def test_hcn_iso_dimer(trans_opt, trans_memory):
calc_kwargs = {
"route": "PM6",
"pal": 4,
"mem": 1000,
}
def calc_getter():
return Gaussian16(**calc_kwargs)
geom = geom_from_library("hcn_iso_pm6_near_ts.xyz")
geom.set_calculator(calc_getter())
geoms = [geom, ]
N_init = np.array(
(0.6333, 0.1061, 0.5678, 0.171, 0.11, 0.3373, 0.0308, 0.1721, 0.282)
)
dimer_kwargs = {
"max_step": 0.04,
"dR_base": 0.01,
"N_init": N_init,
# "rot_opt": "mb",
"trans_opt": trans_opt,
"trans_memory": trans_memory,
"angle_tol": 5,
# "rot_f_thresh": 1e-4,
# "rot_type": "direct",
"f_thresh": 1e-4,
"f_tran_mod": True,
"multiple_translations": True,
}
dimer_result = dimer_method(geoms, calc_getter, **dimer_kwargs)
return dimer_result
def test_anapotcbm():
calc_getter = AnaPotCBM
# geom = AnaPotCBM().get_geom((0.818, 0.2233, 0.0))
geom = AnaPotCBM().get_geom((0.2, 0.2, 0.0))
# geom = AnaPotCBM().get_geom((0.3, 0.3, 0.0))
# geom = AnaPotCBM().get_geom((0.4, 0.4, 0.0))
# geom = AnaPotCBM().get_geom((0.5, 0.2, 0.0))
geom = AnaPotCBM().get_geom((0.9, 0.8, 0.0))
# geom = AnaPotCBM().get_geom((0.8, 0.7, 0.0))
# geom = AnaPotCBM().get_geom((0.65, 0.7, 0.0))
w, v = np.linalg.eigh(geom.hessian)
print("eigenvals", w)
N_imag = v[:,0]
geoms = [geom, ]
dimer_kwargs = {
"ana_2dpot": True,
"N_init": N_imag,
"rot_type": "fourier",
"trans_opt": "lbfgs",
"f_tran_mod": False,
}
true_ts = (0, 0)
dimer_result = dimer_method(geoms, calc_getter, **dimer_kwargs)
dimer_cycles = dimer_result.dimer_cycles
plot_dimer_cycles(dimer_cycles[-10:], pot=AnaPotCBM(), true_ts=true_ts)
def test_anapot(trans_opt, trans_memory):
geoms = get_geoms()
calc_getter = AnaPot
dimer_kwargs = {
"ana_2dpot": True,
"restrict_step": "max",
"angle_tol": 0.5,
"f_thresh": 1e-4,
"rot_opt": "mb",
"trans_opt": trans_opt,
"trans_memory": trans_memory,
"f_tran_mod": False,
# "multiple_translations": True,
}
result = dimer_method(geoms, calc_getter, **dimer_kwargs)
return result
def test_anapot_rot():
geoms = get_geoms()
calc_getter = AnaPot
dimer_kwargs = {
"ana_2dpot": True,
"restrict_step": "max",
"angle_tol": 0.5,
"f_thresh": 1e-4,
"rot_opt": "mb",
"f_tran_mod": False,
"rot_type": "direct",
# "rot_f_thresh": 0.1,
"multiple_translations": False,
# "max_cycles": 1,
}
result = dimer_method(geoms, calc_getter, **dimer_kwargs)
return result
def test_baker_ts_dimer(name, geom, charge, mult, ref_energy):
print(f"@Got geom '{name}'")
# Load initial dimers
N_init_dict = make_N_init_dict()
calc_kwargs = {
"charge": charge,
"mult": mult,
"pal": 2,
"base_name": Path(name).stem,
}
def calc_getter():
return PySCF(basis="321g", **calc_kwargs)
# def calc_getter():
# return Gaussian16(route="HF/3-21G", **calc_kwargs)
geom.set_calculator(calc_getter())
dimer_kwargs = {
"max_step": 0.25,
# 1e-2 Angstroem in bohr
"dR_base": 0.0189,
"rot_opt": "lbfgs",
# "trans_opt": "mb",
"trans_opt": "lbfgs",
# "trans_memory": 10, # bad idea
"angle_tol": 5,
"f_thresh": 1e-3,
"max_cycles": 50,
"f_tran_mod": True,
# "rot_type": "direct",
"multiple_translations": True,
}
dimer_kwargs["N_init"] = N_init_dict[name]
geoms = (geom, )
results = dimer_method(geoms, calc_getter, **dimer_kwargs)
same_energy = geom.energy == pytest.approx(ref_energy)
print(f"@Same energy: {str(same_energy): >5}, {name}, "
f"{results.force_evals} force evaluations")
if not same_energy:
do_final_hessian(geom)
# This way pytest prints the actual values... instead of just the boolean
assert geom.energy == pytest.approx(ref_energy)
def test_baker_16():
calc_kwargs = {
"route": "HF/3-21G",
"pal": 4,
"mem": 1000,
"charge": -1,
"mult": 1,
}
def calc_getter():
return Gaussian16(**calc_kwargs)
# return XTB(**calc_kwargs)
geom = geom_from_library("baker_ts/16_h2po4_anion.xyz")
geom.set_calculator(calc_getter())
geoms = [geom, ]
downhill = geom_from_library("baker_ts/16_h2po4_anion_downhill.xyz")
N_init = geom.coords - downhill.coords
N_init /= np.linalg.norm(N_init)
dimer_kwargs = {
"max_step": 0.5,
# 1e-2 Angstroem in bohr
"dR_base": 0.0189,
"rot_opt": "lbfgs",
"trans_opt": "lbfgs",
# "trans_opt": "mb",
# "trans_memory": 10,
"angle_tol": 5,
"f_thresh": 1e-3,
"max_cycles": 50,
"f_tran_mod": True,
"rot_type": "fourier",
"multiple_translations": True,
"N_init": N_init,
"max_cycles": 15,
"rot_f_thresh": 1.5e-3,
}
# 55 cycles; no multi trans, no f_tran_mod
# import pdb; pdb.set_trace()
dimer_result = dimer_method(geoms, calc_getter, **dimer_kwargs)
return dimer_result
def test_anapot_cbm_rot():
pot = AnaPot()
geoms = (pot.get_geom((0.44, 1.54, 0)), )
N_init = (-0.2, 1, 0)
calc_getter = AnaPot
dimer_kwargs = {
"ana_2dpot": True,
"restrict_step": "max",
"angle_tol": 0.5,
"f_thresh": 1e-4,
"rot_opt": "lbfgs",
"trans_opt": "lbfgs",
"trans_memory": 5,
"f_tran_mod": False,
"N_init": N_init,
"rot_f_thresh": 1e-2,
# "multiple_translations": True,
}
result = dimer_method(geoms, calc_getter, **dimer_kwargs)
true_ts = (0.61173, 1.49297, 0.)
# plot_dimer_cycles(result.dimer_cycles, pot=AnaPot(), true_ts=true_ts[:2])
return result