Recent Posts

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21
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

spin_system=assume(spin_system,'nmr');
[H,Q]=hamiltonian(spin_system,'comm');
H1=H+orientation(Q,[0,0,0]);

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:

spin_system=assume(spin_system,'nmr');
[H,Q]=hamiltonian(spin_system,'comm');
H2=H+orientation(Q,[gamma,-beta,alpha]);

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?
22
Bug reports / Bug - Transformation Amplitude Table (SDv.15.1b7).
« Last post by sje1g13 on September 14, 2016, 10:35:32 AM »
Hi,

I believe that there is a possible clash between SVv2.15.1b7 and the latest version of Mathematica (11.0.0.0) when using Transformation Amplitude Table.

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

Regards,
Stuart.
23
Excellent, Malcolm!

Thanks so much,
Andy
24
Hi Andy,
 while introducing SD v2.14.3, which is compatible with Mathematica 11, I also located and fixed this problem.
all the best
malcolm
25
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the SpinDynamica symbol Duration conflicts with the newly introduced Mathematica 11 symbol of the same name, and has been replaced by EventDuration.
26
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Note that the SpinDynamica symbol Duration clashes with the Mathematica 11 symbol of the same name and has been superseded by EventDuration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: https://www.dropbox.com/sh/3ib0qrpl6mxguhu/AAAUs8MyIPdu1kxmorDgM7Apa?dl=0
27
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.

Malcolm
28
Examples / 2D spectroscopy
« Last post by MalcolmHLevitt on July 28, 2016, 02:05:40 PM »
Although SpinDynamica does not yet contain a fully general routine for 2D spectral simulation, the attached notebook allows the calculation of 2D spectra in some useful special cases. Code of this kind will be included in SpinDynamica itself, in future releases.

As usual the graphics have been stripped out but will be regenerated upon running the notebook.
29
Hello Malcolm,

I am using version 10.4.1.0.

I am relieved you reproduced my observation. I was starting to think that I must be getting a bit soft in the head.

Enjoy your summer break,
Andy
30
Incredible!

Since I was using a slightly older version of Mathematica (10.3) I decided to update to 10.4 and try again.

This time I got the same behaviour as you!

So there is a subtle difference between Mathematica 10.3 and 10.4 which causes different behaviour for this particular calculation, which is very unexpected. I hope to debug this after my summer break.

There should be no need for you to send me the files I requested in the previous post.

all the best
malcolm
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