root / ase / calculators / abinit.py @ 5
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"""This module defines an ASE interface to ABINIT.
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http://www.abinit.org/
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"""
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import os |
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from glob import glob |
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from os.path import join, isfile, islink |
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import numpy as np |
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from ase.data import chemical_symbols |
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from ase.data import atomic_numbers |
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from ase.units import Bohr, Hartree |
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class Abinit: |
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"""Class for doing ABINIT calculations.
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The default parameters are very close to those that the ABINIT
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Fortran code would use. These are the exceptions::
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calc = Abinit(label='abinit', xc='LDA', pulay=5, mix=0.1)
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Use the set_inp method to set extra INPUT parameters::
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calc.set_inp('nstep', 30)
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"""
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def __init__(self, label='abinit', xc='LDA', kpts=None, nbands=0, |
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width=0.04*Hartree, ecut=None, charge=0, |
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pulay=5, mix=0.1, pps='fhi', toldfe=1.0e-6 |
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): |
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"""Construct ABINIT-calculator object.
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Parameters
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==========
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label: str
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Prefix to use for filenames (label.in, label.txt, ...).
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Default is 'abinit'.
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xc: str
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Exchange-correlation functional. Must be one of LDA, PBE,
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revPBE, RPBE.
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kpts: list of three int
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Monkhost-Pack sampling.
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nbands: int
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Number of bands.
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Default is 0.
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width: float
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Fermi-distribution width in eV.
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Default is 0.04 Hartree.
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ecut: float
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Planewave cutoff energy in eV.
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No default.
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charge: float
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Total charge of the system.
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Default is 0.
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pulay: int
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Number of old densities to use for Pulay mixing.
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mix: float
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Mixing parameter between zero and one for density mixing.
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Examples
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========
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Use default values:
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>>> h = Atoms('H', calculator=Abinit())
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>>> h.center(vacuum=3.0)
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>>> e = h.get_potential_energy()
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"""
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if not nbands > 0: |
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raise ValueError('Number of bands (nbands) not set') |
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if ecut is None: |
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raise ValueError('Planewave cutoff energy in eV (ecut) not set') |
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self.label = label#################### != out |
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self.xc = xc
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self.kpts = kpts
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self.nbands = nbands
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self.width = width
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self.ecut = ecut
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self.charge = charge
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self.pulay = pulay
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self.mix = mix
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self.pps = pps
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self.toldfe = toldfe
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if not pps in ['fhi', 'hgh', 'hgh.sc']: |
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raise ValueError('Unexpected PP identifier %s' % pps) |
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self.converged = False |
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self.inp = {}
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self.n_entries_int = 20 # integer entries per line |
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self.n_entries_float = 8 # float entries per line |
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def update(self, atoms): |
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if (not self.converged or |
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len(self.numbers) != len(atoms) or |
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(self.numbers != atoms.get_atomic_numbers()).any()):
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self.initialize(atoms)
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self.calculate(atoms)
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elif ((self.positions != atoms.get_positions()).any() or |
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(self.pbc != atoms.get_pbc()).any() or |
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(self.cell != atoms.get_cell()).any()):
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self.calculate(atoms)
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def initialize(self, atoms): |
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self.numbers = atoms.get_atomic_numbers().copy()
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self.species = []
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for a, Z in enumerate(self.numbers): |
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if Z not in self.species: |
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self.species.append(Z)
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if 'ABINIT_PP_PATH' in os.environ: |
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pppaths = os.environ['ABINIT_PP_PATH'].split(':') |
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else:
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pppaths = [] |
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self.ppp_list = []
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if self.xc != 'LDA': |
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xcname = 'GGA'
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else:
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xcname = 'LDA'
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for Z in self.species: |
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symbol = chemical_symbols[abs(Z)]
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number = atomic_numbers[symbol] |
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pps = self.pps
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if pps == 'fhi': |
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name = '%02d-%s.%s.fhi' % (number, symbol, xcname)
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elif pps in ('hgh', 'hgh.sc'): |
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hghtemplate = '%d%s.%s.hgh' # E.g. "42mo.6.hgh" |
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# There might be multiple files with different valence
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# electron counts, so we must choose between
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# the ordinary and the semicore versions for some elements.
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#
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# Therefore we first use glob to get all relevant files,
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# then pick the correct one afterwards.
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name = hghtemplate % (number, symbol.lower(), '*')
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found = False
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for path in pppaths: |
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if pps.startswith('hgh'): |
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filenames = glob(join(path, name)) |
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if not filenames: |
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continue
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assert len(filenames) in [0, 1, 2] |
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if pps == 'hgh': |
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selector = min # Lowest possible valence electron count |
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else:
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assert pps == 'hgh.sc' |
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selector = max # Semicore - highest electron count |
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Z = selector([int(os.path.split(name)[1].split('.')[1]) |
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for name in filenames]) |
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name = hghtemplate % (number, symbol.lower(), str(Z))
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filename = join(path, name) |
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if isfile(filename) or islink(filename): |
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found = True
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self.ppp_list.append(filename)
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break
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if not found: |
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raise RuntimeError('No pseudopotential for %s!' % symbol) |
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self.converged = False |
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def get_potential_energy(self, atoms, force_consistent=False): |
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self.update(atoms)
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if force_consistent:
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return self.efree |
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else:
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# Energy extrapolated to zero Kelvin:
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return (self.etotal + self.efree) / 2 |
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def get_number_of_bands(self): |
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return self.nbands |
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def get_kpts_info(self, kpt=0, spin=0, mode='eigenvalues'): |
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return self.read_kpts_info(kpt, spin, mode) |
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def get_k_point_weights(self): |
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return self.get_kpts_info(kpt=0, spin=0, mode='k_point_weights') |
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def get_bz_k_points(self): |
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raise NotImplementedError |
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def get_ibz_k_points(self): |
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return self.get_kpts_info(kpt=0, spin=0, mode='ibz_k_points') |
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def get_fermi_level(self): |
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return self.read_fermi() |
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def get_eigenvalues(self, kpt=0, spin=0): |
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return self.get_kpts_info(kpt, spin, 'eigenvalues') |
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def get_occupations(self, kpt=0, spin=0): |
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return self.get_kpts_info(kpt, spin, 'occupations') |
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def get_forces(self, atoms): |
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self.update(atoms)
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return self.forces.copy() |
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def get_stress(self, atoms): |
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self.update(atoms)
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return self.stress.copy() |
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def calculate(self, atoms): |
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self.positions = atoms.get_positions().copy()
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self.cell = atoms.get_cell().copy()
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self.pbc = atoms.get_pbc().copy()
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self.write_files()
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self.write_inp(atoms)
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abinit = os.environ['ABINIT_SCRIPT']
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locals = {'label': self.label}
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# Now, because (stupidly) abinit when it finds a name it uses nameA
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# and when nameA exists it uses nameB, etc.
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# we need to rename our *.txt file to *.txt.bak
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filename = self.label + '.txt' |
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if islink(filename) or isfile(filename): |
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os.rename(filename, filename+'.bak')
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execfile(abinit, {}, locals) |
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exitcode = locals['exitcode'] |
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if exitcode != 0: |
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raise RuntimeError(('Abinit exited with exit code: %d. ' + |
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'Check %s.log for more information.') %
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(exitcode, self.label))
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self.read()
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self.converged = True |
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def write_files(self): |
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"""Write input parameters to files-file."""
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fh = open(self.label + '.files', 'w') |
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import getpass |
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#find a suitable default scratchdir (should be writeable!)
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username=getpass.getuser() |
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if os.access("/scratch/"+username,os.W_OK): |
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scratch = "/scratch/"+username
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elif os.access("/scratch/",os.W_OK): |
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scratch = "/scratch/"
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else:
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if os.access(os.curdir,os.W_OK):
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scratch = os.curdir #if no /scratch use curdir
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else:
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raise IOError,"No suitable scratch directory and no write access to current dir" |
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fh.write('%s\n' % (self.label+'.in')) # input |
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fh.write('%s\n' % (self.label+'.txt')) # output |
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fh.write('%s\n' % (self.label+'i')) # input |
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fh.write('%s\n' % (self.label+'o')) # output |
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# scratch files
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fh.write('%s\n' % (os.path.join(scratch, self.label+'.abinit'))) |
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# Provide the psp files
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for ppp in self.ppp_list: |
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fh.write('%s\n' % (ppp)) # psp file path |
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fh.close() |
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def set_inp(self, key, value): |
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"""Set INPUT parameter."""
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self.inp[key] = value
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def write_inp(self, atoms): |
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"""Write input parameters to in-file."""
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fh = open(self.label + '.in', 'w') |
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inp = {
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#'SystemLabel': self.label,
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#'LatticeConstant': 1.0,
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'natom': len(atoms), |
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'charge': self.charge, |
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'nband': self.nbands, |
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#'DM.UseSaveDM': self.converged,
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#'SolutionMethod': 'diagon',
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'npulayit': self.pulay, # default 7 |
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'diemix': self.mix |
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} |
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if self.ecut is not None: |
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inp['ecut'] = str(self.ecut)+' eV' # default Ha |
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if self.width is not None: |
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inp['tsmear'] = str(self.width)+' eV' # default Ha |
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fh.write('occopt 3 # Fermi-Dirac smearing\n')
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inp['ixc'] = { # default 1 |
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'LDA': 7, |
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'PBE': 11, |
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'revPBE': 14, |
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'RPBE': 15, |
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'WC': 23 |
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}[self.xc]
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magmoms = atoms.get_initial_magnetic_moments() |
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if magmoms.any():
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inp['nsppol'] = 2 |
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fh.write('spinat\n')
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for n, M in enumerate(magmoms): |
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if M != 0: |
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fh.write('%.14f %.14f %.14f\n' % (0, 0, M)) |
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else:
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inp['nsppol'] = 1 |
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#fh.write('spinat\n')
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#for n, M in enumerate(magmoms):
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# if M != 0:
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# fh.write('%.14f\n' % (M))
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inp.update(self.inp)
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for key, value in inp.items(): |
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if value is None: |
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continue
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if isinstance(value, list): |
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fh.write('%block %s\n' % key)
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for line in value: |
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fh.write(' '.join(['%s' % x for x in line]) + '\n') |
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fh.write('%endblock %s\n' % key)
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|
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unit = keys_with_units.get(inpify(key)) |
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if unit is None: |
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fh.write('%s %s\n' % (key, value))
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else:
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if 'fs**2' in unit: |
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value /= fs**2
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elif 'fs' in unit: |
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value /= fs |
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fh.write('%s %f %s\n' % (key, value, unit))
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|
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fh.write('#Definition of the unit cell\n')
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fh.write('acell\n')
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fh.write('%.14f %.14f %.14f Angstrom\n' % (1.0, 1.0, 1.0)) |
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fh.write('rprim\n')
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for v in self.cell: |
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fh.write('%.14f %.14f %.14f\n' % tuple(v)) |
| 347 |
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fh.write('chkprim 0 # Allow non-primitive cells\n')
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|
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fh.write('#Definition of the atom types\n')
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fh.write('ntypat %d\n' % (len(self.species))) |
| 352 |
fh.write('znucl')
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for n, Z in enumerate(self.species): |
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fh.write(' %d' % (Z))
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fh.write('\n')
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fh.write('#Enumerate different atomic species\n')
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fh.write('typat')
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fh.write('\n')
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self.types = []
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for Z in self.numbers: |
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for n, Zs in enumerate(self.species): |
| 362 |
if Z == Zs:
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self.types.append(n+1) |
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for n, type in enumerate(self.types): |
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fh.write(' %d' % (type)) |
| 366 |
if n > 1 and ((n % self.n_entries_int) == 1): |
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fh.write('\n')
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fh.write('\n')
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|
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fh.write('#Definition of the atoms\n')
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fh.write('xangst\n')
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a = 0
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for pos, Z in zip(self.positions, self.numbers): |
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a += 1
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fh.write('%.14f %.14f %.14f\n' % tuple(pos)) |
| 376 |
|
| 377 |
if self.kpts is not None: |
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fh.write('kptopt %d\n' % (1)) |
| 379 |
fh.write('ngkpt ')
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| 380 |
fh.write('%d %d %d\n' % tuple(self.kpts)) |
| 381 |
|
| 382 |
fh.write('#Definition of the SCF procedure\n')
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| 383 |
fh.write('toldfe %.1g\n' % self.toldfe) |
| 384 |
fh.write('chkexit 1 # abinit.exit file in the running directory terminates after the current SCF\n')
|
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|
| 386 |
fh.close() |
| 387 |
|
| 388 |
def read_fermi(self): |
| 389 |
"""Method that reads Fermi energy in Hartree from the output file
|
| 390 |
and returns it in eV"""
|
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E_f=None
|
| 392 |
filename = self.label + '.txt' |
| 393 |
text = open(filename).read().lower()
|
| 394 |
assert 'error' not in text |
| 395 |
for line in iter(text.split('\n')): |
| 396 |
if line.rfind('fermi (or homo) energy (hartree) =') > -1: |
| 397 |
E_f = float(line.split('=')[1].strip().split()[0]) |
| 398 |
return E_f*Hartree
|
| 399 |
|
| 400 |
def read_kpts_info(self, kpt=0, spin=0, mode='eigenvalues'): |
| 401 |
""" Returns list of eigenvalues, occupations, kpts weights, or
|
| 402 |
kpts coordinates for given kpt and spin"""
|
| 403 |
# output may look like this (or without occupation entries); 8 entries per line:
|
| 404 |
#
|
| 405 |
# Eigenvalues (hartree) for nkpt= 20 k points:
|
| 406 |
# kpt# 1, nband= 3, wtk= 0.01563, kpt= 0.0625 0.0625 0.0625 (reduced coord)
|
| 407 |
# -0.09911 0.15393 0.15393
|
| 408 |
# occupation numbers for kpt# 1
|
| 409 |
# 2.00000 0.00000 0.00000
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| 410 |
# kpt# 2, nband= 3, wtk= 0.04688, kpt= 0.1875 0.0625 0.0625 (reduced coord)
|
| 411 |
# ...
|
| 412 |
#
|
| 413 |
assert mode in ['eigenvalues' , 'occupations', 'ibz_k_points', 'k_point_weights'], 'mode not in [\'eigenvalues\' , \'occupations\', \'ibz_k_points\', \'k_point_weights\']' |
| 414 |
# number of lines of eigenvalues/occupations for a kpt
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| 415 |
n_entry_lines = max(1, int(self.nbands/self.n_entries_float)) |
| 416 |
#
|
| 417 |
filename = self.label + '.txt' |
| 418 |
text = open(filename).read().lower()
|
| 419 |
assert 'error' not in text |
| 420 |
lines = iter(text.split('\n')) |
| 421 |
text_list = [] |
| 422 |
# find the begining line of eigenvalues
|
| 423 |
contains_eigenvalues = False
|
| 424 |
for line in lines: |
| 425 |
#if line.rfind('eigenvalues (hartree) for nkpt') > -1: #MDTMP
|
| 426 |
if line.rfind('eigenvalues ( ev ) for nkpt') > -1: |
| 427 |
n_kpts = int(line.split('nkpt=')[1].strip().split()[0]) |
| 428 |
contains_eigenvalues = True
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| 429 |
break
|
| 430 |
# find the end line of eigenvalues starting from linenum
|
| 431 |
for line in lines: |
| 432 |
text_list.append(line) |
| 433 |
if not line.strip(): # find a blank line |
| 434 |
break
|
| 435 |
# remove last (blank) line
|
| 436 |
text_list = text_list[:-1]
|
| 437 |
|
| 438 |
assert contains_eigenvalues, 'No eigenvalues found in the output' |
| 439 |
|
| 440 |
# join text eigenvalues description with eigenvalues
|
| 441 |
# or occupation numbers for kpt# with occupations
|
| 442 |
contains_occupations = False
|
| 443 |
for line in text_list: |
| 444 |
if line.rfind('occupation numbers') > -1: |
| 445 |
contains_occupations = True
|
| 446 |
break
|
| 447 |
if mode == 'occupations': |
| 448 |
assert contains_occupations, 'No occupations found in the output' |
| 449 |
|
| 450 |
if contains_occupations:
|
| 451 |
range_kpts = 2*n_kpts
|
| 452 |
else:
|
| 453 |
range_kpts = n_kpts |
| 454 |
#
|
| 455 |
values_list = [] |
| 456 |
offset = 0
|
| 457 |
for kpt_entry in range(range_kpts): |
| 458 |
full_line = ''
|
| 459 |
for entry_line in range(n_entry_lines+1): |
| 460 |
full_line = full_line+str(text_list[offset+entry_line])
|
| 461 |
first_line = text_list[offset] |
| 462 |
if mode == 'occupations': |
| 463 |
if first_line.rfind('occupation numbers') > -1: |
| 464 |
# extract numbers
|
| 465 |
full_line = [float(v) for v in full_line.split('#')[1].strip().split()[1:]] |
| 466 |
values_list.append(full_line) |
| 467 |
elif mode in ['eigenvalues', 'ibz_k_points', 'k_point_weights']: |
| 468 |
if first_line.rfind('reduced coord') > -1: |
| 469 |
# extract numbers
|
| 470 |
if mode == 'eigenvalues': |
| 471 |
#full_line = [Hartree*float(v) for v in full_line.split(')')[1].strip().split()[:]] # MDTMP
|
| 472 |
full_line = [float(v) for v in full_line.split(')')[1].strip().split()[:]] |
| 473 |
elif mode == 'ibz_k_points': |
| 474 |
full_line = [float(v) for v in full_line.split('kpt=')[1].strip().split('(')[0].split()] |
| 475 |
else:
|
| 476 |
full_line = float(full_line.split('wtk=')[1].strip().split(',')[0].split()[0]) |
| 477 |
values_list.append(full_line) |
| 478 |
offset = offset+n_entry_lines+1
|
| 479 |
#
|
| 480 |
if mode in ['occupations', 'eigenvalues']: |
| 481 |
return np.array(values_list[kpt])
|
| 482 |
else:
|
| 483 |
return np.array(values_list)
|
| 484 |
|
| 485 |
def read(self): |
| 486 |
"""Read results from ABINIT's text-output file."""
|
| 487 |
filename = self.label + '.txt' |
| 488 |
text = open(filename).read().lower()
|
| 489 |
assert 'error' not in text |
| 490 |
assert 'was not enough scf cycles to converge' not in text |
| 491 |
# some consistency ckecks
|
| 492 |
for line in iter(text.split('\n')): |
| 493 |
if line.rfind('natom ') > -1: |
| 494 |
natom = int(line.split()[-1]) |
| 495 |
assert natom == len(self.numbers) |
| 496 |
for line in iter(text.split('\n')): |
| 497 |
if line.rfind('znucl ') > -1: |
| 498 |
znucl = [float(Z) for Z in line.split()[1:]] |
| 499 |
for n, Z in enumerate(self.species): |
| 500 |
assert Z == znucl[n]
|
| 501 |
lines = text.split('\n')
|
| 502 |
for n, line in enumerate(lines): |
| 503 |
if line.rfind(' typat ') > -1: |
| 504 |
nlines = len(self.numbers) / self.n_entries_int |
| 505 |
typat = [int(t) for t in line.split()[1:]] # first line |
| 506 |
for nline in range(nlines): # remaining lines |
| 507 |
for t in lines[1 + n + nline].split()[:]: |
| 508 |
typat.append(int(t))
|
| 509 |
for n, t in enumerate(self.types): |
| 510 |
assert t == typat[n]
|
| 511 |
|
| 512 |
lines = iter(text.split('\n')) |
| 513 |
# Stress:
|
| 514 |
# Printed in the output in the following format [Hartree/Bohr^3]:
|
| 515 |
# sigma(1 1)= 4.02063464E-04 sigma(3 2)= 0.00000000E+00
|
| 516 |
# sigma(2 2)= 4.02063464E-04 sigma(3 1)= 0.00000000E+00
|
| 517 |
# sigma(3 3)= 4.02063464E-04 sigma(2 1)= 0.00000000E+00
|
| 518 |
for line in lines: |
| 519 |
if line.rfind('cartesian components of stress tensor (hartree/bohr^3)') > -1: |
| 520 |
self.stress = np.empty((3, 3)) |
| 521 |
for i in range(3): |
| 522 |
entries = lines.next().split() |
| 523 |
self.stress[i,i] = float(entries[2]) |
| 524 |
self.stress[min(3, 4-i)-1, max(1, 2-i)-1] = float(entries[5]) |
| 525 |
self.stress[max(1, 2-i)-1, min(3, 4-i)-1] = float(entries[5]) |
| 526 |
self.stress = self.stress*Hartree/Bohr**3 |
| 527 |
break
|
| 528 |
else:
|
| 529 |
raise RuntimeError |
| 530 |
|
| 531 |
# Energy [Hartree]:
|
| 532 |
# Warning: Etotal could mean both electronic energy and free energy!
|
| 533 |
for line in iter(text.split('\n')): |
| 534 |
if line.rfind('>>>>> internal e=') > -1: |
| 535 |
self.etotal = float(line.split('=')[-1])*Hartree |
| 536 |
for line1 in iter(text.split('\n')): |
| 537 |
if line1.rfind('>>>>>>>>> etotal=') > -1: |
| 538 |
self.efree = float(line1.split('=')[-1])*Hartree |
| 539 |
break
|
| 540 |
else:
|
| 541 |
raise RuntimeError |
| 542 |
break
|
| 543 |
else:
|
| 544 |
for line2 in iter(text.split('\n')): |
| 545 |
if line2.rfind('>>>>>>>>> etotal=') > -1: |
| 546 |
self.etotal = float(line2.split('=')[-1])*Hartree |
| 547 |
self.efree = self.etotal |
| 548 |
break
|
| 549 |
else:
|
| 550 |
raise RuntimeError |
| 551 |
|
| 552 |
# Forces:
|
| 553 |
for line in lines: |
| 554 |
if line.rfind('cartesian forces (ev/angstrom) at end:') > -1: |
| 555 |
forces = [] |
| 556 |
for i in range(len(self.numbers)): |
| 557 |
forces.append(np.array([float(f) for f in lines.next().split()[1:]])) |
| 558 |
self.forces = np.array(forces)
|
| 559 |
break
|
| 560 |
else:
|
| 561 |
raise RuntimeError |
| 562 |
|
| 563 |
def inpify(key): |
| 564 |
return key.lower().replace('_', '').replace('.', '').replace('-', '') |
| 565 |
|
| 566 |
|
| 567 |
keys_with_units = {
|
| 568 |
} |
| 569 |
#keys_with_units = {
|
| 570 |
# 'paoenergyshift': 'eV',
|
| 571 |
# 'zmunitslength': 'Bohr',
|
| 572 |
# 'zmunitsangle': 'rad',
|
| 573 |
# 'zmforcetollength': 'eV/Ang',
|
| 574 |
# 'zmforcetolangle': 'eV/rad',
|
| 575 |
# 'zmmaxdispllength': 'Ang',
|
| 576 |
# 'zmmaxdisplangle': 'rad',
|
| 577 |
# 'ecut': 'eV',
|
| 578 |
# 'dmenergytolerance': 'eV',
|
| 579 |
# 'electronictemperature': 'eV',
|
| 580 |
# 'oneta': 'eV',
|
| 581 |
# 'onetaalpha': 'eV',
|
| 582 |
# 'onetabeta': 'eV',
|
| 583 |
# 'onrclwf': 'Ang',
|
| 584 |
# 'onchemicalpotentialrc': 'Ang',
|
| 585 |
# 'onchemicalpotentialtemperature': 'eV',
|
| 586 |
# 'mdmaxcgdispl': 'Ang',
|
| 587 |
# 'mdmaxforcetol': 'eV/Ang',
|
| 588 |
# 'mdmaxstresstol': 'eV/Ang**3',
|
| 589 |
# 'mdlengthtimestep': 'fs',
|
| 590 |
# 'mdinitialtemperature': 'eV',
|
| 591 |
# 'mdtargettemperature': 'eV',
|
| 592 |
# 'mdtargetpressure': 'eV/Ang**3',
|
| 593 |
# 'mdnosemass': 'eV*fs**2',
|
| 594 |
# 'mdparrinellorahmanmass': 'eV*fs**2',
|
| 595 |
# 'mdtaurelax': 'fs',
|
| 596 |
# 'mdbulkmodulus': 'eV/Ang**3',
|
| 597 |
# 'mdfcdispl': 'Ang',
|
| 598 |
# 'warningminimumatomicdistance': 'Ang',
|
| 599 |
# 'rcspatial': 'Ang',
|
| 600 |
# 'kgridcutoff': 'Ang',
|
| 601 |
# 'latticeconstant': 'Ang'}
|