example_fromPDFgui.py

import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import leastsq
from mcalculator import *

# Create the structure
MnOunitCell = np.array([[2.72846725,-1.5752813,0],[0,3.1505626,0],[0,0,7.5936979]])
atomBasis=np.array([[0,0,0],[0.33333,0.666667,0.666667],[0.666667,0.333333,0.333333]])

# Set up the mPDF calculator
mc=mPDFcalculator(MnOunitCell,atomBasis,rmax=20.0,gaussPeakWidth=0.2)

mc.makeAtoms()
mc.svec=2.5*np.array([1.0,-1.0,0])/np.sqrt(2)
mc.kvec=np.array([0,0,1.5])
mc.spinOrigin=mc.atoms[0]
mc.makeSpins()
mc.ffqgrid=np.arange(0,10,0.01)
mc.ff=jCalc(mc.ffqgrid,getFFparams('Mn2'))
mc.calcList=np.arange(1)

# Load the data
PDFfitFile='mPDF_exampleFiles/MnOfit_PDFgui.fgr'
rexp,Drexp=getDiffData([PDFfitFile])
mc.rmin=rexp.min()
mc.rmax=rexp.max()

# Do the refinement
def residual(p,yexp,mcalc):
    mcalc.paraScale,mcalc.ordScale=p
    return yexp-mcalc.calc(both=True)[2]

p0=[5.0,3.0]
pOpt=leastsq(residual,p0,args=(Drexp,mc))
print pOpt

fit=mc.calc(both=True)[2]

# Plot the results
fig=plt.figure()
ax=fig.add_subplot(111)
ax.plot(rexp,Drexp,marker='o',mfc='none',mec='b',linestyle='none')
ax.plot(rexp,fit,'r-',lw=2)
ax.set_xlim(xmin=mc.rmin,xmax=mc.rmax)
ax.set_xlabel('r ($\AA$)')
ax.set_ylabel('D(r) ($\AA^{-2}$)')

plt.show()