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Force-Field Refinement with Mantid Algorithm DSFinterp1DFit

This tutorial shows the steps to refine a molecular dynamics force-field parameter through a best fit problem between simulated and experimental quasi-elastic neutron scattering factor.

of the problem, along with the example we will cover in the ensuing tutorial:


  • Required:
    • Mantid framework for computation and visualization of scientific data. Contains the MantidPlot graphical interface and the Mantid python API. Please follow site instructions for download and installation.
    • Python package dsfinterp
      • Linux: type the command in a terminal: sudo pip install dsfinterp.
      • Windows: open a command prompt and cd to to the bin\ directory of your Mantid installation (e.g. cd C:\MantidInstall\bin\ if your Mantid installation directory is C:\MantidInstall). There, type the command .\python.exe -m pip install dsfinterp.
  • Optional:
    • Namd to perform the molecular dynamics simulations.
    • Sassena to calculate the scattering law, or structure factor.

  • Required:
    • Experimental scattering law files.
    • Sassena output: set of intermediate scattering law files.
    • Fitting python script to be run in MantidPlot or ipython notebook that can be run stand-alone (without MantidPlot).
  • Optional:
    • Namd output: molecular dynamics trajectory files.
    • All files and images included in this presentation are accesible here.


The tutorial is self-contained in the python script file which can be ran in MantidPlot, as well as in the ipython notebook dsfinterp1Dfit_apply.ipynb. which can be ran as stand-alone.

A summary of the steps:
  1. Load experimental scattering law.
  2. Load sassena output, the intermediate scattering law I(Q,t) from the molecular dynamics simulations.
  3. Fast Fourier transform the simulated intermediate scattering law in order to yield the scattering law S(Q,E).
  4. Match the resolutions of the simulated and experimental scattering law.
  5. Make a plot of goodness of fit versus dihedral barrier.
  6. Define the fitting function that will compare the simulated and experimental scattering laws.
  7. Run the fitting procedure.
Once the fitting is done, we can visualize the results of the fit with MantidPlot. Below is a detailed presentation of each step.

Import the Mantid algorithms  we will be using
from mantid.simpleapi import LoadNexus, LoadSassena, Transpose, Rebin, Scale, SassenaFFT, ConvolveWorkspaces, Fit, mtd, DSFinterp

Select the working directory where all files should be placed. In our example, we have:

Input the resolution file, the elastic line.
LoadNexus(Filename='{0}/elastic.nxs'.format(rootd), OutputWorkspace='elastic')

Load the experimental quasi-elastic spectra S(Q,E) at T=200K. It contains 9 spectra, each at different Q's (0.3, 0.5, 0.7,..,1.9), and is defined in the energy domain [-0.15, 0.15]meV
LoadNexus(Filename='{0}/exp200K.nxs'.format(rootd), OutputWorkspace='exp200K')

Load the simulated spectra. We have 14 spectra at different values of the dihedral barrier K from 0.02 to 0.15
parametervalues='0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 0.15'
for K in parametervalues.split():

    Load spectra into Mantid workspace. Each file contains the intermediate structure factor I(Q,t) spectra for
    9 different values of Q (0.3, 0.5, 0.7,..,1.9). The names of the resulting workspaces are incSM0.03, .., incSM0.15
    LoadSassena(Filename='{0}/K{1}/T_200/fqt_inc_run1_rms2first.h5'.format(rootd,K), TimeUnit=1.0, OutputWorkspace='incSMK{0}'.format(K))


I(Q=1.9, E, K=0.06), Linear Scale

I(Q=1.9, E, K=0.06), Log-Log Scale

    What happens if one of the I(Q,t) files contains a different number of Q values? In the following special case, K=0.11, the I(Q,t) file contains spectra
    for values of Q (0.02, 0.03, 0.04, 0.05,...,2.0). Thus, we have to rebin the spectra in the Q-coordinate
    if K=='0.11':
        Transpose(InputWorkspace='incSMK0.11_fqt.Re', OutputWorkspace='incSMK0.11_fqt.Re') 
  from I(Q,t) to I(t,Q)
        Rebin(InputWorkspace='incSMK0.11_fqt.Re', Params=[0.2,0.2,2.0], OutputWorkspace='incSMK0.11_fqt.Re') Rebin in Q to (0.3, 0.5,..,1.9)
        Transpose(InputWorkspace='incSMK0.11_fqt.Re', OutputWorkspace='incSMK0.11_fqt.Re')   from I(t,Q) back to I(Q,t)

        After rebin, the intensities I(Q,t=0) in the resulting spectra are different than for spectra at other K values. We rescale the intensities to match
        Scale(InputWorkspace='incSMK0.11_fqt.Re', factor=0.5, Operation='Multiply', OutputWorkspace='incSMK0.11_fqt.Re')

    Fourier transform I(Q,t) to S(Q,E). Resulting workspaces are incSMK0.03_sqw .., incSMK0.15_sqw
    SassenaFFT(InputWorkspace='incSMK{0}'.format(K), FFTonlyRealpart=1, DetailedBalance=1, Temp=200)

    Rebin S(Q,E) in E to the region [-0.2, 0.2] meV, of the same order as the experimental [-0.15, 0.15] but a bit broader
    Rebin(InputWorkspace='incSMK{0}_sqw'.format(K), Params=[-0.2,0.0004,0.2], OutputWorkspace='incSMK{0}_sqw'.format(K))

    Important remark: the system simulated in one POSS molecule. thus, our simulated system does not take into account the broadening
    due to motions of the molecule center of mass that take place in the crystalline phase. As a result, the elastic line in the simulation
    is over-represented. To correct this shortcoming in the simulations we will remove the simulated elastic line from the simulated S(Q,E)
    and later include a term represented the elastic line in the fitting model.
    ws=mtd['incSMK{0}_sqw'.format(K)]  simulated S(Q,E)
    Remove the elastic line for the spectra at each Q.
    for iQ in range(9):
  not neccessary but just to remind the Q-value
        S(Q,E) for the previous Q. SQE is a list of 1000 intensities versus energy. The elastic line is in the middle of this list, at indexes 499 and 500
        We remove these intensities just by setting these values to the adjacent ones, which are quasi-elastic in nature.

 S(Q=1.9, E, K=0.06) before removal of elastic line.
Notice the Log scale on the Y-axis.

S(Q=1.9, E, K=0.06) after removal of elastic line

We match simulated and experimental resolution by convolving simulated S(Q,E) with the experimental resolution.
The names of the convolved workspaces are simSMK0.03, .., simSMK0.15
for K in parametervalues.split():
    ConvolveWorkspaces(Workspace1='elastic', Workspace2='incSMK{0}_sqw'.format(K), OutputWorkspace='simSMK{0}'.format(K))

The intensities of these convolved workspaces are order of magnitude higher than the intensities from the experimental S(Q,E). This
by itself is not a problem, except that the fitting routine will not be able to compe with such a difference. Thus, we rescale the intensities
of the convolved workspaces in order to bring both simulated and experimental intensities closer to each other.
for K in parametervalues.split():
    Scale(InputWorkspace='simSMK{0}'.format(K), Factor=1.0e-05,Operation='Multiply', OutputWorkspace='simSMK{0}'.format(K))


Before intensity scaling and
convolution with experimental resolution

After intensity scaling and
convolution with the experimental resolution

Previous to the proper fitting, we will do a Chi2 plot versus dihedral barrier K. This will give us a feeling for how the goodness of the fit
changes with the value of the dihedral value K. We use algorithm DSFinterp for this purpose.
We will use the structure factors  simSMK0.03, .., simSMK0.15 from the simulations to construct S(Q,E,K) with
K running from 0.03 to 0.13 every 0.001
parametervalues='0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14'.split()
inputworkspaces=['simSMK{0}'.format(K) for K in parametervalues]  # S(Q,E) from the simulations
targetvalues=[0.03+0.001*i for i in range(101)] #target K varies from 0.03 to 0.13 every 0.001
outputworkspaces=['out{0}'.format(K) for K in targetvalues] # interpolated S(Q,E)

From the simulated structure factors, create interpolated structure factors for each target K
DSFinterp(ParameterValues=[float(K) for K in parametervalues], Workspaces=inputworkspaces, LoadErrors=0,\
    TargetParameters=targetvalues, OutputWorkspaces=outputworkspaces,\
    LocalRegression=1, RegressionWindow=4, RegressionType='quadratic')

For each target K, fit the associated structure factor S(Q=1.9, E, K)to the experimenal S(Q=1.9, E), and extract the Chi2 value from the fitting.
Recall that in S(Q,E) Q goes from 0.03 to 1.9. We select the structure factor with highest Q, Q=1.9, corresponding to L~3Angstroms, to do the fitting.
Among the reported Q-values, Q=1.9 corresponds to a lenght scale most sensitive to methyl rotations
for K in targetvalues:

    Our fitting model is a elastic line at Q=1.9 plus our simulated S(Q=1.9,E) plus a linear background
    fit_string    ='name=TabulatedFunction,Workspace=elastic,WorkspaceIndex=8,Scaling=1.0;'
    fit_string +='name=TabulatedFunction,Workspace=out{0},WorkspaceIndex=8,Scaling=1.0;'.format(K)
    fit_string +='name=LinearBackground,A0=0.0,A1=0.0'

    Algorithm Fit carries out the fitting of the previous model to the experimental S(Q=1.9,E), which is index 8 of workspace exp200K.
    Notice the energy range is [-0.13, 0.1] meV. Outside this energy range, the signal to noise ration of the experimental S(Q=1.9, E)
    is not very reliable.
    Fit(fit_string, InputWorkspace='exp200K', WorkspaceIndex=8, StartX=-0.13, EndX=0.1, CreateOutput = 1 )
    ws=mtd['exp200K_Parameters']  Workspace resulting from the fitting containing the optimal value of the fitting parameters and the Chi2
    print 'K=', K, ' Chi2=', chi2
for outws in outputworkspaces:  DeleteWorkspace(outws)
  a bit of clean-up.

Save chi2 values to file chi2vsK.dat for inspection. Plot this file with your favorite plotting tool
buf='#K Chi2\n'
for i in range(len(targetvalues)):  buf += '{0} {1}\n'.format(targetvalues[i], chi2values[i])
open('/tmp/chi2vsK.dat', 'w').write(buf)

File chi2vsK.dat suggest that the dihedral value yielding a simulated S(Q=1.9,E) that compares optimally with the experimental
S(Q=1.9, E) is Koptimal ~ 0.065. We will use this value as initial guess for fitting S(Q,E) at all Q values.
Below are the initial guess of the fitting parameters. 'Scaling' is the intensity of the elastic line, 'Intensity' is the intensity of the
simulated S(Q,E), and 'K' is the dihedral barrier.
guess={'Scaling':1.0, 'Intensity':1.0, 'K':0.065}

 We will use our simulated structure factors simSMK0.03, .., simSMK0.15 to search for the optimal dihedral barrier
parametervalues='0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14'
inputworkspaces=' '.join( ['simSMK{0}'.format(K) for K in parametervalues.split()])

Cycle over S(Q,E) for different values of Q. We begin with the highest Q, Q=1.9, and work out way to the smallest Q, Q=0.3, doing
a fit at S(Q,E) at each Q
for iw in [8,7,6,5,4,3,2,1,0]:

    Our model is a elastic line plus a  structure factor interpolated from the simulated S(Q,E), plus a linear background
    fit_string = 'name=TabulatedFunction,Workspace=elastic,WorkspaceIndex={0},Scaling={1},constraints=(0.0001<Scaling);'.format(iw,guess['Scaling'])+\
        'name=DSFinterp1DFit,InputWorkspaces="{0}",ParameterValues="{1}",'.format(inputworkspaces,parametervalues) +\
        'LoadErrors=0,LocalRegression=1,RegressionType=quadratic,RegressionWindow=4,' +\
        'WorkspaceIndex={0},Intensity={1},TargetParameter={2},'.format(iw,guess['Intensity'],guess['K']) +\
        'constraints=(0.0001<Intensity);' +\
    Fit(fit_string, InputWorkspace='exp200K', WorkspaceIndex=iw, StartX=-0.13, EndX=0.1, CreateOutput = 1 )

    ws=mtd['exp200K_Parameters'] Workspace resulting from the fitting containing the optimal value of the fitting parameters and the Chi2
    print 'Q=', Q, 'L={0:5.1f}'.format( 6.2832/Q), 'K={0:6.4f}'.format(Koptimal), 'Chi2={0:3.1f}'.format(ws.row(5)['Value'])

    Use the optimal intensities of the elastic line and simulated quasi-elastic line as guesses for the fitting of the S(Q,E) for the next Q

The output of the previous print statement:
 K*  Chi2
0.5 12.6
0.0631 2.0
0.9 7.0
1.3 4.8

Simulations thus predict optimal K in the range [0.0635, 0.0652], a narrow range if we take into account the wide range of length scales.