def expand(names):
"""Expand ranges like H-Li to H, He and Li."""
i = 0
while i < len(names):
name = names[i]
if name.count("-") == 1:
s1, s2 = name.split("-")
Z1 = atomic_numbers.get(s1)
Z2 = atomic_numbers.get(s2)
if Z1 is not None and Z2 is not None:
names[i : i + 1] = chemical_symbols[Z1 : Z2 + 1]
i += Z2 - Z1
i += 1
def expand(self, names):
"""Expand ranges like H-Li to H, He, Li."""
if isinstance(names, str):
names = [names]
newnames = []
for name in names:
if name.count('-') == 1:
s1, s2 = name.split('-')
Z1 = atomic_numbers.get(s1)
Z2 = atomic_numbers.get(s2)
if Z1 is None or Z2 is None:
newnames.append(name)
else:
newnames.extend(chemical_symbols[Z1:Z2 + 1])
else:
newnames.append(name)
return newnames
def expand(self, names):
"""Expand ranges like H-Li to H, He, Li."""
if isinstance(names, str):
names = [names]
newnames = []
for name in names:
if name.count('-') == 1:
s1, s2 = name.split('-')
Z1 = atomic_numbers.get(s1)
Z2 = atomic_numbers.get(s2)
if Z1 is None or Z2 is None:
newnames.append(name)
else:
newnames.extend(chemical_symbols[Z1:Z2 + 1])
else:
newnames.append(name)
return newnames
def con_2_ase(path, boundary = [1,1,1]):
if not path.endswith('.con'):
path += '.con'
f = open(path, 'r')
## seed to random
f.readline()
## time stuff
f.readline()
basis_vec = map(float, f.readline().split())
angle_basis_vec = map(lambda x: x - 90 < _floatErr, map(float, f.readline().split()))
if not np.array(angle_basis_vec).sum():
print "Only orthogonal lattice vectores are accepted!"
return
f.readline()
f.readline()
nrComponents = int(f.readline().strip())
nrAtomsPrType = np.array(map(int, f.readline().split()))
#Masses, skiped in original parser. Same here
f.readline()
#All data is parced into these arrays before Atoms object is created.
pos = np.zeros((nrAtomsPrType.sum(), 3))
atomNumbers = np.zeros(nrAtomsPrType.sum())
filt = np.zeros(nrAtomsPrType.sum(), dtype='int32')
#
for comp in xrange(nrComponents):
element = f.readline().strip()
if element.isdigit():
element = int(element)
else:
element = atomic_numbers.get(element) or self._unkownElement(element)
f.readline()
for i in xrange(nrAtomsPrType[0:comp].sum(), nrAtomsPrType[0:comp+1].sum()):
data = f.readline().split()
pos[i] = map(float, data[:3])
atomNumbers[i] = element
filt[i] = int(data[3])
f.close()
return (ase.Atoms(numbers=atomNumbers, positions=pos, cell=basis_vec, pbc=boundary), abs(filt-1))
def get_positions_from_block(keyword):
# %Coordinates or %ReducedCoordinates -> atomic numbers, positions.
block = kwargs.pop(keyword)
positions = []
numbers = []
tags = []
types = {}
for row in block:
assert len(row) in [ndims + 1, ndims + 2]
row = row[:ndims + 1]
sym = row[0]
assert sym.startswith('"') or sym.startswith("'")
assert sym[0] == sym[-1]
sym = sym[1:-1]
pos0 = np.zeros(3)
ndim = int(kwargs.get('dimensions', 3))
pos0[:ndim] = [float(element) for element in row[1:]]
number = atomic_numbers.get(sym) # Use 0 ~ 'X' for unknown?
tag = 0
if number is None:
if sym not in types:
tag = len(types) + 1
types[sym] = tag
number = 0
tag = types[sym]
tags.append(tag)
numbers.append(number)
positions.append(pos0)
positions = np.array(positions)
tags = np.array(tags, int)
if types:
ase_types = {}
for sym, tag in types.items():
ase_types[('X', tag)] = sym
info = {'types': ase_types} # 'info' dict for Atoms object
else:
tags = None
info = None
return numbers, positions, tags, info
def get_positions_from_block(keyword):
# %Coordinates or %ReducedCoordinates -> atomic numbers, positions.
block = kwargs.pop(keyword)
positions = []
numbers = []
tags = []
types = {}
for row in block:
assert len(row) in [ndims + 1, ndims + 2]
row = row[:ndims + 1]
sym = row[0]
assert sym.startswith('"') or sym.startswith("'")
assert sym[0] == sym[-1]
sym = sym[1:-1]
pos0 = np.zeros(3)
ndim = int(kwargs.get('dimensions', 3))
pos0[:ndim] = [float(element) for element in row[1:]]
number = atomic_numbers.get(sym) # Use 0 ~ 'X' for unknown?
tag = 0
if number is None:
if sym not in types:
tag = len(types) + 1
types[sym] = tag
number = 0
tag = types[sym]
tags.append(tag)
numbers.append(number)
positions.append(pos0)
positions = np.array(positions)
tags = np.array(tags, int)
if types:
ase_types = {}
for sym, tag in types.items():
ase_types[('X', tag)] = sym
info = {'types': ase_types} # 'info' dict for Atoms object
else:
tags = None
info = None
return numbers, positions, tags, info
def parse(self, content):
#the output for atomic coords depends on whether we are doing an optimisation (single point calcs take the form 'atom, flag, x, y ,z' rather than simply 'atom, x, y, z'
opt = 'opt' in content
from ase.data import atomic_numbers
self.data = []
temp_items = content.split(PARA_START)
seq_count = 0
for i in temp_items:
i=i.replace("\n ", "")
if i.endswith(PARA_END):
i = i.replace(PARA_END, "")
i = i.split(FIELD_SEPARATOR)
new_dict = {}
self.data.append(new_dict)
new_dict["Sequence number"] = seq_count
seq_count += 1
for pos in range(len(names)):
if names[pos]!="":
new_dict[names[pos]] = self.auto_type(i[pos])
chm = i[charge_multiplicity].split(",")
new_dict["Charge"] = int(chm[0])
new_dict["Multiplicity"] = int(chm[1])
#Read atoms
atoms = []
positions = []
position = charge_multiplicity+1
if not opt:
atom_flags = []
while position<len(i) and i[position]!="":
s = i[position].split(",")
atoms.append(atomic_numbers.get(s[0], 0))
positions.append([float(s[-3]), float(s[-2]), float(s[-1])])
position = position + 1
atom_flags.append(int(s[1]))
new_dict["Atom_flags"]=atom_flags
new_dict["Atomic_numbers"]=atoms
new_dict["Positions"]=positions
else:
while position<len(i) and i[position]!="":
s = i[position].split(",")
atoms.append(atomic_numbers.get(s[0], 0))
positions.append([float(s[-3]), float(s[-2]), float(s[-1])])
position = position + 1
new_dict["Atomic_numbers"]=atoms
new_dict["Positions"]=positions
#read orbital swaps
orb_swaps = []
if 'alter' in new_dict.get('Root',""):
position +=1
while position<len(i) and i[position]!="":
s = i[position].split(",")
orb_swaps.append(s)
position+=1
new_dict["Orbital_swaps"]=orb_swaps
#Read more variables
position +=1
while position<len(i) and i[position]!="":
s = i[position].split("=")
if len(s)==2:
new_dict[s[0]]=self.auto_type(s[1])
else:
print "Warning: unexpected input ",s
position = position + 1
