def read(self, filename, format='auto'):
"""Same as Structure.read, but update spcgr value in
self.pdffit when parser can get spacegroup.
Return instance of StructureParser used to load the data.
See Structure.read() for more info.
"""
p = Structure.read(self, filename, format)
sg = getattr(p, 'spacegroup', None)
if sg: self.pdffit['spcgr'] = sg.short_name
return p
def read(self, filename, format='auto'):
"""Same as Structure.read, but update spcgr value in
self.pdffit when parser can get spacegroup.
Return instance of StructureParser used to load the data.
See Structure.read() for more info.
"""
p = Structure.read(self, filename, format)
sg = getattr(p, 'spacegroup', None)
if sg: self.pdffit['spcgr'] = sg.short_name
return p
# Discard atom if (x/a)**2 + (y/b)**2 + (z/c)**2 > 1
if d > 1:
delList.append(j)
for i in delList:
newS.pop(i)
return newS
if __name__ == "__main__":
import os.path
datadir = "../../tests/testdata"
S = Structure()
S.read(os.path.join(datadir, "CdSe_bulk.stru"), "pdffit")
newS = makeEllipsoid(S, 12)
newS.write("CdSe_d24.stru", "pdffit")
newS = makeEllipsoid(S, 20, 10, 10)
newS.write("CdSe_a20_b10_c10.stru", "pdffit")
newS = makeEllipsoid(S, 20, 15, 10)
newS.write("CdSe_a20_b15_c10.stru", "pdffit")
S = Structure()
S.read(os.path.join(datadir, "Ni.stru"), "pdffit")
newS = makeEllipsoid(S, 10)
newS.write("Ni_d20.stru", "pdffit")
newS = makeEllipsoid(S, 20, 4)
newS.write("Ni_a20_b4_c20.stru", "pdffit")
newS = makeEllipsoid(S, 20, 15, 10)
newS.write("Ni_a20_b15_c10.stru", "pdffit")
from geometry.composites import cuboctahedron
from geometry.operations import translate, rotate
c0 = translate(cuboctahedron(dist), lat.cartesian(newS[ncenter].xyz))
# Cut out an octahedron
from geometry import locate
N = len(newS)
j = N
for i in xrange(N):
xyz = lat.cartesian(newS[N - 1 - i].xyz)
if locate(xyz, c0) == 1:
newS.pop(N - 1 - i)
return newS
if __name__ == "__main__":
import os.path
datadir = "../../../tests/testdata"
S = Structure()
S.read(os.path.join(datadir, "CdSe_bulk.stru"), "pdffit")
newS = makeCuboctahedron(S, 12)
newS.write("CdSe_cuboct24.stru", "pdffit")
S = Structure()
S.read(os.path.join(datadir, "Ni.stru"), "pdffit")
newS = makeCuboctahedron(S, 10)
newS.write("Ni_cuboct20.stru", "pdffit")