# Copyright (C) 2008 CSC - Scientific Computing Ltd. """This module defines an ASE interface to VASP. Developed on the basis of modules by Jussi Enkovaara and John Kitchin. 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 the environmental flag $VASP_SCRIPT pointing to a python script looking something like:: import os exitcode = os.system('vasp') Alternatively, user can set the environmental flag $VASP_COMMAND pointing to the command use the launch vasp e.g. 'vasp' or 'mpirun -n 16 vasp' http://cms.mpi.univie.ac.at/vasp/ """ import os import sys import re import numpy as np import subprocess from contextlib import contextmanager from pathlib import Path from warnings import warn from typing import Dict, Any from xml.etree import ElementTree import ase from ase.io import read, jsonio from ase.utils import PurePath from ase.calculators import calculator from ase.calculators.calculator import Calculator from ase.calculators.singlepoint import SinglePointDFTCalculator from ase.calculators.vasp.create_input import GenerateVaspInput class Vasp(GenerateVaspInput, Calculator): # type: ignore """ASE interface for the Vienna Ab initio Simulation Package (VASP), with the Calculator 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 ``directory`` is used. txt: bool, None, str or writable object - If txt is None, output stream will be supressed - If txt is '-' 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. Default is 'vasp.out' - Examples: >>> Vasp(label='mylabel', txt='vasp.out') # Redirect stdout >>> Vasp(txt='myfile.txt') # Redirect stdout >>> Vasp(txt='-') # Print vasp output to stdout >>> Vasp(txt=None) # Suppress txt output command: str Custom instructions on how to execute VASP. Has priority over environment variables. """ name = 'vasp' ase_objtype = 'vasp_calculator' # For JSON storage # Environment commands env_commands = ('ASE_VASP_COMMAND', 'VASP_COMMAND', 'VASP_SCRIPT') implemented_properties = [ 'energy', 'free_energy', 'forces', 'dipole', 'fermi', 'stress', 'magmom', 'magmoms' ] # Can be used later to set some ASE defaults default_parameters: Dict[str, Any] = {} def __init__(self, atoms=None, restart=None, directory='.', label='vasp', ignore_bad_restart_file=Calculator._deprecated, command=None, txt='vasp.out', **kwargs): self._atoms = None self.results = {} # Initialize parameter dictionaries GenerateVaspInput.__init__(self) self._store_param_state() # Initialize an empty parameter state # Store calculator from vasprun.xml here - None => uninitialized self._xml_calc = None # Set directory and label self.directory = directory if '/' in label: warn(('Specifying directory in "label" is deprecated, ' 'use "directory" instead.'), np.VisibleDeprecationWarning) if self.directory != '.': raise ValueError('Directory redundantly specified though ' 'directory="{}" and label="{}". ' 'Please omit "/" in label.'.format( self.directory, label)) self.label = label else: self.prefix = label # The label should only contain the prefix if isinstance(restart, bool): if restart is True: restart = self.label else: restart = None Calculator.__init__( self, restart=restart, ignore_bad_restart_file=ignore_bad_restart_file, # We already, manually, created the label label=self.label, atoms=atoms, **kwargs) self.command = command self._txt = None self.txt = txt # Set the output txt stream self.version = None # 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 compatibility. # 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 CalculatorSetupError 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 calculator.CalculatorSetupError(msg) return cmd def set(self, **kwargs): """Override the set function, to test for changes in the Vasp 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: self.label = kwargs.pop('label') if 'directory' in kwargs: # str() call to deal with pathlib objects self.directory = str(kwargs.pop('directory')) if 'txt' in kwargs: self.txt = kwargs.pop('txt') if 'atoms' in kwargs: atoms = kwargs.pop('atoms') self.atoms = atoms # Resets results if 'command' in kwargs: self.command = kwargs.pop('command') changed_parameters.update(Calculator.set(self, **kwargs)) # We might at some point add more to changed parameters, or use it if changed_parameters: self.clear_results() # 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() def reset(self): self.atoms = None self.clear_results() def clear_results(self): self.results.clear() self._xml_calc = None @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.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.txt = mystream with calc.txt_outstream() as out: calc.run(out=out) mystream.close() # Print to stdout calc.txt = '-' with calc.txt_outstream() as out: calc.run(out=out) # output is written to stdout """ txt = self.txt open_and_close = False # Do we open the file? if txt is None: # Suppress stdout out = subprocess.DEVNULL else: if isinstance(txt, str): if txt == '-': # subprocess.call redirects this to stdout out = None else: # Open the file in the work directory txt = self._indir(txt) # We wait with opening the file, until we are inside the # try/finally open_and_close = True elif hasattr(txt, 'write'): out = txt else: raise RuntimeError('txt should either be a string' 'or an I/O stream, got {}'.format(txt)) try: if open_and_close: out = open(txt, 'w') yield out finally: if open_and_close: out.close() def calculate(self, atoms=None, properties=('energy', ), system_changes=tuple(calculator.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. """ # Check for zero-length lattice vectors and PBC # and that we actually have an Atoms object. check_atoms(atoms) self.clear_results() if atoms is not None: self.atoms = atoms.copy() command = self.make_command(self.command) self.write_input(self.atoms, properties, system_changes) with self._txt_outstream() as out: errorcode = self._run(command=command, out=out, directory=self.directory) if errorcode: raise calculator.CalculationFailed( '{} 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, directory=None): """Method to explicitly execute VASP""" if command is None: command = self.command if directory is None: directory = self.directory errorcode = subprocess.call(command, shell=True, stdout=out, cwd=directory) 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 compatibility 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 = Calculator.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 asdict(self): """Return a dictionary representation of the calculator state. Does NOT contain information on the ``command``, ``txt`` or ``directory`` keywords. Contains the following keys: - ``ase_version`` - ``vasp_version`` - ``inputs`` - ``results`` - ``atoms`` (Only if the calculator has an ``Atoms`` object) """ # Get versions asevers = ase.__version__ vaspvers = self.get_version() self._store_param_state() # Update param state # Store input parameters which have been set inputs = { key: value for param_dct in self.param_state.values() for key, value in param_dct.items() if value is not None } dct = { 'ase_version': asevers, 'vasp_version': vaspvers, # '__ase_objtype__': self.ase_objtype, 'inputs': inputs, 'results': self.results.copy() } if self.atoms: # Encode atoms as dict from ase.db.row import atoms2dict dct['atoms'] = atoms2dict(self.atoms) return dct def fromdict(self, dct): """Restore calculator from a :func:`~ase.calculators.vasp.Vasp.asdict` dictionary. Parameters: dct: Dictionary The dictionary which is used to restore the calculator state. """ if 'vasp_version' in dct: self.version = dct['vasp_version'] if 'inputs' in dct: self.set(**dct['inputs']) self._store_param_state() if 'atoms' in dct: from ase.db.row import AtomsRow atoms = AtomsRow(dct['atoms']).toatoms() self.atoms = atoms if 'results' in dct: self.results.update(dct['results']) def write_json(self, filename): """Dump calculator state to JSON file. Parameters: filename: string The filename which the JSON file will be stored to. Prepends the ``directory`` path to the filename. """ filename = self._indir(filename) dct = self.asdict() jsonio.write_json(filename, dct) def read_json(self, filename): """Load Calculator state from an exported JSON Vasp file.""" dct = jsonio.read_json(filename) self.fromdict(dct) def write_input(self, atoms, properties=None, system_changes=None): """Write VASP inputfiles, INCAR, KPOINTS and POTCAR""" # Create the folders where we write the files, if we aren't in the # current working directory. if self.directory != os.curdir and not os.path.isdir(self.directory): os.makedirs(self.directory) 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 Calculator.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 f in ['OUTCAR', 'CONTCAR', 'vasprun.xml']: file = self._indir(f) if not file.is_file(): raise calculator.ReadError( 'VASP outputfile {} was not found'.format(file)) # Build sorting and resorting lists self.read_sort() # Read atoms self.atoms = self.read_atoms() # Read parameters self.read_incar(filename=self._indir('INCAR')) self.read_kpoints(filename=self._indir('KPOINTS')) self.read_potcar(filename=self._indir('POTCAR')) # Read the results from the calculation self.read_results() def _indir(self, filename): """Prepend current directory to filename""" return Path(self.directory) / filename 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 = self._indir('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 atoms = read(self._indir('CONTCAR')) self.initialize(atoms) def read_atoms(self, filename='CONTCAR'): """Read the atoms from file located in the VASP working directory. Defaults to CONTCAR.""" filename = self._indir(filename) return read(filename)[self.resort] 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(self._indir('CONTCAR')) atoms.positions = atoms_sorted[self.resort].positions atoms.cell = atoms_sorted.cell self.atoms = atoms # Creates a copy 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 calc_xml = self._read_xml() xml_results = calc_xml.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) self.version = self.read_version() 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)) self._set_old_keywords() # Store the parameters used for this calculation self._store_param_state() def _set_old_keywords(self): """Store keywords for backwards compatibility wd VASP calculator""" self.spinpol = self.get_spin_polarized() 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() # 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) @property def atoms(self): return self._atoms @atoms.setter def atoms(self, atoms): if atoms is None: self._atoms = None self.clear_results() else: if self.check_state(atoms): self.clear_results() self._atoms = atoms.copy() def load_file(self, filename): """Reads a file in the directory, and returns the lines Example: >>> outcar = load_file('OUTCAR') """ filename = self._indir(filename) with open(filename, 'r') as f: return f.readlines() @contextmanager def load_file_iter(self, filename): """Return a file iterator""" filename = self._indir(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_xml(self) -> SinglePointDFTCalculator: """Read vasprun.xml, and return the last calculator object. Returns calculator from the xml file. Raises a ReadError if the reader is not able to construct a calculator. """ file = self._indir('vasprun.xml') incomplete_msg = ( f'The file "{file}" is incomplete, and no DFT data was available. ' 'This is likely due to an incomplete calculation.') try: _xml_atoms = read(file, index=-1, format='vasp-xml') # Silence mypy, we should only ever get a single atoms object assert isinstance(_xml_atoms, ase.Atoms) except ElementTree.ParseError as exc: raise calculator.ReadError(incomplete_msg) from exc if _xml_atoms is None or _xml_atoms.calc is None: raise calculator.ReadError(incomplete_msg) self._xml_calc = _xml_atoms.calc return self._xml_calc @property def _xml_calc(self) -> SinglePointDFTCalculator: if self.__xml_calc is None: raise RuntimeError(('vasprun.xml data has not yet been loaded. ' 'Run read_results() first.')) return self.__xml_calc @_xml_calc.setter def _xml_calc(self, value): self.__xml_calc = value def get_ibz_k_points(self): calc = self._xml_calc return calc.get_ibz_k_points() def get_kpt(self, kpt=0, spin=0): calc = self._xml_calc return calc.get_kpt(kpt=kpt, spin=spin) def get_eigenvalues(self, kpt=0, spin=0): calc = self._xml_calc return calc.get_eigenvalues(kpt=kpt, spin=spin) def get_fermi_level(self): calc = self._xml_calc return calc.get_fermi_level() def get_homo_lumo(self): calc = self._xml_calc return calc.get_homo_lumo() def get_homo_lumo_by_spin(self, spin=0): calc = self._xml_calc return calc.get_homo_lumo_by_spin(spin=spin) def get_occupation_numbers(self, kpt=0, spin=0): calc = self._xml_calc return calc.get_occupation_numbers(kpt, spin) def get_spin_polarized(self): calc = self._xml_calc return calc.get_spin_polarized() def get_number_of_spins(self): calc = self._xml_calc return calc.get_number_of_spins() def get_number_of_bands(self): return self.results.get('nbands', None) 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): if self.version is None: # Try if we can read the version number self.version = self.read_version() return self.version def read_version(self): """Get the VASP version number""" # The version number is the first occurrence, so we can just # load the OUTCAR, as we will return soon anyway if not os.path.isfile(self._indir('OUTCAR')): return None with self.load_file_iter('OUTCAR') as lines: for line in lines: if ' vasp.' in line: return line[len(' vasp.'):].split()[0] # We didn't find the version 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() if self.input_params.get('pp', None): return self.input_params['pp'].upper() 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) 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 occurrence nidx = -1 for n, line in enumerate(lines): if magstr in line: nidx = n # Read that occurrence 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]) return None 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 "" return line @property def txt(self): return self._txt @txt.setter def txt(self, txt): if isinstance(txt, PurePath): txt = str(txt) 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 line in s: l_ = float(line.split(":")[-1]) xc = np.append(xc, l_) assert len(xc) == 32 return xc ##################################### # Below defines helper functions # for the VASP calculator ##################################### def check_atoms(atoms: ase.Atoms) -> None: """Perform checks on the atoms object, to verify that it can be run by VASP. A CalculatorSetupError error is raised if the atoms are not supported. """ # Loop through all check functions for check in (check_atoms_type, check_cell, check_pbc): check(atoms) def check_cell(atoms: ase.Atoms) -> None: """Check if there is a zero unit cell. Raises CalculatorSetupError if the cell is wrong. """ if atoms.cell.rank < 3: raise calculator.CalculatorSetupError( "The lattice vectors are zero! " "This is the default value - please specify a " "unit cell.") def check_pbc(atoms: ase.Atoms) -> None: """Check if any boundaries are not PBC, as VASP cannot handle non-PBC. Raises CalculatorSetupError. """ if not atoms.pbc.all(): raise calculator.CalculatorSetupError( "Vasp cannot handle non-periodic boundaries. " "Please enable all PBC, e.g. atoms.pbc=True") def check_atoms_type(atoms: ase.Atoms) -> None: """Check that the passed atoms object is in fact an Atoms object. Raises CalculatorSetupError. """ if not isinstance(atoms, ase.Atoms): raise calculator.CalculatorSetupError( ('Expected an Atoms object, ' 'instead got object of type {}'.format(type(atoms))))