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Separating Nuclear Manifolds
Posted: Fri May 08, 2015 8:06 am
by AKittell
Is there a way to visualize the contributions of each nuclear quantum number separately? We are interested in seeing how the mi = +/- 1 manifolds change as a function of rotational correlation time, but want to avoid the effects of overlap.
Re: Separating Nuclear Manifolds
Posted: Fri May 08, 2015 12:50 pm
by Matt Krzyaniak
You can use the output option 'separate' to return the individual transitions contributing to the spectrum.
Add the following bit to your simulation code
Code: Select all
Opt.Output = 'separate';
chili(Sys, Exp, Opt)
Re: Separating Nuclear Manifolds
Posted: Fri May 08, 2015 1:10 pm
by AKittell
Thanks Matt. That's precisely what I was looking for.
For those interested, you can export the simulation into a three column matrix and isolate each column.
Thanks again.
Re: Separating Nuclear Manifolds
Posted: Tue May 12, 2015 9:27 am
by AKittell
After playing around with 'separate' and 'summed' for a while, I've noted that when you include any line broadening, the 'separate' option tends to get a little messed up. I'm currently running simulations with a 0.2 mT line broadening, and that results in identical manifold shapes with different intensities. Remove the broadening, and the manifolds separate correctly. Parameters are below. Let me know if you have the same issue. (EasySpin v 5.0 Beta)
Sys =
g: [2.0088 2.0061 2.0023]
A: [17.3600 12.0400 100.5200]
Nucs: '14N'
tcorr: 1.0000e-08
lw: [0 0] OR lw = [0.2 0]
Exp =
CenterSweep: [338.7000 15]
mwFreq: 9.5000
Opt =
Output: 'separate'
Re: Separating Nuclear Manifolds
Posted: Wed May 13, 2015 12:17 pm
by AKittell
In principle, shouldn't the separate manifolds add up to the summed simulation with a three times the intensity? I have found this not to be the case using chili.
Re: Separating Nuclear Manifolds
Posted: Fri May 15, 2015 7:43 am
by Stefan Stoll
Can you please post your simulation script? Use the "Code" button when composing the reply.
Re: Separating Nuclear Manifolds
Posted: Mon May 18, 2015 6:52 am
by AKittell
Here's the code for summing the separated manifolds:
Code: Select all
Sys.g = [2.0088,2.0061,2.0023];
Sys.A = [6.2*2.8, 4.3*2.8, 35.9*2.8];
Sys.tcorr = 1e-8;
Sys.lw = [0 0];
Sys.Nucs = '14N';
Exp.CenterSweep = [338.7 15];
Exp.mwFreq = 9.5;
Exp.Harmonic = 0;
Exp.nPoints = 4096;
Opt.Output = 'separate';
Opt2.Output = 'summed';
Separated = chili(Sys,Exp,Opt);
Summed = chili(Sys,Exp,Opt2);
Sep0 = Separated(2,1:4096);
Sep_1 = Separated(1,1:4096);
Sep1 = Separated(3,1:4096);
SepSum = (Sep0+Sep_1+Sep1)/3;
plot(SepSum)
hold on
plot(Sep_1/3,'k')
plot(Sep1/3,'k')
plot(Sep0/3,'k')
plot(Summed,'r')
And then watching the manifolds completely change when line broadening is included:
Code: Select all
Sys.g = [2.0088,2.0061,2.0023];
Sys.A = [6.2*2.8, 4.3*2.8, 35.9*2.8];
Sys.tcorr = 1e-8;
Sys.lw = [0 0];
Sys.Nucs = '14N';
Exp.CenterSweep = [338.7 15];
Exp.mwFreq = 9.5;
Exp.Harmonic = 0;
Exp.nPoints = 4096;
Opt.Output = 'separate';
chili(Sys,Exp,Opt)
figure
Sys.lw = [0.05 0];
chili(Sys,Exp,Opt)
Re: Separating Nuclear Manifolds
Posted: Wed May 27, 2015 4:29 pm
by Stefan Stoll
Hi Aaron, thanks for spotting this. This is a bug. Separating transitions does not generally work when using the Stochastic Liouville equation.
Please do not use Opt.Output='separate' with chili. It continues to work correctly for the other simulation functions.