def test_run_dimer_irc():
"""Quick test to see if the Dimer method works well with
the rest."""
run_dict = {
"opt": {
"type": "plbfgs",
"do_hess": True,
},
"irc": {
"type": "imk",
"rms_grad_thresh": 0.001,
},
"endopt": {
"fragments": True,
},
"calc": {
"type": "dimer",
"calc": {
"type": "pyscf",
"basis": "321g",
"pal": 2,
}
},
"xyz": "lib:hcn_ts_hf_321g.xyz",
}
results = run_from_dict(run_dict)
assert results.opt.is_converged
assert results.irc.backward_is_converged
assert results.irc.forward_is_converged
hcn, cnh = results.end_geoms
assert hcn.energy == pytest.approx(-92.33966200907034)
assert cnh.energy == pytest.approx(-92.35408370090339)
def test_hcn_neb():
run_dict = {
"preopt": {
"max_cycles": 3,
},
"interpol": {
"type": "idpp",
"between": 3,
},
"cos": {
"type": "neb",
},
"opt": {
"type": "qm",
"align": True,
},
"calc": {
"type": "pyscf",
"pal": 2,
"basis": "321g",
},
"xyz": ["lib:hcn.xyz", "lib:hcn_iso_ts.xyz", "lib:nhc.xyz"]
}
results = run_from_dict(run_dict)
assert results.cos_opt.is_converged
assert results.cos_opt.cur_cycle == 18
def test_endopt_barriers():
run_dict = {
"geom": {
"type": "redund",
"fn": "splined_hei.xyz",
},
"tsopt": {
"type": "rsirfo",
},
"irc": {
"type": "eulerpc",
"rms_grad_thresh": 0.015,
},
"endopt": {
"thresh": "gau_loose",
},
"calc": {
"type": "xtb",
"pal": 1,
},
}
results = run_from_dict(run_dict)
assert results.ts_opt.is_converged
assert results.ts_opt.cur_cycle == 2
assert results.ts_geom.energy == pytest.approx(-5.38737424)
def test_diels_alder_growing_string():
run_dict = {
"preopt": {
"max_cycles": 5,
},
"cos": {
"type": "gs",
"fix_ends": True,
"max_nodes": 8,
"reparam_check": "rms",
"climb": True,
"climb_rms": 0.02,
},
"opt": {
"type": "string",
"stop_in_when_full": 3,
},
"tsopt": {
"type": "rsirfo",
"do_hess": True,
"hessian_recalc": 5,
},
"irc": {
"type": "eulerpc",
"corr_func": "scipy",
"rms_grad_thresh": 2.5e-3,
},
"endopt": {
"fragments": True,
},
"calc": {
"type": "pyscf",
"pal": 2,
"basis": "321g",
},
"xyz": "lib:diels_alder_interpolated.trj",
"coord_type": "dlc",
}
results = run_from_dict(run_dict)
pprint(results)
assert len(results.preopt_xyz) == 3
assert isinstance(results.cos, ChainOfStates)
assert results.cos_opt.is_converged
assert results.ts_opt.is_converged
assert results.ts_geom._energy == pytest.approx(-231.6032000849316)
assert isinstance(results.ts_geom, Geometry)
assert results.irc.forward_is_converged
assert results.irc.backward_is_converged
assert len(results.end_geoms) == 3
assert results.calc_getter
def test_run_results():
run_dict = {
"xyz": "lib:h2o.xyz",
"calc": {
"type": "pyscf",
"basis": "sto3g"
},
}
results = run_from_dict(run_dict)
calced_geoms = results.calced_geoms
assert len(calced_geoms) == 1
assert results.calc_getter
def test_oniom3():
run_dict = {
"xyz": "lib:oniom3alkyl.pdb",
"coord_type": "redund",
"calc": {
"type": "oniom",
"calcs": {
"real": {
"type": "pyscf",
"basis": "sto3g",
"pal": 2,
},
"mid": {
"type": "pyscf",
"basis": "321g",
"pal": 2,
},
"high": {
"type": "pyscf",
# "basis": "sto3g",
"basis": "431g",
"pal": 2,
},
},
"models": {
"high": {
"inds": list(range(7, 16)),
"calc": "high",
},
"mid": {
"inds": list(range(4, 19)),
"calc": "mid",
},
}
},
"opt": {
"thresh": "gau_tight",
},
}
res = run_from_dict(run_dict)
print()
opt = res.opt
assert opt.is_converged
assert opt.cur_cycle == 7
geom = res.opt_geom
res = do_final_hessian(geom, save_hessian=False)
nus = res.nus
assert nus[-1] == pytest.approx(3747.5594141, abs=1e-2)
assert nus[-5] == pytest.approx(3563.8997581, abs=1e-2)
def test_hcn_neb_dimer_irc():
run_dict = {
"preopt": {
"max_cycles": 3,
},
"interpol": {
"type": "idpp",
"between": 3,
},
"cos": {
"type": "neb",
},
"opt": {
"type": "qm",
"align": True,
"max_cycles": 10,
},
"tsopt": {
"type": "dimer",
"thresh": "gau_tight",
"do_hess": True,
},
"irc": {
"type": "eulerpc",
"rms_grad_thresh": 1e-3,
},
"calc": {
"type": "pyscf",
"pal": 2,
"basis": "321g",
},
"xyz": ["lib:hcn.xyz", "lib:hcn_iso_ts.xyz", "lib:nhc.xyz"]
}
results = run_from_dict(run_dict)
assert results.ts_opt.is_converged
assert results.ts_opt.cur_cycle == 6
assert results.ts_geom.energy == pytest.approx(-92.2460427)
irc = results.irc
assert irc.forward_is_converged
assert irc.forward_cycle == 29
assert irc.backward_is_converged
assert irc.backward_cycle == 36
def test_oniom_microiters():
run_dict = {
"xyz": "lib:oniom_microiters_test.pdb",
# "xyz": "lib:acetaldehyd_oniom.xyz",
"coord_type": "cart",
"calc": {
# "type": "pyscf",
# "basis": "sto-3g",
"type": "oniom",
"calcs": {
"real": {
"type": "pyscf",
"basis": "sto3g",
"pal": 2,
},
"high": {
"type": "pyscf",
"basis": "321g",
"pal": 2,
},
},
"models": {
"high": {
"inds": [10, 11, 12, 13, 14],
# "inds": [4, 5, 6],
"calc": "high",
},
}
},
"opt": {
"micro_cycles": [3, 1],
"type": "oniom",
# "rms_force": 0.0025,
# "rms_force": 0.005,
# "max_cycles": 7,
# "max_cycles": 3,
},
}
res = run_from_dict(run_dict)
print()
def test_run():
run_dict = {
"preopt": {
"max_cycles": 5,
"coord_type": "cart",
},
"interpol": {
"type": "linear",
"between": 12,
"align": False,
},
"cos": {
"type": "neb",
},
"opt": {
"type": "sd",
"align": False,
"rms_force": 1.0,
"dump": False,
},
"tsopt": {
"type": "rsirfo",
"thresh": "gau_tight",
},
"calc": {
"type": "anapot",
},
# Inline xyz
"xyz": """
1
X -1.2 1.4 0.0
1
X 2.0 4.0 0.0
""",
"coord_type": "cart",
}
results = run_from_dict(run_dict)
def test_oniomopt_water_dimer():
run_dict = {
"xyz": "lib:water_dimer_oniomopt_test.pdb",
"coord_type": "cart",
"calc": {
# "type": "pyscf",
# "basis": "sto-3g",
"type": "oniom",
"calcs": {
"real": {
"type": "pyscf",
"basis": "sto3g",
"pal": 2,
},
"high": {
"type": "pyscf",
"basis": "321g",
"pal": 2,
},
},
"models": {
"high": {
"inds": [0, 1, 2],
"calc": "high",
},
}
},
"opt": {
"micro_cycles": [3, 1],
"type": "oniom",
# "rms_force": 0.0025,
"rms_force": 0.005,
"max_cycles": 10,
},
}
res = run_from_dict(run_dict)
print()
def test_hcn_neb():
run_dict = {
"preopt": {
"max_cycles": 3,
},
"interpol": {
"type": "idpp",
"between": 3,
},
"cos": {
"type": "neb",
},
"opt": {
"type": "qm",
"align": True,
},
"tsopt": {
"type": "rsirfo",
},
"calc": {
"type": "pyscf",
"pal": 1,
"basis": "321g",
},
"xyz": ["lib:hcn.xyz", "lib:hcn_iso_ts.xyz", "lib:nhc.xyz"]
}
results = run_from_dict(run_dict)
assert results.cos_opt.is_converged
assert results.cos_opt.cur_cycle == 18
assert results.ts_opt.is_converged
assert results.ts_opt.cur_cycle == 1
with h5py.File("optimization.h5", "r") as handle:
groups = list(handle.keys())
ref_groups = ("first_pre", "last_pre", "opt", "tsopt")
assert set(groups) == set(ref_groups)
def test_yaml_oniom():
run_dict = {
"xyz": "lib:acetaldehyd_oniom.xyz",
"coord_type": "redund",
"calc": {
"type": "oniom",
"calcs": {
"real": {
"type": "g16",
"route": "hf sto-3g",
"pal": 2,
},
"high": {
"type": "g16",
"route": "b3lyp d95v",
"pal": 2,
},
},
"models": {
"high": {
"inds": [4, 5, 6],
"calc": "high",
}
}
},
"opt": {
"thresh": "gau_tight",
}
}
res = run_from_dict(run_dict)
opt = res.opt
assert opt.is_converged
assert opt.cur_cycle == 7
assert res.opt_geom.energy == pytest.approx(-153.07526171)
def test_so3hcl_yaml_mdp():
"""See
https://aip.scitation.org/doi/pdf/10.1063/1.5082885
"""
run_dict = {
"geom": {
"type": "cart",
"fn": "lib:so3hcl_diss_ts_opt.xyz",
},
"calc": {
"type": "xtb",
"pal": 2,
"quiet": True,
},
"mdp": {
# About 5 kcal/mol as given in the paper
"E_excess": 0.0079,
"epsilon": 5e-4,
"ascent_alpha": 0.025,
"term_funcs": {
"hcl_diss": "5,0 > 4.6",
"oh_formed": "1,4 < 1.9",
},
"steps_init": 40,
"steps": 200,
"dt": 0.5,
"seed": 9081302,
"external_md": False,
"max_init_trajs": 1,
},
}
results = run_from_dict(run_dict)
res = results.mdp_result
assert res.md_fin_plus_term == "hcl_diss"
assert res.md_fin_minus_term == "oh_formed"
def run_assert(run_dict, prim_len):
res = run_from_dict(run_dict)
geom = res.calced_geoms[0]
assert geom.energy == pytest.approx(ref_energy)
int_ = geom.internal
assert len(int_.prim_indices_set) == prim_len