def get_fock(mf, h1e, s1e, vhf, dm, cycle=-1, diis=None,
diis_start_cycle=None, level_shift_factor=None, damp_factor=None):
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if isinstance(level_shift_factor, (tuple, list, numpy.ndarray)):
shifta, shiftb = level_shift_factor
else:
shifta = shiftb = level_shift_factor
if isinstance(damp_factor, (tuple, list, numpy.ndarray)):
dampa, dampb = damp_factor
else:
dampa = dampb = damp_factor
f = h1e + vhf
if f.ndim == 2:
f = (f, f)
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = [dm*.5] * 2
if 0 <= cycle < diis_start_cycle-1 and abs(dampa)+abs(dampb) > 1e-4:
f = (hf.damping(s1e, dm[0], f[0], dampa),
hf.damping(s1e, dm[1], f[1], dampb))
if diis and cycle >= diis_start_cycle:
f = diis.update(s1e, dm, f, mf, h1e, vhf)
if abs(shifta)+abs(shiftb) > 1e-4:
f = (hf.level_shift(s1e, dm[0], f[0], shifta),
hf.level_shift(s1e, dm[1], f[1], shiftb))
return numpy.array(f)
def get_fock(mf, h1e, s1e, vhf, dm, cycle=-1, adiis=None,
diis_start_cycle=None, level_shift_factor=None, damp_factor=None):
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if isinstance(level_shift_factor, (tuple, list, numpy.ndarray)):
shifta, shiftb = level_shift_factor
else:
shifta = shiftb = level_shift_factor
if isinstance(damp_factor, (tuple, list, numpy.ndarray)):
dampa, dampb = damp_factor
else:
dampa = dampb = damp_factor
f = h1e + vhf
if f.ndim == 2:
f = (f, f)
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = [dm*.5] * 2
if 0 <= cycle < diis_start_cycle-1 and abs(dampa)+abs(dampb) > 1e-4:
f = (hf.damping(s1e, dm[0], f[0], dampa),
hf.damping(s1e, dm[1], f[1], dampb))
if adiis and cycle >= diis_start_cycle:
f = adiis.update(s1e, dm, f)
if abs(shifta)+abs(shiftb) > 1e-4:
f = (hf.level_shift(s1e, dm[0], f[0], shifta),
hf.level_shift(s1e, dm[1], f[1], shiftb))
return numpy.array(f)
def uhf_get_fock(mf,
emb_pot=None,
proj_pot=None,
h1e=None,
s1e=None,
vhf=None,
dm=None,
cycle=-1,
diis=None,
diis_start_cycle=None,
level_shift_factor=None,
damp_factor=None):
if emb_pot is None: emb_pot = [0.0, 0.0]
if proj_pot is None: proj_pot = [0.0, 0.0]
if h1e is None: h1e = mf.get_hcore()
#if vhf is None: vhf = mf.get_veff(dm=dm)
#For some reason the vhf being passed is wrong I believe.
vhf = mf.get_veff(dm=dm)
f = h1e + vhf
if f.ndim == 2:
f = (f, f)
f[0] = f[0] + emb_pot[0] + proj_pot[0] #Add embedding potential
f[1] = f[1] + emb_pot[1] + proj_pot[1] #Add embedding potential
if cycle < 0 and diis is None: # Not inside the SCF iteration
return f
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if s1e is None: s1e = mf.get_ovlp()
if dm is None: dm = self.make_rdm1()
if isinstance(level_shift_factor, (tuple, list, np.ndarray)):
shifta, shiftb = level_shift_factor
else:
shifta = shiftb = level_shift_factor
if isinstance(damp_factor, (tuple, list, np.ndarray)):
dampa, dampb = damp_factor
else:
dampa = dampb = damp_factor
if isinstance(dm, np.ndarray) and dm.ndim == 2:
dm = [dm * .5] * 2
if 0 <= cycle < diis_start_cycle - 1 and abs(dampa) + abs(dampb) > 1e-4:
f = (hf.damping(s1e, dm[0], f[0],
dampa), hf.damping(s1e, dm[1], f[1], dampb))
if diis and cycle >= diis_start_cycle:
f = diis.update(s1e, dm, f, mf, h1e, vhf)
if abs(shifta) + abs(shiftb) > 1e-4:
f = (hf.level_shift(s1e, dm[0], f[0],
shifta), hf.level_shift(s1e, dm[1], f[1], shiftb))
return np.array(f)
def get_fock(mf,
h1e=None,
s1e=None,
vhf=None,
dm=None,
cycle=-1,
diis=None,
diis_start_cycle=None,
level_shift_factor=None,
damp_factor=None):
h1e_kpts, s_kpts, vhf_kpts, dm_kpts = h1e, s1e, vhf, dm
if h1e_kpts is None: h1e_kpts = mf.get_hcore()
if vhf_kpts is None: vhf_kpts = mf.get_veff(mf.cell, dm_kpts)
f_kpts = h1e_kpts + vhf_kpts
if cycle < 0 and diis is None: # Not inside the SCF iteration
return f_kpts
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if s_kpts is None: s_kpts = mf.get_ovlp()
if dm_kpts is None: dm_kpts = mf.make_rdm1()
if isinstance(level_shift_factor, (tuple, list, np.ndarray)):
shifta, shiftb = level_shift_factor
else:
shifta = shiftb = level_shift_factor
if isinstance(damp_factor, (tuple, list, np.ndarray)):
dampa, dampb = damp_factor
else:
dampa = dampb = damp_factor
if 0 <= cycle < diis_start_cycle - 1 and abs(dampa) + abs(dampb) > 1e-4:
f_a = []
f_b = []
for k, s1e in enumerate(s_kpts):
f_a.append(mol_hf.damping(s1e, dm_kpts[0][k], f_kpts[0][k], dampa))
f_b.append(mol_hf.damping(s1e, dm_kpts[1][k], f_kpts[1][k], dampb))
f_kpts = [f_a, f_b]
if diis and cycle >= diis_start_cycle:
f_kpts = diis.update(s_kpts, dm_kpts, f_kpts, mf, h1e_kpts, vhf_kpts)
if abs(level_shift_factor) > 1e-4:
f_kpts = ([
mol_hf.level_shift(s, dm_kpts[0, k], f_kpts[0, k], shifta)
for k, s in enumerate(s_kpts)
], [
mol_hf.level_shift(s, dm_kpts[1, k], f_kpts[1, k], shiftb)
for k, s in enumerate(s_kpts)
])
return lib.asarray(f_kpts)
def get_fock_(mf, h1e, s1e, vhf, dm, cycle=-1, adiis=None, diis_start_cycle=0, level_shift_factor=0, damp_factor=0):
f = h1e + vhf
if f.ndim == 2:
f = (f, f)
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = [dm * 0.5] * 2
if 0 <= cycle < diis_start_cycle - 1:
f = (hf.damping(s1e, dm[0], f[0], damp_factor), hf.damping(s1e, dm[1], f[1], damp_factor))
if adiis and cycle >= diis_start_cycle:
f = adiis.update(s1e, dm, numpy.array(f))
f = (hf.level_shift(s1e, dm[0], f[0], level_shift_factor), hf.level_shift(s1e, dm[1], f[1], level_shift_factor))
return numpy.array(f)
def get_fock(mf, h1e, s1e, vhf, dm, cycle=-1, adiis=None,
diis_start_cycle=None, level_shift_factor=None,
damp_factor=None):
'''Build fock matrix based on Roothaan's effective fock.
See also :func:`get_roothaan_fock`
'''
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = numpy.array((dm*.5, dm*.5))
# To Get orbital energy in get_occ, we saved alpha and beta fock, because
# Roothaan effective Fock cannot provide correct orbital energy with `eig`
# TODO, check other treatment J. Chem. Phys. 133, 141102
mf._focka_ao = h1e + vhf[0]
mf._fockb_ao = h1e + vhf[1]
f = get_roothaan_fock((mf._focka_ao,mf._fockb_ao), dm, s1e)
if 0 <= cycle < diis_start_cycle-1:
f = hf.damping(s1e, dm[0], f, damp_factor)
if adiis and cycle >= diis_start_cycle:
#f = adiis.update(s1e, dmsf*.5, f)
f = adiis.update(s1e, dm[0], f)
#f = level_shift(s1e, dmsf*.5, f, level_shift_factor)
f = hf.level_shift(s1e, dm[0], f, level_shift_factor)
return f
def get_fock(mf, h1e, s1e, vhf, dm, cycle=-1, diis=None,
diis_start_cycle=None, level_shift_factor=None,
damp_factor=None):
'''Build fock matrix based on Roothaan's effective fock.
See also :func:`get_roothaan_fock`
'''
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = numpy.array((dm*.5, dm*.5))
# To Get orbital energy in get_occ, we saved alpha and beta fock, because
# Roothaan effective Fock cannot provide correct orbital energy with `eig`
# TODO, check other treatment J. Chem. Phys. 133, 141102
mf._focka_ao = h1e + vhf[0]
mf._fockb_ao = h1e + vhf[1]
f = get_roothaan_fock((mf._focka_ao,mf._fockb_ao), dm, s1e)
if 0 <= cycle < diis_start_cycle-1:
f = hf.damping(s1e, dm[0], f, damp_factor)
if diis and cycle >= diis_start_cycle:
#f = diis.update(s1e, dmsf*.5, f, mf, h1e, vhf)
f = diis.update(s1e, dm[0], f, mf, h1e, vhf)
#f = level_shift(s1e, dmsf*.5, f, level_shift_factor)
f = hf.level_shift(s1e, dm[0], f, level_shift_factor)
return f
def get_fock(mf, h1e=None, s1e=None, vhf=None, dm=None, cycle=-1, diis=None,
diis_start_cycle=None, level_shift_factor=None, damp_factor=None):
h1e_kpts, s_kpts, vhf_kpts, dm_kpts = h1e, s1e, vhf, dm
if h1e_kpts is None: h1e_kpts = mf.get_hcore()
if vhf_kpts is None: vhf_kpts = mf.get_veff(mf.cell, dm_kpts)
f_kpts = h1e_kpts + vhf_kpts
if cycle < 0 and diis is None: # Not inside the SCF iteration
return f_kpts
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if s_kpts is None: s_kpts = mf.get_ovlp()
if dm_kpts is None: dm_kpts = mf.make_rdm1()
if 0 <= cycle < diis_start_cycle-1 and abs(damp_factor) > 1e-4:
f_kpts = [mol_hf.damping(s1e, dm_kpts[k] * 0.5, f_kpts[k], damp_factor)
for k, s1e in enumerate(s_kpts)]
if diis and cycle >= diis_start_cycle:
f_kpts = diis.update(s_kpts, dm_kpts, f_kpts, mf, h1e_kpts, vhf_kpts)
if abs(level_shift_factor) > 1e-4:
f_kpts = [mol_hf.level_shift(s, dm_kpts[k], f_kpts[k], level_shift_factor)
for k, s in enumerate(s_kpts)]
return lib.asarray(f_kpts)
def get_fock(mf,
h1e=None,
s1e=None,
vhf=None,
dm=None,
cycle=-1,
diis=None,
diis_start_cycle=None,
level_shift_factor=None,
damp_factor=None):
if h1e is None: h1e = mf.get_hcore()
if vhf is None: vhf = mf.get_veff(mf.mol, dm)
f = h1e + vhf
if f.ndim == 2:
f = (f, f)
if cycle < 0 and diis is None: # Not inside the SCF iteration
return f
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if s1e is None: s1e = mf.get_ovlp()
if dm is None: dm = self.make_rdm1()
if isinstance(level_shift_factor, (tuple, list, numpy.ndarray)):
shifta, shiftb = level_shift_factor
else:
shifta = shiftb = level_shift_factor
if isinstance(damp_factor, (tuple, list, numpy.ndarray)):
dampa, dampb = damp_factor
else:
dampa = dampb = damp_factor
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = [dm * .5] * 2
if 0 <= cycle < diis_start_cycle - 1 and abs(dampa) + abs(dampb) > 1e-4:
f = (hf.damping(s1e, dm[0], f[0],
dampa), hf.damping(s1e, dm[1], f[1], dampb))
if diis and cycle >= diis_start_cycle:
f = diis.update(s1e, dm, f, mf, h1e, vhf)
if abs(shifta) + abs(shiftb) > 1e-4:
f = (hf.level_shift(s1e, dm[0], f[0],
shifta), hf.level_shift(s1e, dm[1], f[1], shiftb))
return numpy.array(f)
def get_fock_(mf, h1e, s1e, vhf, dm, cycle=-1, adiis=None,
diis_start_cycle=None, level_shift_factor=None,
damp_factor=None):
'''Roothaan's effective fock.
Ref. http://www-theor.ch.cam.ac.uk/people/ross/thesis/node15.html
======== ======== ====== =========
space closed open virtual
======== ======== ====== =========
closed Fc Fb Fc
open Fb Fc Fa
virtual Fc Fa Fc
======== ======== ====== =========
where Fc stands for the Fa + Fb
Returns:
(fock_eff, fock_alpha, fock_beta)
Roothaan effective Fock matrix, with UHF alpha and beta Fock matrices.
Attach alpha and beta fock, because Roothaan effective Fock cannot
provide correct orbital energies.
'''
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift_factor
if damp_factor is None:
damp_factor = mf.damp_factor
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = numpy.array((dm*.5, dm*.5))
# Fc = (Fa+Fb)/2
mf._focka_ao = h1e + vhf[0]
fockb_ao = h1e + vhf[1]
fc = (mf._focka_ao + fockb_ao) * .5
# Projector for core, open-shell, and virtual
nao = s1e.shape[0]
pc = numpy.dot(dm[1], s1e)
po = numpy.dot(dm[0]-dm[1], s1e)
pv = numpy.eye(nao) - numpy.dot(dm[0], s1e)
f = reduce(numpy.dot, (pc.T, fc, pc)) * .5
f += reduce(numpy.dot, (po.T, fc, po)) * .5
f += reduce(numpy.dot, (pv.T, fc, pv)) * .5
f += reduce(numpy.dot, (po.T, fockb_ao, pc))
f += reduce(numpy.dot, (po.T, mf._focka_ao, pv))
f += reduce(numpy.dot, (pv.T, fc, pc))
f = f + f.T
if 0 <= cycle < diis_start_cycle-1:
f = hf.damping(s1e, dm[0], f, damp_factor)
if adiis and cycle >= diis_start_cycle:
#f = adiis.update(s1e, dmsf*.5, f)
f = adiis.update(s1e, dm[0], f)
#f = level_shift(s1e, dmsf*.5, f, level_shift_factor)
f = hf.level_shift(s1e, dm[0], f, level_shift_factor)
# attach alpha and beta fock, because Roothaan effective Fock cannot provide
# correct orbital energy. To define orbital energy in mf.eig, we use alpha
# fock and beta fock.
# TODO, check other treatment J. Chem. Phys. 133, 141102
return f
def get_fock(mf, h1e=None, s1e=None, vhf=None, dm=None, cycle=-1, diis=None,
diis_start_cycle=None, level_shift_factor=None, damp_factor=None):
if h1e is None: h1e = mf.get_hcore()
if vhf is None: vhf = mf.get_veff(mf.mol, dm)
f = h1e + vhf
if f.ndim == 2:
f = (f, f)
if cycle < 0 and diis is None: # Not inside the SCF iteration
return f
if diis_start_cycle is None:
diis_start_cycle = mf.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = mf.level_shift
if damp_factor is None:
damp_factor = mf.damp
if s1e is None: s1e = mf.get_ovlp()
if dm is None: dm = self.make_rdm1()
if isinstance(level_shift_factor, (tuple, list, numpy.ndarray)):
shifta, shiftb = level_shift_factor
else:
shifta = shiftb = level_shift_factor
if isinstance(damp_factor, (tuple, list, numpy.ndarray)):
dampa, dampb = damp_factor
else:
dampa = dampb = damp_factor
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = [dm*.5] * 2
if 0 <= cycle < diis_start_cycle-1 and abs(dampa)+abs(dampb) > 1e-4:
f = (hf.damping(s1e, dm[0], f[0], dampa),
hf.damping(s1e, dm[1], f[1], dampb))
if diis and cycle >= diis_start_cycle:
f = diis.update(s1e, dm, f, mf, h1e, vhf)
if abs(shifta)+abs(shiftb) > 1e-4:
f = (hf.level_shift(s1e, dm[0], f[0], shifta),
hf.level_shift(s1e, dm[1], f[1], shiftb))
return numpy.array(f)
def get_fock(self,
h1e,
s1e,
vhf,
dm,
cycle=-1,
adiis=None,
diis_start_cycle=None,
level_shift_factor=None,
damp_factor=None):
# Roothaan's effective fock
# http://www-theor.ch.cam.ac.uk/people/ross/thesis/node15.html
# | closed open virtual
# ----------------------------------------
# closed | Fc Fb Fc
# open | Fb Fc Fa
# virtual | Fc Fa Fc
# Fc = (Fa+Fb)/2
if diis_start_cycle is None:
diis_start_cycle = self.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = self.level_shift
if damp_factor is None:
damp_factor = self.damp
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = numpy.array((dm * .5, dm * .5))
self._focka_ao = h1e + vhf[0]
self._fockb_ao = h1e + vhf[1]
ncore = (self.mol.nelectron - self.mol.spin) // 2
nopen = self.mol.spin
nocc = ncore + nopen
dmsf = dm[0] + dm[1]
mo_space = scipy.linalg.eigh(-dmsf, s1e, type=2)[1]
fa = reduce(numpy.dot, (mo_space.T, self._focka_ao, mo_space))
fb = reduce(numpy.dot, (mo_space.T, self._fockb_ao, mo_space))
feff = (fa + fb) * .5
feff[:ncore, ncore:nocc] = fb[:ncore, ncore:nocc]
feff[ncore:nocc, :ncore] = fb[ncore:nocc, :ncore]
feff[nocc:, ncore:nocc] = fa[nocc:, ncore:nocc]
feff[ncore:nocc, nocc:] = fa[ncore:nocc, nocc:]
cinv = numpy.dot(mo_space.T, s1e)
f = reduce(numpy.dot, (cinv.T, feff, cinv))
if 0 <= cycle < diis_start_cycle - 1:
f = hf.damping(s1e, dm[0], f, damp_factor)
if adiis and cycle >= diis_start_cycle:
f = adiis.update(s1e, dm[0], f)
f = hf.level_shift(s1e, dm[0], f, level_shift_factor)
return f
def get_fock(self, h1e, s1e, vhf, dm, cycle=-1, adiis=None,
diis_start_cycle=None, level_shift_factor=None,
damp_factor=None):
# Roothaan's effective fock
# http://www-theor.ch.cam.ac.uk/people/ross/thesis/node15.html
# | closed open virtual
# ----------------------------------------
# closed | Fc Fb Fc
# open | Fb Fc Fa
# virtual | Fc Fa Fc
# Fc = (Fa+Fb)/2
if diis_start_cycle is None:
diis_start_cycle = self.diis_start_cycle
if level_shift_factor is None:
level_shift_factor = self.level_shift
if damp_factor is None:
damp_factor = self.damp
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = numpy.array((dm*.5, dm*.5))
self._focka_ao = h1e + vhf[0]
self._fockb_ao = h1e + vhf[1]
ncore = (self.mol.nelectron-self.mol.spin) // 2
nopen = self.mol.spin
nocc = ncore + nopen
dmsf = dm[0]+dm[1]
mo_space = scipy.linalg.eigh(-dmsf, s1e, type=2)[1]
fa = reduce(numpy.dot, (mo_space.T, self._focka_ao, mo_space))
fb = reduce(numpy.dot, (mo_space.T, self._fockb_ao, mo_space))
feff = (fa + fb) * .5
feff[:ncore,ncore:nocc] = fb[:ncore,ncore:nocc]
feff[ncore:nocc,:ncore] = fb[ncore:nocc,:ncore]
feff[nocc:,ncore:nocc] = fa[nocc:,ncore:nocc]
feff[ncore:nocc,nocc:] = fa[ncore:nocc,nocc:]
cinv = numpy.dot(mo_space.T, s1e)
f = reduce(numpy.dot, (cinv.T, feff, cinv))
if 0 <= cycle < diis_start_cycle-1:
f = hf.damping(s1e, dm[0], f, damp_factor)
if adiis and cycle >= diis_start_cycle:
f = adiis.update(s1e, dm[0], f)
f = hf.level_shift(s1e, dm[0], f, level_shift_factor)
return f
