Index _ | A | B | C | D | E | F | G | I | L | M | N | P | R | S | T | U | V | W _ __init__() (pyscal.catom.Atom method) (pyscal.core.System method) (pyscal.trajectory.Timeslice method) (pyscal.trajectory.Trajectory method) A add_atoms() (pyscal.core.System method) allaq (pyscal.catom.Atom property) allq (pyscal.catom.Atom property) angular (pyscal.catom.Atom property) Atom (class in pyscal.catom) atoms (pyscal.core.System attribute) (pyscal.core.System property) avg_angular (pyscal.catom.Atom property) avg_disorder (pyscal.catom.Atom property) avg_energy (pyscal.catom.Atom property) avg_entropy (pyscal.catom.Atom property) avg_sij (pyscal.catom.Atom property) avg_volume (pyscal.catom.Atom property) B bonds (pyscal.catom.Atom property) box (pyscal.core.System attribute) (pyscal.core.System property) C calculate_angularcriteria() (pyscal.core.System method) calculate_centrosymmetry() (pyscal.core.System method) calculate_chiparams() (pyscal.core.System method) calculate_cna() (pyscal.core.System method) calculate_disorder() (pyscal.core.System method) calculate_energy() (pyscal.core.System method) calculate_entropy() (pyscal.core.System method) calculate_pmsro() (pyscal.core.System method) calculate_q() (pyscal.core.System method) calculate_rdf() (pyscal.core.System method) calculate_solidneighbors() (pyscal.core.System method) calculate_sro() (pyscal.core.System method) calculate_vorovector() (pyscal.core.System method) centrosymmetry (pyscal.catom.Atom property) chiparams (pyscal.catom.Atom property) cluster (pyscal.catom.Atom property) cluster_atoms() (pyscal.core.System method) cna (pyscal.catom.Atom property) common (pyscal.catom.Atom property) compare_atomic_env() (in module pyscal.misc) condition (pyscal.catom.Atom property) coordination (pyscal.catom.Atom property) custom (pyscal.catom.Atom property) cutoff (pyscal.catom.Atom property) D disorder (pyscal.catom.Atom property) E edge_lengths (pyscal.catom.Atom property) embed_in_cubic_box() (pyscal.core.System method) energy (pyscal.catom.Atom property) entropy (pyscal.catom.Atom property) extract_cubic_box() (pyscal.core.System method) F face_perimeters (pyscal.catom.Atom property) face_vertices (pyscal.catom.Atom property) find_diamond_neighbors() (pyscal.core.System method) find_largestcluster() (pyscal.core.System method) find_neighbors() (pyscal.core.System method) find_solids() (pyscal.core.System method) find_tetrahedral_voids() (in module pyscal.misc) G get_atom() (pyscal.core.System method) get_block() (pyscal.trajectory.Trajectory method) get_concentration() (pyscal.core.System method) get_custom() (pyscal.core.System method) get_distance() (pyscal.core.System method) get_q() (pyscal.catom.Atom method) get_qlm() (pyscal.catom.Atom method) get_qvals() (pyscal.core.System method) ghost (pyscal.catom.Atom property) I id (pyscal.catom.Atom property) identify_diamond() (pyscal.core.System method) iter() (pyscal.trajectory.Trajectory method) iter_atoms() (pyscal.core.System method) L largest_cluster (pyscal.catom.Atom property) load() (pyscal.trajectory.Trajectory method) loc (pyscal.catom.Atom property) local_angles (pyscal.catom.Atom property) M make_crystal() (in module pyscal.crystal_structures) mask (pyscal.catom.Atom property) module pyscal.catom pyscal.core pyscal.crystal_structures pyscal.misc pyscal.traj_process pyscal.trajectory N neighbor_distance (pyscal.catom.Atom property) neighbor_vector (pyscal.catom.Atom property) neighbor_weights (pyscal.catom.Atom property) neighbors (pyscal.catom.Atom property) next_neighbor_distances (pyscal.catom.Atom property) next_neighbors (pyscal.catom.Atom property) P pos (pyscal.catom.Atom property) pyscal.catom module pyscal.core module pyscal.crystal_structures module pyscal.misc module pyscal.traj_process module pyscal.trajectory module R read_file() (in module pyscal.traj_process) read_inputfile() (pyscal.core.System method) remap_atoms() (pyscal.core.System method) repeat() (pyscal.core.System method) reset_neighbors() (pyscal.core.System method) S set_atom() (pyscal.core.System method) set_atom_cutoff() (pyscal.core.System method) set_q() (pyscal.catom.Atom method) show() (pyscal.core.System method) sij (pyscal.catom.Atom property) solid (pyscal.catom.Atom property) split_trajectory() (in module pyscal.traj_process) sro (pyscal.catom.Atom property) structure (pyscal.catom.Atom property) surface (pyscal.catom.Atom property) System (class in pyscal.core) T test() (in module pyscal.core) Timeslice (class in pyscal.trajectory) to_ase() (pyscal.core.System method) (pyscal.trajectory.Timeslice method) to_dict() (pyscal.trajectory.Timeslice method) to_file() (pyscal.core.System method) (pyscal.trajectory.Timeslice method) to_system() (pyscal.trajectory.Timeslice method) Trajectory (class in pyscal.trajectory) type (pyscal.catom.Atom property) U unload() (pyscal.trajectory.Trajectory method) V vertex_numbers (pyscal.catom.Atom property) vertex_positions (pyscal.catom.Atom property) vertex_vectors (pyscal.catom.Atom property) volume (pyscal.catom.Atom property) vorovector (pyscal.catom.Atom property) W write_file() (in module pyscal.traj_process)