"""This module defines an ASE interface to VASP.
The path of the directory containing the pseudopotential
directories (potpaw,potpaw_GGA, potpaw_PBE, ...) should be set
by the environmental flag $VASP_PP_PATH.
The user should also set one of the following environmental flags, which
instructs ASE on how to execute VASP: $ASE_VASP_COMMAND, $VASP_COMMAND, or
$VASP_SCRIPT.
The user can set the environmental flag $VASP_COMMAND pointing
to the command use the launch vasp e.g. 'vasp_std' or 'mpirun -n 16 vasp_std'
Alternatively, the user can also set the environmental flag
$VASP_SCRIPT pointing to a python script looking something like::
import os
exitcode = os.system('vasp_std')
www.vasp.at
"""
from __future__ import print_function, division
import os
import sys
import re
import numpy as np
import subprocess
from contextlib import contextmanager
from warnings import warn
import ase
from ase.io import read
from ase.utils import basestring
from ase.calculators.calculator import (FileIOCalculator, ReadError,
all_changes)
from ase.calculators.vasp.create_input import GenerateVaspInput
[docs]class Vasp2(GenerateVaspInput, FileIOCalculator):
"""ASE interface for the Vienna Ab initio Simulation Package (VASP),
with the FileIOCalculator interface.
Parameters:
atoms: object
Attach an atoms object to the calculator.
label: str
Prefix for the output file, and sets the working directory.
Default is 'vasp'.
directory: str
Set the working directory. Is prepended to ``label``.
restart: str or bool
Sets a label for the directory to load files from.
if :code:`restart=True`, the working directory from
``label`` is used.
txt: bool, None, str or writable object
- If txt is None, default ouput stream will be to PREFIX.out,\
where PREFIX is determined by ``label``, i.e. the default\
would be vasp.out.
- If txt is False or '-' the output will be sent through stdout
- If txt is a string a file will be opened,\
and the output will be sent to that file.
- Finally, txt can also be a an output stream,\
which has a 'write' attribute.
- Example:
>>> Vasp2(label='mylabel', txt=None) # Redirect stdout to :file:`mylabel.out`
>>> Vasp2(txt='myfile.txt') # Redirect stdout to :file:`myfile.txt`
>>> Vasp2(txt='-') # Print vasp output to stdout
command: str
Custom instructions on how to execute VASP. Has priority over
environment variables.
"""
name = 'Vasp2'
# Environment commands
env_commands = ['ASE_VASP_COMMAND', 'VASP_COMMAND', 'VASP_SCRIPT']
implemented_properties = ['energy', 'free_energy', 'forces', 'dipole',
'fermi', 'stress', 'magmom', 'magmoms']
default_parameters = {} # Can be used later to set some ASE defaults
def __init__(self,
atoms=None,
restart=None,
directory='',
label='vasp',
ignore_bad_restart_file=False,
command=None,
txt=None,
**kwargs):
# Initialize parameter dictionaries
GenerateVaspInput.__init__(self)
self._store_param_state() # Initialize an empty parameter state
# Store atoms objects from vasprun.xml here - None => uninitialized
self._xml_data = None
label = os.path.join(directory, label)
if restart is True:
# We restart in the label directory
restart = label
FileIOCalculator.__init__(self, restart, ignore_bad_restart_file,
label, atoms, command, **kwargs)
self.command = command
self.set_txt(txt) # Set the output txt stream
# XXX: This seems to break restarting, unless we return first.
# Do we really still need to enfore this?
# # If no XC combination, GGA functional or POTCAR type is specified,
# # default to PW91. This is mostly chosen for backwards compatiblity.
# if kwargs.get('xc', None):
# pass
# elif not (kwargs.get('gga', None) or kwargs.get('pp', None)):
# self.input_params.update({'xc': 'PW91'})
# # A null value of xc is permitted; custom recipes can be
# # used by explicitly setting the pseudopotential set and
# # INCAR keys
# else:
# self.input_params.update({'xc': None})
def make_command(self, command=None):
"""Return command if one is passed, otherwise try to find
ASE_VASP_COMMAND, VASP_COMMAND or VASP_SCRIPT.
If none are set, a RuntimeError is raised"""
if command:
cmd = command
else:
# Search for the environment commands
for env in self.env_commands:
if env in os.environ:
cmd = os.environ[env].replace('PREFIX', self.prefix)
if env == 'VASP_SCRIPT':
# Make the system python exe run $VASP_SCRIPT
exe = sys.executable
cmd = ' '.join([exe, cmd])
break
else:
msg = ('Please set either command in calculator'
' or one of the following environment'
'variables (prioritized as follows): {}').format(
', '.join(self.env_commands))
raise RuntimeError(msg)
return cmd
def set(self, **kwargs):
"""Override the set function, to test for changes in the
Vasp FileIO Calculator, then call the create_input.set()
on remaining inputs for VASP specific keys.
Allows for setting ``label``, ``directory`` and ``txt``
without resetting the results in the calculator.
"""
changed_parameters = {}
if 'label' in kwargs:
label = kwargs.pop('label')
self.set_label(label)
if 'directory' in kwargs:
# If we explicitly set directory, overwrite the one in label.
# XXX: Should we just raise an error here if clash?
directory = kwargs.pop('directory')
label = os.path.join(directory, self.prefix)
self.set_label(label)
if 'txt' in kwargs:
txt = kwargs.pop('txt')
self.set_txt(txt)
if 'atoms' in kwargs:
atoms = kwargs.pop('atoms')
self.set_atoms(atoms) # Resets results
changed_parameters.update(FileIOCalculator.set(self, **kwargs))
# We might at some point add more to changed parameters, or use it
if changed_parameters:
self.results.clear() # We don't want to clear atoms
if kwargs:
# If we make any changes to Vasp input, we always reset
GenerateVaspInput.set(self, **kwargs)
self.results.clear()
@contextmanager
def txt_outstream(self):
"""Custom function for opening a text output stream. Uses self.txt to determine
the output stream, and accepts a string or an open writable object.
If a string is used, a new stream is opened, and automatically closes
the new stream again when exiting.
Examples:
# Pass a string
calc.set_txt('vasp.out')
with calc.txt_outstream() as out:
calc.run(out=out) # Redirects the stdout to 'vasp.out'
# Use an existing stream
mystream = open('vasp.out', 'w')
calc.set_txt(mystream)
with calc.txt_outstream() as out:
calc.run(out=out)
mystream.close()
# Print to stdout
calc.set_txt(False)
with calc.txt_outstream() as out:
calc.run(out=out) # output is written to stdout
"""
opened = False # Track if we opened a file
out = None # Default
if self.txt:
if isinstance(self.txt, basestring):
out = open(self.txt, 'w')
opened = True
elif hasattr(self.txt, 'write'):
out = self.txt
else:
raise RuntimeError('txt should either be a string'
'or an I/O stream, got {}'.format(
self.txt))
try:
yield out
finally:
if opened:
out.close()
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
"""Do a VASP calculation in the specified directory.
This will generate the necessary VASP input files, and then
execute VASP. After execution, the energy, forces. etc. are read
from the VASP output files.
"""
if atoms is not None:
self.atoms = atoms.copy()
self.check_cell() # Check for zero-length lattice vectors
self._xml_data = None # Reset the stored data
command = self.make_command(self.command)
self.write_input(self.atoms, properties, system_changes)
olddir = os.getcwd()
try:
os.chdir(self.directory)
# Create the text output stream and run VASP
with self.txt_outstream() as out:
errorcode = self._run(command=command, out=out)
finally:
os.chdir(olddir)
if errorcode:
raise RuntimeError('{} in {} returned an error: {:d}'.format(
self.name, self.directory, errorcode))
# Read results from calculation
self.update_atoms(atoms)
self.read_results()
def _run(self, command=None, out=None):
"""Method to explicitly execute VASP"""
if command is None:
command = self.command
errorcode = subprocess.call(command, shell=True, stdout=out)
return errorcode
def check_state(self, atoms, tol=1e-15):
"""Check for system changes since last calculation."""
def compare_dict(d1, d2):
"""Helper function to compare dictionaries"""
# Use symmetric difference to find keys which aren't shared
# for python 2.7 compatiblity
if set(d1.keys()) ^ set(d2.keys()):
return False
# Check for differences in values
for key, value in d1.items():
if np.any(value != d2[key]):
return False
return True
# First we check for default changes
system_changes = FileIOCalculator.check_state(self, atoms, tol=tol)
# We now check if we have made any changes to the input parameters
# XXX: Should we add these parameters to all_changes?
for param_string, old_dict in self.param_state.items():
param_dict = getattr(self, param_string) # Get current param dict
if not compare_dict(param_dict, old_dict):
system_changes.append(param_string)
return system_changes
def _store_param_state(self):
"""Store current parameter state"""
self.param_state = dict(
float_params=self.float_params.copy(),
exp_params=self.exp_params.copy(),
string_params=self.string_params.copy(),
int_params=self.int_params.copy(),
input_params=self.input_params.copy(),
bool_params=self.bool_params.copy(),
list_int_params=self.list_int_params.copy(),
list_bool_params=self.list_bool_params.copy(),
list_float_params=self.list_float_params.copy(),
dict_params=self.dict_params.copy())
def write_input(self, atoms, properties=['energies'],
system_changes=all_changes):
"""Write VASP inputfiles, INCAR, KPOINTS and POTCAR"""
# Create the folders where we write the files, if we aren't in the
# current working directory.
FileIOCalculator.write_input(self, atoms, properties, system_changes)
self.initialize(atoms)
GenerateVaspInput.write_input(self, atoms, directory=self.directory)
def read(self, label=None):
"""Read results from VASP output files.
Files which are read: OUTCAR, CONTCAR and vasprun.xml
Raises ReadError if they are not found"""
if label is None:
label = self.label
FileIOCalculator.read(self, label)
# If we restart, self.parameters isn't initialized
if self.parameters is None:
self.parameters = self.get_default_parameters()
# Check for existence of the necessary output files
for file in ['OUTCAR', 'CONTCAR', 'vasprun.xml']:
filename = os.path.join(self.directory, file)
if not os.path.isfile(filename):
raise ReadError(
'VASP outputfile {} was not found'.format(filename))
# Read atoms
self.atoms = self.read_atoms()
# Build sorting and resorting lists
self.read_sort()
# Read parameters
olddir = os.getcwd()
try:
os.chdir(self.directory)
self.read_incar()
self.read_kpoints()
self.read_potcar()
finally:
os.chdir(olddir)
# Read the results from the calculation
self.read_results()
def read_sort(self):
"""Create the sorting and resorting list from ase-sort.dat.
If the ase-sort.dat file does not exist, the sorting is redone.
"""
sortfile = os.path.join(self.directory, 'ase-sort.dat')
if os.path.isfile(sortfile):
self.sort = []
self.resort = []
with open(sortfile, 'r') as f:
for line in f:
sort, resort = line.split()
self.sort.append(int(sort))
self.resort.append(int(resort))
else:
# Redo the sorting
self.initialize(self.atoms)
def read_atoms(self, filename='CONTCAR'):
"""Read the atoms from file located in the VASP
working directory. Defaults to CONTCAR."""
filename = os.path.join(self.directory, filename)
return read(filename)
def update_atoms(self, atoms):
"""Update the atoms object with new positions and cell"""
if (self.int_params['ibrion'] is not None and
self.int_params['nsw'] is not None):
if self.int_params['ibrion'] > -1 and self.int_params['nsw'] > 0:
# Update atomic positions and unit cell with the ones read
# from CONTCAR.
atoms_sorted = read(os.path.join(self.directory, 'CONTCAR'))
atoms.positions = atoms_sorted[self.resort].positions
atoms.cell = atoms_sorted.cell
self.atoms = atoms.copy()
def check_cell(self, atoms=None):
"""Check if there is a zero unit cell"""
if not atoms:
atoms = self.atoms
if not atoms.cell.any():
raise ValueError("The lattice vectors are zero! "
"This is the default value - please specify a "
"unit cell.")
def read_results(self):
"""Read the results from VASP output files"""
# Temporarily load OUTCAR into memory
outcar = self.load_file('OUTCAR')
# Read the data we can from vasprun.xml
atoms_xml = self._read_from_xml()
xml_results = atoms_xml.calc.results
# Fix sorting
xml_results['forces'] = xml_results['forces'][self.resort]
self.results.update(xml_results)
# Parse the outcar, as some properties are not loaded in vasprun.xml
# We want to limit this as much as possible, as reading large OUTCAR's
# is relatively slow
# Removed for now
# self.read_outcar(lines=outcar)
# Update results dict with results from OUTCAR
# which aren't written to the atoms object we read from
# the vasprun.xml file.
self.converged = self.read_convergence(lines=outcar)
magmom, magmoms = self.read_mag(lines=outcar)
dipole = self.read_dipole(lines=outcar)
nbands = self.read_nbands(lines=outcar)
self.results.update(dict(magmom=magmom,
magmoms=magmoms,
dipole=dipole,
nbands=nbands))
# Stress is not always present.
# Prevent calculation from going into a loop
if 'stress' not in self.results:
self.results.update(dict(stress=None))
# Store keywords for backwards compatiblity
self.spinpol = self.get_spin_polarized()
self.version = self.get_version()
self.energy_free = self.get_potential_energy(force_consistent=True)
self.energy_zero = self.get_potential_energy(force_consistent=False)
self.forces = self.get_forces()
self.fermi = self.get_fermi_level()
self.dipole = self.get_dipole_moment()
# Prevent calculation from going into a loop
self.stress = self.get_property('stress', allow_calculation=False)
self.nbands = self.get_number_of_bands()
# Store the parameters used for this calculation
self._store_param_state()
# Below defines some functions for faster access to certain common keywords
@property
def kpts(self):
"""Access the kpts from input_params dict"""
return self.input_params['kpts']
@kpts.setter
def kpts(self, kpts):
"""Set kpts in input_params dict"""
self.input_params['kpts'] = kpts
@property
def encut(self):
"""Direct access to the encut parameter"""
return self.float_params['encut']
@encut.setter
def encut(self, encut):
"""Direct access for setting the encut parameter"""
self.set(encut=encut)
@property
def xc(self):
"""Direct access to the xc parameter"""
return self.get_xc_functional()
@xc.setter
def xc(self, xc):
"""Direct access for setting the xc parameter"""
self.set(xc=xc)
def set_atoms(self, atoms):
if self.check_state(atoms):
self.results.clear()
self.atoms = atoms.copy()
# Below defines methods for reading output files
def load_file(self, filename):
"""Reads a file in the directory, and returns the lines
Example:
>>> outcar = load_file('OUTCAR')
"""
filename = os.path.join(self.directory, filename)
with open(filename, 'r') as f:
return f.readlines()
@contextmanager
def load_file_iter(self, filename):
"""Return a file iterator"""
filename = os.path.join(self.directory, filename)
with open(filename, 'r') as f:
yield f
def read_outcar(self, lines=None):
"""Read results from the OUTCAR file.
Deprecated, see read_results()"""
if not lines:
lines = self.load_file('OUTCAR')
# Spin polarized calculation?
self.spinpol = self.get_spin_polarized()
self.version = self.get_version()
# XXX: Do we want to read all of this again?
self.energy_free, self.energy_zero = self.read_energy(lines=lines)
self.forces = self.read_forces(lines=lines)
self.fermi = self.read_fermi(lines=lines)
self.dipole = self.read_dipole(lines=lines)
self.stress = self.read_stress(lines=lines)
self.nbands = self.read_nbands(lines=lines)
self.read_ldau()
self.magnetic_moment, self.magnetic_moments = self.read_mag(lines=lines)
def _read_from_xml(self, filename='vasprun.xml', overwrite=False):
"""Read vasprun.xml, and return the last atoms object.
If we have not read the atoms object before, we will read the xml file
Parameters:
filename: str
Filename of the .xml file. Default value: 'vasprun.xml'
overwrite: bool
Force overwrite the existing data in xml_data
Default value: False
"""
if overwrite or not self._xml_data:
self._xml_data = read(os.path.join(self.directory,
filename),
index=-1)
return self._xml_data
def get_ibz_k_points(self):
atoms = self._read_from_xml()
return atoms.calc.ibz_kpts
def get_kpt(self, kpt=0, spin=0):
atoms = self._read_from_xml()
return atoms.calc.get_kpt(kpt=kpt, spin=spin)
def get_eigenvalues(self, kpt=0, spin=0):
atoms = self._read_from_xml()
return atoms.calc.get_eigenvalues(kpt=kpt, spin=spin)
def get_fermi_level(self):
atoms = self._read_from_xml()
return atoms.calc.get_fermi_level()
def get_homo_lumo(self):
atoms = self._read_from_xml()
return atoms.calc.get_homo_lumo()
def get_homo_lumo_by_spin(self, spin=0):
atoms = self._read_from_xml()
return atoms.calc.get_homo_lumo_by_spin(spin=spin)
def get_occupation_numbers(self, kpt=0, spin=0):
atoms = self._read_from_xml()
return atoms.calc.get_occupation_numbers(kpt, spin)
def get_spin_polarized(self):
atoms = self._read_from_xml()
return atoms.calc.get_spin_polarized()
def get_number_of_spins(self):
atoms = self._read_from_xml()
return atoms.calc.get_number_of_spins()
def get_number_of_bands(self):
return self.results['nbands']
def get_number_of_electrons(self, lines=None):
if not lines:
lines = self.load_file('OUTCAR')
nelect = None
for line in lines:
if 'total number of electrons' in line:
nelect = float(line.split('=')[1].split()[0].strip())
break
return nelect
def get_k_point_weights(self):
return self.read_k_point_weights()
def get_dos(self, spin=None, **kwargs):
"""
The total DOS.
Uses the ASE DOS module, and returns a tuple with
(energies, dos).
"""
from ase.dft.dos import DOS
dos = DOS(self, **kwargs)
e = dos.get_energies()
d = dos.get_dos(spin=spin)
return e, d
def get_version(self):
"""Get the VASP version number"""
# The version number is the first occurence, so we can just
# load the OUTCAR, as we will return soon anyway
with self.load_file_iter('OUTCAR') as lines:
for line in lines:
if ' vasp.' in line:
return line[len(' vasp.'):].split()[0]
else:
# We didn't find the verison in VASP
return None
def get_number_of_iterations(self):
return self.read_number_of_iterations()
def read_number_of_iterations(self):
niter = None
with self.load_file_iter('OUTCAR') as lines:
for line in lines:
# find the last iteration number
if '- Iteration' in line:
niter = list(map(int, re.findall(r'\d+', line)))[1]
return niter
def read_number_of_ionic_steps(self):
niter = None
with self.load_file_iter('OUTCAR') as lines:
for line in lines:
if '- Iteration' in line:
niter = list(map(int, re.findall(r'\d+', line)))[0]
return niter
def read_stress(self, lines=None):
"""Read stress from OUTCAR.
Depreciated: Use get_stress() instead.
"""
# We don't really need this, as we read this from vasprun.xml
# keeping it around "just in case" for now
if not lines:
lines = self.load_file('OUTCAR')
stress = None
for line in lines:
if ' in kB ' in line:
stress = -np.array([float(a) for a in line.split()[2:]])
stress = stress[[0, 1, 2, 4, 5, 3]] * 1e-1 * ase.units.GPa
return stress
def read_ldau(self, lines=None):
"""Read the LDA+U values from OUTCAR"""
if not lines:
lines = self.load_file('OUTCAR')
ldau_luj = None
ldauprint = None
ldau = None
ldautype = None
atomtypes = []
# read ldau parameters from outcar
for line in lines:
if line.find('TITEL') != -1: # What atoms are present
atomtypes.append(
line.split()[3].split('_')[0].split('.')[0])
if line.find('LDAUTYPE') != -1: # Is this a DFT+U calculation
ldautype = int(line.split('=')[-1])
ldau = True
ldau_luj = {}
if line.find('LDAUL') != -1:
L = line.split('=')[-1].split()
if line.find('LDAUU') != -1:
U = line.split('=')[-1].split()
if line.find('LDAUJ') != -1:
J = line.split('=')[-1].split()
# create dictionary
if ldau:
for i, symbol in enumerate(atomtypes):
ldau_luj[symbol] = {'L': int(L[i]),
'U': float(U[i]),
'J': float(J[i])}
self.dict_params['ldau_luj'] = ldau_luj
self.ldau = ldau
self.ldauprint = ldauprint
self.ldautype = ldautype
self.ldau_luj = ldau_luj
return ldau, ldauprint, ldautype, ldau_luj
def get_xc_functional(self):
"""Returns the XC functional or the pseudopotential type
If a XC recipe is set explicitly with 'xc', this is returned.
Otherwise, the XC functional associated with the
pseudopotentials (LDA, PW91 or PBE) is returned.
The string is always cast to uppercase for consistency
in checks."""
if self.input_params.get('xc', None):
return self.input_params['xc'].upper()
elif self.input_params.get('pp', None):
return self.input_params['pp'].upper()
else:
raise ValueError('No xc or pp found.')
# Methods for reading information from OUTCAR files:
def read_energy(self, all=None, lines=None):
"""Method to read energy from OUTCAR file.
Depreciated: use get_potential_energy() instead"""
if not lines:
lines = self.load_file('OUTCAR')
[energy_free, energy_zero] = [0, 0]
if all:
energy_free = []
energy_zero = []
for line in lines:
# Free energy
if line.lower().startswith(' free energy toten'):
if all:
energy_free.append(float(line.split()[-2]))
else:
energy_free = float(line.split()[-2])
# Extrapolated zero point energy
if line.startswith(' energy without entropy'):
if all:
energy_zero.append(float(line.split()[-1]))
else:
energy_zero = float(line.split()[-1])
return [energy_free, energy_zero]
def read_forces(self, all=False, lines=None):
"""Method that reads forces from OUTCAR file.
If 'all' is switched on, the forces for all ionic steps
in the OUTCAR file be returned, in other case only the
forces for the last ionic configuration is returned."""
if not lines:
lines = self.load_file('OUTCAR')
if all:
all_forces = []
for n, line in enumerate(lines):
if 'TOTAL-FORCE' in line:
forces = []
for i in range(len(self.atoms)):
forces.append(np.array([float(f) for f in
lines[n + 2 + i].split()[3:6]]))
if all:
all_forces.append(np.array(forces)[self.resort])
if all:
return np.array(all_forces)
else:
return np.array(forces)[self.resort]
def read_fermi(self, lines=None):
"""Method that reads Fermi energy from OUTCAR file"""
if not lines:
lines = self.load_file('OUTCAR')
E_f = None
for line in lines:
if 'E-fermi' in line:
E_f = float(line.split()[2])
return E_f
def read_dipole(self, lines=None):
"""Read dipole from OUTCAR"""
if not lines:
lines = self.load_file('OUTCAR')
dipolemoment = np.zeros([1, 3])
for line in lines:
if 'dipolmoment' in line:
dipolemoment = np.array([float(f) for
f in line.split()[1:4]])
return dipolemoment
def read_mag(self, lines=None):
if not lines:
lines = self.load_file('OUTCAR')
p = self.int_params
q = self.list_float_params
if self.spinpol:
magnetic_moment = self._read_magnetic_moment(lines=lines)
if ((p['lorbit'] is not None and p['lorbit'] >= 10) or
(p['lorbit'] is None and q['rwigs'])):
magnetic_moments = self._read_magnetic_moments(lines=lines)
else:
warn(('Magnetic moment data not written in OUTCAR (LORBIT<10),'
' setting magnetic_moments to zero.\nSet LORBIT>=10'
' to get information on magnetic moments'))
magnetic_moments = np.zeros(len(self.atoms))
else:
magnetic_moment = 0.0
magnetic_moments = np.zeros(len(self.atoms))
return magnetic_moment, magnetic_moments
def _read_magnetic_moments(self, lines=None):
"""Read magnetic moments from OUTCAR.
Only reads the last occurrence. """
if not lines:
lines = self.load_file('OUTCAR')
magnetic_moments = np.zeros(len(self.atoms))
magstr = 'magnetization (x)'
# Search for the last occurence
nidx = -1
for n, line in enumerate(lines):
if magstr in line:
nidx = n
# Read that occurence
if nidx > -1:
for m in range(len(self.atoms)):
magnetic_moments[m] = float(lines[nidx + m + 4].split()[4])
return magnetic_moments[self.resort]
def _read_magnetic_moment(self, lines=None):
"""Read magnetic moment from OUTCAR"""
if not lines:
lines = self.load_file('OUTCAR')
for n, line in enumerate(lines):
if 'number of electron ' in line:
magnetic_moment = float(line.split()[-1])
return magnetic_moment
def read_nbands(self, lines=None):
"""Read number of bands from OUTCAR"""
if not lines:
lines = self.load_file('OUTCAR')
for line in lines:
line = self.strip_warnings(line)
if 'NBANDS' in line:
return int(line.split()[-1])
def read_convergence(self, lines=None):
"""Method that checks whether a calculation has converged."""
if not lines:
lines = self.load_file('OUTCAR')
converged = None
# First check electronic convergence
for line in lines:
if 0: # vasp always prints that!
if line.rfind('aborting loop') > -1: # scf failed
raise RuntimeError(line.strip())
break
if 'EDIFF ' in line:
ediff = float(line.split()[2])
if 'total energy-change' in line:
# I saw this in an atomic oxygen calculation. it
# breaks this code, so I am checking for it here.
if 'MIXING' in line:
continue
split = line.split(':')
a = float(split[1].split('(')[0])
b = split[1].split('(')[1][0:-2]
# sometimes this line looks like (second number wrong format!):
# energy-change (2. order) :-0.2141803E-08 ( 0.2737684-111)
# we are checking still the first number so
# let's "fix" the format for the second one
if 'e' not in b.lower():
# replace last occurrence of - (assumed exponent) with -e
bsplit = b.split('-')
bsplit[-1] = 'e' + bsplit[-1]
b = '-'.join(bsplit).replace('-e', 'e-')
b = float(b)
if [abs(a), abs(b)] < [ediff, ediff]:
converged = True
else:
converged = False
continue
# Then if ibrion in [1,2,3] check whether ionic relaxation
# condition been fulfilled
if ((self.int_params['ibrion'] in [1, 2, 3] and
self.int_params['nsw'] not in [0])):
if not self.read_relaxed():
converged = False
else:
converged = True
return converged
def read_k_point_weights(self, filename='IBZKPT'):
"""Read k-point weighting. Defaults to IBZKPT file."""
lines = self.load_file(filename)
if 'Tetrahedra\n' in lines:
N = lines.index('Tetrahedra\n')
else:
N = len(lines)
kpt_weights = []
for n in range(3, N):
kpt_weights.append(float(lines[n].split()[3]))
kpt_weights = np.array(kpt_weights)
kpt_weights /= np.sum(kpt_weights)
return kpt_weights
def read_relaxed(self, lines=None):
"""Check if ionic relaxation completed"""
if not lines:
lines = self.load_file('OUTCAR')
for line in lines:
if 'reached required accuracy' in line:
return True
return False
def read_spinpol(self, lines=None):
"""Method which reads if a calculation from spinpolarized using OUTCAR.
Depreciated: Use get_spin_polarized() instead.
"""
if not lines:
lines = self.load_file('OUTCAR')
for line in lines:
if 'ISPIN' in line:
if int(line.split()[2]) == 2:
self.spinpol = True
else:
self.spinpol = False
return self.spinpol
def strip_warnings(self, line):
"""Returns empty string instead of line from warnings in OUTCAR."""
if line[0] == "|":
return ""
else:
return line
def set_txt(self, txt):
if txt is None:
# Default behavoir, write to vasp.out
self.txt = self.prefix + '.out'
elif txt == '-' or txt is False:
# We let the output be sent through stdout
# Do we ever want to completely suppress output?
self.txt = False
else:
self.txt = txt
def get_number_of_grid_points(self):
raise NotImplementedError
def get_pseudo_density(self):
raise NotImplementedError
def get_pseudo_wavefunction(self, n=0, k=0, s=0, pad=True):
raise NotImplementedError
def get_bz_k_points(self):
raise NotImplementedError
def read_vib_freq(self, lines=None):
"""Read vibrational frequencies.
Returns list of real and list of imaginary frequencies."""
freq = []
i_freq = []
if not lines:
lines = self.load_file('OUTCAR')
for line in lines:
data = line.split()
if 'THz' in data:
if 'f/i=' not in data:
freq.append(float(data[-2]))
else:
i_freq.append(float(data[-2]))
return freq, i_freq
def get_nonselfconsistent_energies(self, bee_type):
""" Method that reads and returns BEE energy contributions
written in OUTCAR file.
"""
assert bee_type == 'beefvdw'
cmd = 'grep -32 "BEEF xc energy contributions" OUTCAR | tail -32'
p = os.popen(cmd, 'r')
s = p.readlines()
p.close()
xc = np.array([])
for i, l in enumerate(s):
l_ = float(l.split(":")[-1])
xc = np.append(xc, l_)
assert len(xc) == 32
return xc