def test_main(require_vasp):
assert installed()
# simple test calculation of CO molecule
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)],
pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='PBE',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False,
ldipol=True)
co.calc = calc
energy = co.get_potential_energy()
forces = co.get_forces()
dipole_moment = co.get_dipole_moment()
# check that parsing of vasprun.xml file works
conf = read('vasprun.xml')
assert conf.calc.parameters['kpoints_generation']
assert conf.calc.parameters['sigma'] == 1.0
assert conf.calc.parameters['ialgo'] == 68
assert energy - conf.get_potential_energy() == 0.0
assert np.allclose(conf.get_forces(), forces)
assert np.allclose(conf.get_dipole_moment(), dipole_moment, atol=1e-6)
# Cleanup
calc.clean()
def test_vasp2_co(require_vasp):
"""
Run some VASP tests to ensure that the VASP calculator works. This
is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables
"""
from ase.test.calculator.vasp import installed2 as installed
assert installed()
from ase import Atoms
from ase.io import write
from ase.calculators.vasp import Vasp2 as Vasp
import numpy as np
def array_almost_equal(a1, a2, tol=np.finfo(type(1.0)).eps):
"""Replacement for old numpy.testing.utils.array_almost_equal."""
return (np.abs(a1 - a2) < tol).all()
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='PBE',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False)
co.calc = calc
en = co.get_potential_energy()
write('vasp_co.traj', co)
assert abs(en + 14.918933) < 5e-3
# Secondly, check that restart from the previously created VASP output works
calc2 = Vasp(restart=True)
co2 = calc2.get_atoms()
# Need tolerance of 1e-14 because VASP itself changes coordinates
# slightly between reading POSCAR and writing CONTCAR even if no ionic
# steps are made.
assert array_almost_equal(co.positions, co2.positions, 1e-14)
assert en - co2.get_potential_energy() == 0.
assert array_almost_equal(calc.get_stress(co), calc2.get_stress(co2))
assert array_almost_equal(calc.get_forces(co), calc2.get_forces(co2))
assert array_almost_equal(calc.get_eigenvalues(), calc2.get_eigenvalues())
assert calc.get_number_of_bands() == calc2.get_number_of_bands()
assert calc.get_xc_functional() == calc2.get_xc_functional()
# Cleanup
calc.clean()
def test_vasp2_import(require_vasp):
"""
Test if we can find vasp2 using get_calculator()
"""
from ase.test.calculator.vasp import installed2 as installed
from ase.calculators.calculator import get_calculator_class
assert installed()
get_calculator_class('vasp2')
def test_main(require_vasp):
assert installed()
# simple test calculation of CO molecule
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='LDA',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
nbands=12,
istart=0,
nelm=3,
lwave=False,
lcharg=False,
ldipol=True)
co.calc = calc
energy = co.get_potential_energy()
forces = co.get_forces()
dipole_moment = co.get_dipole_moment()
# check that parsing of vasprun.xml file works
conf = read('vasprun.xml')
assert conf.calc.parameters['kpoints_generation']
assert conf.calc.parameters['sigma'] == 1.0
assert conf.calc.parameters['ialgo'] == 68
assert energy - conf.get_potential_energy() == 0.0
# Check some arrays
assert np.allclose(conf.get_forces(), forces)
assert np.allclose(conf.get_dipole_moment(), dipole_moment, atol=1e-6)
# Check k-point-dependent properties
assert len(conf.calc.get_eigenvalues(spin=0)) >= 12
assert conf.calc.get_occupation_numbers()[2] == 2
assert conf.calc.get_eigenvalues(spin=1) is None
kpt = conf.calc.get_kpt(0)
assert kpt.weight == 1.
# Perform a spin-polarised calculation
co.calc.set(ispin=2, ibrion=-1)
co.get_potential_energy()
conf = read('vasprun.xml')
assert len(conf.calc.get_eigenvalues(spin=1)) >= 12
assert conf.calc.get_occupation_numbers(spin=1)[0] == 1.
# Cleanup
calc.clean()
def test_vasp2_cell(require_vasp):
"""
Check the unit cell is handled correctly
"""
import pytest
from ase.test.calculator.vasp import installed2 as installed
from ase.calculators.vasp import Vasp2 as Vasp
from ase.build import molecule
assert installed()
# Molecules come with no unit cell
atoms = molecule('CH4')
calc = Vasp()
with pytest.raises(ValueError):
atoms.calc = calc
atoms.get_total_energy()
def test_vasp2_xc(require_vasp):
"""
Run some tests to ensure that the xc setting in the VASP calculator
works.
"""
from ase.test.calculator.vasp import installed2 as installed
from ase.calculators.vasp import Vasp2 as Vasp
assert installed()
def dict_is_subset(d1, d2):
"""True if all the key-value pairs in dict 1 are in dict 2"""
for key, value in d1.items():
if key not in d2:
return False
elif d2[key] != value:
return False
else:
return True
calc_vdw = Vasp(xc='optb86b-vdw')
assert dict_is_subset({
'param1': 0.1234,
'param2': 1.0
}, calc_vdw.float_params)
calc_hse = Vasp(xc='hse06', hfscreen=0.1, gga='RE', encut=400, sigma=0.5)
assert dict_is_subset({
'hfscreen': 0.1,
'encut': 400,
'sigma': 0.5
}, calc_hse.float_params)
assert dict_is_subset({'gga': 'RE'}, calc_hse.string_params)
def test_vasp2_wdir(require_vasp):
"""
Run tests to ensure that the VASP txt and label arguments function correctly,
i.e. correctly sets the working directories and works in that directory.
This is conditional on the existence of the ASE_VASP_COMMAND, VASP_COMMAND
or VASP_SCRIPT environment variables
"""
import filecmp
import os
from ase.test.calculator.vasp import installed2 as installed
from ase import Atoms
from ase.calculators.vasp import Vasp2 as Vasp
assert installed()
def compare_paths(path1, path2):
assert os.path.abspath(path1) == os.path.abspath(path2)
# Test setup system, borrowed from vasp_co.py
d = 1.14
atoms = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
atoms.center(vacuum=5.)
file1 = '_vasp_dummy_str.out'
file2 = '_vasp_dummy_io.out'
file3 = '_vasp_dummy_2.out'
testdir = '_dummy_txt_testdir'
label = os.path.join(testdir, 'vasp')
# Test
settings = dict(label=label,
xc='PBE',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False)
# Make 2 copies of the calculator object
calc = Vasp(**settings)
calc2 = Vasp(**settings)
# Check the calculator path is the expected path
compare_paths(calc.directory, testdir)
calc.set(txt=file1)
atoms.calc = calc
en1 = atoms.get_potential_energy()
# Check that the output files are in the correct directory
for fi in ['OUTCAR', 'CONTCAR', 'vasprun.xml']:
fi = os.path.join(testdir, fi)
assert os.path.isfile(fi)
# We open file2 in our current directory, so we don't want it to write
# in the label directory
with open(file2, 'w') as f:
calc2.set(txt=f)
atoms.calc = calc2
atoms.get_potential_energy()
# Make sure the two outputfiles are identical
assert filecmp.cmp(os.path.join(calc.directory, file1), file2)
# Test restarting from working directory in test directory
label2 = os.path.join(testdir, file3)
calc2 = Vasp(restart=label, label=label2)
# Check the calculator path is the expected path
compare_paths(calc2.directory, testdir)
assert not calc2.calculation_required(calc2.atoms, ['energy', 'forces'])
en2 = calc2.get_potential_energy()
# Check that the restarted calculation didn't run, i.e. write to output file
assert not os.path.isfile(os.path.join(calc.directory, file3))
# Check that we loaded energy correctly
assert en1 == en2
def test_vasp2_kpoints(require_vasp):
"""
Check the many ways of specifying KPOINTS
"""
import os
from ase.calculators.vasp import Vasp2 as Vasp
from ase.build import bulk
from ase.test.calculator.vasp import installed2 as installed
assert installed()
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
def check_kpoints_line(n, contents):
"""Assert the contents of a line"""
with open('KPOINTS', 'r') as f:
lines = f.readlines()
assert lines[n] == contents
# Default to (1 1 1)
calc = Vasp(gamma=True)
calc.write_kpoints()
check_kpoints_line(2, 'Gamma\n')
check_kpoints_line(3, '1 1 1 \n')
calc.clean()
# 3-tuple prints mesh
calc = Vasp(gamma=False, kpts=(4, 4, 4))
calc.write_kpoints()
check_kpoints_line(2, 'Monkhorst-Pack\n')
check_kpoints_line(3, '4 4 4 \n')
calc.clean()
# Auto mode
calc = Vasp(kpts=20)
calc.write_kpoints()
check_kpoints_line(1, '0\n')
check_kpoints_line(2, 'Auto\n')
check_kpoints_line(3, '20 \n')
calc.clean()
# 1-element list ok, Gamma ok
calc = Vasp(kpts=[20], gamma=True)
calc.write_kpoints()
check_kpoints_line(1, '0\n')
check_kpoints_line(2, 'Auto\n')
check_kpoints_line(3, '20 \n')
calc.clean()
# KSPACING suppresses KPOINTS file
calc = Vasp(kspacing=0.23)
calc.initialize(Al)
calc.write_kpoints()
calc.write_incar(Al)
assert not os.path.isfile('KPOINTS')
with open('INCAR', 'r') as f:
assert ' KSPACING = 0.230000\n' in f.readlines()
calc.clean()
# Negative KSPACING raises an error
calc = Vasp(kspacing=-0.5)
try:
calc.write_kpoints()
except ValueError:
pass
else:
raise AssertionError("Negative KSPACING did not raise ValueError")
calc.clean()
# Explicit weighted points with nested lists, Cartesian if not specified
calc = Vasp(
kpts=[[0.1, 0.2, 0.3, 2], [0.0, 0.0, 0.0, 1], [0.0, 0.5, 0.5, 2]])
calc.write_kpoints()
with open('KPOINTS.ref', 'w') as f:
f.write("""KPOINTS created by Atomic Simulation Environment
3
Cartesian
0.100000 0.200000 0.300000 2.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.500000 2.000000
""")
assert filecmp_ignore_whitespace('KPOINTS', 'KPOINTS.ref')
os.remove('KPOINTS.ref')
# Explicit points as list of tuples, automatic weighting = 1.
calc = Vasp(
kpts=[(0.1, 0.2, 0.3), (0.0, 0.0, 0.0), (0.0, 0.5, 0.5)], reciprocal=True)
calc.write_kpoints()
with open('KPOINTS.ref', 'w') as f:
f.write("""KPOINTS created by Atomic Simulation Environment
3
Reciprocal
0.100000 0.200000 0.300000 1.0
0.000000 0.000000 0.000000 1.0
0.000000 0.500000 0.500000 1.0
""")
assert filecmp_ignore_whitespace('KPOINTS', 'KPOINTS.ref')
os.remove('KPOINTS.ref')
def test_vasp2_Al_volrelax(require_vasp):
"""
Run VASP tests to ensure that relaxation with the VASP calculator works.
This is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables.
"""
from ase.test.calculator.vasp import installed2 as installed
assert installed()
import numpy as np
from ase import io
# QuasiNewton nowadays is an alias for BFGSLineSearch, which is
# broken. Use BFGS instead.
from ase.optimize import BFGS as QuasiNewton
from ase.build import bulk
from ase.calculators.vasp import Vasp2 as Vasp
# -- Perform Volume relaxation within Vasp
def vasp_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA', isif=7, nsw=5,
ibrion=1, ediffg=-1e-3, lwave=False, lcharg=False)
calc.calculate(Al)
# Explicitly parse atomic position output file from Vasp
CONTCAR_Al = io.read('CONTCAR', format='vasp')
print('Stress after relaxation:\n', calc.read_stress())
print('Al cell post relaxation from calc:\n', calc.get_atoms().get_cell())
print('Al cell post relaxation from atoms:\n', Al.get_cell())
print('Al cell post relaxation from CONTCAR:\n', CONTCAR_Al.get_cell())
# All the cells should be the same.
assert (calc.get_atoms().get_cell() == CONTCAR_Al.get_cell()).all()
assert (Al.get_cell() == CONTCAR_Al.get_cell()).all()
return Al
# -- Perform Volume relaxation using ASE with Vasp as force/stress calculator
def ase_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA')
Al.calc = calc
from ase.constraints import StrainFilter
sf = StrainFilter(Al)
qn = QuasiNewton(sf, logfile='relaxation.log')
qn.run(fmax=0.1, steps=5)
print('Stress:\n', calc.read_stress())
print('Al post ASE volume relaxation\n', calc.get_atoms().get_cell())
return Al
# Test function for comparing two cells
def cells_almost_equal(cellA, cellB, tol=0.01):
return (np.abs(cellA - cellB) < tol).all()
# Correct LDA relaxed cell
a_rel = 4.18
LDA_cell = np.diag([a_rel, a_rel, a_rel])
Al_vasp = vasp_vol_relax()
Al_ase = ase_vol_relax()
assert cells_almost_equal(LDA_cell, Al_vasp.get_cell())
assert cells_almost_equal(LDA_cell, Al_ase.get_cell())
# Cleanup
Al_ase.calc.clean()
def test_vasp_net_charge(require_vasp):
"""
Run VASP tests to ensure that determining number of electrons from
user-supplied net charge (via the deprecated net_charge parameter) works
correctly. This is conditional on the existence of the VASP_COMMAND or
VASP_SCRIPT environment variables.
This is mainly a slightly reduced duplicate of the vasp_charge test, but with
flipped signs and with checks that ensure FutureWarning is emitted.
Should be removed along with the net_charge parameter itself at some point.
"""
assert installed()
system = bulk('Al', 'fcc', a=4.5, cubic=True)
# Dummy calculation to let VASP determine default number of electrons
calc = Vasp(xc='LDA', nsw=-1, ibrion=-1, nelm=1, lwave=False, lcharg=False)
calc.calculate(system)
default_nelect_from_vasp = calc.get_number_of_electrons()
assert default_nelect_from_vasp == 12
# Compare VASP's output nelect from before + net charge to default nelect
# determined by us + net charge
with pytest.warns(FutureWarning):
net_charge = -2
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
net_charge=net_charge)
calc.initialize(system)
calc.write_input(system)
calc.read_incar()
assert calc.float_params['nelect'] == default_nelect_from_vasp + net_charge
# Test that conflicts between explicitly given nelect and net charge are
# detected
with pytest.raises(ValueError):
with pytest.warns(FutureWarning):
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
nelect=default_nelect_from_vasp + net_charge + 1,
net_charge=net_charge)
calc.calculate(system)
# Test that conflicts between charge and net_charge are detected
with pytest.raises(ValueError):
with pytest.warns(FutureWarning):
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
charge=-net_charge - 1,
net_charge=net_charge)
calc.calculate(system)
# Test that nothing is written if net charge is 0 and nelect not given
with pytest.warns(FutureWarning):
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
net_charge=0)
calc.initialize(system)
calc.write_input(system)
calc.read_incar()
assert calc.float_params['nelect'] is None
def test_vasp_setup(require_vasp):
"""
Run some tests to ensure that VASP calculator constructs correct POTCAR files
"""
from os import remove
from os.path import isfile
from ase.atoms import Atoms
from ase.calculators.vasp import Vasp
from ase.test.calculator.vasp import installed
assert installed()
def check_potcar(setups, filename='POTCAR'):
"""Return true if labels in setups are found in POTCAR"""
pp = []
with open(filename, 'r') as f:
for line in f:
if 'TITEL' in line.split():
pp.append(line.split()[3])
for setup in setups:
assert setup in pp
# Write some POTCARs and check they are ok
potcar = 'POTCAR'
try:
atoms = Atoms('CaGdCs',
positions=[[0, 0, 1], [0, 0, 2], [0, 0, 3]],
cell=[5, 5, 5])
calc = Vasp(xc='pbe')
calc.initialize(atoms)
calc.write_potcar()
check_potcar(('Ca_pv', 'Gd', 'Cs_sv'), filename=potcar)
calc = Vasp(xc='pbe', setups='recommended')
calc.initialize(atoms)
calc.write_potcar()
check_potcar(('Ca_sv', 'Gd_3', 'Cs_sv'), filename=potcar)
calc = Vasp(xc='pbe', setups='materialsproject')
calc.initialize(atoms)
calc.write_potcar()
check_potcar(('Ca_sv', 'Gd', 'Cs_sv'), filename=potcar)
atoms = Atoms('CaInI',
positions=[[0, 0, 1], [0, 0, 2], [0, 0, 3]],
cell=[5, 5, 5])
calc = Vasp(xc='pbe', setups={'base': 'gw'})
calc.initialize(atoms)
calc.write_potcar()
check_potcar(('Ca_sv_GW', 'In_d_GW', 'I_GW'), filename=potcar)
calc = Vasp(xc='pbe', setups={'base': 'gw', 'I': ''})
calc.initialize(atoms)
calc.write_potcar()
check_potcar(('Ca_sv_GW', 'In_d_GW', 'I'), filename=potcar)
calc = Vasp(xc='pbe', setups={'base': 'gw', 'Ca': '_sv', 2: 'I'})
calc.initialize(atoms)
calc.write_potcar()
check_potcar(('Ca_sv', 'In_d_GW', 'I'), filename=potcar)
finally:
if isfile(potcar):
remove(potcar)
def test_vasp2_check_state(require_vasp):
"""
Run tests to ensure that the VASP check_state() function call works correctly,
i.e. correctly sets the working directories and works in that directory.
This is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables
"""
from ase.test.calculator.vasp import installed2 as installed
import os
from ase import Atoms
from ase.calculators.vasp import Vasp2 as Vasp
assert installed()
# Test setup system, borrowed from vasp_co.py
d = 1.14
atoms = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
atoms.extend(Atoms('CO', positions=[(0, 2, 0), (0, 2, d)]))
atoms.center(vacuum=5.)
# Test
settings = dict(xc='LDA',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False)
s1 = atoms.get_chemical_symbols()
calc = Vasp(**settings)
atoms.calc = calc
en1 = atoms.get_potential_energy()
# Test JSON dumping and restarting works
fi = 'json_test.json'
calc.write_json(filename=fi)
assert os.path.isfile(fi)
calc2 = Vasp()
calc2.read_json(fi)
assert not calc2.calculation_required(atoms, ['energy', 'forces'])
en2 = calc2.get_potential_energy()
assert abs(en1 - en2) < 1e-8
os.remove(fi) # Clean up the JSON file
# Check that the symbols remain in order (non-sorted)
s2 = calc.atoms.get_chemical_symbols()
assert s1 == s2
s3 = sorted(s2)
assert s2 != s3
# Check that get_atoms() doesn't reset results
r1 = dict(calc.results) # Force a copy
calc.get_atoms()
r2 = dict(calc.results)
assert r1 == r2
# Make a parameter change to the calculator
calc.set(sigma=0.5)
# Check that we capture a change for float params
assert calc.check_state(atoms) == ['float_params']
assert calc.calculation_required(atoms, ['energy', 'forces'])
en2 = atoms.get_potential_energy()
# The change in sigma should result in a small change in energy
assert (en1 - en2) > 1e-7
# Now we make a change in input_params instead
calc.kpts = 2
# Check that this requires a new calculation
assert calc.check_state(atoms) == ['input_params']
assert calc.calculation_required(atoms, ['energy', 'forces'])
# Clean up
calc.clean()
def test_vasp_charge(require_vasp):
"""
Run VASP tests to ensure that determining number of electrons from
user-supplied charge works correctly. This is conditional on the existence
of the VASP_COMMAND or VASP_SCRIPT environment variables.
"""
import pytest
from ase.build import bulk
from ase.calculators.vasp import Vasp
from ase.test.calculator.vasp import installed
assert installed()
system = bulk('Al', 'fcc', a=4.5, cubic=True)
# Dummy calculation to let VASP determine default number of electrons
calc = Vasp(xc='LDA', nsw=-1, ibrion=-1, nelm=1, lwave=False, lcharg=False)
calc.calculate(system)
default_nelect_from_vasp = calc.get_number_of_electrons()
assert default_nelect_from_vasp == 12
# Make sure that no nelect was written into INCAR yet (as it wasn't necessary)
calc = Vasp()
calc.read_incar()
assert calc.float_params['nelect'] is None
# Compare VASP's output nelect from before minus charge to default nelect
# determined by us minus charge
charge = -2
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
charge=charge)
calc.initialize(system)
calc.write_input(system)
calc.read_incar()
assert calc.float_params['nelect'] == default_nelect_from_vasp - charge
# Test that conflicts between explicitly given nelect and charge are detected
with pytest.raises(ValueError):
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
nelect=default_nelect_from_vasp - charge + 1,
charge=charge)
calc.calculate(system)
# Test that nothing is written if charge is 0 and nelect not given
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
charge=0)
calc.initialize(system)
calc.write_input(system)
calc.read_incar()
assert calc.float_params['nelect'] is None
# Test that explicitly given nelect still works as expected
calc = Vasp(xc='LDA',
nsw=-1,
ibrion=-1,
nelm=1,
lwave=False,
lcharg=False,
nelect=15)
calc.calculate(system)
assert calc.get_number_of_electrons() == 15
