Index

A

add_7T_a (C function) add_7T_s (C function) add_cluster_to_xyz() (in module tcc_python_scripts.post_processing.cluster_movie_maker) add_mem_sp3b (C function) add_mem_sp3c (C function) add_mem_sp4b (C function) add_mem_sp4c (C function) add_mem_sp5b (C function) add_mem_sp5c (C function)

Add_New_Bond (C function) add_new_voronoi_bond (C function) analyse_cluster_dependencies (C function) are_5A_ring_particles_common (C function) are_5A_spindles_common (C function) Are_All_Bonds_Symmetric (C function) are_clusters_distinct (C function) are_spindles_bonded (C function) AtomSnapshot (class in tcc_python_scripts.file_readers.atom)

B

bond_check_12A_extra_particle (C function) Bonds_BondCheck (C function)

box (tcc_python_scripts.file_readers.snapshot.Snapshot attribute) build_bond_network (C function)

C

cell_list_get_particle_1_neighbours (C function) check_6A (C function) Check_6A_rings_bonded (C function) check_7T_type (C function) check_bond_cut_offs (C function) check_extra_particle_bonds (C function) Check_For_Valid_Bond (C function) check_frame_numbers (C function) check_null_pointer (C function) Check_Num_Bonds (C function) check_ring_bonds (C function) check_rings_are_bonded (C function) check_spindles_are_uncommon_and_unbonded (C function) check_unique_cluster (C function) Clust_Write_11E (C function) Clust_Write_12B (C function) Clust_Write_13A (C function) Cluster_Write_10A (C function) Cluster_Write_10B (C function) Cluster_Write_10K (C function) Cluster_Write_10W (C function) Cluster_Write_11A (C function) Cluster_Write_11B (C function) Cluster_Write_11C (C function) Cluster_Write_12D (C function) Cluster_Write_12K (C function) Cluster_Write_13B (C function) Cluster_Write_13K (C function) Cluster_Write_6Z (C function) Cluster_Write_7K (C function) Cluster_Write_8A (C function) Cluster_Write_8B (C function) Cluster_Write_8K (C function) Cluster_Write_9A (C function) Cluster_Write_9B (C function) Cluster_Write_9k (C function) Cluster_Write_BCC9 (C function) Cluster_Write_FCC (C function) Cluster_Write_HCP (C function) Clusters_Get10A (C function) Clusters_Get10B (C function) Clusters_Get10K (C function) Clusters_Get10W (C function)

Clusters_Get11A (C function) Clusters_Get11B (C function) Clusters_Get11C (C function) Clusters_Get11E_12D (C function) Clusters_Get11F_13K (C function) Clusters_Get11W (C function) Clusters_Get12A (C function) Clusters_Get12B_13A (C function) Clusters_Get12D (C function) Clusters_Get12E (C function) Clusters_Get12K (C function) Clusters_Get13B (C function) Clusters_Get13K (C function) Clusters_Get6Z (C function) Clusters_Get7K (C function) Clusters_Get7T (C function) Clusters_Get8A (C function) Clusters_Get8B (C function) Clusters_Get8K (C function) Clusters_Get9A (C function) Clusters_Get9B_10B_11E_12D (C function) Clusters_Get9K (C function) Clusters_GetBCC_9 (C function) Clusters_GetFCC (C function) Clusters_GetHCP (C function) copy() (tcc_python_scripts.file_readers.snapshot.Snapshot method) count_7A_spindle_bonds (C function) count_bonded_ring_particles (C function) count_bonded_ring_particles_11C (C function) count_bonded_ring_particles_11F (C function) count_bonds_to_7A_ring (C function) count_bonds_to_ring (C function) count_cluster_bonds_to_particle (C function) count_common_particles (C function) count_common_spindle_particles (C function) count_extra_particles (C function) count_frame_cluster_population (C function) count_mean_pop_per_frame (C function) count_number_of_clusters (C function) count_particles_bonded_to_common (C function) count_shared_sp5bs (C function) count_spindles_in_ring (C function) count_uncommon_particles (C function)

D

dimensionality (tcc_python_scripts.file_readers.snapshot.Snapshot attribute)

DynamoSnapshot (class in tcc_python_scripts.file_readers.dynamo)

E

enforce_PBCs (C function)

Error (C function) Error_no_free (C function)

F

fill_cell_list (C function) find_12K_cluster (C function) free_cell_list (C function)

free_frame_variables (C function) free_run_variables (C function) free_xyz_info (C function)

G

get_11W_extra_particle (C function) get_12A_extra_particle (C function) get_12K_ring_bonds (C function) get_6A_clusters (C function) get_all_particle_neighbours (C function) get_basic_clusters (C function) get_basic_sp4_rings (C function) get_basic_sp5_rings (C function) get_bonded_6As (C function) get_bonds_between_rings (C function) Get_Bonds_With_Voronoi (C function) get_box_file_offsets (C function) get_box_size (C function) get_coords_from_line (C function) get_distance_components (C function) get_double_from_string (C function) get_first_8A_type (C function)

get_frame() (tcc_python_scripts.post_processing.cluster_movie_maker.RawFileReader method) get_frame_coordinates_from_xyz (C function) Get_Interparticle_Distance (C function) get_long_from_string (C function) get_new_particle (C function) get_NVT_box (C function) get_particle_1_neighbours (C function) get_scalar_cell_index (C function) get_second_8A_type (C function) get_shell_particle_ids (C function) Get_Simple_Bonds (C function) get_sp3_clusters (C function) get_sp4_clusters (C function) get_sp5_clusters (C function) get_third_8A_type (C function) get_unbonded_5A_particles (C function) get_uncommon_5A_ring_particle (C function) get_uncommon_spindle (C function)

I

initialise_frame_variables (C function) initialise_run_variables (C function) initialize_xyz_info (C function) Insertion_Sort_Bond_Lengths (C function) is_12E_unique (C function)

is_particle_bonded (C function) is_particle_bonded_to_7As (C function) is_particle_in_5A_ring (C function) is_particle_in_cluster (C function) is_particle_spindle_of_5A (C function)

L

loop_over_neighbouring_cells (C function)

loop_over_particles_in_cell (C function)

M

main (C function) main() (in module tcc_python_scripts.post_processing.cluster_movie_maker) (in module tcc_python_scripts.post_processing.cluster_ouptut)

make_directory (C function)

N

net_cluster_calculation() (in module tcc_python_scripts.post_processing.net) NonadditiveError

NoSnapshotError num_particles (tcc_python_scripts.file_readers.snapshot.Snapshot attribute)

O

open_file (C function)

open_raw_files() (in module tcc_python_scripts.post_processing.cluster_movie_maker) open_stats_report_file (C function)

P

parse_box_file (C function) parse_xyz_file (C function) particle_coordinates (tcc_python_scripts.file_readers.snapshot.Snapshot attribute)

prepare_output_file() (in module tcc_python_scripts.post_processing.cluster_movie_maker) print_version_number (C function) process_arguments() (in module tcc_python_scripts.post_processing.cluster_movie_maker) process_num_particles() (tcc_python_scripts.post_processing.cluster_movie_maker.XyzFileReader static method)

Q

quickSort (C function)

R

RawFileReader (class in tcc_python_scripts.post_processing.cluster_movie_maker) read() (in module tcc_python_scripts.file_readers.atom) (in module tcc_python_scripts.file_readers.dynamo) (in module tcc_python_scripts.file_readers.xyz) read_clusters_to_analyse (C function) read_ini_file (C function)

read_single() (tcc_python_scripts.file_readers.snapshot.Snapshot class method) read_trajectory() (tcc_python_scripts.file_readers.snapshot.Snapshot class method) Remove_Unbonded_Neighbours (C function) resize_1D_int (C function) resize_2D_int (C function) run() (tcc_python_scripts.tcc.wrapper.TCCWrapper method)

S

set_tcc_executable_directory() (tcc_python_scripts.tcc.wrapper.TCCWrapper method) set_up_cell_list (C function) setup_6A_rings (C function) setup_cluster_lists (C function) Setup_Output_Files (C function) Snapshot (class in tcc_python_scripts.file_readers.snapshot) (class in tcc_python_scripts.post_processing.cluster_movie_maker) SnapshotIncompleteError sort_list_of_lists_of_ints (C function) species (tcc_python_scripts.file_readers.snapshot.Snapshot attribute) Stats_Report (C function)

stats_report_clusters (C function) stats_report_title (C function) Store_sp3a (C function) Store_sp3b (C function) Store_sp3c (C function) Store_sp4a (C function) Store_sp4b (C function) Store_sp4c (C function) Store_sp5a (C function) Store_sp5b (C function) Store_sp5c (C function) stream_safe_open() (in module tcc_python_scripts.file_readers.snapshot)

T

tcc_executable_directory (tcc_python_scripts.tcc.wrapper.TCCWrapper attribute) tcc_executable_path (tcc_python_scripts.tcc.wrapper.TCCWrapper attribute) tcc_python_scripts.file_readers.atom (module) tcc_python_scripts.file_readers.dynamo (module) tcc_python_scripts.file_readers.snapshot (module) tcc_python_scripts.file_readers.xyz (module) tcc_python_scripts.post_processing.cluster_movie_maker (module)

tcc_python_scripts.post_processing.cluster_ouptut (module) tcc_python_scripts.post_processing.net (module) tcc_python_scripts.tcc.structures (module) tcc_python_scripts.tcc.wrapper (module) TCCWrapper (class in tcc_python_scripts.tcc.wrapper) time (tcc_python_scripts.file_readers.snapshot.Snapshot attribute) too_many_bonds (C function) try_read_line_from_file (C function)

W

working_directory (tcc_python_scripts.tcc.wrapper.TCCWrapper attribute) write() (in module tcc_python_scripts.file_readers.xyz) (tcc_python_scripts.file_readers.snapshot.Snapshot method) write_11F (C function) Write_11W (C function) Write_12A (C function) Write_12E (C function) Write_Bonds_File (C function) Write_Cluster (C function)

Write_Cluster_Centers_xyz (C function) Write_Cluster_Compostions (C function) Write_Cluster_XYZ (C function) write_output_files (C function) Write_Pop_Per_Frame (C function) Write_Raw (C function) Write_Raw_Particle_Types (C function) write_snapshot() (in module tcc_python_scripts.file_readers.xyz) write_xyz() (tcc_python_scripts.post_processing.cluster_movie_maker.Snapshot method)

X

XyzFileReader (class in tcc_python_scripts.post_processing.cluster_movie_maker)

XYZSnapshot (class in tcc_python_scripts.file_readers.xyz)

Z

zero_used_array (C function)