def test():
from hartree_fock import rhf
from Molecule import Molecule
# Make a test molecule for the calculation
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 ",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
def test_contr():
from basis_sto3g import basis_data
from Molecule import Molecule
from Ints import getbasis
from time import time
r = 1 / 0.52918
atoms = Molecule('h2o',
atomlist=[(8, (0, 0, 0)), (1, (r, 0, 0)), (1, (0, 0, r))])
bfs = getbasis(atoms, basis_data)
o_1s = bfs[0]
o_2s = bfs[1]
o_px = bfs[2]
o_py = bfs[3]
o_pz = bfs[4]
h1_s = bfs[5]
h2_s = bfs[6]
t0 = time()
val = \
contr_coulomb(h2_s.pexps,h2_s.pcoefs,h2_s.pnorms,
h2_s.origin,h2_s.powers,
h2_s.pexps,h2_s.pcoefs,h2_s.pnorms,
h2_s.origin,h2_s.powers,
h2_s.pexps,h2_s.pcoefs,h2_s.pnorms,
h2_s.origin,h2_s.powers,
o_pz.pexps,o_pz.pcoefs,o_pz.pnorms,
o_pz.origin,o_pz.powers)
t1 = time()
print val, t1 - t0
def test():
from Ints import getbasis, getints, get2JmK
from hartree_fock import get_nel, get_enuke, get_energy
from LA2 import geigh, mkdens
from IO import mtx2file
from Molecule import Molecule
ConvCriteria = 0.00001
MaxIt = 30
h2o = Molecule("h2o", [(8, (0, 0, 0)), (1, (1.0, 0, 0)), (1, (0, 1.0, 0))], units="Angstrom")
bfs = getbasis(h2o)
S, h, Ints = getints(bfs, h2o)
orbe, orbs = geigh(h, S)
nel = get_nel(h2o)
nocc = int(nel / 2)
enuke = get_enuke(h2o)
eold = 0.0
avg = DIIS2(S)
for i in range(30):
D = mkdens(orbs, 0, nocc)
mtx2file(D)
G = get2JmK(Ints, D)
F = h + G
F = avg.getF(F, D) # do the DIIS extrapolation
orbe, orbs = geigh(F, S)
energy = get_energy(h, F, D, enuke)
print i + 1, energy
if abs(energy - eold) < ConvCriteria:
break
eold = energy
return
def test_contr():
from basis_sto3g import basis_data
from Molecule import Molecule
from Ints import getbasis
from time import time
r = 1/0.52918
atoms=Molecule('h2o',atomlist = [(8,(0,0,0)),(1,(r,0,0)),(1,(0,0,r))])
bfs = getbasis(atoms,basis_data)
o_1s = bfs[0]
o_2s = bfs[1]
o_px = bfs[2]
o_py = bfs[3]
o_pz = bfs[4]
h1_s = bfs[5]
h2_s = bfs[6]
t0 = time()
val = \
contr_coulomb(h2_s.exps(),h2_s.coefs(),h2_s.pnorms(),
h2_s.origin(),h2_s.powers(),
h2_s.exps(),h2_s.coefs(),h2_s.pnorms(),
h2_s.origin(),h2_s.powers(),
h2_s.exps(),h2_s.coefs(),h2_s.pnorms(),
h2_s.origin(),h2_s.powers(),
o_pz.exps(),o_pz.coefs(),o_pz.pnorms(),
o_pz.origin(),o_pz.powers())
t1 = time()
print val,t1-t0
def test():
from Ints import getbasis, getints, get2JmK
from hartree_fock import get_nel, get_enuke, get_energy
from LA2 import geigh, mkdens
from IO import mtx2file
from Molecule import Molecule
ConvCriteria = 0.00001
MaxIt = 30
h2o = Molecule('h2o', [(8, (0, 0, 0)), (1, (1., 0, 0)), (1, (0, 1., 0))],
units='Angstrom')
bfs = getbasis(h2o)
S, h, Ints = getints(bfs, h2o)
orbe, orbs = geigh(h, S)
nel = get_nel(h2o)
nocc = int(nel / 2)
enuke = get_enuke(h2o)
eold = 0.
avg = DIIS2(S)
for i in xrange(30):
D = mkdens(orbs, 0, nocc)
mtx2file(D)
G = get2JmK(Ints, D)
F = h + G
F = avg.getF(F, D) # do the DIIS extrapolation
orbe, orbs = geigh(F, S)
energy = get_energy(h, F, D, enuke)
print i + 1, energy
if abs(energy - eold) < ConvCriteria: break
eold = energy
return
def test():
from Ints import getbasis, getints
from hartree_fock import rhf
from Molecule import Molecule
# Make a test molecule for the calculation
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 ", 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
def hf_force(mol,wf,bname):
# calculates Hartree-Fock derived atomic forces through
# analytic derivatives of the HF energy. Stores the forces
# the atom class which can later be accessed through
# atomlist[j].forces[i] which would give you component i
# of the force on atom j
bset = getbasis(mol.atoms,basis=bname)
if wf.restricted:
rhf_force(mol,wf,bset)
if wf.unrestricted:
uhf_force(mol,wf,bset)
if wf.fixedocc:
fixedocc_uhf_force(mol,wf,bset)
return
def hf_force(mol, wf, bname):
# calculates Hartree-Fock derived atomic forces through
# analytic derivatives of the HF energy. Stores the forces
# the atom class which can later be accessed through
# atomlist[j].forces[i] which would give you component i
# of the force on atom j
bset = getbasis(mol.atoms, basis=bname)
if wf.restricted:
rhf_force(mol, wf, bset)
if wf.unrestricted:
uhf_force(mol, wf, bset)
if wf.fixedocc:
fixedocc_uhf_force(mol, wf, bset)
return
def HFGF(atoms, charge=0):
nclosed, nopen = atoms.get_closedopen()
if nopen: raise Exception("HFGF only works for closed shell cases")
bfs = getbasis(atoms)
nvirt = len(bfs) - nclosed
S, h, Ints = getints(bfs, atoms)
hf_energy, hf_orbe, hf_orbs = scf(atoms, S, h, Ints, charge)
print_orbe(hf_orbe, nclosed, nvirt)
sigma = Sigma2(hf_orbe, hf_orbs, Ints, len(bfs), nclosed)
for i in [4, 5, 6, 7, 8, 9]:
print "Correcting orbital %d, HF Eorb = %f" % (i + 1, hf_orbe[i])
del0, dele = sigma.eval(i)
print "-> Eorb = %f %f" % (hf_orbe[i] + del0, hf_orbe[i] + dele)
return
def test():
# Jaguar gets -0.0276516 h for this:
from Ints import getbasis, getints
from hartree_fock import scf
from IO import mtx2file
from Molecule import Molecule
atoms = Molecule('h2', [(1, (1., 0, 0)), (1, (-1., 0, 0))])
bfs = getbasis(atoms)
S, h, Ints = getints(bfs, atoms)
en, orbe, orbs = scf(atoms, S, h, Ints, 0, 0.0001, 10)
print "SCF completed, E = ", en
emp2 = MP2(Ints, orbs, orbe, 1, 9)
print "MP2 correction = ", emp2
print "Final energy = ", en + emp2
return
def test():
# Jaguar gets -0.0276516 h for this:
from Ints import getbasis,getints
from hartree_fock import scf
from IO import mtx2file
from Molecule import Molecule
atoms = Molecule('h2',[(1,(1.,0,0)),(1,(-1.,0,0))])
bfs = getbasis(atoms)
S,h,Ints = getints(bfs,atoms)
en,orbe,orbs = scf(atoms,S,h,Ints,0,0.0001,10)
print "SCF completed, E = ",en
emp2 = MP2(Ints,orbs,orbe,1,9)
print "MP2 correction = ",emp2
print "Final energy = ",en+emp2
return
def HFGF(atoms,charge=0):
nclosed,nopen = atoms.get_closedopen()
if nopen: raise Exception("HFGF only works for closed shell cases")
bfs = getbasis(atoms)
nvirt = len(bfs)-nclosed
S,h,Ints = getints(bfs,atoms)
hf_energy,hf_orbe,hf_orbs = scf(atoms,S,h,Ints,charge)
print_orbe(hf_orbe,nclosed,nvirt)
sigma = Sigma2(hf_orbe,hf_orbs,Ints,len(bfs),nclosed)
for i in [4,5,6,7,8,9]:
print "Correcting orbital %d, HF Eorb = %f" % (i+1,hf_orbe[i])
del0,dele = sigma.eval(i)
print "-> Eorb = %f %f" % (hf_orbe[i]+del0,hf_orbe[i]+dele)
return
def udft_fixed_occ(atoms,occa, occb, **kwargs):
"""\
occa and occb represent the orbital occupation arrays for
the calculating spin orbitals with holes
udft(atoms,**kwargs) - Unrestricted spin DFT driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
verbose False Output terse information to stdout (default)
True Print out additional information
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
functional SVWN Use the SVWN (LDA) DFT functional (default)
S0 Use the Slater Xalpha DFT functional
BLYP Use the BLYP GGA DFT functional
PBE Use the PBE DFT functional
grid_nrad 32 Number of radial shells per atom
grid_fineness 1 Radial shell fineness. 0->coarse, 1->medium, 2->fine
"""
verbose = kwargs.get('verbose',False)
ConvCriteria = kwargs.get('ConvCriteria',1e-4)
MaxIter = kwargs.get('MaxIter',20)
DoAveraging = kwargs.get('DoAveraging',True)
averaging = kwargs.get('averaging',0.5)
ETemp = kwargs.get('ETemp',False)
functional = kwargs.get('functional','LDA')
#default to LDA which has no correlation since that is easier
kwargs['do_grad_dens'] = need_gradients[functional]
kwargs['do_spin_polarized'] = True
bfs = kwargs.get('bfs',None)
if not bfs:
basis_data = kwargs.get('basis_data',None)
bfs = getbasis(atoms,basis_data)
integrals = kwargs.get('integrals',None)
if integrals:
S,h,Ints = integrals
else:
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
# default medium mesh
grid_nrad = kwargs.get('grid_nrad',32)
grid_fineness = kwargs.get('grid_fineness',1)
gr = MolecularGrid(atoms,grid_nrad,grid_fineness,**kwargs)
gr.set_bf_amps(bfs)
# It would be nice to have a more intelligent treatment of the guess
# so that I could pass in a density rather than a set of orbs.
orbs = kwargs.get('orbs',None)
if not orbs: orbe,orbs = geigh(h,S)
orbsa = orbsb = orbs
nalpha,nbeta = atoms.get_alphabeta()
if verbose:
print "UDFT calculation on %s using functional %s" % (
atoms.name,functional)
print "Nbf = %d" % len(bfs)
print "Nalpha = %d" % nalpha
print "Nbeta = %d" % nbeta
eold = 0.
# Converge the LDA density for the system:
print "Optimization of DFT density"
for i in xrange(MaxIter):
Da = mk_auger_dens(orbsa, occa)
Db = mk_auger_dens(orbsb, occb)
Dab = Da + Db
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)
#remember we must use a functional that has no correlation energy
gr.setdens(Da,Db)
exca,XCa,XCb = getXC(gr,nel,**kwargs)
Fa = h+Ja+Jb+XCa
Fb = h+Ja+Jb+XCb
orbea,orbsa = geigh(Fa,S)
orbeb,orbsb = geigh(Fb,S)
Eone = trace2(Dab,h)
Ej = 0.5*trace2(Dab,Ja+Jb)
Exc = 0.5*exca + 0.5*excb
energy = Eone + Ej + Exc + enuke
print i+1," ",energy," ",Ej," ",Exc
if verbose:
print "%d %10.4f %10.4f %10.4f" % (i,energy,Ej,Exc)
if abs(energy-eold) < ConvCriteria: break
eold = energy
print "Final U%s energy for system %s is %f" % (
functional,atoms.name,energy)
return energy,(orbea,orbeb),(orbsa,orbsb)
def dft_fixed_occ(atoms,occs,**kwargs):
"""\
dft(atoms,**kwargs) - DFT driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
verbose False Output terse information to stdout (default)
True Print out additional information
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
functional SVWN Use the SVWN (LDA) DFT functional (default)
S0 Use the Slater Xalpha DFT functional
BLYP Use the BLYP GGA DFT functional
PBE Use the PBE DFT functional
grid_nrad 32 Number of radial shells per atom
grid_fineness 1 Radial shell fineness. 0->coarse, 1->medium, 2->fine
spin_type A Average occupation method for open shell (default)
R Restricted open shell (not implemented yet)
U Unrestricted open shell (aka spin-polarized dft)
Only A works now. Stay tuned.
"""
verbose = kwargs.get('verbose',False)
ConvCriteria = kwargs.get('ConvCriteria',1e-4)
MaxIter = kwargs.get('MaxIter',20)
DoAveraging = kwargs.get('DoAveraging',True)
ETemp = kwargs.get('ETemp',False)
functional = kwargs.get('functional','SVWN')
kwargs['do_grad_dens'] = need_gradients[functional]
bfs = kwargs.get('bfs',None)
if not bfs:
basis_data = kwargs.get('basis_data',None)
bfs = getbasis(atoms,basis_data)
integrals = kwargs.get('integrals',None)
if integrals:
S,h,Ints = integrals
else:
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
# default medium mesh
grid_nrad = kwargs.get('grid_nrad',32)
grid_fineness = kwargs.get('grid_fineness',1)
gr = MolecularGrid(atoms,grid_nrad,grid_fineness,**kwargs)
gr.set_bf_amps(bfs)
# It would be nice to have a more intelligent treatment of the guess
# so that I could pass in a density rather than a set of orbs.
orbs = kwargs.get('orbs',None)
if orbs is None: orbe,orbs = geigh(h,S)
nclosed,nopen = atoms.get_closedopen()
if verbose:
print "DFT calculation on %s using functional %s" % (
atoms.name,functional)
print "Nbf = %d" % len(bfs)
print "Nclosed = %d" % nclosed
print "Nopen = %d" % nclosed
if nopen: print "Using spin-averaged dft for open shell calculation"
eold = 0.
if DoAveraging:
print "Using DIIS averaging"
avg=DIIS(S)
# Converge the LDA density for the system:
if verbose: print "Optimization of DFT density"
for i in xrange(MaxIter):
#print "SCF Iteration:",i,"Starting Energy:",eold
#save the starting orbitals
oldorbs=orbs
if ETemp:
efermi = get_efermi(nel,orbe,ETemp)
occs = get_fermi_occs(efermi,orbe,ETemp)
D = mkdens_occs(orbs,occs)
entropy = get_entropy(occs,ETemp)
else:
D = mk_auger_dens(orbs, occs)
#D = mkdens_spinavg(orbs,nclosed,nopen)
gr.setdens(D)
J = getJ(Ints,D)
Exc,XC = getXC(gr,nel,**kwargs)
F = h+2*J+XC
if DoAveraging: F = avg.getF(F,D)
orbe,orbs = geigh(F,S)
#pad_out(orbs)
#save the new eigenstates of the fock operator F
neworbs=orbs
#send oldorbs and neworbs to get biorthogonalized method
#orbs = biorthog(neworbs, oldorbs, S, nel)
Ej = 2*trace2(D,J)
Eone = 2*trace2(D,h)
energy = Eone + Ej + Exc + enuke
print i+1," ",energy," ",Ej," ",Exc," ",enuke
if ETemp: energy += entropy
if verbose:
print "%d %10.4f %10.4f %10.4f %10.4f %10.4f" % (
i,energy,Eone,Ej,Exc,enuke)
if abs(energy-eold) < ConvCriteria: break
eold = energy
print "Final %s energy for system %s is %f" % (functional,atoms.name,energy)
return energy,orbe,orbs
def rhf(atoms,**opts):
"""\
rhf(atoms,**opts) - Closed-shell HF driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
"""
ConvCriteria = opts.get('ConvCriteria',1e-10)
MaxIter = opts.get('MaxIter',20)
DoAveraging = opts.get('DoAveraging',False)
ETemp = opts.get('ETemp',False)
logger.info("RHF calculation on %s" % atoms.name)
bfs = opts.get('bfs',None)
if not bfs:
basis_data = opts.get('basis_data',None)
bfs = getbasis(atoms,basis_data)
nclosed,nopen = atoms.get_closedopen()
nocc = nclosed
assert(nopen == 0), "SCF currently only works for closed-shell systems"
logger.info("Nbf = %d" % len(bfs))
logger.info("Nclosed = %d" % nclosed)
integrals = opts.get('integrals', None)
if integrals:
S,h,Ints = integrals
else:
S,h,Ints = getints(bfs,atoms)
nel = atoms.get_nel()
orbs = opts.get('orbs',None)
if orbs is None: orbe,orbs = geigh(h,S)
enuke = atoms.get_enuke()
eold = 0.
if DoAveraging:
logger.info("Using DIIS averaging")
avg = DIIS(S)
logging.debug("Optimization of HF orbitals")
for i in xrange(MaxIter):
if ETemp:
efermi = get_efermi(nel,orbe,ETemp)
occs = get_fermi_occs(efermi,orbe,ETemp)
D = mkdens_occs(orbs,occs)
entropy = get_entropy(occs,ETemp)
else:
D = mkdens(orbs,0,nocc)
G = get2JmK(Ints,D)
F = h+G
if DoAveraging: F = avg.getF(F,D)
orbe,orbs = geigh(F,S)
energy = get_energy(h,F,D,enuke)
if ETemp:
energy += entropy
logging.debug("%d %f" % (i,energy))
if abs(energy-eold) < ConvCriteria: break
logger.info("Iteration: %d Energy: %f EnergyVar: %f"%(i,energy,abs(energy-eold)))
eold = energy
if i < MaxIter:
logger.info("PyQuante converged in %d iterations" % i)
else:
logger.warning("PyQuante failed to converge after %d iterations"
% MaxIter)
logger.info("Final HF energy for system %s is %f" % (atoms.name,energy))
return energy,orbe,orbs
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(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 rhf(atoms, **kwargs):
"""\
rhf(atoms,**kwargs) - Closed-shell HF driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
"""
ConvCriteria = kwargs.get('ConvCriteria', settings.ConvergenceCriteria)
MaxIter = kwargs.get('MaxIter', settings.MaxIter)
DoAveraging = kwargs.get('DoAveraging', settings.Averaging)
ETemp = kwargs.get('ETemp', settings.ElectronTemperature)
logger.info("RHF calculation on %s" % atoms.name)
bfs = getbasis(atoms, **kwargs)
nclosed, nopen = atoms.get_closedopen()
nocc = nclosed
assert (nopen == 0), "SCF currently only works for closed-shell systems"
logger.info("Nbf = %d" % len(bfs))
logger.info("Nclosed = %d" % nclosed)
S, h, Ints = getints(bfs, atoms, **kwargs)
nel = atoms.get_nel()
orbs = kwargs.get('orbs')
if orbs is None: orbe, orbs = geigh(h, S)
enuke = atoms.get_enuke()
eold = 0.
if DoAveraging:
logger.info("Using DIIS averaging")
avg = DIIS(S)
logging.debug("Optimization of HF orbitals")
for i in xrange(MaxIter):
if ETemp:
efermi = get_efermi(nel, orbe, ETemp)
occs = get_fermi_occs(efermi, orbe, ETemp)
D = mkdens_occs(orbs, occs)
entropy = get_entropy(occs, ETemp)
else:
D = mkdens(orbs, 0, nocc)
G = get2JmK(Ints, D)
F = h + G
if DoAveraging: F = avg.getF(F, D)
orbe, orbs = geigh(F, S)
energy = get_energy(h, F, D, enuke)
if ETemp:
energy += entropy
logging.debug("%d %f" % (i, energy))
if abs(energy - eold) < ConvCriteria: break
logger.info("Iteration: %d Energy: %f EnergyVar: %f" %
(i, energy, abs(energy - eold)))
eold = energy
if i < MaxIter:
logger.info("PyQuante converged in %d iterations" % i)
else:
logger.warning("PyQuante failed to converge after %d iterations" %
MaxIter)
logger.info("Final HF energy for system %s is %f" % (atoms.name, energy))
return energy, orbe, orbs
def udft_fixed_occ(atoms, occa, occb, **kwargs):
"""\
occa and occb represent the orbital occupation arrays for
the calculating spin orbitals with holes
udft(atoms,**kwargs) - Unrestricted spin DFT driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
verbose False Output terse information to stdout (default)
True Print out additional information
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
functional SVWN Use the SVWN (LDA) DFT functional (default)
S0 Use the Slater Xalpha DFT functional
BLYP Use the BLYP GGA DFT functional
PBE Use the PBE DFT functional
grid_nrad 32 Number of radial shells per atom
grid_fineness 1 Radial shell fineness. 0->coarse, 1->medium, 2->fine
"""
verbose = kwargs.get('verbose', False)
ConvCriteria = kwargs.get('ConvCriteria', 1e-4)
MaxIter = kwargs.get('MaxIter', 20)
DoAveraging = kwargs.get('DoAveraging', True)
averaging = kwargs.get('averaging', 0.5)
ETemp = kwargs.get('ETemp', False)
functional = kwargs.get('functional', 'LDA')
#default to LDA which has no correlation since that is easier
kwargs['do_grad_dens'] = need_gradients[functional]
kwargs['do_spin_polarized'] = True
bfs = kwargs.get('bfs', None)
if not bfs:
basis_data = kwargs.get('basis_data', None)
bfs = getbasis(atoms, basis_data)
integrals = kwargs.get('integrals', None)
if integrals:
S, h, Ints = integrals
else:
S, h, Ints = getints(bfs, atoms)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
# default medium mesh
grid_nrad = kwargs.get('grid_nrad', 32)
grid_fineness = kwargs.get('grid_fineness', 1)
gr = MolecularGrid(atoms, grid_nrad, grid_fineness, **kwargs)
gr.set_bf_amps(bfs)
# It would be nice to have a more intelligent treatment of the guess
# so that I could pass in a density rather than a set of orbs.
orbs = kwargs.get('orbs', None)
if not orbs: orbe, orbs = geigh(h, S)
orbsa = orbsb = orbs
nalpha, nbeta = atoms.get_alphabeta()
if verbose:
print "UDFT calculation on %s using functional %s" % (atoms.name,
functional)
print "Nbf = %d" % len(bfs)
print "Nalpha = %d" % nalpha
print "Nbeta = %d" % nbeta
eold = 0.
# Converge the LDA density for the system:
print "Optimization of DFT density"
for i in xrange(MaxIter):
Da = mk_auger_dens(orbsa, occa)
Db = mk_auger_dens(orbsb, occb)
Dab = Da + Db
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)
#remember we must use a functional that has no correlation energy
gr.setdens(Da, Db)
exca, XCa, XCb = getXC(gr, nel, **kwargs)
Fa = h + Ja + Jb + XCa
Fb = h + Ja + Jb + XCb
orbea, orbsa = geigh(Fa, S)
orbeb, orbsb = geigh(Fb, S)
Eone = trace2(Dab, h)
Ej = 0.5 * trace2(Dab, Ja + Jb)
Exc = 0.5 * exca + 0.5 * excb
energy = Eone + Ej + Exc + enuke
print i + 1, " ", energy, " ", Ej, " ", Exc
if verbose:
print "%d %10.4f %10.4f %10.4f" % (i, energy, Ej, Exc)
if abs(energy - eold) < ConvCriteria: break
eold = energy
print "Final U%s energy for system %s is %f" % (functional, atoms.name,
energy)
return energy, (orbea, orbeb), (orbsa, orbsb)
def dft_fixed_occ(atoms, occs, **kwargs):
"""\
dft(atoms,**kwargs) - DFT driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
verbose False Output terse information to stdout (default)
True Print out additional information
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
functional SVWN Use the SVWN (LDA) DFT functional (default)
S0 Use the Slater Xalpha DFT functional
BLYP Use the BLYP GGA DFT functional
PBE Use the PBE DFT functional
grid_nrad 32 Number of radial shells per atom
grid_fineness 1 Radial shell fineness. 0->coarse, 1->medium, 2->fine
spin_type A Average occupation method for open shell (default)
R Restricted open shell (not implemented yet)
U Unrestricted open shell (aka spin-polarized dft)
Only A works now. Stay tuned.
"""
verbose = kwargs.get('verbose', False)
ConvCriteria = kwargs.get('ConvCriteria', 1e-4)
MaxIter = kwargs.get('MaxIter', 20)
DoAveraging = kwargs.get('DoAveraging', True)
ETemp = kwargs.get('ETemp', False)
functional = kwargs.get('functional', 'SVWN')
kwargs['do_grad_dens'] = need_gradients[functional]
bfs = kwargs.get('bfs', None)
if not bfs:
basis_data = kwargs.get('basis_data', None)
bfs = getbasis(atoms, basis_data)
integrals = kwargs.get('integrals', None)
if integrals:
S, h, Ints = integrals
else:
S, h, Ints = getints(bfs, atoms)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
# default medium mesh
grid_nrad = kwargs.get('grid_nrad', 32)
grid_fineness = kwargs.get('grid_fineness', 1)
gr = MolecularGrid(atoms, grid_nrad, grid_fineness, **kwargs)
gr.set_bf_amps(bfs)
# It would be nice to have a more intelligent treatment of the guess
# so that I could pass in a density rather than a set of orbs.
orbs = kwargs.get('orbs', None)
if orbs is None: orbe, orbs = geigh(h, S)
nclosed, nopen = atoms.get_closedopen()
if verbose:
print "DFT calculation on %s using functional %s" % (atoms.name,
functional)
print "Nbf = %d" % len(bfs)
print "Nclosed = %d" % nclosed
print "Nopen = %d" % nclosed
if nopen: print "Using spin-averaged dft for open shell calculation"
eold = 0.
if DoAveraging:
print "Using DIIS averaging"
avg = DIIS(S)
# Converge the LDA density for the system:
if verbose: print "Optimization of DFT density"
for i in xrange(MaxIter):
#print "SCF Iteration:",i,"Starting Energy:",eold
#save the starting orbitals
oldorbs = orbs
if ETemp:
efermi = get_efermi(nel, orbe, ETemp)
occs = get_fermi_occs(efermi, orbe, ETemp)
D = mkdens_occs(orbs, occs)
entropy = get_entropy(occs, ETemp)
else:
D = mk_auger_dens(orbs, occs)
#D = mkdens_spinavg(orbs,nclosed,nopen)
gr.setdens(D)
J = getJ(Ints, D)
Exc, XC = getXC(gr, nel, **kwargs)
F = h + 2 * J + XC
if DoAveraging: F = avg.getF(F, D)
orbe, orbs = geigh(F, S)
#pad_out(orbs)
#save the new eigenstates of the fock operator F
neworbs = orbs
#send oldorbs and neworbs to get biorthogonalized method
#orbs = biorthog(neworbs, oldorbs, S, nel)
Ej = 2 * trace2(D, J)
Eone = 2 * trace2(D, h)
energy = Eone + Ej + Exc + enuke
print i + 1, " ", energy, " ", Ej, " ", Exc, " ", enuke
if ETemp: energy += entropy
if verbose:
print "%d %10.4f %10.4f %10.4f %10.4f %10.4f" % (i, energy, Eone,
Ej, Exc, enuke)
if abs(energy - eold) < ConvCriteria: break
eold = energy
print "Final %s energy for system %s is %f" % (functional, atoms.name,
energy)
return energy, orbe, orbs
def udft(atoms,**kwargs):
"""\
udft(atoms,**kwargs) - Unrestricted spin DFT driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
verbose False Output terse information to stdout (default)
True Print out additional information
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
functional SVWN Use the SVWN (LDA) DFT functional (default)
S0 Use the Slater Xalpha DFT functional
BLYP Use the BLYP GGA DFT functional
PBE Use the PBE DFT functional
grid_nrad 32 Number of radial shells per atom
grid_fineness 1 Radial shell fineness. 0->coarse, 1->medium, 2->fine
"""
verbose = kwargs.get('verbose')
ConvCriteria = kwargs.get('ConvCriteria',settings.DFTConvergenceCriteria)
MaxIter = kwargs.get('MaxIter',settings.MaxIter)
DoAveraging = kwargs.get('DoAveraging',settings.DFTAveraging)
ETemp = kwargs.get('ETemp',settings.DFT.ElectronTemperature)
functional = kwargs.get('functional',settings.DFTFunctional)
kwargs['do_grad_dens'] = need_gradients[functional]
kwargs['do_spin_polarized'] = True
bfs = getbasis(atoms,**kwargs)
S,h,Ints = getints(bfs,atoms,**kwargs)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
# default medium mesh
grid_nrad = kwargs.get('grid_nrad',settings.DFTGridRadii)
grid_fineness = kwargs.get('grid_fineness',settings.DFTGridFineness)
gr = MolecularGrid(atoms,grid_nrad,grid_fineness,**kwargs)
gr.set_bf_amps(bfs)
# It would be nice to have a more intelligent treatment of the guess
# so that I could pass in a density rather than a set of orbs.
orbs = kwargs.get('orbs')
if not orbs: orbe,orbs = geigh(h,S)
orbsa = orbsb = orbs
nalpha,nbeta = atoms.get_alphabeta()
if verbose:
print "UDFT calculation on %s using functional %s" \
% (atoms.name,functional)
print "Nbf = %d" % len(bfs)
print "Nalpha = %d" % nalpha
print "Nbeta = %d" % nbeta
eold = 0.
# Converge the LDA density for the system:
if verbose: print "Optimization of DFT density"
for i in xrange(MaxIter):
Da = mkdens(orbsa,0,nalpha)
Db = mkdens(orbsb,0,nbeta)
gr.setdens(Da,Db)
Ja = getJ(Ints,Da)
Jb = getJ(Ints,Db)
Exc,XCa,XCb = getXC(gr,nel,**kwargs)
Fa = h+Ja+Jb-Ka
Fb = h+Ja+Jb-Kb
orbea,orbsa = geigh(Fa,S)
orbeb,orbsb = geigh(Fb,S)
Eja = trace2(D,Ja)
Ejb = trace2(D,Jb)
Eone = 2*trace2(D,h)
energy = Eone + Eja + Ejb + Exc + enuke
if verbose:
print "%d %10.4f %10.4f %10.4f %10.4f %10.4f" % (
i,energy,Eone,Eja+Ejb,Exc,enuke)
if abs(energy-eold) < ConvCriteria: break
eold = energy
print "Final U%s energy for system %s is %f" % (
functional,atoms.name,energy)
return energy,orbe,orbs
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)
def udft(atoms, **kwargs):
"""\
udft(atoms,**kwargs) - Unrestricted spin DFT driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
verbose False Output terse information to stdout (default)
True Print out additional information
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
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
orbs None If not none, the guess orbitals
functional SVWN Use the SVWN (LDA) DFT functional (default)
S0 Use the Slater Xalpha DFT functional
BLYP Use the BLYP GGA DFT functional
PBE Use the PBE DFT functional
grid_nrad 32 Number of radial shells per atom
grid_fineness 1 Radial shell fineness. 0->coarse, 1->medium, 2->fine
"""
verbose = kwargs.get('verbose')
ConvCriteria = kwargs.get('ConvCriteria', settings.DFTConvergenceCriteria)
MaxIter = kwargs.get('MaxIter', settings.MaxIter)
DoAveraging = kwargs.get('DoAveraging', settings.DFTAveraging)
ETemp = kwargs.get('ETemp', settings.DFT.ElectronTemperature)
functional = kwargs.get('functional', settings.DFTFunctional)
kwargs['do_grad_dens'] = need_gradients[functional]
kwargs['do_spin_polarized'] = True
bfs = getbasis(atoms, **kwargs)
S, h, Ints = getints(bfs, atoms, **kwargs)
nel = atoms.get_nel()
enuke = atoms.get_enuke()
# default medium mesh
grid_nrad = kwargs.get('grid_nrad', settings.DFTGridRadii)
grid_fineness = kwargs.get('grid_fineness', settings.DFTGridFineness)
gr = MolecularGrid(atoms, grid_nrad, grid_fineness, **kwargs)
gr.set_bf_amps(bfs)
# It would be nice to have a more intelligent treatment of the guess
# so that I could pass in a density rather than a set of orbs.
orbs = kwargs.get('orbs')
if not orbs: orbe, orbs = geigh(h, S)
orbsa = orbsb = orbs
nalpha, nbeta = atoms.get_alphabeta()
if verbose:
print "UDFT calculation on %s using functional %s" \
% (atoms.name,functional)
print "Nbf = %d" % len(bfs)
print "Nalpha = %d" % nalpha
print "Nbeta = %d" % nbeta
eold = 0.
# Converge the LDA density for the system:
if verbose: print "Optimization of DFT density"
for i in xrange(MaxIter):
Da = mkdens(orbsa, 0, nalpha)
Db = mkdens(orbsb, 0, nbeta)
gr.setdens(Da, Db)
Ja = getJ(Ints, Da)
Jb = getJ(Ints, Db)
Exc, XCa, XCb = getXC(gr, nel, **kwargs)
Fa = h + Ja + Jb - Ka
Fb = h + Ja + Jb - Kb
orbea, orbsa = geigh(Fa, S)
orbeb, orbsb = geigh(Fb, S)
Eja = trace2(D, Ja)
Ejb = trace2(D, Jb)
Eone = 2 * trace2(D, h)
energy = Eone + Eja + Ejb + Exc + enuke
if verbose:
print "%d %10.4f %10.4f %10.4f %10.4f %10.4f" % (
i, energy, Eone, Eja + Ejb, Exc, enuke)
if abs(energy - eold) < ConvCriteria: break
eold = energy
print "Final U%s energy for system %s is %f" % (functional, atoms.name,
energy)
return energy, orbe, orbs
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)
