Recent Posts

1

Examples / Altadena

« Last post by LaurynasDagys on September 01, 2019, 06:32:20 PM »

The attached simulation shows how to use SpinDynamica to calculate NMR spectrum of the ALTADENA experiment.
The experiment is performed by preparing the singlet spin-order in low-field followed by adiabatic transfer to high-field.

The simulation contains two chapters regarding cases of 2 spins and 3 spins whereas the latter one contains a bit more complexity.

The spectra and matrices were removed from to simulation to save file size but are generated with new evaluation.

2

Simulations / Re: Commutator[], Matrixexponential, Subspace

« Last post by Christian Bengs on February 06, 2019, 10:18:05 AM »

Hey Hannes,

Sorry for the late reply, but I've finally had a quick look at your notebook.

1) There is really no need to let SpinDynamica know what a commutator equals when constructing the matrix representation of a superoperator. The commutation relations will be dealt with "automatically".

2) There is really no way to reduce the size of the matrix unless your Hamiltonian might display some symmetry. In this case you can define your own basis and focus on the relevant subspace. A useful syntax to order the matrix into its subspaces is as follows:

Flatten[ConnectedComponents[Rule @@@MatrixRepresentation[H]]["NonzeroPositions"]]]

This will return a permutation that permutes the Hamiltonian into block-diagonal form.

3) The reason the last calculation doesn't stop is because the analytic calculation of the matrix exponential takes very long. You may circumvent the problem by first calculating the matrix exponential in a "simple" basis and then transform back into your preferred basis.

4) Unfortunately SpinDynamica has no capabilities to restrict calculations to a certain subspace atm.

kind regards,

Christian

3

Updates and Messages / SpinDynamica 3.3.2 released

« Last post by Christian Bengs on February 06, 2019, 10:10:47 AM »

SpinDynamica 3.3.2 has been released.

–EigenBasis now takes TargetBasis as an optional argument. The calculated EigenBasis and TargetBasis will be aligned as closely as possible. This should be useful for analysis of adiabatic calculations.
–Some bug fixes and speed improvements to the basis construction of spins with I>1/2.
–The functions SingleTransitionOperator, CoherenceOperator and PopulationOperator now allow for specification of a basis. See the documentation for more details.

Check out the SpinDynamica website for the new release: http://www.spindynamica.soton.ac.uk/2019/02/06/spindynamica-3-3-2/

or download the new version here: http://blog.soton.ac.uk/spindynamica/download/spindynamica-3-3-2/?wpdmdl=1034

4

Simulations / Commutator[], Matrixexponential, Subspace

« Last post by dornenfeld on December 10, 2018, 11:13:46 AM »

Hey everyone,

came along some problems while trying to work with Spindynamica. Tried to formulate all questions in attached mathematica file.
Also want to say thanks for the package overall, its very useful. If you need more clarification, please feel free to ask. Also open to any suggestions.

Really appreciate any help you can provide,
Hannes

5

Updates and Messages / SpinDynamica 3.3.1 released

« Last post by Christian Bengs on November 06, 2018, 11:53:24 AM »

SpinDynamica 3.3.1 has been released.

-The recent update of SpinDynamica introduced some problems with WignerD, these bugs have been fixed now.
-The functionality of CorrelatedEigensystems has been extended to support Liouvillians and arbitrary sets of matrices.
-The usage messages of CorrelatedEigensystems and Adiabatic routines have been extended to be more informative.

Check out the SpinDynamica website for the new release: http://www.spindynamica.soton.ac.uk/2018/11/06/spindynamica-3-3-1/

or download the new version here: http://blog.soton.ac.uk/spindynamica/download/spindynamica-3-3-1/?wpdmdl=1025

6

Updates and Messages / SpinDynamica 3.2.1 released

« Last post by Christian Bengs on October 08, 2018, 11:52:08 AM »

SpinDynamica 3.2.1 has been released.

-SpinDynamica now allows for variable degrees of error trapping via UserLevel. Less error trapping leads to speed improvements for some routines.
-The routine MaximizeTransformationAmplitude has been added to SpinDynamica. MaximizeTransformationAmplitude numerically optimizes a TransformationAmplitude with respect to a set of parameters.
-Several bugs have been fixed, most notably bugs related to the COMPUTE algorithm. Thanks letting us know about these issues.

Check out the SpinDynamica website for a couple more details: http://www.spindynamica.soton.ac.uk/2018/10/08/spindynamica-3-2-1/

and download the new version under this link: http://blog.soton.ac.uk/spindynamica/download/spindynamica-3-2-1/?wpdmdl=1020

7

General Discussion / Re: Zero Field NMR

« Last post by janicke on June 13, 2018, 08:06:02 PM »

Is it possible to extend these calculations to ultra-low field (earth's field).  We are hoping to try and extend the work of Pines, Blumich, and Appelt to look at J couplings in a TerraNova system.  Thanks.

8

Simulations / noob question about CuSO4 pentahydrate

« Last post by Steve on May 22, 2018, 03:19:53 AM »

Hello,

We are developing a low field EPR system as part of a larger project and we are starting with a sample that is CuSO4+5H2O in
polycrystalline form. We have spinach up and running and tried substituting 63Cu for Nitrogen in the powder ESEEM example, also
changing the pulse to a single 90.

Really a zeroth order hack because we are not chemists and lack the necessary expertise to set up that molecule in the spinach
GUI. We found the atom coordinates at one site and managed to get those into the interface but are completely at sea with regards to
setting up the required interactions.

Also, we don't understand the shorthand in the ESEEM powder example anyway. No molecule is setup but some interactions are specified
so our substitution of 63 Cu is done in a kind of informational vacuum. Do we even need to set up the rest of the molecule? Maybe not.

We want to know what to expect when we hit this CuSO4 system with shaped pulses so we can do a good a priori job of setting up the signal
handling and post-processing. Also to know when things are more or less working.

Can you please help us with CuSO4 setup?

thanks,

Steve

9

Updates and Messages / SpinDynamica 3.1.0 released

« Last post by Christian Bengs on February 26, 2018, 03:23:55 PM »

SpinDynamica 3.1.0 has been released.

There are a couple of new features.

-SpinDynamica now contains several new routines for the analysis of adiabatic events (see part 11 of the documentation).
-Documentation on highly polarized spin-systems has been addded (see part 10 of the documentation).
-TransformationAmplitudeTable now supports two or more parameter specifications.
-Introduction of LeftMultiplicationSuperoperator and RightMultiplicationSuperoperator.

A more detailed description of the changes may be found here: http://www.spindynamica.soton.ac.uk/2018/02/26/spindynamica-3-1-0-with-a-couple-new-features/

The version is available under this link: http://blog.soton.ac.uk/spindynamica/download/sdv3-1-0/?wpdmdl=984

10

Bug reports / Not really bug: Calculate Re[wrsk] in Compute and warning if Im[wrsk] too large

« Last post by Andreas Brinkmann on November 06, 2017, 05:10:55 PM »

This is not really a bug, but under non-ideal conditions (large Hamiltonians, non-sufficient accuracy settings), the numerically calculated eigenvalues wrsk in the COMPUTE routine can have a small but significant imaginary part. This can translate to peak frequencies that have an imaginary part if the DigitalFrequencyResolution->True setting fails to "snap" the peak frequency to the frequency grid. In that case the FT might fail.

I would recommend taking Re[wrsk] of the eigenvalues and/or print a warning if the imaginary part is significant.

Please see attached your RotationalResonance.nb Example, that I forced into the above behavior.