def getbfs(coords, gbasis):
"""Convenience function for both wavefunction and density based on PyQuante Ints.py."""
if not _HAS_PYQUANTE:
raise Exception("You need to have PyQuante installed")
mymol = cclib2pyquante.makepyquante(coords, [0 for _ in coords])
sym2powerlist = {
'S' : [(0, 0, 0)],
'P' : [(1, 0, 0), (0, 1, 0), (0, 0, 1)],
'D' : [(2, 0, 0), (0, 2, 0), (0, 0, 2), (1, 1, 0), (0, 1, 1), (1, 0, 1)],
'F' : [(3, 0, 0), (2, 1, 0), (2, 0, 1), (1, 2, 0), (1, 1, 1), (1, 0, 2),
(0, 3, 0), (0, 2, 1), (0, 1, 2), (0, 0, 3)]
}
bfs = []
for i, atom in enumerate(mymol):
bs = gbasis[i]
for sym, prims in bs:
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(), power)
for expnt, coef in prims:
bf.add_primitive(expnt, coef)
bf.normalize()
bfs.append(bf)
return bfs
class TestCGBF(unittest.TestCase):
"""
"""
def setUp(self):
self.gto = CGBF((0,0,0),(1,0,0))
def testAddGTO(self):
pgto = PGBF(0.4,(0,1,1),(0,0,0))
self.gto.add_primitive(0.4,0.5)
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 pyquante_basis(molfbasis,atoms):
from PyQuante.Ints import sym2powerlist
from PyQuante.CGBF import CGBF
bfs = []
for type,atomnum,primlist in molfbasis:
for power in sym2powerlist[type]:
symi,atnoi,xi,yi,zi = atoms[atomnum-1]
x,y,z = toBohr3(xi,yi,zi)
bf = CGBF((x,y,z),power)
for expnt,coef in primlist:
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 getbfs(coords, gbasis):
"""Convenience function for both wavefunction and density based on PyQuante Ints.py."""
if not _HAS_PYQUANTE:
raise Exception("You need to have PyQuante installed")
mymol = cclib2pyquante.makepyquante(coords, [0 for _ in coords])
sym2powerlist = {
'S': [(0, 0, 0)],
'P': [(1, 0, 0), (0, 1, 0), (0, 0, 1)],
'D': [(2, 0, 0), (0, 2, 0), (0, 0, 2), (1, 1, 0), (0, 1, 1),
(1, 0, 1)],
'F': [(3, 0, 0), (2, 1, 0), (2, 0, 1), (1, 2, 0), (1, 1, 1), (1, 0, 2),
(0, 3, 0), (0, 2, 1), (0, 1, 2), (0, 0, 3)]
}
bfs = []
for i, atom in enumerate(mymol):
bs = gbasis[i]
for sym, prims in bs:
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(), power)
for expnt, coef in prims:
bf.add_primitive(expnt, coef)
bf.normalize()
bfs.append(bf)
return bfs
def make_pyquante_basis(atoms,input_bfs):
from PyQuante.Ints import sym2powerlist
from PyQuante.CGBF import CGBF
bfs = []
for atom_index,info in input_bfs:
x,y,z = atoms[atom_index-1].pos()
for type,primlist in info:
for power in sym2powerlist[type]:
bf = CGBF((x,y,z),power)
for expnt,coef in primlist:
bf.add_primitive(expnt,coef)
bf.normalize()
bfs.append(bf)
return bfs
def getbfs(ccdata):
from cclib.bridge import cclib2pyquante
pymol = cclib2pyquante.makepyquante(ccdata)
bfs = []
for i, atom in enumerate(pymol):
bs = ccdata.gbasis[i]
for sym, prims in bs:
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(), power)
for expnt, coef in prims:
bf.add_primitive(expnt, coef)
bf.normalize()
bfs.append(bf)
del cclib2pyquante
return bfs
def make_basis(self):
try:
from PyQuante.CGBF import CGBF
from PyQuante.Ints import sym2powerlist
except:
print "PyQuante not available, using slower routines"
print "Consider installing PyQuante to speed basis function evals"
from Gaussian import CGBF, sym2powerlist
self.pyq_basis = []
for iat,atbasis in self.basis:
origin = tuple(self.geo.atoms[iat-1].get_position())
for type,prims in atbasis:
for power in sym2powerlist[type]:
bf = CGBF(origin,power)
for expnt,coef in prims:
bf.add_primitive(expnt,coef)
bf.normalize()
self.pyq_basis.append(bf)
return
def setUp(self):
self.gto = CGBF((0,0,0),(1,0,0))
print(integral_os)
# take the gradient in the X direction
rp = get_bi_center(za, zb, ra, rb)
ta = 2 * za * (rp[0] - ra[0])
tb = 2 * zb * (rp[0] - rb[0])
print(-(ta + tb) * integral_os)
# ga = PGBF(za, tuple(ra), tuple(la))
# gb = PGBF(zb, tuple(rb), tuple(lb))
# print(ga)
# print(gb)
# # PyQuante includes the normalization prefactor
# integral_pq = ga.overlap(gb) / (ga.norm * gb.norm)
ga = CGBF(origin=tuple(ra), powers=tuple(la), atid=0)
gb = CGBF(origin=tuple(rb), powers=tuple(lb), atid=0)
ga.add_primitive(exponent=za, coefficient=1.0)
gb.add_primitive(exponent=zb, coefficient=1.0)
# print(ga)
# print(gb)
# PyQuante includes the normalization prefactor
integral_pq = ga.overlap(gb) / (ga.pnorms[0] * gb.pnorms[0])
print(integral_pq)
print(der_overlap_element(0, ga, gb))
# print(ga.doverlap(gb, 0))
# print(ga.doverlap_num(gb, 0))
# from mmd.integrals
