def _nto_pairs(
molecule: mtr.Molecule,
settings: mtr.Settings,
num_nto_pairs: int,
n_x: int,
n_y: int,
n_z: int,
) -> mtr.QChemInput:
# number of alpha electrons
n_alpha = int(round((sum(molecule.atomic_numbers) + molecule.charge) / 2))
inp = mtr.QChemInput(settings=mtr.Settings())
for i in range(settings["rem", "cis_n_roots"]):
s = copy.deepcopy(settings)
s["rem", "scf_guess"] = "read"
s["rem", "skip_cis_rpa"] = True
s["rem", "nto_pairs"] = True
s["rem", "make_cube_files"] = "ntos"
s["rem", "cubefile_state"] = i + 1
s["plots", "comment"] = (
f"\n {n_x} -10.0 10.0\n" + f" {n_y} -10.0 10.0\n" +
f" {n_z} -10.0 10.0\n" + f" {2*num_nto_pairs} 0 0 0\n " +
" ".join(f"{n_alpha + i}"
for i in range(-num_nto_pairs + 1, num_nto_pairs + 1)))
inp += mtr.QChemInput(settings=s)
return inp
def compute(
self,
molecule: mtr.Molecule,
settings: Optional[mtr.Settings] = None,
) -> mtr.Quantity:
s = mtr.Settings() if settings is None else copy.deepcopy(settings)
input_settings = self.defaults(s)
neutral_sp = self.engine.single_point_frontier(self.gs_io,
name="neutral")
cation_sp = self.engine.single_point(self.cation_io, name="cation")
anion_sp = self.engine.single_point(self.anion_io, name="anion")
cation = copy.deepcopy(molecule)
cation.charge += 1
cation.multiplicity = cation.multiplicity % 2 + 1
anion = copy.deepcopy(molecule)
anion.charge -= 1
anion.multiplicity = anion.multiplicity % 2 + 1
neutral_sp.requires(
molecule=molecule,
settings=input_settings,
)
cation_sp.requires(
molecule=cation,
settings=input_settings,
)
anion_sp.requires(
molecule=anion,
settings=input_settings,
)
wf = Workflow(neutral_sp, cation_sp, anion_sp)
out = wf.compute()
neutral, h**o, lumo = out["neutral"]
cation = out["cation"]
anion = out["anion"]
ea = neutral - anion
ip = cation - neutral
J_squared = (ip + h**o)**2
if ea > 0 * ea.unit:
J_squared += (ea + lumo)**2
return np.sqrt(J_squared.convert(mtr.eV**2).value.item()) * mtr.eV
def compute(
self,
molecule: mtr.Molecule,
settings: Optional[mtr.Settings] = None,
arguments: Optional[Iterable[str]] = None,
) -> Any:
s = mtr.Settings() if settings is None else copy.deepcopy(settings)
inp = mtr.QChemInput(molecule, settings=self.defaults(s))
with self.io() as io:
inp.write(io.inp)
self.engine.execute(self.io, arguments=arguments)
return self.parse(io.out)
def _objective(omega: float, _alpha: float) -> float:
beta = 1 / epsilon - _alpha
s = mtr.Settings() if settings is None else copy.deepcopy(settings)
s = self.defaults(s)
s["rem", "hf_sr"] = int(round(1000 * _alpha))
s["rem", "hf_lr"] = int(1000 / epsilon)
s["xc_functional"] = (
("X", "HF", _alpha),
("X", "wPBE", beta),
("X", "PBE", 1 - _alpha - beta),
("C", "PBE", 1.0),
)
omega = int(round(1000 * omega))
s["rem", "omega"] = s["rem", "omega2"] = omega
wd = mtr.expand(f"{io.work_dir}/{omega}")
gs_io = mtr.IO("gs.in", "gs.out", wd)
cation_io = mtr.IO("cation.in", "cation.out", wd)
anion_io = mtr.IO("anion.in", "anion.out", wd)
ke = self.engine.koopman_error(gs_io, cation_io, anion_io)
return ke.compute(molecule, s).value
def compute(
self,
molecule: mtr.Molecule,
settings: Optional[mtr.Settings] = None,
num_nto_pairs: Optional[int] = 0,
n_x: Optional[int] = 50,
n_y: Optional[int] = 50,
n_z: Optional[int] = 50,
) -> mtr.Molecule:
s = mtr.Settings() if settings is None else copy.deepcopy(settings)
inp = mtr.QChemInput(molecule, settings=self.defaults(s))
if num_nto_pairs > 0:
inp += _nto_pairs(molecule, s, num_nto_pairs, n_x, n_y, n_z)
with self.io() as io:
inp.write(io.inp)
self.engine.execute(self.io)
molecule.electronic_excitations = self.parse(io.out)
return molecule
def __add__(self, other: mtr.QChemInput) -> str:
return QChemInput(string=str(self) + "\n@@@\n\n" + str(other),
settings=mtr.Settings())
def test_write_qchem_tdscf():
settings = materia.Settings(
dt=0.02,
Stabilize=0,
TCLOn=0,
MaxIter=100,
ApplyImpulse=1,
ApplyCw=0,
FieldFreq=0.7,
Tau=0.07,
FieldAmplitude=0.001,
ExDir=1.0,
EyDir=1.0,
EzDir=1.0,
Print=0,
StatusEvery=10,
SaveDipoles=1,
DipolesEvery=2,
SavePopulations=0,
SaveFockEnergies=0,
WriteDensities=0,
SaveEvery=500,
FourierEvery=5000,
MMUT=1,
LFLPPC=0,
)
out_str = textwrap.dedent(""" dt=0.02
Stabilize=0
TCLOn=0
MaxIter=100
ApplyImpulse=1
ApplyCw=0
FieldFreq=0.7
Tau=0.07
FieldAmplitude=0.001
ExDir=1.0
EyDir=1.0
EzDir=1.0
Print=0
StatusEvery=10
SaveDipoles=1
DipolesEvery=2
SavePopulations=0
SaveFockEnergies=0
WriteDensities=0
SaveEvery=500
FourierEvery=5000
MMUT=1
LFLPPC=0""")
# FIXME: make this test work on Windows using pathlib
mock_open = mock.mock_open()
# mock_expand = mock.MagicMock(side_effect=lambda s: s)
mock_os_makedirs = mock.MagicMock(side_effect=lambda s: s)
with mock.patch("builtins.open", mock_open):
with mock.patch("os.makedirs", mock_os_makedirs):
materia.WriteQChemTDSCF(settings=settings,
work_directory="/mock/path/to/dir").run()
# mock_expand.assert_called_once_with("/mock/path")
mock_os_makedirs.assert_called_once_with("/mock/path/to/dir")
mock_open.assert_called_once_with("/mock/path/to/dir/TDSCF.prm", "w")
mock_open().write.assert_called_once_with(out_str)
def test_vasp_input():
s = mtr.Settings()
s["incar", "PREC"] = "Normal"
s["incar", "ENCUT"] = 550
s["incar", "IBRION"] = -1
s["incar", "NSW"] = 0
s["incar", "ISIF"] = 2
s["incar", "NELMIN"] = 2
s["incar", "EDIFF"] = 1.0e-5
s["incar", "EDIFFG"] = -0.02
s["incar", "VOSKOWN"] = 1
s["incar", "NBLOCK"] = 1
s["incar", "NWRITE"] = 1
s["incar", "NELM"] = 60
s["incar", "LUSE_VDW"] = True
s["incar", "LASPH"] = True
s["incar", "AGGAC"] = 0.0000
s["incar", "GGA"] = "MK"
s["incar", "PARAM1"] = 0.1234
s["incar", "PARAM2"] = 1.0000
s["incar", "ALGO"] = "Normal (blocked Davidson)"
s["incar", "ISPIN"] = 2
s["incar", "INIWAV"] = 1
s["incar", "ISTART"] = 0
s["incar", "ICHARG"] = 2
s["incar", "LWAVE"] = False
s["incar", "LCHARG"] = False
s["incar", "ADDGRID"] = False
s["incar", "ISMEAR"] = 1
s["incar", "SIGMA"] = 0.2
s["incar", "LREAL"] = False
s["incar", "RWIGS"] = (1.17, 0.73)
s["incar", "LDAU"] = True
s["incar", "LDAUTYPE"] = 2
s["incar", "LDAUL"] = (2, -1)
s["incar", "LDAUU"] = (8.00, 0.00)
s["incar", "LDAUJ"] = (4.00, 0.00)
s["incar", "LDAUPRINT"] = 2
s["poscar",
"comment"] = "(Fe2 O3)24 (P1) ~ (COD #9015065)_1_2x2x1_1 0 0 1\
surface_1 (#1)_2x2x1_1 (MD #5) (VASP)"
s["poscar", "scaling"] = 1.0
s["poscar", "bravais_matrix"] = np.hstack([[10.0498, 0, 0], [0, 8.7034, 0],
[0, 0, 28.7163]])
s["poscar", "Direct"] = True
s["poscar", "num_atoms"] = (48, 72)
s["kpoints", "comment"] = "Automatic grid"
s["kpoints", "mesh_type"] = "Gamma"
s["kpoints", "grid"] = (4, 4, 1)
s["kpoints", "shift"] = (0.0, 0.0, 0.0)
vasp_str = """PREC = Normal
ENCUT = 550
IBRION = -1
NSW = 0
ISIF = 2
NELMIN = 2
EDIFF = 1e-05
EDIFFG = -0.02
VOSKOWN = 1
NBLOCK = 1
NWRITE = 1
NELM = 60
LUSE_VDW = .TRUE.
LASPH = .TRUE.
AGGAC = 0.0
GGA = MK
PARAM1 = 0.1234
PARAM2 = 1.0
ALGO = Normal (blocked Davidson)
ISPIN = 2
INIWAV = 1
ISTART = 0
ICHARG = 2
LWAVE = .FALSE.
LCHARG = .FALSE.
ADDGRID = .FALSE.
ISMEAR = 1
SIGMA = 0.2
LREAL = .FALSE.
RWIGS = 1.17 0.73
LDAU = .TRUE.
LDAUTYPE = 2
LDAUL = 2 -1
LDAUU = 8.0 0.0
LDAUJ = 4.0 0.0
LDAUPRINT = 2
(Fe2 O3)24 (P1) ~ (COD #9015065)_1_2x2x1_1 0 0 1 surface_1 (#1)_2x2x1_1 (MD #5) (VASP)
1.0
10.0498 0.0 0.0
0.0 8.7034 0.0
0.0 0.0 28.7163
48 72
Automatic grid
Gamma
4 4 1
0.0 0.0 0.0
"""
assert str(mtr.VASPInput(s) == vasp_str)