def _cache_and_analyze_(self, calcname, E, focka_fockb, dma_dmb, JKidem,
JKcorr, oneRDMcorr_loc, loc2idem, loc2corr,
nelec_idem, oneRDM_loc, oneSDM_loc):
########################################################################################################
self.e_tot = E
self.activeVSPIN = (focka_fockb[0] - focka_fockb[1]) / 2
#self.activeFOCK = get_roothaan_fock (focka_fockb, dma_dmb, np.eye (self.norbs_tot))
self.activeFOCK = (focka_fockb[0] + focka_fockb[1]) / 2
self.activeJKidem = JKidem
self.activeJKcorr = JKcorr
self.oneRDMcorr_loc = oneRDMcorr_loc
self.oneSDMcorr_loc = oneSDM_loc
self.loc2idem = loc2idem
self.nelec_idem = nelec_idem
self.oneRDM_loc = oneRDM_loc
self.oneSDM_loc = oneSDM_loc
########################################################################################################
# Analysis: 1RDM and total energy
print("LASSCF trial wave function total energy: {:.9f}".format(E))
ao2molden, ene_no, occ_no = self.get_trial_nos(aobasis=True,
loc2wmas=loc2corr,
oneRDM_loc=oneRDM_loc,
fock=self.activeFOCK,
jmol_shift=True,
try_symmetrize=True)
if self.mol.verbose:
print("Writing trial wave function molden")
molden.from_mo(self.mol,
calcname + '_trial_wvfn.molden',
ao2molden,
occ=occ_no,
ene=ene_no)
def examine_wmcs (dmet_obj):
loc2wmas = np.concatenate ([f.loc2amo for f in dmet_obj.fragments], axis=1)
loc2wmcs = get_complementary_states (loc2wmas)
print ("Examining whole-molecule active space:")
loc2wmas = dmet_obj.ints.compare_basis_to_loc (loc2wmas, dmet_obj.fragments, quiet=False)[0]
norbs_wmas = np.array ([f.norbs_as for f in dmet_obj.fragments])
print ("Examining whole-molecule core space:")
norbs_wmcs_before = dmet_obj.ints.compare_basis_to_loc (loc2wmcs, dmet_obj.fragments, quiet=True)[1]
norbs_before = norbs_wmas + norbs_wmcs_before
ao2loc = dmet_obj.ints.ao2loc
loc2ao = ao2loc.conjugate ().T
ao2wmcs = np.dot (ao2loc, loc2wmcs)
ao2wmcs_new = boys.Boys (dmet_obj.ints.mol, ao2wmcs).kernel ()
aoOao_inv = np.linalg.inv (np.dot (ao2loc, loc2ao))
loc2wmcs_new = reduce (np.dot, [loc2ao, aoOao_inv, ao2wmcs_new])
loc2wmcs_new, norbs_wmcs_after = dmet_obj.ints.compare_basis_to_loc (loc2wmcs_new, dmet_obj.fragments, quiet=False)
norbs_after = norbs_wmas + norbs_wmcs_after
loc2new = np.append (loc2wmas, loc2wmcs_new, axis=1)
active_flag = np.append (np.ones (loc2wmas.shape[1]), np.zeros (loc2wmcs_new.shape[1]))
print ("Is the new basis orthonormal and complete? {0}".format (is_basis_orthonormal_and_complete (loc2new)))
print ("Fragment-orbital assignment breakdown:")
print ("Frag Before After")
for frag, bef, aft in zip (dmet_obj.fragments, norbs_before, norbs_after):
print ('{:>4s} {:6d} {:5d}'.format (frag.frag_name, int (bef), int (aft)))
filename = 'relocalized_basis.molden'
mol = dmet_obj.ints.mol.copy ()
ao2new = np.dot (dmet_obj.ints.ao2loc, loc2new)
molden.from_mo (mol, filename, ao2new, occ=active_flag)
'''
def make_guess_molden (frag, filename, imp2mo, norbs_cmo, norbs_amo):
norbs_tot = imp2mo.shape[1]
mo_occ = np.zeros (norbs_tot)
norbs_occ = norbs_cmo + norbs_amo
mo_occ[:norbs_cmo] = 2
mo_occ[norbs_cmo:norbs_occ] = 1
mo = reduce (np.dot, (frag.ints.ao2loc, frag.loc2imp, imp2mo))
molden.from_mo (frag.ints.mol, filename, mo, occ=mo_occ)
return
def test_dump_cartesian_gto_symm_orbital(self):
ftmp = tempfile.NamedTemporaryFile()
fname = ftmp.name
pmol = mol.copy()
pmol.cart = True
pmol.build()
mf = scf.RHF(pmol).run()
molden.from_mo(pmol, fname, mf.mo_coeff)
res = molden.read(fname)
mo_coeff = res[2]
self.assertAlmostEqual(abs(mf.mo_coeff - mo_coeff).max(), 0, 12)
def from_sa_mcscf(mc,
fname,
state=None,
cas_natorb=False,
cas_mo_energy=False,
**kwargs):
if state is None:
return from_mcscf(mc, fname, cas_natorb=cas_natorb, **kwargs)
casdm1 = mc.fcisolver.states_make_rdm1(mc.ci, mc.ncas, mc.nelecas)[state]
mo_coeff, mo_ci, mo_energy = mc.canonicalize(ci=mc.ci[state],
cas_natorb=cas_natorb,
casdm1=casdm1)
if not cas_mo_energy:
mo_energy[mc.ncore:][:mc.ncas] = 0.0
# TODO: cleaner interface. Probably invent "state_make_?dm*" functions ("state" singular)
# and apply them also to the StateAverageMCSCFSolver instance
mo_occ = np.zeros_like(mo_energy)
mo_occ[:mc.ncore] = 2.0
ci = mc.ci
ci[state] = mo_ci
mo_occ[mc.ncore:][:mc.ncas] = mc.fcisolver.states_make_rdm1(
ci, mc.ncas, mc.nelecas)[state].diagonal()
return from_mo(mc.mol,
fname,
mo_coeff,
occ=mo_occ,
ene=mo_energy,
**kwargs)
def visualize_mos(mol: gto.mole.Mole,
mo_coeff: np.ndarray,
act_mos: list,
nroot: int = 1,
name: str = 'act_mo',
keepmolden: bool = False,
mo_occ: list = None,
mo_ene: list = None):
r"""Function to visualize the active MOs via Jmol.
Orbitals are counted from 0!
Args:
mol: The molecule in PySCF's gto.Mole() format.
mo_coeff (np.ndarray): The MO coeff. matrix obtained via DMRG.
act_mos (list): The suggested active MOs which will be plotted.
nroot (int): Number of the root that is being plotted.
Only for purpose of naming.
name (str): Prefix of the filename for orbitals.
keepmolden (bool): Keep the molden file used for visualization.
mo_occ (list): MO_occupation to be written in molden file.
mo_ene (list): MO energy to be written in molden file.
"""
# Create molden orbitals
from pyscf.tools import molden
molden.from_mo(mol, 'asf_mos.molden', mo_coeff, ene=mo_ene, occ=mo_occ)
# Write jmol script
with open('plot.spt', 'w') as plotfile:
print('initialize;\nset background [xffffff];\nset frank off;\n',
'set autoBond true;\nset bondRadiusMilliAngstroms 66;\n',
'set bondTolerance 0.5;\nset forceAutoBond false;\n',
'load asf_mos.molden;\nrotate 45 x;\nrotate 45 y;\n', 'zoom 100;'
'',
file=plotfile)
for ii in act_mos:
print('isosurface color yellow purple mo ',
'%s translucent; write PNG 200 "%s_%s_%s.png"' %
(ii + 1, name, nroot, ii),
file=plotfile)
print('exitJmol;\n', file=plotfile)
os.system('jmol plot.spt')
os.remove('plot.spt')
idx_h0_2s = mol.search_ao_label ('0 H 2s')[0]
idx_h1_2s = mol.search_ao_label ('1 H 2s')[0]
dma = np.zeros ((nao, nao))
dmb = np.zeros ((nao, nao))
dma[idx_h0_1s,idx_h0_1s] = dmb[idx_h1_1s,idx_h1_1s] = dma[idx_h0_2s,idx_h0_2s] = dmb[idx_h1_2s,idx_h1_2s] = 1
dm0 = [dma, dmb]
# Restricted mean-field base of MC-SCF objects
mf = scf.RHF (mol).run ()
# MC-PDFT objects
if gsbasis:
gsmo = np.load (gsmofile)
mc = mcpdft.CASSCF (mf, transl_type + fnal, ncas, nelecas, grids_level = 3)
mo = mcscf.project_init_guess (mc, gsmo, prev_mol=gsmol)
molden.from_mo (mol, 'check_projection.molden', mo)
mc.kernel (mo)
mc = mc.as_scanner ()
else:
mc = mcpdft.CASSCF (mf, transl_type + fnal, ncas, nelecas, grids_level = 3).run ().as_scanner ()
np.save (mofile, mc.mo_coeff)
# Do MCSCF scan forwards
table = np.zeros ((HHrange.size, 9))
table[:,0] = HHrange
for ix, HHdist in enumerate (HHrange):
geom = 'H 0 0 0; H 0 0 {:.6f}'.format (HHdist)
table[ix,1] = mc (geom)
table[ix,2] = mc.e_mcscf
table[ix,3:] = list (mc.get_energy_decomposition ())
def solve (frag, guess_1RDM, chempot_imp):
# Augment OEI with the chemical potential
OEI = frag.impham_OEI_C - chempot_imp
# Do I need to get the full RHF solution?
guess_orbs_av = len (frag.imp_cache) == 2 or frag.norbs_as > 0
# Get the RHF solution
mol = gto.Mole()
abs_2MS = int (round (2 * abs (frag.target_MS)))
abs_2S = int (round (2 * abs (frag.target_S)))
sign_MS = int (np.sign (frag.target_MS)) or 1
mol.spin = abs_2MS
mol.verbose = 0
if frag.mol_stdout is None:
mol.output = frag.mol_output
mol.verbose = 0 if frag.mol_output is None else lib.logger.DEBUG
mol.atom.append(('H', (0, 0, 0)))
mol.nelectron = frag.nelec_imp
if frag.enforce_symmetry:
mol.groupname = frag.symmetry
mol.symm_orb = get_subspace_symmetry_blocks (frag.loc2imp, frag.loc2symm)
mol.irrep_name = frag.ir_names
mol.irrep_id = frag.ir_ids
mol.max_memory = frag.ints.max_memory
mol.build ()
if frag.mol_stdout is None:
frag.mol_stdout = mol.stdout
else:
mol.stdout = frag.mol_stdout
mol.verbose = 0 if frag.mol_output is None else lib.logger.DEBUG
if frag.enforce_symmetry: mol.symmetry = True
#mol.incore_anyway = True
mf = scf.RHF(mol)
mf.get_hcore = lambda *args: OEI
mf.get_ovlp = lambda *args: np.eye(frag.norbs_imp)
mf.energy_nuc = lambda *args: frag.impham_CONST
if frag.impham_CDERI is not None:
mf = mf.density_fit ()
mf.with_df._cderi = frag.impham_CDERI
else:
mf._eri = ao2mo.restore(8, frag.impham_TEI, frag.norbs_imp)
mf = fix_my_RHF_for_nonsinglet_env (mf, frag.impham_OEI_S)
mf.__dict__.update (frag.mf_attr)
if guess_orbs_av: mf.max_cycle = 2
mf.scf (guess_1RDM)
if (not mf.converged) and (not guess_orbs_av):
if np.any (np.abs (frag.impham_OEI_S) > 1e-8) and mol.spin != 0:
raise NotImplementedError('Gradient and Hessian fixes for nonsinglet environment of Newton-descent ROHF algorithm')
print ("CASSCF RHF-step not converged on fixed-point iteration; initiating newton solver")
mf = mf.newton ()
mf.kernel ()
# Instability check and repeat
if not guess_orbs_av:
for i in range (frag.num_mf_stab_checks):
if np.any (np.abs (frag.impham_OEI_S) > 1e-8) and mol.spin != 0:
raise NotImplementedError('ROHF stability-check fixes for nonsinglet environment')
mf.mo_coeff = mf.stability ()[0]
guess_1RDM = mf.make_rdm1 ()
mf = scf.RHF(mol)
mf.get_hcore = lambda *args: OEI
mf.get_ovlp = lambda *args: np.eye(frag.norbs_imp)
mf._eri = ao2mo.restore(8, frag.impham_TEI, frag.norbs_imp)
mf = fix_my_RHF_for_nonsinglet_env (mf, frag.impham_OEI_S)
mf.scf (guess_1RDM)
if not mf.converged:
mf = mf.newton ()
mf.kernel ()
E_RHF = mf.e_tot
print ("CASSCF RHF-step energy: {}".format (E_RHF))
# Get the CASSCF solution
CASe = frag.active_space[0]
CASorb = frag.active_space[1]
checkCAS = (CASe <= frag.nelec_imp) and (CASorb <= frag.norbs_imp)
if (checkCAS == False):
CASe = frag.nelec_imp
CASorb = frag.norbs_imp
if (abs_2MS > abs_2S):
CASe = ((CASe + sign_MS * abs_2S) // 2, (CASe - sign_MS * abs_2S) // 2)
else:
CASe = ((CASe + sign_MS * abs_2MS) // 2, (CASe - sign_MS * abs_2MS) // 2)
if frag.impham_CDERI is not None:
mc = mcscf.DFCASSCF(mf, CASorb, CASe)
else:
mc = mcscf.CASSCF(mf, CASorb, CASe)
smult = abs_2S + 1 if frag.target_S is not None else (frag.nelec_imp % 2) + 1
mc.fcisolver = csf_solver (mf.mol, smult, symm=frag.enforce_symmetry)
if frag.enforce_symmetry: mc.fcisolver.wfnsym = frag.wfnsym
mc.max_cycle_macro = 50 if frag.imp_maxiter is None else frag.imp_maxiter
mc.conv_tol = min (1e-9, frag.conv_tol_grad**2)
mc.ah_start_tol = mc.conv_tol / 10
mc.ah_conv_tol = mc.conv_tol / 10
mc.__dict__.update (frag.corr_attr)
mc = fix_my_CASSCF_for_nonsinglet_env (mc, frag.impham_OEI_S)
norbs_amo = mc.ncas
norbs_cmo = mc.ncore
norbs_imo = frag.norbs_imp - norbs_amo
nelec_amo = sum (mc.nelecas)
norbs_occ = norbs_amo + norbs_cmo
#mc.natorb = True
# Guess orbitals
ci0 = None
dm_imp = frag.get_oneRDM_imp ()
fock_imp = mf.get_fock (dm=dm_imp)
if len (frag.imp_cache) == 2:
imp2mo, ci0 = frag.imp_cache
print ("Taking molecular orbitals and ci vector from cache")
elif frag.norbs_as > 0:
nelec_imp_guess = int (round (np.trace (frag.oneRDMas_loc)))
norbs_cmo_guess = (frag.nelec_imp - nelec_imp_guess) // 2
print ("Projecting stored amos (frag.loc2amo; spanning {} electrons) onto the impurity basis and filling the remainder with default guess".format (nelec_imp_guess))
imp2mo, my_occ = project_amo_manually (frag.loc2imp, frag.loc2amo, fock_imp, norbs_cmo_guess, dm=frag.oneRDMas_loc)
elif frag.loc2amo_guess is not None:
print ("Projecting stored amos (frag.loc2amo_guess) onto the impurity basis (no amo dm available)")
imp2mo, my_occ = project_amo_manually (frag.loc2imp, frag.loc2amo_guess, fock_imp, norbs_cmo, dm=None)
frag.loc2amo_guess = None
else:
dm_imp = np.asarray (mf.make_rdm1 ())
while dm_imp.ndim > 2:
dm_imp = dm_imp.sum (0)
imp2mo = mf.mo_coeff
fock_imp = mf.get_fock (dm=dm_imp)
fock_mo = represent_operator_in_basis (fock_imp, imp2mo)
_, evecs = matrix_eigen_control_options (fock_mo, sort_vecs=1)
imp2mo = imp2mo @ evecs
my_occ = ((dm_imp @ imp2mo) * imp2mo).sum (0)
print ("No stored amos; using mean-field canonical MOs as initial guess")
# Guess orbital processing
if callable (frag.cas_guess_callback):
mo = reduce (np.dot, (frag.ints.ao2loc, frag.loc2imp, imp2mo))
mo = frag.cas_guess_callback (frag.ints.mol, mc, mo)
imp2mo = reduce (np.dot, (frag.imp2loc, frag.ints.ao2loc.conjugate ().T, frag.ints.ao_ovlp, mo))
frag.cas_guess_callback = None
# Guess CI vector
if len (frag.imp_cache) != 2 and frag.ci_as is not None:
loc2amo_guess = np.dot (frag.loc2imp, imp2mo[:,norbs_cmo:norbs_occ])
metric = np.arange (CASorb) + 1
gOc = np.dot (loc2amo_guess.conjugate ().T, (frag.ci_as_orb * metric[None,:]))
umat_g, svals, umat_c = matrix_svd_control_options (gOc, sort_vecs=1, only_nonzero_vals=True)
if (svals.size == norbs_amo):
print ("Loading ci guess despite shifted impurity orbitals; singular value error sum: {}".format (np.sum (svals - metric)))
imp2mo[:,norbs_cmo:norbs_occ] = np.dot (imp2mo[:,norbs_cmo:norbs_occ], umat_g)
ci0 = transform_ci_for_orbital_rotation (frag.ci_as, CASorb, CASe, umat_c)
else:
print ("Discarding stored ci guess because orbitals are too different (missing {} nonzero svals)".format (norbs_amo-svals.size))
# Symmetry align if possible
imp2unac = frag.align_imporbs_symm (np.append (imp2mo[:,:norbs_cmo], imp2mo[:,norbs_occ:], axis=1), sorting_metric=fock_imp,
sort_vecs=1, orbital_type='guess unactive', mol=mol)[0]
imp2mo[:,:norbs_cmo] = imp2unac[:,:norbs_cmo]
imp2mo[:,norbs_occ:] = imp2unac[:,norbs_cmo:]
#imp2mo[:,:norbs_cmo] = frag.align_imporbs_symm (imp2mo[:,:norbs_cmo], sorting_metric=fock_imp, sort_vecs=1, orbital_type='guess inactive', mol=mol)[0]
imp2mo[:,norbs_cmo:norbs_occ], umat = frag.align_imporbs_symm (imp2mo[:,norbs_cmo:norbs_occ], sorting_metric=fock_imp,
sort_vecs=1, orbital_type='guess active', mol=mol)
#imp2mo[:,norbs_occ:] = frag.align_imporbs_symm (imp2mo[:,norbs_occ:], sorting_metric=fock_imp, sort_vecs=1, orbital_type='guess external', mol=mol)[0]
if frag.enforce_symmetry:
imp2mo = cleanup_subspace_symmetry (imp2mo, mol.symm_orb)
err_symm = measure_subspace_blockbreaking (imp2mo, mol.symm_orb)
err_orth = measure_basis_nonorthonormality (imp2mo)
print ("Initial symmetry error after cleanup = {}".format (err_symm))
print ("Initial orthonormality error after cleanup = {}".format (err_orth))
if ci0 is not None: ci0 = transform_ci_for_orbital_rotation (ci0, CASorb, CASe, umat)
# Guess orbital printing
if frag.mfmo_printed == False and frag.ints.mol.verbose:
ao2mfmo = reduce (np.dot, [frag.ints.ao2loc, frag.loc2imp, imp2mo])
print ("Writing {} {} orbital molden".format (frag.frag_name, 'CAS guess'))
molden.from_mo (frag.ints.mol, frag.filehead + frag.frag_name + '_mfmorb.molden', ao2mfmo, occ=my_occ)
frag.mfmo_printed = True
elif len (frag.active_orb_list) > 0: # This is done AFTER everything else so that the _mfmorb.molden always has consistent ordering
print('Applying caslst: {}'.format (frag.active_orb_list))
imp2mo = mc.sort_mo(frag.active_orb_list, mo_coeff=imp2mo)
frag.active_orb_list = []
if len (frag.frozen_orb_list) > 0:
mc.frozen = copy.copy (frag.frozen_orb_list)
print ("Applying frozen-orbital list (this macroiteration only): {}".format (frag.frozen_orb_list))
frag.frozen_orb_list = []
if frag.enforce_symmetry: imp2mo = lib.tag_array (imp2mo, orbsym=label_orb_symm (mol, mol.irrep_id, mol.symm_orb, imp2mo, s=mf.get_ovlp (), check=False))
t_start = time.time()
E_CASSCF = mc.kernel(imp2mo, ci0)[0]
if (not mc.converged) and np.all (np.abs (frag.impham_OEI_S) < 1e-8):
mc = mc.newton ()
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
if not mc.converged:
print ('Assuming ci vector is poisoned; discarding...')
imp2mo = mc.mo_coeff.copy ()
mc = mcscf.CASSCF(mf, CASorb, CASe)
smult = abs_2S + 1 if frag.target_S is not None else (frag.nelec_imp % 2) + 1
mc.fcisolver = csf_solver (mf.mol, smult)
E_CASSCF = mc.kernel(imp2mo)[0]
if not mc.converged:
if np.any (np.abs (frag.impham_OEI_S) > 1e-8):
raise NotImplementedError('Gradient and Hessian fixes for nonsinglet environment of Newton-descent CASSCF algorithm')
mc = mc.newton ()
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
assert (mc.converged)
'''
mc.conv_tol = 1e-12
mc.ah_start_tol = 1e-10
mc.ah_conv_tol = 1e-12
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
if not mc.converged:
mc = mc.newton ()
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
#assert (mc.converged)
'''
# Get twoRDM + oneRDM. cs: MC-SCF core, as: MC-SCF active space
# I'm going to need to keep some representation of the active-space orbitals
# Symmetry align if possible
oneRDM_amo, twoRDM_amo = mc.fcisolver.make_rdm12 (mc.ci, mc.ncas, mc.nelecas)
fock_imp = mc.get_fock ()
mc.mo_coeff[:,:norbs_cmo] = frag.align_imporbs_symm (mc.mo_coeff[:,:norbs_cmo], sorting_metric=fock_imp, sort_vecs=1, orbital_type='optimized inactive', mol=mol)[0]
mc.mo_coeff[:,norbs_cmo:norbs_occ], umat = frag.align_imporbs_symm (mc.mo_coeff[:,norbs_cmo:norbs_occ],
sorting_metric=oneRDM_amo, sort_vecs=-1, orbital_type='optimized active', mol=mol)
mc.mo_coeff[:,norbs_occ:] = frag.align_imporbs_symm (mc.mo_coeff[:,norbs_occ:], sorting_metric=fock_imp, sort_vecs=1, orbital_type='optimized external', mol=mol)[0]
if frag.enforce_symmetry:
amo2imp = mc.mo_coeff[:,norbs_cmo:norbs_occ].conjugate ().T
mc.mo_coeff = cleanup_subspace_symmetry (mc.mo_coeff, mol.symm_orb)
umat = umat @ (amo2imp @ mc.mo_coeff[:,norbs_cmo:norbs_occ])
err_symm = measure_subspace_blockbreaking (mc.mo_coeff, mol.symm_orb)
err_orth = measure_basis_nonorthonormality (mc.mo_coeff)
print ("Final symmetry error after cleanup = {}".format (err_symm))
print ("Final orthonormality error after cleanup = {}".format (err_orth))
mc.ci = transform_ci_for_orbital_rotation (mc.ci, CASorb, CASe, umat)
# Cache stuff
imp2mo = mc.mo_coeff #mc.cas_natorb()[0]
loc2mo = np.dot (frag.loc2imp, imp2mo)
imp2amo = imp2mo[:,norbs_cmo:norbs_occ]
loc2amo = loc2mo[:,norbs_cmo:norbs_occ]
frag.imp_cache = [mc.mo_coeff, mc.ci]
frag.ci_as = mc.ci
frag.ci_as_orb = loc2amo.copy ()
t_end = time.time()
# oneRDM
oneRDM_imp = mc.make_rdm1 ()
# twoCDM
oneRDM_amo, twoRDM_amo = mc.fcisolver.make_rdm12 (mc.ci, mc.ncas, mc.nelecas)
oneRDMs_amo = np.stack (mc.fcisolver.make_rdm1s (mc.ci, mc.ncas, mc.nelecas), axis=0)
oneSDM_amo = oneRDMs_amo[0] - oneRDMs_amo[1] if frag.target_MS >= 0 else oneRDMs_amo[1] - oneRDMs_amo[0]
oneSDM_imp = represent_operator_in_basis (oneSDM_amo, imp2amo.conjugate ().T)
print ("Norm of spin density: {}".format (linalg.norm (oneSDM_amo)))
# Note that I do _not_ do the *real* cumulant decomposition; I do one assuming oneSDM_amo = 0.
# This is fine as long as I keep it consistent, since it is only in the orbital gradients for this impurity that
# the spin density matters. But it has to stay consistent!
twoCDM_amo = get_2CDM_from_2RDM (twoRDM_amo, oneRDM_amo)
twoCDM_imp = represent_operator_in_basis (twoCDM_amo, imp2amo.conjugate ().T)
print('Impurity CASSCF energy (incl chempot): {}; spin multiplicity: {}; time to solve: {}'.format (E_CASSCF, spin_square (mc)[1], t_end - t_start))
# Active-space RDM data
frag.oneRDMas_loc = symmetrize_tensor (represent_operator_in_basis (oneRDM_amo, loc2amo.conjugate ().T))
frag.oneSDMas_loc = symmetrize_tensor (represent_operator_in_basis (oneSDM_amo, loc2amo.conjugate ().T))
frag.twoCDMimp_amo = twoCDM_amo
frag.loc2mo = loc2mo
frag.loc2amo = loc2amo
frag.E2_cum = np.tensordot (ao2mo.restore (1, mc.get_h2eff (), mc.ncas), twoCDM_amo, axes=4) / 2
frag.E2_cum += (mf.get_k (dm=oneSDM_imp) * oneSDM_imp).sum () / 4
# The second line compensates for my incorrect cumulant decomposition. Anything to avoid changing the checkpoint files...
# General impurity data
frag.oneRDM_loc = frag.oneRDMfroz_loc + symmetrize_tensor (represent_operator_in_basis (oneRDM_imp, frag.imp2loc))
frag.oneSDM_loc = frag.oneSDMfroz_loc + frag.oneSDMas_loc
frag.twoCDM_imp = None # Experiment: this tensor is huge. Do I actually need to keep it? In principle, of course not.
frag.E_imp = E_CASSCF + np.einsum ('ab,ab->', chempot_imp, oneRDM_imp)
return None
#!/usr/bin/env python
#
# Author: Qiming Sun <*****@*****.**>
#
'''
TDDFT NTO analysis.
'''
from pyscf import gto, dft, tddft
mol = gto.Mole()
mol.build(
atom='H 0 0 0; F 0 0 1.1', # in Angstrom
basis='631g',
symmetry=True,
)
mf = dft.RKS(mol)
mf.xc = 'b3lyp'
mf.kernel()
mytd = tddft.TDDFT(mf)
mytd.kernel()
weights_1, nto_1 = mytd.get_nto(state=1, verbose=4)
weights_2, nto_2 = mytd.get_nto(state=2, verbose=4)
weights_3, nto_3 = mytd.get_nto(state=3, verbose=4)
from pyscf.tools import molden
molden.from_mo(mol, 'nto-td-3.molden', nto_3)
C -1.211265339156 0.699329968382 0.000000000000
C -1.211265339156 -0.699329968382 0.000000000000
H 0.000000000000 2.491406946734 0.000000000000
H 0.000000000000 -2.491406946734 0.000000000000
H 2.157597486829 1.245660462400 0.000000000000
H 2.157597486829 -1.245660462400 0.000000000000
H -2.157597486829 1.245660462400 0.000000000000
H -2.157597486829 -1.245660462400 0.000000000000''',
basis = '6-31g')
mf = scf.RHF(mol)
mf.chkfile = 'benzene-631g.chk'
mf.kernel()
pz_idx = numpy.array([17,20,21,22,23,30,36,41,42,47,48,49])-1
loc_orb = lo.Boys(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'benzene-631g-boys.molden', loc_orb)
import numpy
from pyscf import lib
from pyscf import tools
from pyscf.tools import mo_mapping
mol, mo_energy, mo_coeff, mo_occ, irrep_labels, spins = \
tools.molden.load('benzene-631g-boys.molden')
comp = mo_mapping.mo_comps('C.*2p[yz]', # regular expression
mol, mo_coeff)
mol = lib.chkfile.load_mol('benzene-631g.chk')
mf = scf.RHF(mol)
mf.kernel()
#
# First method is to explicit call the functions provided by molden.py
#
with open('C6H6mo.molden', 'w') as f1:
molden.header(mol, f1)
molden.orbital_coeff(mol, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)
#
# Second method is to simply call from_mo function to write the orbitals
#
c_loc_orth = lo.orth.orth_ao(mol)
molden.from_mo(mol, 'C6H6loc.molden', c_loc_orth)
#
# Molden format does not support high angular momentum basis. To handle the
# orbitals which have l>=5 functions, a hacky way is to call molden.remove_high_l
# function. However, the resultant orbitals may not be orthnormal.
#
mol = gto.M(
atom = 'He 0 0 0',
basis = {'He': gto.expand_etbs(((0, 3, 1., 2.), (5, 2, 1., 2.)))})
mf = scf.RHF(mol).run()
try:
molden.from_mo(mol, 'He_without_h.molden', mf.mo_coeff)
except RuntimeError:
print(' Found l=5 in basis.')
def solve(frag, guess_1RDM, chempot_imp):
# Augment OEI with the chemical potential
OEI = frag.impham_OEI - chempot_imp
# Do I need to get the full RHF solution?
guess_orbs_av = len(frag.imp_cache) == 2 or frag.norbs_as > 0
# Get the RHF solution
mol = gto.Mole()
mol.spin = int(round(2 * frag.target_MS))
mol.verbose = 0 if frag.mol_output is None else lib.logger.DEBUG
mol.output = frag.mol_output
mol.atom.append(('H', (0, 0, 0)))
mol.nelectron = frag.nelec_imp
mol.build()
#mol.incore_anyway = True
mf = scf.RHF(mol)
mf.get_hcore = lambda *args: OEI
mf.get_ovlp = lambda *args: np.eye(frag.norbs_imp)
mf.energy_nuc = lambda *args: frag.impham_CONST
if frag.impham_CDERI is not None:
mf = mf.density_fit()
mf.with_df._cderi = frag.impham_CDERI
else:
mf._eri = ao2mo.restore(8, frag.impham_TEI, frag.norbs_imp)
mf.__dict__.update(frag.mf_attr)
if guess_orbs_av: mf.max_cycle = 2
mf.scf(guess_1RDM)
if (not mf.converged) and (not guess_orbs_av):
print(
"CASSCF RHF-step not converged on fixed-point iteration; initiating newton solver"
)
mf = mf.newton()
mf.kernel()
# Instability check and repeat
if not guess_orbs_av:
for i in range(frag.num_mf_stab_checks):
mf.mo_coeff = mf.stability()[0]
guess_1RDM = mf.make_rdm1()
mf = scf.RHF(mol)
mf.get_hcore = lambda *args: OEI
mf.get_ovlp = lambda *args: np.eye(frag.norbs_imp)
mf._eri = ao2mo.restore(8, frag.impham_TEI, frag.norbs_imp)
mf.scf(guess_1RDM)
if not mf.converged:
mf = mf.newton()
mf.kernel()
print("CASSCF RHF-step energy: {}".format(mf.e_tot))
#print(mf.mo_occ)
'''
idx = mf.mo_energy.argsort()
mf.mo_energy = mf.mo_energy[idx]
mf.mo_coeff = mf.mo_coeff[:,idx]'''
# Get the CASSCF solution
CASe = frag.active_space[0]
CASorb = frag.active_space[1]
checkCAS = (CASe <= frag.nelec_imp) and (CASorb <= frag.norbs_imp)
if (checkCAS == False):
CASe = frag.nelec_imp
CASorb = frag.norbs_imp
if (frag.target_MS > frag.target_S):
CASe = ((CASe // 2) + frag.target_S, (CASe // 2) - frag.target_S)
else:
CASe = ((CASe // 2) + frag.target_MS, (CASe // 2) - frag.target_MS)
if frag.impham_CDERI is not None:
mc = mcscf.DFCASSCF(mf, CASorb, CASe)
else:
mc = mcscf.CASSCF(mf, CASorb, CASe)
norbs_amo = mc.ncas
norbs_cmo = mc.ncore
norbs_imo = frag.norbs_imp - norbs_amo
nelec_amo = sum(mc.nelecas)
norbs_occ = norbs_amo + norbs_cmo
#mc.natorb = True
# Guess orbitals
ci0 = None
if len(frag.imp_cache) == 2:
imp2mo, ci0 = frag.imp_cache
print("Taking molecular orbitals and ci vector from cache")
elif frag.norbs_as > 0:
nelec_imp_guess = int(round(np.trace(frag.oneRDMas_loc)))
norbs_cmo_guess = (frag.nelec_imp - nelec_imp_guess) // 2
print(
"Projecting stored amos (frag.loc2amo; spanning {} electrons) onto the impurity basis and filling the remainder with default guess"
.format(nelec_imp_guess))
imp2mo, my_occ = project_amo_manually(
frag.loc2imp,
frag.loc2amo,
mf.get_fock(dm=frag.get_oneRDM_imp()),
norbs_cmo_guess,
dm=frag.oneRDMas_loc)
elif frag.loc2amo_guess is not None:
print(
"Projecting stored amos (frag.loc2amo_guess) onto the impurity basis (no dm available)"
)
imp2mo, my_occ = project_amo_manually(
frag.loc2imp,
frag.loc2amo_guess,
mf.get_fock(dm=frag.get_oneRDM_imp()),
norbs_cmo,
dm=None)
frag.loc2amo_guess = None
else:
imp2mo = mc.mo_coeff
my_occ = mf.mo_occ
print(
"No stored amos; using mean-field canonical MOs as initial guess")
# Guess orbital processing
if callable(frag.cas_guess_callback):
mo = reduce(np.dot, (frag.ints.ao2loc, frag.loc2imp, imp2mo))
mo = frag.cas_guess_callback(frag.ints.mol, mc, mo)
imp2mo = reduce(np.dot, (frag.imp2loc, frag.ints.ao2loc.conjugate().T,
frag.ints.ao_ovlp, mo))
frag.cas_guess_callback = None
elif len(frag.active_orb_list) > 0:
print('Applying caslst: {}'.format(frag.active_orb_list))
imp2mo = mc.sort_mo(frag.active_orb_list, mo_coeff=imp2mo)
frag.active_orb_list = []
if len(frag.frozen_orb_list) > 0:
mc.frozen = copy.copy(frag.frozen_orb_list)
print("Applying frozen-orbital list (this macroiteration only): {}".
format(frag.frozen_orb_list))
frag.frozen_orb_list = []
# Guess orbital printing
if frag.mfmo_printed == False:
ao2mfmo = reduce(np.dot, [frag.ints.ao2loc, frag.loc2imp, imp2mo])
molden.from_mo(frag.ints.mol,
frag.filehead + frag.frag_name + '_mfmorb.molden',
ao2mfmo,
occ=my_occ)
frag.mfmo_printed = True
# Guess CI vector
if len(frag.imp_cache) != 2 and frag.ci_as is not None:
loc2amo_guess = np.dot(frag.loc2imp, imp2mo[:, norbs_cmo:norbs_occ])
gOc = np.dot(loc2amo_guess.conjugate().T, frag.ci_as_orb)
umat_g, svals, umat_c = matrix_svd_control_options(
gOc, sort_vecs=-1, only_nonzero_vals=True)
if (svals.size == norbs_amo):
print(
"Loading ci guess despite shifted impurity orbitals; singular value sum: {}"
.format(np.sum(svals)))
imp2mo[:, norbs_cmo:norbs_occ] = np.dot(
imp2mo[:, norbs_cmo:norbs_occ], umat_g)
ci0 = transform_ci_for_orbital_rotation(frag.ci_as, CASorb, CASe,
umat_c)
else:
print(
"Discarding stored ci guess because orbitals are too different (missing {} nonzero svals)"
.format(norbs_amo - svals.size))
t_start = time.time()
smult = 2 * frag.target_S + 1 if frag.target_S is not None else (
frag.nelec_imp % 2) + 1
mc.fcisolver = csf_solver(mf.mol, smult)
mc.max_cycle_macro = 50 if frag.imp_maxiter is None else frag.imp_maxiter
mc.ah_start_tol = 1e-10
mc.ah_conv_tol = 1e-10
mc.conv_tol = 1e-9
mc.__dict__.update(frag.corr_attr)
E_CASSCF = mc.kernel(imp2mo, ci0)[0]
if not mc.converged:
mc = mc.newton()
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
if not mc.converged:
print('Assuming ci vector is poisoned; discarding...')
imp2mo = mc.mo_coeff.copy()
mc = mcscf.CASSCF(mf, CASorb, CASe)
smult = 2 * frag.target_S + 1 if frag.target_S is not None else (
frag.nelec_imp % 2) + 1
mc.fcisolver = csf_solver(mf.mol, smult)
E_CASSCF = mc.kernel(imp2mo)[0]
if not mc.converged:
mc = mc.newton()
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
assert (mc.converged)
'''
mc.conv_tol = 1e-12
mc.ah_start_tol = 1e-10
mc.ah_conv_tol = 1e-12
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
if not mc.converged:
mc = mc.newton ()
E_CASSCF = mc.kernel(mc.mo_coeff, mc.ci)[0]
#assert (mc.converged)
'''
# Get twoRDM + oneRDM. cs: MC-SCF core, as: MC-SCF active space
# I'm going to need to keep some representation of the active-space orbitals
imp2mo = mc.mo_coeff #mc.cas_natorb()[0]
loc2mo = np.dot(frag.loc2imp, imp2mo)
imp2amo = imp2mo[:, norbs_cmo:norbs_occ]
loc2amo = loc2mo[:, norbs_cmo:norbs_occ]
frag.imp_cache = [mc.mo_coeff, mc.ci]
frag.ci_as = mc.ci
frag.ci_as_orb = loc2amo.copy()
t_end = time.time()
print(
'Impurity CASSCF energy (incl chempot): {}; spin multiplicity: {}; time to solve: {}'
.format(E_CASSCF,
spin_square(mc)[1], t_end - t_start))
# oneRDM
oneRDM_imp = mc.make_rdm1()
# twoCDM
oneRDM_amo, twoRDM_amo = mc.fcisolver.make_rdm12(mc.ci, mc.ncas,
mc.nelecas)
# Note that I do _not_ do the *real* cumulant decomposition; I do one assuming oneRDMs_amo_alpha = oneRDMs_amo_beta
# This is fine as long as I keep it consistent, since it is only in the orbital gradients for this impurity that
# the spin density matters. But it has to stay consistent!
twoCDM_amo = get_2CDM_from_2RDM(twoRDM_amo, oneRDM_amo)
twoCDM_imp = represent_operator_in_basis(twoCDM_amo, imp2amo.conjugate().T)
# General impurity data
frag.oneRDM_loc = symmetrize_tensor(
frag.oneRDMfroz_loc +
represent_operator_in_basis(oneRDM_imp, frag.imp2loc))
frag.twoCDM_imp = None # Experiment: this tensor is huge. Do I actually need to keep it? In principle, of course not.
frag.E_imp = E_CASSCF + np.einsum('ab,ab->', chempot_imp, oneRDM_imp)
# Active-space RDM data
frag.oneRDMas_loc = symmetrize_tensor(
represent_operator_in_basis(oneRDM_amo,
loc2amo.conjugate().T))
frag.twoCDMimp_amo = twoCDM_amo
frag.loc2mo = loc2mo
frag.loc2amo = loc2amo
frag.E2_cum = 0.5 * np.tensordot(
ao2mo.restore(1, mc.get_h2eff(), mc.ncas), twoCDM_amo, axes=4)
return None
def from_lasscf(las, fname, **kwargs):
mo_coeff, mo_ene, mo_occ = las.canonicalize()[:3]
return from_mo(las.mol, fname, mo_coeff, occ=mo_occ, ene=mo_ene, **kwargs)
''' DF-MP2 natural orbitals for the allyl radical ''' from pyscf.gto import Mole from pyscf.scf import UHF from pyscf.tools import molden from pyscf.mp.dfump2_native import DFMP2 mol = Mole() mol.atom = ''' C -1.1528 -0.1151 -0.4645 C 0.2300 -0.1171 -0.3508 C 0.9378 0.2246 0.7924 H 0.4206 0.5272 1.7055 H 2.0270 0.2021 0.8159 H -1.6484 -0.3950 -1.3937 H -1.7866 0.1687 0.3784 H 0.8086 -0.4120 -1.2337 ''' mol.basis = 'def2-TZVP' mol.spin = 1 mol.build() mf = UHF(mol).run() # MP2 natural occupation numbers and natural orbitals natocc, natorb = DFMP2(mf).make_natorbs() # store the natural orbitals in a molden file molden.from_mo(mol, 'allyl_mp2nat.molden', natorb, occ=natocc)
# # Load MF orbitals # chkname = "_chk/pp_dianion_dz_b3lyp.chk" mol = chkfile.load_mol(chkname) mol.verbose = 5 mf = dft.RKS(mol) mf.__dict__.update(chkfile.load(chkname, "scf")) # # SA-MCSCF # nelecas, ncas = (4, 4) n_states = 3 weights = np.ones(n_states) / n_states mc = mcscf.CASSCF(mf, ncas, nelecas).state_average_(weights) mc.fix_spin(ss=0) mc.natorb = True mc.chkfile = "_chk/pp_dianion_dz_cas_4e_4o.chk" cas_list = [142, 143, 150, 151] mo = mcscf.sort_mo(mc, mf.mo_coeff, cas_list) mc.mc1step(mo) # # Analysis and processing # mc.analyze() molden.from_mcscf(mc, "_molden/pp_dianion_dz_cas_4e_4o.molden") molden.from_mo(mol, "_molden/pp_dianion_dz_cas_4e_4o_alt.molden", mc.mo_coeff)
# UKS comparison (initial guess must break symmetry!)
pks = scf.UKS(mol)
pks.xc = fnal
pks.kernel(dm0)
pks = pks.as_scanner()
hks = scf.UKS(mol)
hks.xc = kshfnal
hks.kernel(dm0)
hks = hks.as_scanner()
# MC-PDFT objects
if gsbasis:
gsmo = np.load(gsmofile)
mc = mcpdft.CASSCF(mf, transl_type + fnal, ncas, nelecas, grids_level=3)
mo = mcscf.project_init_guess(mc, gsmo, prev_mol=gsmol)
molden.from_mo(mol, 'check_projection.molden', mo)
mc.kernel(mo)
mc = mc.as_scanner()
else:
mc = mcpdft.CASSCF(mf, transl_type + fnal, ncas, nelecas,
grids_level=3).run().as_scanner()
mc0 = mcpdft.CASSCF(mf, otfnal0, ncas, nelecas,
grids_level=3).run().as_scanner()
mc1 = mcpdft.CASSCF(mf, otfnal1, ncas, nelecas,
grids_level=3).run().as_scanner()
mc2 = mcpdft.CASSCF(mf, otfnal2, ncas, nelecas,
grids_level=3).run().as_scanner()
molden.from_mcscf(mc0, moldenfile)
np.save(mofile, mc.mo_coeff)
# Do MCSCF scan forwards
def impurity_molden(self,
tag=None,
canonicalize=False,
natorb=False,
molorb=False,
ene=None,
occ=None):
tag = '.' if tag == None else '_' + str(tag) + '.'
filename = self.filehead + self.frag_name + tag + 'molden'
mol = self.ints.mol.copy()
mol.nelectron = self.nelec_imp
mol.spin = int(round(2 * self.target_MS))
oneRDM = self.get_oneRDM_imp()
FOCK = represent_operator_in_basis(
self.ints.loc_rhf_fock_bis(self.oneRDM_loc), self.loc2imp)
ao2imp = np.dot(self.ints.ao2loc, self.loc2imp)
ao2molden = ao2imp
if molorb:
assert (not natorb)
assert (not canonicalize)
ao2molden = np.dot(self.ints.ao2loc, self.loc2mo)
occ = np.einsum('ip,ij,jp->p', self.imp2mo.conjugate(), oneRDM,
self.imp2mo)
ene = np.einsum('ip,ij,jp->p', self.imp2mo.conjugate(), FOCK,
self.imp2mo)
if self.norbs_as > 0:
ene = cas_mo_energy_shift_4_jmol(ene, self.norbs_imp,
self.nelec_imp, self.norbs_as,
self.nelec_as)
if natorb:
assert (not canonicalize)
# Separate active and external (inactive + virtual) orbitals and pry their energies apart by +-1e4 Eh so Jmol sets them
# in the proper order
if self.norbs_as > 0:
imp2xmo = get_complementary_states(self.imp2amo)
FOCK_amo = represent_operator_in_basis(FOCK, self.imp2amo)
FOCK_xmo = represent_operator_in_basis(FOCK, imp2xmo)
oneRDM_xmo = represent_operator_in_basis(oneRDM, imp2xmo)
oneRDM_amo = represent_operator_in_basis(oneRDM, self.imp2amo)
ene_xmo, xmo2molden = matrix_eigen_control_options(
FOCK_xmo, sort_vecs=1, only_nonzero_vals=False)
occ_amo, amo2molden = matrix_eigen_control_options(
oneRDM_amo, sort_vecs=-1, only_nonzero_vals=False)
occ_xmo = np.einsum('ip,ij,jp->p', xmo2molden.conjugate(),
oneRDM_xmo, xmo2molden)
ene_amo = np.einsum('ip,ij,jp->p', amo2molden.conjugate(),
FOCK_amo, amo2molden)
norbs_imo = (self.nelec_imp - self.nelec_as) // 2
occ = np.concatenate(
(occ_xmo[:norbs_imo], occ_amo, occ_xmo[norbs_imo:]))
ene = np.concatenate(
(ene_xmo[:norbs_imo], ene_amo, ene_xmo[norbs_imo:]))
ene = cas_mo_energy_shift_4_jmol(ene, self.norbs_imp,
self.nelec_imp, self.norbs_as,
self.nelec_as)
imp2molden = np.concatenate(
(np.dot(imp2xmo, xmo2molden[:, :norbs_imo]),
np.dot(self.imp2amo, amo2molden),
np.dot(imp2xmo, xmo2molden[:, norbs_imo:])),
axis=1)
else:
occ, imp2molden = matrix_eigen_control_options(
oneRDM, sort_vecs=-1, only_nonzero_vals=False)
ene = np.einsum('ip,ij,jp->p', imp2molden.conjugate(), FOCK,
imp2molden)
ao2molden = np.dot(ao2imp, imp2molden)
elif canonicalize:
# Separate active and external (inactive + virtual) orbitals and pry their energies apart by +-1e4 Eh so Jmol sets them
# in the proper order
if self.norbs_as > 0:
imp2xmo = get_complementary_states(self.imp2amo)
FOCK_amo = represent_operator_in_basis(FOCK, self.imp2amo)
FOCK_xmo = represent_operator_in_basis(FOCK, imp2xmo)
ene_xmo, xmo2molden = matrix_eigen_control_options(
FOCK_xmo, sort_vecs=1, only_nonzero_vals=False)
ene_amo, amo1molden = matrix_eigen_control_options(
FOCK_amo, sort_vecs=1, only_nonzero_vals=False)
norbs_imo = (self.nelec_imp - self.nelec_as) // 2
ene = np.concatenate(
(ene_xmo[:norbs_imo], ene_amo, ene_xmo[norbs_imo:]))
ene = cas_mo_energy_shift_4_jmol(ene, self.norbs_imp,
self.nelec_imp, self.norbs_as,
self.nelec_as)
imp2molden = np.concatenate(
(np.dot(imp2xmo, xmo2molden[:, :norbs_imo]),
np.dot(self.imp2amo, amo2molden),
np.dot(imp2xmo, xmo2molden[:, norbs_imo:])),
axis=1)
else:
ene, imp2molden = matrix_eigen_control_options(
FOCK, sort_vecs=-1, only_nonzero_vals=False)
occ = np.einsum('ip,ij,jp->p', imp2molden.conjugate(), oneRDM,
imp2molden)
ao2molden = np.dot(ao2imp, imp2molden)
molden.from_mo(mol, filename, ao2molden, ene=ene, occ=occ)
mf.chkfile = "_chk/pp_anion_pt_chg_dz_b3lyp.chk" mf.kernel() # mf.analyze() # # Dump orbitals # molden.dump_scf(mf, "_molden/pp_anion_pt_chg_dz_b3lyp.molden") # # SA-MCSCF # nelecas, ncas = (4, 4) n_states = 3 weights = np.ones(n_states) / n_states mc = mcscf.CASSCF(mf, ncas, nelecas).state_average_(weights) mc.fix_spin(ss=0) mc.natorb = True mc.chkfile = "_chk/pp_anion_pt_chg_dz_cas_4e_4o.chk" cas_list = [118, 119, 120, 121] mo = mcscf.sort_mo(mc, mf.mo_coeff, cas_list) mc.mc1step(mo) # # Analysis and processing # mc.analyze() molden.from_mcscf(mc, "_molden/pp_anion_pt_chg_dz_cas.molden") molden.from_mo(mol, "_molden/pp_anion_pt_chg_dz_cas_alt.molden", mc.mo_coeff)
def do_scf(inp):
'''Do the requested SCF.'''
from pyscf import gto, scf, dft, cc, fci, ci, ao2mo, mcscf, mrpt, lib, mp, tdscf
from pyscf.cc import ccsd_t, uccsd_t
import numpy as np
from .fcidump import fcidump
# sort out the method
mol = inp.mol
method = inp.scf.method.lower()
# UHF
if method == 'uhf':
ehf, mSCF = do_hf(inp, unrestricted=True)
print_energy('UHF', ehf)
if inp.scf.exci is not None:
inp.timer.start('TDHF')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDHF')
# RHF
elif method in ('rhf', 'hf'):
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
if inp.scf.exci is not None:
inp.timer.start('TDHF')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDHF')
# CCSD and CCSD(T)
elif method in ('ccsd', 'ccsd(t)', 'uccsd', 'uccsd(t)', 'eomccsd'):
if 'u' in method:
ehf, tSCF = do_hf(inp, unrestricted=True)
print_energy('UHF', ehf)
else:
ehf, tSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('ccsd')
frozen = 0
if inp.scf.freeze is not None: frozen = inp.scf.freeze
if 'u' in method:
mSCF = cc.UCCSD(tSCF, frozen=frozen)
else:
mSCF = cc.CCSD(tSCF, frozen=frozen)
mSCF.max_cycle = inp.scf.maxiter
eccsd, t1, t2 = mSCF.kernel()
print_energy('CCSD', ehf + eccsd)
inp.timer.end('ccsd')
if method == 'eomccsd':
inp.timer.start('eomccsd')
ee = mSCF.eomee_ccsd_singlet(nroots=4)[0]
inp.timer.end('eomccsd')
for i in range(len(ee)):
print_energy('EOM-CCSD {0} (eV)'.format(i+1), ee[i] * 27.2114)
if method in ('ccsd(t)', 'uccsd(t)'):
inp.timer.start('ccsd(t)')
eris = mSCF.ao2mo()
if method == 'ccsd(t)':
e3 = ccsd_t.kernel(mSCF, eris)
else:
e3 = uccsd_t.kernel(mSCF, eris)
print_energy('CCSD(T)', ehf + eccsd + e3)
inp.timer.end('ccsd(t)')
# MP2
elif method == 'mp2':
ehf, tSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('mp2')
frozen = 0
if inp.scf.freeze is not None: frozen = inp.scf.freeze
mSCF = mp.MP2(tSCF, frozen=frozen)
emp2, t2 = mSCF.kernel()
print_energy('MP2', ehf+emp2)
inp.timer.end('mp2')
# CISD
elif method == 'cisd' or method == 'cisd(q)':
ehf, tSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('cisd')
frozen = 0
if inp.scf.freeze is not None: frozen = inp.scf.freeze
mSCF = ci.CISD(tSCF, frozen=frozen)
ecisd = mSCF.kernel()[0]
print_energy('CISD', ehf + ecisd)
inp.timer.end('cisd')
# perform Davison quadruples correction
c0 = np.max(np.abs(mSCF.ci))
c02 = c0**2
ne = mSCF.mol.nelectron
eq = ( 1.0 - c02 ) * ecisd
print_energy('CISD(Q) Davidson', ehf + ecisd + eq)
eq = ( 1.0 - c02 ) / c02 * ecisd
print_energy('CISD(Q) Renomalized-Davidson', ehf + ecisd + eq)
eq = ( 1.0 - c02 ) / ( 2.0 * c02 - 1.0 ) * ecisd
print_energy('CISD(Q) Davison-Silver', ehf + ecisd + eq)
eq = (( 2.0 * c02 ) / ((2.0*c02-1.0)*(1.0 + np.sqrt(1.0 + (8.0*c02*(1.0-c02))
/ ( ne * (2.0*c02-1.0)**2 )))) - 1.0 ) * ecisd
print_energy('CISD(Q) PC', ehf + ecisd + eq)
eq = ( 1.0 - c02 ) / c02 * ((ne-2)*(ne-3.0)) / (ne*(ne-1.0)) * ecisd
print_energy('CISD(Q) MC', ehf + ecisd + eq)
if ne > 2:
eq = ( 2.0 - c02 ) / (2.0 * (ne-1.0)/(ne-2.0) * c02 - 1.0)
else:
eq = 0.0
print_energy('CISD(Q) DD', ehf + ecisd + eq)
# UKS
elif method in ('uks' or 'udft'):
inp.timer.start('uks')
inp.timer.start('grids')
grids = dft.gen_grid.Grids(mol)
grids.level = inp.scf.grid
grids.build()
inp.timer.end('grids')
mSCF = dft.UKS(mol)
mSCF.grids = grids
mSCF.xc = inp.scf.xc
mSCF.conv_tol = inp.scf.conv
mSCF.conv_tol_grad = inp.scf.grad
mSCF.max_cycle = inp.scf.maxiter
mSCF.init_guess = inp.scf.guess
mSCF.small_rho_cutoff = 1e-20
eks = mSCF.kernel()
print_energy('UKS', eks)
inp.timer.end('uks')
if inp.scf.exci is not None:
inp.timer.start('TDDFT')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDDFT')
# RKS
elif method in ('rks', 'ks', 'rdft', 'dft'):
inp.timer.start('ks')
inp.timer.start('grids')
grids = dft.gen_grid.Grids(mol)
grids.level = inp.scf.grid
grids.build()
inp.timer.end('grids')
if mol.nelectron%2 == 0:
mSCF = dft.RKS(mol)
else:
mSCF = dft.ROKS(mol)
mSCF.grids = grids
mSCF.xc = inp.scf.xc
mSCF.conv_tol = inp.scf.conv
mSCF.conv_tol_grad = inp.scf.grad
mSCF.max_cycle = inp.scf.maxiter
mSCF.init_guess = inp.scf.guess
mSCF.small_rho_cutoff = 1e-20
mSCF.damp = inp.scf.damp
mSCF.level_shift = inp.scf.shift
eks = mSCF.kernel()
print_energy('RKS', eks)
inp.timer.end('ks')
if inp.scf.exci is not None:
inp.timer.start('TDDFT')
mtd = do_TDDFT(inp, mSCF)
inp.timer.end('TDDFT')
# Unrestricted FCI
elif method == 'ufci':
ehf, mSCF = do_hf(inp, unrestricted=True)
print_energy('UHF', ehf)
inp.timer.start('fci')
cis = fci.direct_uhf.FCISolver(mol)
norb = mSCF.mo_energy[0].size
nea = (mol.nelectron+mol.spin) // 2
neb = (mol.nelectron-mol.spin) // 2
nelec = (nea, neb)
mo_a = mSCF.mo_coeff[0]
mo_b = mSCF.mo_coeff[1]
h1e_a = reduce(np.dot, (mo_a.T, mSCF.get_hcore(), mo_a))
h1e_b = reduce(np.dot, (mo_b.T, mSCF.get_hcore(), mo_b))
g2e_aa = ao2mo.incore.general(mSCF._eri, (mo_a,)*4, compact=False)
g2e_aa = g2e_aa.reshape(norb,norb,norb,norb)
g2e_ab = ao2mo.incore.general(mSCF._eri, (mo_a,mo_a,mo_b,mo_b), compact=False)
g2e_ab = g2e_ab.reshape(norb,norb,norb,norb)
g2e_bb = ao2mo.incore.general(mSCF._eri, (mo_b,)*4, compact=False)
g2e_bb = g2e_bb.reshape(norb,norb,norb,norb)
h1e = (h1e_a, h1e_b)
eri = (g2e_aa, g2e_ab, g2e_bb)
eci = fci.direct_uhf.kernel(h1e, eri, norb, nelec)[0]
print_energy('FCI', eci)
inp.timer.end('fci')
# FCI
elif method in ('fci'):
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('fci')
if inp.scf.freeze is None:
mCI = fci.FCI(mSCF)
if inp.scf.roots is not None:
mCI.nroots = inp.scf.roots
mCI.kernel()[0]
eci = mCI.eci
else:
nel = mol.nelectron - inp.scf.freeze * 2
ncas = mol.nao_nr() - inp.scf.freeze
if mol.spin == 0:
nelecas = nel
mCI = mcscf.CASCI(mSCF, ncas, nelecas)
mCI.fcisolver = fci.solver(mol)
else:
if mol.spin%2 == 0:
nelecas = (nel//2+mol.spin//2, nel//2-mol.spin//2)
else:
nelecas = (nel//2+mol.spin//2+1, nel//2-mol.spin//2)
mCI = mcscf.CASCI(mSCF, ncas, nelecas)
mCI.fcisolver = fci.direct_spin1.FCISolver(mol)
eci = mCI.kernel()[0]
dm = mCI.make_rdm1()
dip = mSCF.dip_moment(dm=dm)
if inp.scf.roots is None:
print_energy('FCI', eci)
else:
for i in range(inp.scf.roots):
print_energy('FCI {0}'.format(i), eci[i])
inp.timer.end('fci')
# CASCI
elif method == 'casci':
if inp.scf.cas is None and inp.scf.casorb is None:
print ('ERROR: Must specify CAS space or CASORB')
return inp
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
# get cas space
if inp.scf.cas is not None:
if mol.spin == 0:
nelecas = inp.scf.cas[0]
else:
nelecas = (inp.scf.cas[0]//2 + mol.spin//2,
inp.scf.cas[0]//2 - mol.spin//2)
ncasorb = inp.scf.cas[1]
elif inp.scf.casorb is not None:
ncasorb = len(inp.scf.casorb)
nelecas = int(np.sum(mSCF.mo_occ[inp.scf.casorb]))
if inp.scf.casspin is not None:
nelecas = (nelecas//2 + inp.scf.casspin//2,
nelecas//2 - inp.scf.casspin//2)
inp.timer.start('casci')
mCI = mcscf.CASCI(mSCF, ncasorb, nelecas)
if inp.scf.casorb is not None:
mo = mcscf.addons.sort_mo(mCI, np.copy(mSCF.mo_coeff), inp.scf.casorb, 0)
else:
mo = np.copy(mSCF.mo_coeff)
eci = mCI.kernel(mo)[0]
print_energy('CASCI', eci)
inp.timer.end('casci')
# CASSCF
elif method == 'casscf' or method == 'ucasscf':
if inp.scf.cas is None and inp.scf.casorb is None:
print ('ERROR: Must specify CAS space or CASORB')
return inp
lunrestricted = (method == 'ucasscf')
ehf, mSCF = do_hf(inp, unrestricted=lunrestricted)
print_energy('HF', ehf)
# get cas space
if inp.scf.cas is not None:
if mol.spin == 0:
nelecas = inp.scf.cas[0]
else:
nelecas = (inp.scf.cas[0]//2 + mol.spin//2,
inp.scf.cas[0]//2 - mol.spin//2)
ncasorb = inp.scf.cas[1]
elif inp.scf.casorb is not None:
ncasorb = len(inp.scf.casorb)
nelecas = int(np.sum(mSCF.mo_occ[inp.scf.casorb]))
if inp.scf.casspin is not None:
nelecas = (nelecas//2 + inp.scf.casspin//2,
nelecas//2 - inp.scf.casspin//2)
inp.timer.start('casscf')
mCI = mcscf.CASSCF(mSCF, ncasorb, nelecas)
if inp.scf.casorb is not None:
mo = mcscf.addons.sort_mo(mCI, np.copy(mSCF.mo_coeff), inp.scf.casorb, 0)
else:
mo = np.copy(mSCF.mo_coeff)
eci = mCI.kernel(mo)[0]
print_energy('CASSCF', eci)
inp.timer.end('casscf')
# NEVPT2
elif method == 'nevpt2' or method == 'unevpt2':
if inp.scf.cas is None and inp.scf.casorb is None:
print ('ERROR: Must specify CAS space or CASORB')
return inp
ehf, mSCF = do_hf(inp)
print_energy('RHF', ehf)
inp.timer.start('casscf')
# get cas space
if inp.scf.cas is not None:
if mol.spin == 0:
nelecas = inp.scf.cas[0]
else:
nelecas = (inp.scf.cas[0]//2 + mol.spin//2,
inp.scf.cas[0]//2 - mol.spin//2)
ncasorb = inp.scf.cas[1]
elif inp.scf.casorb is not None:
ncasorb = len(inp.scf.casorb)
nelecas = int(np.sum(mSCF.mo_occ[inp.scf.casorb]))
if inp.scf.casspin is not None:
nelecas = (nelecas//2 + inp.scf.casspin//2,
nelecas//2 - inp.scf.casspin//2)
mCI = mcscf.CASSCF(mSCF, ncasorb, nelecas, frozen=inp.scf.freeze)
if inp.scf.casorb is not None:
mo = mcscf.addons.sort_mo(mCI, np.copy(mSCF.mo_coeff), inp.scf.casorb, 0)
else:
mo = np.copy(mSCF.mo_coeff)
eci = mCI.kernel(mo)[0]
print_energy('CASSCF', eci)
inp.timer.end('casscf')
inp.timer.start('nevpt2')
mpt2 = mrpt.NEVPT(mCI)
ept2 = mpt2.kernel() + eci
print_energy('NEVPT2', ept2)
inp.timer.end('nevpt2')
else:
print ('ERROR: Unrecognized SCF method!')
raise SystemExit
# dump fcidump file if needed
if inp.fcidump:
if inp.filename[-4:].lower() == '.inp':
fcifile = inp.filename[:-4] + '.fcidump'
else:
fcifile = inp.filename + '.fcidump'
fcidump(mSCF, filename=fcifile, tol=1e-6)
# plot MOs if needed
if inp.mo2cube:
from .mo_2_cube import save_MOs
save_MOs(inp, mSCF, mSCF.mo_coeff)
# save molden file if needed
if inp.molden:
from pyscf.tools import molden
molden_file = inp.filename[:-4] + '.molden'
molden.from_mo(inp.mol, molden_file, mSCF.mo_coeff, ene=mSCF.mo_energy)
# save and return
inp.mf = mSCF
return inp
# Load MF orbitals # chkname = "_chk/pp_neutral_dz_b3lyp.chk" mol = chkfile.load_mol(chkname) mol.verbose = 5 mf = dft.RKS(mol) mf.__dict__.update(chkfile.load(chkname, "scf")) # # SA-MCSCF # nelecas, ncas = (4, 4) n_states = 3 weights = np.ones(n_states) / n_states mc = mcscf.CASSCF(mf, ncas, nelecas).state_average_(weights) mc.fix_spin(ss=0) mc.natorb = True mc.chkfile = "_chk/pp_neutral_dz_cas_4e_4o.chk" cas_list = [148, 149, 150, 151] mo = mcscf.sort_mo(mc, mf.mo_coeff, cas_list) mc.mc1step(mo) # # Analysis and processing # mc.analyze() molden.from_mo(mol, "_molden/pp_neutral_dz_cas_4e_4o_alt.molden", mc.mo_coeff) molden.from_mcscf(mc, "_molden/pp_neutral_dz_cas_4e_4o.molden")
cell.basis = 'gth-dzv'
cell.pseudo = 'gth-pade'
cell.verbose = 5
cell.build(unit='Angstrom')
mf = scf.RHF(cell)
mf.kernel()
'''
generates IAOs
'''
mo_occ = mf.mo_coeff[:, mf.mo_occ > 0]
#a = lo.iao.iao(cell, mo_occ, minao='minao')
#a = lo.iao.iao(cell, mo_occ, minao='gth-szv')
a = iao.iao(cell, mo_occ, minao='gth-szv', scf_basis=True,
ref_basis='gth-szv') # scf basis
print "IAO shape: ", a.shape
molden.from_mo(cell, 'diamondiao_szv.molden', a)
# Orthogonalize IAO
a = lo.vec_lowdin(a, mf.get_ovlp())
molden.from_mo(cell, 'diamondiao_szv_ortho.molden', a)
loc_obj = lo.PM(cell, a)
cost_before = loc_obj.cost_function()
print "cost function before localization: ", cost_before
loc_orb = loc_obj.kernel()
molden.from_mo(cell, 'diamondiao_szv_PM.molden', loc_orb)
#ibo must take the orthonormalized IAOs
#ibo = lo.ibo.ibo(cell, mo_occ, a)
#print "IBO shape: ", ibo.shape
#molden.from_mo(cell, 'diamondibo_szv_ibo.molden', ibo)
def setup_wm_core_scf(self, fragments, calcname):
self.restore_wm_full_scf()
oneRDMcorr_loc = sum((frag.oneRDMas_loc for frag in fragments))
if np.all(np.isclose(oneRDMcorr_loc, 0)):
print("Null correlated 1-RDM; default settings for wm wvfn")
self.activeFOCK = represent_operator_in_basis(
self.fullFOCKao, self.ao2loc)
self.activeJKidem = self.activeFOCK - self.activeOEI
self.activeJKcorr = np.zeros((self.norbs_tot, self.norbs_tot))
self.oneRDMcorr_loc = oneRDMcorr_loc
self.loc2idem = np.eye(self.norbs_tot)
self.nelec_idem = self.nelec_tot
return
loc2corr = np.concatenate([frag.loc2amo for frag in fragments], axis=1)
loc2idem = get_complementary_states(loc2corr)
evecs = matrix_eigen_control_options(represent_operator_in_basis(
self.loc_oei(), loc2idem),
sort_vecs=1,
only_nonzero_vals=False)[1]
loc2idem = np.dot(loc2idem, evecs)
# I want to alter the outputs of self.loc_oei (), self.loc_rhf_fock (), and the get_wm_1RDM_etc () functions.
# self.loc_oei () = P_idem * (activeOEI + JKcorr) * P_idem
# self.loc_rhf_fock () = P_idem * (activeOEI + JKcorr + JKidem) * P_idem
# The get_wm_1RDM_etc () functions will need to add oneRDMcorr_loc to their final return value
# The chemical potential is so that identically zero eigenvalues from the projection into the idem space don't get confused
# with numerically-zero eigenvalues in the idem space: all occupied orbitals must have negative energy
# Make true output 1RDM from fragments to use as guess for wm mcscf calculation
oneRDMguess_loc = np.zeros_like(oneRDMcorr_loc)
for f in itertools.product(fragments, fragments):
loc2frag = [i.loc2frag for i in f]
oneRDMguess_loc += sum(
(0.5 * project_operator_into_subspace(i.oneRDM_loc, *loc2frag)
for i in f))
nelec_corr = np.trace(oneRDMcorr_loc)
if is_close_to_integer(nelec_corr,
100 * params.num_zero_atol) == False:
raise ValueError(
"nelec_corr not an integer! {}".format(nelec_corr))
nelec_idem = int(round(self.nelec_tot - nelec_corr))
JKcorr = self.loc_rhf_jk_bis(oneRDMcorr_loc)
oneRDMidem_loc = self.get_wm_1RDM_from_scf_on_OEI(
self.loc_oei() + JKcorr,
nelec=nelec_idem,
loc2wrk=loc2idem,
oneRDMguess_loc=oneRDMguess_loc,
output=calcname + '_trial_wvfn.log')
JKidem = self.loc_rhf_jk_bis(oneRDMidem_loc)
print("trace of oneRDMcorr_loc = {}".format(np.trace(oneRDMcorr_loc)))
print("trace of oneRDMidem_loc = {}".format(np.trace(oneRDMidem_loc)))
print("trace of oneRDM_loc in corr basis = {}".format(
np.trace(
represent_operator_in_basis(
oneRDMcorr_loc + oneRDMidem_loc,
orthonormalize_a_basis(loc2corr)))))
svals = get_overlapping_states(loc2idem, loc2corr)[2]
print("trace of <idem|corr|idem> = {}".format(np.sum(svals * svals)))
print(loc2corr.shape)
print(loc2idem.shape)
########################################################################################################
self.activeFOCK = self.activeOEI + JKidem + JKcorr
self.activeJKidem = JKidem
self.activeJKcorr = JKcorr
self.oneRDMcorr_loc = oneRDMcorr_loc
self.loc2idem = loc2idem
self.nelec_idem = nelec_idem
########################################################################################################
# Analysis: 1RDM and total energy
print("Analyzing LASSCF trial wave function")
oei = self.activeOEI + (JKcorr + JKidem) / 2
fock = self.activeFOCK
oneRDM = oneRDMidem_loc + oneRDMcorr_loc
E = self.activeCONST + np.tensordot(oei, oneRDM, axes=2)
for frag in fragments:
if frag.norbs_as > 0:
if frag.E2_cum == 0 and np.amax(np.abs(
frag.twoCDMimp_amo)) > 0:
V = self.dmet_tei(frag.loc2amo)
L = frag.twoCDMimp_amo
frag.E2_cum = np.tensordot(V, L, axes=4) / 2
E += frag.E2_cum
print("LASSCF trial wave function total energy: {:.6f}".format(E))
self.oneRDM_loc = oneRDM
self.e_tot = E
# Molden
fock_idem = represent_operator_in_basis(fock, loc2idem)
oneRDM_corr = represent_operator_in_basis(oneRDM, loc2corr)
idem_evecs = matrix_eigen_control_options(fock_idem,
sort_vecs=1,
only_nonzero_vals=False)[1]
corr_evecs = matrix_eigen_control_options(oneRDM_corr,
sort_vecs=-1,
only_nonzero_vals=False)[1]
loc2molden = np.append(np.dot(loc2idem, idem_evecs),
np.dot(loc2corr, corr_evecs),
axis=1)
wm_ene = np.einsum('ip,ij,jp->p', loc2molden, fock, loc2molden)
wm_ene[-loc2corr.shape[1]:] = 0
wm_occ = np.einsum('ip,ij,jp->p', loc2molden, oneRDM, loc2molden)
ao2molden = np.dot(self.ao2loc, loc2molden)
molden.from_mo(self.mol,
calcname + '_trial_wvfn.molden',
ao2molden,
occ=wm_occ,
ene=wm_ene)
C 3.8560 2.1213 0.1612
C 1.0888 2.4099 0.1396
C 3.0401 0.9977 0.0771
C 1.6565 1.1421 0.0663
H 3.9303 4.2734 0.3007
H 1.4582 4.5312 0.2815
H 4.9448 2.0077 0.1699
H 0.0000 2.5234 0.1311
H 3.4870 0.0000 0.0197
H 1.0145 0.2578 0.0000
''',
basis = 'cc-pvdz',
symmetry = 1)
mf = scf.RHF(mol)
mf.kernel()
#
# First method is to explicit call the functions provided by molden.py
#
with open('C6H6mo.molden', 'w') as f1:
molden.header(mol, f1)
molden.orbital_coeff(mol, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)
#
# Second method is to simply call from_mo function to write the orbitals
#
c_loc_orth = lo.orth.orth_ao(mol)
molden.from_mo(mol, 'C6H6loc.molden', c_loc_orth)
def get_mo_from_h5(mol, h5fname, symmetry=None):
''' Get MO vectors for a pyscf molecule from an h5 file written by OpenMolcas
Args:
mol : instance gto.mole
Must be in the same point group as the OpenMolcas calculation,
or set the symmetry argument
h5fname : str
Path to an h5 file generated by OpenMolcas containing (at
least) groups 'BASIS_FUNCTION_IDS', 'MO_OCCUPATIONS',
'MO_VECTORS', and 'MO_ENERGIES' and additionally 'DESYM_MATRIX'
and 'DESYM_BASIS_FUNCTION_IDS' if symmetry is used.
Kwargs:
symmetry : str
Point group of the calculation in OpenMolcas. If not provided,
mol.groupname is used instead
Returns:
mo_coeff : ndarray of shape (nao_nr, nao_nr)
'''
if symmetry is not None:
mol = mol.copy()
mol.build(symmetry=symmetry)
nao = mol.nao_nr()
with h5py.File(h5fname, 'r') as f:
try:
molcas_basids = f['DESYM_BASIS_FUNCTION_IDS'][()]
molcas_usymm = f['DESYM_MATRIX'][()].reshape(nao, nao)
except KeyError:
assert (not mol.symmetry
), "Can't find desym_ data; mol.symmetry = {}".format(
mol.symmetry)
molcas_basids = f['BASIS_FUNCTION_IDS'][()]
molcas_coeff = f['MO_VECTORS'][()]
mo_energy = f['MO_ENERGIES'][()]
mo_occ = f['MO_OCCUPATIONS'][()]
idx_ao = []
for (c, n, l, m) in molcas_basids:
# 0-index atom list in PySCF, 1-index atom list in Molcas
c -= 1
# Actual principal quantum number in PySCF, 1-indexed list in Molcas
n += l
# l=1, ml=(-1,0,1) is (x,y,z) in PySCF, (y,z,x) in Molcas
if l == 1:
m = m - 2 if m > 0 else m + 1
idx_ao.append(mol.search_ao_nr(c, l, m, n))
idx_ao = np.argsort(np.asarray(idx_ao))
if mol.symmetry:
# I have to figure out what order the Molcas irreps are in on the fly
# because it seems to change depending on the xyz
molcas_usymm = molcas_usymm[:, idx_ao]
proj = np.stack([(np.dot(molcas_usymm, ir_coeff)**2).sum(1)
for ir_coeff in mol.symm_orb],
axis=0)
errstr = ("Can't interpret h5 symmetry information; wrong mol? "
" <mol.symm_orb|desym_matrix> =\n{}").format(proj)
assert (np.allclose(np.amax(proj), 1)), errstr
ix_irrep = np.argmax(proj, axis=0)
uniq_idx = np.sort(np.unique(ix_irrep, return_index=True)[1])
uniq_idx = np.append(uniq_idx, len(ix_irrep))
nmo_irrep = []
for ix, i in enumerate(uniq_idx[:-1]):
j = uniq_idx[ix + 1]
assert (len(np.unique(ix_irrep[i:j])) == 1), errstr
nmo_irrep.append(j - i)
nmo_irrep = np.asarray(nmo_irrep)
usymm_irrep_offset = np.cumsum(nmo_irrep) - nmo_irrep
coeff_irrep_offset = np.cumsum(nmo_irrep**2) - nmo_irrep**2
mo_coeff = np.zeros((nao, nao), dtype=np.float_)
for m_ir, usymm_off, coeff_off in zip(nmo_irrep, usymm_irrep_offset,
coeff_irrep_offset):
i, j = usymm_off, usymm_off + m_ir
u, v = coeff_off, coeff_off + (m_ir**2)
usymm = molcas_usymm[i:j, :].T
coeff = molcas_coeff[u:v].reshape(m_ir, m_ir).T
mo_coeff[:, i:j] = np.dot(usymm, coeff)
else:
assert (molcas_coeff.shape == (
nao**2, )), 'mo_vectors.shape = {} but {} AOs'.format(
molcas_coeff.shape, nao)
mo_coeff = molcas_coeff.reshape(nao, nao)[:, idx_ao].T
# 'mergesort' keeps degenerate or active-space orbitals in the provided order!
# idx_ene = np.argsort (mo_energy, kind='mergesort')
# modified by Dayou: sort by mo_occ first, then mo_energy
sort_key = np.min(mo_energy) * 100000 * mo_occ + mo_energy
idx_ene = np.argsort(sort_key, kind='mergesort')
mo_coeff = mo_coeff[:, idx_ene]
mo_occ = mo_occ[idx_ene]
mo_energy = mo_energy[idx_ene]
if mol.verbose > logger.INFO:
fname = str(mol.output)[:-4] + "_h5debug.molden"
molden.from_mo(mol, fname, mo_coeff, occ=mo_occ, ene=mo_energy)
if mol.symmetry: # assert (symmetry is right)
try:
orbsym = label_orb_symm(mol, mol.irrep_name, mol.symm_orb,
mo_coeff)
except ValueError as e:
raise ValueError(("Problem understanding Molcas symmetry?\n"
"{}").format(str(e)))
return mo_coeff
'''
#
# Modify the default core valence settings for Be and Al
#
# 1 s-shell as core, 1 s-shell + 1 p-shell as valence
lo.set_atom_conf('Be', ('1s', '1s1p'))
# 2 s-shells + 1 p-shell as core, 1 s-shell + 1 p-shell + 1 d-shell as valence
lo.set_atom_conf('Al', ('2s1p', '1s1p1d'))
# double-d shell for Fe, ie taking 3d and 4d orbitals as valence
lo.set_atom_conf('Fe', 'double d')
# double-d shell for Mo, ie taking 4d and 5d orbitals as valence
lo.set_atom_conf('Mo', 'double d')
# Put 3d orbital in valence space for Si
lo.set_atom_conf('Si', 'polarize')
#
# Localize Be12 ring
#
mol = gto.M(atom = [('Be', x) for x in ring.make(12, 2.4)], basis='ccpvtz')
c = lo.orth.orth_ao(mol)
molden.from_mo(mol, 'be12.molden', c)
#
# Localize Al12 ring
#
mol = gto.M(atom = [('Al', x) for x in ring.make(12, 2.4)], basis='ccpvtz')
c = lo.orth.orth_ao(mol)
molden.from_mo(mol, 'al12.molden', c)
C -1.523996730 -0.592207689 0.138683275
H 0.609941801 0.564304456 1.384183068
H 1.228991034 1.489024155 0.015946420
H -1.242251083 1.542928348 0.046243898
H -0.662968178 0.676527364 -1.376503770
H -0.838473936 -1.344174292 0.500629028
H -2.075136399 -0.983173387 -0.703807608
H -2.212637905 -0.323898759 0.926200671
O 1.368219958 -0.565620846 -0.173113101
H 2.250134219 -0.596689848 0.204857736
'''
mol.basis = 'def2-SVP'
mol.build()
# Perform a Hartree-Fock calculation
mf = RHF(mol)
mf.kernel()
# determine the number of occupied orbitals
nocc = numpy.count_nonzero(mf.mo_occ > 0)
# localize the occupied orbitals separately
lmo_occ = cholesky_mos(mf.mo_coeff[:, :nocc])
# localize the virtual orbitals separately
lmo_virt = cholesky_mos(mf.mo_coeff[:, nocc:])
# merge the MO coefficients in one matrix
lmo_merged = numpy.hstack((lmo_occ, lmo_virt))
# dump the merged MO coefficients in a molden file
filename = 'c3h7oh_cholesky.molden'
print('Dumping the orbitals in file:', filename)
molden.from_mo(mol, filename, lmo_merged, occ=mf.mo_occ)
C -1.211265339156 0.699329968382 0.000000000000
C -1.211265339156 -0.699329968382 0.000000000000
H 0.000000000000 2.491406946734 0.000000000000
H 0.000000000000 -2.491406946734 0.000000000000
H 2.157597486829 1.245660462400 0.000000000000
H 2.157597486829 -1.245660462400 0.000000000000
H -2.157597486829 1.245660462400 0.000000000000
H -2.157597486829 -1.245660462400 0.000000000000''',
basis='6-31g')
mf = scf.RHF(mol)
mf.chkfile = 'benzene-631g.chk'
mf.kernel()
pz_idx = numpy.array([17, 20, 21, 22, 23, 30, 36, 41, 42, 47, 48, 49]) - 1
loc_orb = lo.Boys(mol, mf.mo_coeff[:, pz_idx]).kernel()
molden.from_mo(mol, 'benzene-631g-boys.molden', loc_orb)
import numpy
from pyscf import lib
from pyscf import tools
from pyscf.tools import mo_mapping
mol, mo_energy, mo_coeff, mo_occ, irrep_labels, spins = \
tools.molden.load('benzene-631g-boys.molden')
comp = mo_mapping.mo_comps(
'C.*2p[yz]', # regular expression
mol,
mo_coeff)
mol = lib.chkfile.load_mol('benzene-631g.chk')
print (si)
# You can get the 1-RDMs of the SA-LASSCF states like this
states_casdm1s = las.states_make_casdm1s ()
# You can get the 1- and 2-RDMs of the LASSI solutions like this
roots_casdm1s, roots_casdm2s = lassi.roots_make_rdm12s (las, las.ci, si)
# No super-convenient molden API yet
# By default orbitals are state-averaged natural-orbitals at the end
# of the SA-LASSCF calculation
# But you can recanonicalize
print ("\nlasscf_state_0-3.molden: single LAS state NOs, (strictly) unentangled")
for iroot, dm1 in enumerate (states_casdm1s.sum (1)): # spin sum
no_coeff, no_ene, no_occ = las.canonicalize (natorb_casdm1=dm1)[:3]
molden.from_mo (las.mol, 'lasscf_state_{}.molden'.format (iroot),
no_coeff, occ=no_occ, ene=no_ene)
print ("lassi_root_0-3.molden: LASSI eigenstate NOs, (generally) entangled")
for iroot, dm1 in enumerate (roots_casdm1s.sum (1)): # spin sum
no_coeff, no_ene, no_occ = las.canonicalize (natorb_casdm1=dm1)[:3]
molden.from_mo (las.mol, 'lassi_root_{}.molden'.format (iroot),
no_coeff, occ=no_occ, ene=no_ene)
# Beware! Don't do ~~~anything~~ to the si array before you pass it to the
# function above or grab the important data from its attachments!
print ("\nSurely I can type si = si * 1 without any consequences")
si = si * 1
try:
print ("<S**2>:",si.s2)
except AttributeError as e:
print ("Oh no! <S**2> disappeared and all I have now is this error message:")
print ("AttributeError:", str (e))
from pyscf import lo
from pyscf.tools import molden
mol = gto.M(
atom = '''
C 0.000000000000 1.398696930758 0.000000000000
C 0.000000000000 -1.398696930758 0.000000000000
C 1.211265339156 0.699329968382 0.000000000000
C 1.211265339156 -0.699329968382 0.000000000000
C -1.211265339156 0.699329968382 0.000000000000
C -1.211265339156 -0.699329968382 0.000000000000
H 0.000000000000 2.491406946734 0.000000000000
H 0.000000000000 -2.491406946734 0.000000000000
H 2.157597486829 1.245660462400 0.000000000000
H 2.157597486829 -1.245660462400 0.000000000000
H -2.157597486829 1.245660462400 0.000000000000
H -2.157597486829 -1.245660462400 0.000000000000''',
basis = '6-31g')
mf = scf.RHF(mol).run()
pz_idx = numpy.array([17,20,21,22,23,30,36,41,42,47,48,49])-1
loc_orb = lo.Boys(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'boys.molden', loc_orb)
loc_orb = lo.ER(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'edmiston.molden', loc_orb)
loc_orb = lo.PM(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'pm.molden', loc_orb)
#
# Author: Qiming Sun <*****@*****.**>
#
'''
TDDFT NTO analysis.
'''
from pyscf import gto, dft, tddft
mol = gto.Mole()
mol.build(
atom = 'H 0 0 0; F 0 0 1.1', # in Angstrom
basis = '631g',
symmetry = True,
)
mf = dft.RKS(mol)
mf.xc = 'b3lyp'
mf.kernel()
mytd = tddft.TDDFT(mf)
mytd.kernel()
weights_1, nto_1 = mytd.get_nto(state=1, verbose=4)
weights_2, nto_2 = mytd.get_nto(state=2, verbose=4)
weights_3, nto_3 = mytd.get_nto(state=3, verbose=4)
from pyscf.tools import molden
molden.from_mo(mol, 'nto-td-3.molden', nto_3)
mf = scf.RHF(mol)
mf.kernel()
#
# First method is to explicit call the functions provided by molden.py
#
with open("C6H6mo.molden", "w") as f1:
molden.header(mol, f1)
molden.orbital_coeff(mol, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)
#
# Second method is to simply call from_mo function to write the orbitals
#
c_loc_orth = lo.orth.orth_ao(mol)
molden.from_mo(mol, "C6H6loc.molden", c_loc_orth)
#
# Molden format does not support high angular momentum basis. To handle the
# orbitals which have l>=5 functions, a hacky way is to call molden.remove_high_l
# function. However, the resultant orbitals may not be orthnormal.
#
mol = gto.M(atom="He 0 0 0", basis={"He": gto.expand_etbs(((0, 3, 1.0, 2.0), (5, 2, 1.0, 2.0)))})
mf = scf.RHF(mol).run()
try:
molden.from_mo(mol, "He_without_h.molden", mf.mo_coeff)
except RuntimeError:
print(" Found l=5 in basis.")
molden.from_mo(mol, "He_without_h.molden", mf.mo_coeff, ignore_h=True)
def setup_wm_core_scf(self, fragments, calcname):
self.restore_wm_full_scf()
oneRDMcorr_loc = sum((frag.oneRDMas_loc for frag in fragments))
oneSDMcorr_loc = sum((frag.oneSDMas_loc for frag in fragments))
if np.all(np.isclose(oneRDMcorr_loc, 0)):
print("Null correlated 1-RDM; default settings for wm wvfn")
self.oneRDMcorr_loc = oneRDMcorr_loc
self.oneSDMcorr_loc = oneSDMcorr_loc
return
loc2corr = np.concatenate([frag.loc2amo for frag in fragments], axis=1)
# Calculate E2_cum
E2_cum = 0
for frag in fragments:
if frag.norbs_as > 0:
if frag.E2_cum == 0 and np.amax(np.abs(
frag.twoCDMimp_amo)) > 0:
V = self.dmet_tei(frag.loc2amo)
L = frag.twoCDMimp_amo
frag.E2_cum = np.tensordot(V, L, axes=4) / 2
K = self.loc_rhf_k_bis(frag.oneSDMas_loc)
frag.E2_cum += (K * frag.oneSDMas_loc).sum() / 4
E2_cum += frag.E2_cum
loc2idem = get_complementary_states(loc2corr)
test, err = are_bases_orthogonal(loc2idem, loc2corr)
print(
"Testing linear algebra: overlap of active and unactive orbitals = {}"
.format(linalg.norm(err)))
# I want to alter the outputs of self.loc_oei (), self.loc_rhf_fock (), and the get_wm_1RDM_etc () functions.
# self.loc_oei () = P_idem * (activeOEI + JKcorr) * P_idem
# self.loc_rhf_fock () = P_idem * (activeOEI + JKcorr + JKidem) * P_idem
# The get_wm_1RDM_etc () functions will need to add oneRDMcorr_loc to their final return value
# The chemical potential is so that identically zero eigenvalues from the projection into the idem space don't get confused
# with numerically-zero eigenvalues in the idem space: all occupied orbitals must have negative energy
# Make true output 1RDM from fragments to use as guess for wm mcscf calculation
oneRDMguess_loc = np.zeros_like(oneRDMcorr_loc)
for f in itertools.product(fragments, fragments):
loc2frag = [i.loc2frag for i in f]
oneRDMguess_loc += sum(
(0.5 * project_operator_into_subspace(i.oneRDM_loc, *loc2frag)
for i in f))
nelec_corr = np.trace(oneRDMcorr_loc)
if is_close_to_integer(nelec_corr,
100 * params.num_zero_atol) == False:
raise ValueError(
"nelec_corr not an integer! {}".format(nelec_corr))
nelec_idem = int(round(self.nelec_tot - nelec_corr))
if nelec_idem % 2:
raise NotImplementedError("Odd % of unactive electrons")
JKcorr = self.loc_rhf_jk_bis(oneRDMcorr_loc)
oei = self.activeOEI + JKcorr / 2
vk = -self.loc_rhf_k_bis(oneSDMcorr_loc) / 2
working_const = self.activeCONST + (oei * oneRDMcorr_loc).sum() + (
vk * oneSDMcorr_loc).sum() / 2 + E2_cum
oneRDMidem_loc = self.get_wm_1RDM_from_scf_on_OEI(
self.loc_oei() + JKcorr,
nelec=nelec_idem,
loc2wrk=loc2idem,
oneRDMguess_loc=oneRDMguess_loc,
output=calcname + '_trial_wvfn.log',
working_const=working_const)
JKidem = self.loc_rhf_jk_bis(oneRDMidem_loc)
print("trace of oneRDMcorr_loc = {}".format(np.trace(oneRDMcorr_loc)))
print("trace of oneRDMidem_loc = {}".format(np.trace(oneRDMidem_loc)))
print("trace of oneSDMcorr_loc = {}".format(np.trace(oneSDMcorr_loc)))
print("trace of oneRDM_loc in corr basis = {}".format(
np.trace(
represent_operator_in_basis(oneRDMcorr_loc + oneRDMidem_loc,
loc2corr))))
svals = get_overlapping_states(loc2idem, loc2corr)[2]
print("trace of <idem|corr|idem> = {}".format(np.sum(svals * svals)))
print(loc2corr.shape)
print(loc2idem.shape)
dma_dmb = oneRDMidem_loc + oneRDMcorr_loc
dma_dmb = [(dma_dmb + oneSDMcorr_loc) / 2,
(dma_dmb - oneSDMcorr_loc) / 2]
focka_fockb = [JKcorr + vk, JKcorr - vk]
focka_fockb = [self.activeOEI + JKidem + JK for JK in focka_fockb]
oneRDM_loc = oneRDMidem_loc + oneRDMcorr_loc
oneSDM_loc = oneSDMcorr_loc
########################################################################################################
self.activeFOCK = get_roothaan_fock(focka_fockb, dma_dmb,
np.eye(self.norbs_tot))
self.activeJKidem = JKidem
self.activeJKcorr = JKcorr
self.oneRDMcorr_loc = oneRDMcorr_loc
self.loc2idem = loc2idem
self.nelec_idem = nelec_idem
self.oneRDM_loc = oneRDM_loc
self.oneSDM_loc = oneSDM_loc
########################################################################################################
# Analysis: 1RDM and total energy
print("Analyzing LASSCF trial wave function")
jk = np.stack([JKcorr + JKidem, -self.loc_rhf_k_bis(oneSDM_loc) / 2],
axis=0)
dm = np.stack([oneRDM_loc, oneSDM_loc], axis=0)
E = self.activeCONST + (
self.activeOEI * oneRDM_loc).sum() + (jk * dm).sum() / 2 + E2_cum
print("LASSCF trial wave function total energy: {:.6f}".format(E))
self.e_tot = E
# Molden
ao2molden, ene_no, occ_no = self.get_trial_nos(aobasis=True,
loc2wmas=loc2corr,
oneRDM_loc=oneRDM_loc,
fock=self.activeFOCK,
jmol_shift=True,
try_symmetrize=True)
print("Writing trial wave function molden")
molden.from_mo(self.mol,
calcname + '_trial_wvfn.molden',
ao2molden,
occ=occ_no,
ene=ene_no)