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General Discussion / Re: SPINACH-Optimal Control Module-GRAPE-Example
« Last post by AmandeepSingh on September 28, 2016, 10:12:54 AM »
Thank you Prof. Kuprov for the reply. I have a unitary matrix which I need to implement using NMR in an optimized manner. For example in current version of SPINACH, in example section, optimal_control, state_transfer_grape_hcf() function transfer the z-magnetization from proton to fluorine i.e. state changes from I_1z to I_3z. Correspond to this operation there is a unitary matrix. So while executing state_transfer_grape_hcf() the optimization is effectively reproducing the same unitary. And I am expecting that we can implement the optimization results to Bruker spectrometer (I am still trying to find the that how optimization results can be converted to a shape file to be used by spectrometer).
Now query is: Is it possible that I supply  the unitary and other system parameters (e.g. required by sys, inter ... etc) and SPINACH can give me the optimized shape pulse? Or alternatively, I have to specify the Initial state and Desired target state ( I mean there is no option for specifying unitary...!)?

Simulations / Re: Euler angles in orientation.m
« Last post by kuprov on September 27, 2016, 10:42:32 AM »
OK, tracked it down to a stray rotation sign convention. The patch is below -- unzip and put into the corresponding kernel directories, overwirting the pre-existing files. Rotations are now all syncronised to Brink and Satchler - Equation 2.13 and the preceding paragraph. Note that "rotation around Y" means that Z axis is tilting towards X, hence the the different sign pattern in the middle rotation matrix in euler2dcm(). The attached test file is now passed successfully, as well as all the other tests that we typically run for release.
Simulations / Re: Euler angles in orientation.m
« Last post by kuprov on September 25, 2016, 09:47:38 AM »

The most likely answer is that the lectures are wrong -- rotations in Spinach kernel are extensively tested against a dozen different calculation types.
Simulations / Euler angles in orientation.m
« Last post by johncprice on September 25, 2016, 01:24:12 AM »
I have a question about Euler angles in Spinach.

I created a set of spin coordinates, rotated them using Euler angles (alpha,beta,gamma), and then created the full dipole Hamiltonian using


Now I do the same thing another way, by creating a spin system using the un-rotated coordinates and passing the Euler angles to orientation.m as follows:


It works! The two Hamiltonians are the same to high precision for various values of the angles.

But the call to orientation(Q,[gamma,-beta,alpha]) suggests to me that I am using the wrong Euler angle convention.  I am using the one given in Kuprov's lecture sd_m2_lecture_03.pdf which corresponds to gamma rotation about z, beta rotation about y, alpha rotation about z. Is a different one being used?
Bug reports / Bug - Transformation Amplitude Table (SDv.15.1b7).
« Last post by sje1g13 on September 14, 2016, 10:35:32 AM »

I believe that there is a possible clash between SVv2.15.1b7 and the latest version of Mathematica ( when using Transformation Amplitude Table.

A Mathematica/SpinDynamica notebook has been attached. The notebook is commented and should explain the problem sufficiently.

Excellent, Malcolm!

Thanks so much,
Hi Andy,
 while introducing SD v2.14.3, which is compatible with Mathematica 11, I also located and fixed this problem.
all the best
Bug reports / Re: Mathematica 11
« Last post by MalcolmHLevitt on August 16, 2016, 05:07:46 PM »
The latest release 2.14.3 is now compatible with Mathematica 11.

However, the SpinDynamica symbol Duration conflicts with the newly introduced Mathematica 11 symbol of the same name, and has been replaced by EventDuration.
SpinDynamica 2.14.3 has been released.

This version is compatible with Mathematica 11.

Note that the SpinDynamica symbol Duration clashes with the Mathematica 11 symbol of the same name and has been superseded by EventDuration

Download here:
Bug reports / Mathematica 11
« Last post by MalcolmHLevitt on August 15, 2016, 04:14:49 PM »
The latest release of SpinDynamica (2.14.2) does not yet run under the newly-released Mathematica 11. This is because Wolfram have introduced a new built-in symbol Duration which conflicts with its prior definition under SpinDynamica. A Mathematica11 workaround will be released shortly.

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