def iter_bond(x_min, x_max, step=5):
import numpy as np
import matplotlib.pyplot as plt
#from matplotlib.pyplot import plot
from diffpy.Structure import Structure, Atom, Lattice
from diffpy.srreal.pdfcalculator import DebyePDFCalculator
dbc = DebyePDFCalculator()
dbc.qmax = 20
dbc.qmin = 0.5
dbc.rmax = 20
iter_range = np.linspace(x_min, x_max, step)
fig_dim = len(iter_range)
acs = Atom('Cs', [0, 0, 0])
acl = Atom('Cl', [0.5, 0.5, 0.5])
plt.figure()
for ind, val in enumerate(iter_range):
cscl = Structure(atoms=[acs, acl],
lattice=Lattice(val, val, val, 90, 90, 90))
dbc.setStructure(cscl)
(r,g) = dbc()
print(val)
plt.subplot(fig_dim, 1, ind+1)
plt.plot(r,g)
plt.title('bond length = %s' % str(val))
def dbc_iter(struc_f, iter_range):
'''change different range'''
import numpy as np
import matplotlib.pyplot as plt
from diffpy.srreal.pdfcalculator import DebyePDFCalculator
from diffpy.Structure import loadStructure
struc = loadStructure(struc_f)
dbc = DebyePDFCalculator()
dbc.setStructure(struc)
dbc.qmax = 20
dbc.qmin = 0.5
dbc.rmax = 20
#par = eval(para)
#print(dbc.par)
for step in iter_range:
(r,g) = dbc(delta2 = step)
plt.plot(r,g)
#!/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()
# stru.loadStrufile('CdS.cif', 'diffpy', periodic=True)
stru.loadStrufile('cd35se20.xyz', 'diffpy', periodic=False)
stru.parseDiffpyStru()
struparaset = StructureExtParSet('test', stru)
# a = np.zeros_like(struparaset.xyz.value)
# struparaset.xyz = a
# b = np.zeros_like(struparaset.occ.value)
# struparaset.occ = b
from diffpy.srreal.pdfcalculator import PDFCalculator, DebyePDFCalculator
from matplotlib.pyplot import plot, show
pc1 = DebyePDFCalculator()
pc1.rmax = 20
pc1.qmin = 1.0
r1, g1 = pc1(struparaset._getSrRealStructure())
plot(r1, g1)
# xyz = np.array(struparaset.xyz.value)
# struparaset.xyz = xyz * 1.1
# uij = np.array(struparaset.uij.value)
# struparaset.uij = uij * 3.0
struparaset.zoomscale = 1.1
r2, g2 = pc1(struparaset._getSrRealStructure())
plot(r2, g2)
show()
