def from_orca(path="."):
calc = ORCA("")
path = Path(path)
results = calc.parse_hessian(path)
hess = results["hessian"]
np.save("hess", hess)
# hess = np.load("hess.npy")
return hess
def run_cos_opt(cos, Opt, images, **kwargs):
opt = Opt(cos, **kwargs)
for img in cos.images:
img.set_calculator(ORCA())
opt.run()
return opt
def prepare_opt():
ethan_xyz = "xyz_files/ethan.xyz"
atoms, coords = parse_xyz_file(ethan_xyz)
geom = Geometry(atoms, coords.flatten())
geom.set_calculator(ORCA())
return geom, copy.copy(KWARGS)
def prepare_geometry(xyz_fn, keywords):
#blocks = "%pal nprocs 3 end"
blocks = ""
atoms, coords = parse_xyz_file(THIS_DIR / xyz_fn)
coords *= ANG2BOHR
geometry = Geometry(atoms, coords.flatten())
geometry.set_calculator(ORCA(keywords, charge=0, mult=1, blocks=blocks))
hessian = geometry.hessian
return geometry
def prepare_geometry():
keywords = "HF 4-22GSP TightSCF"
xyz_fn = "01_irc_sn2_fluour_transfer_optts.xyz"
#blocks = "%pal nprocs 3 end"
blocks = ""
atoms, coords = parse_xyz_file(THIS_DIR / xyz_fn)
coords *= ANG2BOHR
geometry = Geometry(atoms, coords.flatten())
geometry.set_calculator(ORCA(keywords, charge=-1, mult=1, blocks=blocks))
hessian = geometry.hessian
return geometry, THIS_DIR
def get_geom():
init_logging("./")
geom = geom_from_library("h2.xyz")
kwargs = {
"keywords": "BP86 def2-SV(P)",
"charge": 0,
"mult": 1,
"blocks": "%tddft nroots 2 iroot 1 end",
"track": True,
}
orca = ORCA(**kwargs)
geom.set_calculator(orca)
return geom
def test_do_final_hessian(data_dir):
fn = data_dir / "final_geometry.xyz"
geom = geom_from_xyz_file(fn, coord_type="redund")
calc = ORCA("")
grad = np.load(data_dir / "grad.npy")
hess = np.load(data_dir / "hess.npy")
geom.hessian = hess
geom.gradient = grad
res = do_final_hessian(geom, save_hessian=False)
neg_eigvals = res.neg_eigvals
assert len(neg_eigvals) == 1
np.testing.assert_allclose(neg_eigvals[0], -0.00224392407)
def prepare_geometry(keywords=None, xyz_fn=None):
this_dir = pathlib.Path(os.path.dirname(os.path.realpath(__file__)))
if not keywords:
keywords = "HF STO-3G TightSCF"
if not xyz_fn:
xyz_fn = "hfabstraction_sto3g_ts.xyz"
#blocks = "%pal nprocs 3 end"
blocks = ""
atoms, coords = parse_xyz_file(this_dir / xyz_fn)
coords *= ANG2BOHR
geometry = Geometry(atoms, coords.flatten())
geometry.set_calculator(ORCA(keywords, charge=0, mult=1, blocks=blocks))
hessian = geometry.hessian
return geometry, this_dir
def run_distributed(scheduler=None):
init_logging(THIS_DIR, scheduler)
atoms = ("H", "H")
geoms = list()
for i in range(7):
bond_length = 0.8 + i * 0.2
print(f"{i}: {bond_length:.02f}")
coords = np.array((0., 0., 0., 0., 0., bond_length))
geom = Geometry(atoms, coords)
# def2-TZVP / TDDFT
td_kwargs = {
"keywords": "BP86 def2-TZVP",
"charge": 0,
"mult": 1,
"calc_number": i,
"blocks": "%tddft nroots 2 iroot 1 end",
#"track": True,
"out_dir": THIS_DIR,
}
# def2-SV(P) / Ground state
kwargs = {
"keywords": "BP86 def2-SV(P)",
"charge": 0,
"mult": 1,
"calc_number": i,
"out_dir": THIS_DIR,
}
orca = ORCA(**td_kwargs)
geom.set_calculator(orca)
geoms.append(geom)
neb_kwargs = {
"dask_cluster": scheduler,
}
neb = NEB(geoms, **neb_kwargs)
forces = neb.forces
for f in forces.reshape(-1, 6):
print(f, f"{np.linalg.norm(f):.2f}")
for geom in neb.images:
print(geom.calculator.wfow)
def self_compare_base(geom, wfo_basis):
calc_kwargs = {
"keywords": "B3LYP def2-TZVP",
"blocks": "%tddft nroots 2 maxdim 5 end",
"track": True,
"pal": 4,
}
orca = ORCA(**calc_kwargs)
orca.run_calculation(geom.atoms, geom.coords)
# cis = "calculator_0.000.orca.cis"
# gbw = "calculator_0.000.orca.gbw"
# out = "calculator_0.000.orca.out"
# orca.cis = cis
# orca.gbw = gbw
# orca.out = out
orca.store_wfo_data(geom.atoms, geom.coords)
wfow = orca.wfow
res = wfow.compare(wfow)
print(res)