def reference_mol(mol, minao=MINAO):
'''Create a molecule which uses reference minimal basis'''
pmol = mol.copy()
atoms = [atom for atom in gto.format_atom(pmol.atom, unit=1)]
# remove ghost atoms
pmol.atom = [atom for atom in atoms if not is_ghost_atom(atom[0])]
if len(pmol.atom) != len(atoms):
logger.info(
mol, 'Ghost atoms found in system. '
'Current IAO does not support ghost atoms. '
'They are removed from IAO reference basis.')
if getattr(pmol, 'rcut', None) is not None:
pmol.rcut = None
pmol.build(False, False, basis=minao)
return pmol
def create_mm_mol(atoms_or_coords, charges=None, unit='Angstrom'):
'''Create an MM object based on the given coordinates and charges of MM
particles.
'''
if isinstance(atoms_or_coords, numpy.ndarray):
# atoms_or_coords == np.array([(xx, xx, xx)])
# Patch ghost atoms
atoms = [(0, c) for c in atoms_or_coords]
elif (isinstance(atoms_or_coords, (list, tuple)) and atoms_or_coords
and isinstance(atoms_or_coords[0][1], (int, float))):
# atoms_or_coords == [(xx, xx, xx)]
# Patch ghost atoms
atoms = [(0, c) for c in atoms_or_coords]
else:
atoms = atoms_or_coords
atoms = gto.format_atom(atoms, unit=unit)
return Mole(atoms, charges)
def guess_frag(xyz, frags, chgs, spins, gjfhead, scrfhead, gjfname, basis,
wfnpath):
'''
frags: e.g. [[1], [2]] for N2
chgs: e.g. [0, 0] for N2
spins: e.g. [3, -3] for N2
'''
#mol.build()
print('**** generating fragments ****')
atom = gto.format_atom(xyz, unit=1)
#print(atom)
#fraga, fragb = frags
#chga, chgb = chgs
#spina, spinb = spins
allatom = range(1, len(atom) + 1)
for k in range(len(frags)):
frag = frags[k]
chg = chgs[k]
spin = spins[k]
g_spin = spin_p2g(spin)
atomk = [atom[i - 1] for i in frag]
atomother = [atom[i - 1] for i in allatom if i not in frag]
print('fragment %d, chg %d, spin %d' % (k, chg, spin))
#print(atomk)
with open(gjfname + '%d.gjf' % k, 'w') as f:
f.write(gjfhead)
f.write('%d %d\n' % (chg, g_spin))
for a in atomk:
f.write('%s %10.5f %10.5f %10.5f\n' %
(a[0], a[1][0], a[1][1], a[1][2]))
#f.write('\n')
if basis is not None:
f.write(basis)
#f.write('\n')
f.write(scrfhead)
f.write('ExtraSph=%d\n\n' % len(atomother))
for b in atomother:
rad = radii.uff_radii[b[0]] / 2.0
f.write(' %10.5f %10.5f %10.5f %10.5f\n' %
(b[1][0], b[1][1], b[1][2], rad))
f.write('\n')
if wfnpath is not None:
f.write(wfnpath + '%d.wfn' % k + '\n')
f.write('\n')
)], [1, (
0.,
-.757,
0.587,
)], [1, (
0.,
0.757,
0.587,
)]]
h2o.basis = {
'H': 'cc-pvdz',
'O': 'cc-pvdz',
}
h2o.build()
gpname, origin, axes = geom.detect_symm(h2o._atom)
atoms = gto.format_atom(h2o._atom, origin, axes)
h2o.build(False, False, atom=atoms)
print(gpname)
eql_atoms = geom.symm_identical_atoms(gpname, atoms)
print(symm_adapted_basis(h2o, gpname, eql_atoms)[1])
mol = gto.M(atom=[['H', (0, 0, 0)], ['H', (0, 0, -1)], ['H', (0, 0, 1)]],
basis='ccpvtz',
charge=1)
gpname, orig, axes = geom.detect_symm(mol._atom)
atoms = gto.format_atom(mol._atom, orig, axes)
mol.build(False, False, atom=atoms)
print(gpname)
eql_atoms = geom.symm_identical_atoms(gpname, atoms)
print(symm_adapted_basis(mol, gpname, eql_atoms)[1])
def rigid(internal, var, vrange, unit=1):
for v in vrange:
newint = internal.replace(var, '%f'%v)
newcart = gto.format_atom(newint, unit=unit)
newcart = atm2str(newcart)
print(newcart)
return so, irrep_ids
if __name__ == "__main__":
from pyscf import gto
h2o = gto.Mole()
h2o.verbose = 0
h2o.output = None
h2o.atom = [['O' , (1. , 0. , 0. ,)],
[1 , (0. , -.757 , 0.587,)],
[1 , (0. , 0.757 , 0.587,)] ]
h2o.basis = {'H': 'cc-pvdz',
'O': 'cc-pvdz',}
h2o.build()
gpname, origin, axes = geom.detect_symm(h2o._atom)
atoms = gto.format_atom(h2o._atom, origin, axes)
h2o.build(False, False, atom=atoms)
print(gpname)
eql_atoms = geom.symm_identical_atoms(gpname, atoms)
print(symm_adapted_basis(h2o, gpname, eql_atoms)[1])
mol = gto.M(
atom = [['H', (0,0,0)], ['H', (0,0,-1)], ['H', (0,0,1)]],
basis = 'ccpvtz', charge=1)
gpname, orig, axes = geom.detect_symm(mol._atom)
atoms = gto.format_atom(mol._atom, orig, axes)
mol.build(False, False, atom=atoms)
print(gpname)
eql_atoms = geom.symm_identical_atoms(gpname, atoms)
print(symm_adapted_basis(mol, gpname, eql_atoms)[1])