def print_properties(name, natm, nmo):
aom = numpy.zeros((natm,nmo,nmo))
totaom = numpy.zeros((nmo,nmo))
props = numpy.zeros((natm,NPROPS))
totprops = numpy.zeros((NPROPS))
with h5py.File(name) as f:
for i in range(natm):
idx = 'atom_props'+str(i)
props[i] = f[idx+'/totprops'].value
idx = 'ovlp'+str(i)
aom[i] = f[idx+'/aom'].value
for i in range(natm):
log.info('Follow AOM for atom %d', i)
dump_tri(sys.stdout, aom[i], ncol=NCOL, digits=DIGITS, start=0)
totaom += aom[i]
for j in range(NPROPS):
log.info('Nuclei %d prop %s value : %8.5f', i, PROPS[j], props[i,j])
totprops[j] += props[i,j]
for j in range(NPROPS):
log.info('Tot prop %s value : %8.5f', PROPS[j], totprops[j])
log.info('Follow total AOM')
dump_tri(sys.stdout, totaom, ncol=NCOL, digits=DIGITS, start=0)
i = numpy.identity(nmo)
diff = numpy.linalg.norm(totaom-i)
log.info('Diff in S matrix : %8.5f', diff)
def analyze(self, mo_coeff=None, ci=None, verbose=logger.DEBUG):
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
nelecas = self.nelecas
ncas = self.ncas
ncore = self.ncore
casdm1a, casdm1b = self.fcisolver.make_rdm1s(ci, ncas, nelecas)
mocore = mo_coeff[0][:, :ncore[0]]
mocas = mo_coeff[0][:, ncore[0]:ncore[0] + ncas]
dm1a = numpy.dot(mocore, mocore.T)
dm1a += reduce(numpy.dot, (mocas, casdm1a, mocas.T))
mocore = mo_coeff[1][:, :ncore[1]]
mocas = mo_coeff[1][:, ncore[1]:ncore[1] + ncas]
dm1b = numpy.dot(mocore, mocore.T)
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
if verbose >= logger.INFO:
log = logger.Logger(self.stdout, verbose)
label = self.mol.spheric_labels(True)
if log.verbose >= logger.DEBUG:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
s = reduce(
numpy.dot,
(mo_coeff[0].T, self._scf.get_ovlp(), self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s) > .4)
for i, j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
s = reduce(
numpy.dot,
(mo_coeff[1].T, self._scf.get_ovlp(), self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s) > .4)
for i, j in idx:
log.info('beta <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
log.info('\n** Largest CI components **')
if ci is not None and numpy.ndim(ci) >= 2:
if ci[0].ndim == 2:
for i, state in enumerate(ci):
log.info(
' string alpha, string beta, state %d CI coefficients',
i)
for c, ia, ib in fci.addons.large_ci(
state, self.ncas, self.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
else:
log.info(' string alpha, string beta, CI coefficients')
for c, ia, ib in fci.addons.large_ci(
ci, self.ncas, self.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
return dm1a, dm1b
def analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO):
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(casscf.stdout, verbose)
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci, ncas, nelecas)
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
if log.verbose >= logger.INFO:
label = ['%d%3s %s%-4s' % x for x in casscf.mol.spheric_labels()]
if log.verbose >= logger.DEBUG:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label)
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-(casdm1a+casdm1b), ncore, nocc)
log.info('Natural occ %s', str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k,i] < 0:
ucas[:,i] *= -1
mo_cas = numpy.dot(mo_coeff[:,ncore:nocc], ucas)
log.info('Natural orbital in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
s = reduce(numpy.dot, (casscf.mo_coeff.T, casscf._scf.get_ovlp(),
casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<mo-mcscf|mo-hf> %d, %d, %12.8f', i+1, j+1, s[i,j])
log.info('** Largest CI components **')
log.info(' string alpha, string beta, CI coefficients')
for c,ia,ib in fci.addons.large_ci(ci, casscf.ncas, casscf.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
dm1 = dm1a + dm1b
s = casscf._scf.get_ovlp()
casscf._scf.mulliken_pop(casscf.mol, dm1, s, verbose=log)
casscf._scf.mulliken_pop_meta_lowdin_ao(casscf.mol, dm1, verbose=log)
return dm1a, dm1b
def analyze(self, mo_coeff=None, ci=None, verbose=logger.DEBUG):
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
nelecas = self.nelecas
ncas = self.ncas
ncore = self.ncore
casdm1a, casdm1b = self.fcisolver.make_rdm1s(ci, ncas, nelecas)
mocore = mo_coeff[0][:,:ncore[0]]
mocas = mo_coeff[0][:,ncore[0]:ncore[0]+ncas]
dm1a = numpy.dot(mocore, mocore.T)
dm1a += reduce(numpy.dot, (mocas, casdm1a, mocas.T))
mocore = mo_coeff[1][:,:ncore[1]]
mocas = mo_coeff[1][:,ncore[1]:ncore[1]+ncas]
dm1b = numpy.dot(mocore, mocore.T)
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
if verbose >= logger.INFO:
log = logger.Logger(self.stdout, verbose)
label = self.mol.spheric_labels(True)
if log.verbose >= logger.DEBUG:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
s = reduce(numpy.dot, (mo_coeff[0].T, self._scf.get_ovlp(),
self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d %d %12.8f' % (i+1,j+1,s[i,j]))
s = reduce(numpy.dot, (mo_coeff[1].T, self._scf.get_ovlp(),
self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('beta <mo-mcscf|mo-hf> %d %d %12.8f' % (i+1,j+1,s[i,j]))
log.info('\n** Largest CI components **')
if ci is not None and numpy.ndim(ci) >= 2:
if ci[0].ndim == 2:
for i, state in enumerate(ci):
log.info(' string alpha, string beta, state %d CI coefficients', i)
for c,ia,ib in fci.addons.large_ci(state, self.ncas, self.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
else:
log.info(' string alpha, string beta, CI coefficients')
for c,ia,ib in fci.addons.large_ci(ci, self.ncas, self.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
return dm1a, dm1b
def analyze(self, mo_coeff=None, ci=None, verbose=logger.DEBUG):
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
casdm1a, casdm1b = self.fcisolver.make_rdm1s(ci, ncas, nelecas)
mocore = mo_coeff[0][:,:ncore[0]]
mocas = mo_coeff[0][:,ncore[0]:ncore[0]+ncas]
dm1a = numpy.dot(mocore, mocore.T)
dm1a += reduce(numpy.dot, (mocas, casdm1a, mocas.T))
mocore = mo_coeff[1][:,:ncore[1]]
mocas = mo_coeff[1][:,ncore[1]:ncore[1]+ncas]
dm1b = numpy.dot(mocore, mocore.T)
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
if verbose >= logger.INFO:
log = logger.Logger(self.stdout, verbose)
label = ['%d%3s %s%-4s' % x for x in self.mol.spheric_labels()]
if log.verbose >= logger.DEBUG:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
s = reduce(numpy.dot, (mo_coeff[0].T, self._scf.get_ovlp(),
self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d, %d, %12.8f' % (i+1,j+1,s[i,j]))
s = reduce(numpy.dot, (mo_coeff[1].T, self._scf.get_ovlp(),
self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('beta <mo-mcscf|mo-hf> %d, %d, %12.8f' % (i+1,j+1,s[i,j]))
ss = self.spin_square(ci, mo_coeff, self._scf.get_ovlp())
log.info('\nS^2 = %.7f, 2S+1 = %.7f', ss[0], ss[1])
log.info('\n** Largest CI components **')
log.info(' string alpha, string beta, CI coefficients')
for c,ia,ib in fci.addons.large_ci(ci, self.ncas, self.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
return dm1a, dm1b
def build(self):
t0 = (time.clock(), time.time())
lib.logger.TIMER_LEVEL = 3
self.mol = lib.chkfile.load_mol(self.chkfile)
self.nelectron = self.mol.nelectron
self.charge = self.mol.charge
self.spin = self.mol.spin
self.natm = self.mol.natm
self.coords = numpy.asarray([(numpy.asarray(atom[1])).tolist()
for atom in self.mol._atom])
self.charges = self.mol.atom_charges()
if (self.cas):
self.mo_coeff = lib.chkfile.load(self.chkfile, 'mcscf/mo_coeff')
else:
self.mo_coeff = lib.chkfile.load(self.chkfile, 'scf/mo_coeff')
self.mo_occ = lib.chkfile.load(self.chkfile, 'scf/mo_occ')
nprims, nmo = self.mo_coeff.shape
self.nprims = nprims
self.nmo = nmo
if self.charges[self.inuc] == 1:
self.rad = grid.BRAGG[self.charges[self.inuc]]
else:
self.rad = grid.BRAGG[self.charges[self.inuc]] * 0.5
if (self.corr):
self.rdm1 = lib.chkfile.load(self.chkfile, 'rdm/rdm1')
natocc, natorb = numpy.linalg.eigh(self.rdm1)
natorb = numpy.dot(self.mo_coeff, natorb)
self.mo_coeff = natorb
self.mo_occ = natocc
nocc = self.mo_occ[abs(self.mo_occ) > self.occdrop]
nocc = len(nocc)
self.nocc = nocc
idx = 'atom' + str(self.inuc)
with h5py.File(self.surfile) as f:
self.xnuc = f[idx + '/xnuc'].value
self.xyzrho = f[idx + '/xyzrho'].value
self.npang = f[idx + '/npang'].value
self.ntrial = f[idx + '/ntrial'].value
self.rmin = f[idx + '/rmin'].value
self.rmax = f[idx + '/rmax'].value
self.rsurf = f[idx + '/rsurf'].value
self.nlimsurf = f[idx + '/nlimsurf'].value
self.agrids = f[idx + '/coords'].value
self.brad = self.rmin * self.betafac
if self.verbose >= logger.WARN:
self.check_sanity()
if self.verbose > logger.NOTE:
self.dump_input()
if (self.iqudr == 'legendre'):
self.iqudr = 1
if (self.biqudr == 'legendre'):
self.biqudr = 1
if (self.mapr == 'becke'):
self.mapr = 1
elif (self.mapr == 'exp'):
self.mapr = 2
elif (self.mapr == 'none'):
self.mapr = 0
if (self.bmapr == 'becke'):
self.bmapr = 1
elif (self.bmapr == 'exp'):
self.bmapr = 2
elif (self.bmapr == 'none'):
self.bmapr = 0
if (self.full):
self.nocc = self.nmo
nocc = self.nmo
else:
nocc = self.mo_occ[self.mo_occ > self.occdrop]
nocc = len(nocc)
self.nocc = nocc
self.aom = numpy.zeros((nocc, nocc))
with lib.with_omp_threads(self.nthreads):
aomb = int_beta(self)
aoma = out_beta(self)
idx = 0
for i in range(nocc):
for j in range(i + 1):
self.aom[i, j] = aoma[idx] + aomb[idx]
self.aom[j, i] = self.aom[i, j]
idx += 1
if (self.nmo <= 30):
dump_tri(self.stdout, self.aom, ncol=NCOL, digits=DIGITS, start=0)
logger.info(self, 'Write info to HDF5 file')
atom_dic = {'aom': self.aom}
lib.chkfile.save(self.surfile, 'ovlp' + str(self.inuc), atom_dic)
logger.info(self, '')
logger.info(self, 'AOM of atom %d done', self.inuc)
logger.timer(self, 'AOM build', *t0)
return self
def analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO,
large_ci_tol=.1, **kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(casscf.stdout, verbose)
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
label = casscf.mol.spheric_labels(True)
if isinstance(ci, (tuple, list)):
ci0 = ci[0]
log.info('** Natural natural orbitals are based on the first root **')
else:
ci0 = ci
if ci0 is None and hasattr(casscf, 'casdm1'):
casdm1 = casscf.casdm1
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
elif hasattr(casscf.fcisolver, 'make_rdm1s'):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci0, ncas, nelecas)
casdm1 = casdm1a + casdm1b
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG1:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(ci0, ncas, nelecas)
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k,i] < 0:
ucas[:,i] *= -1
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff[:,ncore:nocc], ucas))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
s = reduce(numpy.dot, (casscf.mo_coeff.T, ovlp_ao, casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<mo-mcscf|mo-hf> %d %d %12.8f', i+1, j+1, s[i,j])
if hasattr(casscf.fcisolver, 'large_ci') and ci is not None:
log.info('** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, civec in enumerate(ci):
res = casscf.fcisolver.large_ci(civec, casscf.ncas, casscf.nelecas)
log.info(' string alpha, string beta, state %d CI coefficient', i)
for c,ia,ib in res:
log.info(' %9s %9s %.12f', ia, ib, c)
else:
log.info(' string alpha, string beta, CI coefficient')
res = casscf.fcisolver.large_ci(ci, casscf.ncas, casscf.nelecas)
for c,ia,ib in res:
log.info(' %9s %9s %.12f', ia, ib, c)
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def analyze(self,
mo_coeff=None,
ci=None,
verbose=None,
large_ci_tol=LARGE_CI_TOL,
with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
log = logger.new_logger(self, verbose)
nelecas = self.nelecas
ncas = self.ncas
ncore = self.ncore
mocore_a = mo_coeff[0][:, :ncore[0]]
mocas_a = mo_coeff[0][:, ncore[0]:ncore[0] + ncas]
mocore_b = mo_coeff[1][:, :ncore[1]]
mocas_b = mo_coeff[1][:, ncore[1]:ncore[1] + ncas]
label = self.mol.ao_labels()
if (isinstance(ci, (list, tuple)) and
not isinstance(self.fcisolver, addons.StateAverageFCISolver)):
log.warn(
'Mulitple states found in UCASCI solver. Density '
'matrix of first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
casdm1a, casdm1b = self.fcisolver.make_rdm1s(civec, ncas, nelecas)
dm1a = numpy.dot(mocore_a, mocore_a.T)
dm1a += reduce(numpy.dot, (mocas_a, casdm1a, mocas_a.T))
dm1b = numpy.dot(mocore_b, mocore_b.T)
dm1b += reduce(numpy.dot, (mocas_b, casdm1b, mocas_b.T))
if log.verbose >= logger.DEBUG2:
log.debug2('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.debug2('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
if log.verbose >= logger.INFO:
ovlp_ao = self._scf.get_ovlp()
occa, ucasa = self._eig(-casdm1a, ncore[0], ncore[0] + ncas)
occb, ucasb = self._eig(-casdm1b, ncore[1], ncore[1] + ncas)
log.info('Natural alpha-occupancy %s', str(-occa))
log.info('Natural beta-occupancy %s', str(-occb))
mocas_a = numpy.dot(mocas_a, ucasa)
mocas_b = numpy.dot(mocas_b, ucasb)
if with_meta_lowdin:
orth_coeff = orth.orth_ao(self.mol, 'meta_lowdin', s=ovlp_ao)
mocas_a = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_a))
mocas_b = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_b))
log.info(
'Natural alpha-orbital (expansion on meta-Lowdin AOs) in CAS space'
)
dump_mat.dump_rec(log.stdout,
mocas_a,
label,
start=1,
**kwargs)
log.info(
'Natural beta-orbital (expansion on meta-Lowdin AOs) in CAS space'
)
dump_mat.dump_rec(log.stdout,
mocas_b,
label,
start=1,
**kwargs)
else:
log.info(
'Natural alpha-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout,
mocas_a,
label,
start=1,
**kwargs)
log.info(
'Natural beta-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout,
mocas_b,
label,
start=1,
**kwargs)
tol = getattr(__config__, 'mcscf_addons_map2hf_tol', 0.4)
s = reduce(numpy.dot,
(mo_coeff[0].T, ovlp_ao, self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s) > tol)
for i, j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
s = reduce(numpy.dot,
(mo_coeff[1].T, ovlp_ao, self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s) > tol)
for i, j in idx:
log.info('beta <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
if hasattr(self.fcisolver, 'large_ci') and ci is not None:
log.info('\n** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, state in enumerate(ci):
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient',
i)
res = self.fcisolver.large_ci(state,
self.ncas,
self.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient'
)
res = self.fcisolver.large_ci(ci,
self.ncas,
self.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
return dm1a, dm1b
def analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO):
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
if mo_coeff is None:
mo_coeff = casscf.mo_coeff
if ci is None:
ci = casscf.ci
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(casscf.stdout, verbose)
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
label = casscf.mol.spheric_labels(True)
if hasattr(casscf.fcisolver, "make_rdm1s"):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci, ncas, nelecas)
casdm1 = casdm1a + casdm1b
mocore = mo_coeff[:, :ncore]
mocas = mo_coeff[:, ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG1:
log.info("alpha density matrix (on AO)")
dump_mat.dump_tri(log.stdout, dm1a, label)
log.info("beta density matrix (on AO)")
dump_mat.dump_tri(log.stdout, dm1b, label)
else:
casdm1 = casscf.fcisolver.make_rdm1(ci, ncas, nelecas)
mocore = mo_coeff[:, :ncore]
mocas = mo_coeff[:, ncore:nocc]
dm1a = numpy.dot(mocore, mocore.T) * 2 + reduce(numpy.dot, (mocas, casdm1, mocas.T))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info("Natural occ %s", str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k, i] < 0:
ucas[:, i] *= -1
mo_cas = numpy.dot(mo_coeff[:, ncore:nocc], ucas)
log.info("Natural orbital in CAS space")
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if casscf._scf.mo_coeff is not None:
s = reduce(numpy.dot, (casscf.mo_coeff.T, casscf._scf.get_ovlp(), casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s) > 0.4)
for i, j in idx:
log.info("<mo-mcscf|mo-hf> %d %d %12.8f", i + 1, j + 1, s[i, j])
if ci is not None:
log.info("** Largest CI components **")
log.info(" string alpha, string beta, CI coefficients")
for c, ia, ib in fci.addons.large_ci(ci, casscf.ncas, casscf.nelecas):
log.info(" %9s %9s %.12f", ia, ib, c)
s = casscf._scf.get_ovlp()
# casscf._scf.mulliken_pop(casscf.mol, dm1, s, verbose=log)
casscf._scf.mulliken_pop_meta_lowdin_ao(casscf.mol, dm1, verbose=log)
return dm1a, dm1b
def analyze(self, mo_coeff=None, ci=None, verbose=None,
large_ci_tol=LARGE_CI_TOL, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
log = logger.new_logger(self, verbose)
nelecas = self.nelecas
ncas = self.ncas
ncore = self.ncore
mocore_a = mo_coeff[0][:,:ncore[0]]
mocas_a = mo_coeff[0][:,ncore[0]:ncore[0]+ncas]
mocore_b = mo_coeff[1][:,:ncore[1]]
mocas_b = mo_coeff[1][:,ncore[1]:ncore[1]+ncas]
label = self.mol.ao_labels()
if (isinstance(ci, (list, tuple)) and
not isinstance(self.fcisolver, addons.StateAverageFCISolver)):
log.warn('Mulitple states found in UCASCI solver. Density '
'matrix of first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
casdm1a, casdm1b = self.fcisolver.make_rdm1s(civec, ncas, nelecas)
dm1a = numpy.dot(mocore_a, mocore_a.T)
dm1a += reduce(numpy.dot, (mocas_a, casdm1a, mocas_a.T))
dm1b = numpy.dot(mocore_b, mocore_b.T)
dm1b += reduce(numpy.dot, (mocas_b, casdm1b, mocas_b.T))
if log.verbose >= logger.DEBUG2:
log.debug2('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.debug2('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
if log.verbose >= logger.INFO:
ovlp_ao = self._scf.get_ovlp()
occa, ucasa = self._eig(-casdm1a, ncore[0], ncore[0]+ncas)
occb, ucasb = self._eig(-casdm1b, ncore[1], ncore[1]+ncas)
log.info('Natural alpha-occupancy %s', str(-occa))
log.info('Natural beta-occupancy %s', str(-occb))
mocas_a = numpy.dot(mocas_a, ucasa)
mocas_b = numpy.dot(mocas_b, ucasb)
if with_meta_lowdin:
orth_coeff = orth.orth_ao(self.mol, 'meta_lowdin', s=ovlp_ao)
mocas_a = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_a))
mocas_b = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_b))
log.info('Natural alpha-orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_a, label, start=1, **kwargs)
log.info('Natural beta-orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_b, label, start=1, **kwargs)
else:
log.info('Natural alpha-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_a, label, start=1, **kwargs)
log.info('Natural beta-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_b, label, start=1, **kwargs)
tol = getattr(__config__, 'mcscf_addons_map2hf_tol', 0.4)
s = reduce(numpy.dot, (mo_coeff[0].T, ovlp_ao, self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s)>tol)
for i,j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d %d %12.8f' % (i+1,j+1,s[i,j]))
s = reduce(numpy.dot, (mo_coeff[1].T, ovlp_ao, self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s)>tol)
for i,j in idx:
log.info('beta <mo-mcscf|mo-hf> %d %d %12.8f' % (i+1,j+1,s[i,j]))
if getattr(self.fcisolver, 'large_ci', None) and ci is not None:
log.info('\n** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, state in enumerate(ci):
log.info(' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient', i)
res = self.fcisolver.large_ci(state, self.ncas, self.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient')
res = self.fcisolver.large_ci(ci, self.ncas, self.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
return dm1a, dm1b
rdm1[i, i] = 2.0
# from AO basis to MO basis
s = coeff.T.dot(s).dot(coeff)
pop = numpy.einsum('ij,ji->', s, rdm1)
lib.logger.info(mol, '* Info on MO basis')
lib.logger.info(mol, 'Population : %12.6f' % pop)
# From MO basis to AO basis
coeff = numpy.linalg.inv(coeff)
s = coeff.T.dot(s).dot(coeff)
pop = numpy.einsum('ij,ji->', s, dm)
lib.logger.info(mol, '* Backtransform from MO to AO basis')
lib.logger.info(mol, 'Population : %12.6f' % pop)
lib.logger.info(mol, '* Overlap on AO basis')
dump_tri(mol.stdout, s, ncol=15, digits=5, start=0)
# Reference AO basis
with h5py.File(name + '_integrals.h5') as f:
sref = f['molecule/overlap'].value
lib.logger.info(mol, '* REF Overlap on AO basis')
dump_tri(mol.stdout, sref, ncol=15, digits=5, start=0)
# Read info from aom program
aom = numpy.zeros((mol.natm, nmo, nmo))
totaom = numpy.zeros((nmo, nmo))
with h5py.File(name + '.chk.h5') as f:
for i in range(mol.natm):
idx = 'ovlp' + str(i)
aom[i] = f[idx + '/aom'].value
for i in range(mol.natm):
def analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(casscf.stdout, verbose)
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
label = casscf.mol.spheric_labels(True)
if hasattr(casscf.fcisolver, 'make_rdm1s'):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci, ncas, nelecas)
casdm1 = casdm1a + casdm1b
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG1:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label)
else:
casdm1 = casscf.fcisolver.make_rdm1(ci, ncas, nelecas)
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k,i] < 0:
ucas[:,i] *= -1
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff[:,ncore:nocc], ucas))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if casscf._scf.mo_coeff is not None:
s = reduce(numpy.dot, (casscf.mo_coeff.T, ovlp_ao, casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<mo-mcscf|mo-hf> %d %d %12.8f', i+1, j+1, s[i,j])
if ci is not None and numpy.ndim(ci) >= 2:
log.info('** Largest CI components **')
if ci[0].ndim == 2:
for i, state in enumerate(ci):
log.info(' string alpha, string beta, state %d CI coefficients', i)
for c,ia,ib in fci.addons.large_ci(state, casscf.ncas, casscf.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
else:
log.info(' string alpha, string beta, CI coefficients')
for c,ia,ib in fci.addons.large_ci(ci, casscf.ncas, casscf.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def build(self):
t0 = (time.clock(), time.time())
lib.logger.TIMER_LEVEL = 3
self.cell = libpbc.chkfile.load_cell(self.chkfile)
self.a = self.cell.lattice_vectors()
self.b = self.cell.reciprocal_vectors()
self.vol = self.cell.vol
self.nelectron = self.cell.nelectron
self.charge = self.cell.charge
self.spin = self.cell.spin
self.natm = self.cell.natm
self.ls = self.cell.get_lattice_Ls(dimension=self.cell.dimension)
self.ls = self.ls[numpy.argsort(lib.norm(self.ls, axis=1))]
self.kpts = lib.chkfile.load(self.chkfile, 'kcell/kpts')
self.nkpts = len(self.kpts)
self.coords = numpy.asarray([(numpy.asarray(atom[1])).tolist()
for atom in self.cell._atom])
self.charges = self.cell.atom_charges()
if self.charges[self.inuc] == 1:
self.rad = grid.BRAGG[self.charges[self.inuc]]
else:
self.rad = grid.BRAGG[self.charges[self.inuc]] * 0.5
idx = 'atom' + str(self.inuc)
with h5py.File(self.surfile) as f:
self.xnuc = f[idx + '/xnuc'].value
self.xyzrho = f[idx + '/xyzrho'].value
self.npang = f[idx + '/npang'].value
self.ntrial = f[idx + '/ntrial'].value
self.rmin = f[idx + '/rmin'].value
self.rmax = f[idx + '/rmax'].value
self.rsurf = f[idx + '/rsurf'].value
self.nlimsurf = f[idx + '/nlimsurf'].value
self.agrids = f[idx + '/coords'].value
self.brad = self.rmin * self.betafac
# TODO: general orbitals
mo_coeff = lib.chkfile.load(self.chkfile, 'scf/mo_coeff')
nprims, nmo = mo_coeff[0].shape
if (self.orbs == -1):
self.orbs = nmo
self.nprims = nprims
self.nmo = self.orbs * self.nkpts
self.mo_coeff = numpy.zeros((self.nprims, self.nmo),
dtype=numpy.complex128)
self.tags = numpy.zeros(self.nmo, dtype=numpy.int32)
ii = 0
for k in range(self.nkpts):
for i in range(self.orbs):
self.mo_coeff[:, ii] = mo_coeff[k][:, i]
self.tags[ii] = k
ii += 1
if self.verbose >= logger.WARN:
self.check_sanity()
if self.verbose > logger.NOTE:
self.dump_input()
if (self.iqudr == 'legendre'):
self.iqudr = 1
if (self.biqudr == 'legendre'):
self.biqudr = 1
if (self.mapr == 'becke'):
self.mapr = 1
elif (self.mapr == 'exp'):
self.mapr = 2
elif (self.mapr == 'none'):
self.mapr = 0
if (self.bmapr == 'becke'):
self.bmapr = 1
elif (self.bmapr == 'exp'):
self.bmapr = 2
elif (self.bmapr == 'none'):
self.bmapr = 0
self.aom = numpy.zeros((self.nmo, self.nmo), dtype=numpy.complex128)
with lib.with_omp_threads(self.nthreads):
aomb = int_beta(self)
aoma = out_beta(self)
idx = 0
for i in range(self.nmo):
for j in range(i + 1):
self.aom[i, j] = aoma[idx] + aomb[idx]
self.aom[j, i] = self.aom[i, j].conj()
idx += 1
norm = float(1.0 / self.nkpts)
self.aom = self.aom * norm
if (self.nmo <= 30):
dump_tri(self.stdout, self.aom, ncol=NCOL, digits=DIGITS, start=0)
logger.info(self, 'Write info to HDF5 file')
atom_dic = {'aom': self.aom}
lib.chkfile.save(self.surfile, 'ovlp' + str(self.inuc), atom_dic)
logger.info(self, '')
logger.info(self, 'AOM of atom %d done', self.inuc)
logger.timer(self, 'AOM build', *t0)
return self
def analyze(self,
mo_coeff=None,
ci=None,
verbose=logger.DEBUG,
large_ci_tol=0.1,
**kwargs):
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
nelecas = self.nelecas
ncas = self.ncas
ncore = self.ncore
casdm1a, casdm1b = self.fcisolver.make_rdm1s(ci, ncas, nelecas)
mocore = mo_coeff[0][:, :ncore[0]]
mocas = mo_coeff[0][:, ncore[0]:ncore[0] + ncas]
dm1a = numpy.dot(mocore, mocore.T)
dm1a += reduce(numpy.dot, (mocas, casdm1a, mocas.T))
mocore = mo_coeff[1][:, :ncore[1]]
mocas = mo_coeff[1][:, ncore[1]:ncore[1] + ncas]
dm1b = numpy.dot(mocore, mocore.T)
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
if verbose >= logger.INFO:
log = logger.Logger(self.stdout, verbose)
label = self.mol.ao_labels()
if log.verbose >= logger.DEBUG:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
s = reduce(
numpy.dot,
(mo_coeff[0].T, self._scf.get_ovlp(), self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s) > .4)
for i, j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
s = reduce(
numpy.dot,
(mo_coeff[1].T, self._scf.get_ovlp(), self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s) > .4)
for i, j in idx:
log.info('beta <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
log.info('\n** Largest CI components **')
if (hasattr(self.fcisolver, 'large_ci') and ci is not None
and numpy.ndim(ci) >= 2):
if ci[0].ndim == 2:
for i, state in enumerate(ci):
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient',
i)
res = self.fcisolver.large_ci(state,
self.ncas,
self.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient'
)
res = self.fcisolver.large_ci(ci,
self.ncas,
self.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
return dm1a, dm1b
def analyze(casscf,
mo_coeff=None,
ci=None,
verbose=logger.INFO,
large_ci_tol=.1,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
log = logger.new_logger(casscf, verbose)
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
label = casscf.mol.ao_labels()
if isinstance(ci, (tuple, list)):
ci0 = ci[0]
log.info('** Natural natural orbitals are based on the first root **')
else:
ci0 = ci
if ci0 is None and hasattr(casscf, 'casdm1'):
casdm1 = casscf.casdm1
mocore = mo_coeff[:, :ncore]
mocas = mo_coeff[:, ncore:nocc]
dm1a = (numpy.dot(mocore, mocore.T) * 2 +
reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
elif hasattr(casscf.fcisolver, 'make_rdm1s'):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci0, ncas, nelecas)
casdm1 = casdm1a + casdm1b
mocore = mo_coeff[:, :ncore]
mocas = mo_coeff[:, ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG2:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(ci0, ncas, nelecas)
mocore = mo_coeff[:, :ncore]
mocas = mo_coeff[:, ncore:nocc]
dm1a = (numpy.dot(mocore, mocore.T) * 2 +
reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k, i] < 0:
ucas[:, i] *= -1
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot,
(orth_coeff.T, ovlp_ao, mo_coeff[:, ncore:nocc], ucas))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1, **kwargs)
if log.verbose >= logger.DEBUG2:
if not casscf.natorb:
log.debug2(
'NOTE: mc.mo_coeff in active space is different to '
'the natural orbital coefficients printed in above.')
log.debug2(
' ** CASCI/CASSCF orbital coefficients (expansion on meta-Lowdin AOs) **'
)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
dump_mat.dump_rec(log.stdout, c, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
s = reduce(numpy.dot,
(casscf.mo_coeff.T, ovlp_ao, casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s) > .4)
for i, j in idx:
log.info('<mo-mcscf|mo-hf> %d %d %12.8f', i + 1, j + 1, s[i,
j])
if hasattr(casscf.fcisolver, 'large_ci') and ci is not None:
log.info('** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, civec in enumerate(ci):
res = casscf.fcisolver.large_ci(civec,
casscf.ncas,
casscf.nelecas,
large_ci_tol,
return_strs=False)
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient',
i)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient'
)
res = casscf.fcisolver.large_ci(ci,
casscf.ncas,
casscf.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def analyze(casscf,
mo_coeff=None,
ci=None,
verbose=None,
large_ci_tol=LARGE_CI_TOL,
with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
log = logger.new_logger(casscf, verbose)
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
mocore = mo_coeff[:, :ncore]
mocas = mo_coeff[:, ncore:nocc]
label = casscf.mol.ao_labels()
if (isinstance(ci, (list, tuple)) and
not isinstance(casscf.fcisolver, addons.StateAverageFCISolver)):
log.warn(
'Mulitple states found in CASCI/CASSCF solver. Density '
'matrix of the first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
if getattr(casscf.fcisolver, 'make_rdm1s', None):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(civec, ncas, nelecas)
casdm1 = casdm1a + casdm1b
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG2:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(civec, ncas, nelecas)
dm1a = (numpy.dot(mocore, mocore.T) * 2 +
reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
mocas = numpy.dot(mocas, ucas)
if with_meta_lowdin:
log.info(
'Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mocas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas))
else:
log.info('Natural orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas, label, start=1, **kwargs)
if log.verbose >= logger.DEBUG2:
if not casscf.natorb:
log.debug2(
'NOTE: mc.mo_coeff in active space is different to '
'the natural orbital coefficients printed in above.')
if with_meta_lowdin:
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
log.debug2('MCSCF orbital (expansion on meta-Lowdin AOs)')
else:
c = mo_coeff
log.debug2('MCSCF orbital (expansion on AOs)')
dump_mat.dump_rec(log.stdout, c, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
addons.map2hf(casscf, casscf._scf.mo_coeff)
if getattr(casscf.fcisolver, 'large_ci', None) and ci is not None:
log.info('** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, civec in enumerate(ci):
res = casscf.fcisolver.large_ci(civec,
casscf.ncas,
casscf.nelecas,
large_ci_tol,
return_strs=False)
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient',
i)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient'
)
res = casscf.fcisolver.large_ci(ci,
casscf.ncas,
casscf.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
if with_meta_lowdin:
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
else:
casscf._scf.mulliken_pop(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def analyze(casscf, mo_coeff=None, ci=None, verbose=None,
large_ci_tol=LARGE_CI_TOL, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
log = logger.new_logger(casscf, verbose)
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
label = casscf.mol.ao_labels()
if (isinstance(ci, (list, tuple)) and
not isinstance(casscf.fcisolver, addons.StateAverageFCISolver)):
log.warn('Mulitple states found in CASCI/CASSCF solver. Density '
'matrix of first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
if getattr(casscf.fcisolver, 'make_rdm1s', None):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(civec, ncas, nelecas)
casdm1 = casdm1a + casdm1b
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG2:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(civec, ncas, nelecas)
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
mocas = numpy.dot(mocas, ucas)
if with_meta_lowdin:
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mocas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas))
else:
log.info('Natural orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas, label, start=1, **kwargs)
if log.verbose >= logger.DEBUG2:
if not casscf.natorb:
log.debug2('NOTE: mc.mo_coeff in active space is different to '
'the natural orbital coefficients printed in above.')
if with_meta_lowdin:
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
log.debug2('MCSCF orbital (expansion on meta-Lowdin AOs)')
else:
c = mo_coeff
log.debug2('MCSCF orbital (expansion on AOs)')
dump_mat.dump_rec(log.stdout, c, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
addons.map2hf(casscf, casscf._scf.mo_coeff)
if getattr(casscf.fcisolver, 'large_ci', None) and ci is not None:
log.info('** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, civec in enumerate(ci):
res = casscf.fcisolver.large_ci(civec, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
log.info(' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient', i)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient')
res = casscf.fcisolver.large_ci(ci, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
if with_meta_lowdin:
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
else:
casscf._scf.mulliken_pop(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b