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Messages - faq_user

Pages: [1] 2
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 / Re: questions about new spinach version
« on: November 15, 2013, 06:02:30 PM »
Thank you very much for your last email. If I want to watch the power dependence of spin locking, I assume there maybe another to do it instead of wiping out zeeman terms, which is an infinite power solution, is there a way to do that in spinach? Also, I really like your lecture materials online, I will be very interested of course in Module III, where the relaxation theory and singlet states will be discussed, do you have a timeline for the course or when probably I will see the rest of module 3 and 4 online? Thanks a lot!

3
Simulations / Re: questions about new spinach version
« on: November 15, 2013, 06:01:55 PM »
Thank you very much for your reply! I am trying your latest published version now, 1.2.1437 but let me make sure I understand it right first.
 
1. I am trying to see spin locking effects on the singlet states. So for example after the M2S sequence I need to quench the chemical shift difference so that no leakage happens from the singlet to the triplet due to the coherent mixing. Please let me know how to implement that in spinach.
 
2. I see the "bas.formalism" input in the new version, I have not tried yet, but this is not in the 1.2.1437 version right? In that case, I will wait for the new version officially coming out. I guess if I can read out the zeeman base density matrix at the end of the evolution it will be very useful. As to calculation itself, I am not sure, does the change into zeeman basis slow down the calculation or increase the demand for RAM since you have an excellent way to store tensors as numbers, if I remembered right.
 
3. For the DFT, I guess I will run some training set to see if they make a systematic difference.
 
Again, thank you very much! I will for sure keep the version you gave me confidential, I notice also that the package you gave me probably is the core not including everything since it is much smaller than the 1.2.1437, but anyway, look forward to your new version!

4
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?

5
Simulations / Re: Spinach software requirements
« on: November 15, 2013, 05:58:06 PM »
I’m assuming that’s always been the case then, so there aren’t earlier versions that don’t have this requirement?

6
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?

7
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?

8
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!

9
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?

10
Simulations / Re: Cross-polarization simulations
« on: May 17, 2012, 04:07:32 PM »
Thank you, that clears it up!

11
Simulations / Re: Cross-polarization simulations
« on: May 17, 2012, 04:06:28 PM »
Thanks, so you are saying I can ignore this?

Path tracing, however, finds different subspaces depending on whether I do it via distances or via the coupling matrix.
(in attached file, I have a linear 4-spin chain). Setting calc_via_distances to 1 does it via distances, and via the matrix otherwise.
 
The appearance of the spectra is also slightly different.

12
Simulations / Re: Cross-polarization simulations
« on: May 17, 2012, 02:31:11 PM »
Thanks, when I do it via this matrix, it appears that it turns on strong isotropic coupling
output log says:

h_superop: strong isotropic coupling term for spins 1,2...
            (LxSx+LySy+LzSz) x 362.6667 Hz

Attached is the script that I used.

13
Simulations / Re: Cross-polarization simulations
« on: May 17, 2012, 02:28:44 PM »
Thanks, this would work for J-couplings, but my understanding is that dipolar couplings are specified via distances only, so opposite ends would not be coupled.

14
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?

15
Simulations / Re: Strongly coupled spin systems.
« on: May 16, 2012, 03:41:22 PM »
Thanks, the repeated simulation for the gradients is how I do it now.
I did not see the shaped pulse example earlier.
That is wonderful, with this example I can set up my own pulses.
Thank you for all your help.

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