Index

A

allaq (pyscal.catom.Atom attribute) allq (pyscal.catom.Atom attribute) angular (pyscal.catom.Atom attribute) Atom (class in pyscal.catom)

atoms (pyscal.core.System attribute) avg_angular (pyscal.catom.Atom attribute) avg_disorder (pyscal.catom.Atom attribute) avg_sij (pyscal.catom.Atom attribute) avg_volume (pyscal.catom.Atom attribute)

B

bond_chain_count (pyscal.catom.Atom attribute)

bonds (pyscal.catom.Atom attribute) box (pyscal.core.System attribute)

C

calculate_adaptive_cna() (pyscal.catom.Atom method) 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_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 attribute)

chiparams (pyscal.catom.Atom attribute) cluster (pyscal.catom.Atom attribute) cluster_atoms() (pyscal.core.System method) common_neighbor_bond_count (pyscal.catom.Atom attribute) common_neighbor_bonds (pyscal.catom.Atom attribute) common_neighbor_count (pyscal.catom.Atom attribute) common_neighbors (pyscal.catom.Atom attribute) compare_atomic_env() (in module pyscal.misc) condition (pyscal.catom.Atom attribute) coordination (pyscal.catom.Atom attribute) custom (pyscal.catom.Atom attribute) cutoff (pyscal.catom.Atom attribute)

D

disorder (pyscal.catom.Atom attribute)

E

edge_lengths (pyscal.catom.Atom attribute)

F

face_perimeters (pyscal.catom.Atom attribute) face_vertices (pyscal.catom.Atom attribute) find_clusters() (pyscal.core.System method)

find_largestcluster() (pyscal.core.System method) find_neighbors() (pyscal.core.System method) find_solids() (pyscal.core.System method)

G

get_atom() (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) greedy_edge_selection() (pyscal.core.System method) greedy_vertex_matching() (pyscal.core.System method)

I

id (pyscal.catom.Atom attribute)

L

largest_cluster (pyscal.catom.Atom attribute) lcutlarge (pyscal.catom.Atom attribute)

lcutsmall (pyscal.catom.Atom attribute) loc (pyscal.catom.Atom attribute) local_angles (pyscal.catom.Atom attribute)

M

make_crystal() (in module pyscal.crystal_structures)

mask (pyscal.catom.Atom attribute)

N

neighbor_distance (pyscal.catom.Atom attribute) neighbor_vector (pyscal.catom.Atom attribute) neighbor_weights (pyscal.catom.Atom attribute)

neighbors (pyscal.catom.Atom attribute) next_neighbor_distances (pyscal.catom.Atom attribute) next_neighbors (pyscal.catom.Atom attribute)

P

pos (pyscal.catom.Atom attribute) pyscal.catom (module) pyscal.core (module)

pyscal.crystal_structures (module) pyscal.misc (module) pyscal.traj_process (module)

R

read_ase() (in module pyscal.traj_process) read_inputfile() (pyscal.core.System method) read_lammps_dump() (in module pyscal.traj_process)

read_mdtraj() (in module pyscal.traj_process) read_poscar() (in module pyscal.traj_process) reset_neighbors() (pyscal.core.System method)

S

set_atom() (pyscal.core.System method) set_q() (pyscal.catom.Atom method) sij (pyscal.catom.Atom attribute) solid (pyscal.catom.Atom attribute) split_traj_lammps_dump() (in module pyscal.traj_process)

split_trajectory() (in module pyscal.traj_process) sro (pyscal.catom.Atom attribute) structure (pyscal.catom.Atom attribute) surface (pyscal.catom.Atom attribute) System (class in pyscal.core)

T

test() (in module pyscal.core)

to_file() (pyscal.core.System method) type (pyscal.catom.Atom attribute)

V

vertex_numbers (pyscal.catom.Atom attribute) vertex_vectors (pyscal.catom.Atom attribute)

volume (pyscal.catom.Atom attribute) vorovector (pyscal.catom.Atom attribute)

W

write_poscar() (in module pyscal.traj_process)

write_structure() (in module pyscal.traj_process)