def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k or ksymb == 'GHOST':
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi-2
else:
fake_chgs.append([mole._charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs, coords)/fake_chgs.sum()
coords = coords - self.charge_center
self.im = numpy.einsum('i,ij,ik->jk', fake_chgs, coords, coords)/fake_chgs.sum()
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1,1), coords))[idx]
def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k or ksymb == 'GHOST':
# Put random charges on the decorated atoms
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi-2
else:
fake_chgs.append([mole._charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs, coords)/fake_chgs.sum()
coords = coords - self.charge_center
self.im = numpy.einsum('i,ij,ik->jk', fake_chgs, coords, coords)/fake_chgs.sum()
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1,1), coords))[idx]
def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k:
# Put random charges on the decorated atoms
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi - 2
elif mole.is_ghost_atom(k):
if ksymb == 'X' or ksymb.upper() == 'GHOST':
fake_chgs.append([.3] * len(lst))
elif ksymb[0] == 'X':
fake_chgs.append([mole.charge(ksymb[1:]) + .3] * len(lst))
elif ksymb[:5] == 'GHOST':
fake_chgs.append([mole.charge(ksymb[5:]) + .3] * len(lst))
else:
fake_chgs.append([mole.charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs,
coords) / fake_chgs.sum()
coords = coords - self.charge_center
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1, 1), coords))[idx]
self.group_atoms_by_distance = []
decimals = int(-numpy.log10(TOLERANCE)) - 1
for index in self.atomtypes.values():
index = numpy.asarray(index)
c = self.atoms[index, 1:]
dists = numpy.around(norm(c, axis=1), decimals)
u, idx = numpy.unique(dists, return_inverse=True)
for i, s in enumerate(u):
self.group_atoms_by_distance.append(index[idx == i])
def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k:
# Put random charges on the decorated atoms
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi-2
elif mole.is_ghost_atom(k):
if ksymb == 'X' or ksymb.upper() == 'GHOST':
fake_chgs.append([.3] * len(lst))
elif ksymb[0] == 'X':
fake_chgs.append([mole.charge(ksymb[1:])+.3] * len(lst))
elif ksymb[:5] == 'GHOST':
fake_chgs.append([mole.charge(ksymb[5:])+.3] * len(lst))
else:
fake_chgs.append([mole.charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs, coords)/fake_chgs.sum()
coords = coords - self.charge_center
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1,1), coords))[idx]
self.group_atoms_by_distance = []
decimals = int(-numpy.log10(TOLERANCE)) - 1
for index in self.atomtypes.values():
index = numpy.asarray(index)
c = self.atoms[index,1:]
dists = numpy.around(norm(c, axis=1), decimals)
u, idx = numpy.unique(dists, return_inverse=True)
for i, s in enumerate(u):
self.group_atoms_by_distance.append(index[idx == i])
