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 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_orca_stable():
init_logging()
geom = geom_from_library("ozone.xyz")
orca_kwargs = {
"keywords": "UHF def2-SVP",
"pal": 1,
"mult": 1,
"charge": 0,
}
calc = ORCA(**orca_kwargs)
geom.set_calculator(calc)
unstable_energy = calc.get_energy(geom.atoms, geom.coords)["energy"]
assert unstable_energy == pytest.approx(-224.0547837492)
calc.do_stable = True
stable_energy = calc.get_energy(geom.atoms, geom.coords)["energy"]
assert stable_energy == pytest.approx(-224.1476205193)
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)
import numpy as np
import pytest
from pysisyphus.calculators.AnaPot import AnaPot
from pysisyphus.calculators.Dimer import Dimer
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.Geometry import Geometry
from pysisyphus.helpers import geom_from_library
from pysisyphus.init_logging import init_logging
from pysisyphus.optimizers.PreconLBFGS import PreconLBFGS
from pysisyphus.testing import using
init_logging()
@pytest.mark.parametrize("rotation_method, ref_cycle", [
("direct", 9),
("fourier", 9),
])
def test_dimer(rotation_method, ref_cycle):
coords = (-0.2, 1.1, 0)
geom = Geometry(("X", ), coords)
N_raw = np.array((0.83, 0.27, 0.))
# New implementation
dimer_kwargs = {
"rotation_method": rotation_method,
"calculator": AnaPot(),
"N_raw": N_raw,
"rotation_remove_trans": False,
}
