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from io import StringIO
import numpy as np
import pytest
from ase.io import read, write
from ase.build import bulk
from ase.calculators.calculator import compare_atoms
from ase.io.abinit import read_abinit_out, read_eig, match_kpt_header
from ase.units import Hartree, Bohr
def test_abinit_inputfile_roundtrip():
m1 = bulk('Ti')
m1.set_initial_magnetic_moments(range(len(m1)))
write('abinit_save.in', images=m1, format='abinit-in')
m2 = read('abinit_save.in', format='abinit-in')
# (How many decimals?)
assert not compare_atoms(m1, m2, tol=1e-7)
# "Hand-written" (reduced) abinit txt file based on v8.0.8 format:
sample_outfile = """\
.Version 8.0.8 of ABINIT
-outvars: echo values of preprocessed input variables --------
natom 2
ntypat 1
rprim 5.0 0.0 0.1
0.0 6.0 0.0
0.0 0.0 7.0
typat 1 1
znucl 8.0
================================
----iterations are completed or convergence reached----
cartesian coordinates (angstrom) at end:
1 2.5 2.5 3.7
2 2.5 2.5 2.5
cartesian forces (eV/Angstrom) at end:
1 -0.1 -0.3 0.4
2 -0.2 -0.4 -0.5
Components of total free energy (in Hartree) :
>>>>>>>>> Etotal= -42.5
Cartesian components of stress tensor (hartree/bohr^3)
sigma(1 1)= 2.3 sigma(3 2)= 3.1
sigma(2 2)= 2.4 sigma(3 1)= 3.2
sigma(3 3)= 2.5 sigma(2 1)= 3.3
END DATASET(S)
"""
def test_read_abinit_output():
fd = StringIO(sample_outfile)
results = read_abinit_out(fd)
assert results.pop('version') == '8.0.8'
atoms = results.pop('atoms')
assert all(atoms.symbols == 'OO')
assert atoms.positions == pytest.approx(
np.array([[2.5, 2.5, 3.7], [2.5, 2.5, 2.5]]))
assert all(atoms.pbc)
assert atoms.cell[:] == pytest.approx(
np.array([[5.0, 0.0, 0.1], [0.0, 6.0, 0.0], [0.0, 0.0, 7.0]]))
ref_stress = pytest.approx([2.3, 2.4, 2.5, 3.1, 3.2, 3.3])
assert results.pop('stress') / (Hartree / Bohr**3) == ref_stress
assert results.pop('forces') == pytest.approx(
np.array([[-0.1, -0.3, 0.4], [-0.2, -0.4, -0.5]]))
for name in 'energy', 'free_energy':
assert results.pop(name) / Hartree == -42.5
assert not results
eig_text = """\
Fermi (or HOMO) energy (hartree) = 0.123 Average Vxc (hartree)= -0.456
Eigenvalues (hartree) for nkpt= 2 k points:
kpt# 1, nband= 3, wtk= 0.1, kpt= 0.2 0.3 0.4 (reduced coord)
-0.2 0.2 0.3
kpt# 2, nband= 3, wtk= 0.2, kpt= 0.3 0.4 0.5 (reduced coord)
-0.3 0.4 0.5
"""
def test_parse_eig_with_fermiheader():
eigval_ref = np.array([
[-0.2, 0.2, 0.3],
[-0.3, 0.4, 0.5]
]).reshape(1, 2, 3) # spin x kpts x bands
kpts_ref = np.array([
[0.2, 0.3, 0.4],
[0.3, 0.4, 0.5]
])
weights_ref = [0.1, 0.2]
eig_buf = StringIO(eig_text)
data = read_eig(eig_buf)
assert data['eigenvalues'] / Hartree == pytest.approx(eigval_ref)
assert data['ibz_kpoints'] == pytest.approx(kpts_ref)
assert data['kpoint_weights'] == pytest.approx(weights_ref)
assert data['fermilevel'] / Hartree == pytest.approx(0.123)
def test_parse_eig_without_fermiheader():
fd = StringIO(eig_text)
next(fd) # Header is omitted e.g. in non-selfconsistent calculations.
data = read_eig(fd)
assert 'fermilevel' not in data
assert {'eigenvalues', 'ibz_kpoints', 'kpoint_weights'} == set(data)
def test_match_kpt_header():
header_line = """\
kpt# 12, nband= 5, wtk= 0.02778, \
kpt= 0.4167 0.4167 0.0833 (reduced coord)
"""
nbands, weight, vector = match_kpt_header(header_line)
assert nbands == 5
assert weight == pytest.approx(0.02778)
assert vector == pytest.approx([0.4167, 0.4167, 0.0833])
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