Exemplo n.º 1
0
 def vtk(self):
     if StructureVis is None:
         raise NotImplementedError("vtk must be present to view.")
     lattice = self.structure.lattice
     vis = StructureVis()
     vis.set_structure(Structure.from_sites(self.structure))
     for v in self.vnodes:
         vis.add_site(PeriodicSite("K", v.frac_coords, lattice))
         vis.add_polyhedron(
             [PeriodicSite("S", c, lattice, coords_are_cartesian=True) for c in v.polyhedron_coords],
             PeriodicSite("Na", v.frac_coords, lattice),
             color="element",
             draw_edges=True,
             edges_color=(0, 0, 0))
     vis.show()
Exemplo n.º 2
0
def compute_environments(chemenv_configuration):
    string_sources = {
        'cif': {
            'string': 'a Cif file',
            'regexp': '.*\.cif$'
        },
        'mp': {
            'string': 'the Materials Project database',
            'regexp': 'mp-[0-9]+$'
        }
    }
    questions = {'c': 'cif'}
    if chemenv_configuration.has_materials_project_access:
        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(chemenv_configuration.materials_project_api_key)
            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_and_occu
                    #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':
                test = input(
                    'Enter index of site(s) for which you want to see the grid of parameters : '
                )
                indices = list(map(int, test.split()))
                print(indices)
                for isite in indices:
                    se.plot_environments(isite,
                                         additional_condition=se.AC.ONLY_ACB)
            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 = []
                    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))
                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._fcoords + 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('')
Exemplo n.º 3
0
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("")
Exemplo n.º 4
0
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_and_occu
                    #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._fcoords + 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('')