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# fmt: off
# flake8: noqa
from pathlib import Path
import numpy as np
import pytest
from ase.io import ParseError, read
from ase.io.aims import read_aims_results
from ase.stress import full_3x3_to_voigt_6_stress
parent = Path(__file__).parents[2]
def test_parse_socketio(testdir):
traj = read(parent / "testdata/aims/socket.out", ":", format="aims-output")
assert len(traj) == 6
p0 = [[0.0, 0.0, 0.0], [0.9584, 0.0, 0.0], [-0.24, 0.9279, 0.0]]
p1 = [
[-0.00044436, 0.00021651, 0.00068957],
[0.96112981, -0.00029923, 0.00096836],
[-0.24091781, 0.93010946, 0.00061317],
]
p_end = [
[-0.00156048, -0.00072446, 0.00045281],
[0.98615072, -0.00962614, -0.00053732],
[-0.25646779, 0.95117586, 0.00820183],
]
assert np.allclose(traj[0].get_positions(), p0)
assert np.allclose(traj[1].get_positions(), p1)
assert np.allclose(traj[-1].get_positions(), p_end)
f0 = [
[-0.481289284665163e00, -0.615051370384412e00, 0.811297123282653e-27],
[0.762033585727896e00, -0.942008578636939e-01, -0.973556547939183e-27],
[-0.280744301062733e00, 0.709252228248106e00, -0.649037698626122e-27],
]
f1 = [
[-0.346210275412861e00, -0.520615919604426e00, -0.966369462150621e-04],
[0.587866333819113e00, -0.830442530429637e-01, 0.171037714240380e-03],
[-0.241656058406252e00, 0.603660172647390e00, -0.744007680253175e-04],
]
f_end = [
[0.492882061544499e00, 0.499117230159087e00, 0.347959116743205e-02],
[-0.724281788245024e00, 0.800633239635954e-01, 0.130633777464187e-02],
[0.231399726700525e00, -0.579180554122683e00, -0.478592894207392e-02],
]
assert np.allclose(traj[0].get_forces(), f0)
assert np.allclose(traj[1].get_forces(), f1)
assert np.allclose(traj[-1].get_forces(), f_end)
def test_parse_md(testdir):
traj = read(parent / "testdata/aims/md.out", ":", format="aims-output")
assert len(traj) == 5
p0 = [[0.0, 0.0, 0.0], [0.9584, 0.0, 0.0], [-0.24, 0.9279, 0.0]]
p1 = [
[0.00247722, -0.00200215, 0.00000000],
[0.93156204, -0.00330135, 0.00000000],
[-0.25248383, 0.96298223, 0.00000000],
]
p_end = [
[-0.00044308, -0.00190646, 0.00000000],
[0.98936333, -0.01341746, -0.00000000],
[-0.26393022, 0.97157934, 0.00000000],
]
assert np.allclose(traj[0].get_positions(), p0)
assert np.allclose(traj[1].get_positions(), p1)
assert np.allclose(traj[-1].get_positions(), p_end)
f0 = [
[-0.481289284665163e00, -0.615051370384412e00, 0.811297123282653e-27],
[0.762033585727896e00, -0.942008578636939e-01, -0.973556547939183e-27],
[-0.280744301062733e00, 0.709252228248106e00, -0.649037698626122e-27],
]
f1 = [
[-0.284519402890037e01, 0.121286349030924e01, 0.691733365155783e-17],
[0.257911758656866e01, -0.471469245294899e-01, -0.730166238143266e-18],
[0.266076442331705e00, -0.116571656577975e01, -0.618716741081841e-17],
]
f_end = [
[0.266848800470869e00, 0.137113486710510e01, 0.717235335588107e-17],
[-0.812308728045051e00, 0.142880785873554e00, 0.874856850626564e-18],
[0.545459927574182e00, -0.151401565297866e01, -0.804721020748119e-17],
]
assert np.allclose(traj[0].get_forces(), f0)
assert np.allclose(traj[1].get_forces(), f1)
assert np.allclose(traj[-1].get_forces(), f_end)
def test_parse_relax(testdir):
traj = read(parent / "testdata/aims/relax.out", ":", format="aims-output")
assert len(traj) == 8
p0 = [[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]]
assert all(np.allclose(at.get_scaled_positions(), p0) for at in traj)
assert all(np.allclose(at.get_forces(), np.zeros((2, 3))) for at in traj)
s0 = full_3x3_to_voigt_6_stress(
[
[0.07748922, 0.0, 0.0],
[0.0, 0.07748923, 0.0],
[0.0, 0.0, 0.07748923],
]
)
s_end = full_3x3_to_voigt_6_stress(
[
[-0.00007093, 0.00001488, 0.00001488],
[0.00001488, -0.00007093, 0.00001488],
[0.00001488, 0.00001488, -0.00007093],
]
)
assert np.allclose(traj[0].get_stress(), s0)
assert np.allclose(traj[-1].get_stress(), s_end)
cell_0 = [
[0.000, 2.903, 2.903],
[2.903, 0.000, 2.903],
[2.903, 2.903, 0.000],
]
cell_end = [
[0.00006390, 2.70950938, 2.70950938],
[2.70950941, 0.00006393, 2.70950939],
[2.70950941, 2.70950939, 0.00006393],
]
assert np.allclose(traj[0].get_cell(), cell_0)
assert np.allclose(traj[-1].get_cell(), cell_end)
def test_parse_singlepoint(testdir):
atoms = read(parent / "testdata/aims/singlepoint.out", format="aims-output")
p0 = [[0.0, 0.0, 0.0], [0.9584, 0.0, 0.0], [-0.24, 0.9279, 0.0]]
assert np.allclose(atoms.get_positions(), p0)
f0 = [
[-0.478299830661005e01, -0.616960341437854e01, 0.162259424656531e-27],
[0.692109878170016e01, -0.419925410034428e00, 0.000000000000000e00],
[-0.213810047509011e01, 0.658952882441297e01, 0.243389136984796e-27],
]
assert np.allclose(atoms.get_forces(), f0)
results = read_aims_results(parent / "testdata/aims/singlepoint.out")
assert np.allclose(results["forces"], f0)
assert np.abs(results["total_energy"] + 2.06302072675943e03) < 1e-15
assert np.abs(results["free_energy"] + 2.06302072675943e03) < 1e-15
assert np.abs(results["energy"] + 2.06302072675943e03) < 1e-15
def test_parse_dfpt_dielectric(testdir):
outfile = parent / "testdata/aims/DFPT_dielectric.out"
atoms = read(outfile, format="aims-output")
diel = atoms.calc.results["dielectric_tensor"]
diel_0 = [
[7.18759265e00, -1.0000000e-15, 1.9000000e-14],
[-1.000000e-15, 7.18759284e00, 2.59000000e-13],
[2.0000000e-14, 2.58000000e-13, 7.1875928e00],
]
assert np.allclose(diel, diel_0)
def test_parse_polarization(testdir):
outfile = parent / "testdata/aims/polarization.out"
atoms = read(outfile, format="aims-output")
polar = atoms.calc.results["polarization"]
polar_0 = [-51.045557E-03, -51.045557E-03, -51.458008E-03]
assert np.allclose(polar, polar_0)
def test_preamble_failed(testdir):
outfile = parent / "testdata/aims/preamble_fail.out"
with pytest.raises(ParseError, match='No SCF steps'):
read(outfile, format="aims-output")
def test_numerical_stress(testdir):
outfile = parent / "testdata/aims/numerical_stress.out"
atoms = read(outfile, format="aims-output")
stress = atoms.get_stress()
stress_actual = [
0.00244726, 0.00267442, 0.00258710, 0.00000005, -0.00000026, -0.00000007
]
assert np.allclose(stress, stress_actual)
def test_spin_collinear_w_md_light(testdir):
"""Issue 3345"""
outfile = parent / "testdata/aims/issue_3345_spin_md_light.out"
atoms = read(outfile, format="aims-output")
e0 = -13.0174218930995
ee = atoms.get_potential_energy()
assert np.allclose(e0, ee)
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