pymatgen.analysis.chemenv.utils.scripts_utils — pymatgen 2020.7.3 documentation

# Source code for pymatgen.analysis.chemenv.utils.scripts_utils

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

    from pymatgen.ext.matproj import MPRester
    from pymatgen.io.cif import CifParser

    try:
        from pymatgen.vis.structure_vtk import StructureVis
        no_vis = False
    except ImportError:
        StructureVis = None  # type: ignore
        no_vis = True

    from pymatgen.core.sites import PeriodicSite
    import re
    from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
    from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import UNCLEAR_ENVIRONMENT_SYMBOL
    from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
    from pymatgen.analysis.chemenv.utils.chemenv_errors import NeighborsNotComputedChemenvError
    from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
    from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import rotateCoords
    from pymatgen.analysis.chemenv.utils.defs_utils import chemenv_citations
    from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy
    from pymatgen.core.structure import Molecule
    from collections import OrderedDict
    import numpy as np

    """
    This module contains some utils for the main script of the chemenv package.
    """

    __author__ = "David Waroquiers"
    __copyright__ = "Copyright 2012, The Materials Project"
    __credits__ = "Geoffroy Hautier"
    __version__ = "2.0"
    __maintainer__ = "David Waroquiers"
    __email__ = "david.waroquiers@gmail.com"
    __date__ = "Feb 20, 2016"

    strategies_class_lookup = OrderedDict()  # type: dict
    strategies_class_lookup['SimplestChemenvStrategy'] = SimplestChemenvStrategy

    # strategies_class_lookup['SimpleAbundanceChemenvStrategy'] = SimpleAbundanceChemenvStrategy
    # strategies_class_lookup['TargettedPenaltiedAbundanceChemenvStrategy'] = TargettedPenaltiedAbundanceChemenvStrategy

    def draw_cg(vis, site, neighbors, cg=None, perm=None, perfect2local_map=None,
                show_perfect=False, csm_info=None, symmetry_measure_type='csm_wcs_ctwcc', perfect_radius=0.1,
                show_distorted=True, faces_color_override=None):
        if show_perfect:
            if csm_info is None:
                raise ValueError('Not possible to show perfect environment without csm_info')
            csm_suffix = symmetry_measure_type[4:]
            perf_radius = (perfect_radius - 0.2) / 0.002
        if perm is not None and perfect2local_map is not None:
            raise ValueError('Only "perm" or "perfect2local_map" should be provided in draw_cg, not both')
        if show_distorted:
            vis.add_bonds(neighbors, site)
            for n in neighbors:
                vis.add_site(n)
        if len(neighbors) < 3:
            if show_distorted:
                vis.add_bonds(neighbors, site, color=[0.0, 1.0, 0.0], opacity=0.4, radius=0.175)
            if show_perfect:
                if len(neighbors) == 2:
                    perfect_geometry = AbstractGeometry.from_cg(cg)
                    trans = csm_info['other_symmetry_measures']['translation_vector_{}'.format(csm_suffix)]
                    rot = csm_info['other_symmetry_measures']['rotation_matrix_{}'.format(csm_suffix)]
                    scale = csm_info['other_symmetry_measures']['scaling_factor_{}'.format(csm_suffix)]
                    points = perfect_geometry.points_wcs_ctwcc()
                    rotated_points = rotateCoords(points, rot)
                    points = [scale * pp + trans for pp in rotated_points]
                    if 'wcs' in csm_suffix:
                        ef_points = points[1:]
                    else:
                        ef_points = points
                    edges = cg.edges(ef_points, input='coords')
                    vis.add_edges(edges, color=[1.0, 0.0, 0.0])
                    for point in points:
                        vis.add_partial_sphere(coords=point, radius=perf_radius, color=[0.0, 0.0, 0.0],
                                               start=0, end=360, opacity=1)
        else:
            if show_distorted:
                if perm is not None:
                    faces = cg.faces(neighbors, permutation=perm)
                    edges = cg.edges(neighbors, permutation=perm)
                elif perfect2local_map is not None:
                    faces = cg.faces(neighbors, perfect2local_map=perfect2local_map)
                    edges = cg.edges(neighbors, perfect2local_map=perfect2local_map)
                else:
                    faces = cg.faces(neighbors)
                    edges = cg.edges(neighbors)
                symbol = list(site.species.keys())[0].symbol
                if faces_color_override:
                    mycolor = faces_color_override
                else:
                    mycolor = [float(i) / 255 for i in vis.el_color_mapping[symbol]]
                vis.add_faces(faces, mycolor, opacity=0.4)
                vis.add_edges(edges)
            if show_perfect:
                perfect_geometry = AbstractGeometry.from_cg(cg)
                trans = csm_info['other_symmetry_measures']['translation_vector_{}'.format(csm_suffix)]
                rot = csm_info['other_symmetry_measures']['rotation_matrix_{}'.format(csm_suffix)]
                scale = csm_info['other_symmetry_measures']['scaling_factor_{}'.format(csm_suffix)]
                points = perfect_geometry.points_wcs_ctwcc()
                rotated_points = rotateCoords(points, rot)
                points = [scale * pp + trans for pp in rotated_points]
                if 'wcs' in csm_suffix:
                    ef_points = points[1:]
                else:
                    ef_points = points
                edges = cg.edges(ef_points, input='coords')
                vis.add_edges(edges, color=[1.0, 0.0, 0.0])
                for point in points:
                    vis.add_partial_sphere(coords=point, radius=perf_radius, color=[0.0, 0.0, 0.0],
                                           start=0, end=360, opacity=1)

    # Visualizing a coordination geometry
    def visualize(cg, zoom=None, vis=None, myfactor=1.0, view_index=True, faces_color_override=None):
        if vis is None:
            vis = StructureVis(show_polyhedron=False, show_unit_cell=False)
        myspecies = ["O"] * (cg.coordination_number + 1)
        myspecies[0] = "Cu"
        coords = [np.zeros(3, np.float) + cg.central_site]

        for pp in cg.points:
            coords.append(np.array(pp) + cg.central_site)
        coords = [cc * myfactor for cc in coords]
        structure = Molecule(species=myspecies, coords=coords)
        vis.set_structure(structure=structure, reset_camera=True)
        # neighbors_list = coords[1:]
        draw_cg(vis, site=structure[0], neighbors=structure[1:], cg=cg, faces_color_override=faces_color_override)
        if view_index:
            for ineighbor, neighbor in enumerate(structure[1:]):
                vis.add_text(neighbor.coords, '{}'.format(ineighbor), color=(0, 0, 0))
        if zoom is not None:
            vis.zoom(zoom)
        return vis

    def welcome(chemenv_config):
        print('Chemical Environment package (ChemEnv)')
        print(chemenv_citations())
        print(chemenv_config.package_options_description())

    def thankyou():
        print('Thank you for using the ChemEnv package')
        print(chemenv_citations())

    def compute_environments(chemenv_configuration):
        string_sources = {'cif': {'string': 'a Cif file', 'regexp': r'.*\.cif$'},
                          'mp': {'string': 'the Materials Project database',
                                 'regexp': r'mp-[0-9]+$'}}
        questions = {'c': 'cif'}
        questions['m'] = 'mp'
        lgf = LocalGeometryFinder()
        lgf.setup_parameters()
        allcg = AllCoordinationGeometries()
        strategy_class = strategies_class_lookup[chemenv_configuration.package_options['default_strategy']['strategy']]
        # TODO: Add the possibility to change the parameters and save them in the chemenv_configuration
        default_strategy = strategy_class()
        default_strategy.setup_options(chemenv_configuration.package_options['default_strategy']['strategy_options'])
        max_dist_factor = chemenv_configuration.package_options['default_max_distance_factor']
        firsttime = True
        while True:
            if len(questions) > 1:
                found = False
                print('Enter the source from which the structure is coming or <q> to quit :')
                for key_character, qq in questions.items():
                    print(' - <{}> for a structure from {}'.format(key_character, string_sources[qq]['string']))
                test = input(' ... ')
                if test == 'q':
                    break
                if test not in list(questions.keys()):
                    for key_character, qq in questions.items():
                        if re.match(string_sources[qq]['regexp'], str(test)) is not None:
                            found = True
                            source_type = qq
                    if not found:
                        print('Wrong key, try again ...')
                        continue
                else:
                    source_type = questions[test]
            else:
                found = False
                source_type = list(questions.values())[0]
            if found and len(questions) > 1:
                input_source = test
            if source_type == 'cif':
                if not found:
                    input_source = input('Enter path to cif file : ')
                cp = CifParser(input_source)
                structure = cp.get_structures()[0]
            elif source_type == 'mp':
                if not found:
                    input_source = input('Enter materials project id (e.g. "mp-1902") : ')
                a = MPRester()
                structure = a.get_structure_by_material_id(input_source)
            lgf.setup_structure(structure)
            print('Computing environments for {} ... '.format(structure.composition.reduced_formula))
            se = lgf.compute_structure_environments(maximum_distance_factor=max_dist_factor)
            print('Computing environments finished')
            while True:
                test = input('See list of environments determined for each (unequivalent) site ? '
                             '("y" or "n", "d" with details, "g" to see the grid) : ')
                strategy = default_strategy
                if test in ['y', 'd', 'g']:
                    strategy.set_structure_environments(se)
                    for eqslist in se.equivalent_sites:
                        site = eqslist[0]
                        isite = se.structure.index(site)
                        try:
                            if strategy.uniquely_determines_coordination_environments:
                                ces = strategy.get_site_coordination_environments(site)
                            else:
                                ces = strategy.get_site_coordination_environments_fractions(site)
                        except NeighborsNotComputedChemenvError:
                            continue
                        if ces is None:
                            continue
                        if len(ces) == 0:
                            continue
                        comp = site.species
                        # ce = strategy.get_site_coordination_environment(site)
                        if strategy.uniquely_determines_coordination_environments:
                            ce = ces[0]
                            if ce is None:
                                continue
                            thecg = allcg.get_geometry_from_mp_symbol(ce[0])
                            mystring = 'Environment for site #{} {} ({}) : {} ({})\n'.format(
                                str(isite), comp.get_reduced_formula_and_factor()[0],
                                str(comp), thecg.name, ce[0])
                        else:
                            mystring = 'Environments for site #{} {} ({}) : \n'.format(
                                str(isite), comp.get_reduced_formula_and_factor()[0], str(comp))
                            for ce in ces:
                                cg = allcg.get_geometry_from_mp_symbol(ce[0])
                                csm = ce[1]['other_symmetry_measures']['csm_wcs_ctwcc']
                                mystring += ' - {} ({}): {:.2f} % (csm : {:2f})\n'.format(cg.name, cg.mp_symbol,
                                                                                          100.0 * ce[2],
                                                                                          csm)
                        if test in ['d', 'g'] and strategy.uniquely_determines_coordination_environments:
                            if thecg.mp_symbol != UNCLEAR_ENVIRONMENT_SYMBOL:
                                mystring += '  <Continuous symmetry measures>  '
                                mingeoms = se.ce_list[isite][thecg.coordination_number][0].minimum_geometries()
                                for mingeom in mingeoms:
                                    csm = mingeom[1]['other_symmetry_measures']['csm_wcs_ctwcc']
                                    mystring += '{} : {:.2f}       '.format(mingeom[0], csm)
                        print(mystring)
                if test == 'g':
                    while True:
                        test = input(
                            'Enter index of site(s) (e.g. 0 1 2, separated by spaces) for which you want to see the grid '
                            'of parameters : ')
                        try:
                            indices = [int(x) for x in test.split()]
                            print(str(indices))
                            for isite in indices:
                                if isite < 0:
                                    raise IndexError
                                se.plot_environments(isite, additional_condition=se.AC.ONLY_ACB)
                            break
                        except ValueError:
                            print('This is not a valid site')
                        except IndexError:
                            print('This site is out of the site range')

                if no_vis:
                    test = input('Go to next structure ? ("y" to do so)')
                    if test == 'y':
                        break
                    continue
                test = input('View structure with environments ? ("y" for the unit cell or "m" for a supercell or "n") : ')
                if test in ['y', 'm']:
                    if test == 'm':
                        mydeltas = []
                        while True:
                            try:
                                test = input('Enter multiplicity (e.g. 3 2 2) : ')
                                nns = test.split()
                                for i0 in range(int(nns[0])):
                                    for i1 in range(int(nns[1])):
                                        for i2 in range(int(nns[2])):
                                            mydeltas.append(np.array([1.0 * i0, 1.0 * i1, 1.0 * i2], np.float))
                                break

                            except (ValueError, IndexError):
                                print('Not a valid multiplicity')
                    else:
                        mydeltas = [np.zeros(3, np.float)]
                    if firsttime:
                        vis = StructureVis(show_polyhedron=False, show_unit_cell=True)
                        vis.show_help = False
                        firsttime = False
                    vis.set_structure(se.structure)
                    strategy.set_structure_environments(se)
                    for isite, site in enumerate(se.structure):
                        try:
                            ces = strategy.get_site_coordination_environments(site)
                        except NeighborsNotComputedChemenvError:
                            continue
                        if len(ces) == 0:
                            continue
                        ce = strategy.get_site_coordination_environment(site)
                        if ce is not None and ce[0] != UNCLEAR_ENVIRONMENT_SYMBOL:
                            for mydelta in mydeltas:
                                psite = PeriodicSite(site.species, site.frac_coords + mydelta, site.lattice,
                                                     properties=site.properties)
                                vis.add_site(psite)
                                neighbors = strategy.get_site_neighbors(psite)
                                draw_cg(vis, psite, neighbors, cg=lgf.allcg.get_geometry_from_mp_symbol(ce[0]),
                                        perm=ce[1]['permutation'])
                    vis.show()
                test = input('Go to next structure ? ("y" to do so) : ')
                if test == 'y':
                    break
            print('')