"corr_first_energy": True,
"corr_bisec_size": 0.0025,
"corr_bisec_energy": True,
}
irc = IMKMod(geom, **irc_kwargs)
irc.run()
# plot_irc(irc, irc.__class__.__name__)
assert_anapot_irc(irc)
@pytest.mark.parametrize("calc_cls, kwargs_", [
pytest.param(PySCF, {
"basis": "321g",
}, marks=using("pyscf")),
pytest.param(Gaussian16, {"route": "HF/3-21G"}, marks=using("gaussian16")),
pytest.param(Turbomole, {
"control_path": "./hf_abstr_control_path",
"pal": 1
},
marks=using("turbomole")),
])
def test_hf_abstraction_dvv(calc_cls, kwargs_, this_dir):
geom = geom_loader("lib:hfabstraction_hf321g_displ_forward.xyz")
calc_kwargs = {
"pal": 2,
}
calc_kwargs.update(kwargs_)
# # "thresh": "gau_loose",
# "max_cycles": 23,
# }
# opt = SteepestDescent(cos, **opt_kwargs)
# # import pdb; pdb.set_trace()
# opt.run()
# run_tsopt_from_cos(cos, tsopt_key, tsopt_kwargs)
@pytest.mark.skip
@pytest.mark.parametrize(
"tsopt_key, tsopt_kwargs",
[
# ("dimer", ),
pytest.param("rsprfo", {}, marks=using("orca")),
])
def test_run_tsopt_from_cos(tsopt_key, tsopt_kwargs):
geoms = geom_from_library("ala_dipeptide_iso_b3lyp_631gd_10_images.trj")
orca_kwargs = {
"keywords": "b3lyp 6-31G* rijcosx",
"pal": 2,
"mem": 2000,
"charge": 0,
"mult": 1,
}
calc_number = 0
def calc_getter():
from pysisyphus.optimizers.PreconLBFGS import PreconLBFGS
from pysisyphus.testing import using
init_logging()
@pytest.fixture
def this_dir(request):
return Path(request.module.__file__).parents[0]
@pytest.mark.parametrize("calc_cls, calc_kwargs, chk_exts", [
pytest.param(ORCA, {
"keywords": "HF def2-SVP",
}, ("gbw", ),
marks=using("orca")),
pytest.param(Gaussian16, {
"route": "HF/def2SVP",
}, ("fchk", ),
marks=using("gaussian16")),
pytest.param(PySCF, {
"method": "scf",
"basis": "def2svp"
}, ("chkfile", ),
marks=using("pyscf")),
pytest.param(Turbomole, {"control_path": "benzene_control_path"},
("mos", ),
marks=using("turbomole")),
pytest.param(Turbomole, {"control_path": "benzene_control_path_uhf"},
("alpha", "beta"),
marks=using("turbomole")),
from pysisyphus.calculators import Gaussian16, Turbomole, ORCA
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.helpers import geom_from_library
from pysisyphus.testing import using
@pytest.mark.parametrize(
"calc_cls, calc_kwargs, ref_energy, ref_force_norm",
[
pytest.param(
ORCA,
{"keywords": "BP86 def2-SVP"},
-40.473648820542,
0.0539577447,
marks=using("orca"),
),
pytest.param(
ORCA,
# DoEq includes interaction between point charges and nuclear
# charges of the actual atoms.
{
"keywords": "BP86 def2-SVP",
"blocks": "%method doEQ true end"
},
-40.448455709343,
0.0539577447,
marks=using("orca"),
),
pytest.param(
Turbomole,
init_logging()
@pytest.fixture
def this_dir(request):
return Path(request.module.__file__).parents[0]
@pytest.mark.parametrize(
"calc_cls, calc_kwargs_",
[
pytest.param(Gaussian16,
{"route": "HF/STO-3G"},
marks=using("gaussian16")),
pytest.param(ORCA,
{"keywords": "HF STO-3G tightscf"},
marks=using("orca")),
# pytest.param(Psi4,
# {"method": "scf", "basis": "sto-3g", "to_set": {"scf_type": "pk"}},
# marks=using("psi4"),
# ),
pytest.param(PySCF,
{"basis": "sto-3g"},
marks=(using("pyscf"), pytest.mark.pyscf)),
pytest.param(Turbomole,
{"control_path": "./control_path_hf_sto3g_gs"},
marks=using("turbomole")),
])
def test_cytosin_gs_opt(calc_cls, calc_kwargs_, this_dir):
import numpy as np
@using("pyscf")
@pytest.mark.parametrize(
"hessian_init, ref_cycle",
[
("calc", 11),
# Converges to wrong minimum
# ("unit", 9),
("fischer", 15),
("lindh", 21),
("simple", 22),
("swart", 15),
pytest.param("xtb", 21, marks=[using("pyscf"),
using("xtb")]),
pytest.param("xtb1", 15, marks=[using("pyscf"),
using("xtb")]),
])
def test_guess_hessians(hessian_init, ref_cycle):
geom = geom_loader("lib:h2o2_hf_321g_opt.xyz", coord_type="redund")
geom.set_calculator(PySCF(basis="def2svp", pal=2))
print("@\tguess_hessian:", hessian_init)
opt_kwargs = {
"hessian_init": hessian_init,
"thresh": "gau_tight",
}
opt = RFOptimizer(geom, **opt_kwargs)
opt.run()
import pytest
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.cos.NEB import NEB
from pysisyphus.helpers import geom_from_library
from pysisyphus.optimizers.QuickMin import QuickMin
from pysisyphus.optimizers.LBFGS import LBFGS
from pysisyphus.testing import using
@pytest.mark.skip
@pytest.mark.parametrize("opt_cls", [
pytest.param(QuickMin, marks=using("pyscf")),
pytest.param(LBFGS, marks=using("pyscf")),
])
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,
@pytest.mark.parametrize("precon", [
True,
False,
])
@pytest.mark.parametrize(
"calc_cls, calc_kwargs, ref_nu_pre, ref_cyc_pre, ref_nu, ref_cyc",
[
pytest.param(
# 1791.60 cm⁻¹ from ORCA itself
ORCA,
{"keywords": "BP86 def2-SVP"},
1793.274093,
3,
1793.293512,
7,
marks=using("orca")),
pytest.param(
# 1691.888 cm⁻¹ from XTB itself
XTB,
{},
1691.052689,
3,
1691.005160,
7,
marks=using("xtb")),
# pytest.param(
# PySCF, {"basis": "321g",},
# 1889.2027727, 16, 1888.9849030442317, 16, marks=using("pyscf")),
pytest.param(PySCF, {
"basis": "def2svp",
"xc": "bp86"
-0.20069873 -0.69255477 1.27610279
""".strip().split(),
dtype=float,
) * ANG2BOHR)
return Geometry(atoms, coords)
@pytest.mark.parametrize(
"calc_cls, calc_kwargs",
[
pytest.param(
Gaussian09,
{
"route": "hf sto-3g",
},
marks=using("gaussian09"),
),
pytest.param(
Gaussian16,
{
"route": "hf sto-3g",
},
marks=using("gaussian16"),
),
pytest.param(
ORCA,
{
"keywords": "hf sto-3g",
},
marks=using("orca"),
),
@pytest.mark.parametrize(
"calc_cls, calc_kwargs, ref_cycle, ccl_dist, oc_dist",
[
pytest.param(
PySCF,
{
"basis": "6-31g*",
"xc": "b3lyp",
"pal": 2
},
29,
4.79584,
2.67745,
marks=using("pyscf"),
),
pytest.param(XTB, {}, 27, 5.26346, 2.62731, marks=using("xtb")),
],
)
def test_ohch3f_anion(calc_cls, calc_kwargs, ref_cycle, ccl_dist, oc_dist):
"""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),