def format_currentstate_for_input(func, name, allButMol=False, **kwargs):
"""Function to return an input file in preprocessed psithon.
Captures memory, molecule, options, function, method, and kwargs.
Used to write distributed (sow/reap) input files.
"""
warnings.warn(
"Using `psi4.driver.p4util.format_currentstate_for_input` is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
commands = """\n# This is a psi4 input file auto-generated from the %s() wrapper.\n\n""" % (
inspect.stack()[1][3])
commands += """memory %d mb\n\n""" % (int(0.000001 * core.get_memory()))
if not allButMol:
molecule = core.get_active_molecule()
molecule.update_geometry()
commands += format_molecule_for_input(molecule)
commands += '\n'
commands += prepare_options_for_modules(changedOnly=True,
commandsInsteadDict=True)
commands += """\n%s('%s', """ % (func.__name__, name.lower())
for key in kwargs.keys():
commands += """%s=%r, """ % (key, kwargs[key])
commands += ')\n\n'
return commands
def format_options_for_input(molecule=None, **kwargs):
"""Function to return a string of commands to replicate the
current state of user-modified options. Used to capture C++
options information for distributed (sow/reap) input files.
.. caution:: Some features are not yet implemented. Buy a developer a coffee.
- Does not cover local (as opposed to global) options.
"""
if molecule is not None:
symmetry = molecule.find_point_group(0.00001).symbol()
commands = ''
commands += """\ncore.set_memory_bytes(%s)\n\n""" % (core.get_memory())
for chgdopt in core.get_global_option_list():
if core.has_global_option_changed(chgdopt):
chgdoptval = core.get_global_option(chgdopt)
if molecule is not None:
if chgdopt.lower() in kwargs:
if symmetry in kwargs[chgdopt.lower()]:
chgdoptval = kwargs[chgdopt.lower()][symmetry]
if isinstance(chgdoptval, str):
commands += """core.set_global_option('%s', '%s')\n""" % (chgdopt, chgdoptval)
# Next four lines were conflict between master and roa branches (TDC, 10/29/2014)
elif isinstance(chgdoptval, int) or isinstance(chgdoptval, float):
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
elif isinstance(chgdoptval, list):
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
else:
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
return commands
def format_options_for_input(molecule=None, **kwargs):
"""Function to return a string of commands to replicate the
current state of user-modified options. Used to capture C++
options information for distributed (sow/reap) input files.
.. caution:: Some features are not yet implemented. Buy a developer a coffee.
- Does not cover local (as opposed to global) options.
"""
if molecule is not None:
symmetry = molecule.find_point_group(0.00001).symbol()
commands = ''
commands += """\ncore.set_memory_bytes(%s)\n\n""" % (core.get_memory())
for chgdopt in core.get_global_option_list():
if core.has_global_option_changed(chgdopt):
chgdoptval = core.get_global_option(chgdopt)
if molecule is not None:
if chgdopt.lower() in kwargs:
if symmetry in kwargs[chgdopt.lower()]:
chgdoptval = kwargs[chgdopt.lower()][symmetry]
if isinstance(chgdoptval, str):
commands += """core.set_global_option('%s', '%s')\n""" % (chgdopt, chgdoptval)
# Next four lines were conflict between master and roa branches (TDC, 10/29/2014)
elif isinstance(chgdoptval, int) or isinstance(chgdoptval, float):
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
elif isinstance(chgdoptval, list):
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
else:
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
return commands
def format_currentstate_for_input(func, name, allButMol=False, **kwargs):
"""Function to return an input file in preprocessed psithon.
Captures memory, molecule, options, function, method, and kwargs.
Used to write distributed (sow/reap) input files.
"""
warnings.warn(
"Using `psi4.driver.p4util.format_currentstate_for_input` is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
commands = """\n# This is a psi4 input file auto-generated from the %s() wrapper.\n\n""" % (inspect.stack()[1][3])
commands += """memory %d mb\n\n""" % (int(0.000001 * core.get_memory()))
if not allButMol:
molecule = core.get_active_molecule()
molecule.update_geometry()
commands += format_molecule_for_input(molecule)
commands += '\n'
commands += prepare_options_for_modules(changedOnly=True, commandsInsteadDict=True)
commands += """\n%s('%s', """ % (func.__name__, name.lower())
for key in kwargs.keys():
commands += """%s=%r, """ % (key, kwargs[key])
commands += ')\n\n'
return commands
def _initialize_jk(self, basis, aux_basis, do_J=True, do_K=True):
jk = core.JK.build(basis, aux_basis)
jk.set_memory(int(float(core.get_global_option("SCF_MEM_SAFETY_FACTOR")) * core.get_memory() / 8))
jk.set_do_J(do_J)
jk.set_do_K(do_K)
jk.print_header()
jk.initialize()
return jk
def scf_initialize(self):
"""Specialized initialization, compute integrals and does everything to prepare for iterations"""
# Figure out memory distributions
# Get memory in terms of doubles
total_memory = (core.get_memory() /
8) * core.get_global_option("SCF_MEM_SAFETY_FACTOR")
# Figure out how large the DFT collocation matrices are
vbase = self.V_potential()
if vbase:
collocation_size = vbase.grid().collocation_size()
if vbase.functional().ansatz() == 1:
collocation_size *= 4 # First derivs
elif vbase.functional().ansatz() == 2:
collocation_size *= 10 # Second derivs
else:
collocation_size = 0
# Change allocation for collocation matrices based on DFT type
scf_type = core.get_global_option('SCF_TYPE').upper()
nbf = self.get_basisset("ORBITAL").nbf()
naux = self.get_basisset("DF_BASIS_SCF").nbf()
if "DIRECT" == scf_type:
jk_size = total_memory * 0.1
elif scf_type.endswith('DF'):
jk_size = naux * nbf * nbf
else:
jk_size = nbf**4
# Give remaining to collocation
if total_memory > jk_size:
collocation_memory = total_memory - jk_size
# Give up to 10% to collocation
elif (total_memory * 0.1) > collocation_size:
collocation_memory = collocation_size
else:
collocation_memory = total_memory * 0.1
if collocation_memory > collocation_size:
collocation_memory = collocation_size
# Set constants
self.iteration_ = 0
self.memory_jk_ = int(total_memory - collocation_memory)
self.memory_collocation_ = int(collocation_memory)
# Print out initial docc/socc/etc data
if core.get_option('SCF', "PRINT") > 0:
core.print_out(" ==> Pre-Iterations <==\n\n")
self.print_preiterations()
# Initialize EFP
efp_enabled = hasattr(self.molecule(), 'EFP')
if efp_enabled:
# EFP: Set QM system, options, and callback. Display efp geom in [A]
efpobj = self.molecule().EFP
core.print_out(efpobj.banner())
core.print_out(
efpobj.geometry_summary(units_to_bohr=constants.bohr2angstroms))
efpptc, efpcoords, efpopts = get_qm_atoms_opts(self.molecule())
efpobj.set_point_charges(efpptc, efpcoords)
efpobj.set_opts(efpopts, label='psi', append='psi')
efpobj.set_electron_density_field_fn(field_fn)
# Initilize all integratals and perform the first guess
if self.attempt_number_ == 1:
mints = core.MintsHelper(self.basisset())
if core.get_global_option('RELATIVISTIC') in ['X2C', 'DKH']:
mints.set_rel_basisset(self.get_basisset('BASIS_RELATIVISTIC'))
mints.one_electron_integrals()
self.initialize_jk(self.memory_jk_)
if self.V_potential():
self.V_potential().build_collocation_cache(
self.memory_collocation_)
core.timer_on("HF: Form core H")
self.form_H()
core.timer_off("HF: Form core H")
if efp_enabled:
# EFP: Add in permanent moment contribution and cache
core.timer_on("HF: Form Vefp")
verbose = core.get_option('SCF', "PRINT")
Vefp = modify_Fock_permanent(self.molecule(),
mints,
verbose=verbose - 1)
Vefp = core.Matrix.from_array(Vefp)
self.H().add(Vefp)
Horig = self.H().clone()
self.Horig = Horig
core.print_out(
" QM/EFP: iterating Total Energy including QM/EFP Induction\n"
)
core.timer_off("HF: Form Vefp")
core.timer_on("HF: Form S/X")
self.form_Shalf()
core.timer_off("HF: Form S/X")
core.timer_on("HF: Guess")
self.guess()
core.timer_off("HF: Guess")
else:
# We're reading the orbitals from the previous set of iterations.
self.form_D()
self.set_energies("Total Energy", self.compute_initial_E())
# turn off VV10 for iterations
if core.get_option(
'SCF', "DFT_VV10_POSTSCF") and self.functional().vv10_b() > 0.0:
core.print_out(" VV10: post-SCF option active \n \n")
self.functional().set_lock(False)
self.functional().set_do_vv10(False)
self.functional().set_lock(True)
def scf_initialize(self):
"""Specialized initialization, compute integrals and does everything to prepare for iterations"""
# Figure out memory distributions
# Get memory in terms of doubles
total_memory = (core.get_memory() /
8) * core.get_global_option("SCF_MEM_SAFETY_FACTOR")
# Figure out how large the DFT collocation matrices are
vbase = self.V_potential()
if vbase:
collocation_size = vbase.grid().collocation_size()
if vbase.functional().ansatz() == 1:
collocation_size *= 4 # First derivs
elif vbase.functional().ansatz() == 2:
collocation_size *= 10 # Second derivs
else:
collocation_size = 0
# Change allocation for collocation matrices based on DFT type
jk = _build_jk(self, total_memory)
jk_size = jk.memory_estimate()
# Give remaining to collocation
if total_memory > jk_size:
collocation_memory = total_memory - jk_size
# Give up to 10% to collocation
elif (total_memory * 0.1) > collocation_size:
collocation_memory = collocation_size
else:
collocation_memory = total_memory * 0.1
if collocation_memory > collocation_size:
collocation_memory = collocation_size
# Set constants
self.iteration_ = 0
self.memory_jk_ = int(total_memory - collocation_memory)
self.memory_collocation_ = int(collocation_memory)
if self.get_print():
core.print_out(" ==> Integral Setup <==\n\n")
# Initialize EFP
efp_enabled = hasattr(self.molecule(), 'EFP')
if efp_enabled:
# EFP: Set QM system, options, and callback. Display efp geom in [A]
efpobj = self.molecule().EFP
core.print_out(efpobj.banner())
core.print_out(
efpobj.geometry_summary(units_to_bohr=constants.bohr2angstroms))
efpptc, efpcoords, efpopts = get_qm_atoms_opts(self.molecule())
efpobj.set_point_charges(efpptc, efpcoords)
efpobj.set_opts(efpopts, label='psi', append='psi')
efpobj.set_electron_density_field_fn(efp_field_fn)
# Initialize all integrals and perform the first guess
if self.attempt_number_ == 1:
mints = core.MintsHelper(self.basisset())
self.initialize_jk(self.memory_jk_, jk=jk)
if self.V_potential():
self.V_potential().build_collocation_cache(
self.memory_collocation_)
core.timer_on("HF: Form core H")
self.form_H()
core.timer_off("HF: Form core H")
if efp_enabled:
# EFP: Add in permanent moment contribution and cache
core.timer_on("HF: Form Vefp")
verbose = core.get_option('SCF', "PRINT")
Vefp = modify_Fock_permanent(self.molecule(),
mints,
verbose=verbose - 1)
Vefp = core.Matrix.from_array(Vefp)
self.H().add(Vefp)
Horig = self.H().clone()
self.Horig = Horig
core.print_out(
" QM/EFP: iterating Total Energy including QM/EFP Induction\n"
)
core.timer_off("HF: Form Vefp")
core.timer_on("HF: Form S/X")
self.form_Shalf()
core.timer_off("HF: Form S/X")
core.print_out("\n ==> Pre-Iterations <==\n\n")
core.timer_on("HF: Guess")
self.guess()
core.timer_off("HF: Guess")
# Print out initial docc/socc/etc data
if self.get_print():
lack_occupancy = core.get_local_option('SCF', 'GUESS') in ['SAD']
if core.get_global_option('GUESS') in ['SAD']:
lack_occupancy = core.get_local_option('SCF',
'GUESS') in ['AUTO']
self.print_preiterations(small=lack_occupancy)
else:
self.print_preiterations(small=lack_occupancy)
else:
# We're reading the orbitals from the previous set of iterations.
self.form_D()
self.set_energies("Total Energy", self.compute_initial_E())
# turn off VV10 for iterations
if core.get_option(
'SCF', "DFT_VV10_POSTSCF") and self.functional().vv10_b() > 0.0:
core.print_out(" VV10: post-SCF option active \n \n")
self.functional().set_lock(False)
self.functional().set_do_vv10(False)
self.functional().set_lock(True)
# Print iteration header
is_dfjk = core.get_global_option('SCF_TYPE').endswith('DF')
diis_rms = core.get_option('SCF', 'DIIS_RMS_ERROR')
core.print_out(" ==> Iterations <==\n\n")
core.print_out(
"%s Total Energy Delta E %s |[F,P]|\n\n"
% (" " if is_dfjk else "", "RMS" if diis_rms else "MAX"))
def get_memory():
"""Function to return the total memory allocation."""
return core.get_memory()
def compute_hessian(self,
wfn,
prog='psi4',
geom=None,
disp_points=3,
disp_size=0.005,
c4executable=None,
c4kw={}):
Natom = self.mol.natom()
if prog.upper() == 'PSI4':
self.pr("(ROA) Computing hessian with Psi4...\n")
#Prepare geometry
if geom is None:
geom = self.analysis_geom_2D
self.mol.set_geometry(core.Matrix.from_array(geom))
self.mol.fix_com(True)
self.mol.fix_orientation(True)
self.mol.reset_point_group('c1')
# core.set_global_option('hessian_write', True)
# compute the hessian, put in numpy format, then write out file15.dat file.
psi4_hess = psi4.hessian(wfn, molecule=self.mol)
npHess = psi4_hess.clone().np
npHess = np.reshape(npHess, (3 * Natom * Natom, 3))
f = open('file15.dat', 'w')
for i in range(npHess.shape[0]):
f.write('{0:20.10f}{1:20.10f}{2:20.10f}\n'.format(
npHess[i][0], npHess[i][1], npHess[i][2]))
f.close()
elif prog.upper() == 'CFOUR':
self.pr("(ROA) Computing hessian with CFOUR...\n")
kw = {
'CALC': wfn.upper(),
# if basis not builtin C4, set BASIS=SPECIAL and SPECIAL_BASIS='name'
'BASIS': core.get_global_option('BASIS'),
#'SPECIAL_BASIS' : '6-31G'
'VIB': 'EXACT',
'UNITS': 'BOHR',
'SCF_CONV': 9,
'MEM_UNIT': 'GB',
'MEMORY_SIZE': round(core.get_memory() // 1e9),
'SCF_DAMP': 600, # CFOUR's SCF is really poor at converging.
'SCF_EXPSTART': 300,
'SCF_MAXCYC': 600,
}
kw.update(c4kw)
atom_symbols = [
self.mol.symbol(at) for at in range(self.mol.natom())
]
if c4executable is None:
c4executable = 'run-cfour'
c4 = CFOUR(self.analysis_geom_2D,
atom_symbols,
kw,
title="hess-calc",
executable=c4executable)
c4.run()
c4h = c4.parseHessian() # read the hessian output file (FCMFINAL)
# Now rotate the Hessian into the original input orientation; fancy!
c4coord = c4.parseGeometry()
rmsd, mill = qcel.molutil.B787(c4coord,
self.analysis_geom_2D,
None,
None,
atoms_map=True,
verbose=False)
c4h[:] = mill.align_hessian(c4h)
c4.writeFile15(c4h)
else:
raise Exception('Other hessian prog not yet implemented')
def compute_dipole_derivatives(self,
wfn,
prog='psi4',
geom=None,
disp_points=3,
disp_size=0.001,
c4kw={}):
Natom = self.mol.natom()
if prog.upper() == 'PSI4':
# Lacking analytic derivatives, we will do fd of applied electric fields. We
# alternately apply + and - electric fields in the x, y, and z directions, and
# then take finite differences to get the dipole moment derivatives.
self.pr(
"(ROA) Computing dipole moment derivatives with Psi4 by f.d...\n"
)
#Prepare geometry
if geom is None:
geom = self.analysis_geom_2D
self.mol.set_geometry(core.Matrix.from_array(geom))
self.mol.fix_com(True)
self.mol.fix_orientation(True)
self.mol.reset_point_group('c1')
N = self.mol.natom()
if disp_points == 3:
lambdas = [-1.0 * disp_size, 1.0 * disp_size]
elif disp_points == 5:
lambdas = [
-2.0 * disp_size, -1.0 * disp_size, 1.0 * disp_size,
+2.0 * disp_size
]
DmuxDx = psi4.core.Matrix("Dipole derivatives mu_x", N, 3)
DmuyDx = psi4.core.Matrix("Dipole derivatives mu_y", N, 3)
DmuzDx = psi4.core.Matrix("Dipole derivatives mu_z", N, 3)
for dipole_xyz, dipole_vector in enumerate([[1, 0, 0], [0, 1, 0],
[0, 0, 1]]):
dx = []
for l in lambdas:
core.set_global_option('perturb_h', True)
core.set_global_option('perturb_with', 'dipole')
scaled_dipole_vector = []
for x in dipole_vector:
scaled_dipole_vector.append(x * l)
core.set_global_option('perturb_dipole',
scaled_dipole_vector)
dx.append(psi4.gradient(wfn))
for A in range(N):
for xyz in range(3):
if disp_points == 3:
val = (dx[1].get(A, xyz) -
dx[0].get(A, xyz)) / (2.0 * disp_size)
elif disp_points == 5:
val = (dx[0].get(A,xyz) - 8.0*dx[1].get(A,xyz) \
+ 8.0*dx[2].get(A,xyz) - dx[3].get(A,xyz)) / (12.0*disp_size)
if dipole_xyz == 0:
DmuxDx.set(A, xyz, val)
elif dipole_xyz == 1:
DmuyDx.set(A, xyz, val)
elif dipole_xyz == 2:
DmuzDx.set(A, xyz, val)
core.set_global_option('PERTURB_H', 0)
core.set_global_option('PERTURB_DIPOLE', '')
# write out a file17 with the dipole moment derivatives
f = open('file17.dat', 'w')
for i in range(N):
f.write('{0:20.10f}{1:20.10f}{2:20.10f}\n'.format(
DmuxDx.get(i, 0), DmuxDx.get(i, 1), DmuxDx.get(i, 2)))
for i in range(N):
f.write('{0:20.10f}{1:20.10f}{2:20.10f}\n'.format(
DmuyDx.get(i, 0), DmuyDx.get(i, 1), DmuyDx.get(i, 2)))
for i in range(N):
f.write('{0:20.10f}{1:20.10f}{2:20.10f}\n'.format(
DmuzDx.get(i, 0), DmuzDx.get(i, 1), DmuzDx.get(i, 2)))
f.close()
elif prog.upper() == 'CFOUR':
self.pr(
"(ROA) Reading dipole moment derivatives from CFOUR's DIPDER.\n"
)
kw = {
'CALC': wfn.upper(),
'BASIS': core.get_global_option('BASIS'),
'VIB': 'EXACT',
'UNITS': 'BOHR',
'VIB': 'EXACT',
'UNITS': 'BOHR',
'SCF_CONV': 9,
'MEM_UNIT': 'GB',
'MEMORY_SIZE': round(core.get_memory() // 1e9),
'SCF_DAMP': 600, # CFOUR's SCF is really poor at converging.
'SCF_EXPSTART': 300,
'SCF_MAXCYC': 600,
}
kw.update(c4kw)
atom_symbols = [
self.mol.symbol(at) for at in range(self.mol.natom())
]
c4 = CFOUR(self.analysis_geom_2D, atom_symbols, kw,
"input for DIPDIR read")
(c4dipx, c4dipy, c4dipz) = c4.parseDIPDER()
# Now rotate to input orientation
c4coord = c4.parseGeometry()
rmsd, mill = qcel.molutil.B787(c4coord,
self.analysis_geom_2D,
None,
None,
atoms_map=True,
verbose=False)
RotMat = mill.rotation
# For each atom for field direction by nuclear direction 3x3 and transform it.
for at in range(Natom):
DIPDERatom = np.zeros((3, 3))
DIPDERatom[0, :] = c4dipx[at, :]
DIPDERatom[1, :] = c4dipy[at, :]
DIPDERatom[2, :] = c4dipz[at, :]
DIPDERatom[:] = np.dot(RotMat.T, np.dot(DIPDERatom, RotMat))
c4dipx[at][:] = DIPDERatom[0, :]
c4dipy[at][:] = DIPDERatom[1, :]
c4dipz[at][:] = DIPDERatom[2, :]
c4.writeFile17(c4dipx, c4dipy, c4dipz)
else:
raise Exception('Other muder prog not yet implemented')
return
def compute(self, client: Optional["FractalClient"] = None):
"""Run quantum chemistry."""
from psi4.driver import pp
if self.computed:
return
if client:
self.computed = True
from qcportal.models import KeywordSet, Molecule
# Build the keywords
keyword_id = client.add_keywords(
[KeywordSet(values=self.keywords)])[0]
# Build the molecule
mol = Molecule(**self.molecule.to_schema(dtype=2))
r = client.add_compute("psi4", self.method, self.basis,
self.driver, keyword_id, [mol])
self.result_id = r.ids[0]
# NOTE: The following will re-run errored jobs by default
if self.result_id in r.existing:
ret = client.query_tasks(base_result=self.result_id)
if ret:
if ret[0].status == "ERROR":
client.modify_tasks("restart",
base_result=self.result_id)
logger.info("Resubmitting Errored Job {}".format(
self.result_id))
elif ret[0].status == "COMPLETE":
logger.debug("Job already completed {}".format(
self.result_id))
else:
logger.debug("Job already completed {}".format(
self.result_id))
else:
logger.debug("Submitting AtomicResult {}".format(
self.result_id))
return
logger.info(
f'<<< JSON launch ... {self.molecule.schoenflies_symbol()} {self.molecule.nuclear_repulsion_energy()}'
)
gof = core.get_output_file()
# EITHER ...
# from psi4.driver import schema_wrapper
# self.result = schema_wrapper.run_qcschema(self.plan())
# ... OR ...
self.result = qcng.compute(
self.plan(),
"psi4",
raise_error=True,
# local_options below suitable for serial mode where each job takes all the resources of the parent Psi4 job.
# distributed runs through QCFractal will likely need a different setup.
local_options={
# B -> GiB
"memory": core.get_memory() / (2**30),
"ncores": core.get_num_threads(),
},
)
# ... END
#pp.pprint(self.result.dict())
#print("... JSON returns >>>")
core.set_output_file(gof, True)
core.reopen_outfile()
logger.debug(pp.pformat(self.result.dict()))
core.print_out(_drink_filter(self.result.dict()["stdout"]))
self.computed = True
def write_zmat(name, dertype, molecule):
"""Returns string with contents of Cfour ZMAT file as gathered from
active molecule, current keyword settings, and cfour {...} block.
"""
# Handle memory
mem = int(0.000001 * core.get_memory())
if mem == 524:
memcmd, memkw = '', {}
else:
memcmd, memkw = qcdb.cfour.muster_memory(mem)
# Handle molecule and basis set
if molecule.name() == 'blank_molecule_psi4_yo':
molcmd, molkw = '', {}
bascmd, baskw = '', {}
core.set_local_option('CFOUR', 'TRANSLATE_PSI4', False)
else:
molecule.update_geometry()
#print(molecule.create_psi4_string_from_molecule())
qcdbmolecule = qcdb.Molecule(
molecule.create_psi4_string_from_molecule())
qcdbmolecule.tagline = molecule.name()
molcmd, molkw = qcdbmolecule.format_molecule_for_cfour()
if core.get_global_option('BASIS') in ["", "(AUTO)"]:
bascmd, baskw = '', {}
else:
user_pg = molecule.schoenflies_symbol()
molecule.reset_point_group(
'c1') # need basis printed for *every* atom
qbs = core.BasisSet.build(molecule, "BASIS",
core.get_global_option('BASIS'))
if qbs.has_ECP():
raise ValidationError("""ECPs not hooked up for Cfour""")
with open('GENBAS', 'w') as cfour_basfile:
cfour_basfile.write(qbs.genbas())
core.print_out(
' GENBAS loaded from Psi4 LibMints for basis %s\n' %
(core.get_global_option('BASIS')))
molecule.reset_point_group(user_pg)
molecule.update_geometry()
bascmd, baskw = qcdbmolecule.format_basis_for_cfour(
qbs.has_puream())
# Handle psi4 keywords implying cfour keyword values
if core.get_option('CFOUR', 'TRANSLATE_PSI4'):
psicmd, psikw = qcdb.cfour.muster_psi4options(
p4util.prepare_options_for_modules(changedOnly=True))
else:
psicmd, psikw = '', {}
# Handle calc type and quantum chemical method
mdccmd, mdckw = qcdb.cfour.muster_modelchem(name, dertype)
# Handle calc type and quantum chemical method
mdccmd, mdckw = qcdb.cfour.muster_modelchem(name, dertype)
# Handle driver vs input/default keyword reconciliation
userkw = p4util.prepare_options_for_modules()
userkw = qcdb.options.reconcile_options(userkw, memkw)
userkw = qcdb.options.reconcile_options(userkw, molkw)
userkw = qcdb.options.reconcile_options(userkw, baskw)
userkw = qcdb.options.reconcile_options(userkw, psikw)
userkw = qcdb.options.reconcile_options(userkw, mdckw)
# Handle conversion of psi4 keyword structure into cfour format
optcmd = qcdb.options.prepare_options_for_cfour(userkw)
# Handle text to be passed untouched to cfour
litcmd = core.get_global_option('LITERAL_CFOUR')
# Assemble ZMAT pieces
zmat = memcmd + molcmd + optcmd + mdccmd + psicmd + bascmd + litcmd
if len(re.findall(r'^\*(ACES2|CFOUR|CRAPS)\(', zmat, re.MULTILINE)) != 1:
core.print_out('\n Faulty ZMAT constructed:\n%s' % (zmat))
raise ValidationError("""
Multiple *CFOUR(...) blocks in input. This usually arises
because molecule or options are specified both the psi4 way through
molecule {...} and set ... and the cfour way through cfour {...}.""")
return zmat
def scf_initialize(self):
"""Specialized initialization, compute integrals and does everything to prepare for iterations"""
# Figure out memory distributions
# Get memory in terms of doubles
total_memory = (core.get_memory() / 8) * core.get_global_option("SCF_MEM_SAFETY_FACTOR")
# Figure out how large the DFT collocation matrices are
vbase = self.V_potential()
if vbase:
collocation_size = vbase.grid().collocation_size()
if vbase.functional().ansatz() == 1:
collocation_size *= 4 # First derivs
elif vbase.functional().ansatz() == 2:
collocation_size *= 10 # Second derivs
else:
collocation_size = 0
# Change allocation for collocation matrices based on DFT type
jk = _build_jk(self, total_memory)
jk_size = jk.memory_estimate()
# Give remaining to collocation
if total_memory > jk_size:
collocation_memory = total_memory - jk_size
# Give up to 10% to collocation
elif (total_memory * 0.1) > collocation_size:
collocation_memory = collocation_size
else:
collocation_memory = total_memory * 0.1
if collocation_memory > collocation_size:
collocation_memory = collocation_size
# Set constants
self.iteration_ = 0
self.memory_jk_ = int(total_memory - collocation_memory)
self.memory_collocation_ = int(collocation_memory)
# Print out initial docc/socc/etc data
if self.get_print():
core.print_out(" ==> Pre-Iterations <==\n\n")
self.print_preiterations()
if self.get_print():
core.print_out(" ==> Integral Setup <==\n\n")
# Initialize EFP
efp_enabled = hasattr(self.molecule(), 'EFP')
if efp_enabled:
# EFP: Set QM system, options, and callback. Display efp geom in [A]
efpobj = self.molecule().EFP
core.print_out(efpobj.banner())
core.print_out(efpobj.geometry_summary(units_to_bohr=constants.bohr2angstroms))
efpptc, efpcoords, efpopts = get_qm_atoms_opts(self.molecule())
efpobj.set_point_charges(efpptc, efpcoords)
efpobj.set_opts(efpopts, label='psi', append='psi')
efpobj.set_electron_density_field_fn(field_fn)
# Initilize all integratals and perform the first guess
if self.attempt_number_ == 1:
mints = core.MintsHelper(self.basisset())
if core.get_global_option('RELATIVISTIC') in ['X2C', 'DKH']:
mints.set_rel_basisset(self.get_basisset('BASIS_RELATIVISTIC'))
mints.one_electron_integrals()
self.initialize_jk(self.memory_jk_, jk=jk)
if self.V_potential():
self.V_potential().build_collocation_cache(self.memory_collocation_)
core.timer_on("HF: Form core H")
self.form_H()
core.timer_off("HF: Form core H")
if efp_enabled:
# EFP: Add in permanent moment contribution and cache
core.timer_on("HF: Form Vefp")
verbose = core.get_option('SCF', "PRINT")
Vefp = modify_Fock_permanent(self.molecule(), mints, verbose=verbose-1)
Vefp = core.Matrix.from_array(Vefp)
self.H().add(Vefp)
Horig = self.H().clone()
self.Horig = Horig
core.print_out(" QM/EFP: iterating Total Energy including QM/EFP Induction\n")
core.timer_off("HF: Form Vefp")
core.timer_on("HF: Form S/X")
self.form_Shalf()
core.timer_off("HF: Form S/X")
core.timer_on("HF: Guess")
self.guess()
core.timer_off("HF: Guess")
else:
# We're reading the orbitals from the previous set of iterations.
self.form_D()
self.set_energies("Total Energy", self.compute_initial_E())
# turn off VV10 for iterations
if core.get_option('SCF', "DFT_VV10_POSTSCF") and self.functional().vv10_b() > 0.0:
core.print_out(" VV10: post-SCF option active \n \n")
self.functional().set_lock(False)
self.functional().set_do_vv10(False)
self.functional().set_lock(True)
def get_memory() -> int:
"""Return the total memory allocation in bytes."""
return core.get_memory()