def _parse(self, silent=False):
poscarfile = self._file
# Read comment line
commentline = poscarfile.readline()
# Read three unit cell lines
self.scale_factor = float(poscarfile.readline()) # lattice constant
vec1line = self.strip_comments(poscarfile.readline())
vec2line = self.strip_comments(poscarfile.readline())
vec3line = self.strip_comments(poscarfile.readline())
self.basis = np.zeros((3, 3))
self.basis[0] = map(float, vec1line.split())
self.basis[1] = map(float, vec2line.split())
self.basis[2] = map(float, vec3line.split())
self.basis *= self.scale_factor
# Read the atom counts line
# and check for optional line containing atom types (VASP >= 5.1)
self.atomtypes = []
sixthline = self.strip_comments(poscarfile.readline())
try:
dummy = int(sixthline.split()[0])
atomcountline = sixthline
except:
self.atomtypes = np.array(
[get_atomic_number_from_symbol(i) for i in sixthline.split()])
atomcountline = self.strip_comments(poscarfile.readline())
self.atomcounts = map(int, atomcountline.split())
self.natoms = sum(self.atomcounts)
if len(self.atomtypes) == 0:
if not silent:
print "Note: Atom types are not specified in '%s'" % self.filename
# assign negastive numbers, so we can still differentiate between the different types
# (this will probably cause som nasty bugs at some time...)
self.atomtypes = np.arange(-1, -len(self.atomcounts) - 1, -1)
# Check for optional line specifying selective dynamics
self.selective_dynamics = False
line = self.strip_comments(poscarfile.readline())
if line[0].upper() == 'S':
self.selective_dynamics = True
line = self.strip_comments(poscarfile.readline())
# Read coordinate type line (direct or cartesian)
self.direct_coords = False
if line[0].upper() == 'D':
self.direct_coords = True
# Atomic positions
self.positions = np.zeros((self.natoms, 3))
for j in range(self.natoms):
line = self.strip_comments(poscarfile.readline())
self.positions[j] = [float(x) for x in (line.split()[0:3])]
if len(self.positions[j]) != 3:
raise IOError(
'POSCAR file %s ended before all coordinates were read in'
% self.filename)
poscarfile.close()
def _parse(self, silent=False):
poscarfile = self._file
# Read comment line
commentline = poscarfile.readline()
# Read three unit cell lines
self.scale_factor = float(poscarfile.readline()) # lattice constant
vec1line = self.strip_comments(poscarfile.readline())
vec2line = self.strip_comments(poscarfile.readline())
vec3line = self.strip_comments(poscarfile.readline())
self.basis = np.zeros((3,3))
self.basis[0] = map(float,vec1line.split())
self.basis[1] = map(float,vec2line.split())
self.basis[2] = map(float,vec3line.split())
self.basis *= self.scale_factor
# Read the atom counts line
# and check for optional line containing atom types (VASP >= 5.1)
self.atomtypes = []
sixthline = self.strip_comments(poscarfile.readline())
try:
dummy = int(sixthline.split()[0])
atomcountline = sixthline
except:
self.atomtypes = np.array([get_atomic_number_from_symbol(i) for i in sixthline.split()])
atomcountline = self.strip_comments(poscarfile.readline())
self.atomcounts = map(int, atomcountline.split())
self.natoms = sum(self.atomcounts)
if len(self.atomtypes) == 0:
if not silent:
print "Note: Atom types are not specified in '%s'" % self.filename
# assign negastive numbers, so we can still differentiate between the different types
# (this will probably cause som nasty bugs at some time...)
self.atomtypes = np.arange(-1,-len(self.atomcounts)-1,-1)
# Check for optional line specifying selective dynamics
self.selective_dynamics = False
line = self.strip_comments(poscarfile.readline())
if line[0].upper() == 'S':
self.selective_dynamics = True
line = self.strip_comments(poscarfile.readline())
# Read coordinate type line (direct or cartesian)
self.direct_coords = False
if line[0].upper() == 'D':
self.direct_coords = True
# Atomic positions
self.positions = np.zeros((self.natoms,3))
for j in range(self.natoms):
line = self.strip_comments(poscarfile.readline())
self.positions[j] = [float(x) for x in (line.split()[0:3])]
if len(self.positions[j]) != 3:
raise IOError('POSCAR file %s ended before all coordinates were read in' % self.filename)
poscarfile.close()
def ionic_steps(self):
atoms = []
for rc in self.doc.xpath("/modeling/atominfo/array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text.strip()))
#atoms = [rc[0].text.strip() for rc in atoms]
atoms = np.array(atoms, dtype=int)
results = self.doc.xpath( "/modeling/calculation")
if results:
return [IonicStep(r, atoms) for r in results]
else:
raise LookupError('Value not found')
def ionic_steps(self):
atoms = []
for rc in self.doc.xpath(
"/modeling/atominfo/array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text.strip()))
#atoms = [rc[0].text.strip() for rc in atoms]
atoms = np.array(atoms, dtype=int)
results = self.doc.xpath("/modeling/calculation")
if results:
return [IonicStep(r, atoms) for r in results]
else:
raise LookupError('Value not found')
def get_named_structure(self, name):
""" Returns a named structure as a oppvasp.Structure object. """
struc = self.doc.xpath("/modeling/structure[@name='%s']" % (name))[0]
basis = struc.xpath("crystal/varray[@name='basis']/v")
basis = [[float(x) for x in p.text.split()] for p in basis]
rec_basis = struc.xpath("crystal/varray[@name='rec_basis']/v")
rec_basis = [[float(x) for x in p.text.split()] for p in rec_basis]
vol = struc.xpath("crystal/i[@name='volume']")[0]
vol = float(vol.text)
pos = struc.xpath("varray[@name='positions']/v")
pos = [[float(x) for x in p.text.split()] for p in pos]
vel = struc.xpath("varray[@name='velocities']/v")
if vel:
vel = [[float(x) for x in p.text.split()] for p in vel]
else:
# Found no velocities
vel = None
forces = struc.xpath("varray[@name='forces']/v")
if forces:
forces = [[float(x) for x in p.text.split()] for p in forces]
else:
# Found no forces
forces = None
atoms = []
for rc in self.doc.xpath(
"/modeling/atominfo/array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text.strip()))
#atoms = [rc[0].text.strip() for rc in atoms]
atoms = np.array(atoms, dtype=int)
return Structure(cell=basis,
atomtypes=atoms,
positions=pos,
velocities=vel,
forces=forces,
coords='direct')
def ionic_steps(self, step = 0):
try:
parser
except:
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='atominfo')
for event, elem in context:
atominfo = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atominfo.append(get_atomic_number_from_symbol(rc[0].text.strip()))
break # avoid scanning the whole file!
context = etree.iterparse(self.filename, tag='calculation')
for event, elem in context:
step = IonicStep(elem, atominfo)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
yield step
def ionic_steps(self, step=0):
try:
parser
except:
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='atominfo')
for event, elem in context:
atominfo = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atominfo.append(
get_atomic_number_from_symbol(rc[0].text.strip()))
break # avoid scanning the whole file!
context = etree.iterparse(self.filename, tag='calculation')
for event, elem in context:
step = IonicStep(elem, atominfo)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
yield step
def set_atomtypes(self, atoms):
"""
If the array is set using a list of atomic symbols,
it will be converted into an array of atomic numbers, so
the following two lines of code are equivalent:
>>> set_atomtypes([14,16,16])
>>> set_atomtypes(['Si','O','O'])
"""
if type(atoms).__name__ == 'ndarray':
self._atomtypes = np.array(atoms, dtype = 'int')
elif type(atoms).__name__ == 'list':
self._atomtypes = np.zeros(len(atoms), dtype = 'int')
for i, atom in enumerate(atoms):
if type(atom).__name__ == 'str':
self._atomtypes[i] = get_atomic_number_from_symbol(atom)
else:
self._atomtypes[i] = atom
elif type(atoms).__name__ == 'NoneType':
self._atomtypes = None
else:
print "Error: atoms must be a list or array"
def set_atomtypes(self, atoms):
"""
If the array is set using a list of atomic symbols,
it will be converted into an array of atomic numbers, so
the following two lines of code are equivalent:
>>> set_atomtypes([14,16,16])
>>> set_atomtypes(['Si','O','O'])
"""
if type(atoms).__name__ == 'ndarray':
self._atomtypes = np.array(atoms, dtype='int')
elif type(atoms).__name__ == 'list':
self._atomtypes = np.zeros(len(atoms), dtype='int')
for i, atom in enumerate(atoms):
if type(atom).__name__ == 'str':
self._atomtypes[i] = get_atomic_number_from_symbol(atom)
else:
self._atomtypes[i] = atom
elif type(atoms).__name__ == 'NoneType':
self._atomtypes = None
else:
print "Error: atoms must be a list or array"
def get_named_structure(self, name):
""" Returns a named structure as a oppvasp.Structure object. """
struc = self.doc.xpath("/modeling/structure[@name='%s']" % (name))[0]
basis = struc.xpath("crystal/varray[@name='basis']/v")
basis = [[float(x) for x in p.text.split()] for p in basis]
rec_basis = struc.xpath("crystal/varray[@name='rec_basis']/v")
rec_basis = [[float(x) for x in p.text.split()] for p in rec_basis]
vol = struc.xpath("crystal/i[@name='volume']")[0]
vol = float(vol.text)
pos = struc.xpath("varray[@name='positions']/v")
pos = [[float(x) for x in p.text.split()] for p in pos]
vel = struc.xpath("varray[@name='velocities']/v")
if vel:
vel = [[float(x) for x in p.text.split()] for p in vel]
else:
# Found no velocities
vel = None
forces = struc.xpath("varray[@name='forces']/v")
if forces:
forces = [[float(x) for x in p.text.split()] for p in forces]
else:
# Found no forces
forces = None
atoms = []
for rc in self.doc.xpath("/modeling/atominfo/array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text.strip()))
#atoms = [rc[0].text.strip() for rc in atoms]
atoms = np.array(atoms, dtype=int)
return Structure( cell = basis, atomtypes = atoms, positions = pos, velocities = vel, forces = forces, coords = 'direct' )
def _get_atoms(self, elem):
atoms = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text))
return np.array(atoms, dtype=int)
def _get_atoms(self, elem):
atoms = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text))
return np.array(atoms, dtype=int)