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<!DOCTYPE html>
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<div class="local-toc"><ul>
<li><a class="reference internal" href="#">pymatgen.io.lobster package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.io.lobster.inputs">pymatgen.io.lobster.inputs module</a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin"><code class="docutils literal notranslate"><span class="pre">Lobsterin</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.AVAILABLEKEYWORDS"><code class="docutils literal notranslate"><span class="pre">Lobsterin.AVAILABLEKEYWORDS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.BOOLEAN_KEYWORDS"><code class="docutils literal notranslate"><span class="pre">Lobsterin.BOOLEAN_KEYWORDS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.FLOAT_KEYWORDS"><code class="docutils literal notranslate"><span class="pre">Lobsterin.FLOAT_KEYWORDS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.LISTKEYWORDS"><code class="docutils literal notranslate"><span class="pre">Lobsterin.LISTKEYWORDS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.STRING_KEYWORDS"><code class="docutils literal notranslate"><span class="pre">Lobsterin.STRING_KEYWORDS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin._get_nbands"><code class="docutils literal notranslate"><span class="pre">Lobsterin._get_nbands()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin._get_potcar_symbols"><code class="docutils literal notranslate"><span class="pre">Lobsterin._get_potcar_symbols()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.as_dict"><code class="docutils literal notranslate"><span class="pre">Lobsterin.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.diff"><code class="docutils literal notranslate"><span class="pre">Lobsterin.diff()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.from_dict"><code class="docutils literal notranslate"><span class="pre">Lobsterin.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.from_file"><code class="docutils literal notranslate"><span class="pre">Lobsterin.from_file()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.get_all_possible_basis_functions"><code class="docutils literal notranslate"><span class="pre">Lobsterin.get_all_possible_basis_functions()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.get_basis"><code class="docutils literal notranslate"><span class="pre">Lobsterin.get_basis()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.standard_calculations_from_vasp_files"><code class="docutils literal notranslate"><span class="pre">Lobsterin.standard_calculations_from_vasp_files()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.write_INCAR"><code class="docutils literal notranslate"><span class="pre">Lobsterin.write_INCAR()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.write_KPOINTS"><code class="docutils literal notranslate"><span class="pre">Lobsterin.write_KPOINTS()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.write_POSCAR_with_standard_primitive"><code class="docutils literal notranslate"><span class="pre">Lobsterin.write_POSCAR_with_standard_primitive()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin.write_lobsterin"><code class="docutils literal notranslate"><span class="pre">Lobsterin.write_lobsterin()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.inputs.get_all_possible_basis_combinations"><code class="docutils literal notranslate"><span class="pre">get_all_possible_basis_combinations()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.io.lobster.lobsterenv">pymatgen.io.lobster.lobsterenv module</a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._asdict"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo._asdict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._field_defaults"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo._field_defaults</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._fields"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo._fields</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._make"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo._make()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._replace"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo._replace()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.atoms"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo.atoms</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.central_isites"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo.central_isites</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.labels"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo.labels</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.list_icohps"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo.list_icohps</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.n_bonds"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo.n_bonds</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.total_icohp"><code class="docutils literal notranslate"><span class="pre">ICOHPNeighborsInfo.total_icohp</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments"><code class="docutils literal notranslate"><span class="pre">LobsterLightStructureEnvironments</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.as_dict"><code class="docutils literal notranslate"><span class="pre">LobsterLightStructureEnvironments.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.from_Lobster"><code class="docutils literal notranslate"><span class="pre">LobsterLightStructureEnvironments.from_Lobster()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.uniquely_determines_coordination_environments"><code class="docutils literal notranslate"><span class="pre">LobsterLightStructureEnvironments.uniquely_determines_coordination_environments</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._adapt_extremum_to_add_cond"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._adapt_extremum_to_add_cond()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._determine_unit_cell"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._determine_unit_cell()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._evaluate_ce"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._evaluate_ce()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._find_environments"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._find_environments()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._find_relevant_atoms_additional_condition"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._find_relevant_atoms_additional_condition()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_atomnumber"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._get_atomnumber()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_icohps"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._get_icohps()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_limit_from_extremum"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._get_limit_from_extremum()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_plot_label"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._get_plot_label()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._split_string"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors._split_string()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.anion_types"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.anion_types</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_anion_types"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.get_anion_types()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_cohps_to_neighbors"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.get_info_cohps_to_neighbors()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_icohps_between_neighbors"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.get_info_icohps_between_neighbors()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_icohps_to_neighbors"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.get_info_icohps_to_neighbors()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_light_structure_environment"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.get_light_structure_environment()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_nn_info"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.plot_cohps_of_neighbors"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.plot_cohps_of_neighbors()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.structures_allowed"><code class="docutils literal notranslate"><span class="pre">LobsterNeighbors.structures_allowed</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.io.lobster.outputs">pymatgen.io.lobster.outputs module</a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Bandoverlaps"><code class="docutils literal notranslate"><span class="pre">Bandoverlaps</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Bandoverlaps._read"><code class="docutils literal notranslate"><span class="pre">Bandoverlaps._read()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Bandoverlaps.has_good_quality_check_occupied_bands"><code class="docutils literal notranslate"><span class="pre">Bandoverlaps.has_good_quality_check_occupied_bands()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Bandoverlaps.has_good_quality_maxDeviation"><code class="docutils literal notranslate"><span class="pre">Bandoverlaps.has_good_quality_maxDeviation()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Charge"><code class="docutils literal notranslate"><span class="pre">Charge</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Charge.get_structure_with_charges"><code class="docutils literal notranslate"><span class="pre">Charge.get_structure_with_charges()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Cohpcar"><code class="docutils literal notranslate"><span class="pre">Cohpcar</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Cohpcar._get_bond_data"><code class="docutils literal notranslate"><span class="pre">Cohpcar._get_bond_data()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar"><code class="docutils literal notranslate"><span class="pre">Doscar</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar.completedos"><code class="docutils literal notranslate"><span class="pre">Doscar.completedos</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar.pdos"><code class="docutils literal notranslate"><span class="pre">Doscar.pdos</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar.tdos"><code class="docutils literal notranslate"><span class="pre">Doscar.tdos</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar.energies"><code class="docutils literal notranslate"><span class="pre">Doscar.energies</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar.tdensities"><code class="docutils literal notranslate"><span class="pre">Doscar.tdensities</span></code></a></li>
<li><a class="reference internal" href="#id0"><code class="docutils literal notranslate"><span class="pre">Doscar.energies</span></code></a></li>
<li><a class="reference internal" href="#id1"><code class="docutils literal notranslate"><span class="pre">Doscar.energies</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar.is_spin_polarized"><code class="docutils literal notranslate"><span class="pre">Doscar.is_spin_polarized</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar._parse_doscar"><code class="docutils literal notranslate"><span class="pre">Doscar._parse_doscar()</span></code></a></li>
<li><a class="reference internal" href="#id2"><code class="docutils literal notranslate"><span class="pre">Doscar.completedos</span></code></a></li>
<li><a class="reference internal" href="#id3"><code class="docutils literal notranslate"><span class="pre">Doscar.energies</span></code></a></li>
<li><a class="reference internal" href="#id4"><code class="docutils literal notranslate"><span class="pre">Doscar.is_spin_polarized</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Doscar.itdensities"><code class="docutils literal notranslate"><span class="pre">Doscar.itdensities</span></code></a></li>
<li><a class="reference internal" href="#id5"><code class="docutils literal notranslate"><span class="pre">Doscar.pdos</span></code></a></li>
<li><a class="reference internal" href="#id6"><code class="docutils literal notranslate"><span class="pre">Doscar.tdensities</span></code></a></li>
<li><a class="reference internal" href="#id7"><code class="docutils literal notranslate"><span class="pre">Doscar.tdos</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Fatband"><code class="docutils literal notranslate"><span class="pre">Fatband</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Fatband.get_bandstructure"><code class="docutils literal notranslate"><span class="pre">Fatband.get_bandstructure()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Grosspop"><code class="docutils literal notranslate"><span class="pre">Grosspop</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Grosspop.get_structure_with_total_grosspop"><code class="docutils literal notranslate"><span class="pre">Grosspop.get_structure_with_total_grosspop()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Icohplist"><code class="docutils literal notranslate"><span class="pre">Icohplist</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Icohplist.icohpcollection"><code class="docutils literal notranslate"><span class="pre">Icohplist.icohpcollection</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Icohplist.icohplist"><code class="docutils literal notranslate"><span class="pre">Icohplist.icohplist</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout"><code class="docutils literal notranslate"><span class="pre">Lobsterout</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_all_info_lines"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_all_info_lines()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_all_warning_lines"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_all_warning_lines()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_dft_program"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_dft_program()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_elements_basistype_basisfunctions"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_elements_basistype_basisfunctions()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_lobster_version"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_lobster_version()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_number_of_spins"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_number_of_spins()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_spillings"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_spillings()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_threads"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_threads()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_timing"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_timing()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._get_warning_orthonormalization"><code class="docutils literal notranslate"><span class="pre">Lobsterout._get_warning_orthonormalization()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout._has_fatband"><code class="docutils literal notranslate"><span class="pre">Lobsterout._has_fatband()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Lobsterout.get_doc"><code class="docutils literal notranslate"><span class="pre">Lobsterout.get_doc()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.MadelungEnergies"><code class="docutils literal notranslate"><span class="pre">MadelungEnergies</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.SitePotential"><code class="docutils literal notranslate"><span class="pre">SitePotential</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.SitePotential.get_structure_with_site_potentials"><code class="docutils literal notranslate"><span class="pre">SitePotential.get_structure_with_site_potentials()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Wavefunction"><code class="docutils literal notranslate"><span class="pre">Wavefunction</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Wavefunction._parse_file"><code class="docutils literal notranslate"><span class="pre">Wavefunction._parse_file()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Wavefunction.get_volumetricdata_density"><code class="docutils literal notranslate"><span class="pre">Wavefunction.get_volumetricdata_density()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Wavefunction.get_volumetricdata_imaginary"><code class="docutils literal notranslate"><span class="pre">Wavefunction.get_volumetricdata_imaginary()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Wavefunction.get_volumetricdata_real"><code class="docutils literal notranslate"><span class="pre">Wavefunction.get_volumetricdata_real()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Wavefunction.set_volumetric_data"><code class="docutils literal notranslate"><span class="pre">Wavefunction.set_volumetric_data()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.Wavefunction.write_file"><code class="docutils literal notranslate"><span class="pre">Wavefunction.write_file()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.io.lobster.outputs.get_orb_from_str"><code class="docutils literal notranslate"><span class="pre">get_orb_from_str()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
</div>
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<section id="module-pymatgen.io.lobster">
<span id="pymatgen-io-lobster-package"></span><h1>pymatgen.io.lobster package<a class="headerlink" href="#module-pymatgen.io.lobster" title="Permalink to this heading"></a></h1>
<p>This package implements modules for input and output to and from Lobster. It
imports the key classes form both lobster.inputs and lobster_outputs to allow most
classes to be simply called as pymatgen.io.lobster.Lobsterin for example, to retain
backwards compatibility.</p>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this heading"></a></h2>
</section>
<section id="module-pymatgen.io.lobster.inputs">
<span id="pymatgen-io-lobster-inputs-module"></span><h2>pymatgen.io.lobster.inputs module<a class="headerlink" href="#module-pymatgen.io.lobster.inputs" title="Permalink to this heading"></a></h2>
<p>Module for reading Lobster input files. For more information
on LOBSTER see www.cohp.de.
If you use this module, please cite:
J. George, G. Petretto, A. Naik, M. Esters, A. J. Jackson, R. Nelson, R. Dronskowski, G.-M. Rignanese, G. Hautier,
“Automated Bonding Analysis with Crystal Orbital Hamilton Populations”,
ChemPlusChem 2022, e202200123,
DOI: 10.1002/cplu.202200123.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Lobsterin</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">settingsdict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>This class can handle and generate lobsterin files
Furthermore, it can also modify INCAR files for lobster, generate KPOINT files for fatband calculations in Lobster,
and generate the standard primitive cells in a POSCAR file that are needed for the fatband calculations.
There are also several standard lobsterin files that can be easily generated.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>settingsdict</strong> – dict to initialize Lobsterin.</p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.AVAILABLEKEYWORDS">
<span class="sig-name descname"><span class="pre">AVAILABLEKEYWORDS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('COHPstartEnergy',</span> <span class="pre">'COHPendEnergy',</span> <span class="pre">'gaussianSmearingWidth',</span> <span class="pre">'useDecimalPlaces',</span> <span class="pre">'COHPSteps',</span> <span class="pre">'basisSet',</span> <span class="pre">'cohpGenerator',</span> <span class="pre">'realspaceHamiltonian',</span> <span class="pre">'realspaceOverlap',</span> <span class="pre">'printPAWRealSpaceWavefunction',</span> <span class="pre">'printLCAORealSpaceWavefunction',</span> <span class="pre">'kSpaceCOHP',</span> <span class="pre">'EwaldSum',</span> <span class="pre">'saveProjectionToFile',</span> <span class="pre">'skipdos',</span> <span class="pre">'skipcohp',</span> <span class="pre">'skipcoop',</span> <span class="pre">'skipcobi',</span> <span class="pre">'skipMadelungEnergy',</span> <span class="pre">'loadProjectionFromFile',</span> <span class="pre">'forceEnergyRange',</span> <span class="pre">'DensityOfEnergy',</span> <span class="pre">'BWDF',</span> <span class="pre">'BWDFCOHP',</span> <span class="pre">'skipPopulationAnalysis',</span> <span class="pre">'skipGrossPopulation',</span> <span class="pre">'userecommendedbasisfunctions',</span> <span class="pre">'skipProjection',</span> <span class="pre">'writeBasisFunctions',</span> <span class="pre">'writeMatricesToFile',</span> <span class="pre">'noFFTforVisualization',</span> <span class="pre">'RMSp',</span> <span class="pre">'onlyReadVasprun.xml',</span> <span class="pre">'noMemoryMappedFiles',</span> <span class="pre">'skipPAWOrthonormalityTest',</span> <span class="pre">'doNotIgnoreExcessiveBands',</span> <span class="pre">'doNotUseAbsoluteSpilling',</span> <span class="pre">'skipReOrthonormalization',</span> <span class="pre">'forceV1HMatrix',</span> <span class="pre">'useOriginalTetrahedronMethod',</span> <span class="pre">'forceEnergyRange',</span> <span class="pre">'bandwiseSpilling',</span> <span class="pre">'kpointwiseSpilling',</span> <span class="pre">'LSODOS',</span> <span class="pre">'basisfunctions',</span> <span class="pre">'cohpbetween',</span> <span class="pre">'createFatband')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.AVAILABLEKEYWORDS" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.BOOLEAN_KEYWORDS">
<span class="sig-name descname"><span class="pre">BOOLEAN_KEYWORDS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('saveProjectionToFile',</span> <span class="pre">'skipdos',</span> <span class="pre">'skipcohp',</span> <span class="pre">'skipcoop',</span> <span class="pre">'skipcobi',</span> <span class="pre">'skipMadelungEnergy',</span> <span class="pre">'loadProjectionFromFile',</span> <span class="pre">'forceEnergyRange',</span> <span class="pre">'DensityOfEnergy',</span> <span class="pre">'BWDF',</span> <span class="pre">'BWDFCOHP',</span> <span class="pre">'skipPopulationAnalysis',</span> <span class="pre">'skipGrossPopulation',</span> <span class="pre">'userecommendedbasisfunctions',</span> <span class="pre">'skipProjection',</span> <span class="pre">'writeBasisFunctions',</span> <span class="pre">'writeMatricesToFile',</span> <span class="pre">'noFFTforVisualization',</span> <span class="pre">'RMSp',</span> <span class="pre">'onlyReadVasprun.xml',</span> <span class="pre">'noMemoryMappedFiles',</span> <span class="pre">'skipPAWOrthonormalityTest',</span> <span class="pre">'doNotIgnoreExcessiveBands',</span> <span class="pre">'doNotUseAbsoluteSpilling',</span> <span class="pre">'skipReOrthonormalization',</span> <span class="pre">'forceV1HMatrix',</span> <span class="pre">'useOriginalTetrahedronMethod',</span> <span class="pre">'forceEnergyRange',</span> <span class="pre">'bandwiseSpilling',</span> <span class="pre">'kpointwiseSpilling',</span> <span class="pre">'LSODOS')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.BOOLEAN_KEYWORDS" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.FLOAT_KEYWORDS">
<span class="sig-name descname"><span class="pre">FLOAT_KEYWORDS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('COHPstartEnergy',</span> <span class="pre">'COHPendEnergy',</span> <span class="pre">'gaussianSmearingWidth',</span> <span class="pre">'useDecimalPlaces',</span> <span class="pre">'COHPSteps')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.FLOAT_KEYWORDS" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.LISTKEYWORDS">
<span class="sig-name descname"><span class="pre">LISTKEYWORDS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('basisfunctions',</span> <span class="pre">'cohpbetween',</span> <span class="pre">'createFatband')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.LISTKEYWORDS" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.STRING_KEYWORDS">
<span class="sig-name descname"><span class="pre">STRING_KEYWORDS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('basisSet',</span> <span class="pre">'cohpGenerator',</span> <span class="pre">'realspaceHamiltonian',</span> <span class="pre">'realspaceOverlap',</span> <span class="pre">'printPAWRealSpaceWavefunction',</span> <span class="pre">'printLCAORealSpaceWavefunction',</span> <span class="pre">'kSpaceCOHP',</span> <span class="pre">'EwaldSum')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.STRING_KEYWORDS" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin._get_nbands">
<span class="sig-name descname"><span class="pre">_get_nbands</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin._get_nbands" title="Permalink to this definition"></a></dt>
<dd><p>Get number of bands.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin._get_potcar_symbols">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_get_potcar_symbols</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">POTCAR_input</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin._get_potcar_symbols" title="Permalink to this definition"></a></dt>
<dd><p>Will return the name of the species in the POTCAR.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>POTCAR_input</strong> (<em>str</em>) – string to potcar file</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of the names of the species in string format</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.as_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>MSONable dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.diff">
<span class="sig-name descname"><span class="pre">diff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.diff" title="Permalink to this definition"></a></dt>
<dd><p>Diff function for lobsterin. Compares two lobsterin and indicates which parameters are the same.
Similar to the diff in INCAR.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#pymatgen.io.lobster.inputs.Lobsterin" title="pymatgen.io.lobster.inputs.Lobsterin"><em>Lobsterin</em></a>) – Lobsterin object to compare to</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>dict with differences and similarities</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.from_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>d</strong> – Dict representation</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Lobsterin</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.from_file">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lobsterin</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.from_file" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>lobsterin</strong> (<em>str</em>) – path to lobsterin.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Lobsterin object</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.get_all_possible_basis_functions">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_all_possible_basis_functions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">potcar_symbols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">address_basis_file_min</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">address_basis_file_max</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.get_all_possible_basis_functions" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Structure object</p></li>
<li><p><strong>potcar_symbols</strong> – list of the potcar symbols</p></li>
<li><p><strong>address_basis_file_min</strong> – path to file with the minimum required basis by the POTCAR</p></li>
<li><p><strong>address_basis_file_max</strong> – path to file with the largest possible basis of the POTCAR.</p></li>
</ul>
</dd>
</dl>
<p>Returns: List of dictionaries that can be used to create new Lobsterin objects in
standard_calculations_from_vasp_files as dict_for_basis</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.get_basis">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_basis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">potcar_symbols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">address_basis_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.get_basis" title="Permalink to this definition"></a></dt>
<dd><p>Will get the basis from given potcar_symbols (e.g., [“Fe_pv”,”Si”]
#include this in lobsterin class.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure object</p></li>
<li><p><strong>potcar_symbols</strong> – list of potcar symbols</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>returns basis</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.standard_calculations_from_vasp_files">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">standard_calculations_from_vasp_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">POSCAR_input</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'POSCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">INCAR_input</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'INCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">POTCAR_input</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Vasprun_output</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'vasprun.xml'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dict_for_basis</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">option</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'standard'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.standard_calculations_from_vasp_files" title="Permalink to this definition"></a></dt>
<dd><p>Will generate Lobsterin with standard settings.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>POSCAR_input</strong> (<em>str</em>) – path to POSCAR</p></li>
<li><p><strong>INCAR_input</strong> (<em>str</em>) – path to INCAR</p></li>
<li><p><strong>POTCAR_input</strong> (<em>str</em>) – path to POTCAR</p></li>
<li><p><strong>dict_for_basis</strong> (<em>dict</em>) – can be provided: it should look the following:
dict_for_basis={“Fe”:’3p 3d 4s 4f’, “C”: ‘2s 2p’} and will overwrite all settings from POTCAR_input</p></li>
<li><p><strong>option</strong> (<em>str</em>) – ‘standard’ will start a normal lobster run where COHPs, COOPs, DOS, CHARGE etc. will be
calculated
‘standard_with_energy_range_from_vasprun’ will start a normal lobster run for entire energy range
of VASP static run. vasprun.xml file needs to be in current directory.
‘standard_from_projection’ will start a normal lobster run from a projection
‘standard_with_fatband’ will do a fatband calculation, run over all orbitals
‘onlyprojection’ will only do a projection
‘onlydos’ will only calculate a projected dos
‘onlycohp’ will only calculate cohp
‘onlycoop’ will only calculate coop
‘onlycohpcoop’ will only calculate cohp and coop</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Lobsterin Object with standard settings</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.write_INCAR">
<span class="sig-name descname"><span class="pre">write_INCAR</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">incar_input</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'INCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">incar_output</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'INCAR.lobster'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">poscar_input</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'POSCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isym</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">-1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">further_settings</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.write_INCAR" title="Permalink to this definition"></a></dt>
<dd><p>Will only make the run static, insert nbands, make ISYM=-1, set LWAVE=True and write a new INCAR.
You have to check for the rest.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>incar_input</strong> (<em>str</em>) – path to input INCAR</p></li>
<li><p><strong>incar_output</strong> (<em>str</em>) – path to output INCAR</p></li>
<li><p><strong>poscar_input</strong> (<em>str</em>) – path to input POSCAR</p></li>
<li><p><strong>isym</strong> (<em>int</em>) – isym equal to -1 or 0 are possible. Current Lobster version only allow -1.</p></li>
<li><p><strong>further_settings</strong> (<em>dict</em>) – A dict can be used to include further settings, e.g. {“ISMEAR”:-5}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.write_KPOINTS">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">write_KPOINTS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">POSCAR_input</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'POSCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">KPOINTS_output</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'KPOINTS.lobster'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reciprocal_density</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isym</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">-1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_grid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_grid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(5,</span> <span class="pre">5,</span> <span class="pre">5)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">line_mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kpoints_line_density</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.01</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.write_KPOINTS" title="Permalink to this definition"></a></dt>
<dd><p>Writes a KPOINT file for lobster (only ISYM=-1 and ISYM=0 are possible), grids are gamma centered.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>POSCAR_input</strong> (<em>str</em>) – path to POSCAR</p></li>
<li><p><strong>KPOINTS_output</strong> (<em>str</em>) – path to output KPOINTS</p></li>
<li><p><strong>reciprocal_density</strong> (<em>int</em>) – Grid density</p></li>
<li><p><strong>isym</strong> (<em>int</em>) – either -1 or 0. Current Lobster versions only allow -1.</p></li>
<li><p><strong>from_grid</strong> (<em>bool</em>) – If True KPOINTS will be generated with the help of a grid given in input_grid. Otherwise,
they will be generated from the reciprocal_density</p></li>
<li><p><strong>input_grid</strong> (<em>list</em>) – grid to generate the KPOINTS file</p></li>
<li><p><strong>line_mode</strong> (<em>bool</em>) – If True, band structure will be generated</p></li>
<li><p><strong>kpoints_line_density</strong> (<em>int</em>) – density of the lines in the band structure</p></li>
<li><p><strong>symprec</strong> (<em>float</em>) – precision to determine symmetry</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.write_POSCAR_with_standard_primitive">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">write_POSCAR_with_standard_primitive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">POSCAR_input</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'POSCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">POSCAR_output</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'POSCAR.lobster'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.01</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.write_POSCAR_with_standard_primitive" title="Permalink to this definition"></a></dt>
<dd><p>Writes a POSCAR with the standard primitive cell. This is needed to arrive at the correct kpath.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>POSCAR_input</strong> (<em>str</em>) – filename of input POSCAR</p></li>
<li><p><strong>POSCAR_output</strong> (<em>str</em>) – filename of output POSCAR</p></li>
<li><p><strong>symprec</strong> (<em>float</em>) – precision to find symmetry</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.Lobsterin.write_lobsterin">
<span class="sig-name descname"><span class="pre">write_lobsterin</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'lobsterin'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">overwritedict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.Lobsterin.write_lobsterin" title="Permalink to this definition"></a></dt>
<dd><p>Writes a lobsterin file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>path</strong> (<em>str</em>) – filename of the lobsterin file that will be written</p></li>
<li><p><strong>overwritedict</strong> (<em>dict</em>) – dict that can be used to overwrite lobsterin, e.g. {“skipdos”: True}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.io.lobster.inputs.get_all_possible_basis_combinations">
<span class="sig-name descname"><span class="pre">get_all_possible_basis_combinations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_basis</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_basis</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.inputs.get_all_possible_basis_combinations" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>min_basis</strong> – list of basis entries: e.g., [‘Si 3p 3s ‘]</p></li>
<li><p><strong>max_basis</strong> – list of basis entries: e.g., [‘Si 3p 3s ‘].</p></li>
</ul>
</dd>
</dl>
<p>Returns: all possible combinations of basis functions, e.g. [[‘Si 3p 3s’]]</p>
</dd></dl>
</section>
<section id="module-pymatgen.io.lobster.lobsterenv">
<span id="pymatgen-io-lobster-lobsterenv-module"></span><h2>pymatgen.io.lobster.lobsterenv module<a class="headerlink" href="#module-pymatgen.io.lobster.lobsterenv" title="Permalink to this heading"></a></h2>
<p>This module provides classes to perform analyses of
the local environments (e.g., finding near neighbors)
of single sites in molecules and structures based on
bonding analysis with Lobster.
If you use this module, please cite:
J. George, G. Petretto, A. Naik, M. Esters, A. J. Jackson, R. Nelson, R. Dronskowski, G.-M. Rignanese, G. Hautier,
“Automated Bonding Analysis with Crystal Orbital Hamilton Populations”,
ChemPlusChem 2022, e202200123,
DOI: 10.1002/cplu.202200123.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ICOHPNeighborsInfo</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">total_icohp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">list_icohps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_bonds</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atoms</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">central_isites</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
<p>Tuple to represent information on relevant bonds
:param total_icohp: sum of icohp values of neighbors to the selected sites [given by the id in structure]
:type total_icohp: float
:param list_icohps: list of summed icohp values for all identified interactions with neighbors
:type list_icohps: list
:param n_bonds: number of identified bonds to the selected sites
:type n_bonds: int
:param labels: labels (from ICOHPLIST) for all identified bonds
:type labels: list(str)
:param atoms: list of list describing the species present in the identified interactions</p>
<blockquote>
<div><p>(names from ICOHPLIST), e.g., [‘Ag3’, ‘O5’]</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>central_isites</strong> (<em>list</em><em>(</em><em>int</em><em>)</em>) – list of the central isite for each identified interaction.</p>
</dd>
</dl>
<p>Create new instance of ICOHPNeighborsInfo(total_icohp, list_icohps, n_bonds, labels, atoms, central_isites)</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._asdict">
<span class="sig-name descname"><span class="pre">_asdict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._asdict" title="Permalink to this definition"></a></dt>
<dd><p>Return a new dict which maps field names to their values.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._field_defaults">
<span class="sig-name descname"><span class="pre">_field_defaults</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{}</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._field_defaults" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._fields">
<span class="sig-name descname"><span class="pre">_fields</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('total_icohp',</span> <span class="pre">'list_icohps',</span> <span class="pre">'n_bonds',</span> <span class="pre">'labels',</span> <span class="pre">'atoms',</span> <span class="pre">'central_isites')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._fields" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._make">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_make</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iterable</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._make" title="Permalink to this definition"></a></dt>
<dd><p>Make a new ICOHPNeighborsInfo object from a sequence or iterable</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._replace">
<span class="sig-name descname"><span class="pre">_replace</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwds</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo._replace" title="Permalink to this definition"></a></dt>
<dd><p>Return a new ICOHPNeighborsInfo object replacing specified fields with new values</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.atoms">
<span class="sig-name descname"><span class="pre">atoms</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.atoms" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 4</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.central_isites">
<span class="sig-name descname"><span class="pre">central_isites</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.central_isites" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 5</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.labels">
<span class="sig-name descname"><span class="pre">labels</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.labels" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 3</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.list_icohps">
<span class="sig-name descname"><span class="pre">list_icohps</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.list_icohps" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.n_bonds">
<span class="sig-name descname"><span class="pre">n_bonds</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">int</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.n_bonds" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.total_icohp">
<span class="sig-name descname"><span class="pre">total_icohp</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo.total_icohp" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LobsterLightStructureEnvironments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">strategy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordination_environments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_nbs_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">neighbors_sets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valences_origin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments" title="pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments"><code class="xref py py-class docutils literal notranslate"><span class="pre">LightStructureEnvironments</span></code></a></p>
<p>Class to store LightStructureEnvironments based on Lobster outputs.</p>
<p>Constructor for the LightStructureEnvironments object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>strategy</strong> – ChemEnv strategy used to get the environments.</p></li>
<li><p><strong>coordination_environments</strong> – The coordination environments identified.</p></li>
<li><p><strong>all_nbs_sites</strong> – All the possible neighbors for each site in the structure.</p></li>
<li><p><strong>neighbors_sets</strong> – The neighbors sets of each site in the structure.</p></li>
<li><p><strong>structure</strong> – The structure.</p></li>
<li><p><strong>valences</strong> – The valences used to get the environments (if needed).</p></li>
<li><p><strong>valences_origin</strong> – How the valences were obtained (e.g. from the Bond-valence analysis or from the original
structure).</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>Bson-serializable dict representation of the LightStructureEnvironments object.
:return: Bson-serializable dict representation of the LightStructureEnvironments object.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.from_Lobster">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_Lobster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">list_ce_symbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">list_csm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">list_permutation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">list_neighsite</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">list_neighisite</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">valences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.from_Lobster" title="Permalink to this definition"></a></dt>
<dd><p>Will set up a LightStructureEnvironments from Lobster.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Structure object</p></li>
<li><p><strong>list_ce_symbol</strong> – list of symbols for coordination environments</p></li>
<li><p><strong>list_csm</strong> – list of continuous symmetry measures</p></li>
<li><p><strong>list_permutation</strong> – list of permutations</p></li>
<li><p><strong>list_neighsite</strong> – list of neighboring sites</p></li>
<li><p><strong>list_neighisite</strong> – list of neighboring isites (number of a site)</p></li>
<li><p><strong>valences</strong> – list of valences</p></li>
</ul>
</dd>
</dl>
<p>Returns: LobsterLightStructureEnvironments</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.uniquely_determines_coordination_environments">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">uniquely_determines_coordination_environments</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterLightStructureEnvironments.uniquely_determines_coordination_environments" title="Permalink to this definition"></a></dt>
<dd><p>True if the coordination environments are uniquely determined.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LobsterNeighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename_ICOHP</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'ICOHPLIST.lobster'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">are_coops</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">are_cobis</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valences</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limits</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">additional_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_bonds_to</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">perc_strength_ICOHP</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noise_cutoff</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valences_from_charges</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename_CHARGE</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">which_charge</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'Mulliken'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adapt_extremum_to_add_cond</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">add_additional_data_sg</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename_blist_sg1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename_blist_sg2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_blist_sg1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'ICOOP'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_blist_sg2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'ICOBI'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.analysis.html#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>This class combines capabilities from LocalEnv and ChemEnv to determine coordination environments based on
bonding analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename_ICOHP</strong> – (str) Path to ICOHPLIST.lobster or ICOOPLIST.lobster or ICOBILIST.lobster</p></li>
<li><p><strong>structure</strong> – (Structure) typically constructed by Structure.from_file(“POSCAR”)</p></li>
<li><p><strong>are_coops</strong> – (bool) if True, the file is a ICOOPLIST.lobster and not a ICOHPLIST.lobster; only tested for
ICOHPLIST.lobster so far</p></li>
<li><p><strong>are_cobis</strong> – (bool) if True, the file is a ICOBILIST.lobster and not a ICOHPLIST.lobster</p></li>
<li><p><strong>valences</strong> (<em>Mulliken</em><em>) </em><em>instead of</em>) – (list[int | float]): gives valence/charge for each element</p></li>
<li><p><strong>limits</strong> (<em>tuple</em><em>[</em><em>float</em><em>, </em><em>float</em><em>] </em><em>| </em><em>None</em>) – limit to decide which ICOHPs (ICOOP or ICOBI) should be considered</p></li>
<li><p><strong>additional_condition</strong> (<em>int</em>) – Additional condition that decides which kind of bonds will be considered
NO_ADDITIONAL_CONDITION = 0
ONLY_ANION_CATION_BONDS = 1
NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2
ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 3
ONLY_ELEMENT_TO_OXYGEN_BONDS = 4
DO_NOT_CONSIDER_ANION_CATION_BONDS=5
ONLY_CATION_CATION_BONDS=6</p></li>
<li><p><strong>only_bonds_to</strong> – (list[str]) will only consider bonds to certain elements (e.g. [“O”] for oxygen)</p></li>
<li><p><strong>perc_strength_ICOHP</strong> – if no limits are given, this will decide which icohps will still be considered (</p></li>
<li><p><strong>to</strong> (<em>relative</em>) – </p></li>
<li><p><strong>ICOHP</strong> (<em>the strongest</em>) – </p></li>
<li><p><strong>noise_cutoff</strong> – if provided hardcodes the lower limit of icohps considered</p></li>
<li><p><strong>valences_from_charges</strong> – if True and path to CHARGE.lobster is provided, will use Lobster charges (</p></li>
<li><p><strong>valences</strong> – </p></li>
<li><p><strong>filename_CHARGE</strong> – (str) Path to Charge.lobster</p></li>
<li><p><strong>which_charge</strong> – (str) “Mulliken” or “Loewdin”</p></li>
<li><p><strong>adapt_extremum_to_add_cond</strong> – (bool) will adapt the limits to only focus on the bonds determined by the</p></li>
<li><p><strong>condition</strong> (<em>additional</em>) – </p></li>
<li><p><strong>add_additional_data_sg</strong> – (bool) will add the information from filename_add_bondinglist_sg1,</p></li>
<li><p><strong>filename_blist_sg1</strong> – (str) Path to additional ICOOP, ICOBI data for structure graphs</p></li>
<li><p><strong>filename_blist_sg2</strong> – (str) Path to dditional ICOOP, ICOBI data for structure graphs</p></li>
<li><p><strong>id_blist_sg1</strong> – (str) Identity of data in filename_blist_sg1,
e.g., “icoop” or “icobi”</p></li>
<li><p><strong>id_blist_sg2</strong> – (str) Identity of data in filename_blist_sg2,
e.g., “icoop” or “icobi”.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._adapt_extremum_to_add_cond">
<span class="sig-name descname"><span class="pre">_adapt_extremum_to_add_cond</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">list_icohps</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percentage</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._adapt_extremum_to_add_cond" title="Permalink to this definition"></a></dt>
<dd><p>Convinicence method for returning the extremum of the given icohps or icoops or icobis list</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>list_icohps</strong> – can be a list of icohps or icobis or icobis</p>
</dd>
</dl>
<p>Returns: min value of input list of icohps / max value of input list of icobis or icobis</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._determine_unit_cell">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_determine_unit_cell</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._determine_unit_cell" title="Permalink to this definition"></a></dt>
<dd><p>Based on the site it will determine the unit cell, in which this site is based.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>site</strong> – site object</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._evaluate_ce">
<span class="sig-name descname"><span class="pre">_evaluate_ce</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lowerlimit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upperlimit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_bonds_to</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">additional_condition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">perc_strength_ICOHP</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adapt_extremum_to_add_cond</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._evaluate_ce" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lowerlimit</strong> – lower limit which determines the ICOHPs that are considered for the determination of the</p></li>
<li><p><strong>neighbors</strong> – </p></li>
<li><p><strong>upperlimit</strong> – upper limit which determines the ICOHPs that are considered for the determination of the</p></li>
<li><p><strong>neighbors</strong> – </p></li>
<li><p><strong>only_bonds_to</strong> – restricts the types of bonds that will be considered</p></li>
<li><p><strong>additional_condition</strong> – Additional condition for the evaluation</p></li>
<li><p><strong>perc_strength_ICOHP</strong> – will be used to determine how strong the ICOHPs (percentage*strongest ICOHP) will be</p></li>
<li><p><strong>evalulation</strong> (<em>that are still considered for the</em>) – </p></li>
<li><p><strong>adapt_extremum_to_add_cond</strong> – will recalculate the limit based on the bonding type and not on the overall</p></li>
<li><p><strong>extremum.</strong> – </p></li>
</ul>
</dd>
</dl>
<p>Returns:</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._find_environments">
<span class="sig-name descname"><span class="pre">_find_environments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">additional_condition</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lowerlimit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upperlimit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_bonds_to</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._find_environments" title="Permalink to this definition"></a></dt>
<dd><p>Will find all relevant neighbors based on certain restrictions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>additional_condition</strong> (<em>int</em>) – additional condition (see above)</p></li>
<li><p><strong>lowerlimit</strong> (<em>float</em>) – lower limit that tells you which ICOHPs are considered</p></li>
<li><p><strong>upperlimit</strong> (<em>float</em>) – upper limit that tells you which ICOHPs are considered</p></li>
<li><p><strong>only_bonds_to</strong> (<em>list</em>) – list of str, e.g. [“O”] that will ensure that only bonds to “O” will be considered</p></li>
</ul>
</dd>
</dl>
<p>Returns:</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._find_relevant_atoms_additional_condition">
<span class="sig-name descname"><span class="pre">_find_relevant_atoms_additional_condition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">isite</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">icohps</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">additional_condition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._find_relevant_atoms_additional_condition" title="Permalink to this definition"></a></dt>
<dd><p>Will find all relevant atoms that fulfill the additional_conditions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>isite</strong> – number of site in structure (starts with 0)</p></li>
<li><p><strong>icohps</strong> – icohps</p></li>
<li><p><strong>additional_condition</strong> (<em>int</em>) – additional condition</p></li>
</ul>
</dd>
</dl>
<p>Returns:</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_atomnumber">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_get_atomnumber</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atomstring</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_atomnumber" title="Permalink to this definition"></a></dt>
<dd><p>Return the number of the atom within the initial POSCAR (e.g., Return 0 for “Na1”).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>atomstring</strong> – string such as “Na1”</p>
</dd>
</dl>
<p>Returns: integer indicating the position in the POSCAR</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_icohps">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_get_icohps</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">icohpcollection</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isite</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lowerlimit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upperlimit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_bonds_to</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_icohps" title="Permalink to this definition"></a></dt>
<dd><p>Return icohp dict for certain site.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>icohpcollection</strong> – Icohpcollection object</p></li>
<li><p><strong>isite</strong> (<em>int</em>) – number of a site</p></li>
<li><p><strong>lowerlimit</strong> (<em>float</em>) – lower limit that tells you which ICOHPs are considered</p></li>
<li><p><strong>upperlimit</strong> (<em>float</em>) – upper limit that tells you which ICOHPs are considered</p></li>
<li><p><strong>only_bonds_to</strong> (<em>list</em>) – list of str, e.g. [“O”] that will ensure that only bonds to “O” will be considered</p></li>
</ul>
</dd>
</dl>
<p>Returns:</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_limit_from_extremum">
<span class="sig-name descname"><span class="pre">_get_limit_from_extremum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">icohpcollection</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percentage</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adapt_extremum_to_add_cond</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">additional_condition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_limit_from_extremum" title="Permalink to this definition"></a></dt>
<dd><p>Return limits for the evaluation of the icohp values from an icohpcollection
Return -float(‘inf’), min(max_icohp*0.15,-0.1). Currently only works for ICOHPs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>icohpcollection</strong> – icohpcollection object</p></li>
<li><p><strong>percentage</strong> – will determine which ICOHPs or ICOOP or ICOBI will be considered</p></li>
<li><p><strong>value</strong><strong>)</strong> (<em>(</em><em>only 0.15 from the maximum</em>) – </p></li>
<li><p><strong>adapt_extremum_to_add_cond</strong> – should the extrumum be adapted to the additional condition</p></li>
<li><p><strong>additional_condition</strong> – additional condition to determine which bonds are relevant</p></li>
</ul>
</dd>
</dl>
<p>Returns: [-inf, min(strongest_icohp*0.15,-noise_cutoff)] / [max(strongest_icohp*0.15, noise_cutoff),inf]</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_plot_label">
<span class="sig-name descname"><span class="pre">_get_plot_label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">per_bond</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._get_plot_label" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors._split_string">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_split_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors._split_string" title="Permalink to this definition"></a></dt>
<dd><p>Will split strings such as “Na1” in “Na” and “1” and return “1”.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>s</strong> (<em>str</em>) – string</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.anion_types">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">anion_types</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.anion_types" title="Permalink to this definition"></a></dt>
<dd><p>Return the types of anions present in crystal structure as a set
Returns: set of Element describing anions in the crystal structure.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_anion_types">
<span class="sig-name descname"><span class="pre">get_anion_types</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_anion_types" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_cohps_to_neighbors">
<span class="sig-name descname"><span class="pre">get_info_cohps_to_neighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path_to_COHPCAR</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'COHPCAR.lobster'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_bonds_to</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">onlycation_isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">per_bond</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">summed_spin_channels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_cohps_to_neighbors" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Return info about the cohps (coops or cobis) as a summed cohp object and a label</dt><dd><p>from all sites mentioned in isites with neighbors.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>path_to_COHPCAR</strong> – str, path to COHPCAR or COOPCAR or COBICAR</p></li>
<li><p><strong>isites</strong> – list of int that indicate the number of the site</p></li>
<li><p><strong>only_bonds_to</strong> – list of str, e.g. [“O”] to only show cohps of anything to oxygen</p></li>
<li><p><strong>onlycation_isites</strong> – if isites=None, only cation sites will be returned</p></li>
<li><p><strong>per_bond</strong> – will normalize per bond</p></li>
<li><p><strong>summed_spin_channels</strong> – will sum all spin channels</p></li>
</ul>
</dd>
</dl>
<p>Returns: label for cohp (str), CompleteCohp object which describes all cohps (coops or cobis) of the sites
as given by isites and the other parameters</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_icohps_between_neighbors">
<span class="sig-name descname"><span class="pre">get_info_icohps_between_neighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">onlycation_isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_icohps_between_neighbors" title="Permalink to this definition"></a></dt>
<dd><p>Return infos about interactions between neighbors of a certain atom.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>isites</strong> – list of site ids, if isite==None, all isites will be used</p></li>
<li><p><strong>onlycation_isites</strong> – will only use cations, if isite==None</p></li>
</ul>
</dd>
</dl>
<p>Returns: ICOHPNeighborsInfo</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_icohps_to_neighbors">
<span class="sig-name descname"><span class="pre">get_info_icohps_to_neighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">onlycation_isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_info_icohps_to_neighbors" title="Permalink to this definition"></a></dt>
<dd><p>This method returns information on the icohps of neighbors for certain sites as identified by their site id.
This is useful for plotting the relevant cohps of a site in the structure.
(could be ICOOPLIST.lobster or ICOHPLIST.lobster or ICOBILIST.lobster)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>isites</strong> – list of site ids. If isite==None, all isites will be used to add the icohps of the neighbors</p></li>
<li><p><strong>onlycation_isites</strong> – if True and if isite==None, it will only analyse the sites of the cations</p></li>
</ul>
</dd>
</dl>
<p>Returns: ICOHPNeighborsInfo</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_light_structure_environment">
<span class="sig-name descname"><span class="pre">get_light_structure_environment</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_cation_environments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_indices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_light_structure_environment" title="Permalink to this definition"></a></dt>
<dd><p>Return a LobsterLightStructureEnvironments object
if the structure only contains coordination environments smaller 13.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>only_cation_environments</strong> – only data for cations will be returned</p></li>
<li><p><strong>only_indices</strong> – will only evaluate the list of isites in this list</p></li>
</ul>
</dd>
</dl>
<p>Returns: LobsterLightStructureEnvironments Object</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_weights</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.get_nn_info" title="Permalink to this definition"></a></dt>
<dd><p>Get coordination number, CN, of site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine CN.</p></li>
<li><p><strong>use_weights</strong> (<em>bool</em>) – flag indicating whether (True)
to use weights for computing the coordination number
or not (False, default: each coordinated site has equal
weight).
True is not implemented for LobsterNeighbors</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>coordination number.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>cn (integer or float)</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.molecules_allowed" title="Permalink to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.plot_cohps_of_neighbors">
<span class="sig-name descname"><span class="pre">plot_cohps_of_neighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path_to_COHPCAR</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'COHPCAR.lobster'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">onlycation_isites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_bonds_to</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">per_bond</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">summed_spin_channels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(-10,</span> <span class="pre">6)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrated</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/io/lobster/lobsterenv.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lobster.lobsterenv.LobsterNeighbors.plot_cohps_of_neighbors" title="Permalink to this definition"></a></dt>
<dd><p>Will plot summed cohps or cobis or coops
(please be careful in the spin polarized case (plots might overlap (exactly!)).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>isites</strong> – list of site ids, if isite==[], all isites will be used to add the icohps of the neighbors</p></li>
<li><p><strong>onlycation_isites</strong> – bool, will only use cations, if isite==[]</p></li>
<li><p><strong>only_bonds_to</strong> – list of str, only anions in this list will be considered</p></li>
<li><p><strong>per_bond</strong> – bool, will lead to a normalization of the plotted COHP per number of bond if True,</p></li>
<li><p><strong>sum</strong> (<em>otherwise the</em>) – </p></li>
<li><p><strong>plotted</strong> (<em>will be</em>) – </p></li>
<li><p><strong>xlim</strong> – list of float, limits of x values</p></li>
<li><p><strong>ylim</strong> – list of float, limits of y values</p></li>
<li><p><strong>integrated</strong> – bool, if true will show integrated cohp instead of cohp</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>plt of the cohps or coops or cobis</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.lobster.lobsterenv.LobsterNeighbors.structures_allowed">