def makeC60():
"""Make the C60 molecule using pyobjcryst."""
from pyobjcryst.crystal import Crystal
from pyobjcryst.molecule import Molecule
from pyobjcryst.scatteringpower import ScatteringPowerAtom
pi = numpy.pi
# make a crystal box to put the molecule in
c = Crystal(1, 1, 1, "P1")
c.SetName("c60frame")
# put a molecule inside the box
m = Molecule(c, "c60")
c.AddScatterer(m)
# Create a dummy atom at the center.
m.AddAtom(0, 0, 0, None, "center")
# Create the scattering power object for the carbon atoms
sp = ScatteringPowerAtom("C", "C")
c.AddScatteringPower(sp)
sp.SetBiso(0.25)
# Add the other atoms. They will be named C1, C2, ..., C60.
for i, l in enumerate(c60xyz.strip().splitlines()):
x, y, z = map(float, l.split())
m.AddAtom(x, y, z, sp, "C%i"%(i+1))
return m
def makeScatterer():
sp = ScatteringPowerAtom("Ni", "Ni")
sp.SetBiso(8*pi*pi*0.003)
sp.B11 = 8*pi*pi*0.003
sp.SetBij(2, 2, 8*pi*pi*0.003)
sp.SetBij(3, 3, 8*pi*pi*0.003)
atom = Atom(0, 0, 0, "Ni", sp)
print(sp.B11)
return sp, atom
def makeC60():
c = Crystal(100, 100, 100, "P1")
c.SetName("c60frame")
m = Molecule(c, "c60")
c.AddScatterer(m)
sp = ScatteringPowerAtom("C", "C")
sp.SetBiso(8*pi*pi*0.003)
c.AddScatteringPower(sp)
for i, l in enumerate(c60xyz.strip().splitlines()):
x, y, z = map(float, l.split())
m.AddAtom(x, y, z, sp, "C%i"%i)
return c
def makeC60():
"""Make a crystal containing the C60 molecule using pyobjcryst."""
pi = numpy.pi
c = Crystal(100, 100, 100, "P1")
c.SetName("c60frame")
m = Molecule(c, "c60")
c.AddScatterer(m)
sp = ScatteringPowerAtom("C", "C")
sp.SetBiso(8*pi*pi*0.003)
#c.AddScatteringPower(sp)
for i, l in enumerate(c60xyz.strip().splitlines()):
x, y, z = map(float, l.split())
m.AddAtom(x, y, z, sp, "C%i"%i)
return c
def makeMnO6():
a = 5.6
crystal = Crystal(a, a, a, "P1")
sp1 = ScatteringPowerAtom("Mn", "Mn")
sp1.SetBiso(8*pi*pi*0.003)
sp2 = ScatteringPowerAtom("O", "O")
sp2.SetBiso(8*pi*pi*0.003)
m = MakeOctahedron(crystal, "MnO6", sp1, sp2, 0.5*a)
crystal.AddScatterer(m)
return crystal
def convertObjcrystStru(self, mode='xyz_c'):
'''
convert self.xxx to objcryst object
only applied to non-periodic structure
'''
if self.periodic:
# raise TypeError('Cannot convert to periodic structure')
if self.rawstype == 'diffpy':
cif = self.rawstru.write('temp.cif', 'cif')
objcryst = CreateCrystalFromCIF(file('temp.cif'))
rv = objcryst
os.remove('temp.cif')
else:
c = Crystal(1, 1, 1, "P1")
c.SetName(self.name)
m = Molecule(c, self.name)
c.AddScatterer(m)
for i in range(self.n):
ele = self.element[i]
sp = ScatteringPowerAtom(self.element[i], ele)
if self.anisotropy[i]:
uij = self.uij_c[i]
sp.B11 = uij[0, 0]
sp.B22 = uij[1, 1]
sp.B33 = uij[2, 2]
sp.B12 = uij[0, 1]
sp.B13 = uij[0, 2]
sp.B23 = uij[1, 2]
else:
biso = np.sum(self.uij_c[i].diagonal()) / 3 * (8 * np.pi ** 2)
sp.SetBiso(biso)
if mode == 'xyz':
x, y, z = map(float, self.xyz[i])
else:
x, y, z = map(float, self.xyz_c[i])
a = m.AddAtom(x, y, z, sp, "%s%i" % (ele, i + 1))
a.Occupancy = self.occ[i]
rv = m
return self.addProp(rv)
def makeLaMnO3():
from pyobjcryst.crystal import Crystal
from pyobjcryst.atom import Atom
from pyobjcryst.molecule import Molecule
from pyobjcryst.scatteringpower import ScatteringPowerAtom
pi = numpy.pi
# It appears that ObjCryst only supports standard symbols
crystal = Crystal(5.486341, 5.619215, 7.628206, "P b n m")
crystal.SetName("LaMnO3")
# La1
sp = ScatteringPowerAtom("La1", "La")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0.996096, 0.0321494, 0.25, "La1", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
# Mn1
sp = ScatteringPowerAtom("Mn1", "Mn")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0, 0.5, 0, "Mn1", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
# O1
sp = ScatteringPowerAtom("O1", "O")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0.0595746, 0.496164, 0.25, "O1", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
# O2
sp = ScatteringPowerAtom("O2", "O")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0.720052, 0.289387, 0.0311126, "O2", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
return crystal
def makeScattererAnisotropic():
sp = ScatteringPowerAtom("Ni", "Ni")
sp.B11 = sp.B22 = sp.B33 = 8*pi*pi*0.003
sp.B12 = sp.B13 = sp.B23 = 0
atom = Atom(0, 0, 0, "Ni", sp)
return sp, atom
def makeScatterer():
sp = ScatteringPowerAtom("Ni", "Ni")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0, 0, 0, "Ni", sp)
return sp, atom
def makeLaMnO3():
crystal = Crystal(5.486341, 5.619215, 7.628206, "P b n m")
crystal.SetName("LaMnO3")
# La1
sp = ScatteringPowerAtom("La1", "La")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0.996096, 0.0321494, 0.25, "La1", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
# Mn1
sp = ScatteringPowerAtom("Mn1", "Mn")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0, 0.5, 0, "Mn1", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
# O1
sp = ScatteringPowerAtom("O1", "O")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0.0595746, 0.496164, 0.25, "O1", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
# O2
sp = ScatteringPowerAtom("O2", "O")
sp.SetBiso(8*pi*pi*0.003)
atom = Atom(0.720052, 0.289387, 0.0311126, "O2", sp)
crystal.AddScatteringPower(sp)
crystal.AddScatterer(atom)
return crystal
from matplotlib.pyplot import plot, show, clf, draw
from diffpy.Structure import Structure
from pyobjcryst.crystal import Crystal
from pyobjcryst.molecule import Molecule
from pyobjcryst.scatteringpower import ScatteringPowerAtom
from diffpy.srreal.pdfcalculator import PDFCalculator, DebyePDFCalculator
# load C60 molecule as a diffpy.Structure object
bucky_diffpy = Structure(filename='datafiles/C60bucky.stru')
# convert to an ObjCryst molecule
c60 = Crystal(1, 1, 1, 'P1')
mc60 = Molecule(c60, "C60")
c60.AddScatterer(mc60)
# Create the scattering power object for the carbon atoms
sp = ScatteringPowerAtom("C", "C")
sp.SetBiso(bucky_diffpy[0].Bisoequiv)
for i, a in enumerate(bucky_diffpy):
cname = "C%i" % (i + 1)
mc60.AddAtom(a.xyz_cartn[0], a.xyz_cartn[1], a.xyz_cartn[2], sp, cname)
# PDF configuration
cfg = { 'qmax' : 25,
'rmin' : 0,
'rmax' : 10.001,
'rstep' : 0.05,
}
# calculate PDF by real-space summation
pc0 = PDFCalculator(**cfg)
r0, g0 = pc0(c60)
