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import pytest
import numpy as np
from ase.io import read
from io import StringIO
@pytest.fixture()
def vasprun():
# "Hand-written" (reduced) vasprun.xml
sample_vasprun = """\
<?xml version="1.0" encoding="ISO-8859-1"?>
<modeling>
<structure name="primitive_cell" >
<crystal>
<varray name="basis" >
<v> 3.16000000 0.00000000 0.00000000 </v>
<v> 0.00000000 3.16000000 0.00000000 </v>
<v> 0.00000000 0.00000000 3.16000000 </v>
</varray>
</crystal>
<varray name="positions" >
<v> 0.00000000 0.00000000 0.00000000 </v>
<v> 0.50000000 0.50000000 0.50000000 </v>
</varray>
</structure>
<kpoints>
<varray name="kpointlist" >
<v> 0.00000000 0.00000000 0.00000000 </v>
</varray>
</kpoints>
<atominfo>
<atoms> 2 </atoms>
<types> 1 </types>
<array name="atoms" >
<set>
<rc><c>W </c><c> 1</c></rc>
<rc><c>W </c><c> 1</c></rc>
</set>
</array>
</atominfo>
<structure name="initialpos" >
<crystal>
<varray name="basis" >
<v> 3.16000000 0.00000000 0.00000000 </v>
<v> 0.00000000 3.16000000 0.00000000 </v>
<v> 0.00000000 0.00000000 3.16000000 </v>
</varray>
<i name="volume"> 31.55449600 </i>
</crystal>
<varray name="positions" >
<v> 0.00000000 0.00000000 0.00000000 </v>
<v> 0.50000000 0.50000000 0.50000000 </v>
</varray>
</structure>
"""
return sample_vasprun
@pytest.fixture()
def calculation():
def factory(test_case_index=0):
# list of dictionaries with the expected values for
# test calculation xml strings
expected_values = [{"e_0_energy": -29.67691672,
"e_fr_energy": -29.67243317,
"forces": np.array([[7.58587457,
-5.22590317,
6.88227285],
[-7.58587457,
5.22590317,
-6.88227285]]),
"stress": np.array([[4300.36902090,
-284.50040544,
-1468.20603140],
[-284.50040595,
4824.17435683,
-1625.37541639],
[-1468.20603158,
-1625.37541697,
5726.84189498]])},
{"e_0_energy": -2.0,
"e_fr_energy": -3.0,
"forces": np.full((2, 3), np.pi),
"stress": np.full((3, 3), 2.0 * np.pi)}
]
e_fr_energy = expected_values[test_case_index]["e_fr_energy"]
e_0_energy = expected_values[test_case_index]["e_0_energy"]
forces = expected_values[test_case_index]["forces"]
stress = expected_values[test_case_index]["stress"]
# "Hand-written" calculation record
sample_calculation = f"""\
<calculation>
<scstep>
<energy>
<i name="e_fr_energy"> 32.61376955 </i>
<i name="e_wo_entrp"> 32.60797165 </i>
<i name="e_0_energy"> 32.61183692 </i>
</energy>
</scstep>
<scstep>
<energy>
<i name="e_fr_energy"> {e_fr_energy:.8f} </i>
<i name="e_wo_entrp"> -29.68588381 </i>
<i name="e_0_energy"> {e_0_energy:.8f} </i>
</energy>
</scstep>
<structure>
<crystal>
<varray name="basis" >
<v> 3.16000000 0.00000000 0.00000000 </v>
<v> 0.00000000 3.16000000 0.00000000 </v>
<v> 0.00000000 0.00000000 3.16000000 </v>
</varray>
<i name="volume"> 31.55449600 </i>
<varray name="rec_basis" >
<v> 0.31645570 0.00000000 0.00000000 </v>
<v> 0.00000000 0.31645570 0.00000000 </v>
<v> 0.00000000 0.00000000 0.31645570 </v>
</varray>
</crystal>
<varray name="positions" >
<v> 0.00000000 0.00000000 0.00000000 </v>
<v> 0.50000000 0.50000000 0.50000000 </v>
</varray>
</structure>
<varray name="forces" >
<v> {forces[0, 0]:.8f} {forces[0, 1]:.8f} {forces[0, 2]:.8f} </v>
<v> {forces[1, 0]:.8f} {forces[1, 1]:.8f} {forces[1, 2]:.8f} </v>
</varray>
<varray name="stress" >
<v> {stress[0, 0]:.8f} {stress[0, 1]:.8f} {stress[0, 2]:.8f} </v>
<v> {stress[1, 0]:.8f} {stress[1, 1]:.8f} {stress[1, 2]:.8f} </v>
<v> {stress[2, 0]:.8f} {stress[2, 1]:.8f} {stress[2, 2]:.8f} </v>
</varray>
<energy>
<i name="e_fr_energy"> {e_fr_energy:.8f} </i>
<i name="e_wo_entrp"> -29.68588381 </i>
<i name="e_0_energy"> {e_0_energy:.8f} </i>
</energy>
"""
return sample_calculation, expected_values[test_case_index]
return factory
def test_atoms(vasprun):
atoms = read(StringIO(vasprun), index=-1, format='vasp-xml')
# check number of atoms
assert len(atoms) == 2
# make sure it is still tungsten
assert all(np.array(atoms.get_chemical_symbols()) == "W")
# check scaled_positions
expected_scaled_positions = np.array([[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5]])
np.testing.assert_allclose(atoms.get_scaled_positions(),
expected_scaled_positions)
expected_cell = np.array([[3.16, 0.0, 0.0],
[0.0, 3.16, 0.0],
[0.0, 0.0, 3.16]])
# check cell
np.testing.assert_allclose(atoms.cell, expected_cell)
# check real positions
np.testing.assert_allclose(atoms.positions,
expected_scaled_positions @
atoms.cell.complete())
def check_calculation(vasprun_record, expected_values, index=-1):
from ase.units import GPa
atoms = read(StringIO(vasprun_record), index=index,
format='vasp-xml')
assert atoms.get_potential_energy() == \
pytest.approx(expected_values["e_0_energy"])
assert (atoms.get_potential_energy(force_consistent=True) ==
pytest.approx(expected_values["e_fr_energy"]))
np.testing.assert_allclose(atoms.get_forces(),
expected_values["forces"])
assertion_stress = -0.1 * GPa * expected_values["stress"]
assertion_stress = assertion_stress.reshape(9)[[0, 4, 8, 5, 2, 1]]
np.testing.assert_allclose(atoms.get_stress(), assertion_stress)
def test_calculation(vasprun, calculation):
calculation_record, expected_values = calculation(test_case_index=0)
check_calculation(vasprun + calculation_record, expected_values)
def test_two_calculations(vasprun, calculation):
(first_calculation_record,
first_expected_values) = calculation(test_case_index=0)
(second_calculation_record,
second_expected_values) = calculation(test_case_index=1)
extended_vasprun = (vasprun +
first_calculation_record + second_calculation_record)
# make sure we have two atoms objects in the list if we read all records
images = read(StringIO(extended_vasprun), index=':', format="vasp-xml")
assert len(images) == 2
check_calculation(extended_vasprun, second_expected_values)
# make sure we can read the first (second from the end)
# calculation by passing index=-2
check_calculation(extended_vasprun, first_expected_values,
index=-2)
def test_corrupted_calculation(vasprun, calculation):
(first_calculation_record,
first_expected_values) = calculation(test_case_index=0)
second_calculation_record, _ = calculation(test_case_index=1)
# corrupted calculation that does not have energy record.
# Thus the parser is expected to read the previous one.
corrupted_record = '\n'.join(second_calculation_record.split('\n')[:-6])
# assert that we actually do have two calculations in the set up
xml_string = vasprun + first_calculation_record + corrupted_record
images = read(StringIO(xml_string), index=':', format="vasp-xml")
assert len(images) == 1
check_calculation(vasprun + first_calculation_record + corrupted_record,
expected_values=first_expected_values,
index=-2)
# check that the parser skips the corrupted last one
# Should there be a warning in this case?
check_calculation(vasprun + first_calculation_record + corrupted_record,
expected_values=first_expected_values,
index=-1)
def test_vasp_parameters(vasprun, calculation):
from collections import OrderedDict
vasp_parameters = """\
<kpoints>
<generation param="Monkhorst-Pack">
<v type="int" name="divisions"> 1 1 1 </v>
<v name="usershift"> 0.00000000 0.00000000 0.00000000 </v>
<v name="genvec1"> 1.00000000 0.00000000 0.00000000 </v>
<v name="genvec2"> 0.00000000 1.00000000 0.00000000 </v>
<v name="genvec3"> 0.00000000 0.00000000 1.00000000 </v>
<v name="shift"> 0.00000000 0.00000000 0.00000000 </v>
</generation>
<varray name="kpointlist" >
<v> 0.00000000 0.00000000 0.00000000 </v>
</varray>
<varray name="weights" >
<v> 1.00000000 </v>
</varray>
</kpoints>
<parameters>
<separator name="electronic" >
<i type="string" name="PREC">medium</i>
<i name="ENMAX"> 500.00000000</i>
<i name="ENAUG"> 373.43800000</i>
<i name="EDIFF"> 1.00000000</i>
<separator name="electronic smearing" >
<i type="int" name="ISMEAR"> 1</i>
<i name="SIGMA"> 0.10000000</i>
<i name="KSPACING"> 0.50000000</i>
</separator>
<separator name="electronic startup" >
<i type="int" name="ISTART"> 0</i>
<i type="int" name="ICHARG"> 2</i>
<i type="int" name="INIWAV"> 1</i>
</separator>
<separator name="electronic exchange-correlation" >
<i type="logical" name="LASPH"> F </i>
<i type="logical" name="LMETAGGA"> F </i>
</separator>
</separator>
<separator name="ionic" >
<i type="int" name="NSW"> 10000</i>
<i type="int" name="IBRION"> 11</i>
<i name="EDIFFG"> 10.00000000</i>
</separator>
<separator name="symmetry" >
<i type="int" name="ISYM"> 0</i>
<i name="SYMPREC"> 0.00001000</i>
</separator>
</parameters>
"""
calculation_record, _ = calculation()
atoms = read(StringIO(vasprun + calculation_record + vasp_parameters),
index=-1, format="vasp-xml")
expected_parameters = \
OrderedDict([('kpoints_generation',
OrderedDict([('divisions', [1, 1, 1]),
('usershift', [0.0, 0.0, 0.0]),
('genvec1', [1.0, 0.0, 0.0]),
('genvec2', [0.0, 1.0, 0.0]),
('genvec3', [0.0, 0.0, 1.0]),
('shift', [0.0, 0.0, 0.0])])),
('prec', 'medium'), ('enmax', 500.0),
('enaug', 373.438), ('ediff', 1.0),
('ismear', 1), ('sigma', 0.1),
('kspacing', 0.5), ('istart', 0),
('icharg', 2), ('iniwav', 1),
('lasph', False), ('lmetagga', False),
('nsw', 10000), ('ibrion', 11), ('ediffg', 10.0),
('isym', 0), ('symprec', 1e-05)])
assert atoms.calc.parameters == expected_parameters
|
