectrum axis generator to the core. The axis can now be computed for 1D spectra based on the simulation parameters of those spectra. Cleared up a bit of documentation. ---- Modified : /Spinach/Spinach core/add_clusters.m Added : /Spinach/Spinach core/axis_1d.m Modified : /Spinach/Spinach core/exchange_superop.m Revision: 318 Author: hannah Date: 31 July 2009 17:31:35 Message: Sorry, a little more tidying. Think this is the last of it. ---- Deleted : /Spinach/Incoming/MARY_relax Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_exchange_sym.m Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_kinetics_sym.m Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_relax_sym.m Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_sym.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red Deleted : /Spinach/Spinach core/ad hoc/pre_SSRsym_liouv_gen.m Deleted : /Spinach/Spinach core/ad hoc/pre_SSRsym_relax_mat_gen.m Deleted : /Spinach/Spinach core/ad hoc/state_list_gen_nonsep_sym.m Deleted : /Spinach/Spinach core/ad hoc/state_list_gen_sep_sym.m Revision: 317 Author: hannah Date: 31 July 2009 17:12:27 Message: The codes to produce MARY simulations have been updated so as to be general for any kind of nuclear spin (also any symmetries). ---- Modified : /Spinach/Incoming Deleted : /Spinach/Incoming/MARY_relax/MARY_general_relax.m Deleted : /Spinach/Incoming/MARY_relax/MARY_pre_SSR_relax.m Deleted : /Spinach/Incoming/MARY_relax/pre_SSR_liouv_gen_relax.m Deleted : /Spinach/Incoming/MARY_relax/pre_SSR_relax_mat_gen.m Deleted : /Spinach/Incoming/MARY_relax/state_list_gen_sep_relax.m Added : /Spinach/Incoming/Pre_computed_liouvillians/gen Added : /Spinach/Spinach core/ad hoc/MARY_exchange.m Added : /Spinach/Spinach core/ad hoc/MARY_kinetics.m Added : /Spinach/Spinach core/ad hoc/MARY_relax.m Added : /Spinach/Spinach core/ad hoc/MARY_simple.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR_exchange.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR_kinetics.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR_relax.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/pre_SSR_liouv_gen.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/pre_SSR_relax_mat_gen.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/state_list_gen.m Deleted : /Spinach/Spinach core/ad hoc/Non_sym_red/state_list_gen_sep.m Added : /Spinach/Spinach core/ad hoc/coeff_table_gen.m Added : /Spinach/Spinach core/ad hoc/irr_sph_ten_product_coefficients Added : /Spinach/Spinach core/ad hoc/irr_sph_ten_product_coefficients/table_of_product_coefficients_for_mult2.mat Added : /Spinach/Spinach core/ad hoc/irr_sph_ten_product_coefficients/table_of_product_coefficients_for_mult3.mat Added : /Spinach/Spinach core/ad hoc/out_dated_functions (Copy from path: /Spinach/Spinach core/ad hoc/Non_sym_red, Revision, 316) Added : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_exchange_sym.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_kinetics_sym.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_relax_sym.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/MARY_pre_SSR_sym.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/pre_SSRsym_liouv_gen.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/pre_SSRsym_relax_mat_gen.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/state_finder.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/state_list_gen_nonsep_sym.m Added : /Spinach/Spinach core/ad hoc/out_dated_functions/state_list_gen_sep_sym.m Added : /Spinach/Spinach core/ad hoc/red_liouv_gen.m Added : /Spinach/Spinach core/ad hoc/red_relax_gen.m Added : /Spinach/Spinach core/ad hoc/sph_ten_qc.m Added : /Spinach/Spinach core/ad hoc/statelist_gen_sep.m Added : /Spinach/Spinach core/ad hoc/statelist_gen_total.m Deleted : /Spinach/Spinach tests/oxford/MARY_general.m Added : /Spinach/Spinach tests/oxford/MARY_general_old.m (Copy from path: /Spinach/Spinach tests/oxford/MARY_general_sym.m, Revision, 316) Modified : /Spinach/Spinach tests/oxford/MARY_general_reference.m Deleted : /Spinach/Spinach tests/oxford/MARY_general_sym.m Added : /Spinach/Spinach tests/oxford/MARY_general_v_old.m (Copy from path: /Spinach/Spinach tests/oxford/MARY_general.m, Revision, 316) Added : /Spinach/Spinach tests/oxford/MARY_generalised.m Revision: 316 Author: hannah Date: 20 July 2009 09:52:52 Message: Tidied up the symmetry pre-reduction a bit for MARY simulations. ---- Modified : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_kinetics_sym.m Modified : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_relax_sym.m Modified : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_sym.m Modified : /Spinach/Spinach core/ad hoc/pre_SSRsym_liouv_gen.m Modified : /Spinach/Spinach core/ad hoc/state_list_gen_sep_sym.m Modified : /Spinach/Spinach tests/oxford/MARY_general.m Modified : /Spinach/Spinach tests/oxford/MARY_general_sym.m Revision: 315 Author: kuprov Date: 09 July 2009 01:41:21 Message: Two example programs for Walter Kockenberger. Demonstrating Spinach implementation of a dipolar-coupled spin chain simulation. ---- Added : /Spinach/Spinach tests/spin_chain_1.m Added : /Spinach/Spinach tests/spin_chain_2.m Revision: 314 Author: kuprov Date: 04 July 2009 01:01:11 Message: Added a pilot implementation of the chemical exchange superoperator. Currently only supports symmetric two-site exchange. Also added the final version of the test script for the chemical exchange superoperator. It tests analytical derivatives with respect to the exchange rate constant as well. ---- Added : /Spinach/Spinach core/exchange_superop.m Added : /Spinach/Spinach tests/exchange_test_1.m Revision: 313 Author: kuprov Date: 26 June 2009 23:20:22 Message: Generalized add_clusters.m to the situation where no clusters were previously defined. Added some memory recycling to prop_gen.m, added some pre-computed clusters, added an exact calculation of a 7-spin solid-state system. ---- Modified : /Spinach/Spinach core/add_clusters.m Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2.mat Modified : /Spinach/Spinach core/prop_gen.m Added : /Spinach/Spinach tests/solids_test_2.m Modified : /Spinach/TODO.txt Revision: 312 Author: kuprov Date: 26 June 2009 19:24:09 Message: Added a solid state test on the system from Niels Chr Nielsen. Unconfirmed data from the Emsley group indicate that five-spin orders are sufficient for MAS NMR experiments. ---- Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach experiments/pulse_acquire.m Added : /Spinach/Spinach tests/molecules/alpha0beta45gamma0.dip Added : /Spinach/Spinach tests/molecules/alpha0beta45gamma90.dip Added : /Spinach/Spinach tests/solids_test_1.m Revision: 311 Author: kuprov Date: 25 June 2009 22:02:42 Message: A system + bath file for Alex Jerschow. Partitions the system into a seven-spin chunk that is simulated exactly and the "rest of it" that is simulated with triples. ---- Added : /Spinach/Spinach tests/bath_test_2.m Modified : /Spinach/TODO.txt Modified : /Spinach/installation.txt Revision: 310 Author: kuprov Date: 19 June 2009 23:46:59 Message: Implemented the spectral differentiation and added a test file for it. Freed-style spectrum calculation (via Liouvillian inverse) definitely has its advantages. ---- Modified : /Spinach/Spinach experiments/derivative_pulse_acquire.m Added : /Spinach/Spinach tests/derivative_test_4.m Modified : /Spinach/TODO.txt Revision: 309 Author: kuprov Date: 18 June 2009 03:04:52 Message: Implemented derivative superoperators into derivative_pulse_acquire and added a test function that uses them. ---- Modified : /Spinach/Spinach experiments/derivative_pulse_acquire.m Added : /Spinach/Spinach tests/derivative_test_3.m Added : /Spinach/TODO.txt Revision: 308 Author: hannah Date: 05 June 2009 14:06:46 Message: Added codes that form the Liouvillian for MARY simulations after symmetry factorisation (made possible because only populated irrep is A1g with characters 1). Can also produce the relaxation superoperator for relaxation on one radical in the symmetry reduced state space. These can be called using MARY_general_sym.m in test/oxford. ---- Added : /Spinach/Incoming/Pre_computed_liouvillians/sym Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR.m Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_exchange.m Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_exchange_sym.m Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_kinetics.m Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_kinetics_sym.m Deleted : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_relax.m Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_relax_sym.m Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_sym.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red Added : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR_exchange.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR_kinetics.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red/MARY_pre_SSR_relax.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red/pre_SSR_liouv_gen.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red/pre_SSR_relax_mat_gen.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red/state_list_gen.m Added : /Spinach/Spinach core/ad hoc/Non_sym_red/state_list_gen_sep.m Deleted : /Spinach/Spinach core/ad hoc/pre_SSR_liouv_gen.m Deleted : /Spinach/Spinach core/ad hoc/pre_SSR_relax_mat_gen.m Added : /Spinach/Spinach core/ad hoc/pre_SSRsym_liouv_gen.m Added : /Spinach/Spinach core/ad hoc/pre_SSRsym_relax_mat_gen.m Deleted : /Spinach/Spinach core/ad hoc/state_list_gen.m Added : /Spinach/Spinach core/ad hoc/state_list_gen_nonsep_sym.m Deleted : /Spinach/Spinach core/ad hoc/state_list_gen_sep.m Added : /Spinach/Spinach core/ad hoc/state_list_gen_sep_sym.m Modified : /Spinach/Spinach tests/oxford/MARY_general.m Modified : /Spinach/Spinach tests/oxford/MARY_general_reference.m Added : /Spinach/Spinach tests/oxford/MARY_general_sym.m Revision: 307 Author: kuprov Date: 27 May 2009 21:56:44 Message: Added the rigid body rotations -- it is now possible to rotate the entire system, including all anisotropic interactions declared therein, as a rigid body using Euler angles. Will be useful for solids... ---- Modified : /Spinach/Spinach core/progmeter.m Added : /Spinach/Spinach core/rotate_system.m Revision: 306 Author: kuprov Date: 27 May 2009 18:05:15 Message: Fixed the bugs and re-introduced the general treatment of anisotropic interactions. As a matter of policy, Spinach will never rotate the static field around the system, it will always rotate the system. ---- Modified : /Spinach/Spinach core/cluster_ham.m Modified : /Spinach/Spinach core/create_ss.m Revision: 305 Author: kuprov Date: 27 May 2009 17:54:03 Message: Revert to the previous revision -- bugs discovered. Will likely have to abandon the tilted fields idea -- much better to rotate the system instead. ---- Modified : /Spinach/Spinach aux/offset.m Modified : /Spinach/Spinach core/cluster_ham.m Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/thermal_dm.m Modified : /Spinach/Spinach kope/rlx_gen_kope.m Modified : /Spinach/installation.txt Revision: 304 Author: kuprov Date: 27 May 2009 16:19:50 Message: Added a fully general implementation of interaction anisotropies and extended the core to handle tilted magnetic fields -- it's now possible to specify B0 as a three-element vector. Proceeding to write a few solid-state tests. ---- Modified : /Spinach/Spinach aux/offset.m Modified : /Spinach/Spinach core/cluster_ham.m Added : /Spinach/Spinach core/clusters/generators_3.mat Added : /Spinach/Spinach core/clusters/state_vectors_3.mat Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/thermal_dm.m Modified : /Spinach/Spinach experiments/derivative_pulse_acquire.m Modified : /Spinach/Spinach experiments/pulse_acquire.m Deleted : /Spinach/Spinach external Modified : /Spinach/Spinach kope/rlx_gen_kope.m Revision: 303 Author: kuprov Date: 26 May 2009 17:10:41 Message: Added a family of uniform icosahedral spherical grids. Will be useful for spherical integration when the solids module is up. ---- Added : /Spinach/Spinach core/grids Added : /Spinach/Spinach core/grids/icosahedral_10242.txt Added : /Spinach/Spinach core/grids/icosahedral_12.txt Added : /Spinach/Spinach core/grids/icosahedral_162.txt Added : /Spinach/Spinach core/grids/icosahedral_2562.txt Added : /Spinach/Spinach core/grids/icosahedral_42.txt Added : /Spinach/Spinach core/grids/icosahedral_642.txt Added : /Spinach/Spinach core/grids/sphere.c Revision: 302 Author: kuprov Date: 26 May 2009 16:48:02 Message: Final touches to the SpinXML schema. ---- Added : /Spinach/XML markup/SpinXML/spinxml_schema.png (Copy from path: /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.png, Revision, 300) Added : /Spinach/XML markup/SpinXML/spinxml_schema.xsd (Copy from path: /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.xsd, Revision, 300) Deleted : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.png Deleted : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.xsd Revision: 301 Author: kuprov Date: 26 May 2009 10:24:24 Message: Updated symmetry syntax in Hannah's test calculations. ---- Modified : /Spinach/Spinach tests/oxford/MARY_full_test.m Modified : /Spinach/Spinach tests/oxford/MARY_general.m Revision: 300 Author: kuprov Date: 25 May 2009 17:09:44 Message: Experimental implementation of progress meter in statelist_gen function. It now gives an indication of how far it's got. Also removed the default setting that prints the cluster list to the console. ---- Deleted : /Spinach/Spinach aux/progmeter.m Modified : /Spinach/Spinach core/cluster_gen.m Added : /Spinach/Spinach core/progmeter.m (Copy from path: /Spinach/Spinach aux/progmeter.m, Revision, 299) Modified : /Spinach/Spinach core/statelist_gen.m Added : /Spinach/Spinach tests/noesy_test_1.m Added : /Spinach/Spinach tests/offset_test_1.m Revision: 299 Author: kuprov Date: 25 May 2009 16:33:46 Message: Replaced a crash with a warning in prop_gen.m; changed the apodization in pulse_acquire to a less drastic function; performed a monumental clean-up in the tests directory. ---- Modified : /Spinach/Spinach core/prop_gen.m Modified : /Spinach/Spinach experiments/pulse_acquire.m Deleted : /Spinach/Spinach tests/ANISOTROPY_test.m Deleted : /Spinach/Spinach tests/MARY_full_test.m Deleted : /Spinach/Spinach tests/MARY_general.m Deleted : /Spinach/Spinach tests/MARY_general_reference.m Deleted : /Spinach/Spinach tests/SSR_mary_test.m Deleted : /Spinach/Spinach tests/big_spin_system.m Added : /Spinach/Spinach tests/cosy_test_1.m (Copy from path: /Spinach/Spinach tests/example_cosy.m, Revision, 295) Added : /Spinach/Spinach tests/cosy_test_2.m (Copy from path: /Spinach/Spinach tests/gaussian_test.m, Revision, 295) Deleted : /Spinach/Spinach tests/custom_operator_test.m Added : /Spinach/Spinach tests/decoupling_test_1.m (Copy from path: /Spinach/Spinach tests/example_pulse_acquire.m, Revision, 295) Deleted : /Spinach/Spinach tests/derivative_cosy_test.m Deleted : /Spinach/Spinach tests/derivative_test.m Added : /Spinach/Spinach tests/derivative_test_1.m (Copy from path: /Spinach/Spinach tests/derivative_cosy_test.m, Revision, 295) Added : /Spinach/Spinach tests/derivative_test_2.m (Copy from path: /Spinach/Spinach tests/derivative_test.m, Revision, 295) Deleted : /Spinach/Spinach tests/example_clustering.ppt Deleted : /Spinach/Spinach tests/example_cosy.m Deleted : /Spinach/Spinach tests/example_mary.m Deleted : /Spinach/Spinach tests/example_metric.m Deleted : /Spinach/Spinach tests/example_pulse_acquire.m Deleted : /Spinach/Spinach tests/gaussian_test.m Deleted : /Spinach/Spinach tests/high_spin_test.m Added : /Spinach/Spinach tests/high_spin_test_1.m (Copy from path: /Spinach/Spinach tests/high_spin_test.m, Revision, 295) Added : /Spinach/Spinach tests/hilbert_space_test_1.m (Copy from path: /Spinach/Spinach tests/mary_test_hilbert.m, Revision, 296) Added : /Spinach/Spinach tests/hilbert_space_test_2.m (Copy from path: /Spinach/Spinach tests/symm_pyrene.m, Revision, 296) Deleted : /Spinach/Spinach tests/homospoil_test.m Added : /Spinach/Spinach tests/homospoil_test_1.m (Copy from path: /Spinach/Spinach tests/homospoil_test.m, Revision, 295) Deleted : /Spinach/Spinach tests/large_cluster_test.m Deleted : /Spinach/Spinach tests/mary_test.m Added : /Spinach/Spinach tests/mary_test_1.m (Copy from path: /Spinach/Spinach tests/SSR_mary_test.m, Revision, 295) Added : /Spinach/Spinach tests/mary_test_2.m (Copy from path: /Spinach/Spinach tests/mary_test_symmetry.m, Revision, 295) Added : /Spinach/Spinach tests/mary_test_3.m (Copy from path: /Spinach/Spinach tests/example_mary.m, Revision, 295) Added : /Spinach/Spinach tests/mary_test_4.m (Copy from path: /Spinach/Spinach tests/mary_test.m, Revision, 295) Deleted : /Spinach/Spinach tests/mary_test_hilbert.m Deleted : /Spinach/Spinach tests/mary_test_symmetry.m Deleted : /Spinach/Spinach tests/metric_test.m Added : /Spinach/Spinach tests/metric_test_1.m (Copy from path: /Spinach/Spinach tests/example_metric.m, Revision, 295) Deleted : /Spinach/Spinach tests/noe_test.m Added : /Spinach/Spinach tests/noe_test_1.m (Copy from path: /Spinach/Spinach tests/noe_test.m, Revision, 295) Deleted : /Spinach/Spinach tests/noesy_test.m Added : /Spinach/Spinach tests/noesy_test_2.m (Copy from path: /Spinach/Spinach tests/noesy_test.m, Revision, 295) Added : /Spinach/Spinach tests/operator_test_1.m (Copy from path: /Spinach/Spinach tests/custom_operator_test.m, Revision, 295) Added : /Spinach/Spinach tests/oxford Added : /Spinach/Spinach tests/oxford/ANISOTROPY_test.m (Copy from path: /Spinach/Spinach tests/ANISOTROPY_test.m, Revision, 295) Added : /Spinach/Spinach tests/oxford/MARY_full_test.m (Copy from path: /Spinach/Spinach tests/MARY_full_test.m, Revision, 295) Added : /Spinach/Spinach tests/oxford/MARY_general.m (Copy from path: /Spinach/Spinach tests/MARY_general.m, Revision, 295) Added : /Spinach/Spinach tests/oxford/MARY_general_reference.m (Copy from path: /Spinach/Spinach tests/MARY_general_reference.m, Revision, 295) Deleted : /Spinach/Spinach tests/progmeter_test.m Added : /Spinach/Spinach tests/pulse_test_1.m (Copy from path: /Spinach/Spinach tests/shaped_pulse_test.m, Revision, 295) Added : /Spinach/Spinach tests/pulse_test_2.m (Copy from path: /Spinach/Spinach tests/sim_pulse_test.m, Revision, 295) Added : /Spinach/Spinach tests/scaling_test_1.m (Copy from path: /Spinach/Spinach tests/big_spin_system.m, Revision, 295) Added : /Spinach/Spinach tests/scaling_test_2.m (Copy from path: /Spinach/Spinach tests/large_cluster_test.m, Revision, 295) Deleted : /Spinach/Spinach tests/shaped_pulse_test.m Deleted : /Spinach/Spinach tests/sim_pulse_test.m Deleted : /Spinach/Spinach tests/symm_pyrene.m Deleted : /Spinach/Spinach tests/symmetry_test.m Added : /Spinach/Spinach tests/symmetry_test_1.m (Copy from path: /Spinach/Spinach tests/symmetry_test.m, Revision, 295) Revision: 298 Author: kuprov Date: 25 May 2009 12:55:07 Message: Realized that the state vectors do not need to be computed in Hilbert space. Started to build the "Illustrations" directory, showcasing Spinach capabilities. ---- Added : /Illustrations Added : /Illustrations/cosy spectrum of strychnine.fig Added : /Illustrations/symmetry factorization of pyrene radical hamiltonian.fig Revision: 297 Author: kuprov Date: 25 May 2009 12:54:44 Message: Realized that the state vectors do not need to be computed in Hilbert space. Started to build the "Illustrations" directory, showcasing Spinach capabilities. ---- Deleted : /Spinach/Spinach core/hilb_state_pregen.m Added : /Spinach/Spinach tests/etalons (Copy from path: /Spinach/Spinach tests/ethalons, Revision, 295) Deleted : /Spinach/Spinach tests/ethalons Revision: 296 Author: kuprov Date: 25 May 2009 12:43:13 Message: Parallelized the symmetrizer, added the pyrene symmetry factorization test, updated the hilbert-space MARY test. ---- Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__3__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__3__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3__2__2.mat Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach tests/mary_test_hilbert.m Added : /Spinach/Spinach tests/symm_pyrene.m Revision: 295 Author: hannah Date: 25 May 2009 11:54:05 Message: Rewritten pre_SSR_relax_mat_gen with spin ordering now back to normal and added it to the adhoc section of core. Removed the other relaxation parts from incoming because no longer required and just a bit confusing with the odd spin ordering. Also updated MARY_general in tests to allow for including relaxation. ---- Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_relax.m Added : /Spinach/Spinach core/ad hoc/pre_SSR_relax_mat_gen.m Modified : /Spinach/Spinach tests/MARY_general.m Revision: 294 Author: kuprov Date: 24 May 2009 21:14:39 Message: Minor fixes and some new pre-computed cluster generators. You can have sizeable clusters in Hilbert space... ---- Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__3__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2__2__2__2__2__2__3__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__3__2__2__2__2__2__2__2__2__2__2__2.mat Modified : /Spinach/Spinach core/hilb_statelist_gen.m Modified : /Spinach/Spinach core/symmetry.m Revision: 293 Author: kuprov Date: 24 May 2009 21:08:06 Message: A syntax update, bigger clusters and a bigger symmetry group - Td(x)Td in the cluster-based MARY test file. ---- Modified : /Spinach/Spinach tests/example_mary.m Revision: 292 Author: kuprov Date: 24 May 2009 21:05:44 Message: Found a nice progress meter function that does not erase any of the console text. Spinach will soon give much better feedback on how it's going. ---- Added : /Spinach/Spinach aux/progmeter.m Added : /Spinach/Spinach tests/progmeter_test.m Revision: 291 Author: kuprov Date: 22 May 2009 00:02:32 Message: Put in a slightly more dramatic example into mary_symmetry_test.m; removed the empty irrep warning from symmetry.m - it already informs the user about irrep populations and that should suffice. ---- Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2__2__2.mat Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach tests/mary_test_hilbert.m Revision: 290 Author: kuprov Date: 21 May 2009 23:33:21 Message: A backwards compatibility fix in analytical_zte.m; a user output bug fix in symmetry.m; file property updates. ---- Modified : /Spinach/Spinach core/add_clusters.m Modified : /Spinach/Spinach core/analytical_zte.m Modified : /Spinach/Spinach core/hilb_state_pregen.m Modified : /Spinach/Spinach core/hilb_statelist_gen.m Modified : /Spinach/Spinach core/singlet.m Modified : /Spinach/Spinach core/symmetry.m Revision: 289 Author: kuprov Date: 21 May 2009 23:05:26 Message: Test implementation of Hilbert space symmetrizer for MARY simulations: mary_test_hilbert.m Three things to note: 1. Very compact implementation of MARY simulator in mary_test_hilbert.m - eight lines, neat and fast. 2. Symmetrization sometimes results in rounding errors that break the Hermitian property and wreak havoc among the eigenvalues, hence the (A+A')/2 steps after the irrep projection. 3. All irreps are populated in Hilbert space, meaning effectively that we are constrained to direct products of Abelian groups. Fortunately the maximal Abelian subgroups of Sn are quite large. ---- Modified : /Spinach/Spinach core/hilb_state_pregen.m Modified : /Spinach/Spinach core/symmetry.m Added : /Spinach/Spinach tests/mary_test_hilbert.m Revision: 288 Author: kuprov Date: 21 May 2009 15:20:35 Message: A couple of steps towards the implementation of Hilbert space symmetrizer. Sort of works, but currently leaks into non-symmetric irreps. Investigating... ---- Added : /Spinach/Spinach core/hilb_state_pregen.m Added : /Spinach/Spinach core/hilb_statelist_gen.m Added : /Spinach/Spinach core/singlet.m Revision: 287 Author: kuprov Date: 19 May 2009 21:15:55 Message: Pilot implementation of the analytical derivative code for 2D NMR sequences. Not much difference from 1D -- the parameter derivatives of all hard pulse propagators are zero. :) ---- Added : /Spinach/Spinach experiments/derivativeCOSY.m Added : /Spinach/Spinach tests/derivative_cosy_test.m Modified : /Spinach/Spinach tests/derivative_test.m Revision: 286 Author: hannah Date: 19 May 2009 17:25:48 Message: Added MARY simulation codes to allow for relaxation of one nucleus following on from NWR block diagonal matrices. NB the ordering of the spins has been changed to allow for easier scaling up of the relaxation matrix..this is only affects numbering of spins for symmetry considerations. ---- Added : /Spinach/Incoming/MARY_relax Added : /Spinach/Incoming/MARY_relax/MARY_general_relax.m Added : /Spinach/Incoming/MARY_relax/MARY_pre_SSR_relax.m Added : /Spinach/Incoming/MARY_relax/pre_SSR_liouv_gen_relax.m Added : /Spinach/Incoming/MARY_relax/pre_SSR_relax_mat_gen.m Added : /Spinach/Incoming/MARY_relax/state_list_gen_sep_relax.m Modified : /Spinach/Spinach core/ad hoc/MARY_pre_SSR.m Revision: 285 Author: kuprov Date: 19 May 2009 10:59:13 Message: Added the S6 group. this is probably the largest group for which the symmetrization is worth it -- with 720 elements the SALCs take longer to build than the time saving they provide in the end... ---- Modified : /Spinach/Spinach core/symmetry_group.m Revision: 284 Author: kuprov Date: 18 May 2009 22:51:26 Message: Created a large-cluster test file -- 22-spin system of strychnine with SSR(4)+JNES clusterization with one manually added 8-spin cluster. The global Liouvillian is computed in about 20 minutes. :) ---- Added : /Spinach/Spinach tests/large_cluster_test.m Revision: 283 Author: kuprov Date: 18 May 2009 22:09:11 Message: Final touches on the new Liouvillian recoupling algorithm. Easily 100 times faster than the original one for the test cases + better scaling. Looks like Konstantin can now have his 8-spin cluster. :) ---- Modified : /Spinach/Spinach core/custom_operator.m Revision: 282 Author: kuprov Date: 18 May 2009 22:00:09 Message: A very serious breakthrough with Liouvillian recoupling. The new procedure is very clear and understandable, and can be carried out at virtually zero memory cost. ---- Added : /Spinach/Documentation/2007-03-27-Sym6-Characters.pdf Added : /Spinach/Documentation/Some data on group direct products.html.URL Modified : /Spinach/Spinach core/liouv_gen.m Revision: 281 Author: kuprov Date: 17 May 2009 19:25:02 Message: A slightly larger example for MARY simulations, involving a TdxC2 symmetry group for six nuclei. ---- Added : /Miscellaneous/Literature/chebyshev propagator.pdf Added : /Miscellaneous/Literature/density matrix renormalization/GetPDFServlet 1.pdf Modified : /Spinach/Spinach tests/mary_test_symmetry.m Revision: 280 Author: kuprov Date: 17 May 2009 15:26:39 Message: Added a user-end function that makes adding clusters slightly more straightforward. It also takes care to eliminate the existing clusters that are now contained within the clusters that the user just added, potentially eliminating redundancy. ---- Added : /Spinach/Spinach core/add_clusters.m Revision: 279 Author: kuprov Date: 17 May 2009 15:15:38 Message: Should now be able to deal with Konstantin's 8-spin Ca hub. Huge matrices (dimensions order 100k) as a result, but the code should manage. Would be wise to make use of ZTE and Krylov (expv.m) propagation. Also eliminated the spin_system.nclusters variable, since the user can alter the cluster list at will -- the code now always explicitly checks how many clusters it has. ---- Modified : /Spinach/Spinach core/cluster_gen.m Modified : /Spinach/Spinach core/custom_operator.m Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach core/statelist_gen.m Revision: 278 Author: kuprov Date: 16 May 2009 17:10:05 Message: Added S5 symmetry group to the group database. ---- Modified : /Spinach/Spinach core/symmetry_group.m Revision: 277 Author: kuprov Date: 15 May 2009 18:07:19 Message: Fully general symmetry module: any number of groups of any number of spins of any spin quantum number. Only partial testing has been carried out thus far (all seems to work for Spin Chemistry simulations), so please double-check against the non-symmetric simulations whenever feasible. Usage examples are given in mary_symmetry_test.m file and in the header of symmetry.m in the core. Note the change in syntax for symmetry.m function -- it now needs curly braces. I'm in the process of testing the code with NMR systems. ---- Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2__2__2.mat Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach experiments/expMARY.m Modified : /Spinach/Spinach tests/mary_test_symmetry.m Revision: 276 Author: kuprov Date: 13 May 2009 20:43:18 Message: Added class structure to the symmetry group database. Useful (in principle) for group direct product implementation. ---- Modified : /Spinach/Spinach core/symmetry_group.m Revision: 275 Author: kuprov Date: 13 May 2009 16:10:14 Message: Some group-theoretical heavy-lifting. Need to generate character and class tables for permutation groups up to order 9 (tert-butyl group) -- a formidable task given that 9!=362880. ---- Added : /Spinach/Spinach core/symmetry_groups Added : /Spinach/Spinach core/symmetry_groups/@permutation Added : /Spinach/Spinach core/symmetry_groups/@permutation/acknowledgement.txt Added : /Spinach/Spinach core/symmetry_groups/@permutation/array.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/cycles.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/display.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/eq.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/inv.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/length.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/longest_cycle.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/matrix.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/mpower.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/mtimes.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/ne.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/permutation.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/random.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/sign.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/size.m Added : /Spinach/Spinach core/symmetry_groups/@permutation/subsref.m Added : /Spinach/Spinach core/symmetry_groups/permutation_group_class_list.m Revision: 274 Author: kuprov Date: 11 May 2009 20:59:42 Message: A lot of monumental improvements in the propagator generator -- included scaling and squaring, tightened up the tolerances to safer levels and introduced an option to compute derivative propagators. Modified the 1D spectrum function to return a complex spectrum rather than plot it. Sorted a few files into appropriate directories. Introduced a derivative test script -- that stuff uses pretty much the whole of the algebraic core at the same time. If that script checks out, Spinach is running as designed. ---- Added : /Spinach/Spinach core/clusters/generators_2__2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3__2.mat Deleted : /Spinach/Spinach core/derivative_prop_gen.m Modified : /Spinach/Spinach core/prop_gen.m Modified : /Spinach/Spinach core/tolerances.m Deleted : /Spinach/Spinach examples Modified : /Spinach/Spinach experiments/derivative_pulse_acquire.m Modified : /Spinach/Spinach experiments/expCOSY.m Modified : /Spinach/Spinach experiments/expNOESY.m Modified : /Spinach/Spinach experiments/pulse_acquire.m Added : /Spinach/Spinach tests/MARY_general.m (Copy from path: /Spinach/Spinach examples/MARY_general.m, Revision, 272) Added : /Spinach/Spinach tests/MARY_general_reference.m (Copy from path: /Spinach/Spinach examples/MARY_general_reference.m, Revision, 272) Added : /Spinach/Spinach tests/big_spin_system.m (Copy from path: /Spinach/Spinach examples/big_spin_system.m, Revision, 272) Deleted : /Spinach/Spinach tests/csa_relaxation.nb Deleted : /Spinach/Spinach tests/dd-csa_cross-correlation.nb Deleted : /Spinach/Spinach tests/dd_relaxation.nb Modified : /Spinach/Spinach tests/derivative_test.m Deleted : /Spinach/Spinach tests/deuterium_standard.m Added : /Spinach/Spinach tests/ethalons Added : /Spinach/Spinach tests/ethalons/csa_relaxation.nb (Copy from path: /Spinach/Spinach tests/csa_relaxation.nb, Revision, 272) Added : /Spinach/Spinach tests/ethalons/dd-csa_cross-correlation.nb (Copy from path: /Spinach/Spinach tests/dd-csa_cross-correlation.nb, Revision, 272) Added : /Spinach/Spinach tests/ethalons/dd_relaxation.nb (Copy from path: /Spinach/Spinach tests/dd_relaxation.nb, Revision, 272) Added : /Spinach/Spinach tests/ethalons/deuterium_standard.m (Copy from path: /Spinach/Spinach tests/deuterium_standard.m, Revision, 272) Added : /Spinach/Spinach tests/example_clustering.ppt (Copy from path: /Spinach/Spinach examples/example_clustering.ppt, Revision, 272) Added : /Spinach/Spinach tests/example_cosy.m (Copy from path: /Spinach/Spinach examples/example_cosy.m, Revision, 272) Added : /Spinach/Spinach tests/example_mary.m (Copy from path: /Spinach/Spinach examples/example_mary.m, Revision, 272) Added : /Spinach/Spinach tests/example_metric.m (Copy from path: /Spinach/Spinach examples/example_metric.m, Revision, 272) Added : /Spinach/Spinach tests/example_pulse_acquire.m (Copy from path: /Spinach/Spinach examples/example_pulse_acquire.m, Revision, 272) Modified : /Spinach/Spinach tests/high_spin_test.m Revision: 273 Author: kuprov Date: 10 May 2009 14:08:35 Message: Wrote a nice contour plotting utility with non-linear adaptive contour spacing. Useful for NMR data where small cross-peaks must be adequately contoured next to large diagonal peaks. Updated COSY and NOESY functions to use it. ---- Added : /Spinach/Spinach aux/contour_plot.m Modified : /Spinach/Spinach aux/g03_parse.m Modified : /Spinach/Spinach core/derivative_prop_gen.m Modified : /Spinach/Spinach experiments/expCOSY.m Modified : /Spinach/Spinach experiments/expNOESY.m Modified : /Spinach/Spinach tests/gaussian_test.m Revision: 272 Author: kuprov Date: 09 May 2009 21:44:05 Message: Major improvement in memory footprint -- should crash a lot less now with the "out of memory" error. ---- Modified : /Spinach/Spinach core/custom_operator.m Modified : /Spinach/Spinach core/rlx_gen.m Revision: 271 Author: kuprov Date: 09 May 2009 17:15:13 Message: Improvements in the Gaussian parser. Introduced the Spinach input generator that translates the data acquired from the Gaussian log into Spinach data structures. Fixed a matrix sparsity bug in the derivative propagator generator. Updated the apodization in pulse_acquire experiment to the fairly mild and data-agnostic sine bell function. Created an example derivative simulation function in the tests directory. Moved the gaussian test file to the new parser. ---- Added : /Miscellaneous/Literature/kruk.pdf Modified : /Spinach/Spinach aux/g03_parse.m Added : /Spinach/Spinach aux/g03_to_spinach.m Modified : /Spinach/Spinach core/derivative_prop_gen.m Added : /Spinach/Spinach experiments/derivative_pulse_acquire.m Modified : /Spinach/Spinach experiments/pulse_acquire.m Added : /Spinach/Spinach tests/derivative_test.m Modified : /Spinach/Spinach tests/gaussian_test.m Revision: 270 Author: kuprov Date: 09 May 2009 12:04:35 Message: A pilot implementation of parameter derivative code -- the derivatives of the simulation with respect to its parameters are computed analytically using the co-propagation formalism (IK's paper in preparation). ---- Modified : /Spinach/Documentation/Spinach manual.docx Added : /Spinach/Spinach core/derivative_prop_gen.m (Copy from path: /Spinach/Spinach core/prop_gen.m, Revision, 264) Revision: 269 Author: kuprov Date: 07 May 2009 11:32:08 Message: Extended the relaxation superoperator theory text to quadratic (quadrupolar, ZFS etc) interactions. Proceeding to update rlx_gen... ---- Modified : /Spinach/Documentation/relaxation_superoperator.docx Modified : /Spinach/Documentation/relaxation_superoperator.pdf Revision: 268 Author: kuprov Date: 07 May 2009 10:25:45 Message: Documentation update complete -- the core is currently fully documented. ---- Modified : /Spinach/Documentation/Spinach manual.docx Added : /Spinach/Documentation/Spinach manual.pdf Modified : /Spinach/Spinach core/path_trace.m Modified : /Spinach/Spinach core/thermal_dm.m Revision: 267 Author: kuprov Date: 07 May 2009 09:48:22 Message: More documentation updates and some renaming to make function names more descriptive. ---- Modified : /Spinach/Documentation/Spinach manual.docx Modified : /Spinach/Spinach core/rlx_gen.m Deleted : /Spinach/Spinach core/sp_den.m Added : /Spinach/Spinach core/spectral_density.m (Copy from path: /Spinach/Spinach core/sp_den.m, Revision, 264) Revision: 266 Author: kuprov Date: 06 May 2009 17:23:56 Message: A lot of additional documentation in the main doc file and throughout the code. Removed the legacy code from the numerical ZTE subroutine and renamed it appropriately (also updated the calls throughout the user-land code). ---- Modified : /Spinach/Documentation/Spinach manual.docx Modified : /Spinach/Spinach core/decouple.m Modified : /Spinach/Spinach core/irr_sph_ten.m Added : /Spinach/Spinach core/numerical_zte.m (Copy from path: /Spinach/Spinach core/prune.m, Revision, 264) Modified : /Spinach/Spinach core/pauli.m Deleted : /Spinach/Spinach core/prune.m Modified : /Spinach/Spinach experiments/expMARY.m Modified : /Spinach/Spinach tests/ANISOTROPY_test.m Revision: 265 Author: kuprov Date: 06 May 2009 16:17:51 Message: 1. Extended analytical ZTE in MARY simulations to arbitrary nuclear spin. Hannah, may I ask you to test it with a couple of symmetry-related 35Cl nuclei against the exact simulation? 2. Implemented a fast-track bypass for the state-cluster cross-membership matrix generation in simulations with only one cluster. 3. Documented the wigner_d.m function. ---- Modified : /Spinach/Spinach core/analytical_zte.m Added : /Spinach/Spinach core/clusters/generators_2__2__3__3__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__4__4.mat Added : /Spinach/Spinach core/clusters/generators_2__2__8__8.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3__3__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__4__4.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__8__8.mat Modified : /Spinach/Spinach core/nucleus.m Modified : /Spinach/Spinach core/statelist_gen.m Modified : /Spinach/Spinach core/wigner_d.m Revision: 264 Author: kuprov Date: 05 May 2009 11:49:06 Message: Documentation update. ---- Modified : /Spinach/Documentation/Spinach manual.docx Revision: 263 Author: hannah Date: 05 May 2009 10:32:41 Message: updated to allow for the inclusion of exchange interaction in MARY simulations ---- Added : /Spinach/Incoming/results Modified : /Spinach/Spinach core/ad hoc/MARY_pre_SSR.m Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_exchange.m Modified : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_kinetics.m Modified : /Spinach/Spinach core/ad hoc/pre_SSR_liouv_gen.m Modified : /Spinach/Spinach examples/MARY_general.m Modified : /Spinach/Spinach examples/MARY_general_reference.m Modified : /Spinach/Spinach tests/MARY_full_test.m Revision: 262 Author: kuprov Date: 28 April 2009 20:10:56 Message: Some more changes to SpinXML in response to Stefan Stoll's comments. This looks good enough for broader community consultation. ---- Modified : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.xsd Revision: 261 Author: kuprov Date: 27 April 2009 09:56:37 Message: Fixed a minor core bug concerning user output in cluster_gen. Plus another test molecule for the Gaussian parser. ---- Modified : /Spinach/Spinach core/cluster_gen.m Modified : /Spinach/Spinach tests/gaussian_test.m Added : /Spinach/Spinach tests/molecules/formyl-mlf.log Revision: 260 Author: kuprov Date: 26 April 2009 14:50:04 Message: A parallel implementation of COSY and NOESY (falling back to serial if the matlab worker pool is not initialized). ---- Modified : /Spinach/Spinach experiments/expCOSY.m Modified : /Spinach/Spinach experiments/expNOESY.m Added : /Spinach/installation.txt Revision: 259 Author: hannah Date: 24 April 2009 15:35:28 Message: Fixed the incomplete reduction bug in path_trace.m, updated the MARY test to wait till the graph is actually displayed before overwriting it. ---- Modified : /Spinach/Spinach core/path_trace.m Modified : /Spinach/Spinach tests/MARY_full_test.m Revision: 258 Author: hannah Date: 24 April 2009 14:48:03 Message: Implemented a path tracing subroutine and updated the MARY function to use it. Easily identifiable independent MARY subspaces are now simulated separately. ---- Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2.mat Added : /Spinach/Spinach core/path_trace.m Modified : /Spinach/Spinach experiments/expMARY.m Revision: 257 Author: hannah Date: 24 April 2009 11:54:21 Message: Hannah's path to MARY (Liouvillian generated directly in the reduced state space). Needs interfacing to the rest of Spinach in a convenient way and general beautification. ---- Deleted : /Spinach/Incoming/A (brief) Progress Report MArch.ppt Deleted : /Spinach/Incoming/Pre_SSR Added : /Spinach/Incoming/Pre_computed_liouvillians/system_0210_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/system_0210_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/system_1111_0qc_zz.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/system_4000_0qc_pm_mp.mat Added : /Spinach/Incoming/Pre_computed_liouvillians/system_4000_0qc_zz.mat Deleted : /Spinach/Incoming/ZTE_1000.m Deleted : /Spinach/Incoming/ZTE_example.m Deleted : /Spinach/Incoming/non_spinach_reference.m Added : /Spinach/Spinach core/ad hoc Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR.m Added : /Spinach/Spinach core/ad hoc/MARY_pre_SSR_kinetics.m Added : /Spinach/Spinach core/ad hoc/pre_SSR_liouv_gen.m Added : /Spinach/Spinach core/ad hoc/state_finder.m Added : /Spinach/Spinach core/ad hoc/state_list_gen.m Added : /Spinach/Spinach core/ad hoc/state_list_gen_sep.m Deleted : /Spinach/Spinach core/liouv_gen_hannah.m Deleted : /Spinach/Spinach core/state_list_gen_hannah.m Added : /Spinach/Spinach examples/MARY_general.m (Copy from path: /Spinach/Incoming/Pre_SSR/MARY_general.m, Revision, 256) Added : /Spinach/Spinach examples/MARY_general_reference.m (Copy from path: /Spinach/Incoming/non_spinach_reference.m, Revision, 256) Revision: 256 Author: kuprov Date: 19 April 2009 13:02:00 Message: Update to SpinXML in response to Stefan Stoll's comments. ---- Modified : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.xsd Revision: 255 Author: kuprov Date: 19 April 2009 12:43:13 Message: Update to SpinXML in response to Stefan Stoll's comments. ---- Modified : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.xsd Revision: 254 Author: kuprov Date: 17 April 2009 17:58:06 Message: Added a Gaussian03 log parser functions and a demonstration calculation computing COSY and NOESY for strychnine starting from XYZ coordinates. Added a distance-based clusterization option to the cluster generator (useful for NOESY runs). Added proximity matrix generator to create_ss.m, set the default proximity cut-off radius at 4 Angstrom. Updated COSY to use an efficient parallel algorithm and full-window sine bell apodization by default. ---- Modified : /Spinach/Spinach aux/g03_parse.m Modified : /Spinach/Spinach core/cluster_gen.m Added : /Spinach/Spinach core/clusters/generators_2__2__2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__3__2.mat Added : /Spinach/Spinach core/clusters/generators_2__3__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__8.mat Added : /Spinach/Spinach core/clusters/generators_3__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_3__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__8.mat Added : /Spinach/Spinach core/clusters/state_vectors_3__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_3__2__2__2__2.mat Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/tolerances.m Deleted : /Spinach/Spinach examples/example_high_spin.m Modified : /Spinach/Spinach experiments/expCOSY.m Deleted : /Spinach/Spinach tests/arbitrary_spin_test.m Added : /Spinach/Spinach tests/deuterium_standard.m (Copy from path: /Spinach/Spinach tests/deuterium_test.m, Revision, 248) Deleted : /Spinach/Spinach tests/deuterium_test.m Added : /Spinach/Spinach tests/gaussian_test.m Added : /Spinach/Spinach tests/high_spin_test.m Modified : /Spinach/Spinach tests/homospoil_test.m Added : /Spinach/Spinach tests/molecules Added : /Spinach/Spinach tests/molecules/strychnine.log Revision: 253 Author: kuprov Date: 16 April 2009 12:34:09 Message: Gaussian03 log parser added. Reads molecular coordinates, hyperfine tensors, g-tensor, shielding tensors and scalar coupling constants (all-atom runs only for the time being). ---- Added : /Spinach/Spinach aux/g03_parse.m Deleted : /Spinach/Spinach aux/pre-programmed pulse sequences Revision: 252 Author: kuprov Date: 15 April 2009 22:30:47 Message: A minor update to expNOESY.m -- removed some spurious output. ---- Modified : /Spinach/Spinach experiments/expNOESY.m Revision: 251 Author: kuprov Date: 14 April 2009 18:24:38 Message: Made the NOESY function run in parallel (defaults to serial on uniprocessor boxes). Realized that the mixing time in gradient-filtered NOESY does not need the coherent Liouvillian, only the relaxation superoperator. The latter has *much* smaller eigenvalues, so the mixing time can be handled in two-three steps instead of thousands. So NOESY can now be computed as fast as COSY. ---- Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2__2.mat Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach experiments/expNOESY.m Modified : /Spinach/Spinach tests/noesy_test.m Modified : /Spinach/Spinach tests/shaped_pulse_test.m Revision: 250 Author: kuprov Date: 13 April 2009 15:13:35 Message: Implemented the gradient-selected NOESY and started updating the relaxation superoperator theory to include quadrupolar processes. Fixed a few bugs in homospoil function and the relaxation superoperator. ---- Added : /Spinach/Documentation/gradient-selected NOESY.pdf Modified : /Spinach/Documentation/relaxation_superoperator.docx Modified : /Spinach/Spinach aux/homospoil.m Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach core/rlx_gen.m Deleted : /Spinach/Spinach experiments/exp2d.m Modified : /Spinach/Spinach experiments/expCOSY.m Added : /Spinach/Spinach experiments/expNOESY.m Added : /Spinach/Spinach tests/noesy_test.m Revision: 249 Author: kuprov Date: 13 April 2009 13:47:11 Message: Fixed a state indexing bug in the relaxation superoperator. Starting to implement NOESY sequence. ---- Modified : /Spinach/Spinach core/rlx_gen.m Revision: 248 Author: kuprov Date: 10 April 2009 12:35:10 Message: Streamlined liouv_gen.m, introduced relaxation superoperator zero tolerance, added a function for generation of thermal equilibrium state vector, updated the NOE example to use it. ---- Modified : /Spinach/Spinach core/liouv_gen.m Added : /Spinach/Spinach core/thermal_dm.m Modified : /Spinach/Spinach core/tolerances.m Modified : /Spinach/Spinach tests/noe_test.m Revision: 247 Author: kuprov Date: 09 April 2009 12:19:31 Message: Implemented relaxation into the recoupling bypass for single-cluster simulations. Added an NOE and DD-CSA test case to the tests directory. ---- Modified : /Spinach/Spinach core/liouv_gen.m Added : /Spinach/Spinach tests/noe_test.m (Copy from path: /Spinach/Spinach tests/rlx_test.m, Revision, 246) Deleted : /Spinach/Spinach tests/rlx_test.m Revision: 246 Author: kuprov Date: 08 April 2009 21:23:27 Message: Implemented a "homospoil" gradient -- a function that wipes away the populations from all states except the zero-projection irreducible spherical tensors. Will be useful in implementing Keeler-style NOESY sequences and a few other places. ---- Added : /Spinach/Spinach aux/homospoil.m Added : /Spinach/Spinach core/clusters/generators_2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2.mat Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/sp_den.m Modified : /Spinach/Spinach core/wigner_d.m Deleted : /Spinach/Spinach examples/example.m Added : /Spinach/Spinach tests/homospoil_test.m Modified : /Spinach/Spinach tests/rlx_test.m Added : /Spinach/Spinach tests/shaped_pulse_test.m (Copy from path: /Spinach/Spinach examples/example.m, Revision, 244) Revision: 245 Author: kuprov Date: 08 April 2009 16:55:29 Message: Modified the relaxation superoperator function. The user can now select from the following options in rlx_gen: 'D' - diagonal terms only 'D+L' - diagonal terms and secular cross-terms between all longitudinal orders 'D+k' - diagonal terms and secular cross terms between spin orders up to order k 'full' - diagonal terms and all secular cross-terms Levels up to D+3 work faster than KP's semantic implementation. Higher orders are probably OK with just the diagonal. ---- Modified : / Added : /Spinach/Spinach core/clusters/generators_2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2.mat Modified : /Spinach/Spinach core/rlx_gen.m Added : /Spinach/Spinach core/sp_den.m Added : /Spinach/Spinach core/wigner_d.m Modified : /Spinach/Spinach examples/big_spin_system.m Deleted : /TODO list.mmap Revision: 244 Author: hannah Date: 19 March 2009 16:27:24 Message: Hopefully the end of my svn related confusion, should now be as indicated for version 242, ie pre_SSR that gives general operators which are then saved. Sorry for the confusion. ---- Replacing : /Spinach/Incoming/Pre_SSR/MARY_general.m Replacing : /Spinach/Incoming/Pre_SSR/MARY_pre_SSR.m Added : /Spinach/Incoming/Pre_SSR/MARY_pre_SSR_kinetics.m Deleted : /Spinach/Incoming/Pre_SSR/ZTE_4000.m Deleted : /Spinach/Incoming/Pre_SSR/lou_ham_hfi_gen.m Deleted : /Spinach/Incoming/Pre_SSR/lou_zeeman_gen.m Added : /Spinach/Incoming/Pre_SSR/pre_SSR_liouv_gen.m Replacing : /Spinach/Incoming/Pre_SSR/state_finder.m Replacing : /Spinach/Incoming/Pre_SSR/state_list_gen.m Replacing : /Spinach/Incoming/Pre_SSR/state_list_gen_sep.m Deleted : /Spinach/Incoming/Pre_SSR/stpos_gen.m Revision: 243 Author: hannah Date: 19 March 2009 15:58:12 Message: Sorry, seem to have added the folder twice. One has now been removed. ---- Deleted : /Spinach/Incoming/Pre_SSR_saving_for_spinach Revision: 242 Author: hannah Date: 19 March 2009 15:56:23 Message: The pre-state space restriction codes have been updated to produce general SSR operators, typical of any spin system with the same number, and type, of spins on each radical. These are then saved so that they need be computed only once. Currently these codes only apply to 1H and 15N. A code to run MARY simulations with ks~=kt has also been added. ---- Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach/MARY_general.m Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach/MARY_pre_SSR.m Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach/MARY_pre_SSR_kinetics.m Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach/pre_SSR_liouv_gen.m Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach/state_finder.m Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach/state_list_gen.m Added : /Spinach/Incoming/Pre_SSR_saving_for_spinach/state_list_gen_sep.m Added : /Spinach/Incoming/Pre_computed_liouvillians Deleted : /Spinach/Incoming/ZTE_2020.m Deleted : /Spinach/Incoming/ZTE_3010.m Deleted : /Spinach/Incoming/ZTE_4000.m Added : /Spinach/Incoming/ZTE_example.m Modified : /Spinach/Incoming/non_spinach_reference.m Deleted : /Spinach/Incoming/state_display.m Revision: 241 Author: kuprov Date: 18 March 2009 18:23:11 Message: Thanks to the vigilance of Hannah's test codes, another bug as been quashed -- T(1,-1) differs from L- by a minus sign. Hannah's tests now check out. ---- Modified : /Spinach/Spinach core/clusters/generators_2__2__2.mat Modified : /Spinach/Spinach core/clusters/state_vectors_2__2__2.mat Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach core/statelist_gen.m Revision: 240 Author: kuprov Date: 18 March 2009 18:03:22 Message: Updated Hannah's test file to use new syntax for custom operators. ---- Modified : /Spinach/Spinach tests/ANISOTROPY_test.m Revision: 239 Author: kuprov Date: 18 March 2009 17:56:18 Message: Fixed the bug in the IST basis set (L+ was renamed into L- and vice versa during the calculation of cluster basis sets). ---- Deleted : /Spinach/Spinach core/clusters/generators_2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2.mat Modified : /Spinach/Spinach core/clusters/generators_2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__3__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__3__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__3__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__4.mat Deleted : /Spinach/Spinach core/clusters/generators_2__8.mat Deleted : /Spinach/Spinach core/clusters/generators_3__2.mat Deleted : /Spinach/Spinach core/clusters/generators_3__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_3__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_3__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_3__2__2__3.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2.mat Modified : /Spinach/Spinach core/clusters/state_vectors_2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__3.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__3.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__3__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__3.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__3__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__3__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__4.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__8.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_3__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_3__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_3__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_3__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_3__2__2__3.mat Modified : /Spinach/Spinach core/statelist_gen.m Revision: 238 Author: hannah Date: 18 March 2009 15:10:35 Message: Test m-files, complete with non spinach reference, for arbitrary isotropic and anisotropic simulations, as requested. ---- Added : /Spinach/Spinach tests/ANISOTROPY_test.m Added : /Spinach/Spinach tests/MARY_full_test.m Revision: 237 Author: hannah Date: 17 March 2009 15:02:13 Message: Just put my presentation from the meeting into Incoming. ---- Added : /Spinach/Incoming/A (brief) Progress Report MArch.ppt Revision: 236 Author: kuprov Date: 15 March 2009 11:54:05 Message: Made the documentation directory more prominent. Please update the docs file with all the changes that you introduce ASAP. ---- Deleted : /Spinach/Debugging Added : /Spinach/Documentation (Copy from path: /Spinach/Spinach core/Spinach core documentation, Revision, 227) Added : /Spinach/Documentation/efficient propagation 1.pdf (Copy from path: /Spinach/Spinach core/Spinach core documentation/efficient propagation 1.pdf, Revision, 233) Added : /Spinach/Documentation/symmetry 1.pdf (Copy from path: /Spinach/Spinach core/Spinach core documentation/symmetry 1.pdf, Revision, 233) Added : /Spinach/Documentation/symmetry 2.pdf (Copy from path: /Spinach/Spinach core/Spinach core documentation/symmetry 2.pdf, Revision, 233) Added : /Spinach/Documentation/symmetry 3.pdf (Copy from path: /Spinach/Spinach core/Spinach core documentation/symmetry 3.pdf, Revision, 233) Revision: 235 Author: kuprov Date: 15 March 2009 11:53:52 Message: Made the documentation directory more prominent. Please update the docs file with all the changes that you introduce ASAP. ---- Deleted : /Spinach/Spinach core/Spinach core documentation Revision: 234 Author: hannah Date: 13 March 2009 16:40:21 Message: Updated pre-SSR codes to be general for spin one nuclei too, also no longer need to change nspins in the state list generator manually. ---- Added : /Spinach/Incoming/Pre_SSR/MARY_general.m Modified : /Spinach/Incoming/Pre_SSR/MARY_pre_SSR.m Added : /Spinach/Incoming/Pre_SSR/ZTE_4000.m Deleted : /Spinach/Incoming/Pre_SSR/hfi_states.m Added : /Spinach/Incoming/Pre_SSR/lou_ham_hfi_gen.m Added : /Spinach/Incoming/Pre_SSR/lou_zeeman_gen.m Deleted : /Spinach/Incoming/Pre_SSR/pm_hfi_2.m Added : /Spinach/Incoming/Pre_SSR/state_list_gen.m Added : /Spinach/Incoming/Pre_SSR/state_list_gen_sep.m Deleted : /Spinach/Incoming/Pre_SSR/statelist_x000.m Deleted : /Spinach/Incoming/Pre_SSR/statelist_x0x0.m Added : /Spinach/Incoming/Pre_SSR/stpos_gen.m Deleted : /Spinach/Incoming/Pre_SSR/zeeman.m Deleted : /Spinach/Incoming/Pre_SSR/zz_hfi_2.m Modified : /Spinach/Incoming/ZTE_2020.m Modified : /Spinach/Incoming/non_spinach_reference.m Revision: 233 Author: kuprov Date: 10 March 2009 16:42:25 Message: Dear All, I am pleased to report that Spinach has been fully generalized to arbitrary spin. So, if anyone fancies a group of four equivalent uranium nuclei (spin 7/2), then just say '235U' in the isotope list and specify your symmetry group. This comes courtesy of the generalized irreducible spherical tensor basis set (of which E, Lz, L+ ,L- are a subset, so nothing changes for spin-1/2). The next core feature to be implemented is group direct product -- currently only one group of equivalent nuclei is supported, because direct products of permutation groups are algebraically tricky. If character table generation for group direct product can be automated efficiently (it definitely looks possible), Spinach will support multiple groups of equivalent uranium (or whatever you like) nuclei in the near future. As I mentioned already, the group theory treatment in Spinach is based on SALCs rather than Clebsch-Gordan expansions, meaning that it is fully general and transparent with respect to SSR, ZTE and particle spin. Best wishes, Ilya. ---- Added : /Spinach/Spinach core/Spinach core documentation/efficient propagation 1.pdf Added : /Spinach/Spinach core/Spinach core documentation/symmetry 1.pdf Added : /Spinach/Spinach core/Spinach core documentation/symmetry 2.pdf Added : /Spinach/Spinach core/Spinach core documentation/symmetry 3.pdf Added : /Spinach/Spinach core/clusters/generators_2.mat Added : /Spinach/Spinach core/clusters/generators_2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__3__2.mat Added : /Spinach/Spinach core/clusters/generators_2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__3__2.mat Added : /Spinach/Spinach core/clusters/generators_2__3__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__4.mat Added : /Spinach/Spinach core/clusters/generators_2__8.mat Added : /Spinach/Spinach core/clusters/generators_3__2.mat Added : /Spinach/Spinach core/clusters/generators_3__2__2.mat Added : /Spinach/Spinach core/clusters/generators_3__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_3__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_3__2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__4.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__8.mat Added : /Spinach/Spinach core/clusters/state_vectors_3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_3__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_3__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_3__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_3__2__2__3.mat Modified : /Spinach/Spinach core/custom_operator.m Modified : /Spinach/Spinach core/nucleus.m Deleted : /Spinach/Spinach core/state2dm.m Modified : /Spinach/Spinach core/state_pregen.m Added : /Spinach/Spinach examples/example_high_spin.m Added : /Spinach/Spinach tests/arbitrary_spin_test.m Revision: 232 Author: kuprov Date: 10 March 2009 12:40:46 Message: Emptied the pre-generated cluster basis sets to prepare for basis set generalization. ---- Deleted : /Spinach/Spinach core/clusters/generators_2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__2__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__2__3__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__3.mat Deleted : /Spinach/Spinach core/clusters/generators_2__3__2.mat Deleted : /Spinach/Spinach core/clusters/generators_2__3__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__2__3.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__3.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__2__3__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__3.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__3__2.mat Deleted : /Spinach/Spinach core/clusters/state_vectors_2__3__2__2.mat Revision: 231 Author: kuprov Date: 10 March 2009 11:46:14 Message: statelist_gen.m updated in preparation for the move to spherical tensor basis (and therefore arbitrary spin) throughout Spinach. ---- Modified : /Spinach/Spinach core/statelist_gen.m Revision: 230 Author: kuprov Date: 05 March 2009 16:45:39 Message: Reduced the output verbosity of custom_operator.m; should implement a verbosity switch at some point. ---- Modified : /Spinach/Spinach core/custom_operator.m Revision: 229 Author: kuprov Date: 26 February 2009 12:48:56 Message: A slight update to MARY function to use the new custom_operator syntax. ---- Modified : /Spinach/Spinach core/custom_operator.m Modified : /Spinach/Spinach core/custom_state.m Modified : /Spinach/Spinach experiments/expMARY.m Revision: 228 Author: kuprov Date: 26 February 2009 12:34:38 Message: Implemented a generalized custom operator generator based on cluster recoupling (was previously combinatorial). Any state on the statelist can now be requested as a Liouville-space operator A(x)E-E(x)A^T. The new procedure is completely agnostic to spin quantum numbers. Can this was the last obstacle left on the path to generalizing the whole of Spinach to arbitrary spin quantum numbers. Proceeding to generalize the basis sets... ---- Deleted : /Spinach/Spinach aux/custom_operator.m Deleted : /Spinach/Spinach aux/custom_state.m Deleted : /Spinach/Spinach aux/operator.m Modified : /Spinach/Spinach core/analytical_zte.m Added : /Spinach/Spinach core/custom_operator.m Added : /Spinach/Spinach core/custom_state.m Modified : /Spinach/Spinach core/decouple.m Modified : /Spinach/Spinach core/irr_sph_ten.m Modified : /Spinach/Spinach core/metric.m Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach core/symmetry_group.m Modified : /Spinach/Spinach core/tolerances.m Modified : /Spinach/Spinach examples/example_cosy.m Added : /Spinach/Spinach tests/custom_operator_test.m Revision: 227 Author: kuprov Date: 25 February 2009 17:31:21 Message: Finally hunted down a very elusive core bug that prevented correct generation of user-specified non-hermitian operators. Proceeding to implement a recoupling-based custom operator generator (Spinach currently uses ad hoc combinatorics which prevents high-spin generalizations). ---- Modified : /Spinach/Spinach core/liouv_gen.m Revision: 226 Author: kuprov Date: 25 February 2009 16:44:44 Message: Added a function to generate single-spin irreducible spherical tensors (based on Ryabov's JMR paper). ---- Added : /Spinach/Spinach core/Spinach core documentation/stevens_operator_basis.pdf Added : /Spinach/Spinach core/irr_sph_ten.m Revision: 225 Author: kuprov Date: 07 February 2009 09:51:37 Message: Cosmetic changes to cluster_gen.m - made the conditional clauses leaner by pulling the repetitive statements out. ---- Modified : /Spinach/Spinach core/cluster_gen.m Revision: 224 Author: kuprov Date: 06 February 2009 21:33:22 Message: Hannah's implementation of MARY crashes. Reverted all Spinach functions to (fully operational) revision 221. Will investigate Hannah's functions tomorrow. ---- Modified : /Spinach/Spinach experiments/expMARY.m Modified : /Spinach/Spinach tests/mary_test_symmetry.m Revision: 223 Author: kuprov Date: 06 February 2009 21:07:22 Message: Reverted Hannah's changes to the core functions -- to avoid breaking Konstantin's code. Core interventions are allowed if and only if the proposed change is fully general with respect to any conceivable purpose. ---- Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/symmetry.m Revision: 222 Author: hannah Date: 06 February 2009 19:01:35 Message: Analytical state space restriction codes added and expMARY updated to follow them. Option added to control whether the singlet states dealt with separately or not. ---- Modified : /Spinach/Incoming/Pre_SSR/MARY_pre_SSR.m Modified : /Spinach/Incoming/Pre_SSR/pm_hfi_2.m Modified : /Spinach/Incoming/Pre_SSR/zeeman.m Modified : /Spinach/Incoming/Pre_SSR/zz_hfi_2.m Added : /Spinach/Spinach aux/preSSR_hfi_pm.m Added : /Spinach/Spinach aux/preSSR_hfi_zz_op.m Added : /Spinach/Spinach aux/preSSR_state_finder.m Added : /Spinach/Spinach aux/preSSR_zeeman.m Modified : /Spinach/Spinach core/create_ss.m Added : /Spinach/Spinach core/liouv_gen_hannah.m Added : /Spinach/Spinach core/state_list_gen_hannah.m Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach experiments/expMARY.m Added : /Spinach/Spinach tests/SSR_mary_test.m Modified : /Spinach/Spinach tests/mary_test_symmetry.m Revision: 221 Author: kuprov Date: 06 February 2009 11:33:13 Message: Implemented a recoupling bypass for the cases where there is just one cluster. Liouvillian is generated using the standard direct product technique in that case. Significant speed-up in MARY simulations. ---- Modified : /Spinach/Spinach core/liouv_gen.m Added : /Spinach/XML markup/SpinXML/Discussion paper on the formalization of pulse sequence description.docx Revision: 220 Author: kuprov Date: 04 February 2009 17:39:54 Message: Updated the MARY script in the exampled directory to use the latest technology. ---- Modified : /Spinach/Spinach examples/example_mary.m Revision: 219 Author: hannah Date: 04 February 2009 13:55:01 Message: It is possible to create the liouvillian initially in a reduced state space. Also, for isotropic hfi the initial states (ie those of the singlet projection operator) do not evolve into communal states, ie each part of the singlet projection operator has its own statelist-which can be produced without making the full liouviliian. Including the symmetry reduction still gives an exact answer to machine precision. And now for the 6 spin system with 4 equivalent H we need a state space of 28 and one of 25 for an exact simulation. ---- Added : /Spinach/Incoming/Pre_SSR Added : /Spinach/Incoming/Pre_SSR/MARY_pre_SSR.m Added : /Spinach/Incoming/Pre_SSR/hfi_states.m Added : /Spinach/Incoming/Pre_SSR/pm_hfi_2.m Added : /Spinach/Incoming/Pre_SSR/state_finder.m Added : /Spinach/Incoming/Pre_SSR/statelist_x000.m Added : /Spinach/Incoming/Pre_SSR/statelist_x0x0.m Added : /Spinach/Incoming/Pre_SSR/zeeman.m Added : /Spinach/Incoming/Pre_SSR/zz_hfi_2.m Modified : /Spinach/Incoming/ZTE_2020.m Modified : /Spinach/Incoming/non_spinach_reference.m Revision: 218 Author: kuprov Date: 04 February 2009 11:28:45 Message: Fixed a few bugs in expMARY.m - replaced OR operators with AND in a couple of conditional clauses. ---- Modified : /Spinach/Spinach experiments/expMARY.m Revision: 217 Author: kuprov Date: 04 February 2009 10:34:11 Message: Realized that MARY dynamics is confined to the fully symmetric irrep. Cleaned up expMARY.m from the remains of the state index diagnostics capability (no longer necessary). ---- Modified : /Spinach/Incoming/ZTE_1000.m Modified : /Spinach/Incoming/ZTE_2020.m Modified : /Spinach/Incoming/ZTE_3010.m Modified : /Spinach/Incoming/ZTE_4000.m Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach experiments/expMARY.m Modified : /Spinach/Spinach tests/mary_test_symmetry.m Revision: 216 Author: kuprov Date: 02 February 2009 18:05:39 Message: Implemented symmetry factorization into the standard MARY function (expMARY.m). The information on how to switch symmetry treatment is in the function header. At the time of writing, a two-electron, four-nucleus system starts off with 4096 states, gets chopped down to 924 states by analytical ZTE, then down to 671 states by numerical ZTE, then down to 191+160+160+160 by the D2h factorizer. Symmetry factorization further cuts the simulation time (mary_test_symmetry.m) from 267 to 84 seconds. The original brute-force 4096x4096 simulation was taking several hours. ---- Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach experiments/expMARY.m Added : /Spinach/Spinach tests/mary_test_symmetry.m Modified : /Spinach/Spinach tests/symmetry_test.m Revision: 215 Author: kuprov Date: 02 February 2009 16:53:44 Message: Some bullet-proofing plus additional diagnostics printout to the command line. A few more groups added. When non-Abelian groups are encountered, the system dynamically decides whether it needs to orthogonalize. ---- Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach tests/symmetry_test.m Revision: 214 Author: kuprov Date: 02 February 2009 15:48:05 Message: Implemented an Abelian group (D2h) for the 4-spin case. MUCH faster, since no need to orthogonalize. D2h recommended for runs with quads of equivalent spins. ---- Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach core/symmetry_group.m Modified : /Spinach/Spinach tests/symmetry_test.m Revision: 213 Author: kuprov Date: 01 February 2009 22:59:42 Message: Pilot implementation of symmetry is up. See symmetry.m, symmetry_test.m and symmetry_group.m files in the core and test directory. Currently using semantic analysis of the state list. ---- Modified : /Spinach/Spinach core/symmetry.m Modified : /Spinach/Spinach tests/symmetry_test.m Revision: 212 Author: kuprov Date: 01 February 2009 16:53:29 Message: Some more coding on the subject of spin equivalence. Realized that full character tables are required, not just class digests. ---- Modified : /Spinach/Spinach core Deleted : /Spinach/Spinach core/group.m Added : /Spinach/Spinach core/symmetry.m Added : /Spinach/Spinach core/symmetry_group.m Added : /Spinach/Spinach tests/symmetry_test.m Modified : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.png Revision: 211 Author: kuprov Date: 01 February 2009 12:13:46 Message: Starting to implement spin equivalence. Hand-coded character tables for 2, 3 and 4 equivalent spins. Will proceed to implement semantic irrep sorting. Should implement a Schur/Frobenius generator for those character tables at some point (10.1002/jcc.540100317). ---- Added : /Spinach/Spinach core/group.m Revision: 210 Author: kuprov Date: 22 January 2009 11:14:17 Message: The clusterizer has been updated to have the baseline description at SSR(4) -- all connected 4-spin subgraphs are included into the cluster list by default. Larger subgraphs are included as necessary: if a spin is directly coupled to more than three others, a bigger cluster will be included. The cluster_gen function has been updated accordingly. State spaces are now bigger by a factor of about two, but still quite manageably sized. Some clipart as well. ---- Added : /Clipart/krylov_subspace_schematic.ai Added : /Clipart/krylov_subspace_schematic.png Added : /Clipart/sequence_compiler.ai Added : /Clipart/sequence_compiler.png Added : /Spinach/Debugging Modified : /Spinach/Spinach aux/diagnostics.m Modified : /Spinach/Spinach core/cluster_gen.m Revision: 209 Author: kuprov Date: 19 January 2009 22:21:12 Message: Added exotic ways of specifying interaction tensors and re-generated the example XML input file. All looks neat and readable now -- all with just three XML classes. Sending out for more consultations. ---- Modified : /Spinach/XML markup/SpinXML/Sample file.xml Modified : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.xsd Revision: 208 Author: kuprov Date: 19 January 2009 22:03:01 Message: A *much* improved XML schema for the spin system description, a result of implementing Malcolm Levitt's comments on the original draft. The pdf of the email exchanges enclosed. Also uploaded the XML schema for MusicXML -- the open source blueprint for the MusicXML format. Not much inspiration from it so far - quite convoluted stuff - but might get some eventually. ---- Deleted : /Spinach/XML markup/Schema - spin system Added : /Spinach/XML markup/SpinXML (Copy from path: /Spinach/XML markup/Schema - spin system, Revision, 207) Added : /Spinach/XML markup/SpinXML/Discussions - Malcolm Levitt.pdf Modified : /Spinach/XML markup/SpinXML/xml_schema_for_spin_system_specification.xsd Added : /Spinach/XML markup/musicxml.xsd Revision: 207 Author: kuprov Date: 14 January 2009 17:34:32 Message: Updated the XML schema for spin system specification. Tensor frame referencing added -- the interaction tensor orientation can now be specified relative to the eigenframe of any other tensor. ---- Added : /Spinach/XML markup/Schema - pulse sequence/pulse sequence schema.xsd Deleted : /Spinach/XML markup/Schema - spin system/XML schema for spin system specification.xsd Added : /Spinach/XML markup/Schema - spin system/xml_schema_for_spin_system_specification.png Added : /Spinach/XML markup/Schema - spin system/xml_schema_for_spin_system_specification.xsd (Copy from path: /Spinach/XML markup/Schema - spin system/XML schema for spin system specification.xsd, Revision, 206) Revision: 206 Author: kuprov Date: 13 January 2009 12:47:37 Message: Path bug fix made consistent -- Konstantin's revision of state_pregen accidentally got committed on top of an earlier fix. ---- Modified : /Spinach/Spinach core/state_pregen.m Revision: 205 Author: kuprov Date: 12 January 2009 17:20:33 Message: Draft XML schema complete for the spin system description. Sending this for discussion to Konstantin & Co, Malcolm Levitt and Paul Hodgkinson. ---- Added : /Spinach/XML markup/Schema - spin system/Sample file.xml Added : /Spinach/XML markup/Schema - spin system/XML schema for spin system specification.xsd Revision: 204 Author: kuprov Date: 12 January 2009 10:42:24 Message: An update to the sequence markup story - a nice piece of software (XML studio) was uploaded, a few new folders created and things sorted a little bit. Proceeding to create XML schema for community preview. ---- Added : /Spinach/XML markup/Discussions Added : /Spinach/XML markup/Discussions/Formal Description of NMR pulse sequences.mmap Added : /Spinach/XML markup/Discussions/Formal Description of NMR pulse sequences.pdf Deleted : /Spinach/XML markup/Formal Description of NMR pulse sequences.mmap Deleted : /Spinach/XML markup/Formal Description of NMR pulse sequences.pdf Added : /Spinach/XML markup/Odds and ends Added : /Spinach/XML markup/Odds and ends/delay.png Added : /Spinach/XML markup/Odds and ends/hard_pi.png Added : /Spinach/XML markup/Odds and ends/hard_pi_half.png Added : /Spinach/XML markup/Odds and ends/hsqc_picture.gif Added : /Spinach/XML markup/Odds and ends/render_sequence.m Added : /Spinach/XML markup/Odds and ends/sequence_elements.ai Added : /Spinach/XML markup/Schema - pulse sequence Added : /Spinach/XML markup/Schema - pulse sequence/pulse_sequence_hsqc.xml Added : /Spinach/XML markup/Schema - spin system Added : /Spinach/XML markup/Software Added : /Spinach/XML markup/Software/XmlStudio.exe Deleted : /Spinach/XML markup/delay.png Deleted : /Spinach/XML markup/hard_pi.png Deleted : /Spinach/XML markup/hard_pi_half.png Deleted : /Spinach/XML markup/hsqc_picture.gif Deleted : /Spinach/XML markup/pulse_sequence_hsqc.xml Deleted : /Spinach/XML markup/render_sequence.m Deleted : /Spinach/XML markup/sequence_elements.ai Revision: 203 Author: kuprov Date: 10 January 2009 18:07:04 Message: An update to the metric function (now includes subspace grouping). A summary of the discussion so far on the subject of standardized pulse sequence and spin system markup. ---- Modified : /Spinach/Spinach core/metric.m Modified : /Spinach/Spinach examples/example_metric.m Added : /Spinach/Spinach tests/metric_test.m Added : /Spinach/XML markup/Formal Description of NMR pulse sequences.mmap Added : /Spinach/XML markup/Formal Description of NMR pulse sequences.pdf Deleted : /Spinach/XML markup/wishes.txt Modified : /TODO list.mmap Revision: 202 Author: pervushin Date: 09 January 2009 03:39:27 Message: Trajectory_kope.m has been changed to provide the local relaxation rates computed as decay of the norm of rho. ---- Modified : /Spinach/Spinach kope/event_table_kope.m Revision: 201 Author: pervushin Date: 09 January 2009 00:37:45 Message: added complete analysis of HNCA 3D with sampling in the Ca indirect dimension. trajectory_kope.m creates an table representation ---- Modified : /Spinach/Spinach core/clusters/generators_2__3__2__2.mat Modified : /Spinach/Spinach core/clusters/state_vectors_2__3__2__2.mat Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDlist_amplitudes.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDlist_amplitudes1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDnames.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDnames1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/events.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/gtable.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/gtable1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/pp_store.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/pp_store_r.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/rho.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/rho1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/compute_all.m Modified : /Spinach/Spinach kope/build_graph_table.m Modified : /Spinach/Spinach kope/centered_pulses_kope.m Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope.m Modified : /Spinach/Spinach kope/delay_kope_dig.m Modified : /Spinach/Spinach kope/event_table_kope.m Modified : /Spinach/Spinach kope/execute_pulse_sequence.m Modified : /Spinach/Spinach kope/pulse_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_dec_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Modified : /Spinach/Spinach kope/reset_pp.m Revision: 200 Author: kuprov Date: 08 January 2009 15:52:05 Message: custom_state.m will alert the user if the state he requests is not in the current state space (it was quietly returning a zero vector before). ---- Modified : /Spinach/Spinach aux/custom_state.m Revision: 199 Author: kuprov Date: 08 January 2009 14:19:53 Message: Trajectory similarity metric function introduced, with an example. All current criteria choices are fairly strict. More lenient similarity criteria in development. ---- Added : /Spinach/Spinach core/clusters/generators_2.mat Added : /Spinach/Spinach core/clusters/generators_2__3__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3__2__2.mat Added : /Spinach/Spinach core/metric.m Added : /Spinach/Spinach examples/big_spin_system.m Added : /Spinach/Spinach examples/example_metric.m Modified : /Spinach/XML markup/pulse_sequence_hsqc.xml Added : /Spinach/XML markup/wishes.txt Added : /TODO list.mmap Revision: 198 Author: kuprov Date: 07 January 2009 12:20:28 Message: 1. Put a minus into the ppm scale in create_ss -- the ppm scale is now the right way around in the pictures. 2. Moved the pulse_acquire.m function into experiments folder. 3. Implemented analytical decoupler (see example_pulse_acquire.m for a usage example). 4. Added a few more pre-computed clusters. ---- Deleted : /Spinach/Spinach aux/pre-programmed pulse sequences/pulse_acquire.m Added : /Spinach/Spinach core/clusters/generators_2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3.mat Modified : /Spinach/Spinach core/create_ss.m Added : /Spinach/Spinach core/decouple.m Modified : /Spinach/Spinach examples/example_pulse_acquire.m Added : /Spinach/Spinach experiments/pulse_acquire.m (Copy from path: /Spinach/Spinach aux/pre-programmed pulse sequences/pulse_acquire.m, Revision, 196) Revision: 197 Author: kuprov Date: 07 January 2009 10:51:00 Message: Fixed the path bug. The program should now correctly handle the situations with nested "Spinach" folders. ---- Modified : /Spinach/Spinach core/create_ss.m Deleted : /Spinach/Spinach core/rte.m Revision: 196 Author: pervushin Date: 07 January 2009 05:27:34 Message: problem in lines 18 to 26 in state_pregen.m. Added deuterium decoupling and deutarated spin system. KOPE ---- Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/generate_spinsys.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/hnca_wC Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/hnca_wC/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/hnca_wC/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/hnca_wC/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/spinsys.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/wave Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/wave/Gauss_5_256.pk Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/wave/Q3.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/wave/Q5.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/wave/Q5tr.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/wave/Sinc1.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D/wave/rect.pk Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/compute_all.asv Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca/rho1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hnca_wN/rho1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/wave/Q3.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/wave/Q5.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/wave/Q5tr.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/wave/Sinc1.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/wave/rect.pk Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/rho1.mat Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope_dig.m Modified : /Spinach/Spinach kope/rlx_gen_kope.m Revision: 195 Author: kuprov Date: 05 January 2009 18:28:51 Message: Cosmetic clean-up of expMARY.m and related functions - moved the optional numerical ZTE to the canonical 'options' variable and updated the downstream code in the Incoming directory. ---- Modified : /Spinach/Incoming/ZTE_1000.m Modified : /Spinach/Incoming/ZTE_2020.m Modified : /Spinach/Incoming/ZTE_3010.m Modified : /Spinach/Incoming/ZTE_4000.m Modified : /Spinach/Spinach experiments/expMARY.m Revision: 194 Author: kuprov Date: 05 January 2009 18:04:48 Message: Halfway to implementing a renderer for XML pulse sequences. The render_sequence.m function (currently incomplete) uses Matlab's implementation of DOM to parse XML and attempts to draw a picture representation of the sequence. Much coding still to be done. ---- Added : /Spinach/XML markup/delay.png Added : /Spinach/XML markup/hard_pi.png Added : /Spinach/XML markup/hard_pi_half.png Modified : /Spinach/XML markup/pulse_sequence_hsqc.xml Added : /Spinach/XML markup/render_sequence.m Added : /Spinach/XML markup/sequence_elements.ai Revision: 193 Author: hannah Date: 05 January 2009 15:24:23 Message: Added a second ZTE "sweep" to the expMARY to further prune down the state space. This does so without reducing accuracy (in the examples used so far). ---- Modified : /Spinach/Incoming/ZTE_1000.m Modified : /Spinach/Incoming/ZTE_2020.m Added : /Spinach/Incoming/ZTE_3010.m Added : /Spinach/Incoming/ZTE_4000.m Added : /Spinach/Incoming/non_spinach_reference.m Added : /Spinach/Incoming/state_display.m Modified : /Spinach/Spinach examples/example_clustering.ppt Modified : /Spinach/Spinach experiments/expMARY.m Modified : /Spinach/Spinach external/modification_for_tensor_coupling/spinach_anisotropy_trial1.m Modified : /Spinach/Spinach tests/sim_pulse_test.m Revision: 192 Author: kuprov Date: 05 January 2009 12:11:20 Message: An initial stab at the XML-based pulse sequence description. The XML as such is pretty straightforward, the devil would be in the parser. ---- Added : /Spinach/XML markup Added : /Spinach/XML markup/hsqc_picture.gif Added : /Spinach/XML markup/pulse_sequence_hsqc.xml Deleted : /Spinach/spin_system_input.txt Revision: 191 Author: pervushin Date: 05 January 2009 00:40:07 Message: hnca with small system calculated including magnetization flowing pathways to be used in diagram preparation. KOPE ---- Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/events.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/pp_store.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/pp_store_r.mat Revision: 190 Author: kuprov Date: 04 January 2009 15:45:52 Message: A wrapper function (expMARY.m) for isotropic singlet-singlet MARY experiments. Includes analytical ZTE by default and deals away with the requirement to have electrons as first two spins. Hannah's examples updated to use the new function -- all much neater now. Some six-spin clusters added to the pre-cooked cluster database. Suggested spin system input file format placed in the root directory -- comments please. ---- Modified : /Spinach/Incoming/ZTE_1000.m Modified : /Spinach/Incoming/ZTE_2020.m Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2__2.mat Modified : /Spinach/Spinach core/create_ss.m Added : /Spinach/Spinach experiments/expMARY.m Modified : /Spinach/Spinach tests/mary_test.m Added : /Spinach/spin_system_input.txt Revision: 189 Author: pervushin Date: 04 January 2009 14:50:12 Message: HNCA experiment is setup. Problem with composite pulse decoupling implementations is temporary alleviated by using high power continuous irradiation. KOPE ---- Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara.bak Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/hmqc/rho1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/compute_all.asv Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-dnietlispach/rho1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1 Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/trosy-st2pt1/rho1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/compute_all.asv Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/pp_store_r.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/spinsys.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/spinsys_relax.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/wave/Q3.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/wave/Q5.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/wave/Q5tr.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/wave/Sinc1.1000 Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/wave/rect.pk Modified : /Spinach/Spinach kope/centered_pulses_kope.asv Modified : /Spinach/Spinach kope/centered_pulses_kope.m Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope_dig.m Modified : /Spinach/Spinach kope/pulse_shaped_dec_kope.m Revision: 188 Author: kuprov Date: 04 January 2009 12:48:25 Message: Disk database implemented for cluster state spaces and generators. state_pregen.m would first look on the disk to see if pre-computed state vectors and generators are available for a given cluster type (all clusters with the same spin multiplicity pattern are algebraically identical). If the file is there, the state vectors and generators are loaded and used without further ado. If the file is not there, everything is computed from scratch and disk database updated. This leads to a considerable speed-up in state_pregen.m, particularly with large clusters. ---- Modified : /Spinach/Spinach aux/delay.m Added : /Spinach/Spinach core/clusters Added : /Spinach/Spinach core/clusters/generators_2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/generators_2__2__2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__3.mat Added : /Spinach/Spinach core/clusters/generators_2__2__3__2.mat Added : /Spinach/Spinach core/clusters/generators_2__3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__2__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__2__3__2.mat Added : /Spinach/Spinach core/clusters/state_vectors_2__3__2.mat Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach examples/example_mary.m Deleted : /Spinach/Spinach tests/delay_test.m Revision: 187 Author: kuprov Date: 30 December 2008 22:51:48 Message: Halfway through the documentation update. Putting the latest functions into the doc file and updating the data structures based on what de facto goes on the current code. Thinking about pre-computing cluster spaces for each unique topology (not too many of those) and storing them on disk. ---- Modified : /Spinach/Spinach core/Spinach core documentation/Data structures.mmap Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Revision: 186 Author: pervushin Date: 29 December 2008 01:43:32 Message: problem with conversion oF SCAlar to matrix bilinear form is fixed in rlx_gen_kope.m. should fit to algebraic core. ---- Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/spinsys.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/spinsys_relax.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/wave Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/wave/Gauss_5_256.pk Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/rlx_gen_kope.m Revision: 185 Author: pervushin Date: 28 December 2008 15:09:37 Message: Updated centered pulse function depending on the number of arguments. This is needed in HNCA experiment. ---- Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara.bak Modified : /Spinach/NMRgenerator kope/tt.mac Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/compute_all.asv Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hmqc/rho1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/compute_all.asv Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/hnca/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/compute_all.asv Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-dnietlispach/rho1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/IDlist_amplitudes1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/IDnames1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/compute_all.asv Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/events.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/gra0.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/gra1.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/gtable1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/pp_store.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/pp_store_r.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/rho1.mat Deleted : /Spinach/Spinach kope/HH_pdb.asv Deleted : /Spinach/Spinach kope/build_graph_table.asv Replacing : /Spinach/Spinach kope/centered_pulses_kope.asv Modified : /Spinach/Spinach kope/centered_pulses_kope.m Deleted : /Spinach/Spinach kope/chop_kope.asv Deleted : /Spinach/Spinach kope/create_pp.asv Modified : /Spinach/Spinach kope/create_pp.m Deleted : /Spinach/Spinach kope/delay_kope.asv Modified : /Spinach/Spinach kope/delay_kope.m Deleted : /Spinach/Spinach kope/event_table_kope.asv Deleted : /Spinach/Spinach kope/execute_pulse_sequence.asv Modified : /Spinach/Spinach kope/fetch_single_transition_kope.m Deleted : /Spinach/Spinach kope/gra.asv Deleted : /Spinach/Spinach kope/kope_hsqc1_tst.asv Deleted : /Spinach/Spinach kope/kope_hsqc1_tst.m Deleted : /Spinach/Spinach kope/kope_hsqc2_tst.asv Deleted : /Spinach/Spinach kope/kope_hsqc2_tst.m Deleted : /Spinach/Spinach kope/kope_hsqc_tst.m Deleted : /Spinach/Spinach kope/kope_shape_tst.m Added : /Spinach/Spinach kope/larger.m Deleted : /Spinach/Spinach kope/pulse_kope.asv Deleted : /Spinach/Spinach kope/pulse_shaped_dec_kope.asv Deleted : /Spinach/Spinach kope/pulse_shaped_kope.asv Deleted : /Spinach/Spinach kope/receiver_kope.asv Deleted : /Spinach/Spinach kope/rlx_gen_kope.asv Deleted : /Spinach/Spinach kope/set_power_kope.asv Deleted : /Spinach/Spinach kope/trajectory_kope.asv Revision: 184 Author: kuprov Date: 27 December 2008 20:55:07 Message: Analytical Zero Track Elimination implemented for singlet-singlet isotropic MARY runs. Hannah's example files updated to use the new syntax. A stub for Redundant Track Elimination added (in writing). ---- Modified : /Spinach/Incoming/ZTE_1000.m Modified : /Spinach/Incoming/ZTE_2020.m Added : /Spinach/Spinach core/analytical_zte.m Added : /Spinach/Spinach core/rte.m Revision: 183 Author: kuprov Date: 26 December 2008 20:29:43 Message: Spinach core and aux functions updated to respect the global tolerance settings. All tolerance parameters documented in the code manual (create_ss section). ---- Modified : /Spinach/Spinach aux/delay.m Modified : /Spinach/Spinach aux/hard_pulse.m Modified : /Spinach/Spinach aux/shaped_pulse.m Modified : /Spinach/Spinach aux/sim_pulse.m Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Revision: 182 Author: kuprov Date: 26 December 2008 15:37:51 Message: Multiple changes related to the introduction of global tolerance control -- the user can now tune all internal tolerances using input parameters. Documentation coming. ---- Modified : /Spinach/Incoming/ZTE_1000.m Modified : /Spinach/Incoming/ZTE_2020.m Modified : /Spinach/Spinach aux/delay.m Deleted : /Spinach/Spinach aux/pre-programmed pulse sequences/cosy.m Modified : /Spinach/Spinach aux/pre-programmed pulse sequences/pulse_acquire.m Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach core/pauli.m Modified : /Spinach/Spinach core/prop_gen.m Modified : /Spinach/Spinach core/prune.m Added : /Spinach/Spinach core/tolerances.m Modified : /Spinach/Spinach examples/example_mary.m Modified : /Spinach/Spinach experiments/expCOSY.m Modified : /Spinach/Spinach tests/delay_test.m Modified : /Spinach/Spinach tests/deuterium_test.m Revision: 181 Author: kuprov Date: 18 December 2008 21:28:50 Message: Zero track elimination subroutine updated, global tolerance control introduced into create_ss function. ---- Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/prune.m Modified : /Spinach/Spinach examples/example_mary.m Revision: 180 Author: hannah Date: 18 December 2008 17:37:06 Message: Added two codes which list the retained and lost spin states during zte. ---- Added : /Spinach/Incoming/ZTE_1000.m Added : /Spinach/Incoming/ZTE_2020.m Revision: 179 Author: kuprov Date: 17 December 2008 05:22:00 Message: Added Zero Track Elimination to the MARY example. In that specific case, the state space dimension is truncated further from 4008 to 179. The calculation result is unaffected. ---- Added : /Spinach/Spinach core/prune.m (Copy from path: /Spinach/Spinach core/prune_pro.m, Revision, 176) Deleted : /Spinach/Spinach core/prune_pro.m Deleted : /Spinach/Spinach core/spinsys_1.mat Modified : /Spinach/Spinach examples/example_mary.m Revision: 178 Author: pervushin Date: 16 December 2008 22:07:50 Message: Sim_pulse is integrated in to the work flow of analysis. Bruker syntax is translated and executed fro 3 spin systems ---- Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/compute_all.m Deleted : /Spinach/Spinach kope/IDlist_amplitudes.mat Deleted : /Spinach/Spinach kope/IDlist_amplitudes1.mat Deleted : /Spinach/Spinach kope/IDnames.mat Deleted : /Spinach/Spinach kope/IDnames1.mat Added : /Spinach/Spinach kope/centered_pulses_kope.asv Added : /Spinach/Spinach kope/centered_pulses_kope.m Deleted : /Spinach/Spinach kope/chnaged.txt Deleted : /Spinach/Spinach kope/events.mat Deleted : /Spinach/Spinach kope/exps/HNCO.asv Deleted : /Spinach/Spinach kope/exps/HNCO.m Deleted : /Spinach/Spinach kope/exps/header_s32.txt Deleted : /Spinach/Spinach kope/exps/hmqc_watergate_sp.m Deleted : /Spinach/Spinach kope/exps/hsqc_13C.m Deleted : /Spinach/Spinach kope/exps/hsqc_15N.m Deleted : /Spinach/Spinach kope/exps/hsqc_15N__events.mat Deleted : /Spinach/Spinach kope/exps/hsqc_15N__pp.mat Deleted : /Spinach/Spinach kope/exps/hsqc_15N__v.mat Deleted : /Spinach/Spinach kope/exps/hsqc_15N_r.mat Deleted : /Spinach/Spinach kope/exps/hsqc_15N_r_events.mat Deleted : /Spinach/Spinach kope/exps/hsqc_15N_r_pp.mat Deleted : /Spinach/Spinach kope/exps/hsqc_15N_r_v.mat Deleted : /Spinach/Spinach kope/exps/hsqc_15N_s11.asv Deleted : /Spinach/Spinach kope/exps/hsqc_15N_s11.m Deleted : /Spinach/Spinach kope/exps/offsets_ppm.txt Deleted : /Spinach/Spinach kope/exps/spinsys_1.mat Deleted : /Spinach/Spinach kope/exps/spinsys_1_r.mat Deleted : /Spinach/Spinach kope/exps/trosy_HNCA.m Deleted : /Spinach/Spinach kope/exps/trosy_HNCACB.m Deleted : /Spinach/Spinach kope/exps/tst.asv Deleted : /Spinach/Spinach kope/exps/tst.m Deleted : /Spinach/Spinach kope/gtable.mat Deleted : /Spinach/Spinach kope/gtable1.mat Deleted : /Spinach/Spinach kope/header_11spins.txt Deleted : /Spinach/Spinach kope/hsqc_15N__events.mat Deleted : /Spinach/Spinach kope/hsqc_15N__pp.mat Deleted : /Spinach/Spinach kope/hsqc_15N__v.mat Deleted : /Spinach/Spinach kope/hsqc_15N_r_events.mat Deleted : /Spinach/Spinach kope/hsqc_15N_r_pp.mat Deleted : /Spinach/Spinach kope/hsqc_15N_r_v.mat Deleted : /Spinach/Spinach kope/non_deut_32spin_header.txt Deleted : /Spinach/Spinach kope/pp_store.mat Deleted : /Spinach/Spinach kope/pp_store_r.mat Deleted : /Spinach/Spinach kope/rho.mat Deleted : /Spinach/Spinach kope/rho1.mat Deleted : /Spinach/Spinach kope/spinsys_1.mat Deleted : /Spinach/Spinach kope/spinsys_1_r.mat Deleted : /Spinach/Spinach kope/tt.txt Revision: 177 Author: pervushin Date: 15 December 2008 13:13:51 Message: Trosy component selection and fixes in fetch function. Change of workflow, generate spin systems seprately from the main. ---- Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara.bak Modified : /Spinach/NMRgenerator kope/tt.mac Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/generate_spinsys.asv Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/generate_spinsys.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/spinsys.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/compute_all.asv Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/trosy-st2pt/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/wave Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/wave/Gauss_5_256.pk Modified : /Spinach/Spinach kope/create_pp.m Added : /Spinach/Spinach kope/fetch_single_transition_kope.m Revision: 176 Author: kuprov Date: 13 December 2008 16:26:20 Message: create_ss and cluster_ham functions have been updated to reflect the changes requested by Hannah - coherent tensor couplings are now accepted as matrices if the user wishes to supply them. See the code manual for the detailed description of how to supply coherent tensor couplings. Major clean-up done inside create_ss, many arguments are now optional - Spinach would not insist on supplying spin names, for example. ---- Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Modified : /Spinach/Spinach core/cluster_ham.m Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach tests/sim_pulse_test.m Revision: 175 Author: pervushin Date: 13 December 2008 12:40:03 Message: Dipolar density calculations are added to match those in rela protein (NS3) and in simulated spin system. Restructuring of experiment input. ---- Added : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara Added : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_27.cara.bak Added : /Spinach/Spinach kope/2JLQ_NS3.pdb Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/compute_all.asv Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/gra1.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/output.txt Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/rho1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/spinsys_1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/15N-HSQC-PFG/spinsys_1_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/generate_spinsys.m Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H/spinsys.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/generate_spinsys.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/spinsys.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/spinsys_relax.mat Added : /Spinach/Spinach kope/HH_densities_NS3.txt Added : /Spinach/Spinach kope/HH_pdb.asv Added : /Spinach/Spinach kope/HH_pdb.m Modified : /Spinach/Spinach kope/Jr.m Added : /Spinach/Spinach kope/hBD3.pdb Added : /Spinach/Spinach kope/rlx_gen_kope.asv Modified : /Spinach/Spinach kope/rlx_gen_kope.m Revision: 174 Author: hannah Date: 12 December 2008 12:51:27 Message: As I wanted to do anisotropic spin chemistry simulations I have modified the structure making and cluster_ham codes to allow for non scalar interactions, that is using tensors. I have saved this under new names so as not to disrupt the core (while I think I've set it so you can specify scalar or tensor input with the former running just as before, I'm not totally confident and don't want to mess anything up -though tests of anisotropy and mary plots seem to work nicely). A couple of examples of anisotropy plots are also included. ---- Added : /Spinach/Spinach external/modification_for_tensor_coupling Added : /Spinach/Spinach external/modification_for_tensor_coupling/cluster_ham2.m Added : /Spinach/Spinach external/modification_for_tensor_coupling/create_ss2.m Added : /Spinach/Spinach external/modification_for_tensor_coupling/referencefor_trial2.m Added : /Spinach/Spinach external/modification_for_tensor_coupling/spinach_anisotropy_trial1.m Added : /Spinach/Spinach external/modification_for_tensor_coupling/spinach_anisotropy_trial2.m Revision: 173 Author: kuprov Date: 07 December 2008 22:46:50 Message: sim_pulse.m function is tested and ready to use. See the file header and the sim_pulse_test.m function in the tests directory for the example of usage. Common grid resampling is used, making sure that accuracy is not lost in the process (the grid is chosen so that the finest pulse is sampled at its original sampling rate, all the rest is interpolated up to that resolution). ---- Modified : /Spinach/Spinach aux/sim_pulse.m Modified : /Spinach/Spinach tests/sim_pulse_test.m Revision: 172 Author: kuprov Date: 07 December 2008 21:57:00 Message: Done implementing sim_pulse, some testing remains. All shaped_pulse results are currently reproduced, trying actual simultaneous pulses. ---- Modified : /Spinach/Spinach aux/sim_pulse.m Added : /Spinach/Spinach tests/sim_pulse_test.m Revision: 171 Author: pervushin Date: 07 December 2008 02:57:23 Message: complete analysis of HSQC experiment using small -11- spin system. This is to be repeated with 32 spins ---- Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDlist_amplitudes.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDlist_amplitudes1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDnames.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDnames1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/compute_all.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/events.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/gra1.m Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/gtable.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/pathway0.pdf Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/pathway1.pdf Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/pp_store.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/pp_store_r.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/rho.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/rho1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/spinsys_1.mat Modified : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/spinsys_1_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/trajectory.txt Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/tst.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/wave Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/wave/Gauss_5_256.pk Revision: 170 Author: pervushin Date: 07 December 2008 02:53:13 Message: Features built on the top of Spinach: 0. Translation of experiments from external repository (built previously by me) to Spinach. 1. Sampling along indirectly acquired dimensions. 1.1 quantization of delays to shorter periods in roder to better sample the trajectory. 2. Checkpoints - selectors of the specified spin states at certain points of the pulse sequence. Maybe it is better to call them bootstraps. 3. Graph analysis of magnetization flows. 4. Analysis of relaxation losses along the trajectory. ---- Modified : /Spinach/Spinach kope/build_graph_table.m Modified : /Spinach/Spinach kope/create_pp.m Revision: 169 Author: kuprov Date: 06 December 2008 17:13:30 Message: Minor changes related to the introduction of the spinnames field (some test files updated) and to the fact that the cluster Hamiltonians are now sparse by default. ---- Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach tests/mary_test.m Modified : /Spinach/Spinach tests/rlx_test.m Revision: 168 Author: pervushin Date: 05 December 2008 12:05:09 Message: A complete example of analysis of real Bruker experiment with graph of magnetization flow is prepared. More are to follow. ---- Added : /Spinach/Spinach aux/pre-programmed pulse sequences/cosy.m Added : /Spinach/Spinach core/spinsys_1.mat Added : /Spinach/Spinach kope/EXPERIMENTS Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_D Added : /Spinach/Spinach kope/EXPERIMENTS/Large_spin_system_H Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDlist_amplitudes1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDnames.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/IDnames1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/compute_all.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/events.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/gra0.m Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/gtable.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/gtable1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/pp_store.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/pp_store_r.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/rho.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/rho1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/spinsys_1.mat Added : /Spinach/Spinach kope/EXPERIMENTS/Small_spin_system/INEPT_HN/spinsys_1_r.mat Modified : /Spinach/Spinach kope/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/IDlist_amplitudes1.mat Modified : /Spinach/Spinach kope/IDnames.mat Added : /Spinach/Spinach kope/IDnames1.mat Modified : /Spinach/Spinach kope/build_graph_table.m Added : /Spinach/Spinach kope/chnaged.txt Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope_dig.m Modified : /Spinach/Spinach kope/event_table_kope.asv Modified : /Spinach/Spinach kope/event_table_kope.m Modified : /Spinach/Spinach kope/events.mat Added : /Spinach/Spinach kope/execute_pulse_sequence.asv Modified : /Spinach/Spinach kope/execute_pulse_sequence.m Added : /Spinach/Spinach kope/exps/hsqc_15N__events.mat Added : /Spinach/Spinach kope/exps/hsqc_15N__pp.mat Added : /Spinach/Spinach kope/exps/hsqc_15N__v.mat Added : /Spinach/Spinach kope/exps/hsqc_15N_r_pp.mat Added : /Spinach/Spinach kope/exps/hsqc_15N_r_v.mat Modified : /Spinach/Spinach kope/exps/hsqc_15N_s11.asv Modified : /Spinach/Spinach kope/exps/hsqc_15N_s11.m Added : /Spinach/Spinach kope/exps/spinsys_1.mat Added : /Spinach/Spinach kope/exps/tst.asv Added : /Spinach/Spinach kope/exps/tst.m Modified : /Spinach/Spinach kope/fetch_state_kope.m Added : /Spinach/Spinach kope/gra.asv Modified : /Spinach/Spinach kope/gra.m Modified : /Spinach/Spinach kope/gtable.mat Added : /Spinach/Spinach kope/gtable1.mat Added : /Spinach/Spinach kope/hsqc_15N__events.mat Added : /Spinach/Spinach kope/hsqc_15N__pp.mat Added : /Spinach/Spinach kope/hsqc_15N__v.mat Added : /Spinach/Spinach kope/hsqc_15N_r_events.mat Added : /Spinach/Spinach kope/hsqc_15N_r_pp.mat Added : /Spinach/Spinach kope/hsqc_15N_r_v.mat Modified : /Spinach/Spinach kope/kope_hsqc2_tst.asv Modified : /Spinach/Spinach kope/kope_hsqc2_tst.m Modified : /Spinach/Spinach kope/pp_store.mat Modified : /Spinach/Spinach kope/pp_store_r.mat Modified : /Spinach/Spinach kope/pulse_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Added : /Spinach/Spinach kope/reset_pp.m Added : /Spinach/Spinach kope/rho.mat Added : /Spinach/Spinach kope/rho1.mat Modified : /Spinach/Spinach kope/set_power_kope.m Modified : /Spinach/Spinach kope/spinsys_1.mat Added : /Spinach/Spinach kope/tt.txt Revision: 167 Author: kuprov Date: 03 December 2008 22:33:30 Message: Halfway through to an implementation of parallel soft pulses on multiple nuclei. Going down the common-grid resampling path, where the common grid duration and discretization are determined by the longest and the finest pulse respectively. Quite a twister currently... ---- Added : /Spinach/Spinach aux/sim_pulse.m Revision: 166 Author: kuprov Date: 02 December 2008 16:21:58 Message: Cleaned up the offset function, updated all example files to include the names of the spins into the program body (should probably make it non-compulsory in future), added a few scribbles about MARY re-encounter functions. ---- Added : /Miscellaneous/MARY theory Added : /Miscellaneous/MARY theory/re-encounter function 1.jpg Added : /Miscellaneous/MARY theory/re-encounter function 2.jpg Modified : /Spinach/Spinach aux/offset.m Modified : /Spinach/Spinach core/create_ss.m Deleted : /Spinach/Spinach examples/example.asv Modified : /Spinach/Spinach examples/example.m Modified : /Spinach/Spinach examples/example_cosy.m Modified : /Spinach/Spinach examples/example_mary.m Modified : /Spinach/Spinach examples/example_pulse_acquire.m Revision: 165 Author: pervushin Date: 01 December 2008 09:33:06 Message: offset.m is modified to take input values in Hz or ppm. General framework for analysis of NMR experiment in NMRgenerator database is provided ---- Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_26.cara Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_26.cara.bak Modified : /Spinach/NMRgenerator kope/tt.mac Modified : /Spinach/Spinach aux/offset.m Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope.m Modified : /Spinach/Spinach kope/execute_pulse_sequence.m Modified : /Spinach/Spinach kope/exps/hsqc_15N_s11.asv Modified : /Spinach/Spinach kope/exps/hsqc_15N_s11.m Modified : /Spinach/Spinach kope/pulse_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Revision: 164 Author: pervushin Date: 28 November 2008 03:27:01 Message: sparse matrices converted to full in diagnostics. several bugs have been fixed. Delays can be performed in steps. ---- Modified : /Spinach/Spinach aux/diagnostics.m Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope.m Modified : /Spinach/Spinach kope/execute_pulse_sequence.m Modified : /Spinach/Spinach kope/exps/hsqc_15N_s11.m Modified : /Spinach/Spinach kope/kope_hsqc2_tst.m Modified : /Spinach/Spinach kope/spinsys_1_r.mat Revision: 163 Author: pervushin Date: 28 November 2008 02:55:04 Message: Setups for several NMR experiments have been added. Magnetization flow graph routines added. p@trosy.com ---- Modified : /Spinach/NMRgenerator kope/tt.mac Modified : /Spinach/Spinach core/create_ss.m Added : /Spinach/Spinach kope/IDlist_amplitudes.mat Added : /Spinach/Spinach kope/IDnames.mat Modified : /Spinach/Spinach kope/build_graph_table.asv Modified : /Spinach/Spinach kope/build_graph_table.m Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope.asv Modified : /Spinach/Spinach kope/delay_kope.m Modified : /Spinach/Spinach kope/delay_kope_dig.m Added : /Spinach/Spinach kope/exps Added : /Spinach/Spinach kope/exps/HNCO.asv Added : /Spinach/Spinach kope/exps/HNCO.m Added : /Spinach/Spinach kope/exps/header_s32.txt Added : /Spinach/Spinach kope/exps/hmqc_watergate_sp.m Added : /Spinach/Spinach kope/exps/hsqc_13C.m Added : /Spinach/Spinach kope/exps/hsqc_15N.m Added : /Spinach/Spinach kope/exps/hsqc_15N_r.mat Added : /Spinach/Spinach kope/exps/hsqc_15N_r_events.mat Added : /Spinach/Spinach kope/exps/hsqc_15N_s11.asv Added : /Spinach/Spinach kope/exps/hsqc_15N_s11.m Added : /Spinach/Spinach kope/exps/offsets_ppm.txt Added : /Spinach/Spinach kope/exps/spinsys_1_r.mat Added : /Spinach/Spinach kope/exps/trosy_HNCA.m Added : /Spinach/Spinach kope/exps/trosy_HNCACB.m Modified : /Spinach/Spinach kope/gra.m Added : /Spinach/Spinach kope/gtable.mat Modified : /Spinach/Spinach kope/kope_hsqc2_tst.m Modified : /Spinach/Spinach kope/pp_store_r.mat Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Modified : /Spinach/Spinach kope/spinsys_1_r.mat Revision: 162 Author: kuprov Date: 27 November 2008 11:27:42 Message: Made Spinach core directory require a lock for edits - seems reasonable given the amount of stuff that currently depends on it. Lock can be obtained via the SVN menu. Changed the repository policy to demand at least 100 characters in the log entry before a change can be committed. ---- Modified : / Modified : /Clipart Modified : /Miscellaneous Modified : /Miscellaneous/Application 1 Modified : /Miscellaneous/Discussions Modified : /Miscellaneous/Dumpster Modified : /Miscellaneous/Dumpster/Cluster size dependence figure Modified : /Miscellaneous/Dumpster/Scaling Modified : /Miscellaneous/Lanczos pruning Modified : /Miscellaneous/Lanczos pruning/illustrations Modified : /Miscellaneous/Literature Modified : /Miscellaneous/Literature/Buevich Modified : /Miscellaneous/Literature/IR multimode analogy Modified : /Miscellaneous/Literature/density matrix renormalization Modified : /Miscellaneous/MEX files Modified : /Miscellaneous/SVD pruning Modified : /Miscellaneous/Sparse matrix exponentials Modified : /Miscellaneous/Spinach logo Modified : /Miscellaneous/ZTE pruning Modified : /Miscellaneous/code from Olga Modified : /Miscellaneous/code from Olga/TheProgram Modified : /Miscellaneous/code from Olga/gaussian_log_files Modified : /Miscellaneous/code from Olga/input_files Modified : /Miscellaneous/code from Olga/results Modified : /Miscellaneous/householder tridiagonalization Modified : /Miscellaneous/old code Modified : /Miscellaneous/strychnine Modified : /Spinach Modified : /Spinach/Incoming Modified : /Spinach/NMRgenerator kope Modified : /Spinach/Spinach aux Modified : /Spinach/Spinach aux/pre-programmed pulse sequences Modified : /Spinach/Spinach aux/wave Modified : /Spinach/Spinach core Modified : /Spinach/Spinach core/Spinach core documentation Modified : /Spinach/Spinach core/Spinach core documentation/Data structures.mmap Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Modified : /Spinach/Spinach core/Spinach core documentation/relaxation_superoperator.docx Modified : /Spinach/Spinach core/Spinach core documentation/relaxation_superoperator.pdf Modified : /Spinach/Spinach core/cluster_gen.m Modified : /Spinach/Spinach core/cluster_ham.m Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/expv.m Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach core/nucleus.m Modified : /Spinach/Spinach core/pauli.m Modified : /Spinach/Spinach core/prop_gen.m Modified : /Spinach/Spinach core/prune_pro.m Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/sanity_check.m Modified : /Spinach/Spinach core/state2dm.m Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach core/statelist_gen.m Modified : /Spinach/Spinach examples Modified : /Spinach/Spinach experiments Modified : /Spinach/Spinach experiments/mary_literature Modified : /Spinach/Spinach external Modified : /Spinach/Spinach kope Modified : /Spinach/Spinach kope/wave Modified : /Spinach/Spinach tests Revision: 161 Author: kuprov Date: 25 November 2008 22:04:03 Message: All bugs ironed in MARY, validation pass. ---- Modified : /Spinach/Spinach examples/example_mary.m Modified : /Spinach/Spinach tests/mary_test.m Revision: 160 Author: kuprov Date: 25 November 2008 21:49:44 Message: A dramatic speed-up for MARY simulations, a bug discovered (factor of ten seems to be lost somewhere in field/time ratio). Investigating... ---- Modified : /Spinach/Spinach examples/example_mary.m Modified : /Spinach/Spinach tests/mary_test.m Revision: 159 Author: kuprov Date: 25 November 2008 17:14:34 Message: MARY validation test using CRT's 1998 paper, halfway done (is her X axis correct in Fig 3?) ---- Added : /Spinach/Spinach experiments/mary_literature Added : /Spinach/Spinach experiments/mary_literature/484287_731197559_713830074.pdf Added : /Spinach/Spinach experiments/mary_literature/e077602.pdf Added : /Spinach/Spinach experiments/mary_literature/ja068209l.pdf Added : /Spinach/Spinach experiments/mary_literature/jp050765z.pdf Added : /Spinach/Spinach experiments/mary_literature/till_et_al.pdf Added : /Spinach/Spinach tests/mary_test.m Revision: 158 Author: kuprov Date: 25 November 2008 14:43:59 Message: m ---- Added : /Spinach/Spinach experiments/expCOSY.m Revision: 157 Author: kuprov Date: 25 November 2008 14:43:41 Message: m ---- Deleted : /Spinach/Spinach experiments/expCosy.m Revision: 156 Author: kuprov Date: 25 November 2008 14:41:25 Message: Deleted the nested repository (not a good idea). ---- Deleted : /README.txt Deleted : /conf Deleted : /db Deleted : /format Deleted : /hooks Deleted : /locks Revision: 155 Author: russell Date: 25 November 2008 02:01:56 Message: ---- Added : /README.txt Added : /conf Added : /conf/authz Added : /conf/passwd Added : /conf/svnserve.conf Added : /db Added : /db/current Added : /db/format Added : /db/fs-type Added : /db/revprops Added : /db/revprops/0 Added : /db/revprops/0/0 Added : /db/revs Added : /db/revs/0 Added : /db/revs/0/0 Added : /db/transactions Added : /db/txn-current Added : /db/txn-current-lock Added : /db/txn-protorevs Added : /db/uuid Added : /db/write-lock Added : /format Added : /hooks Added : /hooks/post-commit.tmpl Added : /hooks/post-lock.tmpl Added : /hooks/post-revprop-change.tmpl Added : /hooks/post-unlock.tmpl Added : /hooks/pre-commit.tmpl Added : /hooks/pre-lock.tmpl Added : /hooks/pre-revprop-change.tmpl Added : /hooks/pre-unlock.tmpl Added : /hooks/start-commit.tmpl Added : /locks Added : /locks/db-logs.lock Added : /locks/db.lock Revision: 154 Author: kuprov Date: 24 November 2008 20:48:15 Message: Minor refinements and documentation for the COSY code. ---- Modified : /Spinach/Spinach aux/custom_state.m Deleted : /Spinach/Spinach aux/pre-programmed pulse sequences/cosy.m Modified : /Spinach/Spinach examples/example_cosy.m Deleted : /Spinach/Spinach experiments/exp2d.asv Modified : /Spinach/Spinach experiments/exp2d.m Deleted : /Spinach/Spinach experiments/expCosy.asv Modified : /Spinach/Spinach experiments/expCosy.m Revision: 153 Author: gareth Date: 24 November 2008 13:25:05 Message: Created a "Spinach experiments" folder, split cosy into expCosy and exp2s. Added a phase cycle. ---- Modified : /Spinach/Spinach examples/example_cosy.m Added : /Spinach/Spinach experiments Added : /Spinach/Spinach experiments/exp2d.asv Added : /Spinach/Spinach experiments/exp2d.m Added : /Spinach/Spinach experiments/expCosy.asv Added : /Spinach/Spinach experiments/expCosy.m Revision: 152 Author: pervushin Date: 24 November 2008 10:21:07 Message: ---- Added : /Spinach/Spinach kope/build_graph_table.asv Added : /Spinach/Spinach kope/build_graph_table.m Added : /Spinach/Spinach kope/gra.m Revision: 151 Author: pervushin Date: 24 November 2008 10:20:38 Message: ---- Modified : /Spinach/Spinach kope/execute_pulse_sequence.m Modified : /Spinach/Spinach kope/kope_hsqc2_tst.m Modified : /Spinach/Spinach kope/pp_store_r.mat Revision: 150 Author: pervushin Date: 23 November 2008 14:05:44 Message: ---- Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_26.cara Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_26.cara.bak Modified : /Spinach/NMRgenerator kope/tt.mac Added : /Spinach/Spinach kope/create_pp.asv Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope.m Added : /Spinach/Spinach kope/execute_pulse_sequence.m Added : /Spinach/Spinach kope/kope_hsqc2_tst.asv Added : /Spinach/Spinach kope/kope_hsqc2_tst.m Modified : /Spinach/Spinach kope/pp_store_r.mat Modified : /Spinach/Spinach kope/pulse_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Revision: 149 Author: kuprov Date: 22 November 2008 18:17:47 Message: A large number of technical changes related to the introduction of electrons to enable SSR calculation of spin dynamics in radical pairs. One global parameter name switch: coh.J -> coh.scalar, instances renamed everywhere. ---- Added : /Spinach/Spinach aux/gauss2mhz.m Modified : /Spinach/Spinach aux/protein.m Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/nucleus.m Modified : /Spinach/Spinach examples/example.m Modified : /Spinach/Spinach examples/example_cosy.m Added : /Spinach/Spinach examples/example_mary.m Modified : /Spinach/Spinach examples/example_pulse_acquire.m Modified : /Spinach/Spinach kope/deut_spin_header.txt Modified : /Spinach/Spinach kope/example.m Modified : /Spinach/Spinach kope/example_sp.m Modified : /Spinach/Spinach kope/header_11spins.txt Modified : /Spinach/Spinach kope/kope_hsqc1_tst.m Modified : /Spinach/Spinach kope/kope_hsqc_tst.m Modified : /Spinach/Spinach kope/kope_shape_tst.m Modified : /Spinach/Spinach kope/non_deut_32spin_header.txt Modified : /Spinach/Spinach tests/rlx_test.m Revision: 148 Author: kuprov Date: 21 November 2008 17:12:18 Message: Removed global Lx and Ly from liouv_gen.m -- given the multi-isotope nature of most runs, the global Lx and Ly operators no longer seem necessary. The custom_operator.m function should suffice from now onwards. ---- Modified : /Spinach/Spinach core/liouv_gen.m Revision: 147 Author: kuprov Date: 21 November 2008 17:04:46 Message: cluster_ham.m now uses the intra-cluster generators pre-computed in state_pregen.m. Some speed-up as a result. This also eliminates a scalar coupling amplitude bug with spins larger than 1/2. ---- Modified : /Spinach/Spinach core/cluster_ham.m Revision: 146 Author: russell Date: 21 November 2008 10:42:15 Message: ---- Added : /Spinach/Spinach kope/delay_kope_dig.m Revision: 145 Author: kuprov Date: 20 November 2008 14:58:20 Message: Implemented the offset function. See the offset.m file in the aux directory. Deleted redundant instances of the diagnostics function. ---- Added : /Spinach/Spinach aux/offset.m Deleted : /Spinach/Spinach kope/diagnostics.m Deleted : /Spinach/Spinach kope/diagnostics_kope.asv Deleted : /Spinach/Spinach kope/diagnostics_kope.m Revision: 144 Author: kuprov Date: 20 November 2008 12:33:12 Message: Cleaned up the diagnostics code. ---- Modified : /Spinach/Spinach aux/diagnostics.m Revision: 143 Author: kuprov Date: 20 November 2008 12:08:35 Message: Hard pulse function implemented. See hard_pulse.m in the aux directory. ---- Added : /Spinach/Spinach aux/hard_pulse.m Revision: 142 Author: kuprov Date: 20 November 2008 10:18:25 Message: Delay operator implemented. See delay.m in the aux directory. ---- Added : /Spinach/Spinach aux/delay.m Added : /Spinach/Spinach tests/delay_test.m Revision: 141 Author: pervushin Date: 20 November 2008 08:59:36 Message: ---- Added : /Spinach/Spinach aux/pad.m Added : /Spinach/Spinach kope/diagnostics.m Modified : /Spinach/Spinach kope/event_table_kope.asv Modified : /Spinach/Spinach kope/event_table_kope.m Added : /Spinach/Spinach kope/events.mat Modified : /Spinach/Spinach kope/kope_hsqc1_tst.m Added : /Spinach/Spinach kope/pp_store_r.mat Added : /Spinach/Spinach kope/spinsys_1_r.mat Modified : /Spinach/Spinach kope/trajectory_kope.m Revision: 140 Author: russell Date: 20 November 2008 01:19:48 Message: ---- Modified : /Spinach/Spinach kope/deut_spin_header.txt Revision: 139 Author: russell Date: 20 November 2008 00:58:22 Message: ---- Modified : /Spinach/Spinach kope/deut_spin_header.txt Revision: 138 Author: russell Date: 19 November 2008 10:41:29 Message: ---- Added : /Spinach/Spinach kope/deut_spin_header.txt Added : /Spinach/Spinach kope/non_deut_32spin_header.txt Revision: 137 Author: pervushin Date: 19 November 2008 02:47:46 Message: diagnostics.m in AUX directory is modified to output the number of the spin states less than 'window' and with amplitudes more than 0.01 (this threshold is currently fixed). Spin states are equipped with IDs and relaxationally coupled network. Currently this is output-ed irrespective of the rlxflag. ---- Modified : /Spinach/Spinach aux/diagnostics.m Modified : /Spinach/Spinach kope/kope_hsqc1_tst.m Revision: 136 Author: kuprov Date: 17 November 2008 08:54:41 Message: Added some PowerPoint and Adobe Illustrator clipart, for use in various talks and posters. ---- Added : /Clipart Added : /Clipart/cluster_recoupling.ai Added : /Clipart/lecture.ppt Added : /Clipart/poster.ai Added : /Clipart/scaling_graph.ai Added : /Clipart/ssr_schematic.ai Revision: 135 Author: kuprov Date: 16 November 2008 20:27:07 Message: Fixed the spin-1 bug -- traced to the orthogonality issue between Lz2 and E in the spin-1 state subspace. Resolved by orthogonalization -- replaced Lz2 by Lz2-2/3. The metric tensor becomes a unit matrix and neat recoupling is achieved. See pulse_acquire_example for a test case. ---- Modified : /Spinach/Spinach core/state2dm.m Modified : /Spinach/Spinach examples/example_pulse_acquire.m Modified : /Spinach/Spinach tests/deuterium_test.m Revision: 134 Author: kuprov Date: 16 November 2008 14:39:10 Message: Spin-1 nuclei have been implemented, but do not produce quantitatively correct results yet - a normalization problem I suspect, investigating... The diagnostics subroutine has been modified to reflect the existence of states beyond Lz, L+ and L-. An exact simulation of a 1H-2H two-spin system has been added to the tests directory -- will be needed to pin down the bug. ---- Modified : /Spinach/Spinach aux/diagnostics.m Added : /Spinach/Spinach aux/pre-programmed pulse sequences/pulse_acquire.m Modified : /Spinach/Spinach core/nucleus.m Added : /Spinach/Spinach examples/example_pulse_acquire.m Added : /Spinach/Spinach tests/deuterium_test.m Revision: 133 Author: kuprov Date: 15 November 2008 20:37:09 Message: Another go at the documentation. ---- Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Revision: 132 Author: kuprov Date: 15 November 2008 17:15:38 Message: Another go at the documentation. ---- Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Revision: 131 Author: kuprov Date: 15 November 2008 08:30:05 Message: Another go at the docs. ---- Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Revision: 130 Author: kuprov Date: 14 November 2008 18:14:04 Message: Another go at the docs. ---- Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Revision: 129 Author: kuprov Date: 13 November 2008 12:44:56 Message: Another go at the core documentation ---- Added : /Spinach/Spinach core/Spinach core documentation/Spinach manual.docx Deleted : /Spinach/Spinach core/Spinach core documentation/Spinach manual.txt Revision: 128 Author: pervushin Date: 13 November 2008 04:19:04 Message: ---- Modified : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/event_table_kope.m Modified : /Spinach/Spinach kope/fetch_state_kope.m Modified : /Spinach/Spinach kope/header_11spins.txt Modified : /Spinach/Spinach kope/kope_hsqc1_tst.asv Modified : /Spinach/Spinach kope/kope_hsqc1_tst.m Modified : /Spinach/Spinach kope/pp_store.mat Modified : /Spinach/Spinach kope/trajectory_kope.m Revision: 127 Author: kuprov Date: 12 November 2008 18:08:38 Message: A minor modification to the example COSY simulation. ---- Modified : /Spinach/Spinach examples/example_cosy.m Revision: 126 Author: kuprov Date: 12 November 2008 18:00:25 Message: Moved the offset specification to ppm. ---- Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach examples/example.m Modified : /Spinach/Spinach examples/example_cosy.m Revision: 125 Author: kuprov Date: 12 November 2008 17:25:12 Message: Moved the calculation of irreducible spherical tensor operators to rlx_gen.m - currently they are only used there. might make it a separate function eventually. ---- Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach examples/example.m Revision: 124 Author: kuprov Date: 12 November 2008 15:37:16 Message: Moved Spinach core completely to sparse matrix algebra. Slightly slower, but memory footprint appears to take precedence at the moment. ---- Modified : /Spinach/Spinach core/create_ss.m Added : /Spinach/Spinach core/nucleus.m Modified : /Spinach/Spinach core/pauli.m Modified : /Spinach/Spinach core/state2dm.m Modified : /Spinach/Spinach core/state_pregen.m Revision: 123 Author: pervushin Date: 12 November 2008 07:42:36 Message: ---- Modified : /Spinach/Spinach kope/create_pp.m Added : /Spinach/Spinach kope/fetch_state_kope.m Modified : /Spinach/Spinach kope/kope_hsqc1_tst.asv Modified : /Spinach/Spinach kope/kope_hsqc1_tst.m Modified : /Spinach/Spinach kope/pp_store.mat Modified : /Spinach/Spinach kope/purge.m Added : /Spinach/Spinach kope/trajectory_kope.asv Added : /Spinach/Spinach kope/trajectory_kope.m Revision: 122 Author: kuprov Date: 07 November 2008 21:21:34 Message: A documentation update, a few extra comments in the code and an example COSY simulation. Also, the shell function for the sanity checker -- at some point we will have to check everything the user supplies for sanity, plus perform on-the-fly sanity evaluation within the running simulations. ---- Added : /Spinach/Spinach aux/pre-programmed pulse sequences Added : /Spinach/Spinach aux/pre-programmed pulse sequences/cosy.m Modified : /Spinach/Spinach core/Spinach core documentation/Spinach manual.txt Modified : /Spinach/Spinach core/create_ss.m Added : /Spinach/Spinach core/sanity_check.m Added : /Spinach/Spinach examples/example_cosy.m Revision: 121 Author: pervushin Date: 07 November 2008 11:15:38 Message: Conversion from Bruker to Spinach. Ready to compute Bruker library using 11 spin system. Construction of 29 spin system is in progress. ---- Modified : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_26.cara Added : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_26.cara.bak Added : /Spinach/NMRgenerator kope/tt.mac Added : /Spinach/Spinach kope/chop_kope.asv Added : /Spinach/Spinach kope/chop_kope.m Added : /Spinach/Spinach kope/create_pp.m Modified : /Spinach/Spinach kope/delay_kope.m Modified : /Spinach/Spinach kope/diagnostics_kope.m Modified : /Spinach/Spinach kope/event_table_kope.m Added : /Spinach/Spinach kope/header_11spins.txt Added : /Spinach/Spinach kope/kope_hsqc1_tst.asv Added : /Spinach/Spinach kope/kope_hsqc1_tst.m Modified : /Spinach/Spinach kope/kope_shape_tst.m Added : /Spinach/Spinach kope/pp_store.mat Modified : /Spinach/Spinach kope/pulse_kope.asv Modified : /Spinach/Spinach kope/pulse_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_kope.asv Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Added : /Spinach/Spinach kope/set_power_kope.asv Modified : /Spinach/Spinach kope/set_power_kope.m Modified : /Spinach/Spinach kope/spinsys_1.mat Revision: 120 Author: pervushin Date: 05 November 2008 07:12:31 Message: Shaped pulses are fixed. kope_shpe_tst.m - checks rectangular, gauss and Q5 pulses. ---- Added : /Spinach/Spinach kope/event_table_kope.asv Added : /Spinach/Spinach kope/event_table_kope.m Modified : /Spinach/Spinach kope/example_sp.m Modified : /Spinach/Spinach kope/kope_shape_tst.m Modified : /Spinach/Spinach kope/pulse_kope.m Modified : /Spinach/Spinach kope/pulse_shaped_kope.asv Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Modified : /Spinach/Spinach kope/receiver_kope.m Revision: 119 Author: pervushin Date: 02 November 2008 14:13:21 Message: Automatic (almost) translation of Bruker experiments to Spinach. Aux functions in 'Spinach kope' are added to calculate rho via pulse program. ---- Added : /Spinach/Spinach examples/example.asv Modified : /Spinach/Spinach examples/example.m Added : /Spinach/Spinach kope/delay_kope.asv Modified : /Spinach/Spinach kope/delay_kope.m Added : /Spinach/Spinach kope/example.m Added : /Spinach/Spinach kope/example_sp.m Modified : /Spinach/Spinach kope/kope_shape_tst.m Added : /Spinach/Spinach kope/pulse_kope.asv Modified : /Spinach/Spinach kope/pulse_kope.m Added : /Spinach/Spinach kope/pulse_shaped_dec_kope.asv Added : /Spinach/Spinach kope/pulse_shaped_dec_kope.m Added : /Spinach/Spinach kope/pulse_shaped_kope.asv Modified : /Spinach/Spinach kope/pulse_shaped_kope.m Added : /Spinach/Spinach kope/receiver_kope.asv Modified : /Spinach/Spinach kope/receiver_kope.m Added : /Spinach/Spinach kope/rect.pk Added : /Spinach/Spinach kope/spinsys_1.mat Added : /Spinach/Spinach kope/wave Added : /Spinach/Spinach kope/wave/Gauss_5_256.pk Added : /Spinach/Spinach kope/wave/Q3.1000 Added : /Spinach/Spinach kope/wave/Q5.1000 Revision: 118 Author: kuprov Date: 30 October 2008 15:01:29 Message: Implemented a better clusterization algorithm and started to write a manual. ---- Added : /Spinach/Spinach core/Spinach core documentation/Spinach manual.txt Modified : /Spinach/Spinach core/cluster_gen.m Modified : /Spinach/Spinach examples/example.m Revision: 117 Author: kuprov Date: 30 October 2008 11:36:22 Message: Obsolete folder deleted. ---- Deleted : /Spinach/Incoming/13_10_08 Revision: 116 Author: pervushin Date: 29 October 2008 15:47:09 Message: NMR generator repository is added Spinach kope contains Pervushin's code to bridge Spinach core with the repository of NMR experiments diagnostics_kope.m is formatted - Ilya, take a look by running kope_hsqc_tst.m ---- Added : /Spinach/NMRgenerator kope Added : /Spinach/NMRgenerator kope/nmrGenerator_version_alpha_26.cara Modified : /Spinach/Spinach examples/example.m Added : /Spinach/Spinach kope Added : /Spinach/Spinach kope/Jr.m Added : /Spinach/Spinach kope/delay_kope.m Added : /Spinach/Spinach kope/diagnostics_kope.asv Added : /Spinach/Spinach kope/diagnostics_kope.m Added : /Spinach/Spinach kope/kope_hsqc_tst.m Added : /Spinach/Spinach kope/kope_shape_tst.m Added : /Spinach/Spinach kope/pad.m Added : /Spinach/Spinach kope/pulse_kope.m Added : /Spinach/Spinach kope/pulse_shaped_kope.m Added : /Spinach/Spinach kope/purge.m Added : /Spinach/Spinach kope/receiver_kope.m Added : /Spinach/Spinach kope/rlx_gen_kope.m Added : /Spinach/Spinach kope/select_state_kope.m Added : /Spinach/Spinach kope/set_power_kope.m Revision: 115 Author: kuprov Date: 29 October 2008 10:46:09 Message: Code for incorporation from Konstantin. ---- Added : /Spinach/Incoming/13_10_08 Added : /Spinach/Incoming/13_10_08/Data structures.mmap Added : /Spinach/Incoming/13_10_08/Gauss_5_256.pk Added : /Spinach/Incoming/13_10_08/INEPT_bruker.asv Added : /Spinach/Incoming/13_10_08/INEPT_bruker.m Added : /Spinach/Incoming/13_10_08/Jr.m Added : /Spinach/Incoming/13_10_08/array.m Added : /Spinach/Incoming/13_10_08/cluster_gen.m Added : /Spinach/Incoming/13_10_08/cluster_ham.m Added : /Spinach/Incoming/13_10_08/compres_out.txt Added : /Spinach/Incoming/13_10_08/compress_shape.m Added : /Spinach/Incoming/13_10_08/compress_shape1.asv Added : /Spinach/Incoming/13_10_08/compress_shape1.m Added : /Spinach/Incoming/13_10_08/compress_shape_imp.m Added : /Spinach/Incoming/13_10_08/cpd Added : /Spinach/Incoming/13_10_08/create_ss.m Added : /Spinach/Incoming/13_10_08/custom_operator.m Added : /Spinach/Incoming/13_10_08/custom_state.m Added : /Spinach/Incoming/13_10_08/delay_kope.asv Added : /Spinach/Incoming/13_10_08/delay_kope.m Added : /Spinach/Incoming/13_10_08/diagnostics.m Added : /Spinach/Incoming/13_10_08/diagnostics_kope.asv Added : /Spinach/Incoming/13_10_08/diagnostics_kope.m Added : /Spinach/Incoming/13_10_08/expv.m Added : /Spinach/Incoming/13_10_08/header_ssr.txt Added : /Spinach/Incoming/13_10_08/hnca13.asv Added : /Spinach/Incoming/13_10_08/hnca13.m Added : /Spinach/Incoming/13_10_08/hnca_bruker.asv Added : /Spinach/Incoming/13_10_08/hnca_bruker.m Added : /Spinach/Incoming/13_10_08/kope_auto.m Added : /Spinach/Incoming/13_10_08/kope_auto_hnca.asv Added : /Spinach/Incoming/13_10_08/kope_auto_hnca.m Added : /Spinach/Incoming/13_10_08/kope_hsqc_tst.asv Added : /Spinach/Incoming/13_10_08/kope_hsqc_tst.m Added : /Spinach/Incoming/13_10_08/kope_phase_cycle_tst.asv Added : /Spinach/Incoming/13_10_08/kope_phase_cycle_tst.m Added : /Spinach/Incoming/13_10_08/kope_relax_tst.m Added : /Spinach/Incoming/13_10_08/kope_relax_tst_old.m Added : /Spinach/Incoming/13_10_08/kope_shape_tst.asv Added : /Spinach/Incoming/13_10_08/kope_shape_tst.m Added : /Spinach/Incoming/13_10_08/kphnca.m Added : /Spinach/Incoming/13_10_08/kphnca10.asv Added : /Spinach/Incoming/13_10_08/kphnca10.m Added : /Spinach/Incoming/13_10_08/kphnca_10.asv Added : /Spinach/Incoming/13_10_08/kphnca_10.m Added : /Spinach/Incoming/13_10_08/liouv_gen.m Added : /Spinach/Incoming/13_10_08/mac Added : /Spinach/Incoming/13_10_08/mac/my.mac Added : /Spinach/Incoming/13_10_08/nmrGenerator_version_alpha_25.cara Added : /Spinach/Incoming/13_10_08/operator.m Added : /Spinach/Incoming/13_10_08/pauli.m Added : /Spinach/Incoming/13_10_08/pp Added : /Spinach/Incoming/13_10_08/prop_gen.m Added : /Spinach/Incoming/13_10_08/prune_pro.m Added : /Spinach/Incoming/13_10_08/pulse_acquire.m Added : /Spinach/Incoming/13_10_08/pulse_kope.asv Added : /Spinach/Incoming/13_10_08/pulse_kope.m Added : /Spinach/Incoming/13_10_08/pulse_shaped_kope.asv Added : /Spinach/Incoming/13_10_08/pulse_shaped_kope.m Added : /Spinach/Incoming/13_10_08/pulse_shaped_kope1.m Added : /Spinach/Incoming/13_10_08/purge.m Added : /Spinach/Incoming/13_10_08/read_wave.asv Added : /Spinach/Incoming/13_10_08/read_wave.m Added : /Spinach/Incoming/13_10_08/read_wave1.asv Added : /Spinach/Incoming/13_10_08/read_wave1.m Added : /Spinach/Incoming/13_10_08/receiver_kope.asv Added : /Spinach/Incoming/13_10_08/receiver_kope.m Added : /Spinach/Incoming/13_10_08/rect.pk Added : /Spinach/Incoming/13_10_08/rlx_gen.m Added : /Spinach/Incoming/13_10_08/rlx_gen_kope.asv Added : /Spinach/Incoming/13_10_08/rlx_gen_kope.m Added : /Spinach/Incoming/13_10_08/rlx_gen_kope_HN.m Added : /Spinach/Incoming/13_10_08/rlx_test.m Added : /Spinach/Incoming/13_10_08/run_me.m Added : /Spinach/Incoming/13_10_08/select_state_kope.m Added : /Spinach/Incoming/13_10_08/set_power_kope.m Added : /Spinach/Incoming/13_10_08/shaped_pulse.m Added : /Spinach/Incoming/13_10_08/shaped_tst.asv Added : /Spinach/Incoming/13_10_08/shaped_tst.m Added : /Spinach/Incoming/13_10_08/simps.m Added : /Spinach/Incoming/13_10_08/state2dm.m Added : /Spinach/Incoming/13_10_08/state_pregen.m Added : /Spinach/Incoming/13_10_08/statelist_gen.m Added : /Spinach/Incoming/13_10_08/total_rotation.asv Added : /Spinach/Incoming/13_10_08/tst.txt Added : /Spinach/Incoming/13_10_08/tst.xls Added : /Spinach/Incoming/13_10_08/tst.xml Added : /Spinach/Incoming/13_10_08/tt.mac Added : /Spinach/Incoming/13_10_08/wave Added : /Spinach/Incoming/13_10_08/wave/CaWurst.400_55k Added : /Spinach/Incoming/13_10_08/wave/CaWurst.600_55k Added : /Spinach/Incoming/13_10_08/wave/Crp60,0.5,20.1 Added : /Spinach/Incoming/13_10_08/wave/Gauss_5_256.pk Added : /Spinach/Incoming/13_10_08/wave/Q3.1000 Added : /Spinach/Incoming/13_10_08/wave/Q5.1000 Added : /Spinach/Incoming/13_10_08/wave/Q5tr.1000 Added : /Spinach/Incoming/13_10_08/wave/ReBurp.pk Added : /Spinach/Incoming/13_10_08/wave/Rect.pk Added : /Spinach/Incoming/13_10_08/wave/SChirp_40k_1300_20 Added : /Spinach/Incoming/13_10_08/wave/Sed.200 Added : /Spinach/Incoming/13_10_08/wave/Sinc.pk Added : /Spinach/Incoming/13_10_08/wave/Sinc1.1000 Added : /Spinach/Incoming/13_10_08/wave/Sinc1.txt Added : /Spinach/Incoming/13_10_08/wave/Sinc1_1000.pk Added : /Spinach/Incoming/13_10_08/wave/sine.pk Added : /Spinach/Incoming/13_10_08/wavegauss.asv Added : /Spinach/Incoming/13_10_08/wavegauss.pk Added : /Spinach/Incoming/13_10_08/wavegausskp Added : /Spinach/Incoming/13_10_08/wavegausskp.asv Added : /Spinach/Incoming/13_10_08/wavegausskp.pk Revision: 114 Author: kuprov Date: 18 October 2008 21:02:52 Message: Fully working control commit - sending this to Pervushin. ---- Modified : /Spinach/Spinach aux/diagnostics.m Deleted : /Spinach/Spinach aux/pulse_shaped_kope.m Deleted : /Spinach/Spinach aux/rectangular_pulse.m Deleted : /Spinach/Spinach aux/set_power_kope.m Deleted : /Spinach/Spinach examples/Gauss.m Deleted : /Spinach/Spinach examples/HNCA_system.m Deleted : /Spinach/Spinach examples/clustering.ppt Added : /Spinach/Spinach examples/example.m Added : /Spinach/Spinach examples/example_clustering.ppt (Copy from path: /Spinach/Spinach examples/clustering.ppt, Revision, 113) Deleted : /Spinach/Spinach examples/pulse_acquire.m Deleted : /Spinach/Spinach examples/q5_pulse.m Deleted : /Spinach/Spinach examples/trosy.m Revision: 113 Author: kuprov Date: 18 October 2008 17:56:54 Message: Starting to modify Konstantin's simulation scripts to bind them to the new content in the core and aux directories. ---- Deleted : /Spinach/Incoming/Jr.m Deleted : /Spinach/Incoming/SSR_relax.nb Deleted : /Spinach/Incoming/clustering.ppt Deleted : /Spinach/Incoming/lio_5H.m Deleted : /Spinach/Incoming/rlx_gen_kope.m Deleted : /Spinach/Incoming/shaped_pulse Added : /Spinach/Spinach examples/Gauss.m Added : /Spinach/Spinach examples/clustering.ppt Modified : /Spinach/Spinach examples/pulse_acquire.m Added : /Spinach/Spinach external/Jr.m Added : /Spinach/Spinach external/SSR_relax.nb Added : /Spinach/Spinach external/lio_5H.m Revision: 112 Author: kuprov Date: 18 October 2008 17:52:33 Message: read_wave.m finalized. ---- Modified : /Spinach/Spinach aux/read_wave.m Revision: 111 Author: kuprov Date: 18 October 2008 16:40:08 Message: An initial pilot fix for the shaped_pulse.m ---- Deleted : /Spinach/Incoming/nuc_declrtn Deleted : /Spinach/Incoming/shaped_pulse/Q5.m Deleted : /Spinach/Incoming/shaped_pulse/pulse_shaped_kope.m Deleted : /Spinach/Incoming/shaped_pulse/set_power_kope.m Added : /Spinach/Spinach aux/pulse_shaped_kope.m Modified : /Spinach/Spinach aux/rectangular_pulse.m Added : /Spinach/Spinach aux/set_power_kope.m Modified : /Spinach/Spinach aux/shaped_pulse.m Modified : /Spinach/Spinach examples/pulse_acquire.m Added : /Spinach/Spinach examples/q5_pulse.m Added : /Spinach/Spinach external Added : /Spinach/Spinach external/rlx_gen_kope.m Revision: 110 Author: kuprov Date: 18 October 2008 14:58:57 Message: Slight update to a waveform reading utility. ---- Modified : /Spinach/Spinach aux/read_wave.m Deleted : /Spinach/Spinach aux/wave/CaWurst.400_55k Deleted : /Spinach/Spinach aux/wave/CaWurst.600_55k Deleted : /Spinach/Spinach aux/wave/Crp60,0.5,20.1 Deleted : /Spinach/Spinach aux/wave/Gauss_5_256.pk Deleted : /Spinach/Spinach aux/wave/Q3.1000 Deleted : /Spinach/Spinach aux/wave/Q5.1000 Deleted : /Spinach/Spinach aux/wave/Q5tr.1000 Deleted : /Spinach/Spinach aux/wave/ReBurp.pk Deleted : /Spinach/Spinach aux/wave/Rect.pk Deleted : /Spinach/Spinach aux/wave/SChirp_40k_1300_20 Deleted : /Spinach/Spinach aux/wave/Sed.200 Deleted : /Spinach/Spinach aux/wave/Sinc.pk Deleted : /Spinach/Spinach aux/wave/Sinc1.1000 Deleted : /Spinach/Spinach aux/wave/Sinc1.txt Deleted : /Spinach/Spinach aux/wave/Sinc1_1000.pk Added : /Spinach/Spinach aux/wave/gaussian_256.pk Added : /Spinach/Spinach aux/wave/q3_1000.pk Added : /Spinach/Spinach aux/wave/q5_1000.pk Added : /Spinach/Spinach aux/wave/reburp_1000.pk Added : /Spinach/Spinach aux/wave/rectangular_128.pk Added : /Spinach/Spinach aux/wave/sed_200.pk Added : /Spinach/Spinach aux/wave/sinc_1000.pk Deleted : /Spinach/Spinach aux/wave/sine.pk Revision: 109 Author: kuprov Date: 18 October 2008 14:23:33 Message: Re-did Konstantin's read_wave.m and fixed a potential phase resampling problem. Added the waveforms he supplied to the aux directory with an acknowledgement. ---- Deleted : /Spinach/Incoming/read_wave.m Deleted : /Spinach/Incoming/shaped_pulse/read_wave1.m Deleted : /Spinach/Incoming/shaped_pulse/wave Added : /Spinach/Spinach aux/read_wave.m Added : /Spinach/Spinach aux/simps.m Added : /Spinach/Spinach aux/wave (Copy from path: /Spinach/Incoming/shaped_pulse/wave, Revision, 108) Added : /Spinach/Spinach aux/wave/acknowledgements.txt Revision: 108 Author: kuprov Date: 18 October 2008 11:16:22 Message: Implemented manual clusterization on Pervushin's request. Fixed a bug in state_pregen.m and made a few minor changes. ---- Added : /Spinach/Incoming/clustering.ppt Added : /Spinach/Incoming/nuc_declrtn Added : /Spinach/Incoming/nuc_declrtn/create_ss.m Added : /Spinach/Incoming/nuc_declrtn/pulse_shaped_kope.m Added : /Spinach/Incoming/shaped_pulse Added : /Spinach/Incoming/shaped_pulse/Gauss.m Added : /Spinach/Incoming/shaped_pulse/Q5.m Added : /Spinach/Incoming/shaped_pulse/cluster_gen.m Added : /Spinach/Incoming/shaped_pulse/cluster_ham.m Added : /Spinach/Incoming/shaped_pulse/create_ss.m Added : /Spinach/Incoming/shaped_pulse/custom_state.m Added : /Spinach/Incoming/shaped_pulse/expv.m Added : /Spinach/Incoming/shaped_pulse/liouv_gen.m Added : /Spinach/Incoming/shaped_pulse/operator.m Added : /Spinach/Incoming/shaped_pulse/pauli.m Added : /Spinach/Incoming/shaped_pulse/prop_gen.m Added : /Spinach/Incoming/shaped_pulse/pulse_shaped_kope.m Added : /Spinach/Incoming/shaped_pulse/read_wave1.m Added : /Spinach/Incoming/shaped_pulse/rlx_gen_kope.m Added : /Spinach/Incoming/shaped_pulse/set_power_kope.m Added : /Spinach/Incoming/shaped_pulse/state2dm.m Added : /Spinach/Incoming/shaped_pulse/state_pregen.m Added : /Spinach/Incoming/shaped_pulse/statelist_gen.m Added : /Spinach/Incoming/shaped_pulse/wave Added : /Spinach/Incoming/shaped_pulse/wave/CaWurst.400_55k Added : /Spinach/Incoming/shaped_pulse/wave/CaWurst.600_55k Added : /Spinach/Incoming/shaped_pulse/wave/Crp60,0.5,20.1 Added : /Spinach/Incoming/shaped_pulse/wave/Gauss_5_256.pk Added : /Spinach/Incoming/shaped_pulse/wave/Q3.1000 Added : /Spinach/Incoming/shaped_pulse/wave/Q5.1000 Added : /Spinach/Incoming/shaped_pulse/wave/Q5tr.1000 Added : /Spinach/Incoming/shaped_pulse/wave/ReBurp.pk Added : /Spinach/Incoming/shaped_pulse/wave/Rect.pk Added : /Spinach/Incoming/shaped_pulse/wave/SChirp_40k_1300_20 Added : /Spinach/Incoming/shaped_pulse/wave/Sed.200 Added : /Spinach/Incoming/shaped_pulse/wave/Sinc.pk Added : /Spinach/Incoming/shaped_pulse/wave/Sinc1.1000 Added : /Spinach/Incoming/shaped_pulse/wave/Sinc1.txt Added : /Spinach/Incoming/shaped_pulse/wave/Sinc1_1000.pk Added : /Spinach/Incoming/shaped_pulse/wave/sine.pk Modified : /Spinach/Spinach core/cluster_gen.m Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach examples/pulse_acquire.m Revision: 107 Author: kuprov Date: 12 October 2008 20:54:51 Message: Miscellaneous fixes and updates. ---- Deleted : /Spinach/Incoming/diagnostics_kope.m Deleted : /Spinach/Incoming/kope_relax_tst.m Added : /Spinach/Spinach examples/HNCA_system.m Modified : /Spinach/Spinach examples/pulse_acquire.m Deleted : /Spinach/Spinach examples/pulse_acquire_soft.m Deleted : /Spinach/Spinach examples/pulse_acquire_zte.m Deleted : /Spinach/Spinach examples/run_me.m Modified : /Spinach/Spinach tests/rlx_test.m Revision: 106 Author: kuprov Date: 12 October 2008 20:46:02 Message: Removed the unconditional relaxation supermatrix generation in liouv_gen.m and replaced it with a flag-based opt-in scheme. ---- Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/liouv_gen.m Modified : /Spinach/Spinach core/rlx_gen.m Revision: 105 Author: kuprov Date: 12 October 2008 20:36:05 Message: Added dipolar harmonization. See code comments for what it is. ---- Modified : /Spinach/Spinach core/rlx_gen.m Revision: 104 Author: kuprov Date: 12 October 2008 18:28:03 Message: Implemented Konstantin's changes into the diagnostics subroutine. ---- Modified : /Spinach/Spinach aux/diagnostics.m Revision: 103 Author: kuprov Date: 12 October 2008 16:03:03 Message: Documentation update. ---- Added : /Spinach/Spinach core/Spinach core documentation (Copy from path: /Spinach/Spinach core/Spinach core documnetation, Revision, 102) Modified : /Spinach/Spinach core/Spinach core documentation/relaxation_superoperator.docx Modified : /Spinach/Spinach core/Spinach core documentation/relaxation_superoperator.pdf Deleted : /Spinach/Spinach core/Spinach core documnetation Revision: 102 Author: kuprov Date: 12 October 2008 15:40:54 Message: File system clean-up. ---- Deleted : /Spinach/Spinach core/Data structures.mmap Added : /Spinach/Spinach core/Spinach core documnetation Added : /Spinach/Spinach core/Spinach core documnetation/Data structures.mmap (Copy from path: /Spinach/Spinach core/Data structures.mmap, Revision, 95) Added : /Spinach/Spinach core/Spinach core documnetation/relaxation_superoperator.docx (Copy from path: /Spinach/Spinach core/relaxation_superoperator.docx, Revision, 95) Added : /Spinach/Spinach core/Spinach core documnetation/relaxation_superoperator.pdf (Copy from path: /Spinach/Spinach core/relaxation_superoperator.pdf, Revision, 97) Deleted : /Spinach/Spinach core/relaxation_superoperator.docx Deleted : /Spinach/Spinach core/relaxation_superoperator.pdf Revision: 101 Author: kuprov Date: 12 October 2008 15:38:08 Message: Implemented the secularity condition into the relaxation superoperator - cross-relaxation now happens only across zero frequency differences in the carrier Hamiltonian, a reasonable assumption at high field, where Redfield theory operates. Plus a significant speed-up -- only a tiny fraction of Redfield supermatrix elements actually needs to be computed. ---- Modified : /Spinach/Spinach core/cluster_ham.m Modified : /Spinach/Spinach core/rlx_gen.m Revision: 100 Author: kuprov Date: 11 October 2008 17:05:31 Message: All Euler anlges and Euler-to-cart transformations have been fixed and unified to Varshalovich B convention. The interesting problem of asymmetry in the relaxation superoperator is probably related to the fact that my operators are all normalized to unity. Might investigate if time permits, but all seems right so far. ---- Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach tests/dd-csa_cross-correlation.nb Modified : /Spinach/Spinach tests/rlx_test.m Revision: 99 Author: kuprov Date: 11 October 2008 15:52:05 Message: Full match achieved between Spinach and BRW engine. Some difference in Euler angle designation remains, courtesy of the impossibly stupid implementation of cart2sph in Matlab. ---- Added : /Spinach/Spinach tests/dd-csa_cross-correlation.nb Modified : /Spinach/Spinach tests/dd_relaxation.nb Modified : /Spinach/Spinach tests/rlx_test.m Revision: 98 Author: kuprov Date: 10 October 2008 15:06:46 Message: Dipolar block checks out in full, on both Palmer's book and the BRW engine. One last thing is to check the DD-CSA cross-correlation. ---- Modified : /Spinach/Spinach core/create_ss.m Added : /Spinach/Spinach tests/dd_relaxation.nb Modified : /Spinach/Spinach tests/rlx_test.m Revision: 97 Author: kuprov Date: 10 October 2008 12:53:25 Message: Finished coding and clean-up of the dipolar side. Testing remains. Konstantin sent some updates, placed them into Incoming. ---- Added : /Spinach/Incoming Added : /Spinach/Incoming/Jr.m Added : /Spinach/Incoming/SSR_relax.nb Added : /Spinach/Incoming/diagnostics_kope.m Added : /Spinach/Incoming/kope_relax_tst.m Added : /Spinach/Incoming/lio_5H.m Added : /Spinach/Incoming/read_wave.m Added : /Spinach/Incoming/rlx_gen_kope.m Modified : /Spinach/Spinach core/create_ss.m Modified : /Spinach/Spinach core/liouv_gen.m Added : /Spinach/Spinach core/relaxation_superoperator.pdf Modified : /Spinach/Spinach core/rlx_gen.m Modified : /Spinach/Spinach core/state_pregen.m Modified : /Spinach/Spinach tests/rlx_test.m Revision: 96 Author: kuprov Date: 25 September 2008 20:55:47 Message: File system clean-up. ---- Deleted : /Spinach aux Deleted : /Spinach core Deleted : /Spinach examples Deleted : /Spinach tests Revision: 95 Author: kuprov Date: 25 September 2008 20:55:21 Message: File system clean-up. ---- Added : /Spinach Added : /Spinach/Spinach aux (Copy from path: /Spinach aux, Revision, 94) Added : /Spinach/Spinach core (Copy from path: /Spinach core, Revision, 94) Added : /Spinach/Spinach examples (Copy from path: /Spinach examples, Revision, 94) Added : /Spinach/Spinach tests (Copy from path: /Spinach tests, Revision, 94) Revision: 94 Author: kuprov Date: 25 September 2008 20:52:42 Message: File system clean-up. ---- Deleted : /Spinach Revision: 93 Author: kuprov Date: 25 September 2008 20:50:55 Message: File system clean-up. ---- Added : /Spinach Revision: 92 Author: kuprov Date: 25 September 2008 20:48:33 Message: File system clean-up. ---- Deleted : /Application 1 Deleted : /Data structures.mmap Deleted : /Discussions Deleted : /Dumpster Deleted : /Lanczos pruning Deleted : /Literature Deleted : /MEX files Added : /Miscellaneous/Application 1 (Copy from path: /Application 1, Revision, 90) Added : /Miscellaneous/Discussions (Copy from path: /Discussions, Revision, 90) Added : /Miscellaneous/Dumpster (Copy from path: /Dumpster, Revision, 90) Added : /Miscellaneous/Lanczos pruning (Copy from path: /Lanczos pruning, Revision, 90) Added : /Miscellaneous/Literature (Copy from path: /Literature, Revision, 90) Added : /Miscellaneous/MEX files (Copy from path: /MEX files, Revision, 90) Added : /Miscellaneous/SVD pruning (Copy from path: /SVD pruning, Revision, 90) Added : /Miscellaneous/Sparse matrix exponentials (Copy from path: /Sparse matrix exponentials, Revision, 90) Added : /Miscellaneous/Spinach logo (Copy from path: /Spinach logo, Revision, 90) Added : /Miscellaneous/ZTE pruning (Copy from path: /ZTE pruning, Revision, 90) Added : /Miscellaneous/code from Olga (Copy from path: /code from Olga, Revision, 90) Added : /Miscellaneous/householder tridiagonalization (Copy from path: /householder tridiagonalization, Revision, 90) Added : /Miscellaneous/old code (Copy from path: /old code, Revision, 90) Added : /Miscellaneous/strychnine (Copy from path: /strychnine, Revision, 90) Deleted : /SVD pruning Deleted : /Sparse matrix exponentials Added : /Spinach aux/custom_operator.m (Copy from path: /custom_operator.m, Revision, 90) Added : /Spinach aux/custom_state.m (Copy from path: /custom_state.m, Revision, 90) Added : /Spinach aux/diagnostics.m (Copy from path: /diagnostics.m, Revision, 90) Added : /Spinach aux/operator.m (Copy from path: /operator.m, Revision, 90) Added : /Spinach aux/protein.m (Copy from path: /protein.m, Revision, 90) Added : /Spinach aux/rectangular_pulse.m (Copy from path: /rectangular_pulse.m, Revision, 90) Added : /Spinach aux/shaped_pulse.m (Copy from path: /shaped_pulse.m, Revision, 90) Added : /Spinach core/Data structures.mmap (Copy from path: /Data structures.mmap, Revision, 90) Added : /Spinach core/cluster_gen.m (Copy from path: /cluster_gen.m, Revision, 90) Added : /Spinach core/cluster_ham.m (Copy from path: /cluster_ham.m, Revision, 90) Added : /Spinach core/create_ss.m (Copy from path: /create_ss.m, Revision, 90) Added : /Spinach core/expv.m (Copy from path: /expv.m, Revision, 90) Added : /Spinach core/liouv_gen.m (Copy from path: /liouv_gen.m, Revision, 90) Added : /Spinach core/pauli.m (Copy from path: /pauli.m, Revision, 90) Added : /Spinach core/prop_gen.m (Copy from path: /prop_gen.m, Revision, 90) Added : /Spinach core/prune_pro.m (Copy from path: /prune_pro.m, Revision, 90) Added : /Spinach core/relaxation_superoperator.docx (Copy from path: /relaxation_superoperator.docx, Revision, 91) Added : /Spinach core/rlx_gen.m (Copy from path: /rlx_gen.m, Revision, 90) Added : /Spinach core/state2dm.m (Copy from path: /state2dm.m, Revision, 90) Added : /Spinach core/state_pregen.m (Copy from path: /state_pregen.m, Revision, 90) Added : /Spinach core/statelist_gen.m (Copy from path: /statelist_gen.m, Revision, 90) Added : /Spinach examples/pulse_acquire.m (Copy from path: /pulse_acquire.m, Revision, 90) Added : /Spinach examples/pulse_acquire_soft.m (Copy from path: /pulse_acquire_soft.m, Revision, 90) Added : /Spinach examples/pulse_acquire_zte.m (Copy from path: /pulse_acquire_zte.m, Revision, 90) Added : /Spinach examples/run_me.m (Copy from path: /run_me.m, Revision, 90) Added : /Spinach examples/trosy.m (Copy from path: /trosy.m, Revision, 90) Deleted : /Spinach logo Added : /Spinach tests/csa_relaxation.nb (Copy from path: /csa_relaxation.nb, Revision, 90) Added : /Spinach tests/rlx_test.m (Copy from path: /rlx_test.m, Revision, 90) Deleted : /ZTE pruning Deleted : /cluster_gen.m Deleted : /cluster_ham.m Deleted : /code from Olga Deleted : /create_ss.m Deleted : /csa_relaxation.nb Deleted : /custom_operator.m Deleted : /custom_state.m Deleted : /diagnostics.m Deleted : /expv.m Deleted : /householder tridiagonalization Deleted : /liouv_gen.m Deleted : /old code Deleted : /operator.m Deleted : /pauli.m Deleted : /prop_gen.m Deleted : /protein.m Deleted : /prune_pro.m Deleted : /pulse_acquire.m Deleted : /pulse_acquire_soft.m Deleted : /pulse_acquire_zte.m Deleted : /rectangular_pulse.m Deleted : /relaxation_superoperator.docx Deleted : /rlx_gen.m Deleted : /rlx_test.m Deleted : /run_me.m Deleted : /shaped_pulse.m Deleted : /state2dm.m Deleted : /state_pregen.m Deleted : /statelist_gen.m Deleted : /strychnine Deleted : /trosy.m Revision: 91 Author: kuprov Date: 25 September 2008 20:44:55 Message: File system clean-up. ---- Added : /Miscellaneous Added : /Spinach aux Added : /Spinach core Added : /Spinach examples Added : /Spinach tests Deleted : /csa_relaxation.docx Added : /relaxation_superoperator.docx Revision: 90 Author: kuprov Date: 24 September 2008 19:57:03 Message: Final double-checked etalon commit before the implementation of dipolar coupling. ---- Modified : /csa_relaxation.nb Modified : /pulse_acquire_soft.m Modified : /rlx_gen.m Revision: 89 Author: kuprov Date: 24 September 2008 15:32:36 Message: Cosmetic speed-ups here and there. Still very slow - must generate sparsity patterns for the relaxation superoperator. ---- Modified : /pulse_acquire_soft.m Modified : /rlx_gen.m Revision: 88 Author: kuprov Date: 24 September 2008 13:03:18 Message: Relaxation superoperator integrated into Spinach. Final testing using pulse sequences remains. ---- Modified : /csa_relaxation.docx Modified : /liouv_gen.m Modified : /pulse_acquire_soft.m Modified : /rlx_gen.m Deleted : /rlx_gen_cluster.m Revision: 87 Author: kuprov Date: 24 September 2008 12:30:25 Message: CSA relaxation superoperator has passed all tests against BRW engine and known analytical results. Congratulations. ---- Modified : /csa_relaxation.nb Modified : /pulse_acquire_soft.m Modified : /rlx_gen_cluster.m Revision: 86 Author: kuprov Date: 24 September 2008 11:48:56 Message: Full match to the analytical result of the BRW processor achieved with zero Euler angles. Now trying arbitrary angles... ---- Added : /Spinach logo Added : /Spinach logo/ik_version_1.ai Modified : /csa_relaxation.docx Added : /csa_relaxation.nb Modified : /pulse_acquire_soft.m Modified : /rlx_gen_cluster.m Revision: 85 Author: kuprov Date: 21 September 2008 15:33:16 Message: Achieved correct answers with 1-spin clusters (six-digit match with analytical results). A mysterious factor of 18 is currently included empirically. ---- Modified : /pulse_acquire_soft.m Modified : /rlx_gen_cluster.m Modified : /state2dm.m Revision: 84 Author: kuprov Date: 20 September 2008 20:02:19 Message: Second stab at the CSA relaxation superoperator. Still doesn't yield anything sensible. ---- Modified : /cluster_ham.m Modified : /liouv_gen.m Modified : /pulse_acquire_soft.m Modified : /rlx_gen_cluster.m Revision: 83 Author: kuprov Date: 20 September 2008 15:27:52 Message: Finished programming the fully general CSA relaxation superoperator. Probably buggy and slow - has yet to be tested. Also added a Word file with the theory behind it - really scary stuff. ---- Added : /csa_relaxation.docx Modified : /pulse_acquire_soft.m Modified : /rlx_gen_cluster.m Revision: 82 Author: kuprov Date: 20 August 2008 19:34:41 Message: Soft pulses implemented. ---- Added : /pulse_acquire_soft.m Modified : /rectangular_pulse.m Modified : /rlx_gen.m Modified : /run_me.m Revision: 81 Author: kuprov Date: 20 August 2008 14:37:47 Message: Coding finished for the shaped pulse function and the rectangular pulse function as a simplified wrapper for it. ---- Added : /rectangular_pulse.m Modified : /run_me.m Added : /shaped_pulse.m Revision: 80 Author: kuprov Date: 20 August 2008 13:42:46 Message: Various minor changes related to the ongoing implementation of the proper relaxation superoperator. ---- Modified : /Data structures.mmap Added : /Literature/jerschow.pdf Modified : /create_ss.m Modified : /rlx_gen.m Added : /rlx_gen_cluster.m Modified : /rlx_test.m Modified : /state_pregen.m Revision: 79 Author: kuprov Date: 19 August 2008 14:57:50 Message: Added Zeeman irreducible spherical tensors to state_pregen.m ---- Modified : /state_pregen.m Revision: 78 Author: kuprov Date: 19 August 2008 11:49:14 Message: Added the local nstates variable. ---- Modified : /statelist_gen.m Revision: 77 Author: kuprov Date: 19 August 2008 10:11:42 Message: Added the relaxation testing snippet. Will now proceed to implement cluster relaxation superoperators. ---- Modified : /pulse_acquire.m Modified : /rlx_gen.m Added : /rlx_test.m Modified : /trosy.m Revision: 76 Author: kuprov Date: 14 August 2008 15:50:18 Message: Added some auxiliary functions. ---- Added : /protein.m Added : /pulse_acquire_zte.m Revision: 75 Author: kuprov Date: 14 July 2008 20:49:07 Message: All done. TROSY shines and rocks. Sending this to Pervushin and Leimkuhler. ---- Added : /custom_operator.m Deleted : /custom_operator_trash.m Modified : /operator.m Modified : /pulse_acquire.m Modified : /run_me.m Added : /trosy.m Revision: 74 Author: kuprov Date: 14 July 2008 20:15:15 Message: A reliable single-spin operator generator obtained. Will now implement the "convenience" thing that used to be called custom_operator.m ---- Modified : /operator.m Modified : /run_me.m Revision: 73 Author: kuprov Date: 14 July 2008 19:07:34 Message: Finally, a fully working bespoke operator generator. Single-spin operators for now, analytical combinatorics. Quite slow, but at least something to start from. The Liouvillian and global Lx, Ly recouplers are completely OK. Something unknown was wrong with the bespoke operator recoupler. Check of the basic recoupling theory works if only a subset of clusters is recoupled. ---- Added : /custom_operator_trash.m Added : /operator.m Modified : /run_me.m Modified : /state_pregen.m Revision: 72 Author: kuprov Date: 10 July 2008 21:01:29 Message: OK, the attempt to create custom operators has failed. Need a different strategy. The code has been rolled back to using the pre-computed Lx, Ly and returned to pulse-acquire type demonstration. It's now a lot neater than it used to be, and we have relaxation after all, but I must make another attempt at custom operators as soon as feasible. ---- Deleted : /custom_operator.m Added : /pulse_acquire.m Modified : /run_me.m Modified : /state_pregen.m Deleted : /trosy.m Revision: 71 Author: kuprov Date: 10 July 2008 20:31:42 Message: Ironed a minor bug in custom_operator.m; why the Ly generation appears to be different from Lx is still a mystery. ---- Modified : /custom_operator.m Modified : /run_me.m Revision: 70 Author: kuprov Date: 10 July 2008 17:30:30 Message: OK, sort of nailed the trosy bit, but there's a nasty bug corrupting the custom operators. Could more or less get around it, but a thorough investigation is due into the origin. Should probably start with the "known working" state before the streamlining. The first selective-pulse revision might be a good start. ---- Modified : /custom_operator.m Modified : /diagnostics.m Modified : /run_me.m Modified : /trosy.m Revision: 69 Author: kuprov Date: 10 July 2008 14:17:22 Message: Created a custom operator generator and fixed a few bugs in the custom state generator. Now proceeding to program the trosy. :) ---- Modified : /custom_operator.m Modified : /custom_state.m Deleted : /pulse_acquire.m Modified : /run_me.m Added : /trosy.m Revision: 68 Author: kuprov Date: 10 July 2008 13:38:45 Message: Added a custom state generator -- to make the program more user-friendly. My arcane statespecs, although quite neat and efficient, are unlikely to be grasped instantaneously by a first-time user... now transforming the custom operator subroutine. ---- Added : /custom_state.m Modified : /pulse_acquire.m Revision: 67 Author: kuprov Date: 09 July 2008 21:03:08 Message: The major code clean-up and introduction of heteronuclei seems to have succeeded. Only TROSY implementation is left, but that should now be straightforward. ---- Modified : /Data structures.mmap Modified : /cluster_gen.m Modified : /cluster_ham.m Modified : /create_ss.m Modified : /liouv_gen.m Modified : /pauli.m Modified : /pulse_acquire.m Deleted : /pulse_acquire_selective.m Modified : /rlx_gen.m Modified : /run_me.m Deleted : /sel_inv.m Modified : /state2dm.m Modified : /state_pregen.m Revision: 66 Author: kuprov Date: 09 July 2008 17:02:34 Message: An excellent create_ss.m - I am quite proud of it. Some significant renaming was done and the new names will need to be propagated through the code as I modify it to include nuclei other than protons. ---- Added : /Data structures.mmap Modified : /create_ss.m Modified : /run_me.m Revision: 65 Author: kuprov Date: 09 July 2008 10:53:14 Message: About to embark on a grand modification effort -- introducing carbon and nitrogen. ---- Modified : /pulse_acquire.m Modified : /run_me.m Revision: 64 Author: kuprov Date: 09 July 2008 10:44:57 Message: m ---- Modified : /sel_inv.m Revision: 63 Author: kuprov Date: 09 July 2008 10:15:57 Message: Fixed a normalization bug in custom_operator.m and added a normalization mode switch to state2dm.m ---- Modified : /custom_operator.m Modified : /sel_inv.m Modified : /state2dm.m Revision: 62 Author: kuprov Date: 08 July 2008 21:47:12 Message: Tightened up the propagator tolerances and added a nice state diagnostics tool that prints the most populated states on user request. Konstantin asked for a tool like that, plus it does indeed look like a handy tool. ---- Added : /diagnostics.m Modified : /prop_gen.m Modified : /rlx_gen.m Modified : /run_me.m Modified : /sel_inv.m Revision: 61 Author: kuprov Date: 08 July 2008 14:15:17 Message: Sort of implemented the DD-CSA cross-correlation. Currently Lz<->2LzSz only and the Euler angles are ignored. Should be fine for the time being -- I only need good estimates for those transition rates, we are in for a demonstrator, not the precision code. ---- Modified : /rlx_gen.m Modified : /sel_inv.m Revision: 60 Author: kuprov Date: 07 July 2008 19:47:38 Message: Implemented dipolar cross-relaxation for single-spin orders. Added a selective inversion experiment to test the outcome. Sort of seems to work, but more testing needs to be done, of course. ---- Modified : /rlx_gen.m Modified : /run_me.m Added : /sel_inv.m Revision: 59 Author: kuprov Date: 07 July 2008 15:28:04 Message: SVN playing up. ---- Added : /Dumpster Added : /Dumpster/75_states.png Added : /Dumpster/CRT_quads_vs_triples.ai Added : /Dumpster/CRT_quads_vs_triples.png Added : /Dumpster/Cluster size dependence figure Added : /Dumpster/Cluster size dependence figure/doubles.eps Added : /Dumpster/Cluster size dependence figure/exact.eps Added : /Dumpster/Cluster size dependence figure/quads.eps Added : /Dumpster/Cluster size dependence figure/singles.eps Added : /Dumpster/Cluster size dependence figure/triples.eps Added : /Dumpster/Scaling Added : /Dumpster/Scaling/18-spin quads.eps Added : /Dumpster/Scaling/30-spin doubles.eps Added : /Dumpster/Scaling/30-spin doubles.png Added : /Dumpster/Scaling/36-spin triples.eps Added : /Dumpster/Scaling/36-spin triples.png Added : /Dumpster/Scaling/Scaling.opj Added : /Dumpster/crt_quads.png Added : /Dumpster/crt_triples.png Added : /Dumpster/final_quints.fig Added : /Dumpster/py_dma_triples.png Added : /Dumpster/quads_1000ns.eps Added : /Dumpster/quads_100ns.eps Added : /Dumpster/quads_10ns.eps Added : /Dumpster/quads_1ns.eps Added : /Dumpster/test1_quads.fig Added : /Dumpster/test1_quints.fig Added : /Dumpster/test1_sexts.fig Added : /Dumpster/test1_triples.fig Added : /Dumpster/test_quads.png Added : /Dumpster/test_triples.png Added : /Dumpster/triples_1000ns.eps Added : /Dumpster/triples_100ns.eps Added : /Dumpster/triples_10ns.eps Added : /Dumpster/triples_1ns.eps Revision: 58 Author: kuprov Date: 07 July 2008 15:26:21 Message: SVN playing up. ---- Deleted : /cluster_treat.m Deleted : /exact_treat.m Deleted : /mary.m Deleted : /padm.m Revision: 57 Author: kuprov Date: 07 July 2008 15:25:10 Message: SVN playing up. ---- Deleted : /75_states.png Deleted : /CRT_quads_vs_triples.ai Deleted : /CRT_quads_vs_triples.png Deleted : /check_it_out.asv Deleted : /cluster_gen.asv Deleted : /cluster_ham.asv Deleted : /cluster_treat.asv Deleted : /create_ss.asv Deleted : /crt_quads.png Deleted : /crt_triples.png Deleted : /exact_treat.asv Deleted : /expv.asv Deleted : /final_quints.fig Deleted : /liouv_gen.asv Deleted : /pauli.asv Deleted : /pervushin_fork Deleted : /prop_gen.asv Deleted : /prune_pro.asv Deleted : /pulse_acquire.asv Deleted : /py_dma_triples.png Deleted : /quads_1000ns.eps Deleted : /quads_100ns.eps Deleted : /quads_10ns.eps Deleted : /quads_1ns.eps Deleted : /run_me.asv Deleted : /spin_system.asv Deleted : /state2dm.asv Deleted : /state_pregen.asv Deleted : /statelist_gen.asv Deleted : /tc5b Deleted : /test1_quads.fig Deleted : /test1_quints.fig Deleted : /test1_sexts.fig Deleted : /test1_triples.fig Deleted : /test_quads.png Deleted : /test_triples.png Deleted : /triples_1000ns.eps Deleted : /triples_100ns.eps Deleted : /triples_10ns.eps Deleted : /triples_1ns.eps Revision: 56 Author: kuprov Date: 07 July 2008 15:12:56 Message: ---- Deleted : /Cluster size dependence figure Deleted : /Scaling Revision: 55 Author: kuprov Date: 07 July 2008 15:09:18 Message: SVN plays up. ---- Added : /custom_operator.m Added : /pulse_acquire_selective.m Added : /rlx_gen.m Revision: 54 Author: kuprov Date: 07 July 2008 15:08:58 Message: DD and CSA self-relaxation implemented without cross-correlations. Pervushin fork moved to mainstream, old code moved to the directory named as such. Some odds and ends collected into a dumpster. ---- Added : /old code Added : /old code/cluster_gen.m Added : /old code/cluster_ham.m Added : /old code/cluster_treat.m Added : /old code/create_ss.m Added : /old code/exact_treat.m Added : /old code/expv.m Added : /old code/liouv_gen.m Added : /old code/mary.m Added : /old code/padm.m Added : /old code/pauli.m Added : /old code/prop_gen.m Added : /old code/prune_pro.m Added : /old code/pulse_acquire.m Added : /old code/run_me.m Added : /old code/state2dm.m Added : /old code/state_pregen.m Added : /old code/statelist_gen.m Revision: 53 Author: kuprov Date: 07 July 2008 15:08:47 Message: ---- Deleted : /ZTE pruning/illustrations Revision: 52 Author: kuprov Date: 07 July 2008 15:06:04 Message: ---- Modified : /cluster_gen.m Modified : /cluster_ham.m Modified : /create_ss.m Modified : /liouv_gen.m Modified : /pauli.m Modified : /prop_gen.m Modified : /prune_pro.m Modified : /pulse_acquire.m Modified : /run_me.m Modified : /state2dm.m Modified : /state_pregen.m Modified : /statelist_gen.m Revision: 51 Author: kuprov Date: 07 July 2008 14:22:12 Message: CSA self-relaxation implemented (no cross-correlations so far). ZTE is playing up when simulation settings change -- must find a reliable pruning criterion. ---- Modified : /pervushin_fork/create_ss.m Modified : /pervushin_fork/pulse_acquire.m Modified : /pervushin_fork/rlx_gen.m Modified : /pervushin_fork/run_me.m Revision: 50 Author: kuprov Date: 07 July 2008 10:17:45 Message: Shifted to real time units, now reading isotopes rather than multiplicities, streamlined the parameter intake, added CSA ingestion. Now asking user for the detection parameters (sweep and npoints) instead of guessing them. ---- Modified : /pervushin_fork/create_ss.m Modified : /pervushin_fork/prune_pro.m Modified : /pervushin_fork/pulse_acquire.m Modified : /pervushin_fork/rlx_gen.m Modified : /pervushin_fork/run_me.m Revision: 49 Author: kuprov Date: 06 July 2008 20:18:40 Message: Took out the exponential envelope and switched completely to the relaxation superoperator -- it currently writes a 10 Hz relaxation rate for the orders that it has to skip. Will now try to move to precise timing sync -- the system thus far was working in whatever dumbass units. Trying to move it to physical time. ---- Modified : /pervushin_fork/pulse_acquire.m Modified : /pervushin_fork/rlx_gen.m Modified : /pervushin_fork/run_me.m Revision: 48 Author: kuprov Date: 06 July 2008 20:05:50 Message: Removed the historical inconsistency between the multiplication by 'i' in the main Liouvillian and other global operators. Beware of the repercussions, but seems to be OK. ---- Modified : /pervushin_fork/liouv_gen.m Modified : /pervushin_fork/prop_gen.m Modified : /pervushin_fork/prune_pro.m Revision: 47 Author: kuprov Date: 06 July 2008 19:57:56 Message: Fixed a bug with distance matrix and put in a rudimentary dipolar relaxation superoperator -- currently only single spin order self-relaxation. ---- Modified : /pervushin_fork/create_ss.m Modified : /pervushin_fork/rlx_gen.m Modified : /pervushin_fork/run_me.m Revision: 46 Author: kuprov Date: 06 July 2008 18:27:08 Message: Switched to dense arithmetic inside state2dm.m Seems to lead to a minor performance gain, but watch out. Oddly enough, the assignment in liouv_gen.m takes an awful lot of time. And the Kronecker products in general would bloody do with a bit of a speed-up. ---- Modified : /pervushin_fork/state2dm.m Modified : /pervushin_fork/state_pregen.m Revision: 45 Author: kuprov Date: 05 July 2008 14:26:43 Message: SVN playing up. ---- Modified : /pervushin_fork Deleted : /pervushin_fork/cluster_gen.asv Deleted : /pervushin_fork/custom_operator.asv Deleted : /pervushin_fork/liouv_gen.asv Deleted : /pervushin_fork/pauli.asv Deleted : /pervushin_fork/prop_gen.asv Deleted : /pervushin_fork/prune_pro.asv Deleted : /pervushin_fork/pulse_acquire.asv Deleted : /pervushin_fork/run_me.asv Deleted : /pervushin_fork/state_pregen.asv Revision: 44 Author: kuprov Date: 05 July 2008 14:25:24 Message: Added the distance matrix calculation to create_ss.m and put in some basic skeleton for rlx_gen.m ---- Modified : /pervushin_fork/create_ss.m Added : /pervushin_fork/rlx_gen.m Revision: 43 Author: kuprov Date: 05 July 2008 13:45:08 Message: Added the coordinates and the correlation time to the spin_system data structure. Both can now be supplied and are ingested correctly, but are thus far unused. ---- Modified : /pervushin_fork/create_ss.m Modified : /pervushin_fork/run_me.asv Modified : /pervushin_fork/run_me.m Revision: 42 Author: kuprov Date: 03 July 2008 17:36:52 Message: ---- Added : /Literature/density matrix renormalization Added : /Literature/density matrix renormalization/0207340v1.pdf Added : /Literature/density matrix renormalization/0303557v1.pdf Added : /Literature/density matrix renormalization/0407066v1.pdf Added : /Literature/density matrix renormalization/0502475v1.pdf Added : /Literature/density matrix renormalization/0603842v1.pdf Added : /Literature/density matrix renormalization/0609039v1.pdf Added : /Literature/density matrix renormalization/GetPDFServlet.pdf Added : /Literature/density matrix renormalization/p2863_1.pdf Added : /Literature/tree-code and fmm in quantum chemistry.pdf Deleted : /Thumbs.db Added : /code from Olga Added : /code from Olga/TheProgram Added : /code from Olga/TheProgram/Arrays.m Added : /code from Olga/TheProgram/ChangingField.m Added : /code from Olga/TheProgram/Fig5_ChangingAngles1.m Added : /code from Olga/TheProgram/Fig5_ChangingAngles2.m Added : /code from Olga/TheProgram/GaussianDataSaving.m Added : /code from Olga/TheProgram/GeneralPart.m Added : /code from Olga/TheProgram/Id.m Added : /code from Olga/TheProgram/ShowFig5.m Added : /code from Olga/TheProgram/Singlet.m Added : /code from Olga/TheProgram/Sm.m Added : /code from Olga/TheProgram/Sp.m Added : /code from Olga/TheProgram/Sp_check.m Added : /code from Olga/TheProgram/SphericCoord.asv Added : /code from Olga/TheProgram/SphericCoord.m Added : /code from Olga/TheProgram/SphericCoordMoving.m Added : /code from Olga/TheProgram/SphericCoord_new.asv Added : /code from Olga/TheProgram/SphericCoord_new.m Added : /code from Olga/TheProgram/SphericCoord_test.asv Added : /code from Olga/TheProgram/SphericCoord_test.m Added : /code from Olga/TheProgram/Sx.m Added : /code from Olga/TheProgram/SxTEST.m Added : /code from Olga/TheProgram/Sy.m Added : /code from Olga/TheProgram/SyTEST.m Added : /code from Olga/TheProgram/Sz.m Added : /code from Olga/TheProgram/SzTEST.m Added : /code from Olga/TheProgram/T20.m Added : /code from Olga/TheProgram/T20norm.m Added : /code from Olga/TheProgram/T2m1.m Added : /code from Olga/TheProgram/T2m1norm.m Added : /code from Olga/TheProgram/T2m2.m Added : /code from Olga/TheProgram/T2m2norm.m Added : /code from Olga/TheProgram/T2p1.m Added : /code from Olga/TheProgram/T2p1norm.m Added : /code from Olga/TheProgram/T2p2.m Added : /code from Olga/TheProgram/T2p2check.m Added : /code from Olga/TheProgram/T2p2norm.m Added : /code from Olga/TheProgram/ToDrawFigureFromDataFile.m Added : /code from Olga/TheProgram/ToDrawFigureFromDataFileMy.m Added : /code from Olga/TheProgram/ToPrintPictures.m Added : /code from Olga/TheProgram/ToPrintPictures1.m Added : /code from Olga/TheProgram/ToPrintPictures_Advanced.m Added : /code from Olga/TheProgram/ToWatch.m Added : /code from Olga/TheProgram/ToWatchFig5.m Added : /code from Olga/TheProgram/ToWatch_ChangingAngles.m Added : /code from Olga/TheProgram/ToWatch_Fig5_100micsec.m Added : /code from Olga/TheProgram/ToWatch_Fig5_200micsec.m Added : /code from Olga/TheProgram/ToWatch_Fig5_5micsec.m Added : /code from Olga/TheProgram/ToWriteMovieA.m Added : /code from Olga/TheProgram/ToWriteMovieAB.m Added : /code from Olga/TheProgram/ToWriteMovieB.m Added : /code from Olga/TheProgram/WignerD.m Added : /code from Olga/TheProgram/Y1m1.m Added : /code from Olga/TheProgram/Y1o0.m Added : /code from Olga/TheProgram/Y1p1.m Added : /code from Olga/TheProgram/checking.m Added : /code from Olga/TheProgram/expv.m Added : /code from Olga/TheProgram/launch.m Added : /code from Olga/TheProgram/prune_pro.m Added : /code from Olga/gaussian_log_files Added : /code from Olga/gaussian_log_files/Isotr_test.log Added : /code from Olga/gaussian_log_files/N2_test_ax_m1_m1.log Added : /code from Olga/gaussian_log_files/flavin_anion_radical_hfc_vacuum.log Added : /code from Olga/gaussian_log_files/flavin_anion_radical_hfc_vacuum_unit_vectors.log Added : /code from Olga/gaussian_log_files/flavin_neutr_rad_hfc_vacuum.log Added : /code from Olga/gaussian_log_files/flavin_neutr_rad_hfc_vacuum_unit_vectors.log Added : /code from Olga/gaussian_log_files/nmrdata.txt Added : /code from Olga/gaussian_log_files/test4.log Added : /code from Olga/gaussian_log_files/trp_cation_rad_hfc_vacuum.log Added : /code from Olga/gaussian_log_files/trp_cation_rad_hfc_vacuum_unit_vectors.log Added : /code from Olga/gaussian_log_files/trp_neutr_rad_ hfc_vacuum.log Added : /code from Olga/gaussian_log_files/trp_neutr_rad_ hfc_vacuum_unit_vectors.log Added : /code from Olga/gaussian_log_files/trp_neutr_rad_ hfc_vacuum_unit_vectors_TEST.log Added : /code from Olga/input_files Added : /code from Olga/input_files/isotr.mat Added : /code from Olga/input_files/test.mat Added : /code from Olga/input_files/test1N.mat Added : /code from Olga/input_files/test_4n.mat Added : /code from Olga/results Added : /code from Olga/results/gaussianData.mat Added : /code from Olga/results/result_isotr.mat Added : /code from Olga/results/result_test.mat Revision: 41 Author: kuprov Date: 14 June 2008 13:41:56 Message: Pervushin fork goes to JMR. ---- Modified : /Thumbs.db Modified : /pervushin_fork/prune_pro.m Revision: 40 Author: kuprov Date: 01 June 2008 15:16:42 Message: An update to prune_pro.m, including ZTE, Lanczos and SVD pruning. ---- Added : /pervushin_fork/prune_pro.asv Modified : /pervushin_fork/prune_pro.m Modified : /pervushin_fork/pulse_acquire.m Modified : /pervushin_fork/run_me.m Revision: 39 Author: kuprov Date: 29 May 2008 10:55:35 Message: ---- Deleted : /pervushin_fork/ssr_code.zip Revision: 38 Author: kuprov Date: 29 May 2008 10:49:49 Message: Selective pulses implemented. ---- Added : /pervushin_fork/custom_operator.asv Added : /pervushin_fork/custom_operator.m Modified : /pervushin_fork/pulse_acquire.asv Added : /pervushin_fork/pulse_acquire_selective.m Modified : /pervushin_fork/run_me.asv Modified : /pervushin_fork/run_me.m Revision: 37 Author: kuprov Date: 28 May 2008 09:43:03 Message: Cosmetic changes. ---- Modified : /pervushin_fork/cluster_gen.m Modified : /pervushin_fork/liouv_gen.m Modified : /pervushin_fork/run_me.m Added : /pervushin_fork/ssr_code.zip Modified : /pervushin_fork/state_pregen.m Revision: 36 Author: kuprov Date: 26 May 2008 21:03:17 Message: Final code without relaxation. Sending it to KP. ---- Modified : /pervushin_fork/run_me.m Revision: 35 Author: kuprov Date: 26 May 2008 20:57:32 Message: Basic pulse-acquire sequence done to Konstantin's specification. Relaxation not included so far. ---- Added : /pervushin_fork/cluster_gen.asv Modified : /pervushin_fork/cluster_gen.m Modified : /pervushin_fork/create_ss.m Added : /pervushin_fork/pulse_acquire.asv Modified : /pervushin_fork/pulse_acquire.m Modified : /pervushin_fork/run_me.m Revision: 34 Author: kuprov Date: 26 May 2008 20:21:18 Message: Adding a cleaned-up version for Konstantin Pervushin. Might be beneficial in the long run, because a significant clean-up ans streamlining has been performed. ---- Added : /pervushin_fork Added : /pervushin_fork/cluster_gen.m Added : /pervushin_fork/cluster_ham.m Added : /pervushin_fork/create_ss.m Added : /pervushin_fork/expv.m Added : /pervushin_fork/liouv_gen.asv Added : /pervushin_fork/liouv_gen.m Added : /pervushin_fork/pauli.asv Added : /pervushin_fork/pauli.m Added : /pervushin_fork/prop_gen.asv Added : /pervushin_fork/prop_gen.m Added : /pervushin_fork/prune_pro.m Added : /pervushin_fork/pulse_acquire.m Added : /pervushin_fork/run_me.asv Added : /pervushin_fork/run_me.m Added : /pervushin_fork/state2dm.m Added : /pervushin_fork/state_pregen.asv Added : /pervushin_fork/state_pregen.m Added : /pervushin_fork/statelist_gen.m Revision: 33 Author: kuprov Date: 26 May 2008 18:48:51 Message: Minor improvements here and there. ---- Deleted : /Davidson diagonalization Deleted : /Direct protein structure fitting Deleted : /Krylov techniques Modified : /Lanczos pruning/lanczos_prune.m Added : /Lanczos pruning/svd_prune.m Modified : /Lanczos pruning/test_system.m Added : /Literature/density matrix purification.pdf Added : /Literature/propagation with a time-dependent Hamiltonian.pdf Added : /SVD pruning Added : /SVD pruning/10_states.eps Added : /SVD pruning/160_states.eps Added : /SVD pruning/20_states.eps Added : /SVD pruning/320_states.eps Added : /SVD pruning/40_states.eps Added : /SVD pruning/420_states.eps Added : /SVD pruning/80_states.eps Added : /SVD pruning/test_system.asv Added : /SVD pruning/test_system.m Modified : /Thumbs.db Added : /ZTE pruning Added : /ZTE pruning/12_states.eps Added : /ZTE pruning/154_states.eps Added : /ZTE pruning/24_states.eps Added : /ZTE pruning/320_states.eps Added : /ZTE pruning/420_states.eps Added : /ZTE pruning/42_states.eps Added : /ZTE pruning/80_states.eps Added : /ZTE pruning/expv.m Added : /ZTE pruning/illustrations Added : /ZTE pruning/test_system.m Added : /ZTE pruning/zte_prune.m Modified : /prop_gen.m Modified : /prune_pro.m Added : /pulse_acquire.asv Modified : /pulse_acquire.m Modified : /run_me.m Deleted : /subgraph enumeration Revision: 32 Author: kuprov Date: 14 May 2008 17:41:02 Message: All fine. About to use SVD instead of the Lanczos procedure, hopefully to make it adaptive and stable. ---- Added : /Lanczos pruning/illustrations/420_states.eps Modified : /Lanczos pruning/lanczos_prune.m Modified : /Lanczos pruning/test_system.m Revision: 31 Author: kuprov Date: 13 May 2008 21:20:45 Message: Final variant and the picture for the poster ---- Added : /Lanczos pruning/illustrations Added : /Lanczos pruning/illustrations/10_states.eps Added : /Lanczos pruning/illustrations/160_states.eps Added : /Lanczos pruning/illustrations/20_states.eps Added : /Lanczos pruning/illustrations/320_states.eps Added : /Lanczos pruning/illustrations/40_states.eps Added : /Lanczos pruning/illustrations/80_states.eps Modified : /Lanczos pruning/lanczos_prune.asv Modified : /Lanczos pruning/test_system.asv Modified : /Lanczos pruning/test_system.m Revision: 30 Author: kuprov Date: 09 May 2008 17:27:10 Message: Very good vanilla Lanczos pruning implementation. ---- Deleted : /Lanczos pruning/lanczos_cosy.asv Deleted : /Lanczos pruning/lanczos_cosy.m Added : /Lanczos pruning/lanczos_prune.asv Added : /Lanczos pruning/lanczos_prune.m Added : /Lanczos pruning/test_system.asv Added : /Lanczos pruning/test_system.m Revision: 29 Author: kuprov Date: 16 April 2008 18:07:57 Message: ---- Modified : /liouv_gen.asv Modified : /liouv_gen.m Revision: 28 Author: kuprov Date: 16 April 2008 16:56:59 Message: Some improvements in the speed of liouv_gen.m ---- Added : /Krylov techniques Added : /Krylov techniques/am64.pdf Added : /Krylov techniques/p130-sidje.pdf Added : /Lanczos pruning/a-stable-lanczos-tridiagonalization.pdf Added : /householder tridiagonalization Added : /householder tridiagonalization/ahbeigs.m Added : /householder tridiagonalization/h_trid.m Modified : /liouv_gen.asv Modified : /liouv_gen.m Modified : /prune_pro.asv Modified : /prune_pro.m Modified : /run_me.m Revision: 27 Author: kuprov Date: 15 April 2008 17:46:08 Message: ---- Added : /Davidson diagonalization/GetPDFServlet.pdf Added : /Literature/Shen PNAS 2008.pdf Modified : /cluster_treat.m Added : /mary.m Modified : /prune_pro.m Added : /pulse_acquire.m Modified : /run_me.asv Modified : /run_me.m Revision: 26 Author: kuprov Date: 14 April 2008 21:14:35 Message: Sorta works with dynamic zero track elimination. Tolerances need to be tightened. Chopped out a lot from the propagator code. ---- Modified : /cluster_treat.asv Modified : /cluster_treat.m Modified : /prop_gen.asv Modified : /prop_gen.m Modified : /prune_pro.m Modified : /run_me.m Revision: 25 Author: kuprov Date: 14 April 2008 19:43:45 Message: ---- Modified : /cluster_treat.m Modified : /prune_pro.asv Modified : /prune_pro.m Modified : /run_me.m Revision: 24 Author: kuprov Date: 14 April 2008 15:45:11 Message: Tentatively got it -- use Krylov to get the first ten steps of the trajectory, then shrink the state space, compute the propagators and go ahead. ---- Modified : /cluster_treat.asv Modified : /cluster_treat.m Modified : /prune_pro.asv Modified : /prune_pro.m Revision: 23 Author: kuprov Date: 14 April 2008 13:42:50 Message: Zero track elimination pruning implemented. Seems to work best. Will now try to avoid computing the propagators. ---- Added : /Application 1 Added : /Application 1/a nice COSY to simulateja711454e.pdf Added : /Davidson diagonalization Added : /Davidson diagonalization/talk05-Ron-Shepard.pdf Added : /Discussions Added : /Discussions/Re libraries.txt Added : /Discussions/libraries.txt Added : /Lanczos pruning/TR_PA_03_25.pdf Added : /Literature/GetPDFServlet.pdf Added : /Literature/child.pdf Modified : /cluster_treat.m Modified : /prune_pro.asv Modified : /prune_pro.m Modified : /run_me.asv Modified : /run_me.m Revision: 22 Author: kuprov Date: 31 March 2008 09:49:19 Message: Just a commit. ---- Added : /Lanczos pruning/a808450e.pdf Modified : /cluster_treat.asv Added : /prune_pro.asv Modified : /run_me.m Revision: 21 Author: kuprov Date: 30 March 2008 21:44:51 Message: Pruning implemented in both 1D and COSY, but, in retrospect obviously, it did not make the calculation any faster. Lanczos pruning just gathers the non-zeros from a big and sparse matrix into a small and dense matrix. The number of multiplications remains the same. ---- Modified : /cluster_treat.asv Modified : /cluster_treat.m Modified : /prune_pro.m Modified : /run_me.m Revision: 20 Author: kuprov Date: 30 March 2008 20:16:29 Message: Lanczos pruning implemented into 1D subroutine. Works like a breeze. ---- Added : /75_states.png Modified : /Thumbs.db Modified : /cluster_treat.asv Modified : /cluster_treat.m Added : /prune_pro.m Modified : /run_me.m Revision: 19 Author: kuprov Date: 30 March 2008 19:09:23 Message: Tolerance-based pruning implemented. ---- Modified : /Lanczos pruning/prune_pro.m Revision: 18 Author: kuprov Date: 30 March 2008 17:17:13 Message: Tolerance-based pruning subroutine ready. ---- Modified : /Lanczos pruning/lanczos_cosy.m Added : /Lanczos pruning/prune_pro.asv Added : /Lanczos pruning/prune_pro.m Added : /Lanczos pruning/simultaneous diophantine approximation.pdf Revision: 17 Author: kuprov Date: 29 March 2008 18:11:57 Message: Pruning subroutine with user-selectable new dimension is ready. Will now re-do it in terms of the relative state vector norm cut-off. ---- Modified : /Lanczos pruning/lanczos_cosy.m Modified : /Lanczos pruning/prune.m Revision: 16 Author: kuprov Date: 29 March 2008 17:52:39 Message: Halfway to creating a robust pruning subroutine. ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Added : /Lanczos pruning/prune.asv Added : /Lanczos pruning/prune.m Revision: 15 Author: kuprov Date: 28 March 2008 13:15:25 Message: All working. Will now return to exact pre-simulation, looks like it works much better and isn't that much more expensive after all. ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 14 Author: kuprov Date: 27 March 2008 18:09:21 Message: Looks like the MGS orthogonalization finally works. The secret was to propagate the spin system far enough between steps and not touch the density matrix as it runs. ---- Modified : /Lanczos pruning/lanczos_cosy.m Revision: 13 Author: kuprov Date: 27 March 2008 17:39:25 Message: ---- Modified : /Lanczos pruning/lanczos_cosy.asv Added : /Lanczos pruning/orthogonalization techniques.pdf Revision: 12 Author: kuprov Date: 26 March 2008 23:42:16 Message: Crude finite-difference pre-run to estimate the state space has been implemented. Quite a few tolerance parameters, damn it. ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 11 Author: kuprov Date: 26 March 2008 22:31:42 Message: SVD works just fine. :) ---- Modified : /Lanczos pruning/lanczos_cosy.m Revision: 10 Author: kuprov Date: 26 March 2008 22:01:42 Message: SVD routine working perfectly. Need an efficient way to compute the initial trajectory (finite-diference?) ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 9 Author: kuprov Date: 26 March 2008 21:31:01 Message: Got the perfectly working code by using orth() on the exact state space trajectory. Will now experiment with SVD cutoffs... ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 8 Author: kuprov Date: 26 March 2008 20:13:56 Message: Stuff works, but it is not overwhelmingly impressive. Will now try to do binary state space traversal. ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 7 Author: kuprov Date: 26 March 2008 17:11:25 Message: Vaguely working. ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 6 Author: kuprov Date: 26 March 2008 16:44:35 Message: Half-way to TDPT state mapping. ---- Added : /Lanczos pruning/JHF paper 1 on basis pruning.pdf Added : /Lanczos pruning/JHF paper 2 on basis pruning.pdf Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Deleted : /Literature/JHF paper 1 on basis pruning.pdf Deleted : /Literature/JHF paper 2 on basis pruning.pdf Revision: 5 Author: kuprov Date: 25 March 2008 17:11:45 Message: Liouville space transfer complete. ---- Modified : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 4 Author: kuprov Date: 25 March 2008 16:33:43 Message: Exact 1D up and running. ---- Added : /Lanczos pruning/lanczos_cosy.asv Modified : /Lanczos pruning/lanczos_cosy.m Revision: 3 Author: kuprov Date: 25 March 2008 15:16:08 Message: ---- Added : /Lanczos pruning Added : /Lanczos pruning/lanczos_cosy.m Added : /Literature/JHF paper 1 on basis pruning.pdf Added : /Literature/JHF paper 2 on basis pruning.pdf Deleted : /Literature/JHF paper on basis pruning.pdf Added : /Literature/chemical_graph_theory_1.pdf Added : /Thumbs.db Deleted : /branches Modified : /prop_gen.m Modified : /run_me.m Deleted : /tags Deleted : /trunk Revision: 2 Author: kuprov Date: 03 March 2008 19:51:18 Message: ---- Added : /CRT_quads_vs_triples.ai Added : /CRT_quads_vs_triples.png Added : /Cluster size dependence figure Added : /Cluster size dependence figure/doubles.eps Added : /Cluster size dependence figure/exact.eps Added : /Cluster size dependence figure/quads.eps Added : /Cluster size dependence figure/singles.eps Added : /Cluster size dependence figure/triples.eps Added : /Direct protein structure fitting Added : /Direct protein structure fitting/cpl.pdf Added : /Direct protein structure fitting/jp0683871.pdf Added : /Direct protein structure fitting/jp0718754.pdf Added : /Literature Added : /Literature/Buevich Added : /Literature/Buevich/Oulu_abs_1994.pdf Added : /Literature/Buevich/Riga_abs_1986.pdf Added : /Literature/IR multimode analogy Added : /Literature/IR multimode analogy/jp072647c.pdf Added : /Literature/IR multimode analogy/jp072880a.pdf Added : /Literature/JHF paper on basis pruning.pdf Added : /Literature/automatic-state-decomposition.pdf Added : /Literature/chemical_graph_theory.pdf Added : /MEX files Added : /MEX files/helloworld.c Added : /MEX files/helloworld.mexw64 Added : /MEX files/timestwo.c Added : /MEX files/timestwo.mexw64 Added : /Scaling Added : /Scaling/18-spin quads.eps Added : /Scaling/30-spin doubles.eps Added : /Scaling/30-spin doubles.png Added : /Scaling/36-spin triples.eps Added : /Scaling/36-spin triples.png Added : /Scaling/Scaling.opj Added : /Sparse matrix exponentials Added : /Sparse matrix exponentials/chbv.m Added : /Sparse matrix exponentials/example.m Added : /Sparse matrix exponentials/expv.m Added : /Sparse matrix exponentials/loadccs.m Added : /Sparse matrix exponentials/loadcoo.m Added : /Sparse matrix exponentials/loadcrs.m Added : /Sparse matrix exponentials/mat2ccs.m Added : /Sparse matrix exponentials/mat2coo.m Added : /Sparse matrix exponentials/mat2crs.m Added : /Sparse matrix exponentials/mexpv.m Added : /Sparse matrix exponentials/padm.m Added : /Sparse matrix exponentials/paper.pdf Added : /Sparse matrix exponentials/phiv.m Added : /check_it_out.asv Added : /cluster_gen.asv Added : /cluster_gen.m Added : /cluster_ham.asv Added : /cluster_ham.m Added : /cluster_treat.asv Added : /cluster_treat.m Added : /create_ss.asv Added : /create_ss.m Added : /crt_quads.png Added : /crt_triples.png Added : /exact_treat.asv Added : /exact_treat.m Added : /expv.asv Added : /expv.m Added : /final_quints.fig Added : /liouv_gen.asv Added : /liouv_gen.m Added : /padm.m Added : /pauli.asv Added : /pauli.m Added : /prop_gen.asv Added : /prop_gen.m Added : /py_dma_triples.png Added : /quads_1000ns.eps Added : /quads_100ns.eps Added : /quads_10ns.eps Added : /quads_1ns.eps Added : /run_me.asv Added : /run_me.m Added : /spin_system.asv Added : /state2dm.asv Added : /state2dm.m Added : /state_pregen.asv Added : /state_pregen.m Added : /statelist_gen.asv Added : /statelist_gen.m Added : /strychnine Added : /strychnine/13C_assignment.gif Added : /strychnine/13C_lines.txt Added : /strychnine/13C_spectrum.gif Added : /strychnine/1H_assignment.gif Added : /strychnine/1H_lines.txt Added : /strychnine/1H_spectrum.gif Added : /strychnine/nmrdata.txt Added : /strychnine/stry_geom.log Added : /strychnine/stry_nmr_cc-pVDZ.log Added : /strychnine/stry_nmr_cc-pVTZ.log Added : /subgraph enumeration Added : /subgraph enumeration/cluster expansion.pdf Added : /subgraph enumeration/kiyomi_Dr_thesis.pdf Added : /subgraph enumeration/subgraph_enumeration_1.pdf Added : /subgraph enumeration/trin_1.pdf Added : /tc5b Added : /tc5b/123.LOG Added : /tc5b/123.gjf Added : /tc5b/PM3_OPT_GASEOUS_DROP.LOG Added : /tc5b/PM3_OPT_GASEOUS_DROP_ONIOM.LOG Added : /tc5b/pm3_opt_gaseous_drop.gjf Added : /tc5b/pm3_opt_gaseous_drop_oniom.gjf Added : /tc5b/pm3_opt_gaseous_drop_oniom_1.gjf Added : /tc5b/pm3_opt_gaseous_drop_oniom_2.gjf Added : /test1_quads.fig Added : /test1_quints.fig Added : /test1_sexts.fig Added : /test1_triples.fig Added : /test_quads.png Added : /test_triples.png Added : /triples_1000ns.eps Added : /triples_100ns.eps Added : /triples_10ns.eps Added : /triples_1ns.eps Revision: 1 Author: VisualSVN Server Date: 03 March 2008 19:50:30 Message: Initial structure. ---- Added : /branches Added : /tags Added : /trunk