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import pytest
import numpy as np
from ase import Atom
from ase.build import bulk
import ase.io
from ase import units
from ase.md.verlet import VelocityVerlet
@pytest.fixture
def Atoms_fcc_Ni_with_H_at_center():
atoms = bulk("Ni", cubic=True)
atoms += Atom("H", position=atoms.cell.diagonal() / 2)
return atoms
@pytest.fixture
def lammps_data_file_Fe(datadir):
return datadir / "lammpslib_simple_input.data"
@pytest.fixture
def calc_params_Fe(lammps_data_file_Fe):
calc_params = {}
calc_params["lammps_header"] = [
"units real",
"atom_style full",
"boundary p p p",
"box tilt large",
"pair_style lj/cut/coul/long 12.500",
"bond_style harmonic",
"angle_style harmonic",
"kspace_style ewald 0.0001",
"kspace_modify gewald 0.01",
f"read_data {lammps_data_file_Fe}",
]
calc_params["lmpcmds"] = []
calc_params["atom_types"] = {"Fe": 1}
calc_params["create_atoms"] = False
calc_params["create_box"] = False
calc_params["boundary"] = False
calc_params["log_file"] = "test.log"
calc_params["keep_alive"] = True
return calc_params
@pytest.fixture
def Atoms_Fe(lammps_data_file_Fe):
Atoms_Fe = ase.io.read(
lammps_data_file_Fe,
format="lammps-data",
Z_of_type={1: 26},
units="real",
)
return Atoms_Fe
@pytest.mark.calculator_lite
@pytest.mark.calculator("lammpslib")
def test_lammpslib_simple(
factory,
calc_params_NiH,
Atoms_fcc_Ni_with_H_at_center,
calc_params_Fe,
Atoms_Fe,
):
"""
Get energy from a LAMMPS calculation of an uncharged system.
This was written to run with the 30 Apr 2019 version of LAMMPS,
for which uncharged systems require the use of 'kspace_modify gewald'.
"""
NiH = Atoms_fcc_Ni_with_H_at_center
# Add a bit of distortion to the cell
NiH.set_cell(
NiH.cell + [[0.1, 0.2, 0.4], [0.3, 0.2, 0.0], [0.1, 0.1, 0.1]],
scale_atoms=True,
)
calc = factory.calc(**calc_params_NiH)
NiH.calc = calc
E = NiH.get_potential_energy()
F = NiH.get_forces()
S = NiH.get_stress()
print("Energy: ", E)
print("Forces:", F)
print("Stress: ", S)
print()
E = NiH.get_potential_energy()
F = NiH.get_forces()
S = NiH.get_stress()
calc = factory.calc(**calc_params_NiH)
NiH.calc = calc
E2 = NiH.get_potential_energy()
F2 = NiH.get_forces()
S2 = NiH.get_stress()
assert E == pytest.approx(E2, rel=1e-4)
assert F == pytest.approx(F2, rel=1e-4)
assert S == pytest.approx(S2, rel=1e-4)
NiH.rattle(stdev=0.2)
E3 = NiH.get_potential_energy()
F3 = NiH.get_forces()
S3 = NiH.get_stress()
print("rattled atoms")
print("Energy: ", E3)
print("Forces:", F3)
print("Stress: ", S3)
print()
assert not np.allclose(E, E3)
assert not np.allclose(F, F3)
assert not np.allclose(S, S3)
# Add another H
NiH += Atom("H", position=NiH.cell.diagonal() / 4)
E4 = NiH.get_potential_energy()
F4 = NiH.get_forces()
S4 = NiH.get_stress()
assert not np.allclose(E4, E3)
assert not np.allclose(F4[:-1, :], F3)
assert not np.allclose(S4, S3)
# the example from the docstring
NiH = Atoms_fcc_Ni_with_H_at_center
calc = factory.calc(**calc_params_NiH)
NiH.calc = calc
print("Energy ", NiH.get_potential_energy())
# a more complicated example, reading in a LAMMPS data file
calc = factory.calc(**calc_params_Fe)
Atoms_Fe.calc = calc
dyn = VelocityVerlet(Atoms_Fe, 1 * units.fs)
energy = Atoms_Fe.get_potential_energy()
assert energy == pytest.approx(2041.411982950972, rel=1e-4)
dyn.run(10)
energy = Atoms_Fe.get_potential_energy()
assert energy == pytest.approx(312.4315854721744, rel=1e-4)
|
