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from ase.atoms import Atoms
import numpy as np
from ase.io.acemolecule import read_acemolecule_out, read_acemolecule_input
import pytest
def test_acemolecule_output():
import ase.units
sample_outfile = """\
==================== Atoms =====================
1 1.000000 2.000000 -0.6
9 -1.000000 3.000000 0.7
==================================================
Total energy = -1.5
!================================================
! Force:: List of total force in atomic unit.
! Atom x y z
! Atom 0 0.1 0.2 0.3
! Atom 1 0.5 0.6 0.7
!================================================
"""
with open('acemolecule_test.log', 'w') as fd:
fd.write(sample_outfile)
#fd = StringIO(sample_outfile)
results = read_acemolecule_out('acemolecule_test.log')
#os.system('rm acemolecule_test.log')
atoms = results['atoms']
assert atoms.positions == pytest.approx(
np.array([[1.0, 2.0, -0.6], [-1.0, 3.0, 0.7]]))
assert all(atoms.symbols == 'HF')
convert = ase.units.Hartree / ase.units.Bohr
assert results['forces'] / convert == pytest.approx(
np.array([[0.1, 0.2, 0.3], [0.5, 0.6, 0.7]]))
assert results['energy'] / ase.units.Hartree == -1.5
def test_acemolecule_input():
sample_inputfile = """\
%% BasicInformation
Type Points
Scaling 0.35
Basis Sinc
Grid Basic
KineticMatrix Finite_Difference
DerivativesOrder 7
GeometryFilename acemolecule_test.xyz
CellDimensionX 3.37316805
CellDimensionY 3.37316805
CellDimensionZ 3.37316805
PointX 16
PointY 16
PointZ 16
Periodicity 3
%% Pseudopotential
Pseudopotential 3
PSFilePath PATH
PSFileSuffix .PBE
%% End
GeometryFormat xyz
%% End
"""
with open('acemolecule_test.inp', 'w') as fd:
fd.write(sample_inputfile)
atoms = Atoms(symbols='HF', positions=np.array([[1.0, 2.0, -0.6], [-1.0, 3.0, 0.7]]))
atoms.write('acemolecule_test.xyz', format='xyz')
atoms = read_acemolecule_input('acemolecule_test.inp')
assert atoms.positions == pytest.approx(
np.array([[1.0, 2.0, -0.6], [-1.0, 3.0, 0.7]]))
assert all(atoms.symbols == 'HF')
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