def getbasis(atoms, basis_data=None, **opts):
"""\
bfs = getbasis(atoms,basis_data=None)
Given a Molecule object and a basis library, form a basis set
constructed as a list of CGBF basis functions objects.
"""
from PyQuante.Basis.basis import BasisSet
return BasisSet(atoms, basis_data, **opts)
# Option to omit f basis functions from imported basis sets
omit_f = opts.get('omit_f', False)
if not basis_data:
from PyQuante.Basis.p631ss import basis_data
elif type(basis_data) == type(''):
# Assume this is a name of a basis set, e.g. '6-31g**'
# and import dynamically
basis_data = get_basis_data(basis_data)
bfs = []
for atom in atoms:
bs = basis_data[atom.atno]
for sym, prims in bs:
if omit_f and sym == "F": continue
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(), power, atom.atid)
for expnt, coef in prims:
bf.add_primitive(expnt, coef)
bf.normalize()
bfs.append(bf)
return bfs
def getbasis(atoms,basis_data=None,**opts):
"""\
bfs = getbasis(atoms,basis_data=None)
Given a Molecule object and a basis library, form a basis set
constructed as a list of CGBF basis functions objects.
"""
from PyQuante.Basis.basis import BasisSet
return BasisSet(atoms, basis_data, **opts)
# Option to omit f basis functions from imported basis sets
omit_f = opts.get('omit_f',False)
if not basis_data:
from PyQuante.Basis.p631ss import basis_data
elif type(basis_data) == type(''):
# Assume this is a name of a basis set, e.g. '6-31g**'
# and import dynamically
basis_data = get_basis_data(basis_data)
bfs = []
for atom in atoms:
bs = basis_data[atom.atno]
for sym,prims in bs:
if omit_f and sym == "F": continue
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(),power,atom.atid)
for expnt,coef in prims:
bf.add_primitive(expnt,coef)
bf.normalize()
bfs.append(bf)
return bfs
def __init__(self, atoms, basis_data=None, **opts):
"""
"""
# Option to omit f basis functions from imported basis sets
omit_f = opts.get('omit_f', False)
if not basis_data:
from PyQuante.Basis.p631ss import basis_data
elif type(basis_data) == type(''):
# Assume this is a name of a basis set, e.g. '6-31g**'
# and import dynamically
basis_data = get_basis_data(basis_data)
# Creating the function lists, by shell and by arbitrary order
bfs = [] # Basis list
shells = [] # Shell list
n = 0
LIST1 = [
] # list of atoms and basis function number # GLOBULION ADD
LIST2 = [
] # list of atoms and basis function type # GLOBULION ADD
for atom in atoms:
bs = basis_data[atom.atno]
for sym, prims in bs: # Shell Symbol S,P,D,F
A = sym2powerlist[sym] # GLOBULION ADD
for ni in xrange(len(sym2powerlist[sym])): # GLOBULION ADD
LIST1.append(n) # GLOBULION ADD
LIST2.append(A[ni])
if omit_f and sym == "F": continue
shell = Shell(sym)
for power in sym2powerlist[sym]:
cgbf = CGBF(atom.pos(), power, atom.atid)
#exps,coefs = zip(*prims)
#primlist = [PrimitiveGTO(alpha,atom.pos(),power) for alpha in exps]
#bf = ContractedGTO(primlist,coefs)
#bf.normalize()
[cgbf.add_primitive(alpha, coef) for alpha, coef in prims]
bfs.append(cgbf) # Normal ordering
# Shell ordering
bfs_index = len(bfs) - 1 # last added
shell.append(cgbf, bfs_index)
shells.append(shell)
n += 1
self.bfs = bfs
self.shells = shells
self.LIST1 = LIST1 # GLOBULION ADD
self.LIST2 = LIST2 # GLOBULION ADD
def __init__(self, atoms, basis_data = None, **opts):
"""
"""
# Option to omit f basis functions from imported basis sets
omit_f = opts.get('omit_f',False)
if not basis_data:
from PyQuante.Basis.p631ss import basis_data
elif type(basis_data) == type(''):
# Assume this is a name of a basis set, e.g. '6-31g**'
# and import dynamically
basis_data = get_basis_data(basis_data)
# Creating the function lists, by shell and by arbitrary order
bfs = [] # Basis list
shells = []# Shell list
n = 0
LIST1 = []# list of atoms and basis function number # GLOBULION ADD
LIST2 = []# list of atoms and basis function type # GLOBULION ADD
for atom in atoms:
bs = basis_data[atom.atno]
for sym,prims in bs: # Shell Symbol S,P,D,F
A = sym2powerlist[sym] # GLOBULION ADD
for ni in xrange(len(sym2powerlist[sym])): # GLOBULION ADD
LIST1.append(n) # GLOBULION ADD
LIST2.append(A[ni])
if omit_f and sym == "F": continue
shell = Shell(sym)
for power in sym2powerlist[sym]:
cgbf = CGBF(atom.pos(), power, atom.atid)
#exps,coefs = zip(*prims)
#primlist = [PrimitiveGTO(alpha,atom.pos(),power) for alpha in exps]
#bf = ContractedGTO(primlist,coefs)
#bf.normalize()
[cgbf.add_primitive(alpha,coef) for alpha,coef in prims]
bfs.append(cgbf) # Normal ordering
# Shell ordering
bfs_index = len(bfs)-1 # last added
shell.append(cgbf, bfs_index)
shells.append(shell)
n+=1
self.bfs = bfs
self.shells = shells
self.LIST1 = LIST1 # GLOBULION ADD
self.LIST2 = LIST2 # GLOBULION ADD
def __init__(self,molecule,**opts):
from PyQuante.Ints import getbasis
from PyQuante.Basis.Tools import get_basis_data
basis_data = opts.get('basis_data')
bfs = opts.get('bfs')
if bfs:
self.bfs = bfs
else:
if not basis_data:
basis = opts.get('basis')
if basis:
basis_data = get_basis_data(basis)
self.bfs = getbasis(molecule,basis_data)
logging.info("%d basis functions" % len(self.bfs))
return
def __init__(self, molecule, **opts):
from PyQuante.Ints import getbasis
from PyQuante.Basis.Tools import get_basis_data
basis_data = opts.get('basis_data')
bfs = opts.get('bfs')
if bfs:
self.bfs = bfs
else:
if not basis_data:
basis = opts.get('basis')
if basis:
basis_data = get_basis_data(basis)
self.bfs = getbasis(molecule, basis_data)
logger.info("%d basis functions" % len(self.bfs))
return
def getbasis(atoms, basis_data=None, **kwargs):
"""\
bfs = getbasis(atoms,basis_data=None)
Given a Molecule object and a basis library, form a basis set
constructed as a list of CGBF basis functions objects.
"""
from PyQuante.Basis.basis import BasisSet
if not basis_data:
basis_data = kwargs.get('basis_data')
if kwargs.get('bfs'):
return kwargs.get('bfs')
elif not basis_data:
basis = kwargs.get('basis')
if basis:
basis_data = get_basis_data(basis)
return BasisSet(atoms, basis_data, **kwargs)
def getbasis(atoms,basis_data=None,**kwargs):
"""\
bfs = getbasis(atoms,basis_data=None)
Given a Molecule object and a basis library, form a basis set
constructed as a list of CGBF basis functions objects.
"""
from PyQuante.Basis.basis import BasisSet
if not basis_data:
basis_data = kwargs.get('basis_data')
if kwargs.get('bfs'):
return kwargs.get('bfs')
elif not basis_data:
basis = kwargs.get('basis')
if basis:
basis_data = get_basis_data(basis)
return BasisSet(atoms, basis_data, **kwargs)