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Messages - kuprov

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Simulations / Re: relaxation time calculation using Spinach
« on: April 21, 2014, 02:49:57 PM »
Dear Scott,

yes, you would get the full relaxation matrix. To extract a specific relaxation rate:

1. Generate the state in question (see state.m).
2. Normalize the state (rho=rho/norm(rho,2))
3. Compute rho'*R*rho

Best wishes,

Simulations / Re: 1H-31P Coupling
« on: November 18, 2013, 08:52:42 AM »
Should be the same as 1H or 13C -- just specify 31P in the isotope list and it would work.

Simulations / Re: Quantum number conversion
« on: November 15, 2013, 06:04:10 PM »
See the lin2lm and lm2lin functions in kernel utilities. The operator and state functions also support direct tensor index specification, such as ‘T2,-2’ in the operator description.

To get Hilbert space operators, switch bas.formalism to ‘zeeman-hilb’.

Simulations / Re: questions about new spinach version
« on: November 15, 2013, 06:02:47 PM »
I’ll cook you a template for the spin-lock simulation, give me a couple of days.
Module III is starting on Wednesday, I will do the first four lectures and Giuseppe Pileio will do the other four. So we’ll get to those singlet lectures in about a month from now.

Simulations / Re: questions about new spinach version
« on: November 15, 2013, 06:02:13 PM »
1.       You can just remove that chemical shift difference from the Hamiltonian manually. There’s an option to the assume() function that allows you to drop all Zeeman interactions. Just make two Hamiltonians – one with Zeeman interactions and one without, and use them as needed.
2.       Yes, bas.formalism is not in the public release yet. It switches Spinach between spherical tensor basis and Zeeman basis. Redfield theory should not be any slower, we use complete basis sets for those calculations anyway.

Simulations / Re: questions about new spinach version
« on: November 15, 2013, 06:01:35 PM »
1.       Spin locking implementation depends on what you need to do – in many cases it simply amounts to putting all Zeeman interactions to zero for a period of time. Which experiment are you simulating?
2.       Yes – the current development version of Spinach can run calculations in both Zeeman and spherical tensor basis sets, you just flick a switch. The operators in the Zeeman basis are built in the usual way with direct products of Pauli matrices followed by the transformation into Liouville space.
3.       Accuracy of quantum chemical CSAs is a bit of a black art, unfortunately. See the last two lectures in the Quantum Chemistry course at – the question of “what works” is basically empirical, and many methods produce right answers for wrong reasons due to error compensation.

Simulations / Re: Spinach software requirements
« on: November 15, 2013, 05:58:29 PM »
Yes, parallelization is fundamental to the kernel architecture, no way to take it out. You would likely appreciate it though – quadrupolar simulations require powder averages, and those would be a factor of eight faster on an eight-core workstation.

Simulations / Re: Spinach software requirements
« on: November 15, 2013, 05:57:39 PM »
Linux should be fine, but parallelization is very deeply integrated – no way to run without the Parallel Computing Toolbox.

Simulations / Re: relaxation time calculation using Spinach
« on: November 15, 2013, 05:55:04 PM »
Yes – see the ESR relaxation calculations in the example set. You would need to generate the relaxation superoperator and then extract <Lz|R|Lz> matrix element for 1/T1 and <L+|R|L+> matrix element for 1/T2.

Simulations / Re: about T1,T2 relaxation theory in spinach
« on: November 15, 2013, 05:53:00 PM »
these are just standard T1 and T2, there isn’t really much to say apart from the top of Page 9 in the manual. As you say, the code is simple.

Spinach bug reports / Re: Paths and parallelization
« on: November 15, 2013, 05:49:41 PM »
Please try the following:

1.   Restarting Matlab – the parallelization error looks like Matlab’s parallel pool getting stuck.
2.   Switching the slash symbols from ‘\’to ‘/’ – if you are running Linux or MacOS, that might be it, the error looks like it simply didn’t find the strychnine Gaussian log.
3.   Make sure Spinach paths occur first on the Matlab path list – that would prevent the spectrum name collision, MathWorks have promised to eliminate the offending function in the future release.

General Discussion / Re: Spin dynamics T-shirt
« on: March 24, 2013, 08:18:43 PM »
These are the people that offered me a lot of money for  8)

General Discussion / Re: Plotting NMR spectrum in Mathematica
« on: January 14, 2013, 09:28:31 AM »
I think matNMR here

has data import facilities for all major vendors.

General Discussion / Re: Plotting NMR spectrum in Mathematica
« on: January 13, 2013, 01:20:12 PM »
So far as I can tell, there's no simple universal option in Mathematica. Some possibilities are discussed here:

In Matlab, the command is


Simulations / Re: Liquid state NMR
« on: October 18, 2012, 07:57:50 PM »
OK, sent you the file -- see if it works as you expect.

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