def _parser_function(self):
"""
Parses the vasprun.xml using the Pymatgen Vasprun function.
"""
vasp_param = {} # ParameterData
parser_warnings = {} # return non-critical errors
vspr = vasp.Vasprun(self._out_folder.get_abs_path('vasprun.xml'),
exception_on_bad_xml=False)
# vasp_param['final_energy'] = vspr.final_energy # This includes PV
vasp_param['energy'] = vspr.ionic_steps[-1]['electronic_steps'][-1][
'e_wo_entrp'] # Pure internal energy (U) as appear in OUTCAR
# construct proper output format
try:
nodes_list = []
parameter_data = ParameterData(dict=vasp_param)
nodes_list.append(('output_parameters', parameter_data))
except Exception, e:
msg = ("Failed to create AiiDA data structures "
"(ParameterData/ArrrayData) from parsed data, "
"with error message:\n>> {}".format(e))
raise OutputParsingError(msg)
def _parser_function(self):
"""
Parses the vasprun.xml using the Pymatgen Vasprun function.
"""
vasp_param = {} # ParameterData
vasp_array = {} # ArrayData
parser_warnings = {} # return non-critical errors
# parameter data keys
_vasprun_keys = [ # directly accessible, by name
# logical
'converged',
'converged_electronic',
'converged_ionic',
'dos_has_errors',
'is_spin',
'is_hubbard',
# value
'efermi'
]
_vasprun_special_keys = [ # can't be accessed directly
# logical
'is_band_gap_direct',
# value
'no_ionic_steps',
'final_energy', # returned as FloatWithUnit
'energy_units',
'free_energy',
'energy_wo_entropy',
'energy_T0',
'entropy_TS',
'no_electronic_steps',
'total_no_electronic_steps',
'band_gap',
'cbm',
'vbm',
]
# array data keys
# TODO
# list --> array; see what exactly ArrayData supports
# parsing output files
try:
vspr = vasp.Vasprun(self._out_folder.get_abs_path('vasprun.xml'))
except Exception, e:
msg = ("Parsing vasprun file in pymatgen failed, "
"with error message:\n>> {}".format(e))
raise OutputParsingError(msg)
def _parser_function(self):
"""
Parses the vasprun.xml using the Pymatgen Vasprun function.
"""
vasp_param = {} # ParameterData
parser_warnings = {} # return non-critical errors
# extract data
try:
with open(self._out_folder.get_abs_path('OUTCAR'), 'r') as f:
text = f.readlines()
except:
print('Error opening')
try:
vspr = vasp.Vasprun(self._out_folder.get_abs_path('vasprun.xml'))
vasp_param['energy'] = vspr.final_energy
# vasp_param['volume'] = vspr.final_structure.lattice.volume #Not here!, not necessary
except Exception, e:
msg = ("Parsing vasprun file in pymatgen failed, "
"with error message:\n>> {}".format(e))
raise OutputParsingError(msg)
def __init__(self,
calcdir,
verbose=True,
read_bands=True,
save_pcalc=False):
""" Note that for memory reasons we do not store pcalc or procar as instance variables.
"""
self.calcdir = calcdir
self.calc = ase.io.read(join(calcdir, 'CONTCAR'))
if verbose: sys.stdout.write('Reading vasprun.xml and bands... ')
pcalc = pyvasp.Vasprun(join(calcdir, 'vasprun.xml'))
if save_pcalc: self.pcalc = pcalc
self.band_gap, self.vbm, self.cbm, self.is_direct = pcalc.eigenvalue_band_properties
if read_bands:
self.bands = pcalc.get_band_structure(join(calcdir, 'KPOINTS'),
line_mode=True)
self.nkpts = len(self.bands.kpoints)
self.nbands = self.bands.nb_bands
if verbose: sys.stdout.write('Reading procar... ')
procar = pyvasp.Procar(join(calcdir, 'PROCAR')) # projected bands
self.bigprocar = self._get_pandas_from_procar(procar)
if verbose: sys.stdout.write('Converting to Pandas... ')
self.bigdos = self._get_bigdos_from_pcalc(pcalc)
self.totdos = self.get_dos_contrib() # Get the total dos
#Other useful information
self.natoms = self.calc.get_number_of_atoms()
self.unscaled_energies = pcalc.tdos.energies
self.scaled_energies = pcalc.tdos.energies - pcalc.efermi
self.emin = self.scaled_energies[0]
self.emax = self.scaled_energies[-1]
self.efermi = pcalc.complete_dos.efermi
self.energy = pcalc.final_energy
if verbose: sys.stdout.write('DONE! :)')
get various data from vasprun.xml
Parameters
----------
vasprun : pymatgen.io.vasp.Vasprun class object
"""
summary = {}
summary['final_energy'] = float(vasprun['output']['final_energy'])
summary['final_energy_per_atom'] = float(
vasprun['output']['final_energy_per_atom'])
summary['volume'] = vasprun['output']['crystal']['lattice']['volume']
kpt = vasprun['input']['kpoints']['kpoints'][0]
summary['total_kpoints'] = kpt[0] * kpt[1] * kpt[2]
summary['kpoints'] = [kpt[0], kpt[1], kpt[2]]
summary['nkpoints'] = vasprun['input']['nkpoints']
summary['encut'] = vasprun['input']['parameters']['ENCUT']
summary['correlation_function'] = vasprun['run_type']
ion_steps = []
### vasprun.xml
vasprun_files = args.vasprun_file.split()
vaspruns = []
for vasprun_file in vasprun_files:
check_file_exist(vasprun_file)
vasprun = pmg_vasp.Vasprun(vasprun_file)
vaspruns.append(vasprun)
_check_single_vasprun_file(vasprun_files)
#!/usr/bin/env python3
from pymatgen.io import vasp
import numpy as np
from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer
import pymatgen
run = vasp.Vasprun('vasprun.xml')
outcar = vasp.Outcar('OUTCAR')
st = run.final_structure
symbols = np.array([x.value for x in st.species])
sa = SpacegroupAnalyzer(st)
print('**************')
print("conventional cell")
print(sa.get_conventional_standard_structure())
print(sa.get_conventional_standard_structure().volume)
print(sa.get_space_group_symbol(), sa.get_space_group_number())
print("******************")
print("Final structure")
print(run.final_structure)
print("vol={}".format(run.final_structure.volume))
print("******************")
print("Bandgap information")
print(run.get_band_structure().get_band_gap())
print("******************")
print("Magnetzation per site")
for ielement in range(len(symbols)):
print("{}-{} {}".format(symbols[ielement], ielement,
outcar.magnetization[ielement]['tot']))
print("******************")
print("Magnetzation per species")
def __init__(self, filename, vasprun='vasprun.xml', fermi=0):
self.readfile(filename)
self.fermi=fermi
self.vasprun = vasp.Vasprun(vasprun)