def create_molecule(selected_nodes, parent=None):
numbers = []
coordinates = []
atoms = list(iter_atoms(selected_nodes))
for atom in atoms:
numbers.append(atom.number)
if parent is None:
coordinates.append(atom.get_absolute_frame().t)
else:
coordinates.append(atom.get_frame_relative_to(parent).t)
result = Molecule(numbers, coordinates)
result.atoms = atoms
return result
def collect_molecules(self, parent, universe=None):
Atom = context.application.plugins.get_node("Atom")
Bond = context.application.plugins.get_node("Bond")
Frame = context.application.plugins.get_node("Frame")
if universe==None:
universe = parent
atom_to_index = {}
atoms_extra = {}
counter = 0
numbers = []
coordinates = []
for child in parent.children:
if isinstance(child, Atom):
atom_to_index[child] = counter
if len(child.extra) > 0:
atoms_extra[counter] = child.extra
counter += 1
numbers.append(child.number)
coordinates.append(child.get_frame_relative_to(universe).t)
if len(numbers) > 0:
molecule = Molecule(numbers, coordinates, parent.name)
molecule.extra = parent.extra
molecule.atoms_extra = atoms_extra
molecule.bonds_extra = {}
pairs = set([])
for child in parent.children:
if isinstance(child, Bond):
atoms = child.get_targets()
pair = frozenset([atom_to_index[atoms[0]], atom_to_index[atoms[1]]])
if len(child.extra) > 0:
molecule.bonds_extra[pair] = child.extra
pairs.add(pair)
if len(pairs) > 0:
molecule.graph = MolecularGraph(pairs, molecule.numbers)
else:
molecule.graph = None
result = [molecule]
else:
result = []
for child in parent.children:
if isinstance(child, Frame):
result.extend(self.collect_molecules(child, universe))
return result
def __init__(self, filename):
"""
Arguments:
| ``filename`` -- The file to load.
"""
self.filename = filename
# auxiliary skip function
def skip_to(f, linestart):
while True:
line = f.readline()
if line.startswith(linestart):
return line
if len(line) == 0:
return
with open(filename) as f:
# Unit cell parameters
line = skip_to(f, ' DIRECT LATTICE VECTOR COMPONENTS (BOHR)')
if line is None:
raise FileFormatError('Could not find the lattice vectors')
f.readline()
f.readline()
vectors = []
for i in range(3):
line = f.readline()
vectors.append([float(word) for word in line.split()[1:]])
vectors = np.array(vectors)
self.unit_cell = UnitCell(vectors.transpose())
# Atomic numbers and coordinates
line = skip_to(f, ' ATOM CARTESIAN COORDINATES (BOHR)')
if line is None:
raise FileFormatError('Could not find the atomic coordinates')
f.readline()
f.readline()
f.readline()
numbers = []
symbols = []
coordinates = []
while True:
line = f.readline()
if line.startswith(' *****'):
break
words = line.split()
numbers.append(int(words[1]))
symbols.append(words[2])
coordinates.append(
[float(words[3]),
float(words[4]),
float(words[5])])
self.mol = Molecule(np.array(numbers),
np.array(coordinates),
symbols=symbols,
unit_cell=self.unit_cell)
# Basis set specification
line = skip_to(f, ' VARIATIONAL BASIS SET')
if line is None:
raise FileFormatError('Could not find the basis set')
f.readline()
f.readline()
f.readline()
f.readline()
f.readline()
f.readline()
self.basisset = {}
last_basis = None
last_contraction = None
while True:
line = f.readline()
if line.startswith(' *****'):
break
if line.startswith(' '):
# add info to the last atomic basis set
assert last_basis is not None
subshell = line[36:40].strip()
if len(subshell) == 0:
subshell = last_contraction[0]
# add a primitive to the contraction
exponent = float(line[40:50])
if subshell == 'S':
values = exponent, float(line[50:60])
elif subshell == 'SP':
values = exponent, float(line[50:60]), float(
line[60:70])
else:
values = exponent, float(line[70:80])
last_contraction[1].append(values)
else:
# define a new contraction
last_contraction = (subshell, [])
last_basis.append(last_contraction)
else:
# add new atoms
symbol = line.split()[1]
if symbol not in self.basisset:
last_basis = []
self.basisset[symbol] = last_basis
# Compute the total number of basis functions (and orbitals).
self.num_basis = 0
subshell_counts = {'S': 1, 'P': 3, 'SP': 4, 'D': 5, 'F': 7, 'G': 9}
for symbol, basis in self.basisset.items():
symbol_count = symbols.count(symbol)
for subshell, contraction in basis:
self.num_basis += symbol_count * subshell_counts[subshell]
# Density matrix.
line = skip_to(f, ' DENSITY MATRIX DIRECT LATTICE')
if line is None:
raise FileFormatError('Could not find the density matrix')
f.readline()
f.readline()
f.readline()
self.density_matrix = np.zeros((self.num_basis, self.num_basis),
float)
j0 = 0
while j0 < self.num_basis:
f.readline()
f.readline()
f.readline()
for i in range(self.num_basis):
line = f.readline()
words = line.split()[1:]
for j1, word in enumerate(words):
self.density_matrix[i, j0 + j1] = float(word)
j0 += 10
