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

from __future__ import division, unicode_literals

"""
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 multienum.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"

import re
import math
import subprocess
import itertools
import logging

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

logger = logging.getLogger(__name__)


# Favor the use of the newer "enum.x" by Gus Hart instead of the older
# "multienum.x"
enum_cmd = which('multienum.x')


@requires(enum_cmd and which('makestr.x'),
          "EnumlibAdaptor requires the executables 'enum.x' or 'multienum.x' "
          "and 'makestr.x' 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):
        """
        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.
        """
        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

    def run(self):
        """
        Run the enumeration.
        """
        # Create a temporary directory for working.
        with ScratchDir(".") as d:
            logger.debug("Temp dir : {}".format(d))
            try:
                # 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 ValueError("Unable to enumerate structure.")
            except Exception:
                import sys
                import traceback

                exc_type, exc_value, exc_traceback = sys.exc_info()
                traceback.print_exception(exc_type, exc_value, exc_traceback,
                                          limit=10, file=sys.stdout)

    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_spacegroup_symbol(),
            fitter.get_spacegroup_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_spacegroup_number()

        curr_sites = list(itertools.chain.from_iterable(disordered_sites))
        min_sgnum = get_sg_info(curr_sites)
        logger.debug("Disorderd sites has sgnum %d" % (
            min_sgnum))
        # It could be that some of the ordered sites has a lower symmetry than
        # the disordered sites.  So we consider the lowest symmetry sites as
        # disordered in our enumeration.
        self.ordered_sites = []
        to_add = []

        if self.check_ordered_symmetry:
            for sites in ordered_sites:
                temp_sites = list(curr_sites) + sites
                sgnum = get_sg_info(temp_sites)
                if sgnum < min_sgnum:
                    logger.debug("Adding {} to sites to be ordered. "
                                 "New sgnum {}"
                                 .format(sites, sgnum))
                    to_add = sites
                    min_sgnum = sgnum

        for sites in ordered_sites:
            if sites == to_add:
                index_species.append(sites[0].specie)
                index_amounts.append(len(sites))
                sp_label = len(index_species) - 1
                logger.debug("Lowest symmetry {} sites are included in enum."
                             .format(sites[0].specie))
                for site in sites:
                    coord_str.append("{} {}".format(
                        coord_format.format(*site.coords),
                        sp_label))
                disordered_sites.append(sites)
            else:
                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("{}".format(len(index_species)))
        output.append("{}".format(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*reduce(lcm,
                                      [f.limit_denominator(