def uhf_fixed_occ(atoms,occa, occb,**opts):
"""\
occa and occb represent the orbital occupation arrays for
the calculating spin orbitals with holes
uhf(atoms,**opts) - Unrestriced Open Shell Hartree Fock
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS averaging for convergence acceleration
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
orbs None If not None, the guess orbitals
"""
from biorthogonal import biorthogonalize,pad_out
ConvCriteria = opts.get('ConvCriteria',1e-5)
MaxIter = opts.get('MaxIter',40)
DoAveraging = opts.get('DoAveraging',True)
averaging = opts.get('averaging',0.5)
ETemp = opts.get('ETemp',False)
bfs = opts.get('bfs',None)
if not bfs:
basis_data = opts.get('basis_data',None)
bfs = getbasis(atoms,basis_data)
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() #pass in opts for multiplicity
S,h,Ints = getints(bfs,atoms)
orbsa = opts.get('orbsa',None)
orbsb = opts.get('orbsb',None)
if (orbsa!=None and orbsb!=None):
orbsa = orbsa
orbsb = orbsb
else:
orbe,orbs = geigh(h,S)
orbea = orbeb = orbe
orbsa = orbsb = orbs
#print "A Trial Orbital Energies:\n", orbea
print "A Trial Orbitals:\n"
pad_out(orbsa)
#print "B Trial Orbital Energies:\n",orbeb
print "B Trial Orbitals:\n"
pad_out(orbsb)
enuke = atoms.get_enuke()
eold = 0.
for i in xrange(MaxIter):
print "SCF Iteration:",i,"Starting Energy:",eold
#save the starting orbitals
oldorbs_a=orbsa
oldorbs_b=orbsb
Da = mk_auger_dens(orbsa,occa)
Db = mk_auger_dens(orbsb,occb)
#Da_std = mkdens(orbsa,0,nalpha)
#Db_std = mkdens(orbsb,0,nbeta)
#pad_out(Da - Da_std ) #use to test mk_aug_dens with ground state occupations
#pad_out(Db - Db_std )
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
orbea,orbsa = geigh(Fa,S)
orbeb,orbsb = geigh(Fb,S)
#save the new orbitals
neworbs_a=orbsa
neworbs_b=orbsb
#now we biorthogonalize the new orbitals to the old ones
#to setup occupation arrays for the next scf cycle
orbsa = biorthogonalize(neworbs_a,oldorbs_a,S,nalpha,occa)
orbsb = biorthogonalize(neworbs_b,oldorbs_b,S,nbeta,occb)
energya = get_energy(h,Fa,Da)
energyb = get_energy(h,Fb,Db)
energy = (energya+energyb)/2+enuke
Dab = Da+Db
Eone = trace2(Dab,h)
Ej = 0.5*trace2(Dab,Ja+Jb)
Ek = -0.5*(trace2(Da,Ka)+trace2(Db,Kb))
#print "%d %f %f %f %f" % (i,energy,Eone,Ej,Ek)
logging.debug("%d %f %f %f %f" % (i,energy,Eone,Ej,Ek))
if abs(energy-eold) < ConvCriteria: break
eold = energy
if i==(MaxIter-1):
print "Warning: Reached maximum number of SCF cycles may want to rerun calculation with more SCF cycles"
logger.info("Final UHF energy for system %s is %f" % (atoms.name,energy))
return energy,(orbea,orbeb),(orbsa,orbsb)
def uhf_fixed_occ(atoms, occa, occb, **kwargs):
"""\
occa and occb represent the orbital occupation arrays for
the calculating spin orbitals with holes
uhf(atoms,**kwargs) - Unrestriced Open Shell Hartree Fock
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS averaging for convergence acceleration
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
orbs None If not None, the guess orbitals
"""
from biorthogonal import biorthogonalize, pad_out
ConvCriteria = kwargs.get('ConvCriteria', settings.ConvergenceCriteria)
MaxIter = kwargs.get('MaxIter', settings.MaxIters)
DoAveraging = kwargs.get('DoAveraging', settings.Averaging)
averaging = kwargs.get('averaging', settings.MixingFraction)
ETemp = kwargs.get('ETemp', settings.ElectronTemperature)
bfs = getbasis(atoms, **kwargs)
S, h, Ints = getints(bfs, atoms, **kwargs)
nel = atoms.get_nel()
nalpha, nbeta = atoms.get_alphabeta() #pass in kwargs for multiplicity
orbsa = kwargs.get('orbsa')
orbsb = kwargs.get('orbsb')
if (orbsa == None or orbsb == None):
orbe, orbs = geigh(h, S)
orbea = orbeb = orbe
orbsa = orbsb = orbs
#print "A Trial Orbital Energies:\n", orbea
print "A Trial Orbitals:\n"
pad_out(orbsa)
#print "B Trial Orbital Energies:\n",orbeb
print "B Trial Orbitals:\n"
pad_out(orbsb)
enuke = atoms.get_enuke()
eold = 0.
for i in xrange(MaxIter):
print "SCF Iteration:", i, "Starting Energy:", eold
#save the starting orbitals
oldorbs_a = orbsa
oldorbs_b = orbsb
Da = mk_auger_dens(orbsa, occa)
Db = mk_auger_dens(orbsb, occb)
#Da_std = mkdens(orbsa,0,nalpha)
#Db_std = mkdens(orbsb,0,nbeta)
#pad_out(Da - Da_std ) #use to test mk_aug_dens with ground state occupations
#pad_out(Db - Db_std )
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
orbea, orbsa = geigh(Fa, S)
orbeb, orbsb = geigh(Fb, S)
#save the new orbitals
neworbs_a = orbsa
neworbs_b = orbsb
#now we biorthogonalize the new orbitals to the old ones
#to setup occupation arrays for the next scf cycle
orbsa = biorthogonalize(neworbs_a, oldorbs_a, S, nalpha, occa)
orbsb = biorthogonalize(neworbs_b, oldorbs_b, S, nbeta, occb)
energya = get_energy(h, Fa, Da)
energyb = get_energy(h, Fb, Db)
energy = (energya + energyb) / 2 + enuke
Dab = Da + Db
Eone = trace2(Dab, h)
Ej = 0.5 * trace2(Dab, Ja + Jb)
Ek = -0.5 * (trace2(Da, Ka) + trace2(Db, Kb))
#print "%d %f %f %f %f" % (i,energy,Eone,Ej,Ek)
logging.debug("%d %f %f %f %f" % (i, energy, Eone, Ej, Ek))
if abs(energy - eold) < ConvCriteria: break
eold = energy
if i == (MaxIter - 1):
print "Warning: Reached maximum number of SCF cycles may want to rerun calculation with more SCF cycles"
logger.info("Final UHF energy for system %s is %f" % (atoms.name, energy))
return energy, (orbea, orbeb), (orbsa, orbsb)
def uhf(atoms,**opts):
"""\
uhf(atoms,**opts) - Unrestriced Open Shell Hartree Fock
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS averaging for convergence acceleration
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
orbs None If not None, the guess orbitals
"""
ConvCriteria = opts.get('ConvCriteria',1e-5)
MaxIter = opts.get('MaxIter',40)
DoAveraging = opts.get('DoAveraging',True)
averaging = opts.get('averaging',0.5)
ETemp = opts.get('ETemp',False)
verbose = opts.get('verbose',False)
bfs = opts.get('bfs',None)
if not bfs:
basis_data = opts.get('basis_data',None)
bfs = getbasis(atoms,basis_data)
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() #pass in opts for multiplicity
S,h,Ints = getints(bfs,atoms)
orbs = opts.get('orbs',None)
if orbs!=None:
#orbsa = orbsb = orbs
orbsa = orbs[0]
orbsb = orbs[1]
else:
orbe,orbs = geigh(h,S)
orbea = orbeb = orbe
orbsa = orbsb = orbs
enuke = atoms.get_enuke()
eold = 0.
logger.info("UHF calculation on %s" % atoms.name)
logger.info("Nbf = %d" % len(bfs))
logger.info("Nalpha = %d" % nalpha)
logger.info("Nbeta = %d" % nbeta)
logger.info("Averaging = %s" % DoAveraging)
logging.debug("Optimization of HF orbitals")
for i in xrange(MaxIter):
if verbose: print "SCF Iteration:",i,"Starting Energy:",eold
if ETemp:
# We have to multiply nalpha and nbeta by 2
# to get the Fermi energies to come out correct:
efermia = get_efermi(2.0*nalpha,orbea,ETemp)
occsa = get_fermi_occs(efermia,orbea,ETemp)
#print "occsa = ",occsa
Da = mkdens_occs(orbsa,occsa)
efermib = get_efermi(2.0*nbeta,orbeb,ETemp)
occsb = get_fermi_occs(efermib,orbeb,ETemp)
#print "occsb = ",occsb
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)
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
orbea,orbsa = geigh(Fa,S)
orbeb,orbsb = geigh(Fb,S)
energya = get_energy(h,Fa,Da)
energyb = get_energy(h,Fb,Db)
energy = (energya+energyb)/2+enuke
Dab = Da+Db
Eone = trace2(Dab,h)
Ej = 0.5*trace2(Dab,Ja+Jb)
Ek = -0.5*(trace2(Da,Ka)+trace2(Db,Kb))
if ETemp: energy += entropy
logger.debug("%d %f %f %f %f" % (i,energy,Eone,Ej,Ek))
if abs(energy-eold) < ConvCriteria: break
eold = energy
logger.info("Final UHF energy for system %s is %f" % (atoms.name,energy))
return energy,(orbea,orbeb),(orbsa,orbsb)
def uhf(atoms, **kwargs):
"""\
uhf(atoms,**kwargs) - Unrestriced Open Shell Hartree Fock
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS averaging for convergence acceleration
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
orbs None If not None, the guess orbitals
"""
ConvCriteria = kwargs.get('ConvCriteria', settings.ConvergenceCriteria)
MaxIter = kwargs.get('MaxIter', settings.MaxIters)
DoAveraging = kwargs.get('DoAveraging', settings.Averaging)
averaging = kwargs.get('averaging', settings.MixingFraction)
ETemp = kwargs.get('ETemp', settings.ElectronTemperature)
verbose = kwargs.get('verbose')
bfs = getbasis(atoms, **kwargs)
S, h, Ints = getints(bfs, atoms, **kwargs)
nel = atoms.get_nel()
nalpha, nbeta = atoms.get_alphabeta() #pass in kwargs for multiplicity
orbs = kwargs.get('orbs')
if orbs != None:
#orbsa = orbsb = orbs
orbsa = orbs[0]
orbsb = orbs[1]
else:
orbe, orbs = geigh(h, S)
orbea = orbeb = orbe
orbsa = orbsb = orbs
enuke = atoms.get_enuke()
eold = 0.
logger.info("UHF calculation on %s" % atoms.name)
logger.info("Nbf = %d" % len(bfs))
logger.info("Nalpha = %d" % nalpha)
logger.info("Nbeta = %d" % nbeta)
logger.info("Averaging = %s" % DoAveraging)
logging.debug("Optimization of HF orbitals")
for i in xrange(MaxIter):
if verbose: print "SCF Iteration:", i, "Starting Energy:", eold
if ETemp:
# We have to multiply nalpha and nbeta by 2
# to get the Fermi energies to come out correct:
efermia = get_efermi(2.0 * nalpha, orbea, ETemp)
occsa = get_fermi_occs(efermia, orbea, ETemp)
#print "occsa = ",occsa
Da = mkdens_occs(orbsa, occsa)
efermib = get_efermi(2.0 * nbeta, orbeb, ETemp)
occsb = get_fermi_occs(efermib, orbeb, ETemp)
#print "occsb = ",occsb
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)
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
orbea, orbsa = geigh(Fa, S)
orbeb, orbsb = geigh(Fb, S)
energya = get_energy(h, Fa, Da)
energyb = get_energy(h, Fb, Db)
energy = (energya + energyb) / 2 + enuke
Dab = Da + Db
Eone = trace2(Dab, h)
Ej = 0.5 * trace2(Dab, Ja + Jb)
Ek = -0.5 * (trace2(Da, Ka) + trace2(Db, Kb))
if ETemp: energy += entropy
logger.debug("%d %f %f %f %f" % (i, energy, Eone, Ej, Ek))
if abs(energy - eold) < ConvCriteria: break
eold = energy
logger.info("Final UHF energy for system %s is %f" % (atoms.name, energy))
return energy, (orbea, orbeb), (orbsa, orbsb)