def test_rwStr_pdb_CdSe(self):
"""check conversion to PDB file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
#print stru.description
s = stru.writeStr(self.format)
# all lines should be 80 characters long
linelens = [len(l) for l in s.split('\n') if l != ""]
self.assertEqual(linelens, len(linelens) * [80])
# now clean and re-read structure
stru = Structure()
stru.readStr(s, self.format)
#print stru.description
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [
stru.lattice.a, stru.lattice.b, stru.lattice.c, stru.lattice.alpha,
stru.lattice.beta, stru.lattice.gamma
]
f_lat = [4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [a0.U[i, i] for i in range(3)]
f_Uii = [0.01303035, 0.01303035, 0.01401959]
self.assertListAlmostEqual(s_Uii, f_Uii)
s_sigUii = [a0.sigU[i, i] for i in range(3)]
f_sigUii = [0.00011127, 0.00011127, 0.00019575]
self.assertListAlmostEqual(s_sigUii, f_sigUii)
s_title = stru.description
f_title = "Cell structure file of CdSe #186"
self.assertEqual(s_title, f_title)
def test_rwStr_pdb_CdSe(self):
"""check conversion to PDB file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
#print stru.description
s = stru.writeStr(self.format)
# all lines should be 80 characters long
linelens = [ len(l) for l in s.split('\n') if l != "" ]
self.assertEqual(linelens, len(linelens)*[80])
# now clean and re-read structure
stru = Structure()
stru.readStr(s, self.format)
#print stru.description
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [ stru.lattice.a, stru.lattice.b, stru.lattice.c,
stru.lattice.alpha, stru.lattice.beta, stru.lattice.gamma ]
f_lat = [ 4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0 ]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [ a0.U[i,i] for i in range(3) ]
f_Uii = [ 0.01303035, 0.01303035, 0.01401959 ]
self.assertListAlmostEqual(s_Uii, f_Uii)
s_sigUii = [ a0.sigU[i,i] for i in range(3) ]
f_sigUii = [ 0.00011127, 0.00011127, 0.00019575 ]
self.assertListAlmostEqual(s_sigUii, f_sigUii)
s_title = stru.description
f_title = "Cell structure file of CdSe #186"
self.assertEqual(s_title, f_title)
def parseLines(self, lines):
"""Parse list of lines in RAWXYZ format.
Return Structure object or raise StructureFormatError.
"""
linefields = [l.split() for l in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop-1]) == 0:
stop -= 1
# get out for empty structure
if start >= stop:
return stru
# here we have at least one valid record line
# figure out xyz layout from the first line for plain and raw formats
floatfields = [ isfloat(f) for f in linefields[start] ]
nfields = len(linefields[start])
if nfields not in (3, 4):
emsg = ("%d: invalid RAWXYZ format, expected 3 or 4 columns" %
(start + 1))
raise StructureFormatError(emsg)
if floatfields[:3] == [True, True, True]:
el_idx, x_idx = (None, 0)
elif floatfields[:4] == [False, True, True, True]:
el_idx, x_idx = (0, 1)
else:
emsg = "%d: invalid RAWXYZ format" % (start + 1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:] :
p_nl += 1
if fields == []:
continue
elif len(fields) != nfields:
emsg = ('%d: all lines must have ' +
'the same number of columns') % p_nl
raise StructureFormatError, emsg
symbol = el_idx is not None and fields[el_idx] or ""
xyz = [ float(f) for f in fields[x_idx:x_idx+3] ]
if len(xyz) == 2:
xyz.append(0.0)
stru.addNewAtom(symbol, xyz=xyz)
except ValueError:
emsg = "%d: invalid number" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
raise StructureFormatError, emsg, exc_traceback
return stru
def supercell(S, mno):
"""Perform supercell expansion for a structure.
New lattice parameters are multiplied and fractional coordinates
divided by corresponding multiplier. New atoms are grouped with
their source in the original cell.
S -- an instance of Structure from matter.
mno -- sequence of 3 integers for cell multipliers along
the a, b and c axes.
Return a new expanded structure instance.
Raise TypeError when S is not Structure instance.
Raise ValueError for invalid mno argument.
"""
# check arguments
if len(mno) != 3:
emsg = "Argument mno must contain 3 numbers."
raise ValueError, emsg
elif min(mno) < 1:
emsg = "Multipliers must be greater or equal 1"
raise ValueError, emsg
if not isinstance(S, Structure):
emsg = "The first argument must be a Structure instance."
raise TypeError, emsg
# convert mno to a tuple of integers so it can be used as range limit.
mno = (int(mno[0]), int(mno[1]), int(mno[2]))
# create return instance
newS = Structure(S)
if mno == (1, 1, 1):
return newS
# back to business
ijklist = [(i,j,k)
for i in range(mno[0])
for j in range(mno[1])
for k in range(mno[2])]
# numpy.floor returns float array
mnofloats = numpy.array(mno, dtype=float)
# build a list of new atoms
newAtoms = []
for a in S:
for ijk in ijklist:
adup = Atom(a)
adup.xyz = (a.xyz + ijk)/mnofloats
newAtoms.append(adup)
# newS can own references in newAtoms, no need to make copies
newS.__setslice__(0, len(newS), newAtoms, copy=False)
# take care of lattice parameters
newS.lattice.setLatPar(
a=mno[0]*S.lattice.a,
b=mno[1]*S.lattice.b,
c=mno[2]*S.lattice.c )
return newS
def parseLines(self, lines):
"""Parse list of lines in RAWXYZ format.
Return Structure object or raise StructureFormatError.
"""
linefields = [l.split() for l in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop - 1]) == 0:
stop -= 1
# get out for empty structure
if start >= stop:
return stru
# here we have at least one valid record line
# figure out xyz layout from the first line for plain and raw formats
floatfields = [isfloat(f) for f in linefields[start]]
nfields = len(linefields[start])
if nfields not in (3, 4):
emsg = ("%d: invalid RAWXYZ format, expected 3 or 4 columns" %
(start + 1))
raise StructureFormatError(emsg)
if floatfields[:3] == [True, True, True]:
el_idx, x_idx = (None, 0)
elif floatfields[:4] == [False, True, True, True]:
el_idx, x_idx = (0, 1)
else:
emsg = "%d: invalid RAWXYZ format" % (start + 1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:]:
p_nl += 1
if fields == []:
continue
elif len(fields) != nfields:
emsg = ('%d: all lines must have ' +
'the same number of columns') % p_nl
raise StructureFormatError, emsg
symbol = el_idx is not None and fields[el_idx] or ""
xyz = [float(f) for f in fields[x_idx:x_idx + 3]]
if len(xyz) == 2:
xyz.append(0.0)
stru.addNewAtom(symbol, xyz=xyz)
except ValueError:
emsg = "%d: invalid number" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
raise StructureFormatError, emsg, exc_traceback
return stru
def setUp(self):
# load test structures once
if TestSuperCell.stru_cdse is None:
cdsefile = os.path.join(testdata_dir, "CdSe_bulk.stru")
TestSuperCell.stru_cdse = Structure(filename=cdsefile)
if TestSuperCell.stru_ni is None:
nifile = os.path.join(testdata_dir, "Ni.stru")
TestSuperCell.stru_ni = Structure(filename=nifile)
# bring them to the instance
self.stru_cdse = TestSuperCell.stru_cdse
self.stru_ni = TestSuperCell.stru_ni
return
def test_dsaworm(self):
'Structure: dsaw orm'
Fe57 = Atom('Fe', mass=57)
Al = Atom('Al')
atoms = [Fe57, Al]
lattice = Lattice(a=1, b=2, c=3, alpha=89, beta=91, gamma=92)
struct = Structure(atoms=atoms, lattice=lattice)
orm = self.orm
structrecord = orm(struct)
orm.save(struct)
struct_loaded = orm.load(Structure, structrecord.id)
props = ['sg', 'description']
for prop in props:
self.assertEqual(getattr(struct_loaded, prop),
getattr(struct, prop))
continue
props = ['a', 'b', 'c', 'alpha', 'beta', 'gamma']
for prop in props:
self.assertEqual(getattr(struct_loaded.lattice, prop),
getattr(struct.lattice, prop))
continue
self.assertEqual(len(struct_loaded), 2)
for atom in struct_loaded:
self.assertEqual(atom.__class__, Atom)
return
def test_NaI(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Na', [0.0, 0.0, 0.0])
at2 = Atom('Na', [0.0, 0.5, 0.5])
at3 = Atom('Na', [0.5, 0.0, 0.5])
at4 = Atom('Na', [0.5, 0.5, 0.0])
at5 = Atom('I', [0.5, 0.5, 0.5])
at6 = Atom('I', [0.0, 0.0, 0.5])
at7 = Atom('I', [0.0, 0.5, 0.0])
at8 = Atom('I', [0.5, 0.0, 0.0])
naI = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8],
lattice = Lattice(6.482, 6.482, 6.482, 90, 90, 90),
sgid = 225 )
lines = []
for sym,pos in zip(naI.symbols, naI.xyz_cartn):
lines.append( sym+' %f %f %f' % tuple(pos) )
lines.append('\n')
naI_sup = supercell(naI, (2,2,2))
for sym,pos in zip(naI_sup.symbols, naI_sup.xyz_cartn):
lines.append(sym+' %f %f %f' % tuple(pos))
expected = open('expected-test_NaI-TestSuperCell').readlines()
self.assertEqual(len(lines), len(expected))
for l1, l2 in zip(lines, expected):
self.assertEqual(l1.strip(), l2.strip())
return
def makeUnitcell():
from matter import Atom, Structure, Lattice
atoms = [Atom('Ni')]
# positions = [(0,0,0)]
cellvectors = [ (3.57,0,0), (0,3.57,0), (0,0,3.57) ]
lattice = Lattice(base=cellvectors)
return Structure(lattice=lattice, atoms=atoms)
def __init__(self, *args, **kwargs):
Structure.__init__(self, *args, **kwargs)
# do not overwrite self.pdffit, when instantiated as a copy
# of existing PDFFitStructure
if not hasattr(self, 'pdffit'):
self.pdffit = {
'scale' : 1.0,
'delta1' : 0.0,
'delta2' : 0.0,
'sratio' : 1.0,
'rcut' : 0.0,
'spcgr' : 'P1',
'spdiameter' : 0.0,
'stepcut' : 0.0,
'dcell' : 6*[0.0],
'ncell' : [1, 1, 1, 0],
}
return
def test_rwStr_xcfg_CdSe(self):
"""check conversion to XCFG file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
s = stru.writeStr(self.format)
stru = Structure()
stru.readStr(s, self.format)
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [ stru.lattice.a, stru.lattice.b, stru.lattice.c,
stru.lattice.alpha, stru.lattice.beta, stru.lattice.gamma ]
f_lat = [ 4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0 ]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [ a0.U[i,i] for i in range(3) ]
f_Uii = [ 0.01303035, 0.01303035, 0.01401959 ]
self.assertListAlmostEqual(s_Uii, f_Uii)
def __init__(self, *args, **kwargs):
Structure.__init__(self, *args, **kwargs)
# do not overwrite self.pdffit, when instantiated as a copy
# of existing PDFFitStructure
if not hasattr(self, 'pdffit'):
self.pdffit = {
'scale': 1.0,
'delta1': 0.0,
'delta2': 0.0,
'sratio': 1.0,
'rcut': 0.0,
'spcgr': 'P1',
'spdiameter': 0.0,
'stepcut': 0.0,
'dcell': 6 * [0.0],
'ncell': [1, 1, 1, 0],
}
return
def test_rwStr_xcfg_CdSe(self):
"""check conversion to XCFG file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
s = stru.writeStr(self.format)
stru = Structure()
stru.readStr(s, self.format)
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [ stru.lattice.a, stru.lattice.b, stru.lattice.c,
stru.lattice.alpha, stru.lattice.beta, stru.lattice.gamma ]
f_lat = [ 4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0 ]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [ a0.U[i,i] for i in range(3) ]
f_Uii = [ 0.01303035, 0.01303035, 0.01401959 ]
self.assertListAlmostEqual(s_Uii, f_Uii)
def readStr(self, s, format='auto'):
"""Same as Structure.readStr, but update spcgr value in
self.pdffit when parser can get spacegroup.
Return instance of StructureParser used to load the data.
See Structure.readStr() for more info.
"""
p = Structure.readStr(self, s, format)
sg = getattr(p, 'spacegroup', None)
if sg: self.pdffit['spcgr'] = sg.short_name
return p
def test_writeStr_xyz_Supercell(self):
at1 = Atom('Al', [0.0, 0.0, 0.0])
at2 = Atom('Al', [0.0, 0.5, 0.5])
at3 = Atom('Al', [0.5, 0.0, 0.5])
at4 = Atom('Al', [0.5, 0.5, 0.0])
self.stru4 = Structure([at1, at2, at3, at4],
lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
sgid=225)
from matter.expansion import supercell
al_333 = supercell(self.stru4, (3, 3, 3))
s1 = al_333.writeStr(self.format)
def readStr(self, s, format='auto'):
"""Same as Structure.readStr, but update spcgr value in
self.pdffit when parser can get spacegroup.
Return instance of StructureParser used to load the data.
See Structure.readStr() for more info.
"""
p = Structure.readStr(self, s, format)
sg = getattr(p, 'spacegroup', None)
if sg: self.pdffit['spcgr'] = sg.short_name
return p
def test1(self):
'makeXYZfileContent'
from matter import Lattice, Atom, Structure
Al = Atom('Al', (0, 0, 0))
Fe = Atom('Fe', (0.5, 0.5, 0.5))
atoms = [Al, Fe]
lattice = Lattice(1, 1, 1, 90, 90, 90)
s = Structure(atoms, lattice)
content = struct_utils.makeXYZfileContent(s, latticeAsDescription=True)
self.assertEqual(len(content), 4)
self.assertEqual(int(content[0]), 2)
self.assertEqual(len(content[1].split(' ')), 9)
return
def test_al_supercell(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Al', [0.0, 0.0, 0.0])
at2 = Atom('Al', [0.0, 0.5, 0.5])
at3 = Atom('Al', [0.5, 0.0, 0.5])
at4 = Atom('Al', [0.5, 0.5, 0.0])
self.stru4 = Structure( [ at1, at2, at3, at4],
lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
sgid = 225 )
al_sup = supercell(self.stru4, (3,3,3))
#print al_sup
return
def test_naI_supercell(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Na', [0.0, 0.0, 0.0])
at2 = Atom('Na', [0.0, 0.5, 0.5])
at3 = Atom('Na', [0.5, 0.0, 0.5])
at4 = Atom('Na', [0.5, 0.5, 0.0])
at5 = Atom('I', [0.5, 0.5, 0.5])
at6 = Atom('I', [0.0, 0.0, 0.5])
at7 = Atom('I', [0.0, 0.5, 0.0])
at8 = Atom('I', [0.5, 0.0, 0.0])
naI = Structure([at1, at2, at3, at4, at5, at6, at7, at8],
lattice=Lattice(6.482, 6.482, 6.482, 90, 90, 90),
sgid=225)
for sym, pos in zip(naI.symbols, naI.xyz_cartn):
print sym + ' %f %f %f' % tuple(pos)
print
naI_sup = supercell(naI, (2, 2, 2))
for sym, pos in zip(naI_sup.symbols, naI_sup.xyz_cartn):
print sym + ' %f %f %f' % tuple(pos)
def save(filename, material):
for geo in material.get_geos():
atoms = geo.get_atoms()
from matter import Structure, Lattice
import matter.Atom as matterAtom
for atom in atoms:
x, y, z = atom.get_xyz()
atno = atom.get_atno()
atoms.append(matterAtom(symbol[atno], [x, y, z]))
cell = geo.get_cell()
a, b, c, alph, bet, gam = cell.abcabg
lattice = Lattice(a, b, c, alph, bet, gam)
stru = Structure(atoms, lattice)
import pickle
output = open(filename, 'wb')
from Utilities import assureCorrectFileEnding
filename = assureCorrectFileEnding(filename, 'pkl')
pickle.dump(stru, output)
output.close()
return
def testWriter(self):
p = getParser()
import matter
a = 1.5
lattice = matter.Lattice(2 * a, 2 * a, 2 * a, 90, 90, 90)
atoms = [matter.Atom('Ni'), matter.Atom('Ni', (0.5, 0.5, 0.5))]
struct = Structure(lattice=lattice, atoms=atoms, sgid=229)
print 'original unitcell, cartesian coords'
print '\n'.join(p.toLines(struct))
print 'original unitcell, fractional coords'
print '\n'.join(p.toLines(struct, use_fractional_coordinates=1))
print 'primitive unitcell, cartesian coords'
print '\n'.join(p.toLines(struct, use_primitive_unitcell=1))
print 'primitive unitcell, fractional coords'
print '\n'.join(
p.toLines(struct,
use_primitive_unitcell=1,
use_fractional_coordinates=1))
return
def parseLines(self, lines):
"""Parse list of lines in XYZ format.
Return Structure object or raise StructureFormatError.
"""
linefields = [l.split() for l in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# first valid line gives number of atoms
try:
lfs = linefields[start]
w1 = linefields[start][0]
if len(lfs) == 1 and str(int(w1)) == w1:
p_natoms = int(w1)
#try to get lattice vectors from description line
try:
latticeVecs = map(float, linefields[start+1])
assert len(latticeVecs)==9
from matter.Lattice import Lattice
reshaped = [latticeVecs[0:3], latticeVecs[3:6], latticeVecs[6:9]]
stru.lattice = Lattice(base=reshaped)
needsDescription = True
except:
needsDescription = False
stru.description = lines[start+1].strip()
start += 2
else:
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError(emsg)
except (IndexError, ValueError):
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError, emsg, exc_traceback
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop-1]) == 0:
stop -= 1
# get out for empty structure
if p_natoms == 0 or start >= stop:
return stru
# here we have at least one valid record line
nfields = len(linefields[start])
if nfields != 4 and nfields != 5:
emsg = "%d: invalid XYZ format, expected 4 or 5 columns" % (start + 1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:] :
p_nl += 1
if fields == []:
continue
elif len(fields) != 4 and len(fields) !=5:
emsg = ('%d: all lines must have ' +
'a symbol, position, and optionally charge') % p_nl
raise StructureFormatError(emsg)
symbol = fields[0]
symbol = symbol[0].upper() + symbol[1:].lower()
xyz = [ float(f) for f in fields[1:4] ]
if len(fields)==5:
charge = float(fields[4])
else:
charge = 0.0
stru.addNewAtom(symbol, xyz=xyz, charge=charge)
except ValueError:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid number format" % p_nl
raise StructureFormatError, emsg, exc_traceback
# finally check if all the atoms have been read
if p_natoms is not None and len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
if needsDescription:
stru.generateDescription()
return stru
def test_load_matter(self):
from matter import Structure, Atom, Lattice
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
a = 2. * 5.663 / 1.889725989 # set a in angstrom
struct = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = Lattice(a, a, a, 90, 90, 90))
#print struct
massList = [50.9415, 55.847]
psList = ['V.pbe-n-van.UPF', 'Fe.pbe-nd-rrkjus.UPF']
#self.input.structure.load(structure = struct, ibrav = 2, massList = massList, psList = psList)
self.input.structure.load(structure=struct,
ibrav=2,
massList=massList,
psList=psList)
answer1 = """"Face Centered Cubic" cell:
-5.66300000 0.00000000 5.66300000
0.00000000 5.66300000 5.66300000
-5.66300000 5.66300000 0.00000000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
#print str(self.input.structure)
self.assertEqual(str(self.input.structure), answer1)
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
a = 2. * 5.663 / 1.889725989 # set a in angstrom
struct2 = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = Lattice(a, a, a, 90, 90, 90))
self.input.structure.load(structure=struct2,
massList=massList,
psList=psList)
answer2 = """"generic" cell:
11.32600000 0.00000000 0.00000000
0.00000000 11.32600000 0.00000000
0.00000000 0.00000000 11.32600000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 2.99673076 0.00000000 0.00000000
V 0.00000000 2.99673076 0.00000000
V 0.00000000 0.00000000 2.99673076
V 2.99673076 2.99673076 0.00000000
V 0.00000000 2.99673076 2.99673076
V 2.99673076 0.00000000 2.99673076
V 2.99673076 2.99673076 2.99673076
V 1.49836538 1.49836538 1.49836538
Fe 4.49509614 1.49836538 1.49836538
V 4.49509614 4.49509614 1.49836538
Fe 1.49836538 4.49509614 1.49836538
Fe 1.49836538 1.49836538 4.49509614
V 4.49509614 1.49836538 4.49509614
Fe 4.49509614 4.49509614 4.49509614
V 1.49836538 4.49509614 4.49509614
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
#print str(self.input.structure)
self.assertEqual(str(self.input.structure), answer2)
def makeMatter():
from matter import Structure, Atom, Lattice
atoms = [Atom('Fe', xyz=(0, 0, 0)), Atom('Al', xyz=(0.5, 0.5, 0.5))]
lattice = Lattice(base=((1., 0, 0), (0, 1., 0), (0, 0, 1.)))
return Structure(atoms, lattice)
d = sum(darray)**0.5
# 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")
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
# USA
# read and view pickled structure object
from matter import Structure, Lattice, Atom
at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
a = 2.4612
c = 6.7079
graphite = Structure([at1, at2], lattice=Lattice(a, a, c, 90, 90, 120))
print graphite
import pickle
output = open('graphite.pkl', 'wb')
pickle.dump(graphite, output)
output.close()
pkl_file = open('graphite.pkl', 'rb')
g2 = pickle.load(pkl_file)
print g2
#m2 = create_nanotube(10,10,10)
#save_file("nano.xyz", m2)
#atoms = m1.get_atoms()
def parseLines(self, lines):
"""Parse list of lines in PDB format.
Return Structure object or raise StructureFormatError.
"""
xcfg_Number_of_particles = None
xcfg_A = None
xcfg_H0 = numpy.zeros((3,3), dtype=float)
xcfg_H0_set = numpy.zeros((3,3), dtype=bool)
xcfg_NO_VELOCITY = False
xcfg_entry_count = None
xcfg_auxiliary = []
p_nl = 0
p_auxiliary_re = re.compile(r"^auxiliary\[(\d+)\] =")
p_auxiliary = {}
try:
stru = Structure()
# ignore trailing blank lines
stop = len(lines)
while stop>0 and lines[stop-1].strip() == "":
stop -= 1
ilines = iter(lines[:stop])
# read XCFG header
for line in ilines:
p_nl += 1
stripped_line = line.strip()
# blank lines and lines starting with # are ignored
if stripped_line == "" or line[0] == '#':
continue
elif xcfg_Number_of_particles is None:
if line.find("Number of particles =") != 0:
emsg = ("%d: first line must " +
"contain 'Number of particles ='") % p_nl
raise StructureFormatError(emsg)
xcfg_Number_of_particles = int(line[21:].split(None, 1)[0])
p_natoms = xcfg_Number_of_particles
elif line.find("A =") == 0:
xcfg_A = float(line[3:].split(None, 1)[0])
elif line.find("H0(") == 0:
i, j = ( int(line[3])-1 , int(line[5])-1 )
xcfg_H0[i,j] = float(line[10:].split(None, 1)[0])
xcfg_H0_set[i,j] = True
elif line.find(".NO_VELOCITY.") == 0:
xcfg_NO_VELOCITY = True
elif line.find("entry_count =") == 0:
xcfg_entry_count = int(line[13:].split(None, 1)[0])
elif p_auxiliary_re.match(line):
m = p_auxiliary_re.match(line)
idx = int(m.group(1))
p_auxiliary[idx] = line[m.end():].split(None, 1)[0]
else:
break
# check header for consistency
if numpy.any(xcfg_H0_set == False):
emsg = "H0 tensor is not properly defined"
raise StructureFormatError(emsg)
p_auxnum = len(p_auxiliary) and max(p_auxiliary.keys())+1
for i in range(p_auxnum):
if not i in p_auxiliary:
p_auxiliary[i] = "aux%d" % i
sorted_aux_keys = p_auxiliary.keys()
sorted_aux_keys.sort()
if p_auxnum != 0:
stru.xcfg = {
'auxiliaries' : [ p_auxiliary[k]
for k in sorted_aux_keys ]
}
if 6-3*xcfg_NO_VELOCITY+len(p_auxiliary) != xcfg_entry_count:
emsg = ("%d: auxiliary fields " +
"not consistent with entry_count") % p_nl
raise StructureFormatError(emsg)
# define proper lattice
stru.lattice.setLatBase(xcfg_H0)
# build p_assign_atom function to assign entries to proper fields
p_exprs = [ "a.xyz[0]=fields[0]",
"a.xyz[1]=fields[1]",
"a.xyz[2]=fields[2]" ]
if not xcfg_NO_VELOCITY:
p_exprs += [ "a.v=numpy.zeros(3, dtype=float)",
"a.v[0]=fields[3]",
"a.v[1]=fields[4]",
"a.v[2]=fields[5]" ]
for idx in sorted_aux_keys:
prop = p_auxiliary[idx]
col = idx + 6 - 3*xcfg_NO_VELOCITY
if prop == "Uiso":
p_exprs.append("a.U[0,0]=a.U[1,1]=a.U[2,2]=" +
"fields[%d]" % col)
elif re.match(r"^U\d\d$", prop) \
and 1<=int(prop[1])<=3 and 1<=int(prop[2])<=3 :
i, j = int(prop[1])-1, int(prop[2])-1
if i==j:
p_exprs.append("a.U[%i,%i]=fields[%d]" % (i, j, col) )
else:
p_exprs.append("a.U[%i,%i]=a.U[%i,%i]=fields[%d]" % \
(i, j, j, i, col) )
else:
p_exprs.append( "a.__dict__[%r]=fields[%d]" % \
(prop, col) )
p_assign_expr = "pass; " + "; ".join(p_exprs[3:])
exec "def p_assign_atom(a, fields) : %s" % p_assign_expr
# here we are inside data
p_element = None
p_nl -= 1
for line in lines[p_nl:stop]:
p_nl += 1
words = line.split()
# ignore atom mass
if len(words) == 1 and isfloat(words[0]):
continue
# parse element allowing empty symbol
elif len(words) <= 1:
w = line.strip()
p_element = w[:1].upper() + w[1:].lower()
elif len(words) == xcfg_entry_count and p_element is not None:
fields = [ float(w) for w in words ]
stru.addNewAtom(p_element, fields[:3])
a = stru.getLastAtom()
a.xyz *= xcfg_A
p_assign_atom(a, fields)
else:
emsg = "%d: invalid record" % p_nl
raise StructureFormatError(emsg)
if len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
except (ValueError, IndexError):
emsg = "%d: file is not in XCFG format" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
raise StructureFormatError, emsg, exc_traceback
return stru
def parseLines(self, lines):
"""Parse list of lines in PDB format.
Return Structure object or raise StructureFormatError.
"""
xcfg_Number_of_particles = None
xcfg_A = None
xcfg_H0 = numpy.zeros((3, 3), dtype=float)
xcfg_H0_set = numpy.zeros((3, 3), dtype=bool)
xcfg_NO_VELOCITY = False
xcfg_entry_count = None
xcfg_auxiliary = []
p_nl = 0
p_auxiliary_re = re.compile(r"^auxiliary\[(\d+)\] =")
p_auxiliary = {}
try:
stru = Structure()
# ignore trailing blank lines
stop = len(lines)
while stop > 0 and lines[stop - 1].strip() == "":
stop -= 1
ilines = iter(lines[:stop])
# read XCFG header
for line in ilines:
p_nl += 1
stripped_line = line.strip()
# blank lines and lines starting with # are ignored
if stripped_line == "" or line[0] == '#':
continue
elif xcfg_Number_of_particles is None:
if line.find("Number of particles =") != 0:
emsg = ("%d: first line must " +
"contain 'Number of particles ='") % p_nl
raise StructureFormatError(emsg)
xcfg_Number_of_particles = int(line[21:].split(None, 1)[0])
p_natoms = xcfg_Number_of_particles
elif line.find("A =") == 0:
xcfg_A = float(line[3:].split(None, 1)[0])
elif line.find("H0(") == 0:
i, j = (int(line[3]) - 1, int(line[5]) - 1)
xcfg_H0[i, j] = float(line[10:].split(None, 1)[0])
xcfg_H0_set[i, j] = True
elif line.find(".NO_VELOCITY.") == 0:
xcfg_NO_VELOCITY = True
elif line.find("entry_count =") == 0:
xcfg_entry_count = int(line[13:].split(None, 1)[0])
elif p_auxiliary_re.match(line):
m = p_auxiliary_re.match(line)
idx = int(m.group(1))
p_auxiliary[idx] = line[m.end():].split(None, 1)[0]
else:
break
# check header for consistency
if numpy.any(xcfg_H0_set == False):
emsg = "H0 tensor is not properly defined"
raise StructureFormatError(emsg)
p_auxnum = len(p_auxiliary) and max(p_auxiliary.keys()) + 1
for i in range(p_auxnum):
if not i in p_auxiliary:
p_auxiliary[i] = "aux%d" % i
sorted_aux_keys = p_auxiliary.keys()
sorted_aux_keys.sort()
if p_auxnum != 0:
stru.xcfg = {
'auxiliaries': [p_auxiliary[k] for k in sorted_aux_keys]
}
if 6 - 3 * xcfg_NO_VELOCITY + len(p_auxiliary) != xcfg_entry_count:
emsg = ("%d: auxiliary fields " +
"not consistent with entry_count") % p_nl
raise StructureFormatError(emsg)
# define proper lattice
stru.lattice.setLatBase(xcfg_H0)
# build p_assign_atom function to assign entries to proper fields
p_exprs = [
"a.xyz[0]=fields[0]", "a.xyz[1]=fields[1]",
"a.xyz[2]=fields[2]"
]
if not xcfg_NO_VELOCITY:
p_exprs += [
"a.v=numpy.zeros(3, dtype=float)", "a.v[0]=fields[3]",
"a.v[1]=fields[4]", "a.v[2]=fields[5]"
]
for idx in sorted_aux_keys:
prop = p_auxiliary[idx]
col = idx + 6 - 3 * xcfg_NO_VELOCITY
if prop == "Uiso":
p_exprs.append("a.U[0,0]=a.U[1,1]=a.U[2,2]=" +
"fields[%d]" % col)
elif re.match(r"^U\d\d$", prop) \
and 1<=int(prop[1])<=3 and 1<=int(prop[2])<=3 :
i, j = int(prop[1]) - 1, int(prop[2]) - 1
if i == j:
p_exprs.append("a.U[%i,%i]=fields[%d]" % (i, j, col))
else:
p_exprs.append("a.U[%i,%i]=a.U[%i,%i]=fields[%d]" % \
(i, j, j, i, col) )
else:
p_exprs.append( "a.__dict__[%r]=fields[%d]" % \
(prop, col) )
p_assign_expr = "pass; " + "; ".join(p_exprs[3:])
exec "def p_assign_atom(a, fields) : %s" % p_assign_expr
# here we are inside data
p_element = None
p_nl -= 1
for line in lines[p_nl:stop]:
p_nl += 1
words = line.split()
# ignore atom mass
if len(words) == 1 and isfloat(words[0]):
continue
# parse element allowing empty symbol
elif len(words) <= 1:
w = line.strip()
p_element = w[:1].upper() + w[1:].lower()
elif len(words) == xcfg_entry_count and p_element is not None:
fields = [float(w) for w in words]
stru.addNewAtom(p_element, fields[:3])
a = stru.getLastAtom()
a.xyz *= xcfg_A
p_assign_atom(a, fields)
else:
emsg = "%d: invalid record" % p_nl
raise StructureFormatError(emsg)
if len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
except (ValueError, IndexError):
emsg = "%d: file is not in XCFG format" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
raise StructureFormatError, emsg, exc_traceback
return stru
def setUp(self):
self.stru = Structure()
self.format = "xcfg"
self.places = 6
def setUp(self):
self.stru = Structure()
self.format = "pdb"
self.places = 3
def setUp(self):
self.stru = Structure()
self.format = "rawxyz"
def parseLines(self, lines):
"""Parse list of lines in XYZ format.
Return Structure object or raise StructureFormatError.
"""
linefields = [l.split() for l in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# first valid line gives number of atoms
try:
lfs = linefields[start]
w1 = linefields[start][0]
if len(lfs) == 1 and str(int(w1)) == w1:
p_natoms = int(w1)
#try to get lattice vectors from description line
try:
latticeVecs = map(float, linefields[start + 1])
assert len(latticeVecs) == 9
from matter.Lattice import Lattice
reshaped = [
latticeVecs[0:3], latticeVecs[3:6], latticeVecs[6:9]
]
stru.lattice = Lattice(base=reshaped)
needsDescription = True
except:
needsDescription = False
stru.description = lines[start + 1].strip()
start += 2
else:
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError(emsg)
except (IndexError, ValueError):
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError, emsg, exc_traceback
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop - 1]) == 0:
stop -= 1
# get out for empty structure
if p_natoms == 0 or start >= stop:
return stru
# here we have at least one valid record line
nfields = len(linefields[start])
if nfields != 4 and nfields != 5:
emsg = "%d: invalid XYZ format, expected 4 or 5 columns" % (start +
1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:]:
p_nl += 1
if fields == []:
continue
elif len(fields) != 4 and len(fields) != 5:
emsg = ('%d: all lines must have ' +
'a symbol, position, and optionally charge') % p_nl
raise StructureFormatError(emsg)
symbol = fields[0]
symbol = symbol[0].upper() + symbol[1:].lower()
xyz = [float(f) for f in fields[1:4]]
if len(fields) == 5:
charge = float(fields[4])
else:
charge = 0.0
stru.addNewAtom(symbol, xyz=xyz, charge=charge)
except ValueError:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid number format" % p_nl
raise StructureFormatError, emsg, exc_traceback
# finally check if all the atoms have been read
if p_natoms is not None and len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
if needsDescription:
stru.generateDescription()
return stru
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")
def parseLines(self, lines):
"""Parse list of lines in XYZ format.
Return Structure object or raise StructureFormatError.
"""
linefields = [l.split() for l in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# first valid line gives number of atoms
try:
lfs = linefields[start]
w1 = linefields[start][0]
if len(lfs) == 1 and str(int(w1)) == w1:
p_natoms = int(w1)
stru.title = lines[start+1].strip()
start += 2
else:
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError(emsg)
except (IndexError, ValueError):
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError, emsg, exc_traceback
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop-1]) == 0:
stop -= 1
# get out for empty structure
if p_natoms == 0 or start >= stop:
return stru
# here we have at least one valid record line
nfields = len(linefields[start])
if nfields != 4:
emsg = "%d: invalid XYZ format, expected 4 columns" % (start + 1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:] :
p_nl += 1
if fields == []:
continue
elif len(fields) != nfields:
emsg = ('%d: all lines must have ' +
'the same number of columns') % p_nl
raise StructureFormatError(emsg)
symbol = fields[0]
symbol = symbol[0].upper() + symbol[1:].lower()
xyz = [ float(f) for f in fields[1:4] ]
stru.addNewAtom(symbol, xyz=xyz)
except ValueError:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid number format" % p_nl
raise StructureFormatError, emsg, exc_traceback
# finally check if all the atoms have been read
if p_natoms is not None and len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
return stru
def setUp(self):
self.stru = Structure()
self.format = 'xyz'
import tempfile
handle, self.tmpname = tempfile.mkstemp()
os.close(handle)
def parseLines(self, lines):
"""Parse list of lines in PDB format.
Return Structure instance or raise StructureFormatError.
"""
try:
stru = Structure()
scale = numpy.identity(3, dtype=float)
scaleU = numpy.zeros(3, dtype=float)
p_nl = 0
for line in lines:
p_nl += 1
# skip blank lines
if not line.strip(): continue
# make sure line has 80 characters
if len(line) < 80:
line = "%-80s" % line
words = line.split()
record = words[0]
if record == "TITLE":
continuation = line[8:10]
if continuation.strip():
stru.description += line[10:].rstrip()
else:
stru.description = line[10:].rstrip()
elif record == "CRYST1":
a = float(line[7:15])
b = float(line[15:24])
c = float(line[24:33])
alpha = float(line[33:40])
beta = float(line[40:47])
gamma = float(line[47:54])
stru.lattice.setLatPar(a, b, c, alpha, beta, gamma)
scale = numpy.transpose(stru.lattice.recbase)
elif record == "SCALE1":
sc = numpy.zeros((3,3), dtype=float)
sc[0,:] = [float(x) for x in line[10:40].split()]
scaleU[0] = float(line[45:55])
elif record == "SCALE2":
sc[1,:] = [float(x) for x in line[10:40].split()]
scaleU[1] = float(line[45:55])
elif record == "SCALE3":
sc[2,:] = [float(x) for x in line[10:40].split()]
scaleU[2] = float(line[45:55])
base = numpy.transpose(numpy.linalg.inv(sc))
abcABGcryst = numpy.array(stru.lattice.abcABG())
stru.lattice.setLatBase(base)
abcABGscale = numpy.array(stru.lattice.abcABG())
reldiff = numpy.fabs(1.0 - abcABGscale/abcABGcryst)
if not numpy.all(reldiff < self.epsilon):
emsg = "%d: " % p_nl + \
"SCALE and CRYST1 are not consistent."
raise StructureFormatError(emsg)
if numpy.any(scaleU != 0.0):
emsg = "Origin offset not yet implemented."
raise NotImplementedError(emsg)
elif record in ("ATOM", "HETATM"):
name = line[12:16].strip()
rc = [float(x) for x in line[30:54].split()]
xyz = numpy.dot(scale, rc) + scaleU
try:
occupancy = float(line[54:60])
except ValueError:
occupancy = 1.0
try:
B = float(line[60:66])
U = numpy.identity(3)*B/(8*pi**2)
except ValueError:
U = numpy.zeros((3,3), dtype=float)
symbol = line[76:78].strip()
if symbol == "":
# get symbol from the first 2 characters of name
symbol = line[12:14].strip()
symbol = symbol[0].upper() + symbol[1:].lower()
#stru.addNewAtom(symbol, occupancy=occupancy, name=name, U=U)
stru.addNewAtom(symbol, occupancy=occupancy, label=name, U=U)
last_atom = stru.getLastAtom()
last_atom.xyz_cartn = rc
elif record == "SIGATM":
sigrc = [float(x) for x in line[30:54].split()]
sigxyz = numpy.dot(scale, sigrc)
try:
sigo = float(line[54:60])
except ValueError:
sigo = 0.0
try:
sigB = float(line[60:66])
sigU = numpy.identity(3)*sigB/(8*pi**2)
except ValueError:
sigU = numpy.zeros((3,3), dtype=float)
last_atom.sigxyz = sigxyz
last_atom.sigo = sigo
last_atom.sigU = sigU
elif record == "ANISOU":
Uij = [ float(x)*1.0e-4 for x in line[28:70].split() ]
for i in range(3):
last_atom.U[i,i] = Uij[i]
last_atom.U[0,1] = last_atom.U[1,0] = Uij[3]
last_atom.U[0,2] = last_atom.U[2,0] = Uij[4]
last_atom.U[1,2] = last_atom.U[2,1] = Uij[5]
elif record == "SIGUIJ":
sigUij = [ float(x)*1.0e-4 for x in line[28:70].split() ]
for i in range(3):
last_atom.sigU[i,i] = sigUij[i]
last_atom.sigU[0,1] = last_atom.sigU[1,0] = sigUij[3]
last_atom.sigU[0,2] = last_atom.sigU[2,0] = sigUij[4]
last_atom.sigU[1,2] = last_atom.sigU[2,1] = sigUij[5]
elif record in P_pdb.validRecords:
pass
else:
emsg = "%d: invalid record name '%r'" % (p_nl, record)
raise StructureFormatError(emsg)
except (ValueError, IndexError):
emsg = "%d: invalid PDB record" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
raise StructureFormatError, emsg, exc_traceback
return stru
def testMatter():
pwInput = PWInput(config=testSCFString)
struct = matter.Structure()
struct.read('data/graphite.cif', format='cif')
#struct.read('data/PbTe.cif', format='cif')
#struct.read('data/Ni.stru', format='pdffit')
#struct.read('data/CdSe-wurtzite.stru', format='pdffit')
print struct
print struct.lattice.base
#struct = Structure(filename='data/Ni.stru')
#struct = Structure(filename='data/graphite.cif')
#struct = Structure(filename='data/PbTe.cif')
#struct = Structure(filename='data/CdSe-wurtzite.stru')
#struct = Structure(pbte)
# does not work well in matter:
#s = pbte.writeStr(format='cif')
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
struct2 = Structure([
at1, at2, at3, at4, at5, at6, at7, at8, at9, at10, at11, at12, at13,
at14, at15, at16
],
lattice=Lattice(2, 2, 2, 90, 90, 90))
#print struct
massList = [50., 55.]
psList = ['ps1', 'ps2']
#massList = [1, 2, 3, 4, 5, 6,1, 2, 3, 4, 5, 6]
#psList = ['ps1', 'ps2', 'ps2', 'ps3', 'ps4','ps1', 'ps2', 'ps2', 'ps3', 'ps4']
# pwInput.structure.load(ibrav = 0, structure = struct, \
# massList = massList, psList = psList)
#pwInput.structure.load(structure = struct )
#print pwInput.structure.atomLabels()
pwInput.structure.load(structure = struct, ibrav = 2, \
massList = massList, psList = psList)
# pwInput.structure.setStructureFromDiffpyStructure(struct, \
# massList = massList,\
# psList = psList)
# pwInput.structure.setReducedStructureFromDiffpyStructure(struct, ibrav = 2, \
# massList = massList,\
# psList = psList)
# this will update string s:
#s = ''
#s = pwInput.structure.toString(string = s)
#pwInput.removeNamelist('system')
#pwInput.removeCard('atomic_species')
#pwInput.removeCard('atomic_positions')
#pwInput.removeCard('cell_parameters')
#pwInput.structure.parseInput()
s = pwInput.structure.toString()
#pwInput.structure.atomicPositionsType = 'alat'
#s = pwInput.structure.toString()
#pwInput.structure.save('scf.in')
print s