How to use the zeo.netstorage.AtomNetwork.read_from_CSSR function in ZEO

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

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

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 / 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 / zeoio.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))

ZEO

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

ZPL-2.1
Latest version published 12 months ago

Package Health Score

60 / 100
Full package analysis

Similar packages