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Messages - kuprov

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31
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 18, 2012, 07:42:17 PM »
I've cleaned up the code a bit and I am getting a fairly neat inversion around 55 ppm. Is that what you expect? (see the attachment)

I've emailed you the code and the current version of Spinach (yours is a bit old).

32
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 17, 2012, 06:59:19 PM »
The other thing is that parameters.offset is printing offset, it has no influence on the spin Hamiltonian. The pulse offset must be specified during the call to shaped_pulse function itself.

33
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 17, 2012, 06:54:02 PM »
Ah, looking at your code fragment -- Spinach expects offsets in Hz. Does that solve the problem?

34
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 17, 2012, 06:52:08 PM »
Could I have the code that produced those? It would be a lot easier to see what goes wrong there. If you look inside the shaped_pulse function, you can see easily that the offset is accounted for, so these errors really should not appear.

35
Simulations / Re: Liquid state NMR
« on: October 17, 2012, 06:48:39 PM »
I am still puzzled by your offset troubles -- shaped_pulse does take offsets into account, you can see that yourself if you look into the code. Can you send me the simulation where it does not perform as advertized?

Regarding parallelization, many functions in Spinach would run in parallel -- just run the "matlabpool" command before you run a Spinach simulation.

How many points does your shaped pulse have?

36
Spinach bug reports / Re: Offset problem for shaped pulse
« on: October 15, 2012, 02:00:32 PM »
Hmmm, that shouldn't happen. Looking at it...

37
Simulations / Re: Liquid state NMR
« on: October 15, 2012, 01:59:17 PM »
Looking into it... in principle, the easiest way to run a selective pulse is to specify the spins the operator should act on:

operator(spin_system,{'L+'},{3}) is the L+ on the third spin -- so if you make a pulse operator that only affects your chosen spins, the pulse may well be a hard pulse.

Spinach does include evolution during the shaped pulse -- would you like an option to turn it off?

38
Simulations / Re: Nuclear overhauser effect
« on: September 28, 2012, 04:19:45 PM »
No problem, here are the examples. Should work with Spinach 1.2.1310 or later (make sure the strychnine executable finds the Gaussian log it needs to read).

39
Spinach feature requests / Re: video lectures on Spinach programming
« on: September 28, 2012, 04:17:59 PM »
The liquids_nmr directory in the example set should provide plenty of examples, but I'll see if I can get one written from scratch on video.

40
Simulations / Re: Nuclear overhauser effect
« on: September 28, 2012, 08:59:28 AM »
Yep, there is -- Overhauser DNP and NOESY, see the example set. There is, in fact, a hugely general relaxation theory module supporting both Redfield theory and SLE.

But I guess you would like to have a 1D NMR example. Any specific wishes? We can write you a template.

41
Spinach feature requests / Re: video lectures on Spinach programming
« on: September 27, 2012, 06:31:26 PM »
Working on it. Any suggestions for the topics? If you can list the tough things, I just go through programming them in real time.

42
Spinach feature requests / Re: Function explanation and help
« on: September 19, 2012, 08:54:26 AM »
Another way is to type "help functionname" in the command prompt.

43
Spinach feature requests / Re: Function explanation and help
« on: September 17, 2012, 05:35:10 PM »
Place the cursor on the function and press Ctrl-D.

44
One way is to get your bra-ket density matrices (using kronecker products) and then compute the expansion coefficients with your density matrix, i.e.

rho=a1*A1+a2*A2+...   =>

a_k=trace(A_k'*rho)/norm(A_k);

So standard orthogonal expansion in matrix space, see Lecture 12 of the Spin Dynamics course.

45
Simulations / Re: Cross-polarization simulations
« on: May 17, 2012, 04:07:15 PM »
OK, got it – what you are supplying is not actually the full dipolar coupling, just the secular part of it. It has a trace, and that’s not right because proper DD interaction is traceless. If you supply the full and proper traceless dipolar matrix to Spinach, everything will match.

When you supply coordinates, Spinach actually includes the flip-flop terms into consideration, hence the different result.

In general, Spinach expects that the user will supply “the truth” – i.e. the original unaltered non-approximate interactions. The approximations are applied by setting assumptions during a call to the secularity() function.

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