def run():
args = parse_args(sys.argv[1:])
geoms = geoms_from_trj(
args.trj,
first=args.first,
coord_type="redund",
)
filters = parse_filter(args.filter)
print("Filters", filters)
valid_geoms = list()
invalid_geoms = list()
for i, geom in enumerate(geoms):
internals = get_unique_internals(geom)
valid = all([
is_present == (internal in internals)
for is_present, internal in filters
])
if not valid:
print(f"geom {i+1} is not valid.")
invalid_geoms.append(geom)
else:
valid_geoms.append(geom)
print()
print(f"Found {len(valid_geoms)} valid geometries.")
print(f"Found {len(invalid_geoms)} invalid geometries.")
write_geoms_to_trj(valid_geoms, "filtered_valid.trj")
write_geoms_to_trj(invalid_geoms, "filtered_invalid.trj")
def test_standard_orientation():
geoms = geoms_from_trj(THIS_DIR / "std_orient.trj")
geoms_aligned = list()
for geom in geoms:
geom.standard_orientation()
geoms_aligned.append(geom.principal_axes_are_aligned)
# with open("stdorient.trj", "w") as handle:
# handle.write(make_trj_str_from_geoms(geoms))
assert all(geoms_aligned)
def test_diabatize():
geoms = geoms_from_trj(THIS_DIR /
"ma_proton_transfer/interpolated.trj")[:4]
#in_path = THIS_DIR / "ma_turbo"
in_path = THIS_DIR / "ma_turbo_no_exopt"
calc_kwargs = {
"track": True,
"wfo_basis": "sto-3g",
}
#geoms = geoms_from_trj(THIS_DIR / "biaryl_trj/biaryl_first_13.trj")[:4]
#in_path = THIS_DIR / "biaryl"
#calc_kwargs = {
# "track": True,
# "wfo_basis": "def2-svp",
#}
turbos = list()
wfos = list()
mos = None
np.set_printoptions(precision=2, suppress=True)
# for i, geom in enumerate(geoms):
# pickle_fn = f"wfo_pickle_{i}"
# turbo = Turbomole(in_path, calc_number=i, **calc_kwargs)
# if i > 0:
# turbo.mos = mos
# none_ = turbo.get_tddft(geom.atoms, geom.coords)
# mos = turbo.mos
# print(f"cycle {i}")
# turbos.append(turbo)
# wfos.append(turbo.wfow)
# with open(pickle_fn, "wb") as handle:
# cloudpickle.dump(turbo.wfow, handle)
# if i > 0:
# wfo1 = wfos[i-1]
# inds = wfo1.compare(turbo.wfow)
# print(inds)
mos = natsorted(THIS_DIR.glob("*.mos"))
td_vecs = natsorted(THIS_DIR.glob("*.ciss_a"))
for i, (geom, mos, td_vec) in enumerate(zip(geoms, mos, td_vecs)):
print("cycle", i, geom, mos, td_vec)
turbo = Turbomole(in_path, calc_number=i, **calc_kwargs)
turbo.mos = mos
turbo.td_vec_fn = td_vec
turbo.check_for_root_flip(geom.atoms, geom.coords)
wfos.append(turbo.wfow)
if i > 0:
wfo1 = wfos[i - 1]
inds = wfo1.compare(turbo.wfow)
def parse_opt(self, path, keep_log=False):
xtbopt = path / "xtbopt.xyz"
if not xtbopt.exists():
self.log(f"{self.calc_number:03d} failed")
return None
opt_geom = geom_from_xyz_file(xtbopt)
opt_geom.energy = self.parse_energy(path)
opt_log = None
if keep_log:
opt_log = geoms_from_trj(path / "xtbopt.log")
opt_result = OptResult(opt_geom=opt_geom, opt_log=opt_log)
return opt_result
def test_diabatize():
geoms = geoms_from_trj(THIS_DIR / "ma_proton_transfer/interpolated.trj")
in_path = THIS_DIR / "ma_turbo"
calc_kwargs = {
"track": True,
"wfo_basis": "sto-3g",
}
turbos = list()
wfos = list()
for i, geom in enumerate(geoms):
pickle_fn = f"wfo_pickle_{i}"
turbo = Turbomole(in_path, calc_number=i, **calc_kwargs)
geom.set_calculator(turbo)
forces = geom.forces
print(f"cycle {i}")
turbos.append(turbo)
wfos.append(turbo.wfow)
with open(pickle_fn, "wb") as handle:
cloudpickle.dump(turbo.wfow, handle)
def parse_md(self, path):
assert (path / "xtbmdok").exists(), "File xtbmdok does not exist!"
geoms = geoms_from_trj(path / "xtb.trj")
return geoms