def pymatgen2pychemia(pmg_struct):
"""
Converts a pymatgen structure object into a pychemia
structure object
:param pmg_struct: (pymatgen.Structure) Structure from pymatgen that will be converted
:return:
"""
# if not pmg_struct.is_ordered:
# return None
cell = pmg_struct.lattice_vectors()
reduced = np.array([])
sites = []
symbols = []
occupancies = []
index = 0
for i in pmg_struct:
for j in i.species_and_occu:
symbols.append(j.symbol)
occupancies.append(i.species_and_occu[j])
sites.append(index)
reduced = np.concatenate((reduced, i.frac_coords))
index += 1
reduced.reshape((-1, 3))
return Structure(cell=cell,
reduced=reduced,
symbols=symbols,
sites=sites,
occupancies=occupancies)
def load(filep):
"""
Read an V_sim .ascii file and returns a pychemia
Structure object
Args:
filep: (string) Path to a .ascii file or an
actual file-like object
Returns:
struct: (object) A pychemia Structure object
"""
if isinstance(filep, str):
f = open(filep)
else: # Assume it's a file-like object
f = filep
comment = f.readline()
line = f.readline() + ' ' + f.readline()
box = line.split()
for i in range(len(box)):
box[i] = float(box[i])
keywords = []
positions = []
symbols = []
re_comment = _re.compile('^\s*[#!]')
re_node = _re.compile('^\s*\S+\s+\S+\s+\S+\s+\S+')
while True:
line = f.readline()
if line == '':
break # EOF -> Exit
p = re_comment.match(line)
if p is not None:
# remove comment character at the beginning of line
line = line[p.end():].replace(',', ' ').lower()
if line[:8] == "keyword:":
keywords.extend(line[8:].split())
elif re_node.match(line):
unit = 1.0
if not ("reduced" in keywords):
if ("bohr" in keywords) or ("bohrd0" in keywords) or (
"atomic" in keywords) or ("atomicd0" in keywords):
unit = bohr_angstrom
fields = line.split()
positions.append([
unit * float(fields[0]), unit * float(fields[1]),
unit * float(fields[2])
])
symbols.append(fields[3])
f.close()
if ("surface" in keywords) or ("freeBC" in keywords):
raise NotImplementedError
# create atoms object based on the information
if "angdeg" in keywords:
cell = cell.par_to_cell(box)
else:
unit = 1.0
if ("bohr" in keywords) or ("bohrd0" in keywords) or (
"atomic" in keywords) or ("atomicd0" in keywords):
unit = bohr_angstrom
cell = [[unit * box[0], 0.0, 0.0], [unit * box[1], unit * box[2], 0.0],
[unit * box[3], unit * box[4], unit * box[5]]]
if "reduced" in keywords:
struct = Structure(cell=cell,
reduced=positions,
symbols=symbols,
name=comment)
else:
struct = Structure(cell=cell,
positions=positions,
symbols=symbols,
name=comment)
return struct
def get_structure(self, idtset=None, units='bohr'):
"""
Return the atomic structure from the input object
for a given dataset (no dataset by default)
"""
# NATOM
natom = self.get_value('natom', idtset)
# SYMBOLS
ntypat = self.get_value('ntypat', idtset)
symbols = []
znucl = self.get_value('znucl', idtset)
typat = self.get_value('typat', idtset)
for i in range(natom):
# NOTE: znucl is a real number in OUT.nc
# Alchemic mixing is not allow here
if ntypat == 1:
symbols.append(atomic_symbol(int(znucl)))
else:
symbols.append(atomic_symbol(int(znucl[typat[i] - 1])))
# POSITIONS
xangst = self.get_value('xangst', idtset)
xcart = self.get_value('xcart', idtset)
xred = self.get_value('xred', idtset)
rprim = self.get_value('rprim', idtset)
acell = np.array(self.get_value('acell', idtset))
# Set rprimd and acell using the default values
# if not found
if rprim is None:
rprim = np.identity(3)
else:
rprim = np.array(rprim).reshape((3, 3))
if acell is None:
acell = np.ones(3)
rprimd = np.zeros((3, 3))
rprimd[0] = rprim[0] * acell
rprimd[1] = rprim[1] * acell
rprimd[2] = rprim[2] * acell
if xangst is not None:
xangst = np.array(xangst)
positions = xangst.reshape((natom, 3))
if units == 'bohr':
positions = positions * angstrom_bohr
elif xcart is not None:
xcart = np.array(xcart)
positions = xcart.reshape((natom, 3))
if units == 'angstrom':
positions = positions * bohr_angstrom
elif xred is not None:
xred = np.array(xred)
xred = xred.reshape((natom, 3))
xcart = np.zeros((natom, 3))
# print rprimd
# print xred
for i in range(natom):
xcart[i] = xred[i, 0] * rprimd[0] + xred[i, 1] * rprimd[1] + xred[i, 2] * rprimd[2]
positions = xcart
if units == 'angstrom':
positions = positions * bohr_angstrom
else:
positions = None
if units == 'angstrom':
rprimd = rprimd * bohr_angstrom
# Create an object atomic_structure
structure = Structure(natom=natom, symbols=symbols, positions=positions, cell=rprimd)
return structure