def test():
from UnitCell import UnitCell, Site
from Atom import Atom
uc = UnitCell()
at0 = Atom(symbol="Al")
at1 = Atom(symbol="Fe")
site0 = Site([0.0, 0.0, 0.0], at0)
site1 = Site([0.5, 0.5, 0.5], at1)
uc.addSite(site0, "")
uc.addSite(site1, "")
print uc
print
from python.parsing.parse_phon_results import parse
phonlist = parse("phon.out_dos_noIBZ")
wvectors = [[qx, 0.0, 0.0] for qx in range(30)]
dwc = DebyeWallerCalculator(uc, phonlist, phonlist)
dwlist = [
dwc.getDWFactorForAtom(0, wavevector, 300) for wavevector in wvectors
]
#print dwlist
return dwlist
def test():
from UnitCell import UnitCell,Site
from Atom import Atom
uc = UnitCell()
at0 = Atom(symbol="Al")
at1 = Atom(symbol="Fe")
site0=Site([0.0, 0.0, 0.0],at0)
site1=Site([0.5, 0.5, 0.5],at1)
uc.addSite(site0,"")
uc.addSite(site1, "")
print uc
print
from python.parsing.parse_phon_results import parse
phonlist = parse("phon.out_dos_noIBZ")
wvectors = [[qx, 0.0, 0.0] for qx in range(30)]
dwc = DebyeWallerCalculator(uc, phonlist, phonlist)
dwlist = [dwc.getDWFactorForAtom(0, wavevector, 300) for wavevector in wvectors]
#print dwlist
return dwlist
def buildFromXYZ(self):
"""Builds the unitcell atom coordinates from an XYZ format file."""
self._uc = UnitCell(self._cellvec)
try:
f = open(self._filename, 'r')
except IOError, (errno, strerror):
print "I/O error(%s): %s" % (errno, strerror)
def _create_primitive_unitcell(self):
# the ctor
from UnitCell import UnitCell
base = self._lattice.getPrimitiveLattice(self.sg)
base = numpy.array(base)
puc = UnitCell(base=base)
for atom in self:
if puc.hasAtom(atom): continue
puc.addAtom(atom)
continue
return puc
# check symmetry
sg = self.sg
verdict, atompos, symop = self.symConsistent()
if not verdict:
raise RuntimeError, \
"inconsistent structure: atom position: %s, sym operation %s" % (
atompos, symop)
#
if sg.number == 225:
# face centered--below is only for cubic...need to generalize
a = self.lattice.a
base = numpy.array([[0,1,1], [1,0,1], [1,1,0]])*0.5*a
elif sg.number == 229:
# body centered--below is only for cubic...need to generalize
a = self.lattice.a
base = numpy.array([[1,0,0], [0,1,0], [0.5,0.5,0.5]])*a
elif sg.short_name[0] == 'P':
# primitive
base = self.lattice
else:
# not implemented
return
def _create_primitive_unitcell(self):
# the ctor
from UnitCell import UnitCell
base = self._lattice.getPrimitiveLattice(self.sg)
base = numpy.array(base)
puc = UnitCell(base=base)
for atom in self:
if puc.hasAtom(atom): continue
puc.addAtom(atom)
continue
return puc
# check symmetry
sg = self.sg
verdict, atompos, symop = self.symConsistent()
if not verdict:
raise RuntimeError, \
"inconsistent structure: atom position: %s, sym operation %s" % (
atompos, symop)
#
if sg.number == 225:
# face centered--below is only for cubic...need to generalize
a = self.lattice.a
base = numpy.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]]) * 0.5 * a
elif sg.number == 229:
# body centered--below is only for cubic...need to generalize
a = self.lattice.a
base = numpy.array([[1, 0, 0], [0, 1, 0], [0.5, 0.5, 0.5]]) * a
elif sg.short_name[0] == 'P':
# primitive
base = self.lattice
else:
# not implemented
return
except IOError, (errno, strerror):
print "I/O error(%s): %s" % (errno, strerror)
string = ifile.readlines()
cell_params = []
cell_dict = {}
for parser in cell_parsers:
for data, dataStart, dataEnd in parser.scanString(string):
cell_params.append(data[1])
cell_dict[data[0]]=data[1]
ifile.close()
### end of fix
t=Translator()
t.filenameIn = fileInString
ciflist = t.cifToAtomAndCoordinateList()
cellvectors = MInv(cell_params)
uc = UnitCell(cellvectors)
for item in ciflist:
X = item[0]
pos = [float(x) for x in item[1:4]]
uc.addAtom(Atom(symbol=X), pos, "")
# Note: this only works if elements' symbols in CIF are "Ab" format
#resonators = decorated_resonators
#testLattice = GeneralLayout(resonators , modeType = test1.modeType, name = 'Peter-graphene')
#
#########decorated Euyclidean
#test1 = EuclideanLayout(3,3,lattice_type = 'kagome', modeType = 'FW')
#ucell = UnitCell('PeterChain_tail', side = 1)
#resonators = test1.resonators
#LGresonators = generate_line_graph(resonators)
#resonators = LGresonators
#decorated_resonators = decorate_layout(resonators, ucell.resonators)
#resonators = decorated_resonators
#testLattice = GeneralLayout(resonators , modeType = test1.modeType, name = 'Peter-kagome')
#
#########decorated Euyclidean
test1 = EuclideanLayout(3, 2, lattice_type='Huse', modeType='FW')
ucell = UnitCell('PeterChain_tail', side=1)
resonators = test1.resonators
decorated_resonators = decorate_layout(resonators, ucell.resonators)
resonators = decorated_resonators
testLattice = GeneralLayout(resonators,
modeType=test1.modeType,
name='Peter-HPG')
#
#
#######decorated hyperbolic
#test1 = PlanarLayout(gon = 7, vertex = 3, side =1, radius_method = 'lin')
#test1.populate(2, resonatorsOnly=False)
##resonators = test1.get_all_resonators()
##splitGraph = split_resonators(resonators)
##resonators = splitGraph
#ucell = UnitCell('PeterChain_tail', side = 1)
ifile = open(fileInString, 'r')
except IOError, (errno, strerror):
print "I/O error(%s): %s" % (errno, strerror)
string = ifile.readlines()
cell_params = []
cell_dict = {}
for parser in cell_parsers:
for data, dataStart, dataEnd in parser.scanString(string):
cell_params.append(data[1])
cell_dict[data[0]] = data[1]
ifile.close()
### end of fix
t = Translator()
t.filenameIn = fileInString
ciflist = t.cifToAtomAndCoordinateList()
cellvectors = MInv(cell_params)
uc = UnitCell(cellvectors)
for item in ciflist:
X = item[0]
pos = [float(x) for x in item[1:4]]
uc.addAtom(Atom(symbol=X), pos, "")
# Note: this only works if elements' symbols in CIF are "Ab" format