def setUp(self):
self.P = PdfFit()
self.qmax = 25
self.qdamp = 0.5
self.rmin = 4.0
self.rmax = 10.0
self.bin = 100
def setUp(self):
self.P = PdfFit()
self.P.read_struct(datafile('Ni.stru'))
self.P.read_struct(datafile('PbScW25TiO3.stru'))
self.P.alloc('X', 0.0, 0.05, 0.1, 10, 200)
self.P.alloc('N', 0.0, 0.05, 0.1, 10, 200)
return
def load_ipython_extension(ipython):
from diffpy.pdffit2 import PdfFit
pf = PdfFit()
pdf = EasyPDFPlotting(pf)
print(' Type help(pdffit) or help(topic) for information.\n')
ns = dict(pdffit=PdfFit, pdf=pdf)
pf._exportAll(ns)
ipython.user_ns.update(ns)
return
def calculate(self):
"""do the real calculation
"""
# clean up old results
self.rcalc = []
self.Gcalc = []
# do the job
if len(self.owner.strucs) == 0:
raise ControlConfigError("No structure is given for calculation")
# make sure parameters are initialized
self.owner.updateParameters()
from diffpy.pdffit2 import PdfFit
server = PdfFit()
# structure needs to be read before dataset allocation
for struc in self.owner.strucs:
server.read_struct_string(struc.writeStr('pdffit'))
for key, var in struc.constraints.items():
server.constrain(key.encode('ascii'),
var.formula.encode('ascii'))
# set up dataset
server.alloc(self.stype, self.qmax, self.qdamp, self.rmin, self.rmax,
self.rlen)
server.setvar('qbroad', self.qbroad)
server.setvar('dscale', self.dscale)
# phase related variables
# pair selection applies to current dataset,
# therefore it has to be done after alloc
for phaseidx0, struc in enumerate(self.owner.strucs):
phaseidx1 = phaseidx0 + 1
server.setphase(phaseidx1)
server.setvar('pscale', struc.getvar('pscale'))
server.setvar('spdiameter', struc.getvar('spdiameter'))
struc.applyPairSelection(server, phaseidx1)
# set up parameters
for index, par in self.owner.parameters.items():
server.setpar(index, par.initialValue()) # info[0] = init value
# fix if fixed. Note: all parameters are free after server.reset().
if par.fixed:
server.fixpar(index)
# all ready here
server.calc()
# get results
self.rcalc = server.getR()
self.Gcalc = server.getpdf_fit()
def setUp(self):
self.P = PdfFit()
self.r_data = [0.1, 0.2]
self.Gr_data = [1, 2, 3]
self.qmax = 10
self.qdamp = 0.5
def setUp(self):
self.P = PdfFit()
self.iset = 1
self.i = 1
def setUp(self):
self.P = PdfFit()
self.ip = 1
def setUp(self):
self.P = PdfFit()
self.val = 3.0
def setUp(self):
self.P = PdfFit()
self.par = 1
return
def setUp(self):
self.P = PdfFit()
self.strufile = "temp.stru"
def setUp(self):
self.P = PdfFit()
self.P.read_struct(datafile("Ni.stru"))
def setUp(self):
self.P = PdfFit()
self.iset = 1
self.rmin = 4.0
self.rmax = 10.0
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Perform simple refinement of Ni structure to the experimental x-ray PDF.
Save fitted curve, refined structure and results summary.
'''
from diffpy.pdffit2 import PdfFit
# Create new PDF calculator object.
pf = PdfFit()
# Load data ------------------------------------------------------------------
# Load experimental x-ray PDF data
qmax = 30.0 # Q-cutoff used in PDF calculation in 1/A
qdamp = 0.01 # instrument Q-resolution factor, responsible for PDF decay
pf.read_data('Ni-xray.gr', 'X', qmax, qdamp)
# Load nickel structure, must be in PDFFIT or DISCUS format
pf.read_struct('Ni.stru')
# Configure Refinement -------------------------------------------------------
# Refine lattice parameters a, b, c.
# Make them all equal to parameter @1.
pf.constrain(pf.lat(1), "@1")
pf.constrain(pf.lat(2), "@1")
pf.constrain(pf.lat(3), "@1")
# set initial value of parameter @1
pf.setpar(1, pf.lat(1))
def setUp(self):
self.P = PdfFit()
self.a1 = 1
self.a2 = 2
def setUp(self):
self.P = PdfFit()
self.resfile = "temp.res"
def setUp(self):
self.P = PdfFit()
return
#!/usr/bin/env python
'''Calculate PDF of FCC nickel. Save data to Ni_calculation.cgr.
'''
from diffpy.pdffit2 import PdfFit
# create new PDF calculator object
P = PdfFit()
# load structure file in PDFFIT or DISCUS format
P.read_struct("Ni.stru")
radiation_type = 'X' # x-rays
qmax = 30.0 # Q-cutoff used in PDF calculation in 1/A
qdamp = 0.01 # instrument Q-resolution factor, responsible for PDF decay
rmin = 0.01 # minimum r-value
rmax = 30.0 # maximum r-value
npts = 3000 # number of points in the r-grid
# allocate and configure PDF calculation
P.alloc(radiation_type, qmax, qdamp, rmin, rmax, npts)
P.calc()
P.save_pdf(1, "Ni_calculation.cgr")
