def __init__(self, molecule, **kwargs):
from PyQuante.Convergence import DIIS
from PyQuante.DFunctionals import need_gradients
self.molecule = molecule
logging.info("DFT calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule, **kwargs)
self.integrals = Integrals(molecule, self.basis_set, **kwargs)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.nel = molecule.get_nel()
self.F = self.h
self.functional = kwargs.get('functional', settings.DFTFunctional)
kwargs['do_grad_dens'] = need_gradients[self.functional]
self.setup_grid(molecule, self.basis_set.get(), **kwargs)
self.dmat = None
self.entropy = None
self.DoAveraging = kwargs.get('DoAveraging', settings.DFTAveraging)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed, nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed, nopen))
self.solver = SolverFactory(nel, nclosed, nopen, self.S, **kwargs)
return
def __init__(self,molecule,**kwargs):
from PyQuante.Convergence import DIIS
from PyQuante.DFunctionals import need_gradients
self.molecule = molecule
logging.info("DFT calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule,**kwargs)
self.integrals = Integrals(molecule,self.basis_set,**kwargs)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.nel = molecule.get_nel()
self.F = self.h
self.functional = kwargs.get('functional',settings.DFTFunctional)
kwargs['do_grad_dens'] = need_gradients[self.functional]
self.setup_grid(molecule,self.basis_set.get(),**kwargs)
self.dmat = None
self.entropy = None
self.DoAveraging = kwargs.get('DoAveraging',settings.DFTAveraging)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed,nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed,nopen))
self.solver = SolverFactory(nel,nclosed,nopen,self.S,**kwargs)
return
class HFHamiltonian(AbstractHamiltonian):
method='HF'
def __init__(self,molecule,**kwargs):
from PyQuante.Convergence import DIIS
self.molecule = molecule
logging.info("HF calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule,**kwargs)
self.integrals = Integrals(molecule,self.basis_set,**kwargs)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.F = self.h
self.dmat = None
self.entropy = None
self.DoAveraging = kwargs.get('DoAveraging',settings.Averaging)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed,nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed,nopen))
self.solver = SolverFactory(nel,nclosed,nopen,self.S,**kwargs)
return
def __repr__(self):
lstr = ['Hamiltonian constructed for method %s' % self.method,
repr(self.molecule),
repr(self.basis_set),
repr(self.iterator)]
return '\n'.join(lstr)
def get_energy(self): return self.energy
def iterate(self,**kwargs):
self.iterator.iterate(self,**kwargs)
if self.iterator.converged:
logging.info("Final HF energy for system %s is %f"%(self.molecule.name,self.energy))
return
def update(self,**kwargs):
from PyQuante.LA2 import trace2
from PyQuante.Ints import getJ,getK
if self.DoAveraging and self.dmat is not None:
self.F = self.Averager.getF(self.F,self.dmat)
self.dmat,self.entropy = self.solver.solve(self.F,**kwargs)
D = self.dmat
self.J = getJ(self.ERI,D)
self.Ej = 2*trace2(D,self.J)
self.K = getK(self.ERI,D)
self.Exc = -trace2(D,self.K)
self.Eone = 2*trace2(D,self.h)
self.F = self.h + 2*self.J - self.K
self.energy = self.Eone + self.Ej + self.Exc + self.Enuke + self.entropy
return
def __init__(self, molecule, **kwargs):
from PyQuante.Convergence import DIIS
self.molecule = molecule
logging.info("HF calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule, **kwargs)
self.integrals = Integrals(molecule, self.basis_set, **kwargs)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.F = self.h
self.dmat = None
self.entropy = None
self.DoAveraging = kwargs.get('DoAveraging', settings.Averaging)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed, nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed, nopen))
self.solver = SolverFactory(nel, nclosed, nopen, self.S, **kwargs)
return
def __init__(self,molecule,**opts):
from PyQuante.Convergence import DIIS
self.molecule = molecule
logging.info("HF calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule,**opts)
self.integrals = Integrals(molecule,self.basis_set,**opts)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.F = self.h
self.dmat = None
self.entropy = None
self.DoAveraging = opts.get('DoAveraging',True)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed,nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed,nopen))
self.solver = SolverFactory(nel,nclosed,nopen,self.S,**opts)
return
class DFTHamiltonian(AbstractHamiltonian):
method = 'DFT'
def __init__(self, molecule, **kwargs):
from PyQuante.Convergence import DIIS
from PyQuante.DFunctionals import need_gradients
self.molecule = molecule
logging.info("DFT calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule, **kwargs)
self.integrals = Integrals(molecule, self.basis_set, **kwargs)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.nel = molecule.get_nel()
self.F = self.h
self.functional = kwargs.get('functional', settings.DFTFunctional)
kwargs['do_grad_dens'] = need_gradients[self.functional]
self.setup_grid(molecule, self.basis_set.get(), **kwargs)
self.dmat = None
self.entropy = None
self.DoAveraging = kwargs.get('DoAveraging', settings.DFTAveraging)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed, nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed, nopen))
self.solver = SolverFactory(nel, nclosed, nopen, self.S, **kwargs)
return
def __repr__(self):
lstr = [
'Hamiltonian constructed for method %s' % self.method,
repr(self.molecule),
repr(self.basis_set),
repr(self.iterator)
]
return '\n'.join(lstr)
def get_energy(self):
return self.energy
def iterate(self, **kwargs):
return self.iterator.iterate(self, **kwargs)
def setup_grid(self, molecule, bfs, **kwargs):
#from PyQuante.MolecularGrid import MolecularGrid
from PyQuante.MG2 import MG2 as MolecularGrid
grid_nrad = kwargs.get('grid_nrad', settings.DFTGridRadii)
grid_fineness = kwargs.get('grid_fineness', settings.DFTGridFineness)
self.gr = MolecularGrid(molecule, grid_nrad, grid_fineness, **kwargs)
self.gr.set_bf_amps(bfs)
return
def update(self, **kwargs):
from PyQuante.LA2 import trace2
from PyQuante.Ints import getJ
from PyQuante.dft import getXC
#self.DoAveraging = kwargs.get('DoAveraging',True)
#if self.DoAveraging:
# self.Averager = DIIS(self.S)
if self.DoAveraging and self.dmat is not None:
self.F = self.Averager.getF(self.F, self.dmat)
self.dmat, self.entropy = self.solver.solve(self.F, **kwargs)
D = self.dmat
self.gr.setdens(D)
self.J = getJ(self.ERI, D)
self.Ej = 2 * trace2(D, self.J)
self.Exc, self.XC = getXC(self.gr,
self.nel,
functional=self.functional)
self.Eone = 2 * trace2(D, self.h)
self.F = self.h + 2 * self.J + self.XC
self.energy = self.Eone + self.Ej + self.Exc + self.Enuke + self.entropy
return
class HFHamiltonian(AbstractHamiltonian):
method = 'HF'
def __init__(self, molecule, **kwargs):
from PyQuante.Convergence import DIIS
self.molecule = molecule
logging.info("HF calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule, **kwargs)
self.integrals = Integrals(molecule, self.basis_set, **kwargs)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.F = self.h
self.dmat = None
self.entropy = None
self.DoAveraging = kwargs.get('DoAveraging', settings.Averaging)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed, nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed, nopen))
self.solver = SolverFactory(nel, nclosed, nopen, self.S, **kwargs)
return
def __repr__(self):
lstr = [
'Hamiltonian constructed for method %s' % self.method,
repr(self.molecule),
repr(self.basis_set),
repr(self.iterator)
]
return '\n'.join(lstr)
def get_energy(self):
return self.energy
def iterate(self, **kwargs):
self.iterator.iterate(self, **kwargs)
if self.iterator.converged:
logging.info("Final HF energy for system %s is %f" %
(self.molecule.name, self.energy))
return
def update(self, **kwargs):
from PyQuante.LA2 import trace2
from PyQuante.Ints import getJ, getK
if self.DoAveraging and self.dmat is not None:
self.F = self.Averager.getF(self.F, self.dmat)
self.dmat, self.entropy = self.solver.solve(self.F, **kwargs)
D = self.dmat
self.J = getJ(self.ERI, D)
self.Ej = 2 * trace2(D, self.J)
self.K = getK(self.ERI, D)
self.Exc = -trace2(D, self.K)
self.Eone = 2 * trace2(D, self.h)
self.F = self.h + 2 * self.J - self.K
self.energy = self.Eone + self.Ej + self.Exc + self.Enuke + self.entropy
return
def rhf(mol,
bfs,
S,
Hcore,
Ints,
mu=0,
MaxIter=100,
eps_SCF=1E-4,
_diis_=True):
##########################################################
## Get the system information
##########################################################
# size
nbfs = len(bfs)
# get the nuclear energy
enuke = mol.get_enuke()
# determine the number of electrons
# and occupation numbers
nelec = mol.get_nel()
nclosed, nopen = mol.get_closedopen()
nocc = nclosed
# orthogonalization matrix
X = SymOrthCutoff(S)
if _ee_inter_ == 0:
print '\t\t ==================================================='
print '\t\t == Electrons-Electrons interactions desactivated =='
print '\t\t ==================================================='
if nopen != 0:
print '\t\t ================================================================='
print '\t\t Warning : using restricted HF with open shell is not recommended'
print "\t\t Use only if you know what you're doing"
print '\t\t ================================================================='
# get a first DM
#D = np.zeros((nbfs,nbfs))
L, C = scla.eigh(Hcore, b=S)
D = mkdens(C, 0, nocc)
# initialize the old energy
eold = 0.
# initialize the DIIS
if _diis_:
avg = DIIS(S)
#print '\t SCF Calculations'
for iiter in range(MaxIter):
# form the G matrix from the
# density matrix and the 2electron integrals
G = get2JmK(Ints, D)
# form the Fock matrix
F = Hcore + _ee_inter_ * G + mu
# if DIIS
if _diis_:
F = avg.getF(F, D)
# orthogonalize the Fock matrix
Fp = np.dot(X.T, np.dot(F, X))
# diagonalize the Fock matrix
Lp, Cp = scla.eigh(Fp)
# form the density matrix in the OB
if nopen == 0:
Dp = mkdens(Cp, 0, nocc)
else:
Dp = mkdens_spinavg(Cp, nclosed, nopen)
# pass the eigenvector back to the AO
C = np.dot(X, Cp)
# form the density matrix in the AO
if nopen == 0:
D = mkdens(C, 0, nocc)
#else:
# D = mkdens_spinavg(C,nclosed,nopen)
# compute the total energy
e = np.sum(D * (Hcore + F)) + enuke
print "\t\t Iteration: %d Energy: %f EnergyVar: %f" % (
iiter, e.real, np.abs((e - eold).real))
# stop if done
if (np.abs(e - eold) < eps_SCF):
break
else:
eold = e
if iiter < MaxIter:
print(
"\t\t SCF for HF has converged in %d iterations, Final energy %1.3f Ha\n"
% (iiter, e.real))
else:
print("\t\t SCF for HF has failed to converge after %d iterations")
# compute the density matrix in the
# eigenbasis of F
P = np.dot(Cp.T, np.dot(Dp, Cp))
#print D
return Lp, C, Cp, F, Fp, D, Dp, P, X
class DFTHamiltonian(AbstractHamiltonian):
method='DFT'
def __init__(self,molecule,**kwargs):
from PyQuante.Convergence import DIIS
from PyQuante.DFunctionals import need_gradients
self.molecule = molecule
logging.info("DFT calculation on system %s" % self.molecule.name)
self.basis_set = BasisSet(molecule,**kwargs)
self.integrals = Integrals(molecule,self.basis_set,**kwargs)
self.iterator = SCFIterator()
self.h = self.integrals.get_h()
self.S = self.integrals.get_S()
self.ERI = self.integrals.get_ERI()
self.Enuke = molecule.get_enuke()
self.nel = molecule.get_nel()
self.F = self.h
self.functional = kwargs.get('functional',settings.DFTFunctional)
kwargs['do_grad_dens'] = need_gradients[self.functional]
self.setup_grid(molecule,self.basis_set.get(),**kwargs)
self.dmat = None
self.entropy = None
self.DoAveraging = kwargs.get('DoAveraging',settings.DFTAveraging)
if self.DoAveraging:
self.Averager = DIIS(self.S)
nel = molecule.get_nel()
nclosed,nopen = molecule.get_closedopen()
logging.info("Nclosed/open = %d, %d" % (nclosed,nopen))
self.solver = SolverFactory(nel,nclosed,nopen,self.S,**kwargs)
return
def __repr__(self):
lstr = ['Hamiltonian constructed for method %s' % self.method,
repr(self.molecule),
repr(self.basis_set),
repr(self.iterator)]
return '\n'.join(lstr)
def get_energy(self): return self.energy
def iterate(self,**kwargs): return self.iterator.iterate(self,**kwargs)
def setup_grid(self,molecule,bfs,**kwargs):
#from PyQuante.MolecularGrid import MolecularGrid
from PyQuante.MG2 import MG2 as MolecularGrid
grid_nrad = kwargs.get('grid_nrad',settings.DFTGridRadii)
grid_fineness = kwargs.get('grid_fineness',settings.DFTGridFineness)
self.gr = MolecularGrid(molecule,grid_nrad,grid_fineness,**kwargs)
self.gr.set_bf_amps(bfs)
return
def update(self,**kwargs):
from PyQuante.LA2 import trace2
from PyQuante.Ints import getJ
from PyQuante.dft import getXC
#self.DoAveraging = kwargs.get('DoAveraging',True)
#if self.DoAveraging:
# self.Averager = DIIS(self.S)
if self.DoAveraging and self.dmat is not None:
self.F = self.Averager.getF(self.F,self.dmat)
self.dmat,self.entropy = self.solver.solve(self.F,**kwargs)
D = self.dmat
self.gr.setdens(D)
self.J = getJ(self.ERI,D)
self.Ej = 2*trace2(D,self.J)
self.Exc,self.XC = getXC(self.gr,self.nel,
functional=self.functional)
self.Eone = 2*trace2(D,self.h)
self.F = self.h+2*self.J+self.XC
self.energy = self.Eone + self.Ej + self.Exc + self.Enuke + self.entropy
return
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"
print energy, "(benchmark = -1.122956)"
def rhf(mol, bfs, S, Hcore, Ints, MaxIter=100, eps_SCF=1E-4, _diis_=True):
##########################################################
## Get the system information
##########################################################
# size
nbfs = len(bfs)
# get the nuclear energy
enuke = mol.get_enuke()
# determine the number of electrons
# and occupation numbers
nelec = mol.get_nel()
nclosed, nopen = mol.get_closedopen()
nocc = nclosed
if nopen != 0:
print '\t\t ================================================================='
print '\t\t Warning : using restricted HF with open shell is not recommended'
print "\t\t Use only if you know what you're doing"
print '\t\t ================================================================='
# get a first DM
#D = np.zeros((nbfs,nbfs))
L, C = scla.eigh(Hcore, b=S)
D = mkdens(C, 0, nocc)
# initialize the old energy
eold = 0.
# initialize the DIIS
if _diis_:
avg = DIIS(S)
#print '\t SCF Calculations'
for iiter in range(MaxIter):
# form the G matrix from the
# density matrix and the 2electron integrals
G = get2JmK_mpi(Ints, D)
# form the Fock matrix
F = Hcore + G
# if DIIS
if _diis_:
F = avg.getF(F, D)
# diagonalize the Fock matrix
L, C = scla.eigh(F, b=S)
# new density mtrix
D = mkdens(C, 0, nocc)
# compute the total energy
e = np.sum(D * (Hcore + F)) + enuke
print "\t\t Iteration: %d Energy: %f EnergyVar: %f" % (
iiter, e.real, np.abs((e - eold).real))
# stop if done
if (np.abs(e - eold) < eps_SCF):
break
else:
eold = e
if iiter < MaxIter - 1:
print(
"\t\t SCF for HF has converged in %d iterations, Final energy %1.3f Ha\n"
% (iiter, e.real))
else:
print("\t\t SCF for HF has failed to converge after %d iterations")
sys.exit()
# compute the density matrix in the
# eigenabsis of the Fock matrix
# orthogonalization matrix
X = SymOrthCutoff(S)
Xm1 = np.linalg.inv(X)
# density matrix in ortho basis
Dp = np.dot(Xm1, np.dot(D, Xm1.T))
# eigenvector in ortho basis
Cp = np.dot(Xm1, C)
# density matrix
P = np.dot(Cp.T, np.dot(Dp, Cp))
# done
return L, C, P