Resolution function and PARAMETERS for SANS #972
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| @@ -433,7 +464,7 @@ | |||
| parse("SOLVATION_CORRECTION", correction); | |||
| rho_corr=rho-correction; | |||
| if(onebead) log.printf(" Solvation density contribution: %lf\n", correction); | |||
| if((atomistic||martini)&&(rho_corr!=rho)) log.printf(" Solvation density contribution is taken into account in ONEBEAD only\n"); | |||
| if((atomistic||martini||fromfile)&&(rho_corr!=rho)) log.printf(" Solvation density contribution is taken into account in ONEBEAD only\n"); | |||
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| std::vector<Vector> old_deriv(deriv); | ||
| memset(&deriv[0][0], 0.0, deriv.size() * sizeof deriv[0]); | ||
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| unsigned nt=OpenMP::getNumThreads(); |
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| std::vector<Vector> old_deriv(deriv); | ||
| memset(&deriv[0][0], 0.0, deriv.size() * sizeof deriv[0]); | ||
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| unsigned nt=OpenMP::getNumThreads(); |
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## master #972 +/- ##
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- Coverage 85.11% 85.09% -0.02%
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Files 601 601
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@hmcezar thanks! I will look into the pull request and the i0 intensity issue possibly next week. |
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No problem! Let me know if you need anything from my side. |
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merging! @hmcezar could you send me a working example with the Iq0 normalisation issue? something that can be run with plumed driver would be great |
Description
This PR contains the implementation of a resolution function for the SAS spectra and enables using user-provided
PARAMETERSfor computing SANS.I also implemented an option called
PARAMETERSFILE, that can be used to provide a text file containing all thePARAMETERSinstead of including them in the main input (when you have to specify thePARAMETERSfor thousands of beads, this makes the input more readable).To avoid increasing the computational cost too much when using the resolution function, splines are used to get the intensities and derivatives for
qnot provided by the user.A description of the resolution function implementation and on how one can use the
PARAMETERSin case of CG simulations can be seen in this paper.A bit of context in the paper and implementation:
Last summer (before you pushed the SANS implementation in
SAXS.cppand reworked the code for theONEBEADimplementation) I needed to perform metainference simulations biasing the SANS spectrum for a collaboration.I implemented it in my sans branch and have been using it ever since.
The difference between what is implemented in
SANS.cppin that branch and this PR is basically the normalization, which used to setI(q_0) = 1, withq_0being the lowestq, and now uses the same normalization you are using.About the normalization, I performed a couple of tests, and it seems that in some cases, even when the spectra is flat for low q, the calculated curve is not set to 1 at
q=0.Instead, one has to use a reasonably large
SCALEwith metainference (around 25 for one of my systems) to get a good match between the experimental curve withI(q=0)=1and the computed curve.This is true for both SAXS and SANS, so this is not something that comes from my implementation.
However, if you use a reasonable value for the
SCALE, the curves match and everything works as it should.Anyways, let me know if you need anything else regarding this PR.
Target release
I would like my code to appear in release 2.9
Type of contribution
Copyright
Tests