def __init__(self, name = "pdf"):
"""Initialize the generator.
"""
from diffpy.srreal.pdfcalculator import DebyePDFCalculator
BasePDFGenerator.__init__(self, name)
self._setCalculator(DebyePDFCalculator())
return
def __init__(self, name = "pdf"):
"""Initialize the generator.
"""
BasePDFGenerator.__init__(self, name)
self._setCalculator(DebyePDFCalculator())
return
def setUp(self):
self.pc = PDFCalculator()
self.dbpc = DebyePDFCalculator()
self.pwm = MyPWM()
self.pc.peakwidthmodel = self.pwm
self.dbpc.peakwidthmodel = self.pwm
return
def test_fq(nisph20):
sc = SASCalculator(rmax=22)
dbpc = DebyePDFCalculator(rmax=sc.rmax, qmax=sc.qmax, qstep=sc.qstep)
sc.eval(nisph20)
dbpc.eval(nisph20)
assert numpy.array_equal(dbpc.qgrid, sc.qgrid)
assert numpy.allclose(dbpc.fq, sc.fq)
return
def setUp(self):
self.dpdfc = DebyePDFCalculator()
if not TestDebyePDFCalculator.bucky:
TestDebyePDFCalculator.bucky = (
loadDiffPyStructure('C60bucky.stru'))
if not TestDebyePDFCalculator.tio2rutile:
TestDebyePDFCalculator.tio2rutile = (
loadDiffPyStructure('TiO2_rutile-fit.stru'))
return
def test_picking_owned(self):
'''verify pickling of envelopes owned by PDF calculators.
'''
pc = PDFCalculator()
dbpc = DebyePDFCalculator()
ltb = LocalTable()
ltb.setCustomAs('Na', 'Na', 37)
ltb.foo = 'bar'
pc.scatteringfactortable = ltb
dbpc.scatteringfactortable = ltb
self.assertIs(ltb, pc.scatteringfactortable)
self.assertIs(ltb, dbpc.scatteringfactortable)
pc2 = pickle.loads(pickle.dumps(pc))
dbpc2 = pickle.loads(pickle.dumps(dbpc))
self.assertEqual('localtable', pc2.scatteringfactortable.type())
self.assertEqual('localtable', dbpc2.scatteringfactortable.type())
self.assertEqual(37, pc2.scatteringfactortable.lookup('Na'))
self.assertEqual(37, dbpc2.scatteringfactortable.lookup('Na'))
self.assertEqual('bar', pc2.scatteringfactortable.foo)
self.assertEqual('bar', dbpc2.scatteringfactortable.foo)
return
# 'rmin' : 0,
# 'rmax' : 70,
# 'rstep': 0.01}
#
#cfg_dpc3 = {'qmax' : 100,
# 'qmin' : 0,
# 'rmin' : 0,
# 'rmax' : 100,
# 'rstep': 0.01}
# calculate PDF by real-space summation
pc0 = PDFCalculator(**cfg_pc)
r0, g0 = pc0(nkl_crystal)
# calcualte PDF by DPC
pc1 = DebyePDFCalculator(**cfg_dpc1)
r1, g1 = pc1(nkl_crystal)
#pc2 = DebyePDFCalculator(**cfg_dpc2)
#r2, g2 = pc2(nkl_crystal)
#
#pc3 = DebyePDFCalculator(**cfg_dpc3)
#r3, g3 = pc3(nkl_crystal)
rou = 4 / 3.52**3 ## atomic density
plt.plot(r0, g0, "b-", lw=2, label="PC")
plt.plot(r1, g1, "r-", lw=2, label="DPC, rmax = 40 A")
plt.plot(r1, g1 - 4 * np.pi * rou * r1, "k-", label="DPC, minus 4*pi*rou*r")
#plt.plot(r2, g2 + 60, "k-", lw=2, label = "DPC, rmax = 70 A")
#plt.plot(r3, g3 + 90, "m-", lw=2, label = "DPC, rmax = 100 A")
nkl_crystal.Uisoequiv = 0.005
cfg_pc = {'rmin': 0, 'rmax': 20, 'rstep': 0.01}
cfg_dpc1 = {'qmax': 100, 'qmin': 0, 'rmin': 0, 'rmax': 40, 'rstep': 0.01}
cfg_dpc2 = {'qmax': 100, 'qmin': 0, 'rmin': 0, 'rmax': 70, 'rstep': 0.01}
cfg_dpc3 = {'qmax': 100, 'qmin': 0, 'rmin': 0, 'rmax': 100, 'rstep': 0.01}
# calculate PDF by real-space summation
pc0 = PDFCalculator(**cfg_pc)
r0, g0 = pc0(nkl_crystal)
# calcualte PDF by DPC
pc1 = DebyePDFCalculator(**cfg_dpc1)
r1, g1 = pc1(nkl_crystal)
pc2 = DebyePDFCalculator(**cfg_dpc2)
r2, g2 = pc2(nkl_crystal)
pc3 = DebyePDFCalculator(**cfg_dpc3)
r3, g3 = pc3(nkl_crystal)
plt.plot(r0, g0, "b-", lw=2, label="PC")
plt.plot(r1, g1 + 30, "r-", lw=2, label="DPC, rmax = 40 A")
plt.plot(r2, g2 + 60, "k-", lw=2, label="DPC, rmax = 70 A")
plt.plot(r3, g3 + 90, "m-", lw=2, label="DPC, rmax = 100 A")
plt.legend(loc=0)
plt.xlabel("Radial Distance (r)", fontsize=15)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from diffpy.Structure import loadStructure
from diffpy.srreal.pdfcalculator import DebyePDFCalculator
from matplotlib.pyplot import plot, show
c60 = loadStructure('c60.stru')
dpc = DebyePDFCalculator()
dpc.qmax = 20
dpc.rmax = 20
r3, g3 = dpc(c60, qmin=0)
r4, g4 = dpc(c60, qmin=1)
plot(r3, g3, r4, g4)
show()
