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 makeLaMnO3():
from pyobjcryst.crystal import Crystal
from pyobjcryst.atom import Atom
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 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
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