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test_vasprun.py
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test_vasprun.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
import numpy as np
from pyiron.vasp.vasprun import Vasprun, VasprunError
from pyiron.atomistics.structure.atoms import Atoms
from pyiron.dft.waves.electronic import ElectronicStructure
__author__ = "surendralal"
class TestVasprun(unittest.TestCase):
"""
Testing the Vasprun() module.
"""
@classmethod
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.vp_list = list()
cls.direc = os.path.join(
cls.file_location, "../static/vasp_test_files/vasprun_samples"
)
file_list = sorted(os.listdir(cls.direc))
del file_list[file_list.index("vasprun_spoilt.xml")]
cls.num_species = [3, 1, 2, 2, 3, 4, 4, 2]
for f in file_list:
vp = Vasprun()
filename = posixpath.join(cls.direc, f)
vp.from_file(filename)
cls.vp_list.append(vp)
def test_from_file(self):
vp = Vasprun()
filename = posixpath.join(self.direc, "vasprun_spoilt.xml")
self.assertRaises(VasprunError, vp.from_file, filename)
def test_parse_generator(self):
for vp in self.vp_list:
self.assertIsInstance(vp.vasprun_dict["generator"], dict)
self.assertTrue("program" in vp.vasprun_dict["generator"].keys())
self.assertTrue("version" in vp.vasprun_dict["generator"].keys())
self.assertTrue("time" in vp.vasprun_dict["generator"].keys())
self.assertTrue("subversion" in vp.vasprun_dict["generator"].keys())
self.assertTrue("platform" in vp.vasprun_dict["generator"].keys())
self.assertTrue("date" in vp.vasprun_dict["generator"].keys())
def test_parse_incar(self):
for vp in self.vp_list:
self.assertIsInstance(vp.vasprun_dict["incar"], dict)
def test_parse_kpoints(self):
for vp in self.vp_list:
d = vp.vasprun_dict["kpoints"]
self.assertIsInstance(d, dict)
self.assertIsInstance(d["generation"], dict)
if d["generation"]["scheme"] in ["Monkhorst-Pack", "Gamma"]:
self.assertIsInstance(d["generation"]["divisions"], np.ndarray)
self.assertIsInstance(d["generation"]["genvec"], np.ndarray)
self.assertIsInstance(d["generation"]["shift"], np.ndarray)
self.assertIsInstance(d["generation"]["usershift"], np.ndarray)
self.assertTrue(len(d["generation"]["divisions"]) == 3)
self.assertTrue(len(d["generation"]["genvec"]) == 3)
self.assertTrue(len(d["generation"]["genvec"].T) == 3)
self.assertTrue(len(d["generation"]["shift"]) == 3)
self.assertTrue(len(d["generation"]["usershift"]) == 3)
if d["generation"]["scheme"] in ["listgenerated"]:
self.assertIsInstance(d["line_mode_kpoints"], np.ndarray)
self.assertTrue(len(d["line_mode_kpoints"][-1]), 3)
self.assertIsInstance(d["kpoint_list"], np.ndarray)
self.assertIsInstance(d["kpoint_weights"], np.ndarray)
self.assertEqual(len(d["kpoint_list"]), len(d["kpoint_weights"]))
self.assertTrue(len(d["kpoint_list"].T) == 3)
self.assertIsInstance(d["kpoint_weights"][-1], (float, np.float))
def test_parse_atom_info(self):
for vp in self.vp_list:
d = vp.vasprun_dict["atominfo"]
self.assertIsInstance(d, dict)
self.assertIsInstance(d["species_dict"], dict)
self.assertIsInstance(d["species_list"], list)
n_atoms = 0
for key, value in d["species_dict"].items():
n_atoms += d["species_dict"][key]["n_atoms"]
self.assertEqual(n_atoms, len(d["species_list"]))
def test_parse_structure(self):
for vp in self.vp_list:
for pos_tag in ["init_structure", "final_structure"]:
d = vp.vasprun_dict[pos_tag]
self.assertIsInstance(d["positions"], np.ndarray)
if "selective_dynamics" in d.keys():
self.assertIsInstance(d["selective_dynamics"], np.ndarray)
def test_parse_sc_step(self):
for vp in self.vp_list:
d = vp.vasprun_dict
self.assertIsInstance(d["scf_energies"], list)
self.assertIsInstance(d["scf_dipole_moments"], list)
def test_parse_calc(self):
for vp in self.vp_list:
d = vp.vasprun_dict
self.assertIsInstance(d["positions"], np.ndarray)
self.assertIsInstance(d["forces"], np.ndarray)
self.assertIsInstance(d["cells"], np.ndarray)
self.assertEqual(len(d["cells"]), len(d["positions"]))
self.assertEqual(len(d["forces"]), len(d["positions"]))
self.assertEqual(len(d["total_energies"]), len(d["positions"]))
self.assertEqual(len(d["forces"]), len(d["scf_energies"]))
self.assertEqual(len(d["forces"]), len(d["scf_dipole_moments"]))
self.assertEqual(len(d["forces"].T), 3)
self.assertEqual(len(d["positions"].T), 3)
self.assertFalse(len(d["positions"][d["positions"] > 1.01]) > 0)
self.assertFalse(np.max(d["positions"]) > 1.01)
self.assertEqual(np.shape(d["cells"][0]), np.shape(np.eye(3)))
self.assertIsInstance(d["grand_eigenvalue_matrix"], np.ndarray)
self.assertIsInstance(d["grand_occupancy_matrix"], np.ndarray)
self.assertEqual(
np.shape(d["grand_occupancy_matrix"]),
np.shape(d["grand_eigenvalue_matrix"]),
)
[n_spin, n_kpts, n_bands] = np.shape(d["grand_occupancy_matrix"])
self.assertEqual(len(d["kpoints"]["kpoint_list"]), n_kpts)
self.assertEqual(len(d["kpoints"]["kpoint_list"]), n_kpts)
self.assertGreaterEqual(n_spin, 1)
self.assertGreaterEqual(n_bands, 1)
def test_pdos_parser(self):
for vp in self.vp_list:
d = vp.vasprun_dict
if "efermi" in d.keys():
self.assertIsInstance(d["efermi"], float)
if "grand_dos_matrix" in d.keys():
[n_spin0, n_kpts0, n_bands0] = np.shape(d["grand_occupancy_matrix"])
[n_spin, n_kpts, n_bands, n_atoms, n_orbitals] = np.shape(
d["grand_dos_matrix"]
)
self.assertEqual(len(d["kpoints"]["kpoint_list"]), n_kpts)
self.assertEqual(len(d["positions"][0]), n_atoms)
self.assertEqual(n_spin, n_spin0)
self.assertEqual(n_bands, n_bands0)
self.assertEqual(n_kpts, n_kpts0)
self.assertIsInstance(d["grand_dos_matrix"], np.ndarray)
self.assertIsInstance(d["orbital_dict"], dict)
self.assertEqual(len(d["orbital_dict"].keys()), n_orbitals)
def test_parse_parameters(self):
for vp in self.vp_list:
d = vp.vasprun_dict
self.assertIsInstance(d, dict)
def test_get_initial_structure(self):
for vp in self.vp_list:
basis = vp.get_initial_structure()
self.assertIsInstance(basis, Atoms)
self.assertTrue(np.max(basis.get_scaled_positions()) < 1.01)
def test_get_final_structure(self):
for vp in self.vp_list:
basis = vp.get_final_structure()
self.assertIsInstance(basis, Atoms)
self.assertTrue(np.max(basis.get_scaled_positions()) < 1.01)
self.assertFalse(np.max(basis.positions) < 1.01)
def test_get_electronic_structure(self):
for vp in self.vp_list:
es_obj = vp.get_electronic_structure()
self.assertIsInstance(es_obj, ElectronicStructure)
if "grand_dos_matrix" in vp.vasprun_dict.keys():
[_, n_kpts, n_bands, _, _] = np.shape(
vp.vasprun_dict["grand_dos_matrix"]
)
self.assertEqual(len(es_obj.kpoints), n_kpts)
self.assertEqual(len(es_obj.kpoints[0].bands), n_bands)
def test_species_info(self):
for i, vp in enumerate(self.vp_list):
self.assertEqual(
len(vp.vasprun_dict["atominfo"]["species_dict"].keys()),
self.num_species[i],
)
self.assertEqual(
vp.get_initial_structure().get_number_of_species(), self.num_species[i]
)
self.assertEqual(
vp.get_final_structure().get_number_of_species(), self.num_species[i]
)
if __name__ == "__main__":
unittest.main()