Source code for ase.calculators.castep

# -*- coding: utf-8 -*-
"""This module defines an interface to CASTEP for
    use by the ASE (Webpage: http://wiki.fysik.dtu.dk/ase)

Authors:
    Max Hoffmann, max.hoffmann@ch.tum.de
    Joerg Meyer, joerg.meyer@ch.tum.de
    Simon P. Rittmeyer, simon.rittmeyer@tum.de

Contributors:
    Juan M. Lorenzi, juan.lorenzi@tum.de
    Georg S. Michelitsch, georg.michelitsch@tch.tum.de
    Reinhard J. Maurer, reinhard.maurer@yale.edu
    Simone Sturniolo, simone.sturniolo@stfc.ac.uk
"""

import difflib
import numpy as np
import os
import re
import glob
import shutil
import sys
import json
import time
import tempfile
import warnings
import subprocess
from copy import deepcopy
from collections import namedtuple
from itertools import product

import ase
import ase.units as units
from ase.calculators.general import Calculator
from ase.calculators.calculator import compare_atoms
from ase.calculators.calculator import PropertyNotImplementedError
from ase.calculators.calculator import kpts2sizeandoffsets
from ase.dft.kpoints import BandPath
from ase.utils import basestring
from ase.parallel import paropen
from ase.io.castep import read_param
from ase.io.castep import read_bands
from ase.constraints import FixCartesian

__all__ = [
    'Castep',
    'CastepCell',
    'CastepParam',
    'create_castep_keywords']

contact_email = 'simon.rittmeyer@tum.de'

# A convenient table to avoid the previously used "eval"
_tf_table = {
    '': True,  # Just the keyword is equivalent to True
    'True': True,
    'False': False}


def _self_getter(getf):
    # A decorator that makes it so that if no 'atoms' argument is passed to a
    # getter function, self.atoms is used instead

    def decor_getf(self, atoms=None, *args, **kwargs):

        if atoms is None:
            atoms = self.atoms

        return getf(self, atoms, *args, **kwargs)

    return decor_getf


[docs]class Castep(Calculator): r""" CASTEP Interface Documentation Introduction ============ CASTEP_ [1]_ W_ is a software package which uses density functional theory to provide a good atomic-level description of all manner of materials and molecules. CASTEP can give information about total energies, forces and stresses on an atomic system, as well as calculating optimum geometries, band structures, optical spectra, phonon spectra and much more. It can also perform molecular dynamics simulations. The CASTEP calculator interface class offers intuitive access to all CASTEP settings and most results. All CASTEP specific settings are accessible via attribute access (*i.e*. ``calc.param.keyword = ...`` or ``calc.cell.keyword = ...``) Getting Started: ================ Set the environment variables appropriately for your system. >>> export CASTEP_COMMAND=' ... ' >>> export CASTEP_PP_PATH=' ... ' Note: alternatively to CASTEP_PP_PATH one can set PSPOT_DIR as CASTEP consults this by default, i.e. >>> export PSPOT_DIR=' ... ' Running the Calculator ====================== The default initialization command for the CASTEP calculator is .. class:: Castep(directory='CASTEP', label='castep') To do a minimal run one only needs to set atoms, this will use all default settings of CASTEP, meaning LDA, singlepoint, etc.. With a generated *castep_keywords.json* in place all options are accessible by inspection, *i.e.* tab-completion. This works best when using ``ipython``. All options can be accessed via ``calc.param.<TAB>`` or ``calc.cell.<TAB>`` and documentation is printed with ``calc.param.<keyword> ?`` or ``calc.cell.<keyword> ?``. All options can also be set directly using ``calc.keyword = ...`` or ``calc.KEYWORD = ...`` or even ``ialc.KeYwOrD`` or directly as named arguments in the call to the constructor (*e.g.* ``Castep(task='GeometryOptimization')``). If using this calculator on a machine without CASTEP, one might choose to copy a *castep_keywords.json* file generated elsewhere in order to access this feature: the file will be used if located in the working directory, *$HOME/.ase/* or *ase/ase/calculators/* within the ASE library. The file should be generated the first time it is needed, but you can generate a new keywords file in the currect directory with ``python -m ase.calculators.castep``. All options that go into the ``.param`` file are held in an ``CastepParam`` instance, while all options that go into the ``.cell`` file and don't belong to the atoms object are held in an ``CastepCell`` instance. Each instance can be created individually and can be added to calculators by attribute assignment, *i.e.* ``calc.param = param`` or ``calc.cell = cell``. All internal variables of the calculator start with an underscore (_). All cell attributes that clearly belong into the atoms object are blocked. Setting ``calc.atoms_attribute`` (*e.g.* ``= positions``) is sent directly to the atoms object. Arguments: ========== ========================= ==================================================== Keyword Description ========================= ==================================================== ``directory`` The relative path where all input and output files will be placed. If this does not exist, it will be created. Existing directories will be moved to directory-TIMESTAMP unless self._rename_existing_dir is set to false. ``label`` The prefix of .param, .cell, .castep, etc. files. ``castep_command`` Command to run castep. Can also be set via the bash environment variable ``CASTEP_COMMAND``. If none is given or found, will default to ``castep`` ``check_castep_version`` Boolean whether to check if the installed castep version matches the version from which the available options were deduced. Defaults to ``False``. ``castep_pp_path`` The path where the pseudopotentials are stored. Can also be set via the bash environment variables ``PSPOT_DIR`` (preferred) and ``CASTEP_PP_PATH``. Will default to the current working directory if none is given or found. Note that pseudopotentials may be generated on-the-fly if they are not found. ``find_pspots`` Boolean whether to search for pseudopotentials in ``<castep_pp_path>`` or not. If activated, files in this directory will be checked for typical names. If files are not found, they will be generated on the fly, depending on the ``_build_missing_pspots`` value. A RuntimeError will be raised in case multiple files per element are found. Defaults to ``False``. ``keyword_tolerance`` Integer to indicate the level of tolerance to apply validation of any parameters set in the CastepCell or CastepParam objects against the ones found in castep_keywords. Levels are as following: 0 = no tolerance, keywords not found in castep_keywords will raise an exception 1 = keywords not found will be accepted but produce a warning (default) 2 = keywords not found will be accepted silently 3 = no attempt is made to look for castep_keywords.json at all ========================= ==================================================== Additional Settings =================== ========================= ==================================================== Internal Setting Description ========================= ==================================================== ``_castep_command`` (``=castep``): the actual shell command used to call CASTEP. ``_check_checkfile`` (``=True``): this makes write_param() only write a continue or reuse statement if the addressed .check or .castep_bin file exists in the directory. ``_copy_pspots`` (``=False``): if set to True the calculator will actually copy the needed pseudo-potential (\*.usp) file, usually it will only create symlinks. ``_link_pspots`` (``=True``): if set to True the calculator will actually will create symlinks to the needed pseudo potentials. Set this option (and ``_copy_pspots``) to False if you rather want to access your pseudo potentials using the PSPOT_DIR environment variable that is read by CASTEP. *Note:* This option has no effect if ``copy_pspots`` is True.. ``_build_missing_pspots`` (``=True``): if set to True, castep will generate missing pseudopotentials on the fly. If not, a RuntimeError will be raised if not all files were found. ``_export_settings`` (``=True``): if this is set to True, all calculator internal settings shown here will be included in the .param in a comment line (#) and can be read again by merge_param. merge_param can be forced to ignore this directive using the optional argument ``ignore_internal_keys=True``. ``_force_write`` (``=True``): this controls wether the \*cell and \*param will be overwritten. ``_prepare_input_only`` (``=False``): If set to True, the calculator will create \*cell und \*param file but not start the calculation itself. If this is used to prepare jobs locally and run on a remote cluster it is recommended to set ``_copy_pspots = True``. ``_castep_pp_path`` (``='.'``) : the place where the calculator will look for pseudo-potential files. ``_find_pspots`` (``=False``): if set to True, the calculator will try to find the respective pseudopotentials from <_castep_pp_path>. As long as there are no multiple files per element in this directory, the auto-detect feature should be very robust. Raises a RuntimeError if required files are not unique (multiple files per element). Non existing pseudopotentials will be generated, though this could be dangerous. ``_rename_existing_dir`` (``=True``) : when using a new instance of the calculator, this will move directories out of the way that would be overwritten otherwise, appending a date string. ``_set_atoms`` (``=False``) : setting this to True will overwrite any atoms object previously attached to the calculator when reading a \.castep file. By de- fault, the read() function will only create a new atoms object if none has been attached and other- wise try to assign forces etc. based on the atom's positions. ``_set_atoms=True`` could be necessary if one uses CASTEP's internal geometry optimization (``calc.param.task='GeometryOptimization'``) because then the positions get out of sync. *Warning*: this option is generally not recommended unless one knows one really needs it. There should never be any need, if CASTEP is used as a single-point calculator. ``_track_output`` (``=False``) : if set to true, the interface will append a number to the label on all input and output files, where n is the number of calls to this instance. *Warning*: this setting may con- sume a lot more disk space because of the additio- nal \*check files. ``_try_reuse`` (``=_track_output``) : when setting this, the in- terface will try to fetch the reuse file from the previous run even if _track_output is True. By de- fault it is equal to _track_output, but may be overridden. Since this behavior may not always be desirable for single-point calculations. Regular reuse for *e.g.* a geometry-optimization can be achieved by setting ``calc.param.reuse = True``. ``_pedantic`` (``=False``) if set to true, the calculator will inform about settings probably wasting a lot of CPU time or causing numerical inconsistencies. ========================= ==================================================== Special features: ================= ``.dryrun_ok()`` Runs ``castep_command seed -dryrun`` in a temporary directory return True if all variables initialized ok. This is a fast way to catch errors in the input. Afterwards _kpoints_used is set. ``.merge_param()`` Takes a filename or filehandler of a .param file or CastepParam instance and merges it into the current calculator instance, overwriting current settings ``.keyword.clear()`` Can be used on any option like ``calc.param.keyword.clear()`` or ``calc.cell.keyword.clear()`` to return to the CASTEP default. ``.initialize()`` Creates all needed input in the ``_directory``. This can then copied to and run in a place without ASE or even python. ``.set_pspot('<library>')`` This automatically sets the pseudo-potential for all present species to ``<Species>_<library>.usp``. Make sure that ``_castep_pp_path`` is set correctly. Note that there is no check, if the file actually exists. If it doesn't castep will crash! You may want to use ``find_pspots()`` instead. ``.find_pspots(pspot=<library>, suffix=<suffix>)`` This automatically searches for pseudopotentials of type ``<Species>_<library>.<suffix>`` or ``<Species>-<library>.<suffix>`` in ``castep_pp_path` (make sure this is set correctly). Note that ``<Species>`` will be searched for case insensitive. Regular expressions are accepted, and arguments ``'*'`` will be regarded as bash-like wildcards. Defaults are any ``<library>`` and any ``<suffix>`` from ``['usp', 'UPF', 'recpot']``. If you have well-organized folders with pseudopotentials of one kind, this should work with the defaults. ``print(calc)`` Prints a short summary of the calculator settings and atoms. ``ase.io.castep.read_seed('path-to/seed')`` Given you have a combination of seed.{param,cell,castep} this will return an atoms object with the last ionic positions in the .castep file and all other settings parsed from the .cell and .param file. If no .castep file is found the positions are taken from the .cell file. The output directory will be set to the same directory, only the label is preceded by 'copy_of\_' to avoid overwriting. ``.set_kpts(kpoints)`` This is equivalent to initialising the calculator with ``calc = Castep(kpts=kpoints)``. ``kpoints`` can be specified in many convenient forms: simple Monkhorst-Pack grids can be specified e.g. ``(2, 2, 3)`` or ``'2 2 3'``; lists of specific weighted k-points can be given in reciprocal lattice coordinates e.g. ``[[0, 0, 0, 0.25], [0.25, 0.25, 0.25, 0.75]]``; a dictionary syntax is available for more complex requirements e.g. ``{'size': (2, 2, 2), 'gamma': True}`` will give a Gamma-centered 2x2x2 M-P grid, ``{'density': 10, 'gamma': False, 'even': False}`` will give a mesh with density of at least 10 Ang (based on the unit cell of currently-attached atoms) with an odd number of points in each direction and avoiding the Gamma point. ``.set_bandpath(bandpath)`` This is equivalent to initialialising the calculator with ``calc=Castep(bandpath=bandpath)`` and may be set simultaneously with *kpts*. It allows an electronic band structure path to be set up using ASE BandPath objects. This enables a band structure calculation to be set up conveniently using e.g. calc.set_bandpath(atoms.cell.bandpath().interpolate(npoints=200)) ``.band_structure(bandfile=None)`` Read a band structure from _seedname.bands_ file. This returns an ase BandStructure object which may be plotted with e.g. ``calc.band_structure().plot()`` Notes/Issues: ============== * Currently *only* the FixAtoms *constraint* is fully supported for reading and writing. There is some experimental support for the FixCartesian constraint. * There is no support for the CASTEP *unit system*. Units of eV and Angstrom are used throughout. In particular when converting total energies from different calculators, one should check that the same CODATA_ version is used for constants and conversion factors, respectively. .. _CASTEP: http://www.castep.org/ .. _W: https://en.wikipedia.org/wiki/CASTEP .. _CODATA: https://physics.nist.gov/cuu/Constants/index.html .. [1] S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. J. Probert, K. Refson, M. C. Payne Zeitschrift für Kristallographie 220(5-6) pp.567- 570 (2005) PDF_. .. _PDF: http://www.tcm.phy.cam.ac.uk/castep/papers/ZKristallogr_2005.pdf End CASTEP Interface Documentation """ # Class attributes ! # keys set through atoms object atoms_keys = [ 'charges', 'ionic_constraints', 'lattice_abs', 'lattice_cart', 'positions_abs', 'positions_abs_final', 'positions_abs_intermediate', 'positions_frac', 'positions_frac_final', 'positions_frac_intermediate'] atoms_obj_keys = [ 'dipole', 'energy_free', 'energy_zero', 'fermi', 'forces', 'nbands', 'positions', 'stress', 'pressure'] internal_keys = [ '_castep_command', '_check_checkfile', '_copy_pspots', '_link_pspots', '_find_pspots', '_build_missing_pspots', '_directory', '_export_settings', '_force_write', '_label', '_prepare_input_only', '_castep_pp_path', '_rename_existing_dir', '_set_atoms', '_track_output', '_try_reuse', '_pedantic'] def __init__(self, directory='CASTEP', label='castep', castep_command=None, check_castep_version=False, castep_pp_path=None, find_pspots=False, keyword_tolerance=1, **kwargs): self.__name__ = 'Castep' # initialize the ase.calculators.general calculator Calculator.__init__(self) from ase.io.castep import write_cell self._write_cell = write_cell castep_keywords = CastepKeywords(make_param_dict(), make_cell_dict(), [], [], 0) if keyword_tolerance < 3: try: castep_keywords = import_castep_keywords(castep_command) except CastepVersionError as e: if keyword_tolerance == 0: raise e else: warnings.warn(str(e)) self._kw_tol = keyword_tolerance keyword_tolerance = max(keyword_tolerance, 2) # 3 not accepted below self.param = CastepParam(castep_keywords, keyword_tolerance=keyword_tolerance) self.cell = CastepCell(castep_keywords, keyword_tolerance=keyword_tolerance) ################################### # Calculator state variables # ################################### self._calls = 0 self._castep_version = castep_keywords.castep_version # collects warning from .castep files self._warnings = [] # collects content from *.err file self._error = None # warnings raised by the ASE interface self._interface_warnings = [] # store to check if recalculation is necessary self._old_atoms = None self._old_cell = None self._old_param = None ################################### # Internal keys # # Allow to tweak the behavior # ################################### self._opt = {} self._castep_command = get_castep_command(castep_command) self._castep_pp_path = get_castep_pp_path(castep_pp_path) self._check_checkfile = True self._copy_pspots = False self._link_pspots = True self._find_pspots = find_pspots self._build_missing_pspots = True self._directory = os.path.abspath(directory) self._export_settings = True self._force_write = True self._label = label self._prepare_input_only = False self._rename_existing_dir = True self._set_atoms = False self._track_output = False self._try_reuse = False # turn off the pedantic user warnings self._pedantic = False # will be set on during runtime self._seed = None ################################### # (Physical) result variables # ################################### self.atoms = None # initialize result variables self._forces = None self._energy_total = None self._energy_free = None self._energy_0K = None self._energy_total_corr = None self._efermi = None self._ibz_kpts = None self._ibz_weights = None self._band_structure = None # dispersion corrections self._dispcorr_energy_total = None self._dispcorr_energy_free = None self._dispcorr_energy_0K = None # spins and hirshfeld volumes self._spins = None self._hirsh_volrat = None # Mulliken charges self._mulliken_charges = None # Hirshfeld charges self._hirshfeld_charges = None self._number_of_cell_constraints = None self._output_verbosity = None self._stress = None self._pressure = None self._unit_cell = None self._kpoints = None # pointers to other files used at runtime self._check_file = None self._castep_bin_file = None # plane wave cutoff energy (may be derived during PP generation) self._cut_off_energy = None # runtime information self._total_time = None self._peak_memory = None # check version of CASTEP options module against current one if check_castep_version: local_castep_version = get_castep_version(self._castep_command) if not hasattr(self, '_castep_version'): print('No castep version found') return if not local_castep_version == self._castep_version: print(('The options module was generated from version %s\n' 'while your are currently using CASTEP version %s') % (self._castep_version, get_castep_version(self._castep_command))) self._castep_version = local_castep_version # processes optional arguments in kw style for keyword, value in kwargs.items(): # first fetch special keywords issued by ASE CLI if keyword == 'kpts': self.set_kpts(value) elif keyword == 'bandpath': self.set_bandpath(value) elif keyword == 'xc': self.xc_functional = value elif keyword == 'ecut': self.cut_off_energy = value else: # the general case self.__setattr__(keyword, value) def band_structure(self, bandfile=None): from ase.dft.band_structure import BandStructure if bandfile is None: bandfile = os.path.join(self._directory, self._seed) + '.bands' if not os.path.exists(bandfile): raise ValueError('Cannot find band file "{}".'.format(bandfile)) kpts, weights, eigenvalues, efermi = read_bands(bandfile) # Get definitions of high-symmetry points special_points = self.atoms.cell.bandpath(npoints=0).special_points bandpath = BandPath(self.atoms.cell, kpts=kpts, special_points=special_points) return BandStructure(bandpath, eigenvalues, reference=efermi) def set_bandpath(self, bandpath): """Set a band structure path from ase.dft.kpoints.BandPath object This will set the bs_kpoint_list block with a set of specific points determined in ASE. bs_kpoint_spacing will not be used; to modify the number of points, consider using e.g. bandpath.resample(density=20) to obtain a new dense path. Args: bandpath (:obj:`ase.dft.kpoints.BandPath` or None): Set to None to remove list of band structure points. Otherwise, sampling will follow BandPath parameters. """ def clear_bs_keywords(): bs_keywords = product({'bs_kpoint', 'bs_kpoints'}, {'path', 'path_spacing', 'list', 'mp_grid', 'mp_spacing', 'mp_offset'}) for bs_tag in bs_keywords: setattr(self.cell, '_'.join(bs_tag), None) if bandpath is None: clear_bs_keywords() elif isinstance(bandpath, BandPath): clear_bs_keywords() self.cell.bs_kpoint_list = [' '.join(map(str, row)) for row in bandpath.kpts] else: raise TypeError('Band structure path must be an ' 'ase.dft.kpoint.BandPath object') def set_kpts(self, kpts): """Set k-point mesh/path using a str, tuple or ASE features Args: kpts (None, tuple, str, dict): This method will set the CASTEP parameters kpoints_mp_grid, kpoints_mp_offset and kpoints_mp_spacing as appropriate. Unused parameters will be set to None (i.e. not included in input files.) If kpts=None, all these parameters are set as unused. The simplest useful case is to give a 3-tuple of integers specifying a Monkhorst-Pack grid. This may also be formatted as a string separated by spaces; this is the format used internally before writing to the input files. A more powerful set of features is available when using a python dictionary with the following allowed keys: - 'size' (3-tuple of int) mesh of mesh dimensions - 'density' (float) for BZ sampling density in points per recip. Ang ( kpoint_mp_spacing = 1 / (2pi * density) ). An explicit MP mesh will be set to allow for rounding/centering. - 'spacing' (float) for BZ sampling density for maximum space between sample points in reciprocal space. This is numerically equivalent to the inbuilt ``calc.cell.kpoint_mp_spacing``, but will be converted to 'density' to allow for rounding/centering. - 'even' (bool) to round each direction up to the nearest even number; set False for odd numbers, leave as None for no odd/even rounding. - 'gamma' (bool) to offset the Monkhorst-Pack grid to include (0, 0, 0); set False to offset each direction avoiding 0. """ def clear_mp_keywords(): mp_keywords = product({'kpoint', 'kpoints'}, {'mp_grid', 'mp_offset', 'mp_spacing', 'list'}) for kp_tag in mp_keywords: setattr(self.cell, '_'.join(kp_tag), None) # Case 1: Clear parameters with set_kpts(None) if kpts is None: clear_mp_keywords() pass # Case 2: list of explicit k-points with weights # e.g. [[ 0, 0, 0, 0.125], # [ 0, -0.5, 0, 0.375], # [-0.5, 0, -0.5, 0.375], # [-0.5, -0.5, -0.5, 0.125]] elif (isinstance(kpts, (tuple, list)) and isinstance(kpts[0], (tuple, list))): if not all(map((lambda row: len(row) == 4), kpts)): raise ValueError( 'In explicit kpt list each row should have 4 elements') clear_mp_keywords() self.cell.kpoint_list = [' '.join(map(str, row)) for row in kpts] # Case 3: list of explicit kpts formatted as list of str # i.e. the internal format of calc.kpoint_list split on \n # e.g. ['0 0 0 0.125', '0 -0.5 0 0.375', '-0.5 0 -0.5 0.375'] elif isinstance(kpts, (tuple, list)) and isinstance(kpts[0], str): if not all(map((lambda row: len(row.split()) == 4), kpts)): raise ValueError( 'In explicit kpt list each row should have 4 elements') clear_mp_keywords() self.cell.kpoint_list = kpts # Case 4: list or tuple of MP samples e.g. [3, 3, 2] elif isinstance(kpts, (tuple, list)) and isinstance(kpts[0], int): if len(kpts) != 3: raise ValueError('Monkhorst-pack grid should have 3 values') clear_mp_keywords() self.cell.kpoint_mp_grid = '%d %d %d' % tuple(kpts) # Case 5: str representation of Case 3 e.g. '3 3 2' elif isinstance(kpts, str): self.set_kpts([int(x) for x in kpts.split()]) # Case 6: dict of options e.g. {'size': (3, 3, 2), 'gamma': True} # 'spacing' is allowed but transformed to 'density' to get mesh/offset elif isinstance(kpts, dict): kpts = kpts.copy() if (kpts.get('spacing') is not None and kpts.get('density') is not None): raise ValueError( 'Cannot set kpts spacing and density simultaneously.') else: if kpts.get('spacing') is not None: kpts = kpts.copy() spacing = kpts.pop('spacing') kpts['density'] = 1 / (np.pi * spacing) clear_mp_keywords() size, offsets = kpts2sizeandoffsets(atoms=self.atoms, **kpts) self.cell.kpoint_mp_grid = '%d %d %d' % tuple(size) self.cell.kpoint_mp_offset = '%f %f %f' % tuple(offsets) # Case 7: some other iterator. Try treating as a list: elif hasattr(kpts, '__iter__'): self.set_kpts(list(kpts)) # Otherwise, give up else: raise TypeError('Cannot interpret kpts of this type') def todict(self, skip_default=True): """Create dict with settings of .param and .cell""" dct = {} dct['param'] = self.param.get_attr_dict() dct['cell'] = self.cell.get_attr_dict() return dct def check_state(self, atoms, tol=1e-15): """Check for system changes since last calculation.""" return compare_atoms(self._old_atoms, atoms) def _castep_find_last_record(self, castep_file): """Checks wether a given castep file has a regular ending message following the last banner message. If this is the case, the line number of the last banner is message is return, otherwise False. returns (record_start, record_end, end_found, last_record_complete) """ if isinstance(castep_file, basestring): castep_file = paropen(castep_file, 'r') file_opened = True else: file_opened = False record_starts = [] while True: line = castep_file.readline() if 'Welcome' in line and 'CASTEP' in line: record_starts = [castep_file.tell()] + record_starts if not line: break if record_starts == []: print('Could not find CASTEP label in result file: %s' % castep_file) print('Are you sure this is a .castep file?') return # search for regular end of file end_found = False # start to search from record beginning from the back # and see if record_end = -1 for record_nr, record_start in enumerate(record_starts): castep_file.seek(record_start) while True: line = castep_file.readline() if not line: break if 'warn' in line.lower(): self._warnings.append(line) if 'Finalisation time =' in line: end_found = True record_end = castep_file.tell() break if end_found: break if file_opened: castep_file.close() if end_found: # record_nr == 0 corresponds to the last record here if record_nr == 0: return (record_start, record_end, True, True) else: return (record_start, record_end, True, False) else: return (0, record_end, False, False) def read(self, castep_file=None): """Read a castep file into the current instance.""" _close = True if castep_file is None: if self._castep_file: castep_file = self._castep_file out = paropen(castep_file, 'r') else: print('No CASTEP file specified') return if not os.path.exists(castep_file): print('No CASTEP file found') elif isinstance(castep_file, basestring): out = paropen(castep_file, 'r') else: # in this case we assume that we have a fileobj already, but check # for attributes in order to avoid extended EAFP blocks. out = castep_file # look before you leap... attributes = ['name', 'seek', 'close', 'readline', 'tell'] for attr in attributes: if not hasattr(out, attr): raise TypeError( '"castep_file" is neither str nor valid fileobj') castep_file = out.name _close = False if self._seed is None: self._seed = os.path.splitext(os.path.basename(castep_file))[0] err_file = '%s.0001.err' % self._seed if os.path.exists(err_file): err_file = paropen(err_file) self._error = err_file.read() err_file.close() # we return right-away because it might # just be here from a previous run # look for last result, if several CASTEP # run are appended record_start, record_end, end_found, _\ = self._castep_find_last_record(out) if not end_found: print('No regular end found in %s file' % castep_file) print(self._error) if _close: out.close() return # we return here, because the file has no a regular end # now iterate over last CASTEP output in file to extract information # could be generalized as well to extract trajectory from file # holding several outputs n_cell_const = 0 forces = [] # HOTFIX: # we have to initialize the _stress variable as a zero array # otherwise the calculator crashes upon pickling trajectories # Alternative would be to raise a NotImplementedError() which # is also kind of not true, since we can extract stresses if # the user configures CASTEP to print them in the outfile # stress = [] stress = np.zeros([3, 3]) hirsh_volrat = [] # Two flags to check whether spin-polarized or not, and whether # Hirshfeld volumes are calculated spin_polarized = False calculate_hirshfeld = False mulliken_analysis = False hirshfeld_analysis = False kpoints = None positions_frac_list = [] out.seek(record_start) while True: # TODO: add a switch if we have a geometry optimization: record # atoms objects for intermediate steps. try: # in case we need to rewind back one line, we memorize the bit # position of this line in the file. # --> see symops problem below _line_start = out.tell() line = out.readline() if not line or out.tell() > record_end: break elif 'Hirshfeld Analysis' in line: hirshfeld_charges = [] hirshfeld_analysis = True # skip the separating line line = out.readline() # this is the headline line = out.readline() if 'Charge' in line: # skip the next separator line line = out.readline() while True: line = out.readline() fields = line.split() if len(fields) == 1: break else: hirshfeld_charges.append(float(fields[-1])) elif 'stress calculation' in line: if line.split()[-1].strip() == 'on': self.param.calculate_stress = True elif 'basis set accuracy' in line: self.param.basis_precision = line.split()[-1] elif 'plane wave basis set cut-off' in line: # NB this is set as a private "result" attribute to avoid # conflict with input option basis_precision cutoff = float(line.split()[-2]) self._cut_off_energy = cutoff if self.param.basis_precision.value is None: self.param.cut_off_energy = cutoff elif 'total energy / atom convergence tol.' in line: elec_energy_tol = float(line.split()[-2]) self.param.elec_energy_tol = elec_energy_tol elif 'convergence tolerance window' in line: elec_convergence_win = int(line.split()[-2]) self.param.elec_convergence_win = elec_convergence_win elif re.match(r'\sfinite basis set correction\s*:', line): finite_basis_corr = line.split()[-1] fbc_possibilities = {'none': 0, 'manual': 1, 'automatic': 2} fbc = fbc_possibilities[finite_basis_corr] self.param.finite_basis_corr = fbc elif 'Treating system as non-metallic' in line: self.param.fix_occupancy = True elif 'max. number of SCF cycles:' in line: max_no_scf = float(line.split()[-1]) self.param.max_scf_cycles = max_no_scf elif 'density-mixing scheme' in line: mixing_scheme = line.split()[-1] self.param.mixing_scheme = mixing_scheme elif 'dump wavefunctions every' in line: no_dump_cycles = float(line.split()[-3]) self.param.num_dump_cycles = no_dump_cycles elif 'optimization strategy' in line: lspl = line.split(":") if lspl[0].strip() != 'optimization strategy': # This can happen in iprint: 3 calculations continue if 'memory' in line: self.param.opt_strategy = 'Memory' if 'speed' in line: self.param.opt_strategy = 'Speed' elif 'calculation limited to maximum' in line: calc_limit = float(line.split()[-2]) self.param.run_time = calc_limit elif 'type of calculation' in line: lspl = line.split(":") if lspl[0].strip() != 'type of calculation': # This can happen in iprint: 3 calculations continue calc_type = lspl[-1] calc_type = re.sub(r'\s+', ' ', calc_type) calc_type = calc_type.strip() if calc_type != 'single point energy': calc_type_possibilities = { 'geometry optimization': 'GeometryOptimization', 'band structure': 'BandStructure', 'molecular dynamics': 'MolecularDynamics', 'optical properties': 'Optics', 'phonon calculation': 'Phonon', 'E-field calculation': 'Efield', 'Phonon followed by E-field': 'Phonon+Efield', 'transition state search': 'TransitionStateSearch', 'Magnetic Resonance': 'MagRes', 'Core level spectra': 'Elnes', 'Electronic Spectroscopy': 'ElectronicSpectroscopy' } ctype = calc_type_possibilities[calc_type] self.param.task = ctype elif 'using functional' in line: used_functional = line.split(":")[-1] used_functional = re.sub(r'\s+', ' ', used_functional) used_functional = used_functional.strip() if used_functional != 'Local Density Approximation': used_functional_possibilities = { 'Perdew Wang (1991)': 'PW91', 'Perdew Burke Ernzerhof': 'PBE', 'revised Perdew Burke Ernzerhof': 'RPBE', 'PBE with Wu-Cohen exchange': 'WC', 'PBE for solids (2008)': 'PBESOL', 'Hartree-Fock': 'HF', 'Hartree-Fock +': 'HF-LDA', 'Screened Hartree-Fock': 'sX', 'Screened Hartree-Fock + ': 'sX-LDA', 'hybrid PBE0': 'PBE0', 'hybrid B3LYP': 'B3LYP', 'hybrid HSE03': 'HSE03', 'hybrid HSE06': 'HSE06' } used_func = used_functional_possibilities[used_functional] self.param.xc_functional = used_func elif 'output verbosity' in line: iprint = int(line.split()[-1][1]) if int(iprint) != 1: self.param.iprint = iprint elif 'treating system as spin-polarized' in line: spin_polarized = True self.param.spin_polarized = spin_polarized elif 'treating system as non-spin-polarized' in line: spin_polarized = False elif 'Number of kpoints used' in line: kpoints = int(line.split('=')[-1].strip()) elif 'Unit Cell' in line: lattice_real = [] lattice_reci = [] while True: line = out.readline() fields = line.split() if len(fields) == 6: break for i in range(3): lattice_real.append([float(f) for f in fields[0:3]]) lattice_reci.append([float(f) for f in fields[3:7]]) line = out.readline() fields = line.split() elif 'Cell Contents' in line: while True: line = out.readline() if 'Total number of ions in cell' in line: n_atoms = int(line.split()[7]) if 'Total number of species in cell' in line: int(line.split()[7]) fields = line.split() if len(fields) == 0: break elif 'Fractional coordinates of atoms' in line: species = [] custom_species = None # A CASTEP special thing positions_frac = [] # positions_cart = [] while True: line = out.readline() fields = line.split() if len(fields) == 7: break for n in range(n_atoms): spec_custom = fields[1].split(':', 1) elem = spec_custom[0] if len(spec_custom) > 1 and custom_species is None: # Add it to the custom info! custom_species = list(species) species.append(elem) if custom_species is not None: custom_species.append(fields[1]) positions_frac.append([float(s) for s in fields[3:6]]) line = out.readline() fields = line.split() positions_frac_list.append(positions_frac) elif 'Files used for pseudopotentials' in line: while True: line = out.readline() if 'Pseudopotential generated on-the-fly' in line: continue fields = line.split() if (len(fields) >= 2): elem, pp_file = fields self.cell.species_pot = (elem, pp_file) else: break elif 'k-Points For BZ Sampling' in line: # TODO: generalize for non-Monkhorst Pack case # (i.e. kpoint lists) - # kpoints_offset cannot be read this way and # is hence always set to None while True: line = out.readline() if not line.strip(): break if 'MP grid size for SCF calculation' in line: # kpoints = ' '.join(line.split()[-3:]) # self.kpoints_mp_grid = kpoints # self.kpoints_mp_offset = '0. 0. 0.' # not set here anymore because otherwise # two calculator objects go out of sync # after each calculation triggering unnecessary # recalculation break elif 'Symmetry and Constraints' in line: # this is a bit of a hack, but otherwise the read_symops # would need to re-read the entire file. --> just rewind # back by one line, so the read_symops routine can find the # start of this block. out.seek(_line_start) self.read_symops(castep_castep=out) elif 'Number of cell constraints' in line: n_cell_const = int(line.split()[4]) elif 'Final energy' in line: self._energy_total = float(line.split()[-2]) elif 'Final free energy' in line: self._energy_free = float(line.split()[-2]) elif 'NB est. 0K energy' in line: self._energy_0K = float(line.split()[-2]) # check if we had a finite basis set correction elif 'Total energy corrected for finite basis set' in line: self._energy_total_corr = float(line.split()[-2]) # Add support for dispersion correction # filtering due to SEDC is done in get_potential_energy elif 'Dispersion corrected final energy' in line: self._dispcorr_energy_total = float(line.split()[-2]) elif 'Dispersion corrected final free energy' in line: self._dispcorr_energy_free = float(line.split()[-2]) elif 'dispersion corrected est. 0K energy' in line: self._dispcorr_energy_0K = float(line.split()[-2]) # remember to remove constraint labels in force components # (lacking a space behind the actual floating point number in # the CASTEP output) elif '******************** Forces *********************'\ in line or\ '************** Symmetrised Forces ***************'\ in line or\ '************** Constrained Symmetrised Forces ****'\ '**********'\ in line or\ '******************** Constrained Forces **********'\ '**********'\ in line or\ '******************* Unconstrained Forces *********'\ '**********'\ in line: fix = [] fix_cart = [] forces = [] while True: line = out.readline() fields = line.split() if len(fields) == 7: break for n in range(n_atoms): consd = np.array([0, 0, 0]) fxyz = [0, 0, 0] for (i, force_component) in enumerate(fields[-4:-1]): if force_component.count("(cons'd)") > 0: consd[i] = 1 fxyz[i] = float(force_component.replace( "(cons'd)", '')) if consd.all(): fix.append(n) elif consd.any(): fix_cart.append(FixCartesian(n, consd)) forces.append(fxyz) line = out.readline() fields = line.split() # add support for Hirshfeld analysis elif 'Hirshfeld / free atomic volume :' in line: # if we are here, then params must be able to cope with # Hirshfeld flag (if castep_keywords.py matches employed # castep version) calculate_hirshfeld = True hirsh_volrat = [] while True: line = out.readline() fields = line.split() if len(fields) == 1: break for n in range(n_atoms): hirsh_atom = float(fields[0]) hirsh_volrat.append(hirsh_atom) while True: line = out.readline() if 'Hirshfeld / free atomic volume :' in line or\ 'Hirshfeld Analysis' in line: break line = out.readline() fields = line.split() elif '***************** Stress Tensor *****************'\ in line or\ '*********** Symmetrised Stress Tensor ***********'\ in line: stress = [] while True: line = out.readline() fields = line.split() if len(fields) == 6: break for n in range(3): stress.append([float(s) for s in fields[2:5]]) line = out.readline() fields = line.split() line = out.readline() if "Pressure:" in line: self._pressure = float(line.split()[-2]) * units.GPa elif ('BFGS: starting iteration' in line or 'BFGS: improving iteration' in line): if n_cell_const < 6: lattice_real = [] lattice_reci = [] # backup previous configuration first: # for highly symmetric systems (where essentially only the # stress is optimized, but the atomic positions) positions # are only printed once. if species: prev_species = deepcopy(species) if positions_frac: prev_positions_frac = deepcopy(positions_frac) species = [] positions_frac = [] forces = [] # HOTFIX: # Same reason for the stress initialization as before # stress = [] stress = np.zeros([3, 3]) # extract info from the Mulliken analysis elif 'Atomic Populations' in line: # sometimes this appears twice in a castep file mulliken_charges = [] spins = [] mulliken_analysis = True # skip the separating line line = out.readline() # this is the headline line = out.readline() if 'Charge' in line: # skip the next separator line line = out.readline() while True: line = out.readline() fields = line.split() if len(fields) == 1: break # the check for len==7 is due to CASTEP 18 outformat changes if spin_polarized: if len(fields) != 7: spins.append(float(fields[-1])) mulliken_charges.append(float(fields[-2])) else: mulliken_charges.append(float(fields[-1])) # There is actually no good reason to get out of the loop # already at this point... or do I miss something? # elif 'BFGS: Final Configuration:' in line: # break elif 'warn' in line.lower(): self._warnings.append(line) # fetch some last info elif 'Total time' in line: pattern = r'.*=\s*([\d\.]+) s' self._total_time = float(re.search(pattern, line).group(1)) elif 'Peak Memory Use' in line: pattern = r'.*=\s*([\d]+) kB' self._peak_memory = int(re.search(pattern, line).group(1)) except Exception as exception: sys.stderr.write(line + '|-> line triggered exception: ' + str(exception)) raise if _close: out.close() # in highly summetric crystals, positions and symmetry are only printed # upon init, hence we here restore these original values if not positions_frac: positions_frac = prev_positions_frac if not species: species = prev_species if not spin_polarized: # set to zero spin if non-spin polarized calculation spins = np.zeros(len(positions_frac)) positions_frac_atoms = np.array(positions_frac) forces_atoms = np.array(forces) spins_atoms = np.array(spins) if mulliken_analysis: mulliken_charges_atoms = np.array(mulliken_charges) else: mulliken_charges_atoms = np.zeros(len(positions_frac)) if hirshfeld_analysis: hirshfeld_charges_atoms = np.array(hirshfeld_charges) else: hirshfeld_charges_atoms = None if calculate_hirshfeld: hirsh_atoms = np.array(hirsh_volrat) else: hirsh_atoms = np.zeros_like(spins) if self.atoms and not self._set_atoms: # compensate for internal reordering of atoms by CASTEP # using the fact that the order is kept within each species # positions_frac_ase = self.atoms.get_scaled_positions(wrap=False) atoms_assigned = [False] * len(self.atoms) # positions_frac_castep_init = np.array(positions_frac_list[0]) positions_frac_castep = np.array(positions_frac_list[-1]) # species_castep = list(species) forces_castep = np.array(forces) hirsh_castep = np.array(hirsh_volrat) spins_castep = np.array(spins) mulliken_charges_castep = np.array(mulliken_charges_atoms) # go through the atoms position list and replace # with the corresponding one from the # castep file corresponding atomic number for iase in range(n_atoms): for icastep in range(n_atoms): if (species[icastep] == self.atoms[iase].symbol and not atoms_assigned[icastep]): positions_frac_atoms[iase] = \ positions_frac_castep[icastep] forces_atoms[iase] = np.array(forces_castep[icastep]) if iprint > 1 and calculate_hirshfeld: hirsh_atoms[iase] = np.array(hirsh_castep[icastep]) if spin_polarized: # reordering not necessary in case all spins == 0 spins_atoms[iase] = np.array(spins_castep[icastep]) mulliken_charges_atoms[iase] = np.array( mulliken_charges_castep[icastep]) atoms_assigned[icastep] = True break if not all(atoms_assigned): not_assigned = [i for (i, assigned) in zip(range(len(atoms_assigned)), atoms_assigned) if not assigned] print('%s atoms not assigned.' % atoms_assigned.count(False)) print('DEBUGINFO: The following atoms where not assigned: %s' % not_assigned) else: self.atoms.set_scaled_positions(positions_frac_atoms) else: # If no atoms, object has been previously defined # we define it here and set the Castep() instance as calculator. # This covers the case that we simply want to open a .castep file. # The next time around we will have an atoms object, since # set_calculator also set atoms in the calculator. if self.atoms: constraints = self.atoms.constraints else: constraints = [] atoms = ase.atoms.Atoms(species, cell=lattice_real, constraint=constraints, pbc=True, scaled_positions=positions_frac, ) if custom_species is not None: atoms.new_array('castep_custom_species', np.array(custom_species)) if self.param.spin_polarized: # only set magnetic moments if this was a spin polarized # calculation # this one fails as is atoms.set_initial_magnetic_moments(magmoms=spins_atoms) if mulliken_analysis: atoms.set_initial_charges(charges=mulliken_charges_atoms) atoms.set_calculator(self) self._kpoints = kpoints self._forces = forces_atoms # stress in .castep file is given in GPa: self._stress = np.array(stress) * units.GPa self._hirsh_volrat = hirsh_atoms self._spins = spins_atoms self._mulliken_charges = mulliken_charges_atoms self._hirshfeld_charges = hirshfeld_charges_atoms if self._warnings: print('WARNING: %s contains warnings' % castep_file) for warning in self._warnings: print(warning) # reset self._warnings = [] # Read in eigenvalues from bands file bands_file = castep_file[:-7] + '.bands' if (self.param.task.value is not None and self.param.task.value.lower() == 'bandstructure'): self._band_structure = self.band_structure(bandfile=bands_file) else: (self._ibz_kpts, self._ibz_weights, self._eigenvalues, self._efermi) = read_bands(filename=bands_file) def read_symops(self, castep_castep=None): # TODO: check that this is really backwards compatible # with previous routine with this name... """Read all symmetry operations used from a .castep file.""" if castep_castep is None: castep_castep = self._seed + '.castep' if isinstance(castep_castep, basestring): if not os.path.isfile(castep_castep): print('Warning: CASTEP file %s not found!' % castep_castep) f = paropen(castep_castep, 'r') _close = True else: # in this case we assume that we have a fileobj already, but check # for attributes in order to avoid extended EAFP blocks. f = castep_castep # look before you leap... attributes = ['name', 'readline', 'close'] for attr in attributes: if not hasattr(f, attr): raise TypeError('read_castep_castep_symops: castep_castep ' 'is not of type str nor valid fileobj!') castep_castep = f.name _close = False while True: line = f.readline() if not line: return if 'output verbosity' in line: iprint = line.split()[-1][1] # filter out the default if int(iprint) != 1: self.param.iprint = iprint if 'Symmetry and Constraints' in line: break if self.param.iprint.value is None or int(self.param.iprint.value) < 2: self._interface_warnings.append( 'Warning: No symmetry' 'operations could be read from %s (iprint < 2).' % f.name) return while True: line = f.readline() if not line: break if 'Number of symmetry operations' in line: nsym = int(line.split()[5]) # print "nsym = %d" % nsym # information about symmetry related atoms currently not read symmetry_operations = [] for _ in range(nsym): rotation = [] displacement = [] while True: if 'rotation' in f.readline(): break for _ in range(3): line = f.readline() rotation.append([float(r) for r in line.split()[1:4]]) while True: if 'displacement' in f.readline(): break line = f.readline() displacement = [float(d) for d in line.split()[1:4]] symop = {'rotation': rotation, 'displacement': displacement} self.symmetry_ops = symop self.symmetry = symmetry_operations print('Symmetry operations successfully read from %s' % f.name) print(self.cell.symmetry_ops) break # only close if we opened the file in this routine if _close: f.close() def get_hirsh_volrat(self): """ Return the Hirshfeld volumes. """ return self._hirsh_volrat def get_spins(self): """ Return the spins from a plane-wave Mulliken analysis. """ return self._spins def get_mulliken_charges(self): """ Return the charges from a plane-wave Mulliken analysis. """ return self._mulliken_charges def get_hirshfeld_charges(self): """ Return the charges from a Hirshfeld analysis. """ return self._hirshfeld_charges def get_total_time(self): """ Return the total runtime """ return self._total_time def get_peak_memory(self): """ Return the peak memory usage """ return self._peak_memory def set_label(self, label): """The label is part of each seed, which in turn is a prefix in each CASTEP related file. """ # we may think about changing this in future to set `self._directory` # and `self._label`, as one would expect self._label = label def set_pspot(self, pspot, elems=None, notelems=None, clear=True, suffix='usp'): """Quickly set all pseudo-potentials: Usually CASTEP psp are named like <Elem>_<pspot>.<suffix> so this function function only expects the <LibraryName>. It then clears any previous pseudopotential settings apply the one with <LibraryName> for each element in the atoms object. The optional elems and notelems arguments can be used to exclusively assign to some species, or to exclude with notelemens. Parameters :: - elems (None) : set only these elements - notelems (None): do not set the elements - clear (True): clear previous settings - suffix (usp): PP file suffix """ if self._find_pspots: if self._pedantic: print('Warning: <_find_pspots> = True') print('Do you really want to use `set_pspots()`') print('This does not check whether the PP files exist.') print( 'You may rather want to use `find_pspots()` with the same <pspot>.') if clear and not elems and not notelems: self.cell.species_pot.clear() for elem in set(self.atoms.get_chemical_symbols()): if elems is not None and elem not in elems: continue if notelems is not None and elem in notelems: continue self.cell.species_pot = (elem, '%s_%s.%s' % (elem, pspot, suffix)) def find_pspots(self, pspot='.+', elems=None, notelems=None, clear=True, suffix='(usp|UPF|recpot)'): r"""Quickly find and set all pseudo-potentials by searching in castep_pp_path: This one is more flexible than set_pspots, and also checks if the files are actually available from the castep_pp_path. Essentially, the function parses the filenames in <castep_pp_path> and does a regex matching. The respective pattern is: r"^(<elem>|<elem.upper()>|elem.lower()>(_|-)<pspot>\.<suffix>$" In most cases, it will be sufficient to not specify anything, if you use standard CASTEP USPPs with only one file per element in the <castep_pp_path>. The function raises a `RuntimeError` if there is some ambiguity (multiple files per element). Parameters :: - pspots ('.+') : as defined above, will be a wildcard if not specified. - elems (None) : set only these elements - notelems (None): do not set the elements - clear (True): clear previous settings - suffix (usp|UPF|recpot): PP file suffix """ if clear and not elems and not notelems: self.cell.species_pot.clear() if not os.path.isdir(self._castep_pp_path): if self._pedantic: print('Cannot search directory:\n {}\nFolder does not exist'.format( self._castep_pp_path)) return # translate the bash wildcard syntax to regex if pspot == '*': pspot = '.*' if suffix == '*': suffix = '.*' if pspot == '*': pspot = '.*' # GBRV USPPs have a strnage naming schme pattern = r'^({elem}|{elem_upper}|{elem_lower})(_|-){pspot}\.{suffix}$' for elem in set(self.atoms.get_chemical_symbols()): if elems is not None and elem not in elems: continue if notelems is not None and elem in notelems: continue p = pattern.format(elem=elem, elem_upper=elem.upper(), elem_lower=elem.lower(), pspot=pspot, suffix=suffix) pps = [] for f in os.listdir(self._castep_pp_path): if re.match(p, f): pps.append(f) if not pps: if self._pedantic: print('Pseudopotential for species {} not found!'.format(elem)) elif not len(pps) == 1: raise RuntimeError('Pseudopotential for species ''{} not unique!\n'.format(elem) + 'Found the following files in {}\n'.format(self._castep_pp_path) + '\n'.join([' {}'.format(pp) for pp in pps]) + '\nConsider a stricter search pattern in `find_pspots()`.') else: self.cell.species_pot = (elem, pps[0]) @property def name(self): """Return the name of the calculator (string). """ return self.__name__ def get_property(self, name, atoms=None, allow_calculation=True): # High-level getter for compliance with the database module... # in principle this would not be necessary any longer if we properly # based this class on `Calculator` if name == 'forces': return self.get_forces(atoms) elif name == 'energy': return self.get_potential_energy(atoms) elif name == 'stress': return self.get_stress(atoms) elif name == 'charges': return self.get_charges(atoms) else: raise PropertyNotImplementedError @_self_getter def get_forces(self, atoms): """Run CASTEP calculation if needed and return forces.""" self.update(atoms) return np.array(self._forces) @_self_getter def get_total_energy(self, atoms): """Run CASTEP calculation if needed and return total energy.""" self.update(atoms) return self._energy_total @_self_getter def get_total_energy_corrected(self, atoms): """Run CASTEP calculation if needed and return total energy.""" self.update(atoms) return self._energy_total_corr @_self_getter def get_free_energy(self, atoms): """Run CASTEP calculation if needed and return free energy. Only defined with smearing.""" self.update(atoms) return self._energy_free @_self_getter def get_0K_energy(self, atoms): """Run CASTEP calculation if needed and return 0K energy. Only defined with smearing.""" self.update(atoms) return self._energy_0K @_self_getter def get_potential_energy(self, atoms, force_consistent=False): # here for compatibility with ase/calculators/general.py # but accessing only _name variables """Return the total potential energy.""" self.update(atoms) if force_consistent: # Assumption: If no dispersion correction is applied, then the # respective value will default to None as initialized. if self._dispcorr_energy_free is not None: return self._dispcorr_energy_free else: return self._energy_free else: if self._energy_0K is not None: if self._dispcorr_energy_0K is not None: return self._dispcorr_energy_0K else: return self._energy_0K else: if self._dispcorr_energy_total is not None: return self._dispcorr_energy_total else: if self._energy_total_corr is not None: return self._energy_total_corr else: return self._energy_total @_self_getter def get_stress(self, atoms): """Return the stress.""" self.update(atoms) # modification: we return the Voigt form directly to get rid of the # annoying user warnings stress = np.array([self._stress[0, 0], self._stress[1, 1], self._stress[2, 2], self._stress[1, 2], self._stress[0, 2], self._stress[0, 1]]) # return self._stress return stress @_self_getter def get_pressure(self, atoms): """Return the pressure.""" self.update(atoms) return self._pressure @_self_getter def get_unit_cell(self, atoms): """Return the unit cell.""" self.update(atoms) return self._unit_cell @_self_getter def get_kpoints(self, atoms): """Return the kpoints.""" self.update(atoms) return self._kpoints @_self_getter def get_number_cell_constraints(self, atoms): """Return the number of cell constraints.""" self.update(atoms) return self._number_of_cell_constraints @_self_getter def get_charges(self, atoms): """Run CASTEP calculation if needed and return Mulliken charges.""" self.update(atoms) return np.array(self._mulliken_charges) @_self_getter def get_magnetic_moments(self, atoms): """Run CASTEP calculation if needed and return Mulliken charges.""" self.update(atoms) return np.array(self._spins) def set_atoms(self, atoms): """Sets the atoms for the calculator and vice versa.""" atoms.pbc = [True, True, True] self.__dict__['atoms'] = atoms.copy() self.atoms._calc = self def update(self, atoms): """Checks if atoms object or calculator changed and runs calculation if so. """ if self.calculation_required(atoms): self.calculate(atoms) def calculation_required(self, atoms, _=None): """Checks wether anything changed in the atoms object or CASTEP settings since the last calculation using this instance. """ # SPR: what happens with the atoms parameter here? Why don't we use it? # from all that I can tell we need to compare against atoms instead of # self.atoms # if not self.atoms == self._old_atoms: if not atoms == self._old_atoms: return True if self._old_param is None or self._old_cell is None: return True if not self.param._options == self._old_param._options: return True if not self.cell._options == self._old_cell._options: return True return False def calculate(self, atoms): """Write all necessary input file and call CASTEP.""" self.prepare_input_files(atoms, force_write=self._force_write) if not self._prepare_input_only: self.run() self.read() # we need to push the old state here! # although run() pushes it, read() may change the atoms object # again. # yet, the old state is supposed to be the one AFTER read() self.push_oldstate() def push_oldstate(self): """This function pushes the current state of the (CASTEP) Atoms object onto the previous state. Or in other words after calling this function, calculation_required will return False and enquiry functions just report the current value, e.g. get_forces(), get_potential_energy(). """ # make a snapshot of all current input # to be able to test if recalculation # is necessary self._old_atoms = self.atoms.copy() self._old_param = deepcopy(self.param) self._old_cell = deepcopy(self.cell) def initialize(self, *args, **kwargs): """Just an alias for prepar_input_files to comply with standard function names in ASE. """ self.prepare_input_files(*args, **kwargs) def prepare_input_files(self, atoms=None, force_write=None): """Only writes the input .cell and .param files and return This can be useful if one quickly needs to prepare input files for a cluster where no python or ASE is available. One can than upload the file manually and read out the results using Castep().read(). """ if self.param.reuse.value is None: if self._pedantic: print('You have not set e.g. calc.param.reuse = True') print('Reusing a previous calculation may save CPU time!\n') print( 'The interface will make sure by default, a .check exists') print( 'file before adding this statement to the .param file.\n') if self.param.num_dump_cycles.value is None: if self._pedantic: print('You have not set e.g. calc.param.num_dump_cycles = 0.') print('This can save you a lot of disk space. One only needs') print('*wvfn* if electronic convergence is not achieved.\n') from ase.io.castep import write_param if atoms is None: atoms = self.atoms else: self.atoms = atoms if force_write is None: force_write = self._force_write # if we have new instance of the calculator, # move existing results out of the way, first if (os.path.isdir(self._directory) and self._calls == 0 and self._rename_existing_dir): if os.listdir(self._directory) == []: os.rmdir(self._directory) else: # rename appending creation date of the directory ctime = time.localtime(os.lstat(self._directory).st_ctime) os.rename(self._directory, '%s.bak-%s' % (self._directory, time.strftime('%Y%m%d-%H%M%S', ctime))) # create work directory if not os.path.isdir(self._directory): os.makedirs(self._directory, 0o775) # we do this every time, not only upon first call # if self._calls == 0: self._fetch_pspots() # if _try_reuse is requested and this # is not the first run, we try to find # the .check file from the previous run # this is only necessary if _track_output # is set to true if self._try_reuse and self._calls > 0: if os.path.exists(self._abs_path(self._check_file)): self.param.reuse = self._check_file elif os.path.exists(self._abs_path(self._castep_bin_file)): self.param.reuse = self._castep_bin_file self._seed = self._build_castep_seed() self._check_file = '%s.check' % self._seed self._castep_bin_file = '%s.castep_bin' % self._seed self._castep_file = self._abs_path('%s.castep' % self._seed) # write out the input file self._write_cell(self._abs_path('%s.cell' % self._seed), self.atoms, castep_cell=self.cell, force_write=force_write) if self._export_settings: interface_options = self._opt else: interface_options = None write_param(self._abs_path('%s.param' % self._seed), self.param, check_checkfile=self._check_checkfile, force_write=force_write, interface_options=interface_options,) def _build_castep_seed(self): """Abstracts to construction of the final castep <seed> with and without _tracking_output. """ if self._track_output: return '%s-%06d' % (self._label, self._calls) else: return '%s' % (self._label) def _abs_path(self, path): # Create an absolute path for a file to put in the working directory return os.path.join(self._directory, path) def run(self): """Simply call castep. If the first .err file contains text, this will be printed to the screen. """ # change to target directory self._calls += 1 # run castep itself stdout, stderr = shell_stdouterr('%s %s' % (self._castep_command, self._seed), cwd=self._directory) if stdout: print('castep call stdout:\n%s' % stdout) if stderr: print('castep call stderr:\n%s' % stderr) # shouldn't it be called after read()??? # self.push_oldstate() # check for non-empty error files err_file = self._abs_path('%s.0001.err' % self._seed) if os.path.exists(err_file): err_file = open(err_file) self._error = err_file.read() err_file.close() if self._error: raise RuntimeError(self._error) def __repr__(self): """Returns generic, fast to capture representation of CASTEP settings along with atoms object. """ expr = '' expr += '-----------------Atoms--------------------\n' if self.atoms is not None: expr += str('%20s\n' % self.atoms) else: expr += 'None\n' expr += '-----------------Param keywords-----------\n' expr += str(self.param) expr += '-----------------Cell keywords------------\n' expr += str(self.cell) expr += '-----------------Internal keys------------\n' for key in self.internal_keys: expr += '%20s : %s\n' % (key, self._opt[key]) return expr def __getattr__(self, attr): """___getattr___ gets overloaded to reroute the internal keys and to be able to easily store them in in the param so that they can be read in again in subsequent calls. """ if attr in self.internal_keys: return self._opt[attr] if attr in ['__repr__', '__str__']: raise AttributeError elif attr not in self.__dict__: raise AttributeError else: return self.__dict__[attr] def __setattr__(self, attr, value): """We overload the settattr method to make value assignment as pythonic as possible. Internal values all start with _. Value assigment is case insensitive! """ if attr.startswith('_'): # internal variables all start with _ # let's check first if they are close but not identical # to one of the switches, that the user accesses directly similars = difflib.get_close_matches(attr, self.internal_keys, cutoff=0.9) if attr not in self.internal_keys and similars: print('Warning: You probably tried one of: %s' % similars) print('but typed %s' % attr) if attr in self.internal_keys: self._opt[attr] = value if attr == '_track_output': if value: self._try_reuse = True if self._pedantic: print('You switched _track_output on. This will') print('consume a lot of disk-space. The interface') print('also switched _try_reuse on, which will') print('try to find the last check file. Set') print('_try_reuse = False, if you need') print('really separate calculations') elif '_try_reuse' in self._opt and self._try_reuse: self._try_reuse = False if self._pedantic: print('_try_reuse is set to False, too') else: self.__dict__[attr] = value return elif attr in ['atoms', 'cell', 'param']: if value is not None: if attr == 'atoms' and not isinstance(value, ase.atoms.Atoms): raise TypeError( '%s is not an instance of ase.atoms.Atoms.' % value) elif attr == 'cell' and not isinstance(value, CastepCell): raise TypeError('%s is not an instance of CastepCell.' % value) elif attr == 'param' and not isinstance(value, CastepParam): raise TypeError('%s is not an instance of CastepParam.' % value) # These 3 are accepted right-away, no matter what self.__dict__[attr] = value return elif attr in self.atoms_obj_keys: # keywords which clearly belong to the atoms object are # rerouted to go there self.atoms.__dict__[attr] = value return elif attr in self.atoms_keys: # CASTEP keywords that should go into the atoms object # itself are blocked print('Ignoring setings of "%s", since this has to be set\n' 'through the atoms object' % attr) return attr = attr.lower() if attr not in (list(self.cell._options.keys()) + list(self.param._options.keys())): # what is left now should be meant to be a castep keyword # so we first check if it defined, and if not offer some error # correction if self._kw_tol == 0: similars = difflib.get_close_matches( attr, self.cell._options.keys() + self.param._options.keys()) if similars: raise UserWarning('Option "%s" not known! You mean "%s"?' % (attr, similars[0])) else: raise UserWarning('Option "%s" is not known!' % attr) else: warnings.warn('Option "%s" is not known - please set any new' ' options directly in the .cell or .param ' 'objects' % attr) return # here we know it must go into one of the component param or cell # so we first determine which one if attr in self.param._options.keys(): comp = 'param' elif attr in self.cell._options.keys(): comp = 'cell' else: raise UserWarning('Programming error: could not attach ' 'the keyword to an input file') self.__dict__[comp].__setattr__(attr, value) def merge_param(self, param, overwrite=True, ignore_internal_keys=False): """Parse a param file and merge it into the current parameters.""" if isinstance(param, CastepParam): for key, option in param._options.items(): if option.value is not None: self.param.__setattr__(key, option.value) return elif isinstance(param, basestring): param_file = open(param, 'r') _close = True else: # in this case we assume that we have a fileobj already, but check # for attributes in order to avoid extended EAFP blocks. param_file = param # look before you leap... attributes = ['name', 'close' 'readlines'] for attr in attributes: if not hasattr(param_file, attr): raise TypeError('"param" is neither CastepParam nor str ' 'nor valid fileobj') param = param_file.name _close = False self, int_opts = read_param(fd=param_file, calc=self, get_interface_options=True) # Add the interface options for k, val in int_opts.items(): if (k in self.internal_keys and not ignore_internal_keys): if val in _tf_table: val = _tf_table[val] self._opt[k] = val if _close: param_file.close() def dryrun_ok(self, dryrun_flag='-dryrun'): """Starts a CASTEP run with the -dryrun flag [default] in a temporary and check wether all variables are initialized correctly. This is recommended for every bigger simulation. """ from ase.io.castep import write_param temp_dir = tempfile.mkdtemp() self._fetch_pspots(temp_dir) seed = 'dryrun' self._write_cell(os.path.join(temp_dir, '%s.cell' % seed), self.atoms, castep_cell=self.cell) # This part needs to be modified now that we rely on the new formats.py # interface if not os.path.isfile(os.path.join(temp_dir, '%s.cell' % seed)): print('%s.cell not written - aborting dryrun' % seed) return write_param(os.path.join(temp_dir, '%s.param' % seed), self.param, ) stdout, stderr = shell_stdouterr(('%s %s %s' % (self._castep_command, seed, dryrun_flag)), cwd=temp_dir) if stdout: print(stdout) if stderr: print(stderr) result_file = open(os.path.join(temp_dir, '%s.castep' % seed)) txt = result_file.read() ok_string = r'.*DRYRUN finished.*No problems found with input files.*' match = re.match(ok_string, txt, re.DOTALL) m = re.search(r'Number of kpoints used =\s*([0-9]+)', txt) if m: self._kpoints = int(m.group(1)) else: print('Couldn\'t fetch number of kpoints from dryrun CASTEP file') err_file = os.path.join(temp_dir, '%s.0001.err' % seed) if match is None and os.path.exists(err_file): err_file = open(err_file) self._error = err_file.read() err_file.close() result_file.close() shutil.rmtree(temp_dir) # re.match return None is the string does not match return match is not None # this could go into the Atoms() class at some point... def _get_number_in_species(self, at, atoms=None): """Return the number of the atoms within the set of it own species. If you are an ASE commiter: why not move this into ase.atoms.Atoms ?""" if atoms is None: atoms = self.atoms numbers = atoms.get_atomic_numbers() n = numbers[at] nis = numbers.tolist()[:at + 1].count(n) return nis def _get_absolute_number(self, species, nic, atoms=None): """This is the inverse function to _get_number in species.""" if atoms is None: atoms = self.atoms ch = atoms.get_chemical_symbols() ch.reverse() total_nr = 0 assert nic > 0, 'Number in species needs to be 1 or larger' while True: if ch.pop() == species: if nic == 1: return total_nr nic -= 1 total_nr += 1 def _fetch_pspots(self, directory=None): """Put all specified pseudo-potentials into the working directory. """ # should be a '==' right? Otherwise setting _castep_pp_path is not # honored. if (not os.environ.get('PSPOT_DIR', None) and self._castep_pp_path == os.path.abspath('.')): # By default CASTEP consults the environment variable # PSPOT_DIR. If this contains a list of colon separated # directories it will check those directories for pseudo- # potential files if not in the current directory. # Thus if PSPOT_DIR is set there is nothing left to do. # If however PSPOT_DIR was been accidentally set # (e.g. with regards to a different program) # setting CASTEP_PP_PATH to an explicit value will # still be honored. return if directory is None: directory = self._directory if not os.path.isdir(self._castep_pp_path): print('PSPs directory %s not found' % self._castep_pp_path) pspots = {} if self._find_pspots: self.find_pspots() if self.cell.species_pot.value is not None: for line in self.cell.species_pot.value.split('\n'): line = line.split() if line: pspots[line[0]] = line[1] for species in self.atoms.get_chemical_symbols(): if not pspots or species not in pspots.keys(): if self._build_missing_pspots: if self._pedantic: print('Warning: you have no PP specified for %s.' % species) print('CASTEP will now generate an on-the-fly potentials.') print('For sake of numerical consistency and efficiency') print('this is discouraged.') else: raise RuntimeError('Warning: you have no PP specified for %s.' % species) if self.cell.species_pot.value: for (species, pspot) in pspots.items(): orig_pspot_file = os.path.join(self._castep_pp_path, pspot) cp_pspot_file = os.path.join(directory, pspot) if (os.path.exists(orig_pspot_file) and not os.path.exists(cp_pspot_file)): if self._copy_pspots: shutil.copy(orig_pspot_file, directory) elif self._link_pspots: os.symlink(orig_pspot_file, cp_pspot_file) else: if self._pedantic: print("""\ Warning: PP files have neither been linked nor copied to the working directory. Make sure to set the evironment variable PSPOT_DIR accordingly!""")
def get_castep_version(castep_command): """This returns the version number as printed in the CASTEP banner. For newer CASTEP versions ( > 6.1) the --version command line option has been added; this will be attempted first. """ temp_dir = tempfile.mkdtemp() jname = 'dummy_jobname' stdout, stderr = '', '' fallback_version = 16. # CASTEP 16.0 and 16.1 report version wrongly try: stdout, stderr = subprocess.Popen( castep_command.split() + ['--version'], stderr=subprocess.PIPE, stdout=subprocess.PIPE, cwd=temp_dir, universal_newlines=True).communicate() if 'CASTEP version' not in stdout: stdout, stderr = subprocess.Popen( castep_command.split() + [jname], stderr=subprocess.PIPE, stdout=subprocess.PIPE, cwd=temp_dir, universal_newlines=True).communicate() except: msg = '' msg += 'Could not determine the version of your CASTEP binary \n' msg += 'This usually means one of the following \n' msg += ' * you do not have CASTEP installed \n' msg += ' * you have not set the CASTEP_COMMAND to call it \n' msg += ' * you have provided a wrong CASTEP_COMMAND. \n' msg += ' Make sure it is in your PATH\n\n' msg += stdout msg += stderr raise CastepVersionError(msg) if 'CASTEP version' in stdout: output_txt = stdout.split('\n') version_re = re.compile(r'CASTEP version:\s*([0-9\.]*)') else: output = open(os.path.join(temp_dir, '%s.castep' % jname)) output_txt = output.readlines() output.close() version_re = re.compile(r'(?<=CASTEP version )[0-9.]*') shutil.rmtree(temp_dir) for line in output_txt: if 'CASTEP version' in line: try: return float(version_re.findall(line)[0]) except ValueError: # Fallback for buggy --version on CASTEP 16.0, 16.1 return fallback_version def create_castep_keywords(castep_command, filename='castep_keywords.json', force_write=True, path='.', fetch_only=None): """This function allows to fetch all available keywords from stdout of an installed castep binary. It furthermore collects the documentation to harness the power of (ipython) inspection and type for some basic type checking of input. All information is stored in a JSON file that is not distributed by default to avoid breaking the license of CASTEP. """ # Takes a while ... # Fetch all allowed parameters # fetch_only : only fetch that many parameters (for testsuite only) suffixes = ['cell', 'param'] filepath = os.path.join(path, filename) if os.path.exists(filepath) and not force_write: print('CASTEP Options Module file exists.') print('You can overwrite it by calling') print('python castep.py -f [CASTEP_COMMAND].') return False # Not saving directly to file her to prevent half-generated files # which will cause problems on future runs castep_version = get_castep_version(castep_command) help_all, _ = shell_stdouterr('%s -help all' % castep_command) # Filter out proper keywords try: # The old pattern does not math properly as in CASTEP as of v8.0 there # are some keywords for the semi-empircal dispersion correction (SEDC) # which also include numbers. if castep_version < 7.0: pattern = r'((?<=^ )[A-Z_]{2,}|(?<=^)[A-Z_]{2,})' else: pattern = r'((?<=^ )[A-Z_\d]{2,}|(?<=^)[A-Z_\d]{2,})' raw_options = re.findall(pattern, help_all, re.MULTILINE) except: print('Problem parsing: %s' % help_all) raise types = set() levels = set() processed_n = 0 to_process = len(raw_options[:fetch_only]) processed_options = {sf: {} for sf in suffixes} for o_i, option in enumerate(raw_options[:fetch_only]): doc, _ = shell_stdouterr('%s -help %s' % (castep_command, option)) # Stand Back! I know regular expressions (http://xkcd.com/208/) :-) match = re.match(r'(?P<before_type>.*)Type: (?P<type>.+?)\s+' + r'Level: (?P<level>[^ ]+)\n\s*\n' + r'(?P<doc>.*?)(\n\s*\n|$)', doc, re.DOTALL) processed_n += 1 if match is not None: match = match.groupdict() # JM: uncomment lines in following block to debug issues # with keyword assignment during extraction process from CASTEP suffix = None if re.findall(r'PARAMETERS keywords:\n\n\s?None found', doc): suffix = 'cell' if re.findall(r'CELL keywords:\n\n\s?None found', doc): suffix = 'param' if suffix is None: print('%s -> not assigned to either' ' CELL or PARAMETERS keywords' % option) option = option.lower() mtyp = match.get('type', None) mlvl = match.get('level', None) mdoc = match.get('doc', None) if mtyp is None: warnings.warn('Found no type for %s' % option) continue if mlvl is None: warnings.warn('Found no level for %s' % option) continue if mdoc is None: warnings.warn('Found no doc string for %s' % option) continue types = types.union([mtyp]) levels = levels.union([mlvl]) processed_options[suffix][option] = { 'keyword': option, 'option_type': mtyp, 'level': mlvl, 'docstring': mdoc } processed_n += 1 frac = (o_i + 1.0) / to_process sys.stdout.write('\rProcessed: [{0}] {1:>3.0f}%'.format( '#' * int(frac * 20) + ' ' * (20 - int(frac * 20)), 100 * frac)) sys.stdout.flush() else: warnings.warn('create_castep_keywords: Could not process %s' % option) sys.stdout.write('\n') sys.stdout.flush() processed_options['types'] = list(types) processed_options['levels'] = list(levels) processed_options['castep_version'] = castep_version json.dump(processed_options, open(filepath, 'w'), indent=4) print('\nCASTEP v%s, fetched %s keywords' % (castep_version, processed_n)) return True class CastepOption(object): """"A CASTEP option. It handles basic conversions from string to its value type.""" default_convert_types = { 'boolean (logical)': 'bool', 'defined': 'bool', 'string': 'str', 'integer': 'int', 'real': 'float', 'integer vector': 'int_vector', 'real vector': 'float_vector', 'physical': 'float_physical', 'block': 'block' } def __init__(self, keyword, level, option_type, value=None, docstring='No information available'): self.keyword = keyword self.level = level self.type = option_type self._value = value self.__doc__ = docstring @property def value(self): if self._value is not None: if self.type.lower() in ('integer vector', 'real vector', 'physical'): return ' '.join(map(str, self._value)) elif self.type.lower() in ('boolean (logical)', 'defined'): return str(self._value).upper() else: return str(self._value) @property def raw_value(self): # The value, not converted to a string return self._value @value.setter def value(self, val): if val is None: self.clear() return ctype = self.default_convert_types.get(self.type.lower(), 'str') typeparse = '_parse_%s' % ctype try: self._value = getattr(self, typeparse)(val) except ValueError: raise ConversionError(ctype, self.keyword, val) def clear(self): """Reset the value of the option to None again""" self._value = None @staticmethod def _parse_bool(value): try: value = _tf_table[str(value).strip().title()] except (KeyError, ValueError): raise ValueError() return value @staticmethod def _parse_str(value): value = str(value) return value @staticmethod def _parse_int(value): value = int(value) return value @staticmethod def _parse_float(value): value = float(value) return value @staticmethod def _parse_int_vector(value): # Accepts either a string or an actual list/numpy array of ints if isinstance(value, basestring): if ',' in value: value = value.replace(',', ' ') value = list(map(int, value.split())) value = np.array(value) if value.shape != (3,) or value.dtype != int: raise ValueError() return list(value) @staticmethod def _parse_float_vector(value): # Accepts either a string or an actual list/numpy array of floats if isinstance(value, basestring): if ',' in value: value = value.replace(',', ' ') value = list(map(float, value.split())) value = np.array(value) * 1.0 if value.shape != (3,) or value.dtype != float: raise ValueError() return list(value) @staticmethod def _parse_float_physical(value): # If this is a string containing units, saves them if isinstance(value, basestring): value = value.split() try: l = len(value) except TypeError: l = 1 value = [value] if l == 1: try: value = (float(value[0]), '') except (TypeError, ValueError): raise ValueError() elif l == 2: try: value = (float(value[0]), value[1]) except (TypeError, ValueError, IndexError): raise ValueError() else: raise ValueError() return value @staticmethod def _parse_block(value): if isinstance(value, basestring): return value elif hasattr(value, '__getitem__'): return '\n'.join(value) # Arrays of lines else: raise ValueError() def __repr__(self): if self._value: expr = ('Option: {keyword}({type}, {level}):\n{_value}\n' ).format(**self.__dict__) else: expr = ('Option: {keyword}[unset]({type}, {level})' ).format(**self.__dict__) return expr def __eq__(self, other): if not isinstance(other, CastepOption): return False else: return self.__dict__ == other.__dict__ class CastepOptionDict(object): """A dictionary-like object to hold a set of options for .cell or .param files loaded from a dictionary, for the sake of validation. Replaces the old CastepCellDict and CastepParamDict that were defined in the castep_keywords.py file. """ def __init__(self, options=None): object.__init__(self) self._options = {} # ComparableDict is not needed any more as # CastepOptions can be compared directly now for kw in options: opt = CastepOption(**options[kw]) self._options[opt.keyword] = opt self.__dict__[opt.keyword] = opt class CastepInputFile(object): """Master class for CastepParam and CastepCell to inherit from""" _keyword_conflicts = [] def __init__(self, options_dict=None, keyword_tolerance=1): object.__init__(self) if options_dict is None: options_dict = CastepOptionDict({}) self._options = options_dict._options self.__dict__.update(self._options) # keyword_tolerance means how strict the checks on new attributes are # 0 = no new attributes allowed # 1 = new attributes allowed, warning given # 2 = new attributes allowed, silent self._perm = np.clip(keyword_tolerance, 0, 2) # Compile a dictionary for quick check of conflict sets self._conflict_dict = {kw: set(cset).difference({kw}) for cset in self._keyword_conflicts for kw in cset} def __repr__(self): expr = '' is_default = True for key, option in sorted(self._options.items()): if option.value is not None: is_default = False expr += ('%20s : %s\n' % (key, option.value)) if is_default: expr = 'Default\n' expr += 'Keyword tolerance: {0}'.format(self._perm) return expr def __setattr__(self, attr, value): # Hidden attributes are treated normally if attr.startswith('_'): self.__dict__[attr] = value return if attr not in self._options.keys(): if self._perm > 0: # Do we consider it a string or a block? is_str = isinstance(value, basestring) is_block = False if ((hasattr(value, '__getitem__') and not is_str) or (is_str and len(value.split('\n')) > 1)): is_block = True if self._perm == 0: similars = difflib.get_close_matches(attr, self._options.keys()) if similars: raise UserWarning(('Option "%s" not known! You mean "%s"?') % (attr, similars[0])) else: raise UserWarning('Option "%s" is not known!' % attr) elif self._perm == 1: warnings.warn(('Option "%s" is not known and will ' 'be added as a %s') % (attr, ('block' if is_block else 'string'))) attr = attr.lower() opt = CastepOption(keyword=attr, level='Unknown', option_type='block' if is_block else 'string') self._options[attr] = opt self.__dict__[attr] = opt else: attr = attr.lower() opt = self._options[attr] if not opt.type.lower() == 'block' and isinstance(value, basestring): value = value.replace(':', ' ') # If it is, use the appropriate parser, unless a custom one is defined attrparse = '_parse_%s' % attr.lower() # Check for any conflicts cset = self._conflict_dict.get(attr.lower(), {}) for c in cset: if (c in self._options and self._options[c].value): warnings.warn( 'option "{attr}" conflicts with "{conflict}" in ' 'calculator. Setting "{conflict}" to ' 'None.'.format(attr=attr, conflict=c)) self._options[c].value = None if hasattr(self, attrparse): self._options[attr].value = self.__getattribute__(attrparse)(value) else: self._options[attr].value = value def __getattr__(self, name): if name[0] == '_' or self._perm == 0: raise AttributeError() if self._perm == 1: warnings.warn('Option %s is not known, returning None' % (name)) return CastepOption(keyword='none', level='Unknown', option_type='string', value=None) def get_attr_dict(self, raw=False, types=False): """Settings that go into .param file in a traditional dict""" attrdict = {k: o.raw_value if raw else o.value for k, o in self._options.items() if o.value is not None} if types: for key, val in attrdict.items(): attrdict[key] = (val, self._options[key].type) return attrdict class CastepParam(CastepInputFile): """CastepParam abstracts the settings that go into the .param file""" _keyword_conflicts = [{'cut_off_energy', 'basis_precision'}, ] def __init__(self, castep_keywords, keyword_tolerance=1): self._castep_version = castep_keywords.castep_version CastepInputFile.__init__(self, castep_keywords.CastepParamDict(), keyword_tolerance) @property def castep_version(self): return self._castep_version # .param specific parsers def _parse_reuse(self, value): try: if self._options['continuation'].value: print('Cannot set reuse if continuation is set, and') print('vice versa. Set the other to None, if you want') print('this setting.') return None except KeyError: pass return 'default' if (value is True) else str(value) def _parse_continuation(self, value): try: if self._options['reuse'].value: print('Cannot set reuse if continuation is set, and') print('vice versa. Set the other to None, if you want') print('this setting.') return None except KeyError: pass return 'default' if (value is True) else str(value) class CastepCell(CastepInputFile): """CastepCell abstracts all setting that go into the .cell file""" _keyword_conflicts = [ {'kpoint_mp_grid', 'kpoint_mp_spacing', 'kpoint_list', 'kpoints_mp_grid', 'kpoints_mp_spacing', 'kpoints_list'}, {'bs_kpoint_mp_grid', 'bs_kpoint_mp_spacing', 'bs_kpoint_list', 'bs_kpoint_path', 'bs_kpoints_mp_grid', 'bs_kpoints_mp_spacing', 'bs_kpoints_list', 'bs_kpoints_path'}, {'spectral_kpoint_mp_grid', 'spectral_kpoint_mp_spacing', 'spectral_kpoint_list', 'spectral_kpoint_path', 'spectral_kpoints_mp_grid', 'spectral_kpoints_mp_spacing', 'spectral_kpoints_list', 'spectral_kpoints_path'}, {'phonon_kpoint_mp_grid', 'phonon_kpoint_mp_spacing', 'phonon_kpoint_list', 'phonon_kpoint_path', 'phonon_kpoints_mp_grid', 'phonon_kpoints_mp_spacing', 'phonon_kpoints_list', 'phonon_kpoints_path'}, {'fine_phonon_kpoint_mp_grid', 'fine_phonon_kpoint_mp_spacing', 'fine_phonon_kpoint_list', 'fine_phonon_kpoint_path'}, {'magres_kpoint_mp_grid', 'magres_kpoint_mp_spacing', 'magres_kpoint_list', 'magres_kpoint_path'}, {'elnes_kpoint_mp_grid', 'elnes_kpoint_mp_spacing', 'elnes_kpoint_list', 'elnes_kpoint_path'}, {'optics_kpoint_mp_grid', 'optics_kpoint_mp_spacing', 'optics_kpoint_list', 'optics_kpoint_path'}, {'supercell_kpoint_mp_grid', 'supercell_kpoint_mp_spacing', 'supercell_kpoint_list', 'supercell_kpoint_path'},] def __init__(self, castep_keywords, keyword_tolerance=1): self._castep_version = castep_keywords.castep_version CastepInputFile.__init__(self, castep_keywords.CastepCellDict(), keyword_tolerance) @property def castep_version(self): return self._castep_version # .cell specific parsers def _parse_species_pot(self, value): # Single tuple if isinstance(value, tuple) and len(value) == 2: value = [value] # List of tuples if hasattr(value, '__getitem__'): pspots = [tuple(map(str.strip, x)) for x in value] if not all(map(lambda x: len(x) == 2, value)): print('Please specify pseudopotentials in python as') print('a tuple or a list of tuples formatted like:') print('(species, file), e.g. ("O", "path-to/O_OTFG.usp")') print('Anything else will be ignored') return None text_block = self._options['species_pot'].value text_block = text_block if text_block else '' # Remove any duplicates for pp in pspots: text_block = re.sub(r'\n?\s*%s\s+.*' % pp[0], '', text_block) if pp[1]: text_block += '\n%s %s' % pp return text_block def _parse_symmetry_ops(self, value): if not isinstance(value, tuple) \ or not len(value) == 2 \ or not value[0].shape[1:] == (3, 3) \ or not value[1].shape[1:] == (3,) \ or not value[0].shape[0] == value[1].shape[0]: warnings.warn('Invalid symmetry_ops block, skipping') return # Now on to print... text_block = '' for op_i, (op_rot, op_tranls) in enumerate(zip(*value)): text_block += '\n'.join([' '.join([str(x) for x in row]) for row in op_rot]) text_block += '\n' text_block += ' '.join([str(x) for x in op_tranls]) text_block += '\n\n' return text_block def _parse_positions_abs_intermediate(self, value): if not isinstance(value, ase.atoms.Atoms): raise TypeError('castep.cell.positions_abs_intermediate/product ' 'expect Atoms object') text_block = 'ang\n' for elem, pos in zip(value.get_chemical_symbols(), value.get_positions()): text_block += (' %4s %9.6f %9.6f %9.6f\n' % (elem, pos[0], pos[1], pos[2])) return text_block def _parse_positions_abs_product(self, value): return self._positions_abs_intermediate(self, value) def _parse_positions_frac_intermediate(self, value): if not isinstance(value, ase.atoms.Atoms): raise TypeError('castep.cell.positions_frac_intermediate/product ' 'expect Atoms object') text_block = 'ang\n' for elem, pos in zip(value.get_chemical_symbols(), value.get_scaled_positions()): text_block += (' %4s %9.6f %9.6f %9.6f\n' % (elem, pos[0], pos[1], pos[2])) return text_block def _parse_positions_frac_product(self, value): return self._positions_frac_intermediate(self, value) CastepKeywords = namedtuple('CastepKeywords', ['CastepParamDict', 'CastepCellDict', 'types', 'levels', 'castep_version']) # We keep this just for naming consistency with older versions def make_cell_dict(data=None): data = data if data is not None else {} class CastepCellDict(CastepOptionDict): def __init__(self): CastepOptionDict.__init__(self, data) return CastepCellDict def make_param_dict(data=None): data = data if data is not None else {} class CastepParamDict(CastepOptionDict): def __init__(self): CastepOptionDict.__init__(self, data) return CastepParamDict class CastepVersionError(Exception): """No special behaviour, works to signal when Castep can not be found""" pass class ConversionError(Exception): """Print customized error for options that are not converted correctly and point out that they are maybe not implemented, yet""" def __init__(self, key_type, attr, value): Exception.__init__(self) self.key_type = key_type self.value = value self.attr = attr def __str__(self): return 'Could not convert %s = %s to %s\n' \ % (self.attr, self.value, self.key_type) \ + 'This means you either tried to set a value of the wrong\n'\ + 'type or this keyword needs some special care. Please feel\n'\ + 'to add it to the corresponding __setattr__ method and send\n'\ + 'the patch to %s, so we can all benefit.' % (contact_email) def get_castep_pp_path(castep_pp_path=''): """Abstract the quest for a CASTEP PSP directory.""" if castep_pp_path: return os.path.abspath(os.path.expanduser(castep_pp_path)) elif 'PSPOT_DIR' in os.environ: return os.environ['PSPOT_DIR'] elif 'CASTEP_PP_PATH' in os.environ: return os.environ['CASTEP_PP_PATH'] else: return os.path.abspath('.') def get_castep_command(castep_command=''): """Abstract the quest for a castep_command string.""" if castep_command: return castep_command elif 'CASTEP_COMMAND' in os.environ: return os.environ['CASTEP_COMMAND'] else: return 'castep' def shell_stdouterr(raw_command, cwd=None): """Abstracts the standard call of the commandline, when we are only interested in the stdout and stderr """ stdout, stderr = subprocess.Popen(raw_command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True, shell=True, cwd=cwd).communicate() return stdout.strip(), stderr.strip() def import_castep_keywords(castep_command='', filename='castep_keywords.json', path='.'): # Search for castep_keywords.json (or however it's called) in multiple # paths searchpaths = [path, os.path.expanduser('~/.ase'), os.path.join(ase.__path__[0], 'calculators')] try: kwfile = sum([glob.glob(os.path.join(sp, filename)) for sp in searchpaths], [])[0] except IndexError: print(""" Generating CASTEP keywords JSON file... hang on. The CASTEP keywords JSON file contains abstractions for CASTEP input parameters (for both .cell and .param input files), including some format checks and descriptions. The latter are extracted from the internal online help facility of a CASTEP binary, thus allowing to easily keep the calculator synchronized with (different versions of) the CASTEP code. Consequently, avoiding licensing issues (CASTEP is distributed commercially by accelrys), we consider it wise not to provide the file in the first place. """) create_castep_keywords(get_castep_command(castep_command), filename=filename, path=path) print("""\n\n Stored %s in %s. Copy it to your ASE installation under ase/calculators for system-wide installation """ % (filename, os.path.abspath(path))) print("""\n\n Using a *nix OS this can be a simple as\nmv %s %s""" % (os.path.join(os.path.abspath(path), filename), os.path.join(os.path.dirname(ase.__file__), 'calculators'))) kwfile = os.path.join(path, filename) # Now create the castep_keywords object proper kwdata = json.load(open(kwfile)) # This is a bit awkward, but it's necessary for backwards compatibility param_dict = make_param_dict(kwdata['param']) cell_dict = make_cell_dict(kwdata['cell']) castep_keywords = CastepKeywords(param_dict, cell_dict, kwdata['types'], kwdata['levels'], kwdata['castep_version']) return castep_keywords if __name__ == '__main__': print('When called directly this calculator will fetch all available') print('keywords from the binarys help function into a ') print('castep_keywords.json in the current directory %s' % os.getcwd()) print('For system wide usage, it can be copied into an ase installation') print('at ASE/calculators.\n') print('This castep_keywords.json usually only needs to be generated once') print('for a CASTEP binary/CASTEP version.') import optparse parser = optparse.OptionParser() parser.add_option( '-f', '--force-write', dest='force_write', help='Force overwriting existing castep_keywords.json', default=False, action='store_true') (options, args) = parser.parse_args() if args: opt_castep_command = ''.join(args) else: opt_castep_command = '' generated = create_castep_keywords(get_castep_command(opt_castep_command), force_write=options.force_write) if generated: try: with open('castep_keywords.json') as f: json.load(f) except Exception as e: print(e) print('Ooops, something went wrong with the CASTEP keywords') else: print('Import works. Looking good!')