def test_to_hdf(self):
if sys.version_info[0] >= 3:
filename = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../../static/dft/test_es_hdf.h5",
)
abs_filename = os.path.abspath(filename)
hdf_obj = FileHDFio(abs_filename)
es_obj_old = self.es_list[1]
es_obj_old.to_hdf(hdf_obj, group_name="written_es")
es_obj_new = ElectronicStructure()
es_obj_new.from_hdf(hdf=hdf_obj, group_name="written_es")
self.assertTrue(
np.array_equal(
hdf_obj["written_es/dos/grand_dos_matrix"],
es_obj_old.grand_dos_matrix,
))
self.assertEqual(es_obj_old.efermi, es_obj_new.efermi)
self.assertEqual(es_obj_old.is_metal, es_obj_new.is_metal)
self.assertEqual(es_obj_old.vbm, es_obj_new.vbm)
self.assertEqual(es_obj_old.cbm, es_obj_new.cbm)
self.assertTrue(
np.array_equal(es_obj_new.grand_dos_matrix,
es_obj_old.grand_dos_matrix))
self.assertTrue(
np.array_equal(es_obj_new.resolved_densities,
es_obj_old.resolved_densities))
def from_file(self, filename):
with open(filename, "r") as f:
es_obj = ElectronicStructure()
lines = f.readlines()
details_trigger = "# of k-points:"
details_ready = False
kpoint_trigger = "k-point"
band_trigger = "band"
num_atoms = 0
for i, line in enumerate(lines):
line = line.strip()
if details_trigger in line:
num_kpts, num_bands, num_atoms = self._get_details(line)
details_ready = True
if details_ready:
if kpoint_trigger in line.split():
kpt, weight = self._get_kpoint_details(line)
es_obj.add_kpoint(value=kpt, weight=weight)
if band_trigger in line.split():
eigenvalue, occupancy = self._get_band_details(line)
es_obj.kpoints[-1].add_band(eigenvalue=eigenvalue,
occupancy=occupancy)
band_obj = es_obj.kpoints[-1].bands[-1]
band_obj.resolved_dos_matrix, band_obj.orbital_resolved_dos, band_obj.atom_resolved_dos = self._get_dos_matrix(
lines[i + 2:i + num_atoms + 4])
return es_obj
def get_electronic_structure(self):
"""
Gets the electronic structure instance from the hdf5 file
Returns:
pyiron.atomistics.waves.electronic.ElectronicStructure instance
"""
if self.status not in ["finished", "warning", "not_converged"]:
return
else:
with self.project_hdf5.open("output") as ho:
es_obj = ElectronicStructure()
es_obj.from_hdf(ho)
return es_obj
def setUpClass(cls):
cls.es_list = list()
cls.es_obj = ElectronicStructure()
file_list = ["vasprun_1.xml", "vasprun_2.xml"]
for f in file_list:
vp = Vasprun()
direc = os.path.abspath(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../../static/vasp_test_files/vasprun_samples"))
filename = posixpath.join(direc, f)
vp.from_file(filename)
es = vp.get_electronic_structure()
cls.es_list.append(es)
def test_from_hdf(self):
filename = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../../static/dft/es_hdf.h5")
abs_filename = os.path.abspath(filename)
hdf_obj = FileHDFio(abs_filename)
es_obj_old = ElectronicStructure()
es_obj_old.from_hdf_old(hdf_obj, "es_old")
es_obj_new = ElectronicStructure()
es_obj_new.from_hdf(hdf=hdf_obj, group_name="es_new")
self.assertEqual(es_obj_old.efermi, es_obj_new.efermi)
self.assertEqual(es_obj_old.is_metal, es_obj_new.is_metal)
self.assertEqual(es_obj_old.vbm, es_obj_new.vbm)
self.assertEqual(es_obj_old.cbm, es_obj_new.cbm)
self.assertTrue(
np.array_equal(es_obj_new.grand_dos_matrix,
es_obj_old.grand_dos_matrix))
def get_electronic_structure(self):
"""
Get's the electronic structure from the VASP calculation
Returns:
pyiron.atomistics.waves.electronic.ElectronicStructure: The electronic structure object
"""
es_obj = ElectronicStructure()
es_obj.kpoint_list = self.vasprun_dict["kpoints"]["kpoint_list"]
es_obj.kpoint_weights = self.vasprun_dict["kpoints"]["kpoint_weights"]
es_obj.eigenvalue_matrix = self.vasprun_dict[
"grand_eigenvalue_matrix"][0, :, :]
es_obj.occupancy_matrix = self.vasprun_dict["grand_occupancy_matrix"][
0, :, :]
if "grand_dos_matrix" in self.vasprun_dict.keys():
es_obj.grand_dos_matrix = self.vasprun_dict["grand_dos_matrix"]
if "efermi" in self.vasprun_dict.keys():
es_obj.efermi = self.vasprun_dict["efermi"]
if "spin_dos_energies" in self.vasprun_dict.keys():
es_obj.dos_energies = self.vasprun_dict["spin_dos_energies"][0]
es_obj.dos_densities = self.vasprun_dict["spin_dos_density"]
es_obj.dos_idensities = self.vasprun_dict["spin_dos_idensity"]
if "resolved_dos_matrix" in self.vasprun_dict.keys():
es_obj.resolved_densities = self.vasprun_dict[
"resolved_dos_matrix"]
es_obj.orbital_dict = self.vasprun_dict["orbital_dict"]
es_obj.generate_from_matrices()
return es_obj