def run_hf(xyz, basis, charge=0, multiplicity=1, conv_tol=None,
conv_tol_grad=1e-8, max_iter=150):
basis_remap = {
"sto3g": "sto-3g",
"def2tzvp": "def2-tzvp",
"ccpvdz": "cc-pvdz",
}
with tempfile.TemporaryDirectory() as tmpdir:
infile = os.path.join(tmpdir, "vlx.in")
outfile = os.path.join(tmpdir, "vlx.out")
with open(infile, "w") as fp:
lines = ["@jobs", "task: hf", "@end", ""]
lines += ["@method settings",
"basis: {}".format(basis_remap.get(basis, basis)),
"@end"]
lines += ["@molecule",
"charge: {}".format(charge),
"multiplicity: {}".format(multiplicity),
"units: bohr",
"xyz:\n{}".format("\n".join(xyz.split(";"))),
"@end"]
fp.write("\n".join(lines))
task = vlx.MpiTask([infile, outfile], MPI.COMM_WORLD)
scfdrv = vlx.ScfRestrictedDriver(task.mpi_comm, task.ostream)
# elec. gradient norm
scfdrv.conv_thresh = conv_tol_grad
scfdrv.max_iter = max_iter
scfdrv.compute(task.molecule, task.ao_basis, task.min_basis)
scfdrv.task = task
return scfdrv
def run_scf(self, mol, conv_thresh=1e-6):
inp = str(pathlib.Path(self.get_workdir()) / f'{mol}.inp')
out = str(pathlib.Path(self.get_workdir()) / f'{mol}.out')
self.task = vlx.MpiTask((inp, out), self.comm)
if self.task.molecule.get_multiplicity() == 1:
self.scf_driver = vlx.ScfRestrictedDriver(self.comm,
self.task.ostream)
else:
self.scf_driver = vlx.ScfUnrestrictedDriver(
self.comm, self.task.ostream)
self.scf_driver.conv_thresh = conv_thresh
self.scf_driver.compute(self.task.molecule, self.task.ao_basis,
self.task.min_basis)
def run_hf(xyz,
basis,
charge=0,
multiplicity=1,
conv_tol_grad=1e-8,
max_iter=150,
pe_options=None):
basis_remap = {
"sto3g": "sto-3g",
"def2tzvp": "def2-tzvp",
"ccpvdz": "cc-pvdz",
}
with tempfile.TemporaryDirectory() as tmpdir:
infile = os.path.join(tmpdir, "vlx.in")
outfile = os.path.join(tmpdir, "vlx.out")
with open(infile, "w") as fp:
lines = ["@jobs", "task: hf", "@end", ""]
lines += [
"@method settings",
"basis: {}".format(basis_remap.get(basis, basis))
]
# TODO: PE results in VeloxChem are currently wrong, because
# polarizabilities are always made isotropic
if pe_options:
potfile = pe_options["potfile"]
lines += ["pe: yes", f"potfile: {potfile}"]
lines += ["@end"]
lines += [
"@molecule", "charge: {}".format(charge),
"multiplicity: {}".format(multiplicity), "units: bohr",
"xyz:\n{}".format("\n".join(xyz.split(";"))), "@end"
]
fp.write("\n".join(lines))
task = MpiTask([infile, outfile], MPI.COMM_WORLD)
scfdrv = vlx.ScfRestrictedDriver(task.mpi_comm, task.ostream)
scfdrv.update_settings(task.input_dict['scf'],
task.input_dict['method_settings'])
# elec. gradient norm
scfdrv.conv_thresh = conv_tol_grad
scfdrv.max_iter = max_iter
scfdrv.compute(task.molecule, task.ao_basis, task.min_basis)
scfdrv.task = task
return scfdrv
with open(infile, "w") as fp:
fp.write("""
@jobs
task: hf
@end
@method settings
basis: sto-3g
@end
@molecule
charge: 0
multiplicity: 1
units: bohr
xyz:
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
@end
""")
task = MpiTask([infile, outfile], MPI.COMM_WORLD)
scfdrv = vlx.ScfRestrictedDriver(task.mpi_comm, task.ostream)
scfdrv.conv_thresh = 1e-8
scfdrv.compute(task.molecule, task.ao_basis, task.min_basis)
scfdrv.task = task
# Run an adc2 calculation:
state = adcc.adc2(scfdrv, n_singlets=5)
print(state.describe())
method_settings = {}
comm = MPI.COMM_WORLD
ostream = vlx.OutputStream(sys.stdout)
molecule = vlx.Molecule.read_str(molecule_string, units='angs')
basis = vlx.MolecularBasis.read(molecule, basis_set_label)
ostream.print_block(molecule.get_string())
ostream.print_block(basis.get_string('Atomic Basis', molecule))
ostream.flush()
# SCF calculation
# Do SCF again with non-custom routine
scfdrv = vlx.ScfRestrictedDriver(comm, ostream)
scfdrv.update_settings(scf_settings, method_settings)
scfdrv.compute(molecule, basis)
MOs = scfdrv.scf_tensors['C']
F = scfdrv.scf_tensors['F'][0]
# AO integrals (pq|rs)
n_ao = MOs.shape[0]
pqrs = np.zeros((n_ao, n_ao, n_ao, n_ao))
eri_drv = vlx.ElectronRepulsionIntegralsDriver(comm)
eri_drv.compute_in_mem(molecule, basis, pqrs)
# MO integrals (tu|vw), chemists' notation
tqrs = np.einsum('pqrs,pt->tqrs', pqrs, MOs, optimize=True)