def test_augment_coordinates_silyl(augment, ref_cycle):
geom = geom_from_library("baker_ts/18_silyene_insertion.xyz",
coord_type="redund")
opt_kwargs = {
"thresh": "baker",
"max_cycles": 100,
"dump": True,
"trust_radius": 0.3,
"trust_max": 0.3,
"augment_bonds": augment,
}
calc_kwargs = {
"charge": 0,
"mult": 1,
"pal": 4,
}
calc = PySCF(basis="321g", **calc_kwargs)
geom.set_calculator(calc)
opt = RSIRFOptimizer(geom, **opt_kwargs)
opt.run()
assert opt.is_converged
assert opt.cur_cycle == ref_cycle
ref_en = -367.20778
assert opt.geometry.energy == pytest.approx(ref_en)
def test_afir():
"""Example (R1) from
https://aip.scitation.org/doi/pdf/10.1063/1.3457903?class=pdf
See Fig. 2 and Fig. 4
"""
geom = geom_loader("lib:ohch3f_anion_cs.xyz")
# OH group is a fragment
fragment_indices = [
(5, 6),
]
calc = PySCF(basis="6-31g*", xc="b3lyp", pal=2, charge=-1)
gamma = 100
afir = AFIR(calc, fragment_indices, gamma)
geom.set_calculator(afir)
opt = RFOptimizer(geom, dump=True, trust_max=.3)
opt.run()
assert opt.is_converged
assert opt.cur_cycle == 47
# Broken C-Cl bond
c3d = geom.coords3d
assert np.linalg.norm(c3d[0] - c3d[4]) == pytest.approx(4.805665, abs=1e-4)
# Formed O-C bond
assert np.linalg.norm(c3d[0] - c3d[5]) == pytest.approx(2.674330, abs=1e-4)
def calc_getter(calc_number):
calc_kwargs = {
"charge": +1,
"mult": 1,
"pal": 2,
"basis": "321g",
"calc_number": calc_number,
}
calc = PySCF(**calc_kwargs)
return calc
def test_baker_tsopt(name, results_bag):
charge, mult, ref_energy = get_baker_ts_data()[name]
geom = geom_loader(
f"lib:baker_ts/{name}",
coord_type="redund",
coord_kwargs={
"rebuild": True,
},
)
# geom.jmol()
calc_kwargs = {
"charge": charge,
"mult": mult,
"pal": 1,
}
print(f"@Running {name}")
geom.set_calculator(PySCF(basis="321g", **calc_kwargs))
# geom.set_calculator(ORCA(keywords="HF 3-21G", **calc_kwargs))
if geom.coord_type != "cart":
geom = augment_bonds(geom)
opt_kwargs = {
"thresh": "baker",
"max_cycles": 50,
"trust_radius": 0.1,
"trust_max": 0.3,
"min_line_search": True,
"max_line_search": True,
}
opt = RSPRFOptimizer(geom, **opt_kwargs)
# opt = RSIRFOptimizer(geom, **opt_kwargs)
# opt = TRIM(geom, **opt_kwargs)
opt.run()
# Without symmetry restriction this lower lying TS will be obtained.
# if name.startswith("22_"):
# ref_energy = -242.25695787
results_bag.cycles = opt.cur_cycle + 1
results_bag.is_converged = opt.is_converged
results_bag.energy = geom.energy
results_bag.ref_energy = ref_energy
print(f"\t@Converged: {opt.is_converged}, {opt.cur_cycle+1} cycles")
assert geom.energy == pytest.approx(ref_energy)
print("\t@Energies match!")
return opt.cur_cycle + 1
def test_opt_load_save_hessian(this_dir):
geom = geom_loader("lib:acetaldehyd.xyz", coord_type="redund")
calc = PySCF(basis="321g", pal=2)
geom.set_calculator(calc)
opt_kwargs = {
"hessian_recalc": 1,
"hessian_init": this_dir / "inp_hess_calc_cyc_0.h5",
}
opt = RFOptimizer(geom, **opt_kwargs)
opt.run()
assert opt.is_converged
assert opt.cur_cycle == 2
assert geom.energy == pytest.approx(-152.05524620313963)
def test_irc_load_save_hessian(this_dir):
geom = geom_loader("lib:hcn_iso_hf_sto3g_ts_opt.xyz")
calc = PySCF(basis="sto3g", pal=2)
geom.set_calculator(calc)
irc_kwargs = {
"rms_grad_thresh": 1e-3,
"hessian_init": this_dir / "inp_hess_init_irc.h5",
"hessian_recalc": 2,
"max_cycles": 5,
}
irc = EulerPC(geom, **irc_kwargs)
irc.run()
assert irc.forward_cycle == 5
assert irc.backward_cycle == 5
def water():
geom = geom_loader("lib:h2o.xyz")
init_logging()
calc_kwargs = {
"xc": "pbe0",
"method": "tddft",
"basis": "sto3g",
"nstates": 2,
"root": 1,
# OverlapCalculator specific
"track": True,
"cdds": "calc",
"ovlp_type": "tden",
}
calc = PySCF(**calc_kwargs)
geom.set_calculator(calc)
return geom
def test_diels_alder_neb(opt_cls):
geoms = geom_from_library("diels_alder_interpolated.trj")
for i, geom in enumerate(geoms):
calc_kwargs = {
"basis": "sto3g",
"pal": 2,
"calc_number": i,
}
calc = PySCF(**calc_kwargs)
geom.set_calculator(calc)
neb = NEB(geoms)
opt_kwargs = {
"dump": True,
"align": True,
"max_cycles": 15,
}
opt = opt_cls(neb, **opt_kwargs)
opt.run()