Index

A

a (pychemia.crystal.lattice.Lattice attribute) AbiFiles (class in pychemia.code.abinit.abifiles) abihelp() (in module pychemia.code.abinit.utils) AbinitJob (class in pychemia.code.abinit.abinit) AbinitOutput (class in pychemia.code.abinit.output) Ackley (class in pychemia.utils.metaheuristics) active_workdirs (pychemia.evaluator.vasp_evaluator.RelaxPopulation attribute) actives (pychemia.population.realfunction.RealFunction attribute) actives_in_generation (pychemia.searcher.searcher.Searcher attribute) add_atom() (pychemia.core.structure.Structure method) add_children() (pychemia.db.repo.StructureEntry method) add_entry() (pychemia.db.repo.StructureRepository method) add_file() (pychemia.db.queue.PyChemiaQueue method) add_from_db() (pychemia.population.relaxstructures.RelaxStructures method) add_input_file() (pychemia.db.queue.PyChemiaQueue method) add_kpt() (pychemia.crystal.kpoints.KPoints method) add_many_entries() (pychemia.db.repo.StructureRepository method) add_original_file() (pychemia.db.repo.StructureEntry method) add_parents() (pychemia.db.repo.StructureEntry method) add_property() (pychemia.db.repo.PropertiesEntry method) add_random() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) add_status() (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) add_tags() (pychemia.db.repo.StructureEntry method)

add_vacuum() (pychemia.core.structure.Structure method) adjust_reduced() (pychemia.core.structure.Structure method) advance() (pychemia.searcher.searcher.Searcher method) Al2O3() (in module pychemia.crystal.samples) align_inertia_momenta() (pychemia.core.structure.Structure method) align_with_axis() (pychemia.core.structure.Structure method) (pychemia.crystal.lattice.Lattice method) align_with_plane() (pychemia.core.structure.Structure method) (pychemia.crystal.lattice.Lattice method) all_distances() (pychemia.analysis.analysis.StructureAnalysis method) all_distances_by_species() (pychemia.analysis.analysis.StructureAnalysis method) (pychemia.analysis.cluster.ClusterAnalysis method) all_tests_functions() (in module pychemia.utils.metaheuristics) alpha (pychemia.crystal.lattice.Lattice attribute) amu_emass (in module pychemia.utils.constants) angle_between_vectors() (in module pychemia.utils.mathematics) angle_vector() (in module pychemia.utils.mathematics) angle_vectors() (in module pychemia.utils.mathematics) angles (pychemia.crystal.lattice.Lattice attribute) AntColony (class in pychemia.searcher.ant) apply_rotation() (in module pychemia.utils.mathematics) atom_name() (pychemia.code.abinit.input.InputVariables method) atomic_number() (in module pychemia.utils.periodic) atomic_symbol() (in module pychemia.utils.periodic) atoms_in_box() (pychemia.core.structure.Structure method) attach_to_facet() (in module pychemia.analysis.surface) Avogadro (in module pychemia.utils.constants)

B

b (pychemia.crystal.lattice.Lattice attribute) basedir (pychemia.code.abinit.abifiles.AbiFiles attribute) basic_analysis() (pychemia.code.dftb.dftb.DFTBplus method) basic_driver() (pychemia.code.dftb.dftb.DFTBplus method) basic_hamiltonian() (pychemia.code.dftb.dftb.DFTBplus method) basic_input() (pychemia.code.dftb.dftb.DFTBplus method) basic_options() (pychemia.code.dftb.dftb.DFTBplus method) basic_parser_options() (pychemia.code.dftb.dftb.DFTBplus method) Beale (class in pychemia.utils.metaheuristics) BeeAlgorithm (class in pychemia.searcher.bee)

best_encut (pychemia.code.vasp.task.convergence.ConvergenceCutOffEnergy attribute) best_kpoints (pychemia.code.vasp.task.convergence.ConvergenceKPointGrid attribute) beta (pychemia.crystal.lattice.Lattice attribute) BField_Tesla (in module pychemia.utils.constants) block() (in module pychemia.utils.periodic) block_from_string() (pychemia.io.cif.CIF method) bohr_angstrom (in module pychemia.utils.constants) bonds_coordination() (pychemia.analysis.analysis.StructureAnalysis method) Booth (class in pychemia.utils.metaheuristics) broken_function() (in module pychemia.utils.tests.test_doctest_utils) BukinN6 (class in pychemia.utils.metaheuristics)

C

c (pychemia.crystal.lattice.Lattice attribute) canonical_form() (pychemia.core.structure.Structure method) cartesian2reduced() (pychemia.crystal.lattice.Lattice method) cartesian_distances() (pychemia.analysis.matching.StructureMatch method) cartesian_to_spherical() (in module pychemia.utils.mathematics) CaTiO3() (in module pychemia.crystal.samples) cell (pychemia.crystal.lattice.Lattice attribute) cell_displacement() (pychemia.analysis.matching.StructureMatch method) cell_to_reduced() (in module pychemia.io.ascii) center_mass() (pychemia.core.structure.Structure method) change_kinetic_energy() (in module pychemia.code.octopus.analysis) charge_in_sphere() (in module pychemia.code.octopus.analysis) check_duplicates() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) check_output() (pychemia.test.doctest_2to3.DocTestChecker method) check_results() (in module pychemia.test.test_zexample2) CIF (class in pychemia.io.cif) cif_expand() (in module pychemia.io.cif) CIFStructure (class in pychemia.io.cif) clean() (pychemia.code.abinit.abifiles.AbiFiles method) (pychemia.code.abinit.input.InputVariables method) (pychemia.code.vasp.vasp.VaspJob method) (pychemia.db.db.PyChemiaDB method) (pychemia.db.repo.StructureRepository method) (pychemia.searcher.searcher.Searcher method) cleanall() (pychemia.code.abinit.abifiles.AbiFiles method) cleaned_from_duplicates() (pychemia.population.relaxstructures.RelaxStructures method) cleaner() (pychemia.code.vasp.task.relax.IonRelaxation method) (pychemia.code.vasp.task.stregth.IdealStrength method) close_distances() (pychemia.analysis.analysis.StructureAnalysis method) cluster_evaluator() (in module pychemia.evaluator.cluster) cluster_fb_evaluator() (in module pychemia.evaluator.cluster_fireball) cluster_fb_launcher() (in module pychemia.evaluator.cluster_fireball) cluster_fb_worker() (in module pychemia.evaluator.cluster_fireball) cluster_launcher() (in module pychemia.evaluator.cluster) cluster_minimal_distance() (in module pychemia.core.structure) cluster_relaxation() (pychemia.code.fireball.fireball.FireBall method) cluster_worker() (in module pychemia.evaluator.cluster)

ClusterAnalysis (class in pychemia.analysis.cluster) ClusterMatch (class in pychemia.analysis.cluster) cmd_exists() (in module pychemia.external.symmol.symmol) Codes (class in pychemia.code.codes) collect_data() (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) Composition (class in pychemia.core.composition) composition (pychemia.core.composition.Composition attribute) (pychemia.core.structure.Structure attribute) Convergence (class in pychemia.code.vasp.task.convergence) ConvergenceCutOffEnergy (class in pychemia.code.vasp.task.convergence) ConvergenceKPointGrid (class in pychemia.code.vasp.task.convergence) convert_color() (in module pychemia.utils.computing) convert_value() (in module pychemia.code.fireball.fireball) coordinate() (pychemia.population.realfunction.RealFunction method) coordinates() (in module pychemia.code.octopus) copy() (pychemia.core.structure.Structure method) (pychemia.crystal.lattice.Lattice method) correct_extras() (pychemia.searcher.searcher.Searcher method) covalent_radius() (in module pychemia.utils.periodic) covalent_volume() (pychemia.core.composition.Composition method) cpk_color() (in module pychemia.utils.periodic) Cr() (in module pychemia.crystal.samples) create() (pychemia.code.abinit.abifiles.AbiFiles method) create_database() (in module pychemia.db.db) create_dirs() (pychemia.code.vasp.task.relax.IonRelaxation method) (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) create_foragers() (pychemia.searcher.bee.BeeAlgorithm method) create_input() (pychemia.external.findsym.FindSym method) create_inputs() (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) create_static() (pychemia.db.db.PyChemiaDB method) create_user() (in module pychemia.db.db) creation() (in module pychemia.test.test_zexample1) cross() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) CrossInTray (class in pychemia.utils.metaheuristics) crystal_system() (pychemia.crystal.symmetry.CrystalSymmetry method) CrystalSymmetry (class in pychemia.crystal.symmetry) CrystalSymmetryTest (class in pychemia.crystal.tests.test_symmetry)

D

datamining() (in module pychemia.test.test_zexample1) debug_evaluation() (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) deep_unicode() (in module pychemia.utils.computing) deflection() (in module pychemia.code.octopus.analysis) deform_cell() (pychemia.analysis.changer.StructureChanger method) del_atom() (pychemia.core.structure.Structure method) del_entry() (pychemia.db.repo.StructureRepository method) del_status() (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) density (pychemia.core.structure.Structure attribute) DFTBplus (class in pychemia.code.dftb.dftb) diff_values_matrix() (pychemia.population.relaxstructures.RelaxStructures method) dipolx_in_sphere() (in module pychemia.code.octopus.analysis) direct_move() (in module pychemia.population.ljcluster) DirectEvaluator (class in pychemia.evaluator.direct_evaluator) disable() (pychemia.population.realfunction.RealFunction method) discrete_radial_distribution_function() (pychemia.analysis.cluster.ClusterAnalysis method) distance() (in module pychemia.utils.mathematics) (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method)

distance2() (pychemia.core.structure.Structure method) (pychemia.crystal.lattice.Lattice method) distance_matrix() (pychemia.analysis.cluster.ClusterAnalysis method) (pychemia.core.structure.Structure method) (pychemia.population.relaxstructures.RelaxStructures method) distance_matrix_by_species() (pychemia.analysis.cluster.ClusterAnalysis method) distances (pychemia.analysis.analysis.StructureAnalysis attribute) distances() (in module pychemia.utils.mathematics) distances_in_sphere() (pychemia.crystal.lattice.Lattice method) dmatpawu2params() (in module pychemia.population.orbitaldftu) do_mixing() (in module pychemia.analysis.splitting) doctest_suite() (in module pychemia.test.doctest_2to3) DocTestChecker (class in pychemia.test.doctest_2to3)

E

e_Cb (in module pychemia.utils.constants) Easom (class in pychemia.utils.metaheuristics) Eggholder (class in pychemia.utils.metaheuristics) elastic_moduli() (in module pychemia.code.vasp.task.elastic) ElasticModuli (class in pychemia.code.vasp.task.elastic) electronegativity() (in module pychemia.utils.periodic) enable() (pychemia.population.realfunction.RealFunction method) energy (pychemia.code.vasp.outcar.VaspOutput attribute) energy() (in module pychemia.code.octopus) enforce_generation_size() (pychemia.searcher.searcher.Searcher method) error() (pychemia.code.abinit.htmlparser.MyHTMLParser method) evaluate() (pychemia.evaluator.function.FunctionEvaluator method) (pychemia.evaluator.functional.Evaluator method) (pychemia.population.ljcluster.LJCluster method) (pychemia.population.realfunction.RealFunction method)

evaluate_entry() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) Evaluator (class in pychemia.evaluator) (class in pychemia.evaluator.functional) evaluator() (in module pychemia.searcher.tests.test_searcher_clusters) execute() (in module pychemia.code.octopus.input) (in module pychemia.evaluator) (pychemia.code.abinit.abifiles.AbiFiles method) execution() (in module pychemia.test.test_zexample1) ExecutionRepository (class in pychemia.db.repo) ext_gcd() (in module pychemia.analysis.surface)

F

filename (pychemia.code.abinit.abifiles.AbiFiles attribute) files (pychemia.code.abinit.abifiles.AbiFiles attribute) files_presence() (pychemia.code.vasp.vasp.VaspAnalyser method) finalize() (pychemia.code.abinit.abinit.AbinitJob method) (pychemia.code.codes.Codes method) (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.fireball.fireball.FireBall method) (pychemia.code.vasp.vasp.VaspJob method) find_AnBm() (pychemia.db.db.PyChemiaDB method) find_composition() (pychemia.db.db.PyChemiaDB method) find_new_seed() (in module pychemia.analysis.surface) find_primitive() (pychemia.crystal.symmetry.CrystalSymmetry method) FindSym (class in pychemia.external.findsym) FireBall (class in pychemia.code.fireball.fireball) FireFly (class in pychemia.searcher.firefly) first_run() (pychemia.code.vasp.task.relax.IonRelaxation method) flip_status() (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) fminimum() (pychemia.utils.metaheuristics.OptimizationTestFunction method) formula (pychemia.core.composition.Composition attribute) (pychemia.core.structure.Structure attribute) formula_parser() (pychemia.core.composition.Composition static method) formula_to_list() (pychemia.core.composition.Composition static method) fp_oganov() (pychemia.analysis.analysis.StructureAnalysis method) free_energy() (pychemia.code.vasp.outcar.VaspOutput method) frexp10() (in module pychemia.utils.mathematics) from_dict() (pychemia.code.fireball.fireball.FireBall static method) (pychemia.core.structure.Structure static method) (pychemia.crystal.kpoints.KPoints class method) (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms static method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) (pychemia.utils.serializer.PyChemiaJsonable class method)

from_file() (pychemia.io.cif.CIF static method) from_parameters_to_cell() (pychemia.crystal.lattice.Lattice static method) from_string() (pychemia.io.cif.CIF static method) from_structure() (pychemia.code.abinit.input.InputVariables method) fromdict() (pychemia.code.vasp.vasp.VaspJob method) (pychemia.db.repo.StructureRepository method) full_version() (pychemia.Version static method) function() (pychemia.utils.metaheuristics.Ackley static method) (pychemia.utils.metaheuristics.Beale static method) (pychemia.utils.metaheuristics.Booth static method) (pychemia.utils.metaheuristics.BukinN6 static method) (pychemia.utils.metaheuristics.CrossInTray static method) (pychemia.utils.metaheuristics.Easom static method) (pychemia.utils.metaheuristics.Eggholder static method) (pychemia.utils.metaheuristics.GoldsteinPrice static method) (pychemia.utils.metaheuristics.HolderTable static method) (pychemia.utils.metaheuristics.LeviN13 static method) (pychemia.utils.metaheuristics.Matyas static method) (pychemia.utils.metaheuristics.McCormick static method) (pychemia.utils.metaheuristics.OptimizationTestFunction static method) (pychemia.utils.metaheuristics.Rosenbrock static method) (pychemia.utils.metaheuristics.SchafferN2 static method) (pychemia.utils.metaheuristics.SchafferN4 static method) (pychemia.utils.metaheuristics.Sphere static method) (pychemia.utils.metaheuristics.StyblinskiTang static method) (pychemia.utils.metaheuristics.ThreeHump static method) FunctionEvaluator (class in pychemia.evaluator.function) FunctionObjectiveFunction (class in pychemia.evaluator.function) funx2() (in module pychemia.population.tests.test_population)

G

gamma (pychemia.crystal.lattice.Lattice attribute) gcd (pychemia.core.composition.Composition attribute) gea_all_angles() (in module pychemia.utils.mathematics) gea_angles() (in module pychemia.utils.mathematics) gea_matrix_a() (in module pychemia.utils.mathematics) gea_orthogonal_from_angles() (in module pychemia.utils.mathematics) generic_serializer() (in module pychemia.utils.serializer) GeneticAlgorithm (class in pychemia.searcher.genetic) get_all_entries (pychemia.db.repo.StructureRepository attribute) get_all_generations() (pychemia.searcher.searcher.Searcher method) get_all_shells() (pychemia.code.dftb.dftb.DFTBplus method) get_all_splitted_compositions() (in module pychemia.analysis.splitting) get_bonds() (pychemia.analysis.analysis.StructureAnalysis method) get_bonds_coordination() (pychemia.analysis.analysis.StructureAnalysis method) get_brillouin() (pychemia.crystal.lattice.Lattice method) get_cell() (pychemia.core.structure.Structure method) get_center_vector() (in module pychemia.analysis.surface) get_composition() (pychemia.core.structure.Structure method) get_correlation_params() (pychemia.population.orbitaldftu.OrbitalDFTU method) get_cut_planes() (in module pychemia.analysis.splitting) get_database() (in module pychemia.db.db) get_defined_variables() (pychemia.code.vasp.incar.InputVariables method) get_delaunay_reduction() (in module pychemia.core.delaunay) get_density_of_kpoints() (pychemia.crystal.kpoints.KPoints method) get_dicts() (pychemia.db.db.PyChemiaDB method) get_distance() (pychemia.core.structure.Structure method) get_dmatpawu() (pychemia.code.abinit.output.AbinitOutput method) get_dtsets_keys() (pychemia.code.abinit.input.InputVariables method) get_duplicates() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) get_elastic_moduli() (pychemia.code.vasp.task.elastic.ElasticModuli method) get_energetics() (pychemia.code.abinit.output.AbinitOutput method) get_energy() (pychemia.code.lennardjones.lj.LennardJones method) get_entry() (pychemia.db.db.PyChemiaDB method) get_facets() (in module pychemia.analysis.surface) get_fdata_info() (in module pychemia.code.fireball.fireball) get_final_correlation_matrices_from_output() (in module pychemia.population.orbitaldftu) get_final_dmatpawu() (in module pychemia.population.orbitaldftu) get_final_geometry() (pychemia.code.abinit.task.relax.IonRelaxation method) (pychemia.code.dftb.task.relax.Relaxation method) (pychemia.code.relaxator.Relaxator method) (pychemia.code.vasp.task.relax.IonRelaxation method) get_float() (in module pychemia.utils.computing) get_forces() (pychemia.code.lennardjones.lj.LennardJones method) (pychemia.population.ljcluster.LJCluster method) get_forces_stress_energy() (pychemia.code.abinit.task.relax.IonRelaxation method) (pychemia.code.dftb.task.relax.Relaxation method) (pychemia.code.relaxator.Relaxator method) (pychemia.code.vasp.task.relax.IonRelaxation method) get_formulas() (pychemia.db.repo.StructureRepository method) get_general_timing() (pychemia.code.vasp.outcar.VaspOutput method) get_generation() (pychemia.searcher.searcher.Searcher method) get_geometry() (pychemia.code.dftb.dftb.DFTBplus method) get_input_filename() (pychemia.code.abinit.abifiles.AbiFiles method) get_input_structure() (pychemia.db.queue.PyChemiaQueue method) get_input_variables() (pychemia.db.queue.PyChemiaQueue method) get_int() (in module pychemia.utils.computing) get_jobs() (in module pychemia.runner.pbs) get_last_iteration() (in module pychemia.code.octopus.analysis) get_lattice() (pychemia.io.cif.CIFStructure method) get_list_candidates() (pychemia.evaluator.direct_evaluator.DirectEvaluator method) get_magnetization() (pychemia.code.vasp.outcar.VaspOutput method) get_magnitude_forces() (pychemia.code.lennardjones.lj.LennardJones method) get_matching_options() (in module pychemia.analysis.splitting) get_max_angular_momentum() (pychemia.code.dftb.dftb.DFTBplus method) get_max_force_stress() (pychemia.code.relaxator.Relaxator method) (pychemia.population.relaxstructures.RelaxStructures method)

get_mechanical_properties() (pychemia.code.vasp.task.elastic.ElasticModuli method) get_memory_used() (pychemia.code.vasp.outcar.VaspOutput method) get_minimal_splitting() (pychemia.analysis.splitting.SplitMatch method) get_new_structure() (pychemia.crystal.symmetry.CrystalSymmetry method) get_occupation_matrix() (pychemia.code.abinit.output.AbinitOutput method) get_onion_layers() (in module pychemia.analysis.surface) get_out_filename() (pychemia.code.abinit.abifiles.AbiFiles method) get_output() (pychemia.code.abinit.abifiles.AbiFiles method) get_output_filename() (pychemia.code.abinit.abifiles.AbiFiles method) get_output_structure() (pychemia.db.queue.PyChemiaQueue method) get_outputs() (pychemia.code.abinit.abinit.AbinitJob method) (pychemia.code.codes.Codes method) (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.fireball.fireball.FireBall method) (pychemia.code.vasp.vasp.VaspJob method) get_params() (pychemia.searcher.annealing.SimulatedAnnealing method) (pychemia.searcher.ant.AntColony method) (pychemia.searcher.bee.BeeAlgorithm method) (pychemia.searcher.firefly.FireFly method) (pychemia.searcher.genetic.GeneticAlgorithm method) (pychemia.searcher.grey.GreyWolf method) (pychemia.searcher.harmony.HarmonySearch method) (pychemia.searcher.mhm.MinimaHoppingMethod method) (pychemia.searcher.searcher.Searcher method) (pychemia.searcher.swarm.ParticleSwarm method) (pychemia.searcher.swarm2.ParticleSwarm method) get_path() (pychemia.crystal.lattice.Lattice method) get_pattern() (in module pychemia.population.orbitaldftu) get_plot_matrices() (pychemia.utils.metaheuristics.OptimizationTestFunction method) get_point_group() (in module pychemia.external.symmol.symmol) get_potcar_info() (in module pychemia.code.vasp.poscar) get_reduced_bases() (in module pychemia.core.delaunay) get_shells() (pychemia.code.dftb.dftb.DFTBplus static method) get_shortest_bases_from_extented_bases() (in module pychemia.core.delaunay) get_sigma_epsilon() (pychemia.code.lennardjones.lj.LennardJones method) get_simple_match() (pychemia.analysis.splitting.SplitMatch method) get_simple_split_sites() (in module pychemia.analysis.splitting) get_singlecifs() (in module pychemia.io.cif) get_space_group_symop_operation_xyz() (in module pychemia.io.cif) get_space_group_type() (pychemia.crystal.symmetry.CrystalSymmetry method) get_spacegroup() (pychemia.crystal.symmetry.CrystalSymmetry method) get_species() (in module pychemia.code.vasp.poscar) get_species_from_hex() (pychemia.core.composition.Composition static method) get_species_list() (in module pychemia.code.vasp.poscar) get_split_sites() (in module pychemia.analysis.splitting) get_structure() (pychemia.code.abinit.input.InputVariables method) (pychemia.db.db.PyChemiaDB method) (pychemia.db.queue.PyChemiaQueue method) (pychemia.population.ljcluster.LJCluster method) (pychemia.population.relaxstructures.RelaxStructures method) get_surface_atoms() (in module pychemia.analysis.surface) get_surface_atoms_new() (in module pychemia.analysis.surface) get_symmetry() (pychemia.crystal.symmetry.CrystalSymmetry method) get_symmetry_dataset() (pychemia.crystal.symmetry.CrystalSymmetry method) get_symmetry_operations() (pychemia.io.cif.CIFStructure method) get_tags() (pychemia.db.db.PyChemiaDB method) get_value() (pychemia.code.abinit.input.InputVariables method) get_values() (pychemia.evaluator.function.FunctionObjectiveFunction method) (pychemia.evaluator.functional.ObjectiveFunction method) (pychemia.population.realfunction.RealFunction method) get_vars() (in module pychemia.code.octopus.input) get_wigner_seitz() (pychemia.crystal.lattice.Lattice method) get_wigner_seitz_container() (pychemia.crystal.lattice.Lattice method) GoldsteinPrice (class in pychemia.utils.metaheuristics) gram_smith() (in module pychemia.utils.mathematics) gram_smith_qr() (in module pychemia.utils.mathematics) GreyWolf (class in pychemia.searcher.grey) group() (in module pychemia.utils.periodic)

H

Ha_cmm1 (in module pychemia.utils.constants) Ha_eV (in module pychemia.utils.constants) Ha_J (in module pychemia.utils.constants) Ha_K (in module pychemia.utils.constants) Ha_meV (in module pychemia.utils.constants) HaBohr3_GPa (in module pychemia.utils.constants) hall_number() (pychemia.crystal.symmetry.CrystalSymmetry method) handle_data() (pychemia.code.abinit.htmlparser.MyHTMLParser method) handle_endtag() (pychemia.code.abinit.htmlparser.MyHTMLParser method) handle_starttag() (pychemia.code.abinit.htmlparser.MyHTMLParser method)

hardness() (pychemia.analysis.analysis.StructureAnalysis method) hardness_old() (pychemia.analysis.analysis.StructureAnalysis method) hardness_XX() (pychemia.analysis.analysis.StructureAnalysis method) HarmonySearch (class in pychemia.searcher.harmony) has_connection() (in module pychemia.db.db) (in module pychemia.population.tests.test_population) has_forces_stress_energy() (pychemia.code.vasp.outcar.VaspOutput method) has_variable() (pychemia.code.abinit.input.InputVariables method) hashfile() (in module pychemia.utils.computing) hirshfeld() (in module pychemia.code.octopus.analysis) HolderTable (class in pychemia.utils.metaheuristics)

I

IdealStrength (class in pychemia.code.vasp.task.stregth) ids_sorted() (pychemia.evaluator.function.FunctionObjectiveFunction method) (pychemia.evaluator.functional.ObjectiveFunction method) inertia_matrix() (pychemia.core.structure.Structure method) info() (in module pychemia) initialize() (pychemia.code.abinit.abinit.AbinitJob method) (pychemia.code.codes.Codes method) (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.fireball.fireball.FireBall method) (pychemia.code.vasp.task.polarization.Polarization method) (pychemia.code.vasp.vasp.VaspJob method) (pychemia.evaluator.Evaluator method) (pychemia.evaluator.function.FunctionEvaluator method) (pychemia.evaluator.function.FunctionObjectiveFunction method) (pychemia.evaluator.functional.Evaluator method) (pychemia.evaluator.functional.ObjectiveFunction method) (pychemia.runner.pbs.PBSRunner method) (pychemia.runner.runner.Runner method) InputVariables (class in pychemia.code.abinit.input) (class in pychemia.code.octopus.input) (class in pychemia.code.vasp.incar) insert() (pychemia.core.structure.Structure method) (pychemia.db.db.PyChemiaDB method) integral_gaussian() (in module pychemia.utils.mathematics)

integrate_x() (pychemia.code.octopus.input.OpenDX method) inverse (pychemia.crystal.lattice.Lattice attribute) InvFineStruct (in module pychemia.utils.constants) IonRelaxation (class in pychemia.code.abinit.task.relax) (class in pychemia.code.vasp.task.relax) is_converge (pychemia.code.vasp.task.convergence.Convergence attribute) is_crystal (pychemia.core.structure.Structure attribute) is_evaluated() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) is_finished (pychemia.code.abinit.output.AbinitOutput attribute) (pychemia.code.vasp.outcar.VaspOutput attribute) is_inside() (pychemia.population.realfunction.RealFunction method) is_locked() (pychemia.db.db.PyChemiaDB method) is_multistructure() (in module pychemia.io.cif) is_perfect (pychemia.core.structure.Structure attribute) is_periodic (pychemia.core.structure.Structure attribute) is_running (pychemia.evaluator.Evaluator attribute) (pychemia.evaluator.function.FunctionEvaluator attribute) (pychemia.evaluator.functional.Evaluator attribute) iterations() (pychemia.code.vasp.outcar.VaspOutput method) iterative_rotation_angles() (in module pychemia.utils.mathematics)

J

job_ecut_convergence() (pychemia.code.abinit.abinit.AbinitJob method) job_ion_relax() (pychemia.code.abinit.abinit.AbinitJob method)

job_static() (pychemia.code.abinit.abinit.AbinitJob method) (pychemia.code.vasp.vasp.VaspJob method)

K

kb_HaK (in module pychemia.utils.constants) kpoint_convergence() (in module pychemia.code.dftb.task.kpconv)

KPointConvergence (class in pychemia.code.dftb.task.kpconv) KPoints (class in pychemia.crystal.kpoints) KPointsTest (class in pychemia.crystal.tests.test_kpoints)

L

Lattice (class in pychemia.crystal.lattice) lattice (pychemia.core.structure.Structure attribute) lcm() (in module pychemia.utils.mathematics) length_vector() (in module pychemia.utils.mathematics) length_vectors() (in module pychemia.utils.mathematics) lengths (pychemia.crystal.lattice.Lattice attribute) LennardJones (class in pychemia.code.lennardjones.lj) LeviN13 (class in pychemia.utils.metaheuristics) LiF() (in module pychemia.crystal.samples) link_fdata() (pychemia.code.fireball.fireball.FireBall method) link_slater_koster() (pychemia.code.dftb.dftb.DFTBplus method) lj_compact_evaluate() (in module pychemia.code.lennardjones.lj) lj_energy() (in module pychemia.code.lennardjones.lj) lj_forces() (in module pychemia.code.lennardjones.lj) lj_gradient() (in module pychemia.code.lennardjones.lj) LJCluster (class in pychemia.population.ljcluster) load() (in module pychemia.io.ascii) (in module pychemia.io.xyz) (pychemia.code.abinit.task.relax.IonRelaxation method) (pychemia.code.abinit.task.static.StaticCalculation method) (pychemia.code.tasks.Task method) (pychemia.code.vasp.task.convergence.ConvergenceCutOffEnergy method) (pychemia.code.vasp.task.convergence.ConvergenceKPointGrid method) (pychemia.code.vasp.task.elastic.ElasticModuli method) (pychemia.code.vasp.task.polarization.Polarization method) (pychemia.code.vasp.task.relax.IonRelaxation method) (pychemia.code.vasp.task.static.StaticCalculation method) (pychemia.code.vasp.task.stregth.IdealStrength method) (pychemia.db.repo.PropertiesEntry method) (pychemia.db.repo.StructureEntry method) (pychemia.db.repo.StructureRepository method)

load_json() (pychemia.code.vasp.vasp.VaspJob method) (pychemia.core.structure.Structure static method) load_originals() (pychemia.db.repo.StructureEntry method) load_structure_json() (in module pychemia.core.structure) local_minimization() (pychemia.code.lennardjones.lj.LennardJones method) lock() (pychemia.db.db.PyChemiaDB method)

M

magnitude_velocity() (in module pychemia.code.octopus.analysis) map_to_all() (pychemia.db.db.PyChemiaDB method) mass() (in module pychemia.utils.periodic) match() (pychemia.analysis.cluster.ClusterMatch method) match_atoms() (pychemia.analysis.matching.StructureMatch method) match_shape() (pychemia.analysis.matching.StructureMatch method) match_size() (pychemia.analysis.matching.StructureMatch method) matrix_from_eig() (in module pychemia.utils.mathematics) Matyas (class in pychemia.utils.metaheuristics) max_kpoints() (pychemia.crystal.kpoints.KPoints static method) maxforce() (pychemia.population.ljcluster.LJCluster method) McCormick (class in pychemia.utils.metaheuristics) mechanical_properties() (in module pychemia.code.vasp.task.elastic) member_str() (pychemia.population.realfunction.RealFunction method) members (pychemia.population.realfunction.RealFunction attribute) merge() (in module pychemia.code.abinit.input) (pychemia.db.repo.StructureRepository method) merge2entries() (pychemia.db.repo.StructureRepository method) merge_restart() (in module pychemia.code.octopus.merge) metadatafromdict() (pychemia.db.repo.StructureEntry method) metadatatodict() (pychemia.db.repo.StructureEntry method) metric (pychemia.crystal.lattice.Lattice attribute) MgB2() (in module pychemia.crystal.samples) MgO() (in module pychemia.crystal.samples) MinimaHoppingMethod (class in pychemia.searcher.mhm) minimal_distance() (pychemia.crystal.lattice.Lattice method) minimal_distances() (pychemia.crystal.lattice.Lattice method) minimum() (pychemia.utils.metaheuristics.Ackley method) (pychemia.utils.metaheuristics.Beale method) (pychemia.utils.metaheuristics.Booth method) (pychemia.utils.metaheuristics.BukinN6 method) (pychemia.utils.metaheuristics.CrossInTray method) (pychemia.utils.metaheuristics.Easom method) (pychemia.utils.metaheuristics.Eggholder method) (pychemia.utils.metaheuristics.GoldsteinPrice method) (pychemia.utils.metaheuristics.HolderTable method) (pychemia.utils.metaheuristics.LeviN13 method) (pychemia.utils.metaheuristics.Matyas method) (pychemia.utils.metaheuristics.McCormick method) (pychemia.utils.metaheuristics.OptimizationTestFunction method) (pychemia.utils.metaheuristics.Rosenbrock method) (pychemia.utils.metaheuristics.SchafferN2 method) (pychemia.utils.metaheuristics.SchafferN4 method) (pychemia.utils.metaheuristics.Sphere method) (pychemia.utils.metaheuristics.StyblinskiTang method) (pychemia.utils.metaheuristics.ThreeHump method)

modify_input() (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) moment_of_inertia() (pychemia.core.structure.Structure method) move() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) move_one_atom() (pychemia.analysis.changer.StructureChanger method) move_random() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) move_to_minima() (pychemia.code.lennardjones.lj.LennardJones method) movement_sweep() (in module pychemia.population.ljcluster) MyHTMLParser (class in pychemia.code.abinit.htmlparser) MyTestCase (class in pychemia.code.vasp.tests.test_vasp) (class in pychemia.utils.tests.test_doctest_utils)

N

NaCl() (in module pychemia.crystal.samples) natom (pychemia.core.composition.Composition attribute) ndim (pychemia.population.orbitaldftu.OrbitalDFTU attribute) netcdf2dict() (in module pychemia.code.abinit.output) (in module pychemia.code.abinit.utils) new_entry() (pychemia.db.queue.PyChemiaQueue method) (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method)

new_identifier() (pychemia.population.realfunction.RealFunction static method) (pychemia.population.relaxstructures.RelaxStructures static method) nkpt (pychemia.crystal.kpoints.KPoints attribute) NonCollinearMagMoms (class in pychemia.population.noncollinearmagmoms) notest_dftu() (pychemia.population.tests.test_population.PopulationTest method) notest_searcher() (in module pychemia.searcher.tests.test_searcher_clusters) notest_structure() (pychemia.population.tests.test_population.PopulationTest method) nsites (pychemia.core.structure.Structure attribute) nspecies (pychemia.core.composition.Composition attribute) (pychemia.core.structure.Structure attribute) number() (pychemia.crystal.symmetry.CrystalSymmetry method) number_of_kpoints (pychemia.crystal.kpoints.KPoints attribute)

O

object_id() (in module pychemia.db.db) ObjectiveFunction (class in pychemia.evaluator.functional) oct_merge() (in module pychemia.code.octopus.merge) OctopusOccupancies (class in pychemia.code.octopus.merge) OctopusRestart (class in pychemia.code.octopus.merge) OctopusStates (class in pychemia.code.octopus.merge) OctopusStatesFile (class in pychemia.code.octopus.merge)

OctopusWavefunctions (class in pychemia.code.octopus.merge) only_ascii() (in module pychemia.utils.computing) OpenDX (class in pychemia.code.octopus.input) OptimizationTestFunction (class in pychemia.utils.metaheuristics) optimized_grid() (pychemia.crystal.kpoints.KPoints class method) OrbitalDFTU (class in pychemia.population.orbitaldftu) outcar_parser() (pychemia.code.vasp.outcar.VaspOutput method)

P

params2dmatpawu() (in module pychemia.population.orbitaldftu) parse_doscar() (pychemia.code.vasp.doscar.VaspDoscar static method) parse_value() (in module pychemia.code.dftb.dftb) parser() (in module pychemia.code.abinit.parser) ParticleSwarm (class in pychemia.searcher.swarm) (class in pychemia.searcher.swarm2) pass_to_new_generation() (pychemia.searcher.searcher.Searcher method) PBSRunner (class in pychemia.runner.pbs) period() (in module pychemia.utils.periodic) periodic_dimensions (pychemia.crystal.lattice.Lattice attribute) permutator() (pychemia.analysis.changer.StructureChanger method) plot() (pychemia.code.abinit.task.relax.IonRelaxation method) (pychemia.code.abinit.task.static.StaticCalculation method) (pychemia.code.tasks.Task method) (pychemia.code.vasp.task.convergence.ConvergenceCutOffEnergy method) (pychemia.code.vasp.task.convergence.ConvergenceKPointGrid method) (pychemia.code.vasp.task.elastic.ElasticModuli method) (pychemia.code.vasp.task.polarization.Polarization method) (pychemia.code.vasp.task.relax.IonRelaxation method) (pychemia.code.vasp.task.static.StaticCalculation method) (pychemia.code.vasp.task.stregth.IdealStrength method) plot_simple() (in module pychemia.code.abinit.utils) Polarization (class in pychemia.code.vasp.task.polarization) PopulationTest (class in pychemia.population.tests.test_population) positions2reduced() (pychemia.core.structure.Structure method) postprocess() (pychemia.code.vasp.task.polarization.Polarization method) prepare_folder() (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) print_all() (pychemia.code.dftb.dftb.DFTBplus method) print_block() (pychemia.code.dftb.dftb.DFTBplus static method) print_status() (pychemia.searcher.searcher.Searcher method) print_vector() (in module pychemia.analysis.surface) process_scouts() (pychemia.searcher.bee.BeeAlgorithm method) product_of_inertia() (pychemia.core.structure.Structure method) projector() (in module pychemia.utils.mathematics) PropertiesEntry (class in pychemia.db.repo) psp_name() (in module pychemia.code.abinit.utils) pychemia (module) pychemia.analysis (module) pychemia.analysis.analysis (module) pychemia.analysis.changer (module) pychemia.analysis.cluster (module) pychemia.analysis.matching (module) pychemia.analysis.splitting (module) pychemia.analysis.surface (module) pychemia.code (module) pychemia.code.abinit (module) pychemia.code.abinit.abifiles (module) pychemia.code.abinit.abinit (module) pychemia.code.abinit.htmlparser (module) pychemia.code.abinit.input (module) pychemia.code.abinit.output (module) pychemia.code.abinit.parser (module) pychemia.code.abinit.task (module) pychemia.code.abinit.task.relax (module) pychemia.code.abinit.task.static (module) pychemia.code.abinit.tests (module) pychemia.code.abinit.tests.test_abinit (module) pychemia.code.abinit.utils (module) pychemia.code.codes (module) pychemia.code.dftb (module) pychemia.code.dftb.dftb (module) pychemia.code.dftb.task (module) pychemia.code.dftb.task.kpconv (module) pychemia.code.dftb.task.relax (module) pychemia.code.dftb.task.static (module) pychemia.code.fireball (module) pychemia.code.fireball.fireball (module) pychemia.code.fireball.task (module) pychemia.code.lennardjones (module) pychemia.code.lennardjones.lj (module) pychemia.code.octopus (module) pychemia.code.octopus.analysis (module) pychemia.code.octopus.input (module) pychemia.code.octopus.merge (module) pychemia.code.relaxator (module) pychemia.code.tasks (module) pychemia.code.vasp (module) pychemia.code.vasp.doscar (module) pychemia.code.vasp.incar (module) pychemia.code.vasp.kpoints (module) pychemia.code.vasp.outcar (module) pychemia.code.vasp.poscar (module) pychemia.code.vasp.queue (module) pychemia.code.vasp.task (module) pychemia.code.vasp.task.convergence (module) pychemia.code.vasp.task.elastic (module) pychemia.code.vasp.task.polarization (module) pychemia.code.vasp.task.relax (module) pychemia.code.vasp.task.static (module) pychemia.code.vasp.task.stregth (module) pychemia.code.vasp.tests (module)

pychemia.code.vasp.tests.test_vasp (module) pychemia.code.vasp.vasp (module) pychemia.core (module) pychemia.core.composition (module) pychemia.core.delaunay (module) pychemia.core.from_file (module) pychemia.core.structure (module) pychemia.core.tests (module) pychemia.core.tests.test_core (module) pychemia.core.tests.test_doctest (module) pychemia.crystal (module) pychemia.crystal.kpoints (module) pychemia.crystal.lattice (module) pychemia.crystal.samples (module) pychemia.crystal.symmetry (module) pychemia.crystal.tests (module) pychemia.crystal.tests.test_doctest (module) pychemia.crystal.tests.test_kpoints (module) pychemia.crystal.tests.test_symmetry (module) pychemia.db (module) pychemia.db.db (module) pychemia.db.queue (module) pychemia.db.repo (module) pychemia.db.tests (module) pychemia.db.tests.test_queue (module) pychemia.evaluator (module) pychemia.evaluator.cluster (module) pychemia.evaluator.cluster_fireball (module) pychemia.evaluator.direct_evaluator (module) pychemia.evaluator.function (module) pychemia.evaluator.functional (module) pychemia.evaluator.vasp_evaluator (module) pychemia.external (module) pychemia.external.ase (module) pychemia.external.findsym (module) pychemia.external.pymatgen (module) pychemia.external.symmol (module) pychemia.external.symmol.symmol (module) pychemia.io (module) pychemia.io.ascii (module) pychemia.io.cif (module) pychemia.io.xyz (module) pychemia.md (module) pychemia.md.verlet (module) pychemia.population (module) pychemia.population.ljcluster (module) pychemia.population.noncollinearmagmoms (module) pychemia.population.orbitaldftu (module) pychemia.population.realfunction (module) pychemia.population.relaxstructures (module) pychemia.population.tests (module) pychemia.population.tests.test_popu_noncoll (module) pychemia.population.tests.test_population (module) pychemia.runner (module) pychemia.runner.pbs (module) pychemia.runner.runner (module) pychemia.searcher (module) pychemia.searcher.annealing (module) pychemia.searcher.ant (module) pychemia.searcher.bee (module) pychemia.searcher.firefly (module) pychemia.searcher.genetic (module) pychemia.searcher.grey (module) pychemia.searcher.harmony (module) pychemia.searcher.mhm (module) pychemia.searcher.searcher (module) pychemia.searcher.swarm (module) pychemia.searcher.swarm2 (module) pychemia.searcher.tests (module) pychemia.searcher.tests.test_searcher_clusters (module) pychemia.searcher.tests.test_searcher_functions (module) pychemia.searcher.tests.test_searcher_noncollinear (module) pychemia.test (module) pychemia.test.doctest_2to3 (module) pychemia.test.test_00 (module) pychemia.test.test_bin (module) pychemia.test.test_zexample1 (module) pychemia.test.test_zexample2 (module) pychemia.utils (module) pychemia.utils.computing (module) pychemia.utils.constants (module) pychemia.utils.mathematics (module) pychemia.utils.metaheuristics (module) pychemia.utils.periodic (module) pychemia.utils.serializer (module) pychemia.utils.tests (module) pychemia.utils.tests.test_doctest_utils (module) pychemia.utils.tests.test_periodic (module) pychemia.utils.tests.test_serializer (module) pychemia.web (module) PyChemiaDB (class in pychemia.db.db) PyChemiaJsonable (class in pychemia.utils.serializer) PyChemiaQueue (class in pychemia.db.queue)

Q

quality() (pychemia.code.dftb.task.relax.Relaxation method)

R

radius (pychemia.analysis.analysis.StructureAnalysis attribute) random_attaching() (in module pychemia.analysis.surface) random_cell() (pychemia.core.structure.Structure static method) (pychemia.crystal.lattice.Lattice static method) random_change() (pychemia.analysis.changer.StructureChanger method) random_cluster() (pychemia.core.structure.Structure static method) random_deform_cell() (pychemia.analysis.changer.StructureChanger method) random_move_many_atoms() (pychemia.analysis.changer.StructureChanger method) random_move_one_atom() (pychemia.analysis.changer.StructureChanger method) random_permutator() (pychemia.analysis.changer.StructureChanger method) random_population() (pychemia.population.realfunction.RealFunction method) random_structure() (in module pychemia.core.structure) read_detailed_out() (in module pychemia.code.dftb.dftb) read_dftb_stdout() (in module pychemia.code.dftb.dftb) read_eigen() (in module pychemia.code.fireball.fireball) read_file() (in module pychemia.utils.computing) read_final_fireball_relax() (in module pychemia.code.fireball.fireball) read_fireball_in() (in module pychemia.code.fireball.fireball) read_fireball_stdout() (in module pychemia.code.fireball.fireball) read_geometry_bas() (in module pychemia.code.fireball.fireball) read_geometry_gen() (in module pychemia.code.dftb.dftb) read_incar() (in module pychemia.code.vasp.incar) (pychemia.code.vasp.vasp.VaspJob method) read_input() (pychemia.code.dftb.dftb.DFTBplus static method) read_kpoints() (in module pychemia.code.vasp.kpoints) (pychemia.code.vasp.vasp.VaspJob method) read_lvs() (in module pychemia.code.fireball.fireball) read_output_netcdf() (pychemia.code.abinit.output.AbinitOutput static method) read_param() (in module pychemia.code.fireball.fireball) read_poscar() (in module pychemia.code.vasp.poscar) (pychemia.code.vasp.vasp.VaspJob method) read_vasp_stdout() (in module pychemia.code.vasp.outcar) RealFunction (class in pychemia.population.realfunction) rebuild() (pychemia.db.repo.StructureRepository method) reciprocal() (pychemia.crystal.lattice.Lattice method) recover() (pychemia.code.vasp.task.convergence.ConvergenceKPointGrid method) (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) (pychemia.searcher.searcher.Searcher method) reduce_bases() (in module pychemia.core.delaunay) reduced2cartesian() (pychemia.crystal.lattice.Lattice method) reduced2positions() (pychemia.core.structure.Structure method) reduced_displacement() (pychemia.analysis.matching.StructureMatch method) refine() (pychemia.db.repo.StructureRepository method) (pychemia.population.ljcluster.LJCluster method) refine_cell() (pychemia.crystal.symmetry.CrystalSymmetry method) refine_progressive() (pychemia.population.ljcluster.LJCluster method) Relaxation (class in pychemia.code.dftb.task.relax) relaxation_info() (pychemia.code.vasp.outcar.VaspOutput method) relaxation_status() (pychemia.code.relaxator.Relaxator method) Relaxator (class in pychemia.code.relaxator) RelaxPopulation (class in pychemia.evaluator.vasp_evaluator) RelaxStructures (class in pychemia.population.relaxstructures) reload() (pychemia.code.abinit.output.AbinitOutput method) (pychemia.code.vasp.outcar.VaspOutput method) relocate_to_cm() (pychemia.core.structure.Structure method) replace_by_changed() (pychemia.searcher.searcher.Searcher method) replace_by_other() (pychemia.searcher.searcher.Searcher method) replace_by_random() (pychemia.searcher.searcher.Searcher method) replace_failed() (pychemia.db.db.PyChemiaDB method) (pychemia.population.realfunction.RealFunction method) (pychemia.searcher.searcher.Searcher method) report() (pychemia.code.abinit.task.relax.IonRelaxation method) (pychemia.code.abinit.task.static.StaticCalculation method) (pychemia.code.tasks.Task method) (pychemia.code.vasp.task.convergence.ConvergenceCutOffEnergy method) (pychemia.code.vasp.task.convergence.ConvergenceKPointGrid method) (pychemia.code.vasp.task.elastic.ElasticModuli method) (pychemia.code.vasp.task.polarization.Polarization method) (pychemia.code.vasp.task.relax.IonRelaxation method) (pychemia.code.vasp.task.static.StaticCalculation method) (pychemia.code.vasp.task.stregth.IdealStrength method)

report_cover() (in module pychemia.runner.pbs) report_end() (pychemia.code.tasks.Task method) roll_outputs() (pychemia.code.dftb.dftb.DFTBplus method) Rosenbrock (class in pychemia.utils.metaheuristics) rotate_along_indices() (in module pychemia.analysis.surface) rotate_towards_axis() (in module pychemia.utils.mathematics) rotation() (pychemia.core.structure.Structure method) rotation_matrix_around_axis_angle() (in module pychemia.utils.mathematics) rotation_matrix_ndim() (in module pychemia.utils.mathematics) rotation_matrix_numpy() (in module pychemia.utils.mathematics) rotation_matrix_weave() (in module pychemia.utils.mathematics) rotation_move() (in module pychemia.population.ljcluster) rotation_ndim() (in module pychemia.utils.mathematics) rotation_x() (in module pychemia.utils.mathematics) rotation_y() (in module pychemia.utils.mathematics) rotation_z() (in module pychemia.utils.mathematics) round() (pychemia.core.structure.Structure method) round_small() (in module pychemia.utils.mathematics) run() (pychemia.code.abinit.task.relax.IonRelaxation method) (pychemia.code.abinit.task.static.StaticCalculation method) (pychemia.code.codes.Codes method) (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.dftb.task.kpconv.KPointConvergence method) (pychemia.code.dftb.task.relax.Relaxation method) (pychemia.code.dftb.task.static.StaticCalculation method) (pychemia.code.fireball.fireball.FireBall method) (pychemia.code.relaxator.Relaxator method) (pychemia.code.tasks.Task method) (pychemia.code.vasp.task.convergence.ConvergenceCutOffEnergy method) (pychemia.code.vasp.task.convergence.ConvergenceKPointGrid method) (pychemia.code.vasp.task.elastic.ElasticModuli method) (pychemia.code.vasp.task.polarization.Polarization method) (pychemia.code.vasp.task.relax.IonRelaxation method) (pychemia.code.vasp.task.static.StaticCalculation method) (pychemia.code.vasp.task.stregth.IdealStrength method) (pychemia.code.vasp.vasp.VaspAnalyser method) (pychemia.evaluator.Evaluator method) (pychemia.evaluator.direct_evaluator.DirectEvaluator method) (pychemia.evaluator.function.FunctionEvaluator method) (pychemia.evaluator.functional.Evaluator method) (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) (pychemia.external.findsym.FindSym method) (pychemia.md.verlet.Verlet method) (pychemia.runner.runner.Runner method) (pychemia.searcher.searcher.Searcher method) run_multidirs() (pychemia.runner.runner.Runner method) run_multidirs_nonstop() (pychemia.runner.runner.Runner method) run_one() (pychemia.searcher.annealing.SimulatedAnnealing method) (pychemia.searcher.ant.AntColony method) (pychemia.searcher.bee.BeeAlgorithm method) (pychemia.searcher.firefly.FireFly method) (pychemia.searcher.genetic.GeneticAlgorithm method) (pychemia.searcher.grey.GreyWolf method) (pychemia.searcher.harmony.HarmonySearch method) (pychemia.searcher.mhm.MinimaHoppingMethod method) (pychemia.searcher.searcher.Searcher method) (pychemia.searcher.swarm.ParticleSwarm method) (pychemia.searcher.swarm2.ParticleSwarm method) run_status() (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.fireball.fireball.FireBall method) Runner (class in pychemia.runner.runner)

S

save() (in module pychemia.io.ascii) (in module pychemia.io.xyz) (pychemia.code.tasks.Task method) (pychemia.code.vasp.task.polarization.Polarization method) (pychemia.db.repo.PropertiesEntry method) (pychemia.db.repo.StructureEntry method) (pychemia.db.repo.StructureRepository method) (pychemia.population.realfunction.RealFunction method) save_generations() (pychemia.searcher.searcher.Searcher method) save_info() (pychemia.population.realfunction.RealFunction method) (pychemia.searcher.searcher.Searcher method) save_json() (pychemia.code.dftb.task.kpconv.KPointConvergence method) (pychemia.code.dftb.task.static.StaticCalculation method) (pychemia.code.vasp.vasp.VaspJob method) (pychemia.core.structure.Structure method) (pychemia.db.db.PyChemiaDB method) save_to_file() (pychemia.utils.serializer.PyChemiaJsonable method) scale() (pychemia.core.structure.Structure method) (pychemia.crystal.lattice.Lattice method) SchafferN2 (class in pychemia.utils.metaheuristics) SchafferN4 (class in pychemia.utils.metaheuristics) Searcher (class in pychemia.searcher.searcher) searcher() (in module pychemia.searcher.tests.test_searcher_clusters) searcher_name (pychemia.searcher.searcher.Searcher attribute) SearcherTest (class in pychemia.searcher.tests.test_searcher_clusters) (class in pychemia.searcher.tests.test_searcher_functions) (class in pychemia.searcher.tests.test_searcher_noncollinear) SerializerTest (class in pychemia.utils.tests.test_serializer) set_cell() (pychemia.core.structure.Structure method) set_density_for_restart() (pychemia.code.vasp.incar.InputVariables method) set_ecut() (pychemia.code.abinit.abinit.AbinitJob method) set_electron_scf() (pychemia.code.vasp.incar.InputVariables method) set_encut() (pychemia.code.vasp.incar.InputVariables method) set_generation() (pychemia.searcher.searcher.Searcher method) set_grid() (pychemia.crystal.kpoints.KPoints method) set_input() (pychemia.code.abinit.abifiles.AbiFiles method) (pychemia.db.queue.PyChemiaQueue method) set_input_structure() (pychemia.db.queue.PyChemiaQueue method) set_input_variables() (pychemia.code.vasp.vasp.VaspJob method) set_inputs() (pychemia.code.abinit.abinit.AbinitJob method) (pychemia.code.codes.Codes method) (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.fireball.fireball.FireBall method) (pychemia.code.vasp.vasp.VaspJob method) set_ion_relax() (pychemia.code.vasp.incar.InputVariables method) set_ismear() (pychemia.code.vasp.incar.InputVariables method) set_job_settings() (pychemia.db.queue.PyChemiaQueue method) set_kpoints() (pychemia.code.abinit.abinit.AbinitJob method) (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.vasp.vasp.VaspJob method) set_kpoints_list() (pychemia.crystal.kpoints.KPoints method) set_mag_moments() (pychemia.core.structure.Structure method) set_minimal_schema() (pychemia.db.db.PyChemiaDB method) (pychemia.db.queue.PyChemiaQueue method) set_minimum() (pychemia.code.vasp.incar.InputVariables method) set_mit_settings() (pychemia.code.vasp.incar.InputVariables method) set_output_structure() (pychemia.db.queue.PyChemiaQueue method) set_params() (pychemia.code.dftb.task.relax.Relaxation method) (pychemia.searcher.annealing.SimulatedAnnealing method) (pychemia.searcher.ant.AntColony method) (pychemia.searcher.bee.BeeAlgorithm method) (pychemia.searcher.firefly.FireFly method) (pychemia.searcher.genetic.GeneticAlgorithm method) (pychemia.searcher.grey.GreyWolf method) (pychemia.searcher.harmony.HarmonySearch method) (pychemia.searcher.mhm.MinimaHoppingMethod method) (pychemia.searcher.searcher.Searcher method) (pychemia.searcher.swarm.ParticleSwarm method) (pychemia.searcher.swarm2.ParticleSwarm method) set_periodicity() (pychemia.core.structure.Structure method) (pychemia.crystal.lattice.Lattice method)

set_positions() (pychemia.core.structure.Structure method) set_psps() (pychemia.code.abinit.abifiles.AbiFiles method) (pychemia.code.abinit.abinit.AbinitJob method) set_reduced() (pychemia.core.structure.Structure method) set_rough_relaxation() (pychemia.code.vasp.incar.InputVariables method) set_run() (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) set_slater_koster() (pychemia.code.dftb.dftb.DFTBplus method) set_static() (pychemia.code.dftb.dftb.DFTBplus method) set_structure() (pychemia.db.queue.PyChemiaQueue method) set_template() (pychemia.runner.pbs.PBSRunner method) set_value() (pychemia.code.abinit.input.InputVariables method) (pychemia.population.realfunction.RealFunction method) set_walltime() (pychemia.runner.pbs.PBSRunner method) shortest_triple_set() (in module pychemia.utils.mathematics) Si() (in module pychemia.crystal.samples) sieve_atkin() (in module pychemia.utils.mathematics) signature() (pychemia.core.structure.Structure method) SimulatedAnnealing (class in pychemia.searcher.annealing) SiO2() (in module pychemia.crystal.samples) Site (class in pychemia.core.structure) SiteSet (class in pychemia.core.structure) SnO2() (in module pychemia.crystal.samples) sort_axes() (pychemia.core.structure.Structure method) sort_sites() (pychemia.core.structure.Structure method) sort_sites_using_list() (pychemia.core.structure.Structure method) sorted_formula() (pychemia.core.composition.Composition method) Sp_Lt (in module pychemia.utils.constants) species (pychemia.core.composition.Composition attribute) (pychemia.core.structure.Structure attribute) species_encoded() (pychemia.core.composition.Composition method) species_hex() (pychemia.core.composition.Composition method) spglib_cell (pychemia.crystal.symmetry.CrystalSymmetry attribute) spglib_version() (in module pychemia.crystal.symmetry) Sphere (class in pychemia.utils.metaheuristics) spherical_to_cartesian() (in module pychemia.utils.mathematics) split_data() (pychemia.io.cif.CIF method) split_varname() (in module pychemia.code.abinit.utils) SplitMatch (class in pychemia.analysis.splitting) standarize_cell() (pychemia.crystal.symmetry.CrystalSymmetry method) StaticCalculation (class in pychemia.code.abinit.task.static) (class in pychemia.code.dftb.task.static) (class in pychemia.code.vasp.task.static) status() (pychemia.code.tasks.Task method) (pychemia.code.vasp.task.polarization.Polarization method) steepest_descent() (pychemia.code.lennardjones.lj.LennardJones method) stop() (pychemia.evaluator.Evaluator method) (pychemia.evaluator.function.FunctionEvaluator method) (pychemia.evaluator.functional.Evaluator method) str_entry() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) stretch() (pychemia.crystal.lattice.Lattice method) Structure (class in pychemia.core.structure) structure_distances() (pychemia.analysis.analysis.StructureAnalysis method) structure_entry() (pychemia.db.repo.StructureRepository method) structure_from_file() (in module pychemia.core.from_file) StructureAnalysis (class in pychemia.analysis.analysis) StructureChanger (class in pychemia.analysis.changer) StructureEntry (class in pychemia.db.repo) StructureMatch (class in pychemia.analysis.matching) StructureRepository (class in pychemia.db.repo) StyblinskiTang (class in pychemia.utils.metaheuristics) submit() (pychemia.runner.pbs.PBSRunner method) supercell() (pychemia.core.structure.Structure method) symbol() (pychemia.crystal.symmetry.CrystalSymmetry method) symbols (pychemia.core.composition.Composition attribute) symmetrize() (in module pychemia.code.dftb.task.relax) (pychemia.crystal.symmetry.CrystalSymmetry method)

T

Task (class in pychemia.code.tasks) test() (pychemia.utils.tests.test_doctest_utils.MyTestCase method) test_abinit() (in module pychemia.code.abinit.tests.test_abinit) test_abinit2xyz() (in module pychemia.test.test_bin) test_abinit_abifiles() (in module pychemia.code.abinit.tests.test_abinit) test_abinit_input() (in module pychemia.code.abinit.tests.test_abinit) test_abinit_parser() (in module pychemia.code.abinit.tests.test_abinit) test_abinit_utils() (in module pychemia.code.abinit.tests.test_abinit) test_atomicnumber() (in module pychemia.utils.tests.test_periodic) test_bad_outcar() (pychemia.code.vasp.tests.test_vasp.MyTestCase method) test_composition() (in module pychemia.core.tests.test_core) (in module pychemia.core.tests.test_doctest) test_computing() (in module pychemia.utils.tests.test_doctest_utils) test_covalent_radius() (in module pychemia.utils.tests.test_periodic) test_encut_setup() (pychemia.code.vasp.tests.test_vasp.MyTestCase method) test_euclidean() (pychemia.population.tests.test_population.PopulationTest method) test_example1() (in module pychemia.test.test_zexample1) test_example2() (in module pychemia.test.test_zexample2) test_firefly() (pychemia.searcher.tests.test_searcher_clusters.SearcherTest method) (pychemia.searcher.tests.test_searcher_functions.SearcherTest method) (pychemia.searcher.tests.test_searcher_noncollinear.SearcherTest method) test_genetic() (pychemia.searcher.tests.test_searcher_clusters.SearcherTest method) (pychemia.searcher.tests.test_searcher_functions.SearcherTest method) (pychemia.searcher.tests.test_searcher_noncollinear.SearcherTest method) test_good() (in module pychemia.test.test_00) test_harmony() (pychemia.searcher.tests.test_searcher_clusters.SearcherTest method) (pychemia.searcher.tests.test_searcher_functions.SearcherTest method) (pychemia.searcher.tests.test_searcher_noncollinear.SearcherTest method) test_incar() (pychemia.code.vasp.tests.test_vasp.MyTestCase method) test_lattice() (in module pychemia.crystal.tests.test_doctest) test_ljcluster() (pychemia.population.tests.test_population.PopulationTest method) test_mass() (in module pychemia.utils.tests.test_periodic) test_mathematics() (in module pychemia.utils.tests.test_doctest_utils) test_noncoll() (pychemia.population.tests.test_population.PopulationTest method) test_optimized_grid() (pychemia.crystal.tests.test_kpoints.KPointsTest method) (pychemia.crystal.tests.test_symmetry.CrystalSymmetryTest method)

test_outcar() (pychemia.code.vasp.tests.test_vasp.MyTestCase method) test_periodic() (in module pychemia.utils.tests.test_doctest_utils) test_plot_bonds() (in module pychemia.test.test_bin) test_plot_hist() (in module pychemia.test.test_bin) test_popu_noncoll() (in module pychemia.population.tests.test_popu_noncoll) test_poscar() (pychemia.code.vasp.tests.test_vasp.MyTestCase method) test_queue() (in module pychemia.db.tests.test_queue) test_serializer() (pychemia.utils.tests.test_serializer.SerializerTest method) test_structure() (in module pychemia.core.tests.test_core) (in module pychemia.core.tests.test_doctest) test_swarm() (pychemia.searcher.tests.test_searcher_clusters.SearcherTest method) (pychemia.searcher.tests.test_searcher_functions.SearcherTest method) test_symbol() (in module pychemia.utils.tests.test_periodic) test_symmetry() (in module pychemia.crystal.tests.test_doctest) test_utils() (in module pychemia.utils.tests.test_periodic) test_valence() (in module pychemia.utils.tests.test_periodic) test_vaspjob() (pychemia.code.vasp.tests.test_vasp.MyTestCase method) test_xyz2abinit() (in module pychemia.test.test_bin) ThreeHump (class in pychemia.utils.metaheuristics) Time_Sec (in module pychemia.utils.constants) TiO2_anatase() (in module pychemia.crystal.samples) to_dict (pychemia.code.fireball.fireball.FireBall attribute) (pychemia.code.vasp.outcar.VaspOutput attribute) (pychemia.code.vasp.vasp.VaspJob attribute) (pychemia.core.structure.Structure attribute) (pychemia.crystal.kpoints.KPoints attribute) (pychemia.population.ljcluster.LJCluster attribute) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms attribute) (pychemia.population.orbitaldftu.OrbitalDFTU attribute) (pychemia.population.relaxstructures.RelaxStructures attribute) (pychemia.searcher.searcher.Searcher attribute) (pychemia.utils.serializer.PyChemiaJsonable attribute) to_json (pychemia.utils.serializer.PyChemiaJsonable attribute) todict() (pychemia.db.repo.StructureRepository method) trial_division() (in module pychemia.utils.mathematics)

U

unit_vector() (in module pychemia.utils.mathematics) unit_vectors() (in module pychemia.utils.mathematics) unlock() (pychemia.db.db.PyChemiaDB method) unlock_all() (pychemia.evaluator.direct_evaluator.DirectEvaluator method) update() (pychemia.code.vasp.task.relax.IonRelaxation method) (pychemia.code.vasp.vasp.VaspJob method) (pychemia.db.db.PyChemiaDB method) (pychemia.evaluator.vasp_evaluator.RelaxPopulation method)

update_generation() (pychemia.searcher.searcher.Searcher method) update_history() (pychemia.evaluator.vasp_evaluator.RelaxPopulation method) update_lineages() (pychemia.searcher.searcher.Searcher method)

V

valence() (in module pychemia.utils.periodic) valence_electrons() (pychemia.core.structure.Structure method) value() (pychemia.population.ljcluster.LJCluster method) (pychemia.population.noncollinearmagmoms.NonCollinearMagMoms method) (pychemia.population.orbitaldftu.OrbitalDFTU method) (pychemia.population.realfunction.RealFunction method) (pychemia.population.relaxstructures.RelaxStructures method) value_in_sphere() (in module pychemia.code.octopus.analysis) values (pychemia.core.composition.Composition attribute) variables (pychemia.code.vasp.vasp.VaspJob attribute)

VaspAnalyser (class in pychemia.code.vasp.vasp) VaspDoscar (class in pychemia.code.vasp.doscar) VaspJob (class in pychemia.code.vasp.vasp) VaspOutput (class in pychemia.code.vasp.outcar) vector_set_perpendicular() (in module pychemia.utils.mathematics) Verlet (class in pychemia.md.verlet) Version (class in pychemia) view_projections() (pychemia.code.abinit.input.InputVariables method) volume (pychemia.core.structure.Structure attribute) (pychemia.crystal.lattice.Lattice attribute)

W

which() (in module pychemia.test.test_zexample1) (in module pychemia.test.test_zexample2) workdirs (pychemia.evaluator.vasp_evaluator.RelaxPopulation attribute) worker_star() (in module pychemia.core.structure) wrap2_pmhalf() (in module pychemia.utils.mathematics) write() (pychemia.code.abinit.abifiles.AbiFiles method) (pychemia.code.abinit.input.InputVariables method) (pychemia.code.octopus.input.InputVariables method) (pychemia.code.octopus.merge.OctopusOccupancies method) (pychemia.code.octopus.merge.OctopusStates method) (pychemia.code.octopus.merge.OctopusWavefunctions method) (pychemia.code.vasp.incar.InputVariables method) write_abifiles() (pychemia.code.abinit.abinit.AbinitJob method) write_abiinput() (pychemia.code.abinit.abinit.AbinitJob method) write_all() (pychemia.code.abinit.abinit.AbinitJob method) write_basis() (pychemia.code.fireball.fireball.FireBall method) write_change() (pychemia.population.realfunction.RealFunction method) (pychemia.searcher.searcher.Searcher method)

write_cif() (pychemia.external.findsym.FindSym method) write_from_queue() (in module pychemia.code.vasp.queue) write_geometry_bas() (in module pychemia.code.fireball.fireball) write_incar() (in module pychemia.code.vasp.incar) (pychemia.code.vasp.vasp.VaspJob method) write_input() (pychemia.code.dftb.dftb.DFTBplus method) (pychemia.code.fireball.fireball.FireBall method) write_input_files() (pychemia.db.queue.PyChemiaQueue method) write_key() (pychemia.code.abinit.input.InputVariables method) (pychemia.code.vasp.incar.InputVariables method) write_kpoints() (in module pychemia.code.vasp.kpoints) (pychemia.code.fireball.fireball.FireBall method) (pychemia.code.vasp.vasp.VaspJob method) write_lattice() (pychemia.code.fireball.fireball.FireBall method) write_pbs() (pychemia.runner.pbs.PBSRunner method) write_poscar() (in module pychemia.code.vasp.poscar) (pychemia.code.vasp.vasp.VaspJob method) write_potcar() (in module pychemia.code.vasp.poscar) (pychemia.code.vasp.vasp.VaspJob method)

X

xyz2input() (in module pychemia.code.abinit.input)

Z

ZnO() (in module pychemia.crystal.samples)