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from io import StringIO
import numpy as np
import pytest
from ase.io import read
from ase.io.formats import match_magic
import ase.units as units
buf = r"""
Entering Gaussian System, Link 0=g16
...
******************************************
Gaussian 16: ES64L-G16RevA.03 25-Dec-2016
6-Apr-2021
******************************************
...
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 1.1 2.2 3.3
2 1 0 4.4 5.5 6.6
3 1 0 7.7 8.8 9.9
---------------------------------------------------------------------
...
SCF Done: E(RB3LYP) = -12.3456789 A.U. after 9 cycles
...
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 8 0.1 0.2 0.3
2 1 0.4 0.5 0.6
3 1 0.7 0.8 0.9
-------------------------------------------------------------------
"""
def test_match_magic():
bytebuf = buf.encode('ascii')
assert match_magic(bytebuf).name == 'gaussian-out'
def test_gaussian_out():
fd = StringIO(buf)
atoms = read(fd, format='gaussian-out')
assert str(atoms.symbols) == 'OH2'
assert atoms.positions == pytest.approx(np.array([
[1.1, 2.2, 3.3],
[4.4, 5.5, 6.6],
[7.7, 8.8, 9.9],
]))
assert not any(atoms.pbc)
assert atoms.cell.rank == 0
energy = atoms.get_potential_energy()
forces = atoms.get_forces()
assert energy / units.Ha == pytest.approx(-12.3456789)
assert forces / (units.Ha / units.Bohr) == pytest.approx(np.array([
[0.1, 0.2, 0.3],
[0.4, 0.5, 0.6],
[0.7, 0.8, 0.9],
]))
|
