def rohf_wag(atoms, noccsh=None, f=None, a=None, b=None, **kwargs):
"""\
rohf(atoms,noccsh=None,f=None,a=None,b=None,**kwargs):
Restricted open shell HF driving routine
atoms A Molecule object containing the system of interest
"""
ConvCriteria = kwargs.get('ConvCriteria', settings.ConvergenceCriteria)
MaxIter = kwargs.get('MaxIter', settings.MaxIter)
DoAveraging = kwargs.get('DoAveraging', settings.Averaging)
verbose = kwargs.get('verbose')
bfs = getbasis(atoms, **kwargs)
S, h, Ints = getints(bfs, atoms, **kwargs)
nel = atoms.get_nel()
orbs = kwargs.get('orbs')
if orbs is None:
orbe, orbs = geigh(h, nS)
nclosed, nopen = atoms.get_closedopen()
nocc = nopen + nclosed
if not noccsh: noccsh = get_noccsh(nclosed, nopen)
nsh = len(noccsh)
nbf = norb = len(bfs)
if not f:
f, a, b = get_fab(nclosed, nopen)
if verbose:
print "ROHF calculation"
print "nsh = ", nsh
print "noccsh = ", noccsh
print "f = ", f
print "a_ij: "
for i in xrange(nsh):
for j in xrange(i + 1):
print a[i, j],
print
print "b_ij: "
for i in xrange(nsh):
for j in xrange(i + 1):
print b[i, j],
print
enuke = atoms.get_enuke()
energy = eold = 0.
for i in xrange(MaxIter):
Ds = get_os_dens(orbs, f, noccsh)
Hs = get_os_hams(Ints, Ds)
orbs = rotion(orbs, h, Hs, f, a, b, noccsh)
orbe, orbs = ocbse(orbs, h, Hs, f, a, b, noccsh)
orthogonalize(orbs, S)
# Compute the energy
eone = sum(f[ish] * trace2(Ds[ish], h) for ish in xrange(nsh))
energy = enuke + eone + sum(orbe[:nocc])
print energy, eone
if abs(energy - eold) < ConvCriteria: break
eold = energy
return energy, orbe, orbs
def gamess_basisInfo(mol, basis_set):
atom_types = [atno2type(atom.atno) for atom in mol.atoms]
bfs = getbasis(mol, basis_set)
currentId = -1
basis_str = ""
shell_id = 1
gauss_id = 1
for bfindx in range(len(bfs)):
bf = bfs[bfindx]
if bf.atid != currentId:
currentId = bf.atid
basis_str += '%s\n\n' % (atom_types[bf.atid])
for prim in bf.prims:
if prim.powers[1] == 0 and prim.powers[2] == 0:
sym = power2sym(prim.powers)
basis_str += " {:d} {:s} {:d}".format(
shell_id, sym, gauss_id)
basis_str += " {:12.7f} {:12.12f}\n".format(
prim.exp, prim.coef)
gauss_id += 1
count = True
if count:
shell_id += 1
basis_str += '\n'
count = False
return basis_str, shell_id - 1
def rohf_wag(atoms,noccsh=None,f=None,a=None,b=None,**kwargs):
"""\
rohf(atoms,noccsh=None,f=None,a=None,b=None,**kwargs):
Restricted open shell HF driving routine
atoms A Molecule object containing the system of interest
"""
ConvCriteria = kwargs.get('ConvCriteria',settings.ConvergenceCriteria)
MaxIter = kwargs.get('MaxIter',settings.MaxIter)
DoAveraging = kwargs.get('DoAveraging',settings.Averaging)
verbose = kwargs.get('verbose')
bfs = getbasis(atoms,**kwargs)
S,h,Ints = getints(bfs,atoms,**kwargs)
nel = atoms.get_nel()
orbs = kwargs.get('orbs')
if orbs is None:
orbe,orbs = geigh(h,nS)
nclosed,nopen = atoms.get_closedopen()
nocc = nopen+nclosed
if not noccsh: noccsh = get_noccsh(nclosed,nopen)
nsh = len(noccsh)
nbf = norb = len(bfs)
if not f:
f,a,b = get_fab(nclosed,nopen)
if verbose:
print "ROHF calculation"
print "nsh = ",nsh
print "noccsh = ",noccsh
print "f = ",f
print "a_ij: "
for i in xrange(nsh):
for j in xrange(i+1):
print a[i,j],
print
print "b_ij: "
for i in xrange(nsh):
for j in xrange(i+1):
print b[i,j],
print
enuke = atoms.get_enuke()
energy = eold = 0.
for i in xrange(MaxIter):
Ds = get_os_dens(orbs,f,noccsh)
Hs = get_os_hams(Ints,Ds)
orbs = rotion(orbs,h,Hs,f,a,b,noccsh)
orbe,orbs = ocbse(orbs,h,Hs,f,a,b,noccsh)
orthogonalize(orbs,S)
# Compute the energy
eone = sum(f[ish]*trace2(Ds[ish],h) for ish in xrange(nsh))
energy = enuke+eone+sum(orbe[:nocc])
print energy,eone
if abs(energy-eold) < ConvCriteria: break
eold = energy
return energy,orbe,orbs
def __init__(self,molecule,**kwargs):
from PyQuante.Ints import getbasis
from PyQuante.Basis.Tools import get_basis_data
self.bfs = getbasis(molecule,**kwargs)
logging.info("%d basis functions" % len(self.bfs))
return
def test_mol(mol, **opts):
basis_data = opts.get('basis_data', None)
do_python_tests = opts.get('do_python_tests', True)
make_hf_driver(mol, basis_data=basis_data)
if do_python_tests:
bfs = getbasis(mol, basis_data)
S = getS(bfs)
T = getT(bfs)
V = getV(bfs, mol)
Ints = get2ints(bfs)
nclosed, nopen = mol.get_closedopen()
enuke = mol.get_enuke()
assert nopen == 0
h = T + V
orbe, orbs = GHeigenvectors(h, S)
print "Eval of h: ",
print orbe
for i in range(10):
D = mkdens(orbs, 0, nclosed)
J = getJ(Ints, D)
K = getK(Ints, D)
orbe, orbs = GHeigenvectors(h + 2 * J - K, S)
eone = TraceProperty(D, h)
ej = TraceProperty(D, J)
ek = TraceProperty(D, K)
energy = enuke + 2 * eone + 2 * ej - ek
print i, energy, enuke, eone, ej, ek
return
def test_mol(mol,**opts):
basis_data = opts.get('basis_data',None)
do_python_tests = opts.get('do_python_tests',True)
make_hf_driver(mol,basis_data=basis_data)
if do_python_tests:
bfs = getbasis(mol,basis_data)
S= getS(bfs)
T = getT(bfs)
V = getV(bfs,mol)
Ints = get2ints(bfs)
nclosed,nopen = mol.get_closedopen()
enuke = mol.get_enuke()
assert nopen==0
h = T+V
orbe,orbs = GHeigenvectors(h,S)
print "Eval of h: ",
print orbe
for i in range(10):
D = mkdens(orbs,0,nclosed)
J = getJ(Ints,D)
K = getK(Ints,D)
orbe,orbs = GHeigenvectors(h+2*J-K,S)
eone = TraceProperty(D,h)
ej = TraceProperty(D,J)
ek = TraceProperty(D,K)
energy = enuke+2*eone+2*ej-ek
print i,energy,enuke,eone,ej,ek
return
def __init__(self, molecule, **kwargs):
from PyQuante.Ints import getbasis
from PyQuante.Basis.Tools import get_basis_data
self.bfs = getbasis(molecule, **kwargs)
logging.info("%d basis functions" % len(self.bfs))
return
def get_orbitalList(mol, basis_set):
bfs = getbasis(mol, basis_set)
g_basis = [[] for i in mol.atoms]
# check for duplicates
last_sym = 'N'
last_pair = (0.0, 0.0)
last_atid = -1
# iterate bfs
for i_bf in range(len(bfs)):
bf = bfs[i_bf]
sym = power2sym(bf.powers)
cgbf = (sym, [])
for prim in bf.prims:
pair = (prim.exp, prim.coef)
cgbf[1].append(pair)
if (last_sym != sym) or (pair != last_pair) or (last_atid != bf.atid):
g_basis[bf.atid].append(cgbf)
last_sym = sym
last_pair = pair
last_atid = bf.atid
return g_basis
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 main():
dirname = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(dirname, 'LiH.xyz')
mol = Molecule.from_file(filename, format='xyz')
bfs = getbasis(mol.atoms, 'sto-3g')
print(der_overlap_matrix(0, bfs))
return
def main():
dirname = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(dirname, 'LiH.xyz')
mol = Molecule.from_file(filename, format='xyz')
bfs = getbasis(mol.atoms, 'sto-3g')
print(der_overlap_matrix(0, bfs))
return
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 gamess_orbInfo(mol, basis_set):
atom_types = [atno2type(atom.atno) for atom in mol.atoms]
bfs = getbasis(mol, basis_set)
bfs_atids = []
bfs_atypes = []
bfs_sym = []
for bfindx in range(len(bfs)):
bf = bfs[bfindx]
bfs_atids.append(bf.atid + 1)
bfs_atypes.append(atom_types[bf.atid])
bfs_sym.append(gamess_power2xyz(bf.powers))
return bfs_atids, bfs_atypes, bfs_sym
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 create_Orbital_file(
filename,
mol,
basis_set,
orbitals,
orb_e,
):
'''
Creates a orbital file with extension .out
that can be used with Avogadro
for 3D orbital viewing.
Based on a dummy GAMESS file.
INPUTS:
filename --> a string to be used for the name of the file, duh
mol --> a PyQuante Molecule object
basis_set -> a string indicating the basis_set used
orbitals -> a matrix that containts the coefficients for the orbitals
orb_e -> an array of orbital energies
'''
template_file = 'files/template_mo.out'
new_file = '%s.out' % filename
replaceDict = {}
# general mol info
replaceDict['{#Molname}'] = mol.name
replaceDict['{#XYZ}'] = xyz_text(mol)
replaceDict['{#Natoms}'] = len(mol.atoms)
replaceDict['{#Nelectrons}'] = mol.get_nel()
(nalpha, nbeta) = mol.get_alphabeta()
replaceDict['{#Nalpha}'] = nalpha
replaceDict['{#Nbeta}'] = nbeta
replaceDict['{#Charge}'] = mol.charge
replaceDict['{#Multiplicity}'] = mol.multiplicity
# Basis set info
basis_str, nshells = gamess_basisInfo(mol, basis_set)
replaceDict['{#BasisInfo}'] = basis_str
replaceDict['{#Nbfs}'] = len(getbasis(mol, basis_set))
replaceDict['{#Nshells}'] = nshells
# Orbital Info
replaceDict['{#Orbitals}'] = gamess_orbStr(mol, basis_set, orbitals, orb_e)
# create file
replace_allnew(template_file, new_file, replaceDict)
print('======================')
print('Created %s successfully!' % new_file)
print('View it now with Avogadro!')
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 make_hf_driver(atoms, **opts):
basis_data = opts.get('basis_data', None)
do_print_one = opts.get('do_print_one', False)
do_print_two = opts.get('do_print_two', False)
maxiter = opts.get('maxiter', 5)
nat = len(atoms)
bfs = getbasis(atoms, basis_data)
nbf = len(bfs)
nbf2 = nbf * nbf
nint = nbf * (nbf + 1) * (nbf * nbf + nbf + 2) / 8
nclosed, nopen = atoms.get_closedopen()
enuke = atoms.get_enuke()
assert nopen == 0, "code only works for closed-shell systems"
nprim = 0
for bf in bfs:
nprim += len(bf._prims)
atnos, xs, ys, zs = get_adat(atoms)
atno_array = output_elements_table(atnos, 'atno', 'int')
x_array = output_elements_table(xs, 'x', 'double')
y_array = output_elements_table(ys, 'y', 'double')
z_array = output_elements_table(zs, 'z', 'double')
# Print out data over contracted bfs:
xcenter, ycenter, zcenter, lpower, mpower, npower, normcs, istarts, nprims = get_cdat(
bfs)
xcenter_array = output_elements_table(xcenter, 'xcenter', 'double')
ycenter_array = output_elements_table(ycenter, 'ycenter', 'double')
zcenter_array = output_elements_table(zcenter, 'zcenter', 'double')
lpower_array = output_elements_table(lpower, 'lpower', 'int')
mpower_array = output_elements_table(mpower, 'mpower', 'int')
npower_array = output_elements_table(npower, 'npower', 'int')
normc_array = output_elements_table(normcs, 'normc', 'double')
istart_array = output_elements_table(istarts, 'istart', 'int')
nprim_array = output_elements_table(nprims, 'nprim', 'int')
# print out data over primitive bfs:
alpha, coef, normp = get_pdat(bfs)
alpha_array = output_elements_table(alpha, 'alpha', 'double')
coef_array = output_elements_table(coef, 'coef', 'double')
normp_array = output_elements_table(normp, 'normp', 'double')
template = open("main_template.c").read()
open("%s.c" % atoms.name, 'w').write(template % locals())
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 __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 __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 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 __init__(self,natom, R, basis_input="ccpvtz",LDA=False):
if basis_input =='2dp':
basis_data='6-311g++(2d,2p)'
elif basis_input =='3dp':
basis_data='6-311g++(3d,3p)'
elif basis_input =='3df':
basis_data='6-311g++(3df,3pd)'
elif basis_input =='ccpvtz':
basis_data="ccpvtz"
elif basis_input =='631ss':
basis_data = '6-31g**++'
elif basis_input =='ccpvdz':
basis_data="ccpvdz"
elif basis_input =='p6311ss':
basis_data = '6-311g**'
elif basis_input =='juho_':
basis_data = 'juho_'
elif basis_input =='1s':
basis_data = 'sto-6g'
atoms = Molecule('H2',atomlist=[(natom,(0,0,0)),(natom,(R,0,0))])
self.bfs = getbasis(atoms,basis_data)
self.S, self.h, self.Ints = getints(self.bfs, atoms)
M = len(self.S)
ist, dict_ist = index_double(M)
M2 = len(ist)
UH_g = zeros((M2,M2),float)
UF_g = zeros((M2,M2),float)
for il,(i,j) in enumerate(ist):
UH_g[il] = fetch_jints(self.Ints,i,j,M)
UF_g[il] = fetch_kints(self.Ints,i,j,M)
#Diagonalize GTO: H2+ basis
self.eival, self.eivec = geigh(self.h,self.S)
#h0 within H2+ basis
h0 = trans_2matrix(self.h,self.eivec)
#UH and UF within H2+ basis: T1[ad,il]*UH_g(ijkl)*T1.T[jk,bc]
UH = trans_4matrix(UH_g, self.eivec)
UF = trans_4matrix(UF_g, self.eivec)
self.inputs = (2*h0,2*UH,2*UF)
if LDA:
self.gr = gto_lda_inputs(self.bfs,atoms)
def make_hf_driver(atoms,**opts):
basis_data = opts.get('basis_data',None)
do_print_one = opts.get('do_print_one',False)
do_print_two = opts.get('do_print_two',False)
maxiter = opts.get('maxiter',5)
nat = len(atoms)
bfs = getbasis(atoms,basis_data)
nbf = len(bfs)
nbf2 = nbf*nbf
nint = nbf*(nbf+1)*(nbf*nbf+nbf+2)/8
nclosed,nopen = atoms.get_closedopen()
enuke = atoms.get_enuke()
assert nopen==0, "code only works for closed-shell systems"
nprim = 0
for bf in bfs: nprim += len(bf._prims)
atnos,xs,ys,zs = get_adat(atoms)
atno_array = output_elements_table(atnos,'atno','int')
x_array = output_elements_table(xs,'x','double')
y_array = output_elements_table(ys,'y','double')
z_array = output_elements_table(zs,'z','double')
# Print out data over contracted bfs:
xcenter,ycenter,zcenter,lpower,mpower,npower,normcs,istarts,nprims = get_cdat(bfs)
xcenter_array = output_elements_table(xcenter,'xcenter','double')
ycenter_array = output_elements_table(ycenter,'ycenter','double')
zcenter_array = output_elements_table(zcenter,'zcenter','double')
lpower_array = output_elements_table(lpower,'lpower','int')
mpower_array = output_elements_table(mpower,'mpower','int')
npower_array = output_elements_table(npower,'npower','int')
normc_array = output_elements_table(normcs,'normc','double')
istart_array = output_elements_table(istarts,'istart','int')
nprim_array = output_elements_table(nprims,'nprim','int')
# print out data over primitive bfs:
alpha,coef,normp = get_pdat(bfs)
alpha_array = output_elements_table(alpha,'alpha','double')
coef_array = output_elements_table(coef,'coef','double')
normp_array = output_elements_table(normp,'normp','double')
template = open("main_template.c").read()
open("%s.c" % atoms.name,'w').write(template % locals())
return
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 get_orbitalInfo(mol, basis_set):
if isinstance(basis_set, basestring):
bfs = getbasis(mol, basis_set)
else:
bfs = basis_set
g_basis = [[] for i in mol.atoms]
for i_bf in range(len(bfs)):
bf = bfs[i_bf]
cgbf = (power2sym(bf.powers), power2xyz(bf.powers), [])
for prim in bf.prims:
cgbf[2].append((prim.exp, prim.coef))
g_basis[bf.atid].append(cgbf)
return g_basis, len(bfs)
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 test_grad(atoms,**opts):
basis = opts.get('basis',None)
verbose = opts.get('verbose',False)
bfs = getbasis(atoms,basis)
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
energy, orbe, orbs = dft(atoms,return_flag=1)
nclosed,nopen = atoms.get_closedopen()
D = mkdens_spinavg(orbs,nclosed,nopen)
# Now set up a minigrid on which to evaluate the density and gradients:
npts = opts.get('npts',1)
d = opts.get('d',1e-4)
# generate any number of random points, and compute
# analytical and numeric gradients:
print "Computing Grad Rho for Molecule %s" % atoms.name
maxerr = -1
for i in range(npts):
x,y,z = rand_xyz()
rho = get_rho(x,y,z,D,bfs)
rho_px = get_rho(x+d,y,z,D,bfs)
rho_mx = get_rho(x-d,y,z,D,bfs)
rho_py = get_rho(x,y+d,z,D,bfs)
rho_my = get_rho(x,y-d,z,D,bfs)
rho_pz = get_rho(x,y,z+d,D,bfs)
rho_mz = get_rho(x,y,z-d,D,bfs)
gx,gy,gz = get_grad_rho(x,y,z,D,bfs)
gx_num = (rho_px-rho_mx)/2/d
gy_num = (rho_py-rho_my)/2/d
gz_num = (rho_pz-rho_mz)/2/d
dx,dy,dz = gx-gx_num,gy-gy_num,gz-gz_num
error = sqrt(dx*dx+dy*dy+dz*dz)
maxerr = max(error,maxerr)
print " Point %10.6f %10.6f %10.6f %10.6f" % (x,y,z,error)
print " Numerical %10.6f %10.6f %10.6f" % (gx_num,gy_num,gz_num)
print " Analytic %10.6f %10.6f %10.6f" % (gx,gy,gz)
print "The maximum error in the gradient calculation is ",maxerr
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():
#from PyQuante.Basis.sto3g import basis_data
from PyQuante.Basis.p631ss import basis_data
r = 1/0.52918
atoms=Molecule('h2o',atomlist = [(8,(0,0,0)),(1,(r,0,0)),(1,(0,r,0))])
inttol = 1e-6 # Tolerance to which integrals must be equal
bfs = getbasis(atoms,basis_data)
print "Int times: "
t0 = time()
int0 = get2ints(bfs,chgpcc)
t1 = time()
print "CHGP Ints: ",t1-t0
int1 = get2ints(bfs,cryscc)
t2 = time()
print "CRys Ints: ",t2-t1
assert maxdiff(int0,int1)<inttol
int1 = get2ints(bfs,ccc)
t3 = time()
print "CINTS Ints: ",t3-t2
assert maxdiff(int0,int1)<inttol
ints1 = get2ints(bfs,hgpcc)
t4 = time()
print "HGP Ints: ",t4-t3
assert maxdiff(int0,int1)<inttol
int1 = get2ints(bfs,ryscc)
t5 = time()
print "Rys Ints: ",t5-t4
assert maxdiff(int0,int1)<inttol
int1 = get2ints(bfs,pycc)
t6 = time()
print "Py Ints: ",t6-t5
assert maxdiff(int0,int1)<inttol
def test():
#from PyQuante.Basis.sto3g import basis_data
from PyQuante.Basis.p631ss import basis_data
r = 1 / 0.52918
atoms = Molecule('h2o',
atomlist=[(8, (0, 0, 0)), (1, (r, 0, 0)), (1, (0, r, 0))])
inttol = 1e-6 # Tolerance to which integrals must be equal
bfs = getbasis(atoms, basis_data)
print "Int times: "
t0 = time()
int0 = get2ints(bfs, chgpcc)
t1 = time()
print "CHGP Ints: ", t1 - t0
int1 = get2ints(bfs, cryscc)
t2 = time()
print "CRys Ints: ", t2 - t1
assert maxdiff(int0, int1) < inttol
int1 = get2ints(bfs, ccc)
t3 = time()
print "CINTS Ints: ", t3 - t2
assert maxdiff(int0, int1) < inttol
ints1 = get2ints(bfs, hgpcc)
t4 = time()
print "HGP Ints: ", t4 - t3
assert maxdiff(int0, int1) < inttol
int1 = get2ints(bfs, ryscc)
t5 = time()
print "Rys Ints: ", t5 - t4
assert maxdiff(int0, int1) < inttol
int1 = get2ints(bfs, pycc)
t6 = time()
print "Py Ints: ", t6 - t5
assert maxdiff(int0, int1) < inttol
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 bfs_filter(natom, atoms, basis_data):
symlist = {
'S' : [1],
'P' : [1,0,0],
#'P' : [1,1,1],
'D' : [1,0,0,1,0,1],
'F' : [0,0,0,0,0,0,0,0,0,0],
}
import PyQuante.Basis.Tools as tools
basis_info = tools.get_basis_data(basis_data)[natom]
bfs_sym = []
for sym in basis_info:
bfs_sym += symlist[sym[0]]
bfs_sym = 2*bfs_sym
bfs0 = getbasis(atoms,basis_data)
M = len(bfs0)
bfs = []
for il in range(M):
if bfs_sym[il]==1:
bfs.append(bfs0[il])
return bfs
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 __init__(self, name='molecule', atomlist=[], **opts):
self.name = name
self.atoms = []
self.basis = []
self.grid = None
units = opts.get('units', 'bohr')
units = units.lower()[:4]
assert units in allowed_units
self.units = units
if atomlist: self.add_atuples(atomlist)
self.charge = int(opts.get('charge', 0))
self.multiplicity = int(opts.get('multiplicity', 1))
# basis set
self.bfs = None
self.basis_name = None
if 'basis' in opts.keys():
self.bfs = getbasis(self, opts['basis'])
self.basis_name = opts['basis']
# method
self.method = None
if 'method' in opts.keys():
self.method = opts['method']
return
def __init__(self,name='molecule',atomlist=[],**opts):
self.name = name
self.atoms = []
self.basis = []
self.grid = None
units = opts.get('units','bohr')
units = units.lower()[:4]
assert units in allowed_units
self.units = units
if atomlist: self.add_atuples(atomlist)
self.charge = int(opts.get('charge',0))
self.multiplicity = int(opts.get('multiplicity',1))
# basis set
self.bfs = None
self.basis_name = None
if 'basis' in opts.keys():
self.bfs = getbasis(self,opts['basis'])
self.basis_name = opts['basis']
# method
self.method = None
if 'method' in opts.keys():
self.method = opts['method']
return
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 new_grid_tester():
from PyQuante.TestMolecules import he,h2
from PyQuante.MolecularGrid import MolecularGrid
from PyQuante.Ints import getbasis
from PyQuante import SCF
mol = h2
gr = MolecularGrid(mol,do_grad_dens=True)
gr2 = MG2(mol,do_grad_dens=True)
print "test_length: ",test_length(gr,gr2)
print "test_distance: ",test_distance(gr,gr2)
bfs = getbasis(mol)
gr.set_bf_amps(bfs)
gr2.add_basis(bfs)
print "test_bfgrid: ",test_bfgrid(gr,gr2)
# This is a little weird, but now use the hf density matrix to
# test whether the densities are the same
hf = SCF(mol)
hf.iterate()
gr.setdens(hf.dmat)
gr2.set_density(hf.dmat)
print "test_density: ",test_density(gr,gr2)
print "test_gamma: ",test_gamma(gr,gr2)
def new_grid_tester():
from PyQuante.TestMolecules import he,h2
from PyQuante.MolecularGrid import MolecularGrid
from PyQuante.Ints import getbasis
from PyQuante import SCF
mol = h2
gr = MolecularGrid(mol,do_grad_dens=True)
gr2 = MG2(mol,do_grad_dens=True)
print "test_length: ",test_length(gr,gr2)
print "test_distance: ",test_distance(gr,gr2)
bfs = getbasis(mol)
gr.set_bf_amps(bfs)
gr2.add_basis(bfs)
print "test_bfgrid: ",test_bfgrid(gr,gr2)
# This is a little weird, but now use the hf density matrix to
# test whether the densities are the same
hf = SCF(mol)
hf.iterate()
gr.setdens(hf.dmat)
gr2.set_density(hf.dmat)
print "test_density: ",test_density(gr,gr2)
print "test_gamma: ",test_gamma(gr,gr2)
def oep_uhf_an(atoms,orbsa,orbsb,**opts):
"""oep_hf - Form the optimized effective potential for HF exchange.
Implementation of Wu and Yang's Approximate Newton Scheme
from J. Theor. Comp. Chem. 2, 627 (2003).
oep_uhf(atoms,orbs,**opts)
atoms A Molecule object containing a list of the atoms
orbs A matrix of guess orbitals
Options
-------
bfs None The basis functions to use for the wfn
pbfs None The basis functions to use for the pot
basis_data None The basis data to use to construct bfs
integrals None The one- and two-electron integrals to use
If not None, S,h,Ints
"""
maxiter = opts.get('maxiter',100)
tol = opts.get('tol',1e-5)
ETemp = opts.get('ETemp',False)
bfs = opts.get('bfs',None)
if not bfs:
basis = opts.get('basis',None)
bfs = getbasis(atoms,basis)
# The basis set for the potential can be set different from
# that used for the wave function
pbfs = opts.get('pbfs',None)
if not pbfs: pbfs = bfs
npbf = len(pbfs)
integrals = opts.get('integrals',None)
if integrals:
S,h,Ints = integrals
else:
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
nclosed,nopen = atoms.get_closedopen()
nalpha,nbeta = nclosed+nopen,nclosed
Enuke = atoms.get_enuke()
# Form the OEP using Yang/Wu, PRL 89 143002 (2002)
nbf = len(bfs)
norb = nbf
ba = zeros(npbf,'d')
bb = zeros(npbf,'d')
# Form and store all of the three-center integrals
# we're going to need.
# These are <ibf|gbf|jbf> (where 'bf' indicates basis func,
# as opposed to MO)
# N^3 storage -- obviously you don't want to do this for
# very large systems
Gij = []
for g in range(npbf):
gmat = zeros((nbf,nbf),'d')
Gij.append(gmat)
gbf = pbfs[g]
for i in range(nbf):
ibf = bfs[i]
for j in range(i+1):
jbf = bfs[j]
gij = three_center(ibf,gbf,jbf)
gmat[i,j] = gij
gmat[j,i] = gij
# Compute the Fermi-Amaldi potential based on the LDA density.
# We're going to form this matrix from the Coulombic matrix that
# arises from the input orbitals. D0 and J0 refer to the density
# matrix and corresponding Coulomb matrix
D0 = mkdens(orbsa,0,nalpha)+mkdens(orbsb,0,nbeta)
J0 = getJ(Ints,D0)
Vfa = ((nel-1.)/nel)*J0
H0 = h + Vfa
eold = 0
for iter in range(maxiter):
Hoepa = get_Hoep(ba,H0,Gij)
Hoepb = get_Hoep(ba,H0,Gij)
orbea,orbsa = geigh(Hoepa,S)
orbeb,orbsb = geigh(Hoepb,S)
if ETemp:
efermia = get_efermi(2*nalpha,orbea,ETemp)
occsa = get_fermi_occs(efermia,orbea,ETemp)
Da = mkdens_occs(orbsa,occsa)
efermib = get_efermi(2*nbeta,orbeb,ETemp)
occsb = get_fermi_occs(efermib,orbeb,ETemp)
Db = mkdens_occs(orbsb,occsb)
entropy = 0.5*(get_entropy(occsa,ETemp)+get_entropy(occsb,ETemp))
else:
Da = mkdens(orbsa,0,nalpha)
Db = mkdens(orbsb,0,nbeta)
J = getJ(Ints,Da) + getJ(Ints,Db)
Ka = getK(Ints,Da)
Kb = getK(Ints,Db)
energy = (trace2(2*h+J-Ka,Da)+trace2(2*h+J-Kb,Db))/2\
+Enuke
if ETemp: energy += entropy
if abs(energy-eold) < tol:
break
else:
eold = energy
logging.debug("OEP AN Opt: %d %f" % (iter,energy))
# Do alpha and beta separately
# Alphas
dV_ao = J-Ka-Vfa
dV = matrixmultiply(orbsa,matrixmultiply(dV_ao,transpose(orbsa)))
X = zeros((nbf,nbf),'d')
c = zeros(nbf,'d')
for k in range(nbf):
Gk = matrixmultiply(orbsa,matrixmultiply(Gij[k],
transpose(orbsa)))
for i in range(nalpha):
for a in range(nalpha,norb):
c[k] += dV[i,a]*Gk[i,a]/(orbea[i]-orbea[a])
for l in range(nbf):
Gl = matrixmultiply(orbsa,matrixmultiply(Gij[l],
transpose(orbsa)))
for i in range(nalpha):
for a in range(nalpha,norb):
X[k,l] += Gk[i,a]*Gl[i,a]/(orbea[i]-orbea[a])
# This should actually be a pseudoinverse...
ba = solve(X,c)
# Betas
dV_ao = J-Kb-Vfa
dV = matrixmultiply(orbsb,matrixmultiply(dV_ao,transpose(orbsb)))
X = zeros((nbf,nbf),'d')
c = zeros(nbf,'d')
for k in range(nbf):
Gk = matrixmultiply(orbsb,matrixmultiply(Gij[k],
transpose(orbsb)))
for i in range(nbeta):
for a in range(nbeta,norb):
c[k] += dV[i,a]*Gk[i,a]/(orbeb[i]-orbeb[a])
for l in range(nbf):
Gl = matrixmultiply(orbsb,matrixmultiply(Gij[l],
transpose(orbsb)))
for i in range(nbeta):
for a in range(nbeta,norb):
X[k,l] += Gk[i,a]*Gl[i,a]/(orbeb[i]-orbeb[a])
# This should actually be a pseudoinverse...
bb = solve(X,c)
logging.info("Final OEP energy = %f" % energy)
return energy,(orbea,orbeb),(orbsa,orbsb)
def oep_hf_an(atoms,orbs,**opts):
"""oep_hf - Form the optimized effective potential for HF exchange.
Implementation of Wu and Yang's Approximate Newton Scheme
from J. Theor. Comp. Chem. 2, 627 (2003).
oep_hf(atoms,orbs,**opts)
atoms A Molecule object containing a list of the atoms
orbs A matrix of guess orbitals
Options
-------
bfs None The basis functions to use for the wfn
pbfs None The basis functions to use for the pot
basis_data None The basis data to use to construct bfs
integrals None The one- and two-electron integrals to use
If not None, S,h,Ints
"""
maxiter = opts.get('maxiter',100)
tol = opts.get('tol',1e-5)
bfs = opts.get('bfs',None)
if not bfs:
basis = opts.get('basis',None)
bfs = getbasis(atoms,basis)
# The basis set for the potential can be set different from
# that used for the wave function
pbfs = opts.get('pbfs',None)
if not pbfs: pbfs = bfs
npbf = len(pbfs)
integrals = opts.get('integrals',None)
if integrals:
S,h,Ints = integrals
else:
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
nocc,nopen = atoms.get_closedopen()
Enuke = atoms.get_enuke()
# Form the OEP using Yang/Wu, PRL 89 143002 (2002)
nbf = len(bfs)
norb = nbf
bp = zeros(nbf,'d')
bvec = opts.get('bvec',None)
if bvec:
assert len(bvec) == npbf
b = array(bvec)
else:
b = zeros(npbf,'d')
# Form and store all of the three-center integrals
# we're going to need.
# These are <ibf|gbf|jbf> (where 'bf' indicates basis func,
# as opposed to MO)
# N^3 storage -- obviously you don't want to do this for
# very large systems
Gij = []
for g in range(npbf):
gmat = zeros((nbf,nbf),'d')
Gij.append(gmat)
gbf = pbfs[g]
for i in range(nbf):
ibf = bfs[i]
for j in range(i+1):
jbf = bfs[j]
gij = three_center(ibf,gbf,jbf)
gmat[i,j] = gij
gmat[j,i] = gij
# Compute the Fermi-Amaldi potential based on the LDA density.
# We're going to form this matrix from the Coulombic matrix that
# arises from the input orbitals. D0 and J0 refer to the density
# matrix and corresponding Coulomb matrix
D0 = mkdens(orbs,0,nocc)
J0 = getJ(Ints,D0)
Vfa = (2*(nel-1.)/nel)*J0
H0 = h + Vfa
b = zeros(nbf,'d')
eold = 0
for iter in range(maxiter):
Hoep = get_Hoep(b,H0,Gij)
orbe,orbs = geigh(Hoep,S)
D = mkdens(orbs,0,nocc)
Vhf = get2JmK(Ints,D)
energy = trace2(2*h+Vhf,D)+Enuke
if abs(energy-eold) < tol:
break
else:
eold = energy
logging.debug("OEP AN Opt: %d %f" % (iter,energy))
dV_ao = Vhf-Vfa
dV = matrixmultiply(transpose(orbs),matrixmultiply(dV_ao,orbs))
X = zeros((nbf,nbf),'d')
c = zeros(nbf,'d')
Gkt = zeros((nbf,nbf),'d')
for k in range(nbf):
# This didn't work; in fact, it made things worse:
Gk = matrixmultiply(transpose(orbs),matrixmultiply(Gij[k],orbs))
for i in range(nocc):
for a in range(nocc,norb):
c[k] += dV[i,a]*Gk[i,a]/(orbe[i]-orbe[a])
for l in range(nbf):
Gl = matrixmultiply(transpose(orbs),matrixmultiply(Gij[l],orbs))
for i in range(nocc):
for a in range(nocc,norb):
X[k,l] += Gk[i,a]*Gl[i,a]/(orbe[i]-orbe[a])
# This should actually be a pseudoinverse...
b = solve(X,c)
logging.info("Final OEP energy = %f" % energy)
return energy,orbe,orbs
def oep(atoms,orbs,energy_func,grad_func=None,**opts):
"""oep - Form the optimized effective potential for a given energy expression
oep(atoms,orbs,energy_func,grad_func=None,**opts)
atoms A Molecule object containing a list of the atoms
orbs A matrix of guess orbitals
energy_func The function that returns the energy for the given method
grad_func The function that returns the force for the given method
Options
-------
verbose False Output terse information to stdout (default)
True Print out additional information
ETemp False Use ETemp value for finite temperature DFT (default)
float Use (float) for the electron temperature
bfs None The basis functions to use. List of CGBF's
basis_data None The basis data to use to construct bfs
integrals None The one- and two-electron integrals to use
If not None, S,h,Ints
"""
verbose = opts.get('verbose',False)
ETemp = opts.get('ETemp',False)
opt_method = opts.get('opt_method','BFGS')
bfs = opts.get('bfs',None)
if not bfs:
basis = opts.get('basis',None)
bfs = getbasis(atoms,basis)
# The basis set for the potential can be set different from
# that used for the wave function
pbfs = opts.get('pbfs',None)
if not pbfs: pbfs = bfs
npbf = len(pbfs)
integrals = opts.get('integrals',None)
if integrals:
S,h,Ints = integrals
else:
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
nocc,nopen = atoms.get_closedopen()
Enuke = atoms.get_enuke()
# Form the OEP using Yang/Wu, PRL 89 143002 (2002)
nbf = len(bfs)
norb = nbf
bp = zeros(nbf,'d')
bvec = opts.get('bvec',None)
if bvec:
assert len(bvec) == npbf
b = array(bvec)
else:
b = zeros(npbf,'d')
# Form and store all of the three-center integrals
# we're going to need.
# These are <ibf|gbf|jbf> (where 'bf' indicates basis func,
# as opposed to MO)
# N^3 storage -- obviously you don't want to do this for
# very large systems
Gij = []
for g in range(npbf):
gmat = zeros((nbf,nbf),'d')
Gij.append(gmat)
gbf = pbfs[g]
for i in range(nbf):
ibf = bfs[i]
for j in range(i+1):
jbf = bfs[j]
gij = three_center(ibf,gbf,jbf)
gmat[i,j] = gij
gmat[j,i] = gij
# Compute the Fermi-Amaldi potential based on the LDA density.
# We're going to form this matrix from the Coulombic matrix that
# arises from the input orbitals. D0 and J0 refer to the density
# matrix and corresponding Coulomb matrix
D0 = mkdens(orbs,0,nocc)
J0 = getJ(Ints,D0)
Vfa = (2*(nel-1.)/nel)*J0
H0 = h + Vfa
b = fminBFGS(energy_func,b,grad_func,
(nbf,nel,nocc,ETemp,Enuke,S,h,Ints,H0,Gij),
logger=logging)
energy,orbe,orbs = energy_func(b,nbf,nel,nocc,ETemp,Enuke,
S,h,Ints,H0,Gij,return_flag=1)
return energy,orbe,orbs
energy = get_energy(h,F,D,enuke)
print "%d %f" % (i,energy)
if abs(energy-eold) < 1e-4: break
eold = energy
print "Final HF energy for system %s is %f" % (atoms.name,energy)
return energy,orbe,orbs
# Data
Li_x1 = -0.200966
H_x1 = 1.399033
Li_x2 = -0.351691
H_x2 = 2.448309
# Construct a molecule:
LiH1 = Molecule('LiH1',[('Li',(Li_x1,0,0)),('H',(H_x1,0,0))],units='Angs')
bfs1 = getbasis(LiH1)
S1,h1,Ints1 = getints(bfs1,LiH1)
simple_hf(LiH1,S1,h1,Ints1)
# Make another molecule
LiH2 = Molecule('LiH2',[('Li',(Li_x2,0,0)),('H',(H_x2,0,0))],units='Angs')
bfs2 = getbasis(LiH2)
S2,h2,Ints2 = getints(bfs2,LiH2)
simple_hf(LiH2,S2,h2,Ints2)
# Make a superset of the two basis sets:
bfs_big = bfs1 + bfs2
# and make a basis set with it:
S1a,h1a,Ints1a = getints(bfs_big,LiH1)
simple_hf(LiH1,S1a,h1a,Ints1a)
from PyQuante import Molecule
from PyQuante.Ints import getbasis
h2 = Molecule('h2',[('H',(0,0,-0.5)),('H',(0,0,0.5))],units='Angs')
basis = getbasis(h2,basis_data='sto-3g')
nbf = len(basis)
h2.inertial()
print "STO-3G z"
for i in range(nbf):
for j in range(nbf):
print i,j,basis[i].multipole(basis[j],0,0,1)
# Sheesh! I don't have 6-31g in PyQuante
print '6-31G CH4 1'
ch4 = Molecule('ch4',
[('C',(0.0, 0.0, 0.0)),
('H',(0.0, 0.0, 1.083658)),
('H',(1.021683, 0.0, -0.361219)),
('H',(-0.510841, 0.884804, -0.361219)),
('H',(-0.510841,-0.884804, -0.361219)),],
units='Angs')
ch4.inertial()
# This should give the same results, but without the inertial coordinate
# transformation
#ch4 = Molecule('ch4',
# [(6,( 0.0000000000,-0.0000000781, 0.0000001487)),
# (1,( 0.0000000000,-0.6085461813,-1.9553066848)),
molec = Molecule('mol',[(K,(0,0,0))])
# Create a basis for this molecule
# Access the CGBF atributes of the CGBF number n by doing
# basis.bfs[CGBF_n].atribute (or, since it has some operator overloading defined,
# basis[n] = basis.bfs[n])
# E.g. basis.bfs[0].powers (basis[0].powers)
# One can also access the contraction coefficients and the exponents of the
# PGBF making up the CGBF by doing
# basis[CGBF_n].pcoefs[PGBF_i]
# basis[CGBF_n].pexps[PGBF_i]
# Use "6-31g**" for "best" results
# Use "STO-3G" for debbuging
bas = getbasis(molec,basis_data="6-31g**")
# Grab length of basis and number of electrons and print - some of this
# obviously will not make sense if there's more than one type of atom
lenBasis = 2*len(bas)
nEle = molec.get_nel()
nucNum = nEle # Nuclear number - one of the reasons this only works
# for atoms.
# If we want molecules, we must be able to change this
# according to the molecule
lenNPartBasis = math.factorial(lenBasis)/(math.factorial(nEle) * \
math.factorial(lenBasis-nEle) )
print "\n"
print "Using a single particle spatial basis consisting of", lenBasis/2, \
"contracted gaussians."
def test():
from PyQuante import Molecule
from mpi4py import MPI
############################
# Initialize MPI
############################
comm = MPI.COMM_WORLD
rank = comm.rank
############################
if rank == 0:
print '\n'
print '#' * 60
print '# Parallel PyQuante'
print '# Integral calculation with MPI'
print '#' * 60
tinit = time.time()
print '\n'
#####################################
# Creates the molecule
#####################################
mol = 'benzene.xyz'
units = 'angs'
basis_set = '6-31g'
# read the xyz file of the molecule
if rank == 0:
print '\t Read molecule position'
f = open(mol, 'r')
data = f.readlines()
f.close
# create the molecule object
xyz = []
for i in range(2, len(data)):
d = data[i].split()
xyz.append((d[0], (float(d[1]), float(d[2]), float(d[3]))))
natom = len(xyz)
mol = Molecule(name='molecule', units=units)
mol.add_atuples(xyz)
nelec = mol.get_nel()
#####################################
# get the basis function
#####################################
basis = getbasis(mol, basis_set)
nbfs = len(basis)
nclosed, nopen = mol.get_closedopen()
nocc = nclosed
#####################################
# Print for debug
#####################################
if rank == 0:
print '\t Basis %s' % basis_set
print '\t %d basis functions' % (nbfs)
print '\t %d shells\n ' % (len(basis.shells))
if 0:
for i in range(nbfs):
print basis[i]
comm.barrier()
#####################################
# compute all the integrals
#####################################
S, h, Ints = getints_mpi(basis, mol, rank, comm, _debug_=True)
comm.barrier()
if rank == 0:
tfinal = time.time()
print '\n\t Total computation time %f ' % (tfinal - tinit)
def EN2(molecule, **kwargs): #
"General wrapper for the simple CI method"
nalpha, nbeta = molecule.get_alphabeta()
bfs = getbasis(molecule)
S, h, Ints = getints(bfs, molecule)
energy, (orbea, orbeb), (orbsa, orbsb) = uhf(molecule,
integrals=(S, h, Ints),
bfs=bfs,
**kwargs)
EHF = energy
print "The Hatree-Fock energy is ", EHF
#compute the transformed molecular orbital integrals
aamoints, nbf = TransformInts(Ints, orbsa, orbsa, nalpha)
bbmoints, nbf = TransformInts(Ints, orbsb, orbsb, nbeta)
abmoints, nbf = TransformInts(Ints, orbsa, orbsb, nalpha)
#Initialize the fractional occupations:
Yalpha = zeros((nbf), 'd')
Ybeta = zeros((nbf), 'd')
#set up the occupied and virtual orbitals
aoccs = range(nalpha)
boccs = range(nbeta)
avirt = range(nalpha, nbf) #numbers of alpha virtual orbitals
bvirt = range(nbeta, nbf) #numbers of beta virtual orbitals
######## Computation of the primary energy correction #########
#Set initial correction terms to zero
Ec1 = 0.
sum = 0.
z = 1.
#compute correction term for two alpha electrons
for a in aoccs:
for b in xrange(a):
for r in avirt:
for s in xrange(nalpha, r):
arbs = aamoints[ijkl2intindex(a, r, b, s)]
asbr = aamoints[ijkl2intindex(a, s, b, r)]
rraa = aamoints[ijkl2intindex(r,r,a,a)] - \
aamoints[ijkl2intindex(r,a,a,r)]
rrbb = aamoints[ijkl2intindex(r,r,b,b)] - \
aamoints[ijkl2intindex(r,b,b,r)]
ssaa = aamoints[ijkl2intindex(s,s,a,a)] - \
aamoints[ijkl2intindex(s,a,a,s)]
ssbb = aamoints[ijkl2intindex(s,s,b,b)] - \
aamoints[ijkl2intindex(s,b,b,s)]
rrss = aamoints[ijkl2intindex(r,r,s,s)] - \
aamoints[ijkl2intindex(r,s,s,r)]
aabb = aamoints[ijkl2intindex(a,a,b,b)] - \
aamoints[ijkl2intindex(a,b,b,a)]
eigendif = (orbea[r] + orbea[s] - orbea[a] - orbea[b])
delcorr = (-rraa - rrbb - ssaa - ssbb + rrss + aabb)
delta = eigendif + delcorr * z
Eio = (arbs - asbr)
x = -Eio / delta
if abs(x) > 1:
print "Warning a large x value has been ",\
"discovered with x = ",x
x = choose(x < 1, (1, x))
x = choose(x > -1, (-1, x))
sum += x * x
Yalpha[a] -= x * x
Yalpha[b] -= x * x
Yalpha[r] += x * x
Yalpha[s] += x * x
Ec1 += x * Eio
#compute correction term for two beta electrons
for a in boccs:
for b in xrange(a):
for r in bvirt:
for s in xrange(nbeta, r):
arbs = bbmoints[ijkl2intindex(a, r, b, s)]
asbr = bbmoints[ijkl2intindex(a, s, b, r)]
rraa = bbmoints[ijkl2intindex(r,r,a,a)] - \
bbmoints[ijkl2intindex(r,a,a,r)]
rrbb = bbmoints[ijkl2intindex(r,r,b,b)] - \
bbmoints[ijkl2intindex(r,b,b,r)]
ssaa = bbmoints[ijkl2intindex(s,s,a,a)] - \
bbmoints[ijkl2intindex(s,a,a,s)]
ssbb = bbmoints[ijkl2intindex(s,s,b,b)] - \
bbmoints[ijkl2intindex(s,b,b,s)]
rrss = bbmoints[ijkl2intindex(r,r,s,s)] - \
bbmoints[ijkl2intindex(r,s,s,r)]
aabb = bbmoints[ijkl2intindex(a,a,b,b)] - \
bbmoints[ijkl2intindex(a,b,b,a)]
eigendif = (orbeb[r] + orbeb[s] - orbeb[a] - orbeb[b])
delcorr = (-rraa - rrbb - ssaa - ssbb + rrss + aabb)
delta = eigendif + delcorr * z
Eio = (arbs - asbr)
x = -Eio / delta
if abs(x) > 1: print "Warning a large x value has ",\
"been discovered with x = ",x
x = choose(x < 1, (1, x))
x = choose(x > -1, (-1, x))
sum += x * x
Ybeta[a] -= x * x
Ybeta[b] -= x * x
Ybeta[r] += x * x
Ybeta[s] += x * x
Ec1 += x * Eio
#compute correction term for one alpha and one beta electron
for a in aoccs:
for b in boccs:
for r in avirt:
for s in bvirt:
arbs = abmoints[ijkl2intindex(a, r, b, s)]
rraa = aamoints[ijkl2intindex(r,r,a,a)] - \
aamoints[ijkl2intindex(r,a,a,r)]
rrbb = abmoints[ijkl2intindex(r, r, b, b)]
aass = abmoints[ijkl2intindex(a, a, s, s)]
ssbb = bbmoints[ijkl2intindex(s,s,b,b)] - \
bbmoints[ijkl2intindex(s,b,b,s)]
rrss = abmoints[ijkl2intindex(r, r, s, s)]
aabb = abmoints[ijkl2intindex(a, a, b, b)]
eigendif = (orbea[r] + orbeb[s] - orbea[a] - orbeb[b])
delcorr = (-rraa - rrbb - aass - ssbb + rrss + aabb)
delta = eigendif + delcorr * z
Eio = arbs
x = -Eio / delta
if abs(x) > 1: print "Warning a large x value has ",\
"been discovered with x = ",x
x = choose(x < 1, (1, x))
x = choose(x > -1, (-1, x))
sum += x * x
Yalpha[a] -= x * x
Ybeta[b] -= x * x
Yalpha[r] += x * x
Ybeta[s] += x * x
Ec1 += x * Eio
#compute the fractional occupations of the occupied orbitals
for a in aoccs:
Yalpha[a] = 1 + Yalpha[a]
for b in boccs:
Ybeta[b] = 1 + Ybeta[b]
#for a in xrange(nbf):
#print "For alpha = ",a,"the fractional occupation is ",Yalpha[a]
#print "For beta = ",a,"the fractional occupation is ",Ybeta[a]
#print the energy and its corrections
E = energy + Ec1
print "The total sum of excitations is ", sum
print "The primary correlation correction is ", Ec1
print "The total energy is ", E
return E
def rohf(atoms,**opts):
"""\
rohf(atoms,**opts) - Restriced Open Shell Hartree Fock
atoms A Molecule object containing the molecule
"""
ConvCriteria = opts.get('ConvCriteria',1e-5)
MaxIter = opts.get('MaxIter',40)
DoAveraging = opts.get('DoAveraging',True)
averaging = opts.get('averaging',0.95)
verbose = opts.get('verbose',True)
bfs = opts.get('bfs',None)
if not bfs:
basis_data = opts.get('basis_data',None)
bfs = getbasis(atoms,basis_data)
nbf = len(bfs)
integrals = opts.get('integrals', None)
if integrals:
S,h,Ints = integrals
else:
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
nalpha,nbeta = atoms.get_alphabeta()
S,h,Ints = getints(bfs,atoms)
orbs = opts.get('orbs',None)
if orbs is None:
orbe,orbs = geigh(h,S)
norbs = nbf
enuke = atoms.get_enuke()
eold = 0.
if verbose: print "ROHF calculation on %s" % atoms.name
if verbose: print "Nbf = %d" % nbf
if verbose: print "Nalpha = %d" % nalpha
if verbose: print "Nbeta = %d" % nbeta
if verbose: print "Averaging = %s" % DoAveraging
print "Optimization of HF orbitals"
for i in xrange(MaxIter):
if verbose: print "SCF Iteration:",i,"Starting Energy:",eold
Da = mkdens(orbs,0,nalpha)
Db = mkdens(orbs,0,nbeta)
if DoAveraging:
if i:
Da = averaging*Da + (1-averaging)*Da0
Db = averaging*Db + (1-averaging)*Db0
Da0 = Da
Db0 = Db
Ja = getJ(Ints,Da)
Jb = getJ(Ints,Db)
Ka = getK(Ints,Da)
Kb = getK(Ints,Db)
Fa = h+Ja+Jb-Ka
Fb = h+Ja+Jb-Kb
energya = get_energy(h,Fa,Da)
energyb = get_energy(h,Fb,Db)
eone = (trace2(Da,h) + trace2(Db,h))/2
etwo = (trace2(Da,Fa) + trace2(Db,Fb))/2
energy = (energya+energyb)/2 + enuke
print i,energy,eone,etwo,enuke
if abs(energy-eold) < ConvCriteria: break
eold = energy
Fa = ao2mo(Fa,orbs)
Fb = ao2mo(Fb,orbs)
# Building the approximate Fock matrices in the MO basis
F = 0.5*(Fa+Fb)
K = Fb-Fa
# The Fock matrix now looks like
# F-K | F + K/2 | F
# ---------------------------------
# F + K/2 | F | F - K/2
# ---------------------------------
# F | F - K/2 | F + K
# Make explicit slice objects to simplify this
do = slice(0,nbeta)
so = slice(nbeta,nalpha)
uo = slice(nalpha,norbs)
F[do,do] -= K[do,do]
F[uo,uo] += K[uo,uo]
F[do,so] += 0.5*K[do,so]
F[so,do] += 0.5*K[so,do]
F[so,uo] -= 0.5*K[so,uo]
F[uo,so] -= 0.5*K[uo,so]
orbe,mo_orbs = eigh(F)
orbs = matrixmultiply(orbs,mo_orbs)
if verbose:
print "Final ROHF energy for system %s is %f" % (atoms.name,energy)
return energy,orbe,orbs
def main(argv):
parser = argparse.ArgumentParser(
description='Hartree Fock Calculation from scratch')
# molecule information
parser.add_argument('mol', help='xyz file of the molecule', type=str)
parser.add_argument('-basis',
default='sto-3g',
help='basis set to be used in the calculation',
type=str)
parser.add_argument('-charge',
default=0,
help='Charge of the system',
type=float)
parser.add_argument('-units',
default='angs',
help='Units in the xyz file',
type=str)
# HF calculations
parser.add_argument('-MaxIter',
default=100,
help='Maximum number of SCF iterations',
type=int)
parser.add_argument('-eps_SCF',
default=1E-4,
help='Criterion for SCF termination',
type=float)
# field information
parser.add_argument('-ffreq',
default=0.1,
help='Frequency of the field',
type=float)
parser.add_argument('-fint',
default=0.05,
help='Intensity of the field',
type=float)
parser.add_argument('-ft0',
default=0.5,
help='center of the field for gsin',
type=float)
parser.add_argument('-fsigma',
default=0.25,
help='sigma of the field for gsin',
type=float)
parser.add_argument('-fform', default='sin', help='field form', type=str)
parser.add_argument('-fdir',
default='x',
help='direction of the field',
type=str)
# Propagation
parser.add_argument('-tmax',
default=200,
help='maximum evolution time',
type=float)
parser.add_argument('-nT',
default=200,
help='number of time step',
type=int)
parser.add_argument('-time_unit',
default='au',
help='unit of tmax',
type=str)
# export
parser.add_argument('-nb_print_mo',
default=10,
help='Number of orbitals to be written',
type=int)
'''
Possible basis
'3-21g' 'sto3g' 'sto-3g' 'sto-6g'
'6-31g' '6-31g**' '6-31g(d,p)' '6-31g**++' '6-31g++**' '6-311g**' '6-311g++(2d,2p)'
'6-311g++(3d,3p)' '6-311g++(3df,3pd)'
'lacvp'
'ccpvdz' 'cc-pvdz' 'ccpvtz' 'cc-pvtz' 'ccpvqz' 'cc-pvqz' 'ccpv5z' 'cc-pv5z' 'ccpv6z' 'cc-pv6z'
'augccpvdz' 'aug-cc-pvdz' 'augccpvtz' 'aug-cc-pvtz' 'augccpvqz'
'aug-cc-pvqz' 'augccpv5z' 'aug-cc-pv5z' 'augccpv6z' 'aug-cc-pv6z'
'dzvp':'dzvp',
'''
# done
args = parser.parse_args()
print '\n\n=================================================='
print '== PyQuante - Time-dependent hartree-fock =='
print '==================================================\n'
#-------------------------------------------------------------------------------------------
#
# PREPARE SIMULATIONS
#
#-------------------------------------------------------------------------------------------
##########################################################
## Read Molecule
##########################################################
# read the xyz file of the molecule
print '\t Read molecule position'
f = open(args.mol, 'r')
data = f.readlines()
f.close
# get the molecule name
name_mol = re.split(r'\.|/', args.mol)[-2]
# create the molecule object
xyz = []
for i in range(2, len(data)):
d = data[i].split()
xyz.append((d[0], (float(d[1]), float(d[2]), float(d[3]))))
natom = len(xyz)
mol = Molecule(name=name_mol, units=args.units)
mol.add_atuples(xyz)
mol.set_charge(args.charge)
nelec = mol.get_nel()
if np.abs(args.charge) == 1:
mol.set_multiplicity(2)
if args.charge > 1:
print 'charge superior to one are not implemented'
# get the basis function
bfs = getbasis(mol, args.basis)
nbfs = len(bfs)
nclosed, nopen = mol.get_closedopen()
nocc = nclosed
print '\t\t Molecule %s' % args.mol
print '\t\t Basis %s' % args.basis
print '\t\t %d basis functions' % (nbfs)
if _print_basis_:
for i in range(nbfs):
print bfs[i]
# compute all the integrals
print '\n\t Compute the integrals and form the matrices'
S, Hcore, Ints = getints(bfs, mol)
print '\t Compute the transition dipole moments'
mu_at = compute_dipole_atoms(bfs, args.fdir)
##########################################################
## Compute the HF GROUND STATE
##########################################################
print '\n\t Compute the ground state HF Ground State\n\t',
print '-' * 50
L, C, Cp, F0, F0p, D, Dp, P, X = rhf(mol,
bfs,
S,
Hcore,
Ints,
MaxIter=args.MaxIter,
eps_SCF=args.eps_SCF)
print '\t Energy of the HF orbitals\n\t',
print '-' * 50
index_homo = nocc - 1
nb_print = int(min(nbfs, args.nb_print_mo) / 2)
for ibfs in range(index_homo - nb_print + 1, index_homo + nb_print + 1):
print '\t\t orb %02d \t occ %1.1f \t\t Energy %1.3f Ha' % (
ibfs, np.abs(2 * P[ibfs, ibfs].real), L[ibfs].real)
# store the field free eigenstates
C0 = np.copy(C)
C0p = np.copy(Cp)
# invert of the X matrix
Xm1 = np.linalg.inv(X)
##########################################################
## Transform the matrices in the OB
##########################################################
# pass the other matrices as well
Hcore_p = simx(Hcore, X, 'T')
mu_at_p = simx(mu_at, X, 'T')
# copy the Fock matrix
Fp = np.copy(F0p)
# transtion matrix at t=0
mup = mu_at_p
# check if everythong is ok
if _check_ortho_:
w, u = np.linalg.eigh(F0p)
if np.sum(np.abs(w - L)) > 1E-3:
print '\t == Warning orthonormalisation issue'
sys.exit()
#-------------------------------------------------------------------------------------------
#
# TEST IF EVERYTHING IS OF SO FAR
#
#-------------------------------------------------------------------------------------------
# verify the basis transformation between
# Atomic Orbitals and Orthonormal orbitals
#
if _test_:
print '\n\t Run Check on the matrices'
#print'\n'
#print'='*40
print '\t\t Verify the basis transformation from diagonal to AO basis ',
x = np.dot(np.diag(L), np.linalg.inv(C))
x = np.dot(C, x)
x = np.dot(S, x)
if np.abs(np.sum(x - F0)) < 1E-3:
print '\t Check'
else:
print '\t NOT OK'
#print'='*40
if _verbose_:
print '\t\t reconstructed Fock matrix'
print x
print '\t\t original Fock matrix'
print F0
#print'\n\t'
#print'='*40
print '\t\t Verify the basis transformation from AO to diagonal basis ',
y = np.dot(F0, C)
y = np.dot(np.linalg.inv(S), y)
y = np.dot(np.linalg.inv(C), y)
if np.abs(np.sum(y - np.diag(L))) < 1E-3:
print '\t Check'
else:
print '\t NOT OK'
#print'='*40
if _verbose_:
print '\t\t reconstructed eigenvalues'
print y
print '\t\t original eigenvalues'
print L
#
# verify the basis transformation between
# Atomic Orbitals and Orthonormal orbitals
#
if _test_:
#print'\n'
#print'='*40
print '\t\t Verify the basis transformation from AO basis to ORTHO basis ',
#print'='*40
if np.abs(np.sum(D - np.dot(X, np.dot(Dp, X.T)))) < 1E-3:
print '\t Check'
else:
print '\t NOT OK'
if _verbose_:
print '\t\t reconstructed density in the AO'
print np.dot(X, np.dot(Dp, X.T))
print '\t\t Original density in the AO'
print D
#
# verify the basis transformation between
# Atomic Orbitals and Orthonormal orbitals
#
if _test_:
#print'\n'
#print'='*40
print '\t\t Verify the basis transformation from AO basis to ORTHO basis ',
#print'='*40
if np.abs(np.sum(Dp - np.dot(Xm1, np.dot(D, Xm1.T)))) < 1E-3:
print '\t Check'
else:
print '\t NOT OK'
if _verbose_:
print '\t\t reconstructed density in the OB'
print np.dot(Xm1, np.dot(D, Xm1.T))
print '\t\t original density in the OB'
print Dp
# test if the Fock matrix and densitu matrix in OB
# share the same eigenbasis
# due to degeneracies in the density matrix only a few
# eigenvectors might be the same
if _verbose_:
print '\t\t verify that the Fock matrix and the density matrix '
print '\t\t in the ORTHOGONAL BASIS have the same eigenvector',
lf, cf = scla.eigh(F0p)
r = 1E-6 * np.random.rand(nbfs, nbfs)
r += r.T
ld, cd = scla.eigh(Dp + r)
x1 = simx(Dp, cf, 'N')
x2 = simx(F0p, cd, 'N')
s1 = np.sum(np.abs(x1 - np.diag(np.diag(x1))))
s2 = np.sum(np.abs(x2 - np.diag(np.diag(x2))))
if s1 < 1E-6 and s2 < 1E-6:
print '\t\t Check'
else:
print '\t\t NOT OK'
if _verbose_:
print '\t\tDensity matrix in eigenbasis of the Fock matrix'
print np.array_str(x1, suppress_small=True)
print '\t\t\Fock matrix in eigenbasis of the Density matrix'
print np.array_str(x2, suppress_small=True)
print '\n'
print '\t\t',
print '=' * 40
print '\t\teigenvector/eigenvalues of the fock matrix'
print lf
print cf
print ''
print '\t\teigenvector/eigenvalues of the density matrix'
print ld
print cd
print '\t\t',
print '=' * 40
#
# check the initial population of the molecular orbital
#
if _verbose_:
print '\t\t',
print '=' * 40
print '\t\t Initial population of the molecular orbitals'
print '\t\t ',
for i in range(len(P)):
print '%1.3f ' % (P[i, i].real),
print ''
print '\t\t',
print '=' * 40
#
#-------------------------------------------------------------------------------------------
#
# SIMUALTIONS
#
#-------------------------------------------------------------------------------------------
##########################################################
## Define time and outputs
##########################################################
if args.time_unit == 'fs':
tmax_convert = args.tmax * 1E-15 / au2s
elif args.time_unit == 'ps':
tmax_convert = args.tmax * 1E-12 / au2s
elif args.time_unit == 'au':
tmax_convert = args.tmax
# a few shortcut
ffreq = args.ffreq
fint = args.fint
ft0 = args.ft0 * tmax_convert
fsigma = args.fsigma * tmax_convert
fform = args.fform
# readjust the frequency in case it is not specified
if ffreq < 0:
ffreq = L[nocc] - L[nocc - 1]
print '\n\t Field frequency adjusted to %f' % (ffreq)
T = np.linspace(0, tmax_convert, args.nT)
Tplot = np.linspace(0, args.tmax, args.nT)
FIELD = np.zeros(args.nT)
N = np.zeros((nbfs, args.nT))
Q = np.zeros((natom, args.nT))
mu0 = 0
for i in range(natom):
Q[i, :] = mol[i].Z
mu0 += mol[i].Z * mol.atoms[i].r[0]
MU = mu0 * np.ones(args.nT)
dt = T[1] - T[0]
##########################################################
## Loop over time
##########################################################
print '\n'
print '\t Compute the TDHF dynamics'
print '\t Simulation done at %d percent' % (0),
for iT in range(0, args.nT):
################################################################
## TIMER
################################################################
if iT * 10 % int(args.nT) == 0:
sys.stdout.write('\r\t Simulation done at %d percent' %
(iT * 100 / args.nT))
sys.stdout.flush()
################################################################
## Compute the observable
################################################################
# compute the Lowdin atomic charges
for iorb in range(nbfs):
atid = bfs[iorb].atid
Q[atid, iT] -= 2 * Dp[iorb, iorb].real
# compute the population of the orbitals
for iorb in range(nbfs):
N[iorb,
iT] = (np.dot(C0p[:, iorb], np.dot(Dp.real, C0p[:, iorb].T)) /
np.linalg.norm(C0p[:, iorb])**2).real
# compute the instantaneous dipole
MU[iT] -= np.trace(np.dot(mu_at, D)).real
######################################
## Propagation
######################################
if _predict_ and iT < args.nT - 1:
# predict the density matrix
dp = propagate_dm(Dp, Fp, dt, method='relax')
#predicted dm in AO basis
d = np.dot(X, np.dot(dp, X.T))
# value of the field
fp1 = compute_field(T[iT + 1],
ffreq=ffreq,
fint=fint,
t0=ft0,
s=fsigma,
fform=fform)
mup_p1 = mu_at_p * fp1
# predicted fock matrix
fp = compute_F(d, Hcore_p, X, Ints, mup_p1)
# form the intermediate fock matrix
fm = 0.5 * (Fp + fp)
# propagte the density matrix with that
Dp = propagate_dm(Dp, fm, dt, method='relax')
else:
# propagte the density matrix with that
Dp = propagate_dm(Dp, Fp, dt, method='relax')
######################################
## New Density Matrix in AO
######################################
# DM in AO basis
D = np.dot(X, np.dot(Dp, X.T))
######################################
## New Field
######################################
# value of the field
FIELD[iT] = compute_field(T[iT],
ffreq=ffreq,
fint=fint,
t0=ft0,
s=fsigma,
fform=fform)
mup = mu_at_p * FIELD[iT]
######################################
## New Fock Matrix
######################################
# new Fock matrix
Fp = compute_F(D, Hcore_p, X, Ints, mup)
sys.stdout.write('\r\t Simulation done at 100 percent')
# save all the data
print '\n\t Save data\n'
np.savetxt('time.dat', Tplot)
np.savetxt('orb_pops.dat', N)
np.savetxt('charges.dat', Q)
np.savetxt('dipole.dat', MU)
np.savetxt('field.dat', FIELD)
#-------------------------------------------------------------------------------------------
#
# EXPORT THE RESULTS
#
#-------------------------------------------------------------------------------------------
##########################################################
## PLOT THE DATA WITH MATPLOTLIB
##########################################################
if _plot_:
plot(Tplot, FIELD, N, Q, MU, cutlow=0.05, cuthigh=0.9)
##########################################################
## Export the MO in VMD Format
##########################################################
if _export_mo_:
print '\t Export MO Gaussian Cube format'
index_homo = nocc - 1
nb_print = int(min(nbfs, args.nb_print_mo) / 2)
fmo_names = []
for ibfs in range(index_homo - nb_print + 1,
index_homo + nb_print + 1):
if ibfs <= index_homo:
motyp = 'occ'
else:
motyp = 'virt'
file_name = mol.name + '_mo' + '_' + motyp + '_%01d.cube' % (index)
xyz_min, nb_pts, spacing = mesh_orb(file_name, mol, bfs, C0, ibfs)
fmo_names.append(file_name)
##########################################################
## Export the MO
## in bvox Blender format
##########################################################
if _export_blender_:
print '\t Export MO volumetric data for Blender'
bvox_files_mo = []
for fname in fmo_names:
fn = cube2blender(fname)
bvox_files_mo.append(fn)
##########################################################
## Create the
## Blender script to visualize the orbitals
##########################################################
path_to_files = os.getcwd()
pdb_file = name_mol + '.pdb'
create_pdb(pdb_file, args.mol, args.units)
# create the blender file
blname = name_mol + '_mo_volumetric.py'
create_blender_script_mo(blname, xyz_min, nb_pts, spacing,
pdb_file, bvox_files_mo, path_to_files)
##########################################################
## Export the MO DYNAMICS in VMD Format
##########################################################
if _export_mo_dynamics_:
# step increment
nstep_mo = 4
# resolution i.e. point per angstrom
ppa = 1
# just a test
norm = 1 - np.min(N[0, :])
# loop to create all the desired cube files
fdyn_elec, fdyn_hole = [], []
for iT in range(0, args.nT, nstep_mo):
if iT * 10 % int(args.nT) == 0:
sys.stdout.write(
'\r\t Export Cube File \t\t\t\t %d percent done' %
(iT * 100 / args.nT))
sys.stdout.flush()
felec, fhole, xyz_min, nb_pts, spacing = mesh_exc_dens(
mol, bfs, N, C0, iT, nocc, resolution=ppa)
fdyn_elec.append(felec)
fdyn_hole.append(fhole)
sys.stdout.write('\r\t Export Cube File \t\t\t\t 100 percent done\n')
# create the vmd script to animate the voxel
create_vmd_anim(mol.name, args.nT, nstep_mo)
##########################################################
## Export the DYN
## in bvox Blender format
##########################################################
if _export_blender_:
print '\t Export volumetric data for Blender'
# create the bvox files for electron
bvox_files_dyn_elec = []
for fname in fdyn_elec:
fn = cube2blender(fname)
bvox_files_dyn_elec.append(fn)
# create the bvox files for holes
bvox_files_dyn_hole = []
for fname in fdyn_hole:
fn = cube2blender(fname)
bvox_files_dyn_hole.append(fn)
# create the pdb file
pdb_file = name_mol + '.pdb'
create_pdb(pdb_file, args.mol, args.units)
# path to files
path_to_files = os.getcwd()
# create the blender script
blname = name_mol + '_traj_volumetric.py'
create_blender_script_traj(blname, xyz_min, nb_pts, spacing,
pdb_file, bvox_files_dyn_elec,
bvox_files_dyn_hole, path_to_files)
print '\n\n=================================================='
print '== Calculation done =='
print '==================================================\n'
from PyQuante.TestMolecules import h2
from PyQuante.LA2 import geigh,mkdens
from PyQuante.Ints import get2JmK,getbasis,getints
from PyQuante.Convergence import DIIS
from PyQuante.hartree_fock import get_energy
bfs = getbasis(h2,basis="3-21g")
nclosed,nopen = h2.get_closedopen()
nocc = nclosed
nel = h2.get_nel()
S,h,Ints = getints(bfs,h2)
orbe,orbs = geigh(h,S)
enuke = h2.get_enuke()
eold = 0
avg = DIIS(S)
for i in range(20):
D = mkdens(orbs,0,nocc)
G = get2JmK(Ints,D)
F = h+G
F = avg.getF(F,D)
orbe,orbs = geigh(F,S)
energy = get_energy(h,F,D,enuke)
print i,energy,energy-eold
if abs(energy-eold)<1e-5:
break
eold = energy
print "Converged"
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 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)