def test_vasp_calling(cmd, poscar):
cleanup_vasp_run()
structure = dft_input_to_structure(poscar)
forces1 = run_dft('.', cmd, structure=structure, en=False)
forces2, energy2 = run_dft('.', cmd, structure=structure, en=True)
forces3 = parse_dft_forces('./test_files/test_vasprun.xml')
forces4, energy4 = parse_dft_forces_and_energy(
'./test_files/test_vasprun.xml')
vr_step = Vasprun('./test_files/test_vasprun.xml').ionic_steps[-1]
ref_forces = vr_step['forces']
ref_energy = vr_step['electronic_steps'][-1]['e_0_energy']
assert len(forces1) == len(ref_forces)
assert len(forces2) == len(ref_forces)
assert len(forces3) == len(ref_forces)
assert len(forces4) == len(ref_forces)
for i in range(structure.nat):
assert np.isclose(forces1[i], ref_forces[i]).all()
assert np.isclose(forces2[i], ref_forces[i]).all()
assert np.isclose(forces3[i], ref_forces[i]).all()
assert np.isclose(forces4[i], ref_forces[i]).all()
assert energy2 == ref_energy
assert energy4 == ref_energy
cleanup_vasp_run()
def test_run_dft_par():
os.system('cp test_files/test_POSCAR ./POSCAR')
test_structure = dft_input_to_structure('./POSCAR')
for dft_command in [None]:
with raises(FileNotFoundError):
run_dft_par('POSCAR',
test_structure,
dft_command=dft_command,
n_cpus=2)
call_string = "echo 'testing_call'"
forces = run_dft_par('POSCAR',
test_structure,
dft_command=call_string,
n_cpus=1,
serial_prefix=' ',
dft_out='test_files/test_vasprun.xml',
screen_out='TEST_CALL_OUT')
with open("TEST_CALL_OUT", 'r') as f:
assert 'testing_call' in f.readline()
os.system('rm ./TEST_CALL_OUT')
assert isinstance(forces, np.ndarray)
def test_run_dft_par():
os.system("cp test_files/test_POSCAR ./POSCAR")
test_structure = dft_input_to_structure("./POSCAR")
for dft_command in [None]:
with raises(FileNotFoundError):
run_dft_par("POSCAR", test_structure, dft_command=dft_command, n_cpus=2)
call_string = "echo 'testing_call'"
forces = run_dft_par(
"POSCAR",
test_structure,
dft_command=call_string,
n_cpus=1,
serial_prefix=" ",
dft_out="test_files/test_vasprun.xml",
screen_out="TEST_CALL_OUT",
)
with open("TEST_CALL_OUT", "r") as f:
assert "testing_call" in f.readline()
os.system("rm ./TEST_CALL_OUT")
assert isinstance(forces, np.ndarray)
def test_vasp_input_edit():
os.system('cp test_files/test_POSCAR ./POSCAR')
structure = dft_input_to_structure('./test_files/test_POSCAR')
structure.positions[0] += np.random.randn(3)
new_file = edit_dft_input_positions('./POSCAR', structure=structure)
final_structure = dft_input_to_structure(new_file)
assert np.isclose(final_structure.vec1, structure.vec1, atol=1e-4).all()
assert np.isclose(final_structure.positions[0],
structure.positions[0],
atol=1e-4).all()
os.system('rm ./POSCAR')
os.system('rm ./POSCAR.bak')
def test_structure_parsing(poscar):
structure = dft_input_to_structure(poscar)
pmg_struct = Poscar.from_file(poscar).structure
assert len(structure.species_labels) == len(pmg_struct)
assert (structure.cell == pmg_struct.lattice.matrix).all()
for i, spec in enumerate(structure.species_labels):
assert spec == pmg_struct[i].specie.symbol
assert np.isclose(structure.positions, pmg_struct.cart_coords).all()
def test_vasp_calling_fail(cmd, poscar):
structure = dft_input_to_structure(poscar)
with raises(FileNotFoundError):
_ = run_dft('.', cmd, structure=structure, en=False)
def test_input_to_structure(poscar):
assert isinstance(dft_input_to_structure(poscar), Structure)