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Topics - faq_user

Pages: [1]
1
Simulations / Quantum number conversion
« on: November 15, 2013, 06:03:52 PM »
I am trying out the new version, 1.3.1916 spinach. I am looking for the easiest way to convert the (L,M) index the "stateinfo" function generates to maybe Hilbert space matrix representation in the end. I would like to know if you have any suggestions on how to do that. Right now I am looking through the stateinfo function to see how you did the index conversion from 0,1,2,3 to (L,M). Thanks a lot!

2
Simulations / questions about new spinach version
« on: November 15, 2013, 06:01:08 PM »
1. Is there a function you have written for spin-locking? I had an impression there is, but I cannot find it.

2. Is there a way now to conveniently extract the density matrix information from the tensor operator basis to the zeeman base matrix? I built each state like the singlet state before, but it is tedious for larger spin system.

3. I noticed in the JACS paper, you use M06/cc-pVTZ to simulate the system, have you compared the performace with b3lyp or other functional/basis set combination?

3
Simulations / Spinach software requirements
« on: November 15, 2013, 05:57:14 PM »
The website states that the minimum supported version of Matlab is 2013a (64-bit version) with Parallel Computing Toolbox. Is this toolbox necessary, or is it only really needed for working on more advanced processes?

We were also thinking of running Matlab on a linux distribution. Would there be any issues for Spinach with doing this that you know of?

4
Simulations / relaxation time calculation using Spinach
« on: November 15, 2013, 05:54:16 PM »
Dear Prof. Kuprov,
I want to extract T1 and T2 relaxation time in a ESR calculation. Is it possible with Spinach code?

5
Simulations / about T1,T2 relaxation theory in spinach
« on: November 15, 2013, 05:50:54 PM »
Dear professor Kuprov,
I learn the relaxation superoperator in source file ‘relaxation.m’, and I wonder if there is any reference documentation recommendable about T1,T2 relaxation theory part (although it seems simple from the code)?
Thanks a lot!

6
Spinach bug reports / Paths and parallelization
« on: November 15, 2013, 05:48:17 PM »
Dear Ilya,
 
meanwhile I'm using spinach 1.3.1980 + matlab R2013a. In order to prepare for some 2D experiments, I tried to run nmr_liquids/hmqc_strychnine.m without any changes. Instead of a 2D plot I obtain the following error text at the end of the protocol output:
 
[...allel_function > (parfor body) > basis > banner ]  ===========================================
[...allel_function > (parfor body) > basis > banner ]  =                                         =
[...allel_function > (parfor body) > basis > banner ]  =                BASIS SET                =
[...allel_function > (parfor body) > basis > banner ]  =                                         =
[...allel_function > (parfor body) > basis > banner ]  ===========================================
[...allel_function > (parfor body) > basis > banner ]   
[...ine > parallel_function > (parfor body) > basis ]  spherical tensor basis set using Liouville space matrix formalism.
[...ine > parallel_function > (parfor body) > basis ]  IK-2 approximation - spin correlations involving all nearest neighbours of each spin on the coupling graph.
[...ine > parallel_function > (parfor body) > basis ]  IK-2 approximation - spin correlations up to order 1 between all spins within 4 Angstrom of each other.
[...ine > parallel_function > (parfor body) > basis ]  scalar couplings will be used to build the coupling graph.
[...ine > parallel_function > (parfor body) > basis ]  coupling tensors with norm below 1e-05 will be ignored.
[...ine > parallel_function > (parfor body) > basis ]  connectivity matrix density 11.1531%
[...ine > parallel_function > (parfor body) > basis ]  proximity matrix density 4.3478%
[...ine > parallel_function > (parfor body) > basis ]  WARNING - the system contains 9 non-interacting subsystems.
[...ine > parallel_function > (parfor body) > basis ]  23 subgraphs generated from coupling data.
[...ine > parallel_function > (parfor body) > basis ]  23 subgraphs generated from proximity data.
[...ine > parallel_function > (parfor body) > basis ]  removing identical subgraphs...
[...ine > parallel_function > (parfor body) > basis ]  generated 23 subgraphs of size 1
[...ine > parallel_function > (parfor body) > basis ]  generated 7 subgraphs of size 2
[...ine > parallel_function > (parfor body) > basis ]  generated 7 subgraphs of size 3
[...ine > parallel_function > (parfor body) > basis ]  generated 2 subgraphs of size 4
[...ine > parallel_function > (parfor body) > basis ]  building basis descriptor...
Error using Composite/subsref (line 64)
An invalid indexing request was made.

Error in basis (line 219)
        basis_spec=vertcat(basis_spec{:});

Error in hmqc_strychnine>(parfor body) (line 47)
    subsystem=basis(subsystems{n},bas);

Error in hmqc_strychnine (line 44)
parfor n=1:numel(subsystems)

Caused by:
    Error using Composite/subsref (line 64)
    An invalid indexing request was made.
        Error using Composite/errorIfRemoteOperationInProgress (line 170)
        The Composite value cannot be accessed because
        a remote operation is in progress.
 
This error appears also with any of the other 2D examples.
Because in some 1D runs, matlab R2013a denied the use of the name "spectrum" (obviously they want to give up their function spectrum), I changed "spectrum" to "spectrum1" in my pulse_acquire.m-files runs and got nice spectra.
If I try this workaround with hmqc_strychnine.m I obtain immediately
 
>> hmqc_strychnine
Error using textscan
Invalid file identifier.  Use fopen to generate a valid file identifier.

Error in g03_parse (line 25)
g03_output=textscan(file_id,'%s','bufsize',65536,'delimiter','\n');

Error in hmqc_strychnine_mt (line 12)
[sys,inter]=g03_to_spinach(g03_parse('..\standard_systems\strychnine.log'),...
 
>>
 
I don't know how to solve the problem. Might there be difficulties in the interaction of spinach with this matlab version?

7
Simulations / Cross-polarization simulations
« on: May 17, 2012, 02:28:06 PM »
I noticed you have absorbing boundaries in one of your CP examples. Is it also possible to implement periodic boundary conditions?

8
Simulations / Solid state simulations
« on: May 16, 2012, 01:59:12 PM »
I was hoping that you could help me with this. I played with your nmr_solids_1.m example, and tried to make a 'manual' pulse via the operators and evolution (see attached). The results are not the same. The 'manual' approach produces only one line, which the 'pulse_acquire' function produces a doublet, as it should. I am assuming I am doing something wrong here, but can't figure out what it is. Can you help me with this?

9
Simulations / Strongly coupled spin systems.
« on: May 16, 2012, 01:51:01 PM »
I am using it a lot and have integrated it with my own Matlab code to simulate spectra for metabolomics.
In general the simulations are very fast, which is one of the primary reasons I like to use your code over my own, much slower, density matrix-based code.

However, occasionally I encounter a spin-system that takes much longer to simulate. The reason clearly has to do with how strongly coupled the spin-system under investigation is. I have attached two examples. Both use 7 spins, but differ in the amount of strong coupling. The weak system simulates in 4 seconds, whereas the strong system takes 40 seconds! Am I doing something stupid or is this difference inherent to the spinach algorithm?

I know that in my own density-matrix-based code only the number of spins determines the calculation time, not the scalar couplings. But of course in that program the calculation becomes impossibly slow for more than 7-8 spins.

Please let me know if there is anything I can do to speed up the calculation.

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