/
test_vasp.py
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/
test_vasp.py
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# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
import unittest
import os
import posixpath
from pyiron.atomistics.structure.atoms import CrystalStructure
from pyiron.vasp.base import Input, Output
from pyiron_base import ProjectHDFio, Project
from pyiron.vasp.potential import VaspPotentialSetter
from pyiron.vasp.vasp import Vasp
from pyiron.vasp.metadyn import VaspMetadyn
from pyiron.vasp.structure import read_atoms
import numpy as np
__author__ = "Sudarsan Surendralal"
class TestVasp(unittest.TestCase):
"""
Tests the pyiron.objects.hamilton.dft.vasp.Vasp class
"""
@classmethod
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "test_vasp"))
cls.job = cls.project.create_job("Vasp", "trial")
cls.job_spin = cls.project.create_job("Vasp", "spin")
cls.job_spin.structure = CrystalStructure("Fe", BravaisBasis="bcc", a=2.83)
cls.job_spin.structure = cls.job_spin.structure.repeat(2)
cls.job_spin.structure[2] = "Se"
cls.job_spin.structure[3] = "O"
cls.job_metadyn = cls.project.create_job("VaspMetadyn", "trial_metadyn")
cls.job_complete = Vasp(
project=ProjectHDFio(project=cls.project, file_name="vasp_complete"),
job_name="vasp_complete",
)
poscar_file = posixpath.join(
cls.execution_path, "../static/vasp_test_files/full_job_sample/POSCAR"
)
cls.job_complete.structure = read_atoms(poscar_file, species_from_potcar=True)
poscar_file = posixpath.join(
cls.execution_path, "../static/vasp_test_files/poscar_samples/POSCAR_metadyn"
)
cls.job_metadyn.structure = read_atoms(poscar_file)
@classmethod
def tearDownClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(cls.execution_path, "test_vasp"))
project.remove_jobs_silently(recursive=True)
project.remove(enable=True)
def setUp(self):
self.job.structure = None
def test_list_potentials(self):
self.assertEqual(sorted([
'Fe', 'Fe_GW', 'Fe_pv', 'Fe_sv', 'Fe_sv_GW', 'Se', 'Se_GW',
'O', 'O_GW', 'O_GW_new', 'O_h', 'O_s', 'O_s_GW'
]), sorted(self.job_spin.list_potentials()))
self.assertEqual(
sorted(['Fe', 'Fe_GW', 'Fe_pv', 'Fe_sv', 'Fe_sv_GW']),
sorted(self.job_complete.list_potentials())
)
self.job_spin.potential["Fe"] = 'Fe_sv_GW'
self.job_complete.potential.Fe = 'Fe_sv_GW'
self.assertEqual('Fe_sv_GW', list(self.job_spin.potential.to_dict().values())[0])
self.assertEqual('Fe_sv_GW', list(self.job_complete.potential.to_dict().values())[0])
self.job_complete.potential["Fe"] = 'Fe'
self.job_spin.potential.Fe = 'Fe'
def test_init(self):
self.assertEqual(self.job.__name__, "Vasp")
self.assertEqual(self.job._sorted_indices, None)
self.assertIsInstance(self.job.input, Input)
self.assertIsInstance(self.job._output_parser, Output)
self.assertIsInstance(self.job._potential, VaspPotentialSetter)
self.assertTrue(self.job._compress_by_default)
self.assertEqual(self.job.get_eddrmm_handling(), "warn")
self.assertIsInstance(self.job_metadyn, Vasp)
self.assertIsInstance(self.job_metadyn, VaspMetadyn)
self.assertTrue(self.job_metadyn.input.incar["LBLUEOUT"])
def test_eddrmm(self):
self.job.set_eddrmm_handling("ignore")
self.assertEqual(self.job.get_eddrmm_handling(), "ignore")
self.job.set_eddrmm_handling("restart")
self.assertEqual(self.job.get_eddrmm_handling(), "restart")
self.job.set_eddrmm_handling()
self.assertEqual(self.job.get_eddrmm_handling(), "warn")
self.assertRaises(ValueError, self.job.set_eddrmm_handling, status="blah")
def test_rwigs(self):
rwigs_dict = {"Fe": 1.1, "Se": 2.2, "O": 3.3, "N": 4.4}
rwigs_dict_wrong_1 = {"Fe": "not a float", "Se": 2.2, "O": 3.3, "N": 4.4}
rwigs_dict_wrong_2 = {"Fe": 1.1}
self.assertIsNone(self.job_spin.get_rwigs())
self.assertRaises(AssertionError, self.job_spin.set_rwigs, rwigs_dict="not a dict")
self.assertRaises(ValueError, self.job_spin.set_rwigs, rwigs_dict=rwigs_dict_wrong_1)
self.assertRaises(ValueError, self.job_spin.set_rwigs, rwigs_dict=rwigs_dict_wrong_2)
self.job_spin.set_rwigs(rwigs_dict)
rwigs_dict_out = self.job_spin.get_rwigs()
for key in rwigs_dict_out.keys():
self.assertEqual(rwigs_dict_out[key], rwigs_dict[key])
def test_spin_constraints(self):
self.job_spin.spin_constraints = 1
self.assertTrue(self.job_spin.spin_constraints)
self.job_spin.spin_constraints = 2
self.assertTrue(self.job_spin.spin_constraints)
del self.job_spin.input.incar["I_CONSTRAINED_M"]
self.assertFalse(self.job_spin.spin_constraints)
def test_spin_constraint(self):
rwigs_dict = {"Fe": 1.1, "Se": 2.2, "O": 3.3, "N": 4.4}
self.assertRaises(
AssertionError,
self.job_spin.set_spin_constraint,
lamb=0.5,
rwigs_dict=rwigs_dict,
direction="not a bool",
norm=False
)
self.assertRaises(
AssertionError,
self.job_spin.set_spin_constraint,
lamb=0.5,
rwigs_dict=rwigs_dict,
direction=True,
norm="not a bool"
)
self.assertRaises(
AssertionError,
self.job_spin.set_spin_constraint,
lamb="not a float",
rwigs_dict=rwigs_dict,
direction=True,
norm=False
)
self.assertRaises(
ValueError,
self.job_spin.set_spin_constraint,
lamb=0.5,
rwigs_dict=rwigs_dict,
direction=False,
norm=False
)
self.assertRaises(
ValueError,
self.job_spin.set_spin_constraint,
lamb=0.5,
rwigs_dict=rwigs_dict,
direction=False,
norm=True
)
self.job_spin.set_spin_constraint(lamb=0.5, rwigs_dict=rwigs_dict, direction=True, norm=False)
self.assertEqual(self.job_spin.input.incar["LAMBDA"], 0.5)
self.assertEqual(self.job_spin.input.incar["I_CONSTRAINED_M"], 1)
rwigs_dict_out = self.job_spin.get_rwigs()
for key in rwigs_dict_out.keys():
self.assertEqual(rwigs_dict_out[key], rwigs_dict[key])
self.job_spin.set_spin_constraint(lamb=0.5, rwigs_dict=rwigs_dict, direction=True, norm=True)
self.assertEqual(self.job_spin.input.incar["I_CONSTRAINED_M"], 2)
def test_potential(self):
self.assertEqual(self.job.potential, self.job._potential)
def test_plane_wave_cutoff(self):
self.assertIsInstance(self.job.plane_wave_cutoff, (float, int, type(None)))
# self.assertIsInstance(self.job.plane_wave_cutoff, (float, int))
self.job.plane_wave_cutoff = 350
self.assertEqual(self.job.input.incar["ENCUT"], 350)
self.assertEqual(self.job.plane_wave_cutoff, 350)
self.assertEqual(self.job.plane_wave_cutoff, self.job.encut)
self.job.encut = 450
self.assertEqual(self.job.encut, 450)
self.assertEqual(self.job.input.incar["ENCUT"], 450)
self.assertEqual(self.job.plane_wave_cutoff, 450)
def test_exchange_correlation_functional(self):
self.assertEqual(self.job.exchange_correlation_functional, "GGA")
self.assertEqual(self.job.input.potcar["xc"], "GGA")
self.job.exchange_correlation_functional = "LDA"
self.assertEqual(self.job.exchange_correlation_functional, "LDA")
self.assertEqual(self.job.input.potcar["xc"], "LDA")
def test_get_nelect(self):
atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
self.job.structure = atoms
self.assertEqual(self.job.get_nelect(), 10)
def test_write_magmoms(self):
magmom = np.arange(8.)
magmom_ncl = np.zeros([8, 3])
magmom_ncl[:, 0] = magmom / 2
magmom_ncl[:, 1] = magmom
magmom_ncl[:, 2] = magmom ** 2
magmom_str = "0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0"
magmom_ncl_str =\
"0.0 0.0 0.0 0.5 1.0 1.0 1.0 2.0 4.0 1.5 3.0 9.0 " \
"2.0 4.0 16.0 2.5 5.0 25.0 3.0 6.0 36.0 3.5 7.0 49.0"
self.job.structure = CrystalStructure("Fe", BravaisBasis="bcc", a=2.83)
self.job.structure = self.job.structure.repeat(2)
self.job.structure.set_initial_magnetic_moments(magmom)
self.job.input.incar["ISPIN"] = 1
self.job.write_magmoms()
self.assertIsNone(self.job.input.incar["MAGMOM"])
self.assertEqual(self.job.input.incar["ISPIN"], 1)
del self.job.input.incar["ISPIN"]
self.job.write_magmoms()
self.assertEqual(self.job.input.incar["ISPIN"], 2)
self.assertEqual(self.job.input.incar["MAGMOM"], magmom_str)
del self.job.input.incar["MAGMOM"]
self.job.structure.set_initial_magnetic_moments(magmom_ncl)
self.job.set_spin_constraint(lamb=1.0, rwigs_dict={"Fe": 2.5}, direction=True, norm=True)
self.job.write_magmoms()
self.assertEqual(self.job.input.incar["LNONCOLLINEAR"], True)
self.assertEqual(self.job.input.incar["MAGMOM"], magmom_ncl_str)
self.assertEqual(self.job.input.incar["M_CONSTR"], magmom_ncl_str)
del self.job.input.incar["MAGMOM"]
del self.job.input.incar["M_CONSTR"]
del self.job.input.incar["LNONCOLLINEAR"]
del self.job.input.incar["RWIGS"]
self.assertRaises(ValueError, self.job.write_magmoms)
self.job.input.incar["RWIGS"] = "2.5"
del self.job.input.incar["LAMBDA"]
self.assertRaises(ValueError, self.job.write_magmoms)
def test_set_empty_states(self):
atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
self.job.structure = atoms
self.job.set_empty_states(n_empty_states=10)
self.assertEqual(self.job.input.incar["NBANDS"], 15)
self.job.structure = atoms.repeat([3, 1, 1])
self.job.set_empty_states(n_empty_states=10)
self.assertEqual(self.job.input.incar["NBANDS"], 25)
def test_calc_static(self):
self.job.calc_static(
electronic_steps=90,
retain_charge_density=True,
retain_electrostatic_potential=True,
)
self.assertEqual(self.job.input.incar["IBRION"], -1)
self.assertEqual(self.job.input.incar["NELM"], 90)
self.assertEqual(self.job.input.incar["LVTOT"], True)
self.assertEqual(self.job.input.incar["LCHARG"], True)
def test_set_structure(self):
self.assertEqual(self.job.structure, None)
atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
self.job.structure = atoms
self.assertEqual(self.job.structure, atoms)
self.job.structure = None
self.assertEqual(self.job.structure, None)
self.job.structure = atoms
self.assertEqual(self.job.structure, atoms)
def test_list_potenitals(self):
self.assertRaises(ValueError, self.job.list_potentials)
def test_run_complete(self):
self.job_complete.exchange_correlation_functional = "PBE"
self.job_complete.set_occupancy_smearing(smearing="fermi", width=0.2)
self.job_complete.calc_static()
self.job_complete.set_convergence_precision(electronic_energy=1e-7)
self.job_complete.write_electrostatic_potential = False
self.assertEqual(self.job_complete.input.incar["SIGMA"], 0.2)
self.assertEqual(self.job_complete.input.incar["LVTOT"], False)
self.assertEqual(self.job_complete.input.incar["EDIFF"], 1e-7)
file_directory = posixpath.join(
self.execution_path, "../static/vasp_test_files/full_job_sample"
)
self.job_complete.restart_file_list.append(
posixpath.join(file_directory, "vasprun.xml")
)
self.job_complete.restart_file_list.append(
posixpath.join(file_directory, "OUTCAR")
)
self.job_complete.run(run_mode="manual")
self.job_complete.status.collect = True
self.job_complete.run()
nodes = [
"positions",
"temperature",
"energy_tot",
"steps",
"positions",
"forces",
"cells",
"pressures",
]
with self.job_complete.project_hdf5.open("output/generic") as h_gen:
hdf_nodes = h_gen.list_nodes()
self.assertTrue(all([node in hdf_nodes for node in nodes]))
nodes = [
"energy_free",
"energy_int",
"energy_zero",
"final_magmoms",
"magnetization",
"n_elect",
"scf_dipole_mom",
"scf_energy_free",
"scf_energy_int",
"scf_energy_zero",
]
with self.job_complete.project_hdf5.open("output/generic/dft") as h_dft:
hdf_nodes = h_dft.list_nodes()
self.assertTrue(all([node in hdf_nodes for node in nodes]))
nodes = ["efermi", "eig_matrix", "k_points", "k_weights", "occ_matrix"]
with self.job_complete.project_hdf5.open(
"output/electronic_structure"
) as h_dft:
hdf_nodes = h_dft.list_nodes()
self.assertTrue(all([node in hdf_nodes for node in nodes]))
job_chg_den = self.job_complete.restart_from_charge_density(job_name="chg")
self.assertEqual(job_chg_den.structure, self.job_complete.get_structure(-1))
self.assertTrue(
posixpath.join(self.job_complete.working_directory, "CHGCAR")
in job_chg_den.restart_file_list
)
with job_chg_den.project_hdf5.open("output") as h_out:
self.assertTrue(h_out.list_nodes() == [])
self.assertTrue(h_out.list_groups() == [])
with job_chg_den.project_hdf5.open("input") as h_in:
self.assertFalse(h_in.list_nodes() == [])
self.assertFalse(h_in.list_groups() == [])
job_wave = self.job_complete.restart_from_wave_functions(job_name="wave")
self.assertEqual(job_wave.structure, self.job_complete.get_structure(-1))
self.assertTrue(
posixpath.join(self.job_complete.working_directory, "WAVECAR")
in job_wave.restart_file_list
)
with job_wave.project_hdf5.open("output") as h_out:
self.assertTrue(h_out.list_nodes() == [])
self.assertTrue(h_out.list_groups() == [])
with job_wave.project_hdf5.open("input") as h_in:
self.assertFalse(h_in.list_nodes() == [])
self.assertFalse(h_in.list_groups() == [])
job_chg_wave = self.job_complete.restart_from_wave_and_charge(
job_name="chg_wave"
)
self.assertEqual(job_chg_wave.structure, self.job_complete.get_structure(-1))
self.assertTrue(
posixpath.join(self.job_complete.working_directory, "WAVECAR")
in job_chg_wave.restart_file_list
)
self.assertTrue(
posixpath.join(self.job_complete.working_directory, "CHGCAR")
in job_chg_wave.restart_file_list
)
for key, val in job_chg_wave.restart_file_dict.items():
self.assertTrue(key, val)
with job_chg_wave.project_hdf5.open("output") as h_out:
self.assertTrue(h_out.list_nodes() == [])
self.assertTrue(h_out.list_groups() == [])
with job_chg_wave.project_hdf5.open("input") as h_in:
self.assertFalse(h_in.list_nodes() == [])
self.assertFalse(h_in.list_groups() == [])
def test_vasp_metadyn(self):
self.job_metadyn.set_primitive_constraint("bond_1", "bond", atom_indices=[0, 2], increment=1e-4)
self.job_metadyn.set_primitive_constraint("bond_2", "bond", atom_indices=[0, 3], increment=1e-4)
self.job_metadyn.set_complex_constraint("combine", "linear_combination", {"bond_1": 1, "bond_2": -1},
increment=1e-4)
self.job_metadyn.write_constraints()
constraints = self.job_metadyn.input.iconst._dataset["Value"]
for val in ['R 1 6 0', 'R 1 2 0', 'S 1 -1 0']:
self.assertTrue(val in constraints)
def test_setting_input(self):
self.job.set_convergence_precision(electronic_energy=1e-7, ionic_force_tolerance=0.1)
self.assertEqual(self.job.input.incar["EDIFF"], 1e-7)
self.assertEqual(self.job.input.incar["EDIFFG"], -0.1)
self.job.calc_minimize()
self.assertEqual(self.job.input.incar["EDIFFG"], -0.01)
self.job.calc_minimize(ionic_energy=1e-4)
self.assertEqual(self.job.input.incar["EDIFFG"], 0.0001)
self.job.calc_minimize(ionic_forces=1e-3)
self.assertEqual(self.job.input.incar["EDIFFG"], -0.001)
self.assertEqual(self.job.input.incar["EDIFF"], 1e-7)
if __name__ == "__main__":
unittest.main()