How to use ZEO - 10 common examples

To help you get started, we’ve selected a few ZEO examples, based on popular ways it is used in public projects.

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github materialsproject / pymatgen / pymatgen / io / zeopp.py View on Github external
Returns:
        volume: floating number representing the volume of void
    """
    with ScratchDir('.'):
        name = "temp_zeo"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)

        rad_file = None
        if rad_dict:
            rad_file = name + ".rad"
            with open(rad_file, 'w') as fp:
                for el in rad_dict.keys():
                    fp.write("{0}     {1}".format(el, rad_dict[el]))

        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, True, rad_file)
        vol_str = volume(atmnet, 0.3, probe_rad, 10000)
        sa_str = surface_area(atmnet, 0.3, probe_rad, 10000)
        vol = None
        sa = None
        for line in vol_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
                    vol = -1.0
                    break
                if float(fields[1]) == 0:
                    vol = -1.0
                    break
                vol = float(fields[3])
        for line in sa_str.split("\n"):
            if "Number_of_pockets" in line:
github materialsproject / pymatgen / pymatgen / io / zeoio.py View on Github external
Returns:
        volume: floating number representing the volume of void
    """
    with ScratchDir('.'):
        name = "temp_zeo"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)

        rad_file = None
        if rad_dict:
            rad_file = name + ".rad"
            with open(rad_file, 'w') as fp:
                for el in rad_dict.keys():
                    fp.write("{0}     {1}".format(el, rad_dict[el]))

        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, True, rad_file)
        vol_str = volume(atmnet, 0.3, probe_rad, 10000)
        sa_str = surface_area(atmnet, 0.3, probe_rad, 10000)
        vol = None
        sa = None
        for line in vol_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
                    vol = -1.0
                    break
                if float(fields[1]) == 0:
                    vol = -1.0
                    break
                vol = float(fields[3])
        for line in sa_str.split("\n"):
            if "Number_of_pockets" in line:
github materialsproject / pymatgen / pymatgen / io / zeopp.py View on Github external
with ScratchDir('.'):
        name = "temp_zeo1"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)
        rad_file = None
        rad_flag = False

        if rad_dict:
            rad_file = name + ".rad"
            rad_flag = True
            with open(rad_file, 'w+') as fp:
                for el in rad_dict.keys():
                    fp.write("{} {}\n".format(el, rad_dict[el].real))

        atmnet = AtomNetwork.read_from_CSSR(
            zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
        out_file = "temp.res"
        atmnet.calculate_free_sphere_parameters(out_file)
        if os.path.isfile(out_file) and os.path.getsize(out_file) > 0:
            with open(out_file, "rt") as fp:
                output = fp.readline()
        else:
            output = ""
    fields = [val.strip() for val in output.split()][1:4]
    if len(fields) == 3:
        fields = [float(field) for field in fields]
        free_sphere_params = {'inc_sph_max_dia': fields[0],
                              'free_sph_max_dia': fields[1],
                              'inc_sph_along_free_sph_path_max_dia': fields[2]}
    return free_sphere_params
github materialsproject / pymatgen / pymatgen / io / zeoio.py View on Github external
"""
    with ScratchDir('.'):
        name = "temp_zeo"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)

        rad_file = None
        if rad_dict:
            rad_file = name + ".rad"
            with open(rad_file, 'w') as fp:
                for el in rad_dict.keys():
                    fp.write("{0}     {1}".format(el, rad_dict[el]))

        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, True, rad_file)
        vol_str = volume(atmnet, 0.3, probe_rad, 10000)
        sa_str = surface_area(atmnet, 0.3, probe_rad, 10000)
        vol = None
        sa = None
        for line in vol_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
                    vol = -1.0
                    break
                if float(fields[1]) == 0:
                    vol = -1.0
                    break
                vol = float(fields[3])
        for line in sa_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
github materialsproject / pymatgen / pymatgen / io / zeopp.py View on Github external
"""
    with ScratchDir('.'):
        name = "temp_zeo"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)

        rad_file = None
        if rad_dict:
            rad_file = name + ".rad"
            with open(rad_file, 'w') as fp:
                for el in rad_dict.keys():
                    fp.write("{0}     {1}".format(el, rad_dict[el]))

        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, True, rad_file)
        vol_str = volume(atmnet, 0.3, probe_rad, 10000)
        sa_str = surface_area(atmnet, 0.3, probe_rad, 10000)
        vol = None
        sa = None
        for line in vol_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
                    vol = -1.0
                    break
                if float(fields[1]) == 0:
                    vol = -1.0
                    break
                vol = float(fields[3])
        for line in sa_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
github materialsproject / pymatgen / pymatgen / io / zeoio.py View on Github external
volume: floating number representing the volume of void
    """
    with ScratchDir('.'):
        name = "temp_zeo"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)

        rad_file = None
        if rad_dict:
            rad_file = name + ".rad"
            with open(rad_file, 'w') as fp:
                for el in rad_dict.keys():
                    fp.write("{0}     {1}".format(el, rad_dict[el]))

        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, True, rad_file)
        vol_str = volume(atmnet, 0.3, probe_rad, 10000)
        sa_str = surface_area(atmnet, 0.3, probe_rad, 10000)
        vol = None
        sa = None
        for line in vol_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
                    vol = -1.0
                    break
                if float(fields[1]) == 0:
                    vol = -1.0
                    break
                vol = float(fields[3])
        for line in sa_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
github materialsproject / pymatgen / pymatgen / io / zeopp.py View on Github external
volume: floating number representing the volume of void
    """
    with ScratchDir('.'):
        name = "temp_zeo"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)

        rad_file = None
        if rad_dict:
            rad_file = name + ".rad"
            with open(rad_file, 'w') as fp:
                for el in rad_dict.keys():
                    fp.write("{0}     {1}".format(el, rad_dict[el]))

        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, True, rad_file)
        vol_str = volume(atmnet, 0.3, probe_rad, 10000)
        sa_str = surface_area(atmnet, 0.3, probe_rad, 10000)
        vol = None
        sa = None
        for line in vol_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
                if float(fields[1]) > 1:
                    vol = -1.0
                    break
                if float(fields[1]) == 0:
                    vol = -1.0
                    break
                vol = float(fields[3])
        for line in sa_str.split("\n"):
            if "Number_of_pockets" in line:
                fields = line.split()
github materialsproject / pymatgen / pymatgen / io / zeoio.py View on Github external
with ScratchDir('.'):
        name = "temp_zeo1"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)
        rad_file = None
        rad_flag = False

        if rad_dict:
            rad_file = name + ".rad"
            rad_flag = True
            with open(rad_file, 'w+') as fp:
                for el in rad_dict.keys():
                    fp.write("{} {}\n".format(el, rad_dict[el].real))

        atmnet = AtomNetwork.read_from_CSSR(
                zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
        vornet, vor_edge_centers, vor_face_centers = \
            atmnet.perform_voronoi_decomposition()
        vornet.analyze_writeto_XYZ(name, probe_rad, atmnet)
        voro_out_filename = name + '_voro.xyz'
        voro_node_mol = ZeoVoronoiXYZ.from_file(voro_out_filename).molecule

    species = ["X"] * len(voro_node_mol.sites)
    coords = []
    prop = []
    for site in voro_node_mol.sites:
        coords.append(list(site.coords))
        prop.append(site.properties['voronoi_radius'])

    lattice = Lattice.from_lengths_and_angles(
        structure.lattice.abc, structure.lattice.angles)
github materialsproject / pymatgen / pymatgen / io / zeopp.py View on Github external
unit cell defined by the lattice of input structure
        voronoi face centers as pymatgen.core.structure.Strucutre within the
        unit cell defined by the lattice of input structure
    """

    with ScratchDir('.'):
        name = "temp_zeo1"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)
        rad_flag = True
        rad_file = name + ".rad"
        with open(rad_file, 'w+') as fp:
            for el in rad_dict.keys():
                print("{} {}".format(el, rad_dict[el].real), file=fp)

        atmnet = AtomNetwork.read_from_CSSR(
            zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
        # vornet, vor_edge_centers, vor_face_centers = \
        #        atmnet.perform_voronoi_decomposition()
        red_ha_vornet = \
            prune_voronoi_network_close_node(atmnet)
        # generate_simplified_highaccuracy_voronoi_network(atmnet)
        # get_nearest_largest_diameter_highaccuracy_vornode(atmnet)
        red_ha_vornet.analyze_writeto_XYZ(name, probe_rad, atmnet)
        voro_out_filename = name + '_voro.xyz'
        voro_node_mol = ZeoVoronoiXYZ.from_file(voro_out_filename).molecule

    species = ["X"] * len(voro_node_mol.sites)
    coords = []
    prop = []
    for site in voro_node_mol.sites:
        coords.append(list(site.coords))
github materialsproject / pymatgen / pymatgen / io / zeopp.py View on Github external
with ScratchDir('.'):
        name = "temp_zeo1"
        zeo_inp_filename = name + ".cssr"
        ZeoCssr(structure).write_file(zeo_inp_filename)
        rad_file = None
        rad_flag = False

        if rad_dict:
            rad_file = name + ".rad"
            rad_flag = True
            with open(rad_file, 'w+') as fp:
                for el in rad_dict.keys():
                    fp.write("{} {}\n".format(el, rad_dict[el].real))

        atmnet = AtomNetwork.read_from_CSSR(
            zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
        vornet, vor_edge_centers, vor_face_centers = \
            atmnet.perform_voronoi_decomposition()
        vornet.analyze_writeto_XYZ(name, probe_rad, atmnet)
        voro_out_filename = name + '_voro.xyz'
        voro_node_mol = ZeoVoronoiXYZ.from_file(voro_out_filename).molecule

    species = ["X"] * len(voro_node_mol.sites)
    coords = []
    prop = []
    for site in voro_node_mol.sites:
        coords.append(list(site.coords))
        prop.append(site.properties['voronoi_radius'])

    lattice = Lattice.from_lengths_and_angles(
        structure.lattice.abc, structure.lattice.angles)

ZEO

ZEO - Single-server client-server database server for ZODB

ZPL-2.1
Latest version published 8 months ago

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