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# fmt: off
import numpy as np
import pytest
import ase.io
from ase import Atom, Atoms, units
from ase.build import bulk
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"
return calc_params
@pytest.fixture()
def atoms_Fe(lammps_data_file_Fe):
return ase.io.read(
lammps_data_file_Fe,
format="lammps-data",
Z_of_type={1: 26},
units="real",
)
@pytest.mark.calculator_lite()
@pytest.mark.calculator("lammpslib")
def test_lammpslib_simple(
factory,
calc_params_NiH,
atoms_fcc_Ni_with_H_at_center: Atoms,
):
# TODO: Split the test in a rational way.
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())
@pytest.mark.parametrize("keep_alive", [False, True])
@pytest.mark.calculator_lite()
@pytest.mark.calculator("lammpslib")
def test_read_data(
factory,
calc_params_Fe,
atoms_Fe: Atoms,
keep_alive: bool,
):
"""Test `read_data` and `keep_alive`.
Test if a LAMMPS data file can be read and if both `keep_alive=False` and
`keep_alive=True` work together with `Dynamics`.
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'.
"""
calc = factory.calc(keep_alive=keep_alive, **calc_params_Fe)
atoms_Fe.calc = calc
with VelocityVerlet(atoms_Fe, 1 * units.fs) as dyn:
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)
@pytest.mark.calculator_lite()
@pytest.mark.calculator('lammpslib')
def test_charges_atomic(
factory,
calc_params_NiH: dict,
atoms_fcc_Ni_with_H_at_center: Atoms,
):
"""Test charges for `atom_style atomic`.
Since `atom_style atomic` does not include atomic charges, LAMMPS raises
an error "Cannot set attribute charge for atom style atomic" if we set a
command like 'set atom 1 charge 1.0'.
The above command must therefore be set only when `atom_style` include
atomic charges, and otherwise the command should be skipped.
This test checks if the skipping is properly done.
"""
atoms = atoms_fcc_Ni_with_H_at_center
atoms.set_initial_charges(len(atoms) * [1.0])
atoms.calc = factory.calc(**calc_params_NiH)
atoms.get_potential_energy()
@pytest.mark.calculator_lite()
@pytest.mark.calculator('lammpslib')
def test_charges_full(
factory,
calc_params_Fe: dict,
atoms_Fe: Atoms,
):
"""Test charges for `atom_style full`.
Test if
1. Setting initial charges triggers a new calculation.
2. The energy with charges is different from the energy without charges.
"""
calc = factory.calc(**calc_params_Fe)
atoms_Fe.calc = calc
energy_without_charges = atoms_Fe.get_potential_energy()
atoms_Fe.set_initial_charges(len(atoms_Fe) * [1.0])
energy_with_charges = atoms_Fe.get_potential_energy()
assert energy_with_charges != pytest.approx(energy_without_charges)
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