def iterate(self,**opts):
self.iter = 0
self.etemp = opts.get("etemp",False)
logging.debug("iter Energy <b|b>")
logging.debug("---- ------ -----")
self.b = fminBFGS(self.get_energy,self.b,self.get_gradient,logger=logging)
return
def iterate(self,**kwargs):
self.iter = 0
self.etemp = kwargs.get("etemp",settings.DFTElectronTemperature)
logging.debug("iter Energy <b|b>")
logging.debug("---- ------ -----")
self.b = fminBFGS(self.get_energy,self.b,self.get_gradient,logger=logging)
return
def iterate(self, **opts):
self.iter = 0
self.etemp = opts.get("etemp", False)
logging.debug("iter Energy <b|b>")
logging.debug("---- ------ -----")
self.b = fminBFGS(self.get_energy,
self.b,
self.get_gradient,
logger=logging)
return
def iterate(self, **kwargs):
self.iter = 0
self.etemp = kwargs.get("etemp", settings.DFTElectronTemperature)
logging.debug("iter Energy <b|b>")
logging.debug("---- ------ -----")
self.b = fminBFGS(self.get_energy,
self.b,
self.get_gradient,
logger=logging)
return
def opt(atoms,**kwargs):
from PyQuante.optimize import fminBFGS
c0,Efunc,Ffunc = energy_forces_factories(atoms,**kwargs)
print "C0 = ",c0
# Currently optimization works when I use Energies and numerical
# forces, but not using the analytical forces. Obviously something
# is wrong somewhere here, but I don't have time to fix this now.
# Hopefully the final fix won't be too hard.
copt = fminBFGS(Efunc,c0,Ffunc,avegtol=1e-4)
#copt = fminBFGS(Efunc,c0,None,avegtol=1e-4)
Efinal = Efunc(copt)
return Efinal,copt
def opt(atoms,**kwargs):
from PyQuante.optimize import fminBFGS
c0,Efunc,Ffunc = energy_forces_factories(atoms,**kwargs)
print "C0 = ",c0
# Currently optimization works when I use Energies and numerical
# forces, but not using the analytical forces. Obviously something
# is wrong somewhere here, but I don't have time to fix this now.
# Hopefully the final fix won't be too hard.
copt = fminBFGS(Efunc,c0,Ffunc,avegtol=1e-4)
#copt = fminBFGS(Efunc,c0,None,avegtol=1e-4)
Efinal = Efunc(copt)
return Efinal,copt
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
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 xrange(npbf):
gmat = zeros((nbf, nbf), 'd')
Gij.append(gmat)
gbf = pbfs[g]
for i in xrange(nbf):
ibf = bfs[i]
for j in xrange(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
