def main():
h2 = Molecule('h2',
atomlist = [(1,(0.,0.,0.7)),(1,(0.,0.,-0.7))],
units = 'Bohr')
en,orbe,orbs = rhf(h2,ETemp=1e4)
print "Energy ",en,abs(en-energy)
print "Spectrum ",orbe
return en
def main():
atoms = Molecule('h2',[(1,(1.,0,0)),(1,(-1.,0,0))])
bfs = getbasis(atoms)
S,h,Ints = getints(bfs,atoms)
en,orbe,orbs = rhf(atoms,integrals=(S,h,Ints))
occs = [1.]+[0.]*9
Ecis = CIS(Ints,orbs,orbe,1,9,en)
return Ecis[0]
def calculate(self):
if self.log == 1:
f = open('calc.log','w')
f.close()
configure_output("calc.log")
x_1 = float(self.coor1_x.GetValue())
y_1 = float(self.coor1_y.GetValue())
z_1 = float(self.coor1_z.GetValue())
x_2 = float(self.coor2_x.GetValue())
y_2 = float(self.coor2_y.GetValue())
z_2 = float(self.coor2_z.GetValue())
mol = Molecule('h2',[(self.atom_no_1,(x_1,y_1,z_1)),
(self.atom_no_2,(x_2,y_2,z_2))])
print mol
bf_name = self.Bf_box.GetValue()
#Why?
if bf_name == "sto-3g":
bf_name = "sto-3g"
elif bf_name == "6-31g":
bf_name = "6-31g"
elif bf_name == "3-21g":
bf_name = "3-21g"
elif bf_name == "6-31g**":
bf_name = "6-31g**"
elif bf_name == "6-31g**++":
bf_name = "6-31g**++"
elif bf_name == "6-311g**":
bf_name = "6-311g**"
elif bf_name == "6-311g++(2d,2p)":
bf_name = "6-311g++(2d,2p)"
elif bf_name == "6-311g++(3d,3p)":
bf_name = "6-311g++(3d,3p)"
elif bf_name == "6-311g++(3df,3pd)":
bf_name = "6-311g++(3df,3pd)"
elif bf_name == "sto-6g":
bf_name = "sto-6g"
elif bf_name == "lacvp":
bf_name = "lacvp"
elif bf_name == "cc-pvdz":
bf_name = "cc-pvdz"
elif bf_name == "cc-pvtz":
bf_name = "cc-pvtz"
elif bf_name == "dzvp":
bf_name = "dzvp"
en,orbe,orbs = rhf(mol,basis_data=bf_name)
if self.log == 1:
with open('calc.log','a') as f_handle:
f_handle.write("\norbs is\n")
np.savetxt(f_handle,orbs)
f_handle.write("\norbe is\n")
np.savetxt(f_handle,orbe)
self.console_box.SetValue('energy=%f' % en)
def main():
atoms = Molecule('h2',[(1,(1.,0,0)),(1,(-1.,0,0))])
bfs = getbasis(atoms)
nel = atoms.get_nel()
nbf = len(bfs)
nocc = nel/2
S,h,Ints = getints(bfs,atoms)
en,orbe,orbs = rhf(atoms,integrals=(S,h,Ints),)
emp2 = MP2(Ints,orbs,orbe,nocc,nbf-nocc)
return en+emp2
def test_exx():
logging.basicConfig(filename='test_exx.log',
level=logging.INFO,
format="%(message)s",
filemode='w')
logging.info("Testing EXX functions")
logging.info(time.asctime())
h2o = Molecule('H2O',
atomlist = [(8,(0,0,0)), # the geo corresponds to the
(1,(0.959,0,0)),# one that Yang used
(1,(-.230,0.930,0))],
units = 'Angstrom')
h2 = Molecule('H2',
atomlist = [(1,(0.,0.,0.7)),(1,(0.,0.,-0.7))],
units = 'Bohr')
he = Molecule('He',atomlist = [(2,(0,0,0))])
ne = Molecule('Ne',atomlist = [(10,(0,0,0))])
ohm = Molecule('OH-',atomlist = [(8,(0.0,0.0,0.0)),
(1,(0.971,0.0,0.0))],
units = 'Angstrom',
charge = -1)
be = Molecule('Be',atomlist = [(4,(0.0,0.0,0.0))],
units = 'Angstrom')
lih = Molecule('LiH',
atomlist = [(1,(0,0,1.5)),(3,(0,0,-1.5))],
units = 'Bohr')
#for atoms in [h2,he,be,lih,ohm,ne,h2o]:
for atoms in [h2,lih]:
logging.info("--%s--" % atoms.name)
# Caution: the rydberg molecules (He, Ne) will need a
# much much larger basis set than the default returned
# by getbasis (which is 6-31G**)
bfs = getbasis(atoms)
S,h,Ints = getints(bfs,atoms)
enhf,orbehf,orbshf = rhf(atoms,integrals=(S,h,Ints))
logging.info("HF total energy = %f"% enhf)
enlda,orbelda,orbslda = dft(atoms,
integrals=(S,h,Ints),
bfs = bfs)
logging.info("LDA total energy = %f" % enlda)
energy,orbe_exx,orbs_exx = exx(atoms,orbslda,
integrals=(S,h,Ints),
bfs = bfs,
verbose=True,
opt_method="BFGS")
logging.info("EXX total energy = %f" % energy)
return
def main():
atoms = Molecule('He',
[(2,( .0000000000, .0000000000, .0000000000))],
units='Angstroms')
bfs = getbasis(atoms)
nel = atoms.get_nel()
nbf = len(bfs)
nocc = nel/2
S,h,Ints = getints(bfs,atoms)
en,orbe,orbs = rhf(atoms,integrals=(S,h,Ints))
emp2 = MP2(Ints,orbs,orbe,nocc,nbf-nocc)
return en+emp2
def main():
atoms = Molecule('h2', [(1, (1., 0, 0)), (1, (-1., 0, 0))])
bfs = getbasis(atoms)
nel = atoms.get_nel()
nbf = len(bfs)
nocc = nel / 2
S, h, Ints = getints(bfs, atoms)
en, orbe, orbs = rhf(
atoms,
integrals=(S, h, Ints),
)
emp2 = MP2(Ints, orbs, orbe, nocc, nbf - nocc)
return en + emp2
def main(**opts):
do_oep_an = opts.get('do_oep_an',True)
mol = Molecule('LiH',[(1,(0,0,1.5)),(3,(0,0,-1.5))],units = 'Bohr')
bfs = getbasis(mol)
S,h,Ints = getints(bfs,mol)
E_hf,orbe_hf,orbs_hf = rhf(mol,bfs=bfs,integrals=(S,h,Ints),
DoAveraging=True)
if do_oep_an:
E_exx,orbe_exx,orbs_exx = oep_hf_an(mol,orbs_hf,bfs=bfs,
integrals=(S,h,Ints))
else:
E_exx,orbe_exx,orbs_exx = oep_hf(mol,orbs_hf,bfs=bfs,
integrals=(S,h,Ints))
return E_exx
def main():
LiH = Molecule('lih', [(3, (.0000000000, .0000000000, .0000000000)),
(1, (.0000000000, .0000000000, 1.629912))],
units='Angstroms')
bfs = getbasis(LiH)
nbf = len(bfs)
nocc, nopen = LiH.get_closedopen()
assert nopen == 0
S, h, Ints = getints(bfs, LiH)
en, orbe, orbs = rhf(LiH, integrals=(S, h, Ints))
print "SCF completed, E = ", en
emp2 = MP2(Ints, orbs, orbe, nocc, nbf - nocc)
print "MP2 correction = ", emp2
print "Final energy = ", en + emp2
return en + emp2
def main():
LiH = Molecule('lih',
[(3,( .0000000000, .0000000000, .0000000000)),
(1,( .0000000000, .0000000000,1.629912))],
units='Angstroms')
bfs = getbasis(LiH)
nbf = len(bfs)
nocc,nopen = LiH.get_closedopen()
assert nopen==0
S,h,Ints = getints(bfs,LiH)
en,orbe,orbs = rhf(LiH,integrals=(S,h,Ints))
print "SCF completed, E = ",en
emp2 = MP2(Ints,orbs,orbe,nocc,nbf-nocc)
print "MP2 correction = ",emp2
print "Final energy = ",en+emp2
return en+emp2
def test_old():
from PyQuante.Molecule import Molecule
from PyQuante.Ints import getbasis,getints
from PyQuante.hartree_fock import rhf
logging.basicConfig(level=logging.DEBUG,format="%(message)s")
#mol = Molecule('HF',[('H',(0.,0.,0.)),('F',(0.,0.,0.898369))],
# units='Angstrom')
mol = Molecule('LiH',[(1,(0,0,1.5)),(3,(0,0,-1.5))],units = 'Bohr')
bfs = getbasis(mol)
S,h,Ints = getints(bfs,mol)
print "after integrals"
E_hf,orbe_hf,orbs_hf = rhf(mol,bfs=bfs,integrals=(S,h,Ints),DoAveraging=True)
print "RHF energy = ",E_hf
E_exx,orbe_exx,orbs_exx = exx(mol,orbs_hf,bfs=bfs,integrals=(S,h,Ints))
return
def main():
atoms = Molecule('ch4', [(6, (.0000000000, .0000000000, .0000000000)),
(1, (.0000000000, .0000000000, 1.0836058890)),
(1, (1.0216334297, .0000000000, -.3612019630)),
(1, (-.5108167148, .8847605034, -.3612019630)),
(1, (-.5108167148, -.8847605034, -.3612019630))],
units='Angstroms')
bfs = getbasis(atoms)
nel = atoms.get_nel()
nbf = len(bfs)
nocc = nel / 2
S, h, Ints = getints(bfs, atoms)
en, orbe, orbs = rhf(atoms, integrals=(S, h, Ints))
print "SCF completed, E = ", en
emp2 = MP2(Ints, orbs, orbe, nocc, nbf - nocc)
print "MP2 correction = ", emp2
print "Final energy = ", en + emp2
return en + emp2
def main():
atoms = Molecule('ch4',
[(6,( .0000000000, .0000000000, .0000000000)),
(1,( .0000000000, .0000000000,1.0836058890)),
(1,(1.0216334297, .0000000000,-.3612019630)),
(1,(-.5108167148, .8847605034,-.3612019630)),
(1,(-.5108167148,-.8847605034,-.3612019630))],
units='Angstroms')
bfs = getbasis(atoms)
nel = atoms.get_nel()
nbf = len(bfs)
nocc = nel/2
S,h,Ints = getints(bfs,atoms)
en,orbe,orbs = rhf(atoms,integrals=(S,h,Ints))
print "SCF completed, E = ",en
emp2 = MP2(Ints,orbs,orbe,nocc,nbf-nocc)
print "MP2 correction = ",emp2
print "Final energy = ",en+emp2
return en+emp2
def test(file):
# Make a test molecule for the calculation
p = QMFile(file,mol=1)
h2 = p.get_mol()
#h2 = Molecule('h2',[(1,(1.,0,0)),(1,(-1.,0,0))])
# Get a basis set and compute the integrals.
# normally the routine will do this automatically, but we
# do it explicitly here so that we can pass the same set
# of integrals into the CI code and thus not recompute them.
bfs = getbasis(h2)
S,h,Ints = getints(bfs,h2)
# Compute the HF wave function for our molecule
en,orbe,orbs = rhf(h2,
integrals=(S,h,Ints)
)
print "SCF completed, E = ",en
print " orbital energies "
PRINT (orbe)
# Compute the occupied and unoccupied orbitals, used in the
# CIS program to generate the excitations
nclosed,nopen = h2.get_closedopen()
nbf = len(bfs)
nocc = nclosed+nopen
nvirt = nbf-nocc
# Call the CI program:
#Ecis = CIS(Ints,orbs,orbe,nocc,nvirt,en)
#print "Ecis = ",Ecis
print orbs
CIS_H = CISMatrix(Ints, orbs, en, orbe, nocc, nvirt)
EN, U = linalg.eig(CIS_H)
EE = EN; EE.sort()
print " CIS Energies [eV]"
PRINT ( EE )#* UNITS.HartreeToElectronVolt)
print " First excited state energy = %20.4f" % min(EN)
return
def main(**opts):
do_oep_an = opts.get('do_oep_an', True)
mol = Molecule('LiH', [(1, (0, 0, 1.5)), (3, (0, 0, -1.5))], units='Bohr')
bfs = getbasis(mol)
S, h, Ints = getints(bfs, mol)
E_hf, orbe_hf, orbs_hf = rhf(mol,
bfs=bfs,
integrals=(S, h, Ints),
DoAveraging=True)
if do_oep_an:
E_exx, orbe_exx, orbs_exx = oep_hf_an(mol,
orbs_hf,
bfs=bfs,
integrals=(S, h, Ints))
else:
E_exx, orbe_exx, orbs_exx = oep_hf(mol,
orbs_hf,
bfs=bfs,
integrals=(S, h, Ints))
return E_exx
def test_old():
from PyQuante.Molecule import Molecule
from PyQuante.Ints import getbasis, getints
from PyQuante.hartree_fock import rhf
logging.basicConfig(level=logging.DEBUG, format="%(message)s")
#mol = Molecule('HF',[('H',(0.,0.,0.)),('F',(0.,0.,0.898369))],
# units='Angstrom')
mol = Molecule('LiH', [(1, (0, 0, 1.5)), (3, (0, 0, -1.5))], units='Bohr')
bfs = getbasis(mol)
S, h, Ints = getints(bfs, mol)
print "after integrals"
E_hf, orbe_hf, orbs_hf = rhf(mol,
bfs=bfs,
integrals=(S, h, Ints),
DoAveraging=True)
print "RHF energy = ", E_hf
E_exx, orbe_exx, orbs_exx = exx(mol,
orbs_hf,
bfs=bfs,
integrals=(S, h, Ints))
return
#!/usr/bin/env python
from PyQuante.hartree_fock import rhf
from PyQuante.Molecule import Molecule
from PyQuante.force import *
bl=1.4
mol = Molecule('H2',[(1,(0.,0.,0.)),(1,(0.0,0.0,bl))])
en,orb_en,coefs = rhf(mol,MaxIter=20,basis_data="sto-3g")
bfs = getbasis(mol,'sto-3g')
dHcore_dXa,dHcore_dYa,dHcore_dZa = der_Hcore_matrix(1,bfs,mol.atoms)
dS_dXa,dS_dYa,dS_dZa = der_overlap_matrix(1,bfs)
print "\n*** Analytic gradients ***\n"
print "\ndHcore/dZa\n",dHcore_dZa
print "\ndS/dZa\n",dS_dZa
def main():
r = 1. / 0.52918
h2o = Molecule('h2o',
atomlist=[(8, (0, 0, 0)), (1, (r, 0, 0)), (1, (0, r, 0))])
en, orbe, orbs = rhf(h2o)
return en
def H2O_Molecule(tst,info,auX,auZ):
H2O = Molecule('H2O',
[('O', ( 0.0, 0.0, 0.0)),
('H', ( auX, 0.0, auZ)),
('H', (-auX, 0.0, auZ))],
units='Bohr')
# Get a better energy estimate
if dft:
print "# info=%s A.U.=(%g,%g) " % (info,auX,auZ)
edft,orbe2,orbs2 = dft(H2O,functional='SVWN')
bfs= getbasis(H2O,basis_data=basis_data)
#S is overlap of 2 basis funcs
#h is (kinetic+nucl) 1 body term
#ints is 2 body terms
S,h,ints=getints(bfs,H2O)
#enhf is the Hartee-Fock energy
#orbe is the orbital energies
#orbs is the orbital overlaps
enhf,orbe,orbs=rhf(H2O,integrals=(S,h,ints))
enuke = Molecule.get_enuke(H2O)
# print "orbe=%d" % len(orbe)
temp = matrixmultiply(h,orbs)
hmol = matrixmultiply(transpose(orbs),temp)
MOInts = TransformInts(ints,orbs)
if single:
print "h = \n",h
print "S = \n",S
print "ints = \n",ints
print "orbe = \n",orbe
print "orbs = \n",orbs
print ""
print "Index 0: 1 or 2 in the paper, Index 1: 3 or 4 in the paper (for pqrs)"
print ""
print "hmol = \n",hmol
print "MOInts:"
print "I,J,K,L = PQRS order: Cre1,Cre2,Ann1,Ann2"
if 1:
print "tst=%d info=%s nuc=%.9f Ehf=%.9f" % (tst,info,enuke,enhf),
cntOrbs = 0
maxOrb = 0
npts = len(hmol[:])
for i in xrange(npts):
for j in range(i,npts):
if abs(hmol[i,j]) > 1.0e-7:
print "%d,%d=%.9f" % (i,j,hmol[i,j]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
nbf,nmo = orbs.shape
mos = range(nmo)
for i in mos:
for j in xrange(i+1):
ij = i*(i+1)/2+j
for k in mos:
for l in xrange(k+1):
kl = k*(k+1)/2+l
if ij >= kl:
ijkl = ijkl2intindex(i,j,k,l)
if abs(MOInts[ijkl]) > 1.0e-7:
print "%d,%d,%d,%d=%.9f" % (l,i,j,k,MOInts[ijkl]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
print ""
return (maxOrb,cntOrbs)
def main():
ne = Molecule('Ne',atomlist = [(10,(0,0,0))])
en,orbe,orbs = rhf(ne)
return en
def main():
h2 = Molecule('h2',
atomlist=[(1, (0, 0, 0.6921756113231793)),
(1, (0, 0, -0.6921756113231793))])
en, orbe, orbs = rhf(h2, basis="sto3g")
return en
def main():
he = Molecule('He', atomlist=[(2, (0, 0, 0))])
en, orbe, orbs = rhf(he)
return en
def main():
oh = Molecule('OH-',
atomlist=[(8, (0, 0, 0)), (1, (0.957939 * ang2bohr, 0, 0))],
charge=-1)
en, orbe, orbs = rhf(oh)
return en
def main():
h2 = Molecule("h2", atomlist=[(1, (0.0, 0.0, 0.7)), (1, (0.0, 0.0, -0.7))], units="Bohr")
en, orbe, orbs = rhf(h2, ETemp=1e4)
print "Energy ", en, abs(en - energy)
print "Spectrum ", orbe
return en
def H2O_Molecule(tst, info, auX, auZ):
H2O = Molecule('H2O', [('O', (0.0, 0.0, 0.0)), ('H', (auX, 0.0, auZ)),
('H', (-auX, 0.0, auZ))],
units='Bohr')
# Get a better energy estimate
if dft:
print "# info=%s A.U.=(%g,%g) " % (info, auX, auZ)
edft, orbe2, orbs2 = dft(H2O, functional='SVWN')
bfs = getbasis(H2O, basis_data=basis_data)
#S is overlap of 2 basis funcs
#h is (kinetic+nucl) 1 body term
#ints is 2 body terms
S, h, ints = getints(bfs, H2O)
#enhf is the Hartee-Fock energy
#orbe is the orbital energies
#orbs is the orbital overlaps
enhf, orbe, orbs = rhf(H2O, integrals=(S, h, ints))
enuke = Molecule.get_enuke(H2O)
# print "orbe=%d" % len(orbe)
temp = matrixmultiply(h, orbs)
hmol = matrixmultiply(transpose(orbs), temp)
MOInts = TransformInts(ints, orbs)
if single:
print "h = \n", h
print "S = \n", S
print "ints = \n", ints
print "orbe = \n", orbe
print "orbs = \n", orbs
print ""
print "Index 0: 1 or 2 in the paper, Index 1: 3 or 4 in the paper (for pqrs)"
print ""
print "hmol = \n", hmol
print "MOInts:"
print "I,J,K,L = PQRS order: Cre1,Cre2,Ann1,Ann2"
if 1:
print "tst=%d info=%s nuc=%.9f Ehf=%.9f" % (tst, info, enuke, enhf),
cntOrbs = 0
maxOrb = 0
npts = len(hmol[:])
for i in xrange(npts):
for j in range(i, npts):
if abs(hmol[i, j]) > 1.0e-7:
print "%d,%d=%.9f" % (i, j, hmol[i, j]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
nbf, nmo = orbs.shape
mos = range(nmo)
for i in mos:
for j in xrange(i + 1):
ij = i * (i + 1) / 2 + j
for k in mos:
for l in xrange(k + 1):
kl = k * (k + 1) / 2 + l
if ij >= kl:
ijkl = ijkl2intindex(i, j, k, l)
if abs(MOInts[ijkl]) > 1.0e-7:
print "%d,%d,%d,%d=%.9f" % (l, i, j, k,
MOInts[ijkl]),
cntOrbs += 1
if i > maxOrb: maxOrb = i
if j > maxOrb: maxOrb = j
print ""
return (maxOrb, cntOrbs)
def main():
h2 = Molecule('h2', atomlist=[(1, (0, 0, 0)), (1, (1.0, 0, 0))])
en, orbe, orbs = rhf(h2)
return en
def visualize(self):
if self.log == 1:
f = open('calc.log','w')
f.close()
configure_output("calc.log")
x_1 = float(self.coor1_x.GetValue())
y_1 = float(self.coor1_y.GetValue())
z_1 = float(self.coor1_z.GetValue())
x_2 = float(self.coor2_x.GetValue())
y_2 = float(self.coor2_y.GetValue())
z_2 = float(self.coor2_z.GetValue())
z_pos = float(self.z_pos.GetValue())
mol = Molecule('h2',[(self.atom_no_1,(y_1,x_1,z_1)),
(self.atom_no_2,(y_2,x_2,z_2))],
units='Angstrom')
bf_name = self.Bf_box.GetValue()
#Why?
if bf_name == "sto-3g":
bf_name = "sto-3g"
elif bf_name == "6-31g":
bf_name = "6-31g"
elif bf_name == "3-21g":
bf_name = "3-21g"
elif bf_name == "6-31g**":
bf_name = "6-31g**"
elif bf_name == "6-31g**++":
bf_name = "6-31g**++"
elif bf_name == "6-311g**":
bf_name = "6-311g**"
elif bf_name == "6-311g++(2d,2p)":
bf_name = "6-311g++(2d,2p)"
elif bf_name == "6-311g++(3d,3p)":
bf_name = "6-311g++(3d,3p)"
elif bf_name == "6-311g++(3df,3pd)":
bf_name = "6-311g++(3df,3pd)"
elif bf_name == "sto-6g":
bf_name = "sto-6g"
elif bf_name == "lacvp":
bf_name = "lacvp"
elif bf_name == "cc-pvdz":
bf_name = "cc-pvdz"
elif bf_name == "cc-pvtz":
bf_name = "cc-pvtz"
elif bf_name == "dzvp":
bf_name = "dzvp"
en,orbe,orbs = rhf(mol,basis_data=bf_name)
self.console_box.SetValue('energy=%f' % en)
bfs = getbasis(mol,bf_name)
delta = 0.1
c_range = 5.0
#setting for visualize
x = np.arange(-1*c_range,c_range,delta)
y = np.arange(-1*c_range,c_range,delta)
X,Y = p.meshgrid(x,y)
Z = np.zeros((len(X),len(Y)))
Z_2 = np.zeros((len(X),len(Y)))
#print C matrix
#print "C=",orbs
#bounding = self.orb_bound_box.GetValue()
#calculate wave function
for k,bf in enumerate(bfs.bfs):
for i,x1 in enumerate(x):
for j,y1 in enumerate(y):
#calculate wave function
#basic function multiply
#if bounding == "boundary":
Z[i,j] += bf.amp(x1,y1,z_pos) * orbs[k,0]
#else:
# Z[i,j] += bf.amp(x1,y1,z_pos) * orbs[k,1]
if self.log == 1:
with open('calc.log','a') as f_handle:
f_handle.write("\norbs is\n")
np.savetxt(f_handle,orbs)
f_handle.write("\norbe is\n")
np.savetxt(f_handle,orbe)
##### visualize #####
fig = p.figure()
ax = Axes3D(fig)
#ax.plot_surface(X,Y,Z)
ax.plot_wireframe(X,Y,Z,color = 'b')
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
p.show()
def main():
h2 = Molecule('h2',atomlist=[(1,(0,0,0)),(1,(1.0,0,0))])
en,orbe,orbs = rhf(h2)
return en
def runapp(self):
molecule = self.m
res = rhf(molecule)
SCF(molecule).iterate()
#!/usr/bin/env python
from PyQuante.hartree_fock import rhf
from PyQuante.Molecule import Molecule
from PyQuante.force import *
bl = 1.4
mol = Molecule('H2', [(1, (0., 0., 0.)), (1, (0.0, 0.0, bl))])
en, orb_en, coefs = rhf(mol, MaxIter=20, basis_data="sto-3g")
bfs = getbasis(mol, 'sto-3g')
dHcore_dXa, dHcore_dYa, dHcore_dZa = der_Hcore_matrix(1, bfs, mol.atoms)
dS_dXa, dS_dYa, dS_dZa = der_overlap_matrix(1, bfs)
print "\n*** Analytic gradients ***\n"
print "\ndHcore/dZa\n", dHcore_dZa
print "\ndS/dZa\n", dS_dZa
def main():
ne = Molecule('Ne', atomlist=[(10, (0, 0, 0))])
en, orbe, orbs = rhf(ne)
return en
def main():
h2 = Molecule('h2',atomlist=[(1,(0,0,0.6921756113231793)),(1,(0,0,-0.6921756113231793))])
en,orbe,orbs = rhf(h2,basis="sto3g")
return en
benz = Molecule('benzene', [(6, (0.000, 1.396, 0.000)),
(6, (1.209, 0.698, 0.000)),
(6, (1.209, -0.698, 0.000)),
(6, (0.000, -1.396, 0.000)),
(6, (-1.209, -0.698, 0.000)),
(6, (-1.209, 0.698, 0.000)),
(1, (0.000, 2.479, 0.000)),
(1, (2.147, 1.240, 0.000)),
(1, (2.147, -1.240, 0.000)),
(1, (0.000, -2.479, 0.000)),
(1, (-2.147, -1.240, 0.000)),
(1, (-2.147, 1.240, 0.000))],
units='Angstrom')
print "------------ h2 ------------"
en, orbe, orbs = rhf(h2)
print 'orbe', orbe
print 'orbs', orbs
print "------------ h2o ------------"
en, orbe, orbs = rhf(h2o)
print 'orbe', orbe
print 'orbs', orbs
print "------------ beneze ------------"
en, orbe, orbs = rhf(benz)
def main():
he = Molecule('He',atomlist = [(2,(0,0,0))])
en,orbe,orbs = rhf(he)
return en
def main():
r = 1./0.52918
h2o=Molecule('h2o',atomlist = [(8,(0,0,0)),(1,(r,0,0)),(1,(0,r,0))])
en,orbe,orbs = rhf(h2o)
return en
def main():
oh=Molecule('OH-',
atomlist = [(8,(0,0,0)),(1,(0.957939*ang2bohr,0,0))],
charge=-1)
en,orbe,orbs = rhf(oh)
return en