Source code for pymatgen.command_line.enumlib_caller

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

from __future__ import division, unicode_literals

import re
import math
import subprocess
import itertools
import logging
import glob
import warnings

import numpy as np
from monty.fractions import lcm
import fractions

from six.moves import reduce

from pymatgen.io.vasp.inputs import Poscar
from pymatgen.core.sites import PeriodicSite
from pymatgen.core.structure import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.periodic_table import DummySpecie
from monty.os.path import which
from monty.dev import requires
from monty.tempfile import ScratchDir
from threading import Timer

"""
This module implements an interface to enumlib, Gus Hart"s excellent Fortran
code for enumerating derivative structures.

This module depends on a compiled enumlib with the executables enum.x and
makestr.x available in the path. Please download the library at
http://enum.sourceforge.net/ and follow the instructions in the README to
compile these two executables accordingly.

If you use this module, please cite the following:

Gus L. W. Hart and Rodney W. Forcade, "Algorithm for generating derivative
structures," Phys. Rev. B 77 224115 (26 June 2008)

Gus L. W. Hart and Rodney W. Forcade, "Generating derivative structures from
multilattices: Application to hcp alloys," Phys. Rev. B 80 014120 (July 2009)

Gus L. W. Hart, Lance J. Nelson, and Rodney W. Forcade, "Generating
derivative structures at a fixed concentration," Comp. Mat. Sci. 59
101-107 (March 2012)
"""

__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Jul 16, 2012"


logger = logging.getLogger(__name__)


# Favor the use of the newer "enum.x" by Gus Hart instead of the older
# "multienum.x"
enum_cmd = which('enum.x') or which('multienum.x')
# prefer makestr.x at present
makestr_cmd = which('makestr.x') or which('makeStr.x') or which('makeStr.py')


[docs]@requires(enum_cmd and makestr_cmd, "EnumlibAdaptor requires the executables 'enum.x' or 'multienum.x' " "and 'makestr.x' or 'makeStr.py' to be in the path. Please download the " "library at http://enum.sourceforge.net/ and follow the instructions in " "the README to compile these two executables accordingly.") class EnumlibAdaptor(object): """ An adaptor for enumlib. .. attribute:: structures List of all enumerated structures. """ amount_tol = 1e-5 def __init__(self, structure, min_cell_size=1, max_cell_size=1, symm_prec=0.1, enum_precision_parameter=0.001, refine_structure=False, check_ordered_symmetry=True, timeout=None): """ Initializes the adapter with a structure and some parameters. Args: structure: An input structure. min_cell_size (int): The minimum cell size wanted. Defaults to 1. max_cell_size (int): The maximum cell size wanted. Defaults to 1. symm_prec (float): Symmetry precision. Defaults to 0.1. enum_precision_parameter (float): Finite precision parameter for enumlib. Default of 0.001 is usually ok, but you might need to tweak it for certain cells. refine_structure (bool): If you are starting from a structure that has been relaxed via some electronic structure code, it is usually much better to start with symmetry determination and then obtain a refined structure. The refined structure have cell parameters and atomic positions shifted to the expected symmetry positions, which makes it much less sensitive precision issues in enumlib. If you are already starting from an experimental cif, refinement should have already been done and it is not necessary. Defaults to False. check_ordered_symmetry (bool): Whether to check the symmetry of the ordered sites. If the symmetry of the ordered sites is lower, the lowest symmetry ordered sites is included in the enumeration. This is important if the ordered sites break symmetry in a way that is important getting possible structures. But sometimes including ordered sites slows down enumeration to the point that it cannot be completed. Switch to False in those cases. Defaults to True. timeout (float): If specified, will kill enumlib after specified time in minutes. This can be useful for gracefully handling enumerations in a high-throughput context, for some enumerations which will not terminate in a realistic length of time. """ if refine_structure: finder = SpacegroupAnalyzer(structure, symm_prec) self.structure = finder.get_refined_structure() else: self.structure = structure self.min_cell_size = min_cell_size self.max_cell_size = max_cell_size self.symm_prec = symm_prec self.enum_precision_parameter = enum_precision_parameter self.check_ordered_symmetry = check_ordered_symmetry self.structures = None self.timeout = timeout def run(self): """ Run the enumeration. """ # Create a temporary directory for working. with ScratchDir(".") as d: logger.debug("Temp dir : {}".format(d)) # Generate input files self._gen_input_file() # Perform the actual enumeration num_structs = self._run_multienum() # Read in the enumeration output as structures. if num_structs > 0: self.structures = self._get_structures(num_structs) else: raise EnumError("Unable to enumerate structure.") def _gen_input_file(self): """ Generate the necessary struct_enum.in file for enumlib. See enumlib documentation for details. """ coord_format = "{:.6f} {:.6f} {:.6f}" # Using symmetry finder, get the symmetrically distinct sites. fitter = SpacegroupAnalyzer(self.structure, self.symm_prec) symmetrized_structure = fitter.get_symmetrized_structure() logger.debug("Spacegroup {} ({}) with {} distinct sites".format( fitter.get_space_group_symbol(), fitter.get_space_group_number(), len(symmetrized_structure.equivalent_sites)) ) """ Enumlib doesn"t work when the number of species get too large. To simplify matters, we generate the input file only with disordered sites and exclude the ordered sites from the enumeration. The fact that different disordered sites with the exact same species may belong to different equivalent sites is dealt with by having determined the spacegroup earlier and labelling the species differently. """ # index_species and index_amounts store mappings between the indices # used in the enum input file, and the actual species and amounts. index_species = [] index_amounts = [] # Stores the ordered sites, which are not enumerated. ordered_sites = [] disordered_sites = [] coord_str = [] for sites in symmetrized_structure.equivalent_sites: if sites[0].is_ordered: ordered_sites.append(sites) else: sp_label = [] species = {k: v for k, v in sites[0].species_and_occu.items()} if sum(species.values()) < 1 - EnumlibAdaptor.amount_tol: # Let us first make add a dummy element for every single # site whose total occupancies don't sum to 1. species[DummySpecie("X")] = 1 - sum(species.values()) for sp in species.keys(): if sp not in index_species: index_species.append(sp) sp_label.append(len(index_species) - 1) index_amounts.append(species[sp] * len(sites)) else: ind = index_species.index(sp) sp_label.append(ind) index_amounts[ind] += species[sp] * len(sites) sp_label = "/".join(["{}".format(i) for i in sorted(sp_label)]) for site in sites: coord_str.append("{} {}".format( coord_format.format(*site.coords), sp_label)) disordered_sites.append(sites) def get_sg_info(ss): finder = SpacegroupAnalyzer(Structure.from_sites(ss), self.symm_prec) return finder.get_space_group_number() target_sgnum = get_sg_info(symmetrized_structure.sites) curr_sites = list(itertools.chain.from_iterable(disordered_sites)) sgnum = get_sg_info(curr_sites) ordered_sites = sorted(ordered_sites, key=lambda sites: len(sites)) logger.debug("Disordered sites has sg # %d" % (sgnum)) self.ordered_sites = [] # progressively add ordered sites to our disordered sites # until we match the symmetry of our input structure if self.check_ordered_symmetry: while sgnum != target_sgnum and len(ordered_sites) > 0: sites = ordered_sites.pop(0) temp_sites = list(curr_sites) + sites new_sgnum = get_sg_info(temp_sites) if sgnum != new_sgnum: logger.debug("Adding %s in enum. New sg # %d" % (sites[0].specie, new_sgnum)) index_species.append(sites[0].specie) index_amounts.append(len(sites)) sp_label = len(index_species) - 1 for site in sites: coord_str.append("{} {}".format( coord_format.format(*site.coords), sp_label)) disordered_sites.append(sites) curr_sites = temp_sites sgnum = new_sgnum else: self.ordered_sites.extend(sites) for sites in ordered_sites: self.ordered_sites.extend(sites) self.index_species = index_species lattice = self.structure.lattice output = [self.structure.formula, "bulk"] for vec in lattice.matrix: output.append(coord_format.format(*vec)) output.append("%d" % len(index_species)) output.append("%d" % len(coord_str)) output.extend(coord_str) output.append("{} {}".format(self.min_cell_size, self.max_cell_size)) output.append(str(self.enum_precision_parameter)) output.append("partial") ndisordered = sum([len(s) for s in disordered_sites]) base = int(ndisordered*lcm(*[f.limit_denominator(ndisordered * self.max_cell_size).denominator for f in map(fractions.Fraction, index_amounts)])) # This multiplicative factor of 10 is to prevent having too small bases # which can lead to rounding issues in the next step. # An old bug was that a base was set to 8, with a conc of 0.4:0.6. That # resulted in a range that overlaps and a conc of 0.5 satisfying this # enumeration. See Cu7Te5.cif test file. base *= 10 # base = ndisordered #10 ** int(math.ceil(math.log10(ndisordered))) # To get a reasonable number of structures, we fix concentrations to the # range expected in the original structure. total_amounts = sum(index_amounts) for amt in index_amounts: conc = amt / total_amounts if abs(conc * base - round(conc * base)) < 1e-5: output.append("{} {} {}".format(int(round(conc * base)), int(round(conc * base)), base)) else: min_conc = int(math.floor(conc * base)) output.append("{} {} {}".format(min_conc - 1, min_conc + 1, base)) output.append("") logger.debug("Generated input file:\n{}".format("\n".join(output))) with open("struct_enum.in", "w") as f: f.write("\n".join(output)) def _run_multienum(self): p = subprocess.Popen([enum_cmd], stdout=subprocess.PIPE, stdin=subprocess.PIPE, close_fds=True) if self.timeout: timed_out = False timer = Timer(self.timeout*60, lambda p: p.kill(), [p]) try: timer.start() output = p.communicate()[0].decode("utf-8") finally: if not timer.is_alive(): timed_out = True timer.cancel() if timed_out: raise TimeoutError('Enumeration took too long.') else: output = p.communicate()[0].decode("utf-8") count = 0 start_count = False for line in output.strip().split("\n"): if line.strip().endswith("RunTot"): start_count = True elif start_count and re.match(r"\d+\s+.*", line.strip()): count = int(line.split()[-1]) logger.debug("Enumeration resulted in {} structures".format(count)) return count def _get_structures(self, num_structs): structs = [] if ".py" in makestr_cmd: options = ["-input", "struct_enum.out", str(1), str(num_structs)] else: options = ["struct_enum.out", str(0), str(num_structs - 1)] rs = subprocess.Popen([makestr_cmd] + options, stdout=subprocess.PIPE, stdin=subprocess.PIPE, close_fds=True) stdout, stderr = rs.communicate() if stderr: logger.warning(stderr.decode()) # sites retrieved from enumlib will lack site properties # to ensure consistency, we keep track of what site properties # are missing and set them to None # TODO: improve this by mapping ordered structure to original # disorded structure, and retrieving correct site properties disordered_site_properties = {} if len(self.ordered_sites) > 0: original_latt = self.ordered_sites[0].lattice # Need to strip sites of site_properties, which would otherwise # result in an index error. Hence Structure is reconstructed in # the next step. site_properties = {} for site in self.ordered_sites: for k, v in site.properties.items(): disordered_site_properties[k] = None if k in site_properties: site_properties[k].append(v) else: site_properties[k] = [v] ordered_structure = Structure( original_latt, [site.species_and_occu for site in self.ordered_sites], [site.frac_coords for site in self.ordered_sites], site_properties=site_properties ) inv_org_latt = np.linalg.inv(original_latt.matrix) for file in glob.glob('vasp.*'): with open(file) as f: data = f.read() data = re.sub(r'scale factor', "1", data) data = re.sub(r'(\d+)-(\d+)', r'\1 -\2', data) poscar = Poscar.from_string(data, self.index_species) sub_structure = poscar.structure # Enumeration may have resulted in a super lattice. We need to # find the mapping from the new lattice to the old lattice, and # perform supercell construction if necessary. new_latt = sub_structure.lattice sites = [] if len(self.ordered_sites) > 0: transformation = np.dot(new_latt.matrix, inv_org_latt) transformation = [[int(round(cell)) for cell in row] for row in transformation] logger.debug("Supercell matrix: {}".format(transformation)) s = ordered_structure * transformation sites.extend([site.to_unit_cell for site in s]) super_latt = sites[-1].lattice else: super_latt = new_latt for site in sub_structure: if site.specie.symbol != "X": # We exclude vacancies. sites.append(PeriodicSite(site.species_and_occu, site.frac_coords, super_latt, properties=disordered_site_properties) .to_unit_cell) else: warnings.warn("Skipping sites that include species X.") structs.append(Structure.from_sites(sorted(sites))) logger.debug("Read in a total of {} structures.".format(num_structs)) return structs
[docs]class EnumError(BaseException): pass