def _core_val_ryd_list(mol):
from pyscf.gto.ecp import core_configuration
count = numpy.zeros((mol.natm, 9), dtype=int)
core_lst = []
val_lst = []
rydbg_lst = []
k = 0
for ib in range(mol.nbas):
ia = mol.bas_atom(ib)
# Avoid calling mol.atom_charge because we should include ECP core electrons here
nuc = mole.charge(mol.atom_symbol(ia))
l = mol.bas_angular(ib)
nc = mol.bas_nctr(ib)
nelec_ecp = mol.atom_nelec_core(ia)
ecpcore = core_configuration(nelec_ecp)
coreshell = [int(x) for x in AOSHELL[nuc][0][::2]]
cvshell = [int(x) for x in AOSHELL[nuc][1][::2]]
if mol.cart:
deg = (l + 1) * (l + 2) // 2
else:
deg = 2 * l + 1
for n in range(nc):
if l > 3:
rydbg_lst.extend(range(k, k + deg))
elif ecpcore[l] + count[ia, l] + n < coreshell[l]:
core_lst.extend(range(k, k + deg))
elif ecpcore[l] + count[ia, l] + n < cvshell[l]:
val_lst.extend(range(k, k + deg))
else:
rydbg_lst.extend(range(k, k + deg))
k = k + deg
count[ia, l] += nc
return core_lst, val_lst, rydbg_lst
def _core_val_ryd_list(mol):
from pyscf.gto.ecp import core_configuration
count = numpy.zeros((mol.natm, 9), dtype=int)
core_lst = []
val_lst = []
rydbg_lst = []
k = 0
for ib in range(mol.nbas):
ia = mol.bas_atom(ib)
# Avoid calling mol.atom_charge because we should include ECP core electrons here
nuc = mole.charge(mol.atom_symbol(ia))
l = mol.bas_angular(ib)
nc = mol.bas_nctr(ib)
symb = mol.atom_symbol(ia)
nelec_ecp = mol.atom_nelec_core(ia)
ecpcore = core_configuration(nelec_ecp)
coreshell = [int(x) for x in AOSHELL[nuc][0][::2]]
cvshell = [int(x) for x in AOSHELL[nuc][1][::2]]
if mol.cart:
deg = (l + 1) * (l + 2) // 2
else:
deg = 2 * l + 1
for n in range(nc):
if l > 3:
rydbg_lst.extend(range(k, k+deg))
elif ecpcore[l]+count[ia,l]+n < coreshell[l]:
core_lst.extend(range(k, k+deg))
elif ecpcore[l]+count[ia,l]+n < cvshell[l]:
val_lst.extend(range(k, k+deg))
else:
rydbg_lst.extend(range(k, k+deg))
k = k + deg
count[ia,l] += nc
return core_lst, val_lst, rydbg_lst
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])
def set_atom_conf(element, description):
'''Change the default atomic core and valence configuration to the one
given by "description".
See data/elements.py for the default configuration.
Args:
element : str or int
Element symbol or nuclear charge
description : str or a list of str
| "double p" : double p shell
| "double d" : double d shell
| "double f" : double f shell
| "polarize" : add one polarized shell
| "1s1d" : keep core unchanged and set 1 s 1 d shells for valence
| ("3s2p","1d") : 3 s, 2 p shells for core and 1 d shells for valence
'''
charge = mole.charge(element)
def to_conf(desc):
desc = desc.replace(' ', '').replace('-', '').replace('_', '').lower()
if "doublep" in desc:
desc = '2p'
elif "doubled" in desc:
desc = '2d'
elif "doublef" in desc:
desc = '2f'
elif "polarize" in desc:
loc = AOSHELL[charge][1].find('0')
desc = '1' + AOSHELL[charge][1][loc + 1]
return desc
if isinstance(description, str):
c_desc, v_desc = AOSHELL[charge][0], to_conf(description)
else:
c_desc, v_desc = to_conf(description[0]), to_conf(description[1])
ncore = [int(x) for x in AOSHELL[charge][0][::2]]
ncv = [int(x) for x in AOSHELL[charge][1][::2]]
for i, s in enumerate(('s', 'p', 'd', 'f')):
if s in c_desc:
ncore[i] = int(c_desc.split(s)[0][-1])
if s in v_desc:
ncv[i] = ncore[i] + int(v_desc.split(s)[0][-1])
c_conf = '%ds%dp%dd%df' % tuple(ncore)
cv_conf = '%ds%dp%dd%df' % tuple(ncv)
AOSHELL[charge] = [c_conf, cv_conf]
sys.stderr.write('Update %s conf: core %s core+valence %s\n' %
(element, c_conf, cv_conf))
def set_atom_conf(element, description):
'''Change the default atomic core and valence configuration to the one
given by "description".
See data/elements.py for the default configuration.
Args:
element : str or int
Element symbol or nuclear charge
description : str or a list of str
| "double p" : double p shell
| "double d" : double d shell
| "double f" : double f shell
| "polarize" : add one polarized shell
| "1s1d" : keep core unchanged and set 1 s 1 d shells for valence
| ("3s2p","1d") : 3 s, 2 p shells for core and 1 d shells for valence
'''
charge = mole.charge(element)
def to_conf(desc):
desc = desc.replace(' ','').replace('-','').replace('_','').lower()
if "doublep" in desc:
desc = '2p'
elif "doubled" in desc:
desc = '2d'
elif "doublef" in desc:
desc = '2f'
elif "polarize" in desc:
loc = AOSHELL[charge][1].find('0')
desc = '1' + AOSHELL[charge][1][loc+1]
return desc
if isinstance(description, str):
c_desc, v_desc = AOSHELL[charge][0], to_conf(description)
else:
c_desc, v_desc = to_conf(description[0]), to_conf(description[1])
ncore = [int(x) for x in AOSHELL[charge][0][::2]]
ncv = [int(x) for x in AOSHELL[charge][1][::2]]
for i, s in enumerate(('s', 'p', 'd', 'f')):
if s in c_desc:
ncore[i] = int(c_desc.split(s)[0][-1])
if s in v_desc:
ncv[i] = ncore[i] + int(v_desc.split(s)[0][-1])
c_conf = '%ds%dp%dd%df' % tuple(ncore)
cv_conf = '%ds%dp%dd%df' % tuple(ncv)
AOSHELL[charge] = [c_conf, cv_conf]
sys.stderr.write('Update %s conf: core %s core+valence %s\n' %
(element, c_conf, cv_conf))
def get_nuc_g_factor(symb_or_charge, mass=None):
if isinstance(symb_or_charge, str):
Z = mole.charge(symb_or_charge)
else:
Z = symb_or_charge
# g factor of other isotopes can be found in file nuclear_g_factor.dat
if mass is None:
# The default isotopes
nuc_spin, g_nuc = ISOTOPE_GYRO[Z][0][1:3]
else:
for isotop_mass, nuc_spin, g_nuc in ISOTOPE_GYRO[Z]:
if isotop_mass == mass:
break
else:
raise ValueError('mass=%s not found in isotopes of %s' %
(mass, symb_or_charge))
#gyromag = g_factor_to_gyromagnetic_ratio(g_nuc)
return g_nuc
def get_nuc_g_factor(symb, mass=None):
Z = mole.charge(symb)
# g factor of other isotopes can be found in file nuclear_g_factor.dat
nuc_spin, g_nuc = ISOTOPE_GYRO[Z][1:3]
#gyromag = g_factor_to_gyromagnetic_ratio(g_nuc)
return g_nuc
