Difference between revisions of "Built-in experiments"

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This section contains a brief alphabetic list of the pre-coded pulse sequences supplied with Spinach. If your particular sequence is not listed below, or if you have invented something that is worthy of broad public adoption, drop us a note – we are always interested in expanding Spinach capabilities. With the exceptions noted below, the sequences must be invoked via liquid, crystal, powder and roadmap wrapper functions (see the example set).
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This section contains a list of the pre-programmed pulse sequences supplied with ''Spinach''. Everything is open-source, so feel free to hack and modify as appropriate. If your particular sequence is not listed below, or if you have written something that is worthy of broad public adoption, drop us a note – we are always interested in expanding ''Spinach'' capabilities.  
  
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Unless stated otherwise in the experiment description, all of the functions listed below below should be invoked ''via'' a [[kernel contexts|kernel context]] function that sets the appropriate (solid, liquid, ''etc.'') simulation infrastructure.
 
==General experiments==
 
==General experiments==
  
 
[[acquire.m]] – simple forward time evolution with signal acquisition.
 
[[acquire.m]] – simple forward time evolution with signal acquisition.
  
[[traject.m]] - simple forward time evolution, trajectory is returned.
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[[cpmg.m]] - CPMG echo train with detection.
  
[[slowpass.m]] – slow passage detection - calculates spectrum values at the user specified frequency positions using the Fourier transform of the Liouville - von Neumann equation. The biggest advantage over the fid + fft style detection is easy parallelization and the possibility of getting spectrum values at specific frequencies without recalculating the entire free induction decay.
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[[holeburn.m]] - hole burning experiment.
  
 
[[hp_acquire.m]] – standard hard pulse acquire sequence. The user must supply the pulse operator, the pulse duration and the initial condition.
 
[[hp_acquire.m]] – standard hard pulse acquire sequence. The user must supply the pulse operator, the pulse duration and the initial condition.
 +
 +
[[impound.m]] - captures what it receives from the context function and returns it to the user.
 +
 +
[[levelpop.m]] - energy levels and their populations.
 +
 +
[[relaxan.m]] - automated relaxation theory analysis.
 +
 +
[[slowpass.m]] – calculates spectrum values at the user specified frequency positions using the Fourier transform of the Liouville - von Neumann equation. The biggest advantage over the fid + fft style detection is easy parallelization and the possibility of getting spectrum values at specific frequencies without recalculating the entire free induction decay.
  
 
[[sp_acquire.m]] - a pulse-acquire sequence with a soft pulse.
 
[[sp_acquire.m]] - a pulse-acquire sequence with a soft pulse.
  
[[holeburn.m]] - hole burning experiment.
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[[traject.m]] - simple forward time evolution, trajectory is returned as a stack of density matrices.
 
 
[[levelpop.m]] - energy levels and their populations.
 
  
 
==NMR experiments==
 
==NMR experiments==
  
 
[[clip_hsqc.m]] – CLIP-HSQC pulse sequence.  
 
[[clip_hsqc.m]] – CLIP-HSQC pulse sequence.  
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 +
[[cn2d_sq.m]] – CN2D experiment under MAS, single-quantum.
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 +
[[cn2d_dq.m]] – CN2D experiment under MAS, double-quantum.
  
 
[[cosy.m]] – phase-sensitive COSY pulse sequence.  
 
[[cosy.m]] – phase-sensitive COSY pulse sequence.  
  
[[crosspol.m]] – cross-polarization experiment.  
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[[crosspol.m]] – cross-polarization experiment.
 +
 
 +
[[dante.m]] - DANTE pulse sequence.
  
 
[[dqf_cosy.m]] – phase-sensitive double-quantum filtered COSY pulse sequence
 
[[dqf_cosy.m]] – phase-sensitive double-quantum filtered COSY pulse sequence
Line 31: Line 44:
 
[[hmqc.m]] – magnitude mode HMQC pulse sequence.  
 
[[hmqc.m]] – magnitude mode HMQC pulse sequence.  
  
[[hnco.m]] – Phase-sensitive HNCO pulse sequence from the paper by Lewis Kay and co-authors, using the bidirectional propagation method (paper in press). The sequence is hard-wired to work on 1H, 13C, 15N labelled proteins.  
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[[hnco.m]] – Phase-sensitive HNCO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.  
  
[[hncoca.m]] – Phase-sensitive HNCO pulse sequence from the paper by Bax and Ikura, using the bidirectional propagation method (paper in press). The sequence is hard-wired to work on 1H, 13C, 15N labelled proteins.  
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[[hncoca.m]] – Phase-sensitive HNCO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.  
  
 
[[hsqc.m]] – phase-sensitive HSQC pulse sequence.
 
[[hsqc.m]] – phase-sensitive HSQC pulse sequence.
  
[[lcosy.m]] – localized  COSY pulse sequence.  
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[[lcosy.m]] – localized  COSY pulse sequence.
 +
 
 +
[[m2s.m]] - magnetisation to singlet state.
  
[[cn2d.m]] – CN2D experiment under MAS. See the function header for further information.
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[[mqmas.m]] - 2D multiple-quantum MAS pulse sequence for quadrupolar nuclei.  
 +
 
 +
[[mqs.m]] - 2D multiple-quantum NMR pulse sequence.
  
 
[[noesy.m]] – phase-sensitive homonuclear NOESY pulse sequence.
 
[[noesy.m]] – phase-sensitive homonuclear NOESY pulse sequence.
  
[[roesy.m]] - phase-sensitive homonuclear ROESY pulse sequence.  
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[[noesyhsqc.m]] – phase-sensitive NOESY-HSQC pulse sequence. Hard-wired to 1H, 15N, 1H.
 +
 
 +
[[roesy.m]] - phase-sensitive homonuclear ROESY pulse sequence.
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 +
[[s2m.m]] - singlet state to magnetisation.
  
[[noesyhsqc.m]] – phase-sensitive NOESY-HSQC pulse sequence from the paper by Marion and co-authors. The sequence is hard-wired to 1H, 15N, 1H.
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[[tocsy.m]] - amplitude-mode homonuclear TOCSY.
  
 
==Spatially encoded NMR==
 
==Spatially encoded NMR==
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===Ultrafast and pure-shift NMR===
  
 
[[spencosy.m]] - ultrafast COSY experiment.
 
[[spencosy.m]] - ultrafast COSY experiment.
  
 
[[spendosy.m]] - ultrafast DOSY experiment.
 
[[spendosy.m]] - ultrafast DOSY experiment.
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[[dosy_oneshot.m]] - one-shot DOSY pulse sequence.
  
 
[[spendosycosy.m]] - ultrafast 3D DOSY-COSY experiment.
 
[[spendosycosy.m]] - ultrafast 3D DOSY-COSY experiment.
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[[spendosy_keeler_fit.m]] - original Keeler model data processing for SPEN DOSY.
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[[spendosy_keeler_fit_corr.m]] - corrected Keeler model data processing for SPEN DOSY.
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[[spendosy_frydman_fit.m]] - original Frydman model data processing for SPEN DOSY.
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[[spendosy_keeler_fit_corr.m]] - corrected Frydman model data processing for SPEN DOSY.
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[[spendosy_processing1s.m]] - SPEN DOSY processing, one signal.
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[[spendosy_processing2s.m]] - SPEN DOSY processing, two signals.
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[[stejskal_tanner_analysis.m]] - Stejskal-Tanner analysis of diffusion data.
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[[psyche_1d.m]] - PSYCHE 1D pulse sequence.
  
 
[[diag_psyche_zfilters.m]] - Phase-sensitive homonuclear DIAG pulse sequence.
 
[[diag_psyche_zfilters.m]] - Phase-sensitive homonuclear DIAG pulse sequence.
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===Diffusion NMR===
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[[pfg_spin_echo.m]] - Pulsed field gradient spin echo sequence.
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[[pfg_stim_echo.m]] - Pulsed field gradient stimulated spin echo sequence.
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[[bpp_stim_echo.m]] - Bipolar pulse pair stimulated spin echo sequence.
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===Gradient signal suppression===
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[[dpfgse_select.m]] - DPFGSE signal selection
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[[dpfgse_suppress.m]] - DPFGSE signal suppression
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==Magnetic resonance imaging==
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{{:mri_sequence_list}}
  
 
==Overtone NMR experiments==
 
==Overtone NMR experiments==
Line 76: Line 134:
  
 
[[eseem.m]] – ESEEM pulse sequence.
 
[[eseem.m]] – ESEEM pulse sequence.
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 +
[[fieldsweep.m]] - field sweep ESR experiment using steady state formalism.
  
 
[[hyscore.m]] – HYSCORE experiment.
 
[[hyscore.m]] – HYSCORE experiment.
  
[[oopeseem.m]] - out-of-phase ESEEM expariment.
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[[oopeseem.m]] - out-of-phase ESEEM experiment.
  
 
[[rapidscan.m]] - ESR rapid field scan experiment.
 
[[rapidscan.m]] - ESR rapid field scan experiment.
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 +
[[sifter.m]] - SIFTER experiment
  
 
==DEER/PELDOR experiments==
 
==DEER/PELDOR experiments==
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[[masdnp.m]] - magic angle spinning DNP.
 
[[masdnp.m]] - magic angle spinning DNP.
  
==Paramagnetic shift==
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==Paramagnetic NMR spectroscopy==
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 +
[[centroid.m]] - centre of mass point of a 3D probability density in a cube.
 +
 
 +
[[csa2racs.m]] - residual anisotropic chemical shift.
 +
 
 +
[[eqmag.m]] - molar magnetization vector at the thermal equilibrium.
  
[[ipcs.m]] – spin density recovery from pseudocontact shifts. See function header for further information.
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[[fieldscan_enlev.m]] - energy levels as a function of the magnetic field.
  
[[ippcs.m]] – point electron model fitting to PCS data. See the function header for further information.
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[[fieldscan_magn.m]] - Z magnetisation in a finite-speed field sweep.
  
[[kpcs.m]] – PCS calculation using Kuprov equation. See the function header for further information.
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[[geffect.m]] - Effective g-tensor for a user-specified Kramers doublet.
  
 
[[hfc2pcs.m]] - computes pseudocontact shifts from hyperfine couplings and susceptibility tensors.
 
[[hfc2pcs.m]] - computes pseudocontact shifts from hyperfine couplings and susceptibility tensors.
  
 
[[hfc2pms.m]] - computes paramagnetic shifts (contact + pseudocontact) from hyperfine couplings and susceptibility data.
 
[[hfc2pms.m]] - computes paramagnetic shifts (contact + pseudocontact) from hyperfine couplings and susceptibility data.
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 +
[[ipcs.m]] – tag probability density recovery from pseudocontact shifts..
 +
 +
[[ippcs.m]] – point electron model fitting to PCS data.
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 +
[[kpcs.m]] – PCS calculation using Kuprov equation.
  
 
[[pms2chi.m]] - extracts magnetic susceptibility tensors from paramagnetic shift data.
 
[[pms2chi.m]] - extracts magnetic susceptibility tensors from paramagnetic shift data.
  
 
[[pcs2chi.m]] - extracts rank 2 components of the magnetic susceptibility tensors from pseudocontact shift data.
 
[[pcs2chi.m]] - extracts rank 2 components of the magnetic susceptibility tensors from pseudocontact shift data.
 +
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[[pcs_combi_fit.m]] - PCS data fitting with ambiguous assignments.
  
 
[[ppcs.m]] - Computes pseudocontact shift from a point electron centre at the nuclear coordinates supplied.
 
[[ppcs.m]] - Computes pseudocontact shift from a point electron centre at the nuclear coordinates supplied.
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 +
[[probmax.m]] - maximum point of a 3D probability density in a cube.
  
 
==Exotica==
 
==Exotica==
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[[crazed.m]] – CRAZED sequence, implemented as described in Warren Warren's paper.
  
 
[[rydmr.m]] – singlet-singlet RYDMR experiment with exponential recombination function, as described in the paper by Timmel and co-authors.
 
[[rydmr.m]] – singlet-singlet RYDMR experiment with exponential recombination function, as described in the paper by Timmel and co-authors.
Line 135: Line 214:
 
[[zerofield.m]] - gamma-weighted pulse-acquire sequence in zero field.
 
[[zerofield.m]] - gamma-weighted pulse-acquire sequence in zero field.
  
[[crazed.m]] – CRAZED sequence, implemented as described in Warren Warren's paper.
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[[zulf_abrupt.m]] - zero-field NMR with an abrupt field drop.
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 +
 
 +
''Version 2.1, authors: [[Ilya Kuprov]]''

Revision as of 09:40, 21 July 2018

This section contains a list of the pre-programmed pulse sequences supplied with Spinach. Everything is open-source, so feel free to hack and modify as appropriate. If your particular sequence is not listed below, or if you have written something that is worthy of broad public adoption, drop us a note – we are always interested in expanding Spinach capabilities.

Unless stated otherwise in the experiment description, all of the functions listed below below should be invoked via a kernel context function that sets the appropriate (solid, liquid, etc.) simulation infrastructure.

General experiments

acquire.m – simple forward time evolution with signal acquisition.

cpmg.m - CPMG echo train with detection.

holeburn.m - hole burning experiment.

hp_acquire.m – standard hard pulse acquire sequence. The user must supply the pulse operator, the pulse duration and the initial condition.

impound.m - captures what it receives from the context function and returns it to the user.

levelpop.m - energy levels and their populations.

relaxan.m - automated relaxation theory analysis.

slowpass.m – calculates spectrum values at the user specified frequency positions using the Fourier transform of the Liouville - von Neumann equation. The biggest advantage over the fid + fft style detection is easy parallelization and the possibility of getting spectrum values at specific frequencies without recalculating the entire free induction decay.

sp_acquire.m - a pulse-acquire sequence with a soft pulse.

traject.m - simple forward time evolution, trajectory is returned as a stack of density matrices.

NMR experiments

clip_hsqc.m – CLIP-HSQC pulse sequence.

cn2d_sq.m – CN2D experiment under MAS, single-quantum.

cn2d_dq.m – CN2D experiment under MAS, double-quantum.

cosy.m – phase-sensitive COSY pulse sequence.

crosspol.m – cross-polarization experiment.

dante.m - DANTE pulse sequence.

dqf_cosy.m – phase-sensitive double-quantum filtered COSY pulse sequence

hetcor.m – magnitude mode HETCOR pulse sequence.

hmqc.m – magnitude mode HMQC pulse sequence.

hnco.m – Phase-sensitive HNCO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hncoca.m – Phase-sensitive HNCO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hsqc.m – phase-sensitive HSQC pulse sequence.

lcosy.m – localized COSY pulse sequence.

m2s.m - magnetisation to singlet state.

mqmas.m - 2D multiple-quantum MAS pulse sequence for quadrupolar nuclei.

mqs.m - 2D multiple-quantum NMR pulse sequence.

noesy.m – phase-sensitive homonuclear NOESY pulse sequence.

noesyhsqc.m – phase-sensitive NOESY-HSQC pulse sequence. Hard-wired to 1H, 15N, 1H.

roesy.m - phase-sensitive homonuclear ROESY pulse sequence.

s2m.m - singlet state to magnetisation.

tocsy.m - amplitude-mode homonuclear TOCSY.

Spatially encoded NMR

Ultrafast and pure-shift NMR

spencosy.m - ultrafast COSY experiment.

spendosy.m - ultrafast DOSY experiment.

dosy_oneshot.m - one-shot DOSY pulse sequence.

spendosycosy.m - ultrafast 3D DOSY-COSY experiment.

spendosy_keeler_fit.m - original Keeler model data processing for SPEN DOSY.

spendosy_keeler_fit_corr.m - corrected Keeler model data processing for SPEN DOSY.

spendosy_frydman_fit.m - original Frydman model data processing for SPEN DOSY.

spendosy_keeler_fit_corr.m - corrected Frydman model data processing for SPEN DOSY.

spendosy_processing1s.m - SPEN DOSY processing, one signal.

spendosy_processing2s.m - SPEN DOSY processing, two signals.

stejskal_tanner_analysis.m - Stejskal-Tanner analysis of diffusion data.

psyche_1d.m - PSYCHE 1D pulse sequence.

diag_psyche_zfilters.m - Phase-sensitive homonuclear DIAG pulse sequence.

Diffusion NMR

pfg_spin_echo.m - Pulsed field gradient spin echo sequence.

pfg_stim_echo.m - Pulsed field gradient stimulated spin echo sequence.

bpp_stim_echo.m - Bipolar pulse pair stimulated spin echo sequence.

Gradient signal suppression

dpfgse_select.m - DPFGSE signal selection

dpfgse_suppress.m - DPFGSE signal suppression

Magnetic resonance imaging

basic_1d_hard.m - basic 1D imaging with a hard pulse and a gradient

cpmg_dec.m - CPMG echo train

dwi.m - 2D (spatial) diffusion weighted imaging sequence

epi.m - 2D (spatial) echo planar imaging sequence

fse.m - 2D (spatial) fast spin echo sequence

grad_echo.m - simple gradient echo pulse sequence

phase_enc.m - 2D (spatial) phase encoded imaging.

press_1d.m - 1D (spatial) PRESS sequence

press_2d.m - 2D (spatial) PRESS sequence

press_voxel_1d.m - voxel selection diagnostics for 1D (spatial) PRESS pulse sequence

press_voxel_2d.m - voxel selection diagnostics for 2D (spatial) PRESS pulse sequence

press_voxel_3d.m - voxel selection diagnostics for 2D (spatial) PRESS pulse sequence

slice_phase_enc.m - 3D (spatial) imaging with slice selection followed by phase-encoded acquisition

slice_select_1d.m - slice selection diagnostics

spin_echo.m - simple spin echo pulse sequence

spiral.m - 2D (spatial) imaging with spiral readout

udd_dec.m - Uhrig Dynamic Decoupling (UDD) echo train

uhrig_times.m - timing sequence for UDD echo train

Overtone NMR experiments

overtone_a.m - overtone signal acquisition.

overtone_cp.m - overtone cross-polarisation.

overtone_pa.m - overtone pulse-acquire.

overtone_dante.m - overtone DANTE.

ESR experiments

endor_cw.m – continuous-wave ENDOR pulse sequence.

endor_mims.m – Mims ENDOR pulse sequence.

endor_davies.m - Davies ENDOR pulse sequence.

eseem.m – ESEEM pulse sequence.

fieldsweep.m - field sweep ESR experiment using steady state formalism.

hyscore.m – HYSCORE experiment.

oopeseem.m - out-of-phase ESEEM experiment.

rapidscan.m - ESR rapid field scan experiment.

sifter.m - SIFTER experiment

DEER/PELDOR experiments

deer_3p_hard_echo.m - echo diagnostocs for ideal three-pulse DEER.

deer_3p_hard_deer.m - ideal three-pulse DEER.

deer_3p_soft_deer.m - three-pulse DEER with realistic pulses and orientation selection.

deer_3p_soft_hole.m - pulse hole diagnostics for three-pulse DEER with realistic pulses and orientation selection.

deer_3p_soft_diag.m - full diagnostics suite for three-pulse DEER with realistic pulses and orientation selection.

deer_4p_soft_deer.m - four-pulse DEER with realistic pulses and orientation selection.

deer_4p_soft_hole.m - pulse hole diagnostics for four-pulse DEER with realistic pulses and orientation selection.

deer_4p_soft_diag.m - full diagnostics suite for four-pulse DEER with realistic pulses and orientation selection.

DNP experiments

dnp_field_scan.m – field scan steady-state DNP experiment.

dnp_freq_scan.m – frequency scan steady-state DNP experiment.

solid_effect.m – large-scale simulation of solid effect DNP.

masdnp.m - magic angle spinning DNP.

Paramagnetic NMR spectroscopy

centroid.m - centre of mass point of a 3D probability density in a cube.

csa2racs.m - residual anisotropic chemical shift.

eqmag.m - molar magnetization vector at the thermal equilibrium.

fieldscan_enlev.m - energy levels as a function of the magnetic field.

fieldscan_magn.m - Z magnetisation in a finite-speed field sweep.

geffect.m - Effective g-tensor for a user-specified Kramers doublet.

hfc2pcs.m - computes pseudocontact shifts from hyperfine couplings and susceptibility tensors.

hfc2pms.m - computes paramagnetic shifts (contact + pseudocontact) from hyperfine couplings and susceptibility data.

ipcs.m – tag probability density recovery from pseudocontact shifts..

ippcs.m – point electron model fitting to PCS data.

kpcs.m – PCS calculation using Kuprov equation.

pms2chi.m - extracts magnetic susceptibility tensors from paramagnetic shift data.

pcs2chi.m - extracts rank 2 components of the magnetic susceptibility tensors from pseudocontact shift data.

pcs_combi_fit.m - PCS data fitting with ambiguous assignments.

ppcs.m - Computes pseudocontact shift from a point electron centre at the nuclear coordinates supplied.

probmax.m - maximum point of a 3D probability density in a cube.

Exotica

crazed.m – CRAZED sequence, implemented as described in Warren Warren's paper.

rydmr.m – singlet-singlet RYDMR experiment with exponential recombination function, as described in the paper by Timmel and co-authors.

zerofield.m - gamma-weighted pulse-acquire sequence in zero field.

zulf_abrupt.m - zero-field NMR with an abrupt field drop.


Version 2.1, authors: Ilya Kuprov