Source code for ase.calculators.vasp.vasp

from __future__ import print_function
# 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
from ase.calculators.general import Calculator

import numpy as np

import ase.io
from ase.utils import devnull, basestring

from ase.calculators.singlepoint import SinglePointCalculator
from ase.calculators.calculator import PropertyNotImplementedError
from .create_input import GenerateVaspInput, read_potcar_numbers_of_electrons


[docs]class Vasp(GenerateVaspInput, Calculator): name = 'Vasp' implemented_properties = ['energy', 'forces', 'dipole', 'fermi', 'stress', 'magmom', 'magmoms'] def __init__(self, restart=None, output_template='vasp', track_output=False, **kwargs): GenerateVaspInput.__init__(self) self.restart = restart self.track_output = track_output self.output_template = output_template if restart: self.restart_load() return self.nbands = self.int_params['nbands'] self.atoms = None self.positions = None self.run_counts = 0 # 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}) self.set(**kwargs) def update(self, atoms): if self.calculation_required(atoms, ['energy']): if (((self.atoms is None) or (self.atoms.positions.shape != atoms.positions.shape) )): # Completely new calculation just reusing the same # calculator, so delete any old VASP files found. self.clean() self.calculate(atoms) def calculate(self, atoms): """Generate necessary files in the working directory and run VASP. The method first write VASP input files, then calls the method which executes VASP. When the VASP run is finished energy, forces, etc. are read from the VASP output. """ # Check if there is only a zero unit cell if not atoms.cell.any(): raise ValueError("The lattice vectors are zero! " "This is the default value - please specify a " "unit cell.") # Initialize calculations self.initialize(atoms) # Write input self.write_input(atoms) # Execute VASP self.run() # Read output atoms_sorted = ase.io.read('CONTCAR', format='vasp') 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.positions = atoms_sorted[self.resort].positions atoms.cell = atoms_sorted.cell self.converged = self.read_convergence() self.set_results(atoms) def set_results(self, atoms): self.read(atoms) if self.spinpol: self.magnetic_moment = self.read_magnetic_moment() if (self.int_params['lorbit'] is not None and (self.int_params['lorbit'] >= 10 or self.list_float_params['rwigs'])): self.magnetic_moments = self.read_magnetic_moments(atoms) else: self.magnetic_moments = None self.old_float_params = self.float_params.copy() self.old_exp_params = self.exp_params.copy() self.old_string_params = self.string_params.copy() self.old_int_params = self.int_params.copy() self.old_input_params = self.input_params.copy() self.old_bool_params = self.bool_params.copy() self.old_list_bool_params = self.list_bool_params.copy() self.old_list_int_params = self.list_int_params.copy() self.old_list_float_params = self.list_float_params.copy() self.old_dict_params = self.dict_params.copy() self.atoms = atoms.copy() self.name = 'vasp' self.version = self.read_version() self.niter = self.read_number_of_iterations() self.sigma = self.read_electronic_temperature() self.nelect = self.read_number_of_electrons() def run(self): """Method which explicitely runs VASP.""" if self.track_output: self.out = self.output_template + str(self.run_counts) + '.out' self.run_counts += 1 else: self.out = self.output_template + '.out' stderr = sys.stderr p = self.input_params if p['txt'] is None: sys.stderr = devnull elif p['txt'] == '-': pass elif isinstance(p['txt'], basestring): sys.stderr = open(p['txt'], 'w') if 'VASP_COMMAND' in os.environ: vasp = os.environ['VASP_COMMAND'] exitcode = os.system('%s > %s' % (vasp, self.out)) elif 'VASP_SCRIPT' in os.environ: vasp = os.environ['VASP_SCRIPT'] locals = {} exec(compile(open(vasp).read(), vasp, 'exec'), {}, locals) exitcode = locals['exitcode'] else: raise RuntimeError('Please set either VASP_COMMAND' ' or VASP_SCRIPT environment variable') sys.stderr = stderr if exitcode != 0: raise RuntimeError('Vasp exited with exit code: %d. ' % exitcode) def restart_load(self): """Method which is called upon restart.""" # Try to read sorting file if os.path.isfile('ase-sort.dat'): self.sort = [] self.resort = [] file = open('ase-sort.dat', 'r') lines = file.readlines() file.close() for line in lines: data = line.split() self.sort.append(int(data[0])) self.resort.append(int(data[1])) atoms = ase.io.read('CONTCAR', format='vasp')[self.resort] else: atoms = ase.io.read('CONTCAR', format='vasp') self.sort = list(range(len(atoms))) self.resort = list(range(len(atoms))) self.atoms = atoms.copy() self.read_incar() self.read_outcar() self.set_results(atoms) if not self.float_params['kspacing']: self.read_kpoints() self.read_potcar() self.old_input_params = self.input_params.copy() self.converged = self.read_convergence() def set_atoms(self, atoms): if (atoms != self.atoms): self.converged = None self.atoms = atoms.copy() def get_atoms(self): atoms = self.atoms.copy() atoms.set_calculator(self) return atoms def get_version(self): self.update(self.atoms) return self.version def read_version(self): version = None for line in open('OUTCAR'): if line.find(' vasp.') != -1: # find the first occurrence version = line[len(' vasp.'):].split()[0] break return version def get_potential_energy(self, atoms, force_consistent=False): self.update(atoms) if force_consistent: return self.energy_free else: return self.energy_zero def get_number_of_iterations(self): self.update(self.atoms) return self.niter def read_number_of_iterations(self): niter = None for line in open('OUTCAR'): # find the last iteration number if line.find('- Iteration') != -1: niter = int(line.split(')')[0].split('(')[-1].strip()) return niter def get_electronic_temperature(self): self.update(self.atoms) return self.sigma def read_electronic_temperature(self): sigma = None for line in open('OUTCAR'): if line.find('Fermi-smearing in eV SIGMA') != -1: sigma = float(line.split('=')[1].strip()) return sigma def get_default_number_of_electrons(self, filename='POTCAR'): """Get list of tuples (atomic symbol, number of valence electrons) for each atomtype from a POTCAR file. """ return self.read_default_number_of_electrons(filename) def read_default_number_of_electrons(self, filename='POTCAR'): file_obj = open(filename) r = read_potcar_numbers_of_electrons(file_obj=file_obj) return r def get_number_of_electrons(self): self.update(self.atoms) return self.nelect def read_number_of_electrons(self): nelect = None for line in open('OUTCAR'): if line.find('total number of electrons') != -1: nelect = float(line.split('=')[1].split()[0].strip()) return nelect def get_forces(self, atoms): self.update(atoms) return self.forces def get_stress(self, atoms): self.update(atoms) if self.stress is None: raise PropertyNotImplementedError return self.stress def read_stress(self): stress = None for line in open('OUTCAR'): if line.find(' in kB ') != -1: 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): ldau_luj = None ldauprint = None ldau = None ldautype = None atomtypes = [] # read ldau parameters from outcar for line in open('OUTCAR'): 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 return ldau, ldauprint, ldautype, ldau_luj def calculation_required(self, atoms, quantities): if (((self.positions is None) or (self.atoms != atoms) or (self.float_params != self.old_float_params) or (self.exp_params != self.old_exp_params) or (self.string_params != self.old_string_params) or (self.int_params != self.old_int_params) or (self.bool_params != self.old_bool_params) or (self.list_bool_params != self.old_list_bool_params) or (self.list_int_params != self.old_list_int_params) or (self.list_float_params != self.old_list_float_params) or (self.input_params != self.old_input_params) or (self.dict_params != self.old_dict_params) or not self.converged)): return True if 'magmom' in quantities: return not hasattr(self, 'magnetic_moment') return False def get_number_of_bands(self): return self.nbands def get_k_point_weights(self): self.update(self.atoms) return self.read_k_point_weights() def get_number_of_spins(self): if self.spinpol is None: return 1 else: return 1 + int(self.spinpol) def get_eigenvalues(self, kpt=0, spin=0): self.update(self.atoms) return self.read_eigenvalues(kpt, spin) def get_occupation_numbers(self, kpt=0, spin=0): self.update(self.atoms) return self.read_occupation_numbers(kpt, spin) def get_fermi_level(self): return self.fermi 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 get_ibz_kpoints(self): self.update(self.atoms) return self.read_ibz_kpoints() def get_ibz_k_points(self): return self.get_ibz_kpoints() def get_spin_polarized(self): if not hasattr(self, 'spinpol'): self.spinpol = self.atoms.get_initial_magnetic_moments().any() return self.spinpol def get_magnetic_moment(self, atoms): self.update(atoms) return self.magnetic_moment def get_magnetic_moments(self, atoms): if ((self.int_params['lorbit'] is not None and self.int_params['lorbit'] >= 10) or self.list_float_params['rwigs']): self.update(atoms) return self.magnetic_moments else: return None def get_dipole_moment(self, atoms): """Returns total dipole moment of the system.""" self.update(atoms) return self.dipole 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): [energy_free, energy_zero] = [0, 0] if all: energy_free = [] energy_zero = [] for line in open('OUTCAR', 'r'): # 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, atoms, all=False): """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.""" file = open('OUTCAR', 'r') lines = file.readlines() file.close() n = 0 if all: all_forces = [] for line in lines: if line.rfind('TOTAL-FORCE') > -1: forces = [] for i in range(len(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]) n += 1 if all: return np.array(all_forces) else: return np.array(forces)[self.resort] def read_fermi(self): """Method that reads Fermi energy from OUTCAR file""" E_f = None for line in open('OUTCAR', 'r'): if line.rfind('E-fermi') > -1: E_f = float(line.split()[2]) return E_f def read_dipole(self): dipolemoment = np.zeros([1, 3]) for line in open('OUTCAR', 'r'): if line.rfind('dipolmoment') > -1: dipolemoment = np.array([float(f) for f in line.split()[1:4]]) return dipolemoment def read_magnetic_moments(self, atoms): magnetic_moments = np.zeros(len(atoms)) n = 0 lines = open('OUTCAR', 'r').readlines() for line in lines: if line.rfind('magnetization (x)') > -1: for m in range(len(atoms)): magnetic_moments[m] = float(lines[n + m + 4].split()[4]) n += 1 return np.array(magnetic_moments)[self.resort] def read_magnetic_moment(self): n = 0 for line in open('OUTCAR', 'r'): if line.rfind('number of electron ') > -1: magnetic_moment = float(line.split()[-1]) n += 1 return magnetic_moment def read_nbands(self): for line in open('OUTCAR', 'r'): line = self.strip_warnings(line) if line.rfind('NBANDS') > -1: return int(line.split()[-1]) def strip_warnings(self, line): """Returns empty string instead of line from warnings in OUTCAR.""" if line[0] == "|": return "" else: return line def read_convergence(self): """Method that checks whether a calculation has converged.""" converged = None # First check electronic convergence for line in open('OUTCAR', 'r'): if 0: # vasp always prints that! if line.rfind('aborting loop') > -1: # scf failed raise RuntimeError(line.strip()) break if line.rfind('EDIFF ') > -1: ediff = float(line.split()[2]) if line.rfind('total energy-change') > -1: # 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_ibz_kpoints(self): lines = open('OUTCAR', 'r').readlines() ibz_kpts = [] n = 0 i = 0 for line in lines: if line.rfind('Following cartesian coordinates') > -1: m = n + 2 while i == 0: ibz_kpts.append([float(lines[m].split()[p]) for p in range(3)]) m += 1 if lines[m] == ' \n': i = 1 if i == 1: continue n += 1 ibz_kpts = np.array(ibz_kpts) return np.array(ibz_kpts) def read_k_point_weights(self): file = open('IBZKPT') lines = file.readlines() file.close() 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_eigenvalues(self, kpt=0, spin=0): file = open('EIGENVAL', 'r') lines = file.readlines() file.close() eigs = [] for n in range(8 + kpt * (self.nbands + 2), 8 + kpt * (self.nbands + 2) + self.nbands): eigs.append(float(lines[n].split()[spin + 1])) return np.array(eigs) def read_occupation_numbers(self, kpt=0, spin=0): lines = open('OUTCAR').readlines() nspins = self.get_number_of_spins() start = 0 if nspins == 1: for n, line in enumerate(lines): # find it in the last iteration m = re.search(' k-point *' + str(kpt + 1) + ' *:', line) if m is not None: start = n else: for n, line in enumerate(lines): # find it in the last iteration if line.find(' spin component ' + str(spin + 1)) != -1: start = n for n2, line2 in enumerate(lines[start:]): m = re.search(' k-point *' + str(kpt + 1) + ' *:', line2) if m is not None: start = start + n2 break for n2, line2 in enumerate(lines[start + 2:]): if not line2.strip(): break occ = [] for line in lines[start + 2:start + 2 + n2]: occ.append(float(line.split()[2])) return np.array(occ) def read_relaxed(self): for line in open('OUTCAR', 'r'): if line.rfind('reached required accuracy') > -1: return True return False def read_outcar(self): # Spin polarized calculation? file = open('OUTCAR', 'r') lines = file.readlines() file.close() for line in lines: if line.rfind('ISPIN') > -1: if int(line.split()[2]) == 2: self.spinpol = True else: self.spinpol = None self.energy_free, self.energy_zero = self.read_energy() self.forces = self.read_forces(self.atoms) self.dipole = self.read_dipole() self.fermi = self.read_fermi() self.stress = self.read_stress() self.nbands = self.read_nbands() self.read_ldau() p = self.int_params q = self.list_float_params if self.spinpol: self.magnetic_moment = self.read_magnetic_moment() if ((p['lorbit'] is not None and p['lorbit'] >= 10) or (p['lorbit'] is None and q['rwigs'])): self.magnetic_moments = self.read_magnetic_moments(self.atoms) else: self.magnetic_moments = None self.set(nbands=self.nbands) def read_vib_freq(self): """Read vibrational frequencies. Returns list of real and list of imaginary frequencies.""" freq = [] i_freq = [] with open('OUTCAR', 'r') as fd: lines = fd.readlines() 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 def check_state(self, atoms, tol=1e-15): """Check for system changes since last calculation.""" from ase.calculators.calculator import all_changes, equal if self.atoms is None: system_changes = all_changes[:] else: system_changes = [] if not equal(self.atoms.positions, atoms.positions, tol): system_changes.append('positions') if not equal(self.atoms.numbers, atoms.numbers): system_changes.append('numbers') if not equal(self.atoms.cell, atoms.cell, tol): system_changes.append('cell') if not equal(self.atoms.pbc, atoms.pbc): system_changes.append('pbc') if not equal(self.atoms.get_initial_magnetic_moments(), atoms.get_initial_magnetic_moments(), tol): system_changes.append('initial_magmoms') if not equal(self.atoms.get_initial_charges(), atoms.get_initial_charges(), tol): system_changes.append('initial_charges') return system_changes def get_property(self, name, atoms=None, allow_calculation=True): """Returns the value of a property""" if name not in Vasp.implemented_properties: raise PropertyNotImplementedError if atoms is None: atoms = self.atoms saved_property = { 'energy': 'energy_zero', 'forces': 'forces', 'dipole': 'dipole', 'fermi': 'fermi', 'stress': 'stress', 'magmom': 'magnetic_moment', 'magmoms': 'magnetic_moments' } property_getter = { 'energy': {'function': 'get_potential_energy', 'args': [atoms]}, 'forces': {'function': 'get_forces', 'args': [atoms]}, 'dipole': {'function': 'get_dipole_moment', 'args': [atoms]}, 'fermi': {'function': 'get_fermi_level', 'args': []}, 'stress': {'function': 'get_stress', 'args': [atoms]}, 'magmom': {'function': 'get_magnetic_moment', 'args': [atoms]}, 'magmoms': {'function': 'get_magnetic_moments', 'args': [atoms]} } if allow_calculation: function = property_getter[name]['function'] args = property_getter[name]['args'] result = getattr(self, function)(*args) else: if hasattr(self, saved_property[name]): result = getattr(self, saved_property[name]) else: result = None if isinstance(result, np.ndarray): result = result.copy() return result
class VaspChargeDensity(object): """Class for representing VASP charge density""" def __init__(self, filename='CHG'): # Instance variables self.atoms = [] # List of Atoms objects self.chg = [] # Charge density self.chgdiff = [] # Charge density difference, if spin polarized self.aug = '' # Augmentation charges, not parsed just a big string self.augdiff = '' # Augmentation charge differece, is spin polarized # Note that the augmentation charge is not a list, since they # are needed only for CHGCAR files which store only a single # image. if filename is not None: self.read(filename) def is_spin_polarized(self): if len(self.chgdiff) > 0: return True return False def _read_chg(self, fobj, chg, volume): """Read charge from file object Utility method for reading the actual charge density (or charge density difference) from a file object. On input, the file object must be at the beginning of the charge block, on output the file position will be left at the end of the block. The chg array must be of the correct dimensions. """ # VASP writes charge density as # WRITE(IU,FORM) (((C(NX,NY,NZ),NX=1,NGXC),NY=1,NGYZ),NZ=1,NGZC) # Fortran nested implied do loops; innermost index fastest # First, just read it in for zz in range(chg.shape[2]): for yy in range(chg.shape[1]): chg[:, yy, zz] = np.fromfile(fobj, count=chg.shape[0], sep=' ') chg /= volume def read(self, filename='CHG'): """Read CHG or CHGCAR file. If CHG contains charge density from multiple steps all the steps are read and stored in the object. By default VASP writes out the charge density every 10 steps. chgdiff is the difference between the spin up charge density and the spin down charge density and is thus only read for a spin-polarized calculation. aug is the PAW augmentation charges found in CHGCAR. These are not parsed, they are just stored as a string so that they can be written again to a CHGCAR format file. """ import ase.io.vasp as aiv f = open(filename) self.atoms = [] self.chg = [] self.chgdiff = [] self.aug = '' self.augdiff = '' while True: try: atoms = aiv.read_vasp(f) except (IOError, ValueError, IndexError): # Probably an empty line, or we tried to read the # augmentation occupancies in CHGCAR break f.readline() ngr = f.readline().split() ng = (int(ngr[0]), int(ngr[1]), int(ngr[2])) chg = np.empty(ng) self._read_chg(f, chg, atoms.get_volume()) self.chg.append(chg) self.atoms.append(atoms) # Check if the file has a spin-polarized charge density part, and # if so, read it in. fl = f.tell() # First check if the file has an augmentation charge part (CHGCAR # file.) line1 = f.readline() if line1 == '': break elif line1.find('augmentation') != -1: augs = [line1] while True: line2 = f.readline() if line2.split() == ngr: self.aug = ''.join(augs) augs = [] chgdiff = np.empty(ng) self._read_chg(f, chgdiff, atoms.get_volume()) self.chgdiff.append(chgdiff) elif line2 == '': break else: augs.append(line2) if len(self.aug) == 0: self.aug = ''.join(augs) augs = [] else: self.augdiff = ''.join(augs) augs = [] elif line1.split() == ngr: chgdiff = np.empty(ng) self._read_chg(f, chgdiff, atoms.get_volume()) self.chgdiff.append(chgdiff) else: f.seek(fl) f.close() def _write_chg(self, fobj, chg, volume, format='chg'): """Write charge density Utility function similar to _read_chg but for writing. """ # Make a 1D copy of chg, must take transpose to get ordering right chgtmp = chg.T.ravel() # Multiply by volume chgtmp = chgtmp * volume # Must be a tuple to pass to string conversion chgtmp = tuple(chgtmp) # CHG format - 10 columns if format.lower() == 'chg': # Write all but the last row for ii in range((len(chgtmp) - 1) // 10): fobj.write(' %#11.5G %#11.5G %#11.5G %#11.5G %#11.5G\ %#11.5G %#11.5G %#11.5G %#11.5G %#11.5G\n' % chgtmp[ii * 10:(ii + 1) * 10] ) # If the last row contains 10 values then write them without a # newline if len(chgtmp) % 10 == 0: fobj.write(' %#11.5G %#11.5G %#11.5G %#11.5G %#11.5G' ' %#11.5G %#11.5G %#11.5G %#11.5G %#11.5G' % chgtmp[len(chgtmp) - 10:len(chgtmp)]) # Otherwise write fewer columns without a newline else: for ii in range(len(chgtmp) % 10): fobj.write((' %#11.5G') % chgtmp[len(chgtmp) - len(chgtmp) % 10 + ii]) # Other formats - 5 columns else: # Write all but the last row for ii in range((len(chgtmp) - 1) // 5): fobj.write(' %17.10E %17.10E %17.10E %17.10E %17.10E\n' % chgtmp[ii * 5:(ii + 1) * 5]) # If the last row contains 5 values then write them without a # newline if len(chgtmp) % 5 == 0: fobj.write(' %17.10E %17.10E %17.10E %17.10E %17.10E' % chgtmp[len(chgtmp) - 5:len(chgtmp)]) # Otherwise write fewer columns without a newline else: for ii in range(len(chgtmp) % 5): fobj.write((' %17.10E') % chgtmp[len(chgtmp) - len(chgtmp) % 5 + ii]) # Write a newline whatever format it is fobj.write('\n') # Clean up del chgtmp def write(self, filename='CHG', format=None): """Write VASP charge density in CHG format. filename: str Name of file to write to. format: str String specifying whether to write in CHGCAR or CHG format. """ import ase.io.vasp as aiv if format is None: if filename.lower().find('chgcar') != -1: format = 'chgcar' elif filename.lower().find('chg') != -1: format = 'chg' elif len(self.chg) == 1: format = 'chgcar' else: format = 'chg' f = open(filename, 'w') for ii, chg in enumerate(self.chg): if format == 'chgcar' and ii != len(self.chg) - 1: continue # Write only the last image for CHGCAR aiv.write_vasp(f, self.atoms[ii], direct=True, long_format=False) f.write('\n') for dim in chg.shape: f.write(' %4i' % dim) f.write('\n') vol = self.atoms[ii].get_volume() self._write_chg(f, chg, vol, format) if format == 'chgcar': f.write(self.aug) if self.is_spin_polarized(): if format == 'chg': f.write('\n') for dim in chg.shape: f.write(' %4i' % dim) self._write_chg(f, self.chgdiff[ii], vol, format) if format == 'chgcar': f.write('\n') f.write(self.augdiff) if format == 'chg' and len(self.chg) > 1: f.write('\n') f.close() class VaspDos(object): """Class for representing density-of-states produced by VASP The energies are in property self.energy Site-projected DOS is accesible via the self.site_dos method. Total and integrated DOS is accessible as numpy.ndarray's in the properties self.dos and self.integrated_dos. If the calculation is spin polarized, the arrays will be of shape (2, NDOS), else (1, NDOS). The self.efermi property contains the currently set Fermi level. Changing this value shifts the energies. """ def __init__(self, doscar='DOSCAR', efermi=0.0): """Initialize""" self._efermi = 0.0 self.read_doscar(doscar) self.efermi = efermi # we have determine the resort to correctly map ase atom index to the # POSCAR. self.sort = [] self.resort = [] if os.path.isfile('ase-sort.dat'): file = open('ase-sort.dat', 'r') lines = file.readlines() file.close() for line in lines: data = line.split() self.sort.append(int(data[0])) self.resort.append(int(data[1])) def _set_efermi(self, efermi): """Set the Fermi level.""" ef = efermi - self._efermi self._efermi = efermi self._total_dos[0, :] = self._total_dos[0, :] - ef try: self._site_dos[:, 0, :] = self._site_dos[:, 0, :] - ef except IndexError: pass def _get_efermi(self): return self._efermi efermi = property(_get_efermi, _set_efermi, None, "Fermi energy.") def _get_energy(self): """Return the array with the energies.""" return self._total_dos[0, :] energy = property(_get_energy, None, None, "Array of energies") def site_dos(self, atom, orbital): """Return an NDOSx1 array with dos for the chosen atom and orbital. atom: int Atom index orbital: int or str Which orbital to plot If the orbital is given as an integer: If spin-unpolarized calculation, no phase factors: s = 0, p = 1, d = 2 Spin-polarized, no phase factors: s-up = 0, s-down = 1, p-up = 2, p-down = 3, d-up = 4, d-down = 5 If phase factors have been calculated, orbitals are s, py, pz, px, dxy, dyz, dz2, dxz, dx2 double in the above fashion if spin polarized. """ # Correct atom index for resorting if we need to. This happens when the # ase-sort.dat file exists, and self.resort is not empty. if self.resort: atom = self.resort[atom] # Integer indexing for orbitals starts from 1 in the _site_dos array # since the 0th column contains the energies if isinstance(orbital, int): return self._site_dos[atom, orbital + 1, :] n = self._site_dos.shape[1] if n == 4: norb = {'s': 1, 'p': 2, 'd': 3} elif n == 5: norb = {'s': 1, 'p': 2, 'd': 3, 'f': 4} elif n == 7: norb = {'s+': 1, 's-up': 1, 's-': 2, 's-down': 2, 'p+': 3, 'p-up': 3, 'p-': 4, 'p-down': 4, 'd+': 5, 'd-up': 5, 'd-': 6, 'd-down': 6} elif n == 9: norb = { 's+': 1, 's-up': 1, 's-': 2, 's-down': 2, 'p+': 3, 'p-up': 3, 'p-': 4, 'p-down': 4, 'd+': 5, 'd-up': 5, 'd-': 6, 'd-down': 6, 'f+': 7, 'f-up': 7, 'f-': 8, 'f-down': 8, } elif n == 10: norb = {'s': 1, 'py': 2, 'pz': 3, 'px': 4, 'dxy': 5, 'dyz': 6, 'dz2': 7, 'dxz': 8, 'dx2': 9} elif n == 19: norb = {'s+': 1, 's-up': 1, 's-': 2, 's-down': 2, 'py+': 3, 'py-up': 3, 'py-': 4, 'py-down': 4, 'pz+': 5, 'pz-up': 5, 'pz-': 6, 'pz-down': 6, 'px+': 7, 'px-up': 7, 'px-': 8, 'px-down': 8, 'dxy+': 9, 'dxy-up': 9, 'dxy-': 10, 'dxy-down': 10, 'dyz+': 11, 'dyz-up': 11, 'dyz-': 12, 'dyz-down': 12, 'dz2+': 13, 'dz2-up': 13, 'dz2-': 14, 'dz2-down': 14, 'dxz+': 15, 'dxz-up': 15, 'dxz-': 16, 'dxz-down': 16, 'dx2+': 17, 'dx2-up': 17, 'dx2-': 18, 'dx2-down': 18} elif n == 17: norb = { 's': 1, 'py': 2, 'pz': 3, 'px': 4, 'dxy': 5, 'dyz': 6, 'dz2': 7, 'dxz': 8, 'dx2': 9, 'fy(3x2-y2)': 10, 'fxyz': 11, 'fyz2': 12, 'fz3': 13, 'fxz2': 14, 'fz(x2-y2)': 15, 'fx(x2-3y2)': 16, } elif n == 19: norb = { 's+': 1, 's-up': 1, 's-': 2, 's-down': 2, 'py+': 3, 'py-up': 3, 'py-': 4, 'py-down': 4, 'pz+': 5, 'pz-up': 5, 'pz-': 6, 'pz-down': 6, 'px+': 7, 'px-up': 7, 'px-': 8, 'px-down': 8, 'dxy+': 9, 'dxy-up': 9, 'dxy-': 10, 'dxy-down': 10, 'dyz+': 11, 'dyz-up': 11, 'dyz-': 12, 'dyz-down': 12, 'dz2+': 13, 'dz2-up': 13, 'dz2-': 14, 'dz2-down': 14, 'dxz+': 15, 'dxz-up': 15, 'dxz-': 16, 'dxz-down': 16, 'dx2+': 17, 'dx2-up': 17, 'dx2-': 18, 'dx2-down': 18 } else: norb = { 's+': 1, 's-up': 1, 's-': 2, 's-down': 2, 'py+': 3, 'py-up': 3, 'py-': 4, 'py-down': 4, 'pz+': 5, 'pz-up': 5, 'pz-': 6, 'pz-down': 6, 'px+': 7, 'px-up': 7, 'px-': 8, 'px-down': 8, 'dxy+': 9, 'dxy-up': 9, 'dxy-': 10, 'dxy-down': 10, 'dyz+': 11, 'dyz-up': 11, 'dyz-': 12, 'dyz-down': 12, 'dz2+': 13, 'dz2-up': 13, 'dz2-': 14, 'dz2-down': 14, 'dxz+': 15, 'dxz-up': 15, 'dxz-': 16, 'dxz-down': 16, 'dx2+': 17, 'dx2-up': 17, 'dx2-': 18, 'dx2-down': 18, 'fy(3x2-y2)+': 19, 'fy(3x2-y2)-up': 19, 'fy(3x2-y2)-': 20, 'fy(3x2-y2)-down': 20, 'fxyz+': 21, 'fxyz-up': 21, 'fxyz-': 22, 'fxyz-down': 22, 'fyz2+': 23, 'fyz2-up': 23, 'fyz2-': 24, 'fyz2-down': 24, 'fz3+': 25, 'fz3-up': 25, 'fz3-': 26, 'fz3-down': 26, 'fxz2+': 27, 'fxz2-up': 27, 'fxz2-': 28, 'fxz2-down': 28, 'fz(x2-y2)+': 29, 'fz(x2-y2)-up': 29, 'fz(x2-y2)-': 30, 'fz(x2-y2)-down': 30, 'fx(x2-3y2)+': 31, 'fx(x2-3y2)-up': 31, 'fx(x2-3y2)-': 32, 'fx(x2-3y2)-down': 32, } return self._site_dos[atom, norb[orbital.lower()], :] def _get_dos(self): if self._total_dos.shape[0] == 3: return self._total_dos[1, :] elif self._total_dos.shape[0] == 5: return self._total_dos[1:3, :] dos = property(_get_dos, None, None, 'Average DOS in cell') def _get_integrated_dos(self): if self._total_dos.shape[0] == 3: return self._total_dos[2, :] elif self._total_dos.shape[0] == 5: return self._total_dos[3:5, :] integrated_dos = property(_get_integrated_dos, None, None, 'Integrated average DOS in cell') def read_doscar(self, fname="DOSCAR"): """Read a VASP DOSCAR file""" f = open(fname) natoms = int(f.readline().split()[0]) [f.readline() for nn in range(4)] # Skip next 4 lines. # First we have a block with total and total integrated DOS ndos = int(f.readline().split()[2]) dos = [] for nd in range(ndos): dos.append(np.array([float(x) for x in f.readline().split()])) self._total_dos = np.array(dos).T # Next we have one block per atom, if INCAR contains the stuff # necessary for generating site-projected DOS dos = [] for na in range(natoms): line = f.readline() if line == '': # No site-projected DOS break ndos = int(line.split()[2]) line = f.readline().split() cdos = np.empty((ndos, len(line))) cdos[0] = np.array(line) for nd in range(1, ndos): line = f.readline().split() cdos[nd] = np.array([float(x) for x in line]) dos.append(cdos.T) self._site_dos = np.array(dos) class xdat2traj: def __init__(self, trajectory=None, atoms=None, poscar=None, xdatcar=None, sort=None, calc=None): """ trajectory is the name of the file to write the trajectory to poscar is the name of the poscar file to read. Default: POSCAR """ if not poscar: self.poscar = 'POSCAR' else: self.poscar = poscar if not atoms: # This reads the atoms sorted the way VASP wants self.atoms = ase.io.read(self.poscar, format='vasp') resort_reqd = True else: # Assume if we pass atoms that it is sorted the way we want self.atoms = atoms resort_reqd = False if not calc: self.calc = Vasp() else: self.calc = calc if not sort: if not hasattr(self.calc, 'sort'): self.calc.sort = list(range(len(self.atoms))) else: self.calc.sort = sort self.calc.resort = list(range(len(self.calc.sort))) for n in range(len(self.calc.resort)): self.calc.resort[self.calc.sort[n]] = n if not xdatcar: self.xdatcar = 'XDATCAR' else: self.xdatcar = xdatcar if not trajectory: self.trajectory = 'out.traj' else: self.trajectory = trajectory self.out = ase.io.trajectory.Trajectory(self.trajectory, mode='w') if resort_reqd: self.atoms = self.atoms[self.calc.resort] self.energies = self.calc.read_energy(all=True)[1] # Forces are read with the atoms sorted using resort self.forces = self.calc.read_forces(self.atoms, all=True) def convert(self): lines = open(self.xdatcar).readlines() if len(lines[7].split()) == 0: del(lines[0:8]) elif len(lines[5].split()) == 0: del(lines[0:6]) elif len(lines[4].split()) == 0: del(lines[0:5]) elif lines[7].split()[0] == 'Direct': del(lines[0:8]) step = 0 iatom = 0 scaled_pos = [] for line in lines: if iatom == len(self.atoms): if step == 0: self.out.write_header(self.atoms[self.calc.resort]) scaled_pos = np.array(scaled_pos) # Now resort the positions to match self.atoms self.atoms.set_scaled_positions(scaled_pos[self.calc.resort]) calc = SinglePointCalculator(self.atoms, energy=self.energies[step], forces=self.forces[step]) self.atoms.set_calculator(calc) self.out.write(self.atoms) scaled_pos = [] iatom = 0 step += 1 else: if not line.split()[0] == 'Direct': iatom += 1 scaled_pos.append([float(line.split()[n]) for n in range(3)]) # Write also the last image # I'm sure there is also more clever fix... if step == 0: self.out.write_header(self.atoms[self.calc.resort]) scaled_pos = np.array(scaled_pos)[self.calc.resort] self.atoms.set_scaled_positions(scaled_pos) calc = SinglePointCalculator(self.atoms, energy=self.energies[step], forces=self.forces[step]) self.atoms.set_calculator(calc) self.out.write(self.atoms) self.out.close()