CatKit
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CatKit
CatGen
CatHub
CatFlow
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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W
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X
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Y
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Z
A
add_adsorbate() (catkit.gen.adsorption.Builder method)
(in module catkit.build)
add_adsorbates() (catkit.gen.adsorption.Builder method)
add_atoms() (in module catkit.hub.tools)
add_entry() (catkit.db.Connect method)
adj (catkit.gratoms.Gratoms attribute)
adsorption_sites() (catkit.gen.surface.SlabGenerator method)
AdsorptionSites (class in catkit.gen.adsorption)
align_crystal() (catkit.gen.surface.SlabGenerator method)
array_to_list() (in module catkit.flow.fwio)
atom (catkit.db.Atom_Result attribute)
(catkit.db.Element attribute)
Atom (class in catkit.db)
atom_result (catkit.db.Atom attribute)
(catkit.db.Calculator attribute)
Atom_Result (class in catkit.db)
atoms (catkit.db.Structure attribute)
atoms_id (catkit.db.Atom_Result attribute)
atoms_to_encode() (in module catkit.flow.fwio)
attach_results() (in module catkit.flow.qeio)
autocorrelation() (in module catkit.pawprint.operations)
B
bin_hydrogen() (in module catkit.gen.molecules)
bonding_convolution() (in module catkit.pawprint.operations)
Builder (class in catkit.gen.adsorption)
bulk() (in module catkit.build)
C
calcualtor_id (catkit.db.Structure_Result attribute)
calculator (catkit.db.Atom_Result attribute)
(catkit.db.Entry attribute)
(catkit.db.Structure_Result attribute)
Calculator (class in catkit.db)
calculator_id (catkit.db.Atom_Result attribute)
(catkit.db.Entry attribute)
CathubPostgreSQL (class in catkit.hub.postgresql)
CathubSQLite (class in catkit.hub.cathubsqlite)
catkit.build (module)
catkit.db (module)
catkit.enumeration (module)
catkit.flow (module)
catkit.flow.fwespresso (module)
catkit.flow.fwio (module)
catkit.flow.hpcio (module)
catkit.flow.qeio (module)
catkit.gen (module)
catkit.gen.adsorption (module)
catkit.gen.analysis (module)
catkit.gen.analysis.classifier (module)
catkit.gen.analysis.matching (module)
catkit.gen.analysis.reconfiguration (module)
catkit.gen.molecules (module)
catkit.gen.pathways (module)
catkit.gen.route (module)
catkit.gen.surface (module)
catkit.gen.utils (module)
catkit.gratoms (module)
catkit.hub (module)
catkit.hub.ase_connect (module)
catkit.hub.ase_tools (module)
catkit.hub.ase_tools.gas_phase_references (module)
catkit.hub.cathubsqlite (module)
catkit.hub.convert_traj (module)
catkit.hub.create_user (module)
catkit.hub.db2server (module)
catkit.hub.folder2db (module)
catkit.hub.folder_check (module)
catkit.hub.folderreader (module)
catkit.hub.maintain_server (module)
catkit.hub.organize (module)
catkit.hub.postgresql (module)
catkit.hub.psql_server_connect (module)
catkit.hub.query (module)
catkit.hub.tools (module)
catkit.learn (module)
catkit.pawprint (module)
catkit.pawprint.generator (module)
catkit.pawprint.operations (module)
cd() (in module catkit.flow.qeio)
charge (catkit.db.Atom attribute)
check() (catkit.hub.cathubsqlite.CathubSQLite method)
(catkit.hub.postgresql.CathubPostgreSQL method)
check_ase_ids() (in module catkit.hub.cathubsqlite)
check_in_ase() (in module catkit.hub.ase_tools)
check_publication() (catkit.hub.cathubsqlite.CathubSQLite method)
check_publication_structure() (catkit.hub.cathubsqlite.CathubSQLite method)
check_reaction() (in module catkit.hub.tools)
check_reaction_on_surface() (catkit.hub.cathubsqlite.CathubSQLite method)
check_traj() (in module catkit.hub.ase_tools)
Classifier (class in catkit.gen.analysis)
(class in catkit.gen.analysis.classifier)
clear_prefactor() (in module catkit.hub.ase_tools)
clear_state() (in module catkit.hub.ase_tools)
collect_structures() (in module catkit.hub.organize)
Connect (class in catkit.db)
connectivity (catkit.gratoms.Gratoms attribute)
connectivity_to_edges() (in module catkit.gen.utils)
construct_reference_system() (in module catkit.hub.ase_tools.gas_phase_references)
convert() (in module catkit.hub.query)
convert_miller_index() (in module catkit.gen.surface)
copy() (catkit.gratoms.Gratoms method)
covalent_radii (catkit.db.Element attribute)
create_folders() (in module catkit.hub.organize)
create_table() (catkit.db.FingerprintDB method)
(catkit.gen.pathways.ReactionNetwork method)
create_user() (catkit.hub.postgresql.CathubPostgreSQL method)
D
debug_assert() (in module catkit.hub.ase_tools)
Defaults (class in catkit.gen)
degree (catkit.gratoms.Gratoms attribute)
delete() (catkit.hub.postgresql.CathubPostgreSQL method)
delete_lost_systems() (catkit.hub.maintain_server.MaintainPostgres method)
E
edges (catkit.gratoms.Gratoms attribute)
element (catkit.db.Atom attribute)
Element (class in catkit.db)
element_id (catkit.db.Atom attribute)
encode_to_atoms() (in module catkit.flow.fwio)
energy (catkit.db.Entry attribute)
(catkit.db.Structure_Result attribute)
energy_cutoff (catkit.db.Calculator attribute)
entry (catkit.db.Calculator attribute)
(catkit.db.Structure attribute)
Entry (class in catkit.db)
entry_id (catkit.db.Trajectories attribute)
ex_sites() (catkit.gen.adsorption.Builder method)
execute_graphQL() (in module catkit.hub.query)
expand_cell() (in module catkit.gen.utils)
ext_gcd() (in module catkit.gen.utils)
extract_atoms() (in module catkit.hub.tools)
F
fill_reaction_system() (catkit.hub.maintain_server.MaintainPostgres method)
fingerprint_entry() (catkit.db.FingerprintDB method)
FingerprintDB (class in catkit.db)
Fingerprinter (class in catkit.pawprint)
(class in catkit.pawprint.generator)
fmax (catkit.db.Entry attribute)
FolderReader (class in catkit.hub.folderreader)
fuzzy_match() (in module catkit.hub.organize)
G
generate_indices() (in module catkit.gen.surface)
geometry_hash() (in module catkit.flow.qeio)
get_adsorption_edges() (catkit.gen.adsorption.AdsorptionSites method)
get_adsorption_sites() (in module catkit.gen.adsorption)
get_adsorption_vectors() (catkit.gen.adsorption.AdsorptionSites method)
get_affine_operations() (in module catkit.gen.utils)
get_ase_db() (in module catkit.hub.query)
get_atomic_numbers() (in module catkit.gen.utils)
(in module catkit.hub.ase_tools)
get_atomic_stoichiometry() (in module catkit.hub.ase_tools.gas_phase_references)
get_atoms() (in module catkit.hub.ase_tools)
get_atoms_by_id() (in module catkit.hub.query)
get_atomsrow_by_id() (in module catkit.hub.query)
get_bases() (in module catkit.hub.tools)
get_bulk_composition() (in module catkit.hub.ase_tools)
get_catbase() (in module catkit.hub.tools)
get_chemical_formula() (in module catkit.hub.ase_tools)
(in module catkit.hub.organize)
get_chemical_tags() (catkit.gratoms.Gratoms method)
get_connectivity() (catkit.gen.adsorption.AdsorptionSites method)
(in module catkit.pawprint.generator)
get_coordinates() (catkit.gen.adsorption.AdsorptionSites method)
get_cutoff_neighbors() (in module catkit.gen.utils)
get_degenerate_indices() (in module catkit.gen.surface)
get_energies() (in module catkit.hub.ase_tools)
get_energy() (in module catkit.hub.ase_tools)
get_energy_diff() (in module catkit.hub.ase_tools)
get_fingerprints() (catkit.db.FingerprintDB method)
get_formula_from_numbers() (in module catkit.hub.ase_tools)
get_fp() (catkit.pawprint.Fingerprinter method)
(catkit.pawprint.generator.Fingerprinter method)
get_heppel_sellers() (in module catkit.gen.route)
get_key_value_list() (in module catkit.hub.cathubsqlite)
get_key_value_str() (in module catkit.hub.cathubsqlite)
(in module catkit.hub.postgresql)
get_last_id() (catkit.hub.cathubsqlite.CathubSQLite method)
get_layers() (in module catkit.hub.ase_tools)
get_n_layers() (in module catkit.hub.ase_tools)
get_neb() (in module catkit.flow.fwespresso)
get_neighbor_symbols() (catkit.gratoms.Gratoms method)
get_nnodes() (in module catkit.flow.hpcio)
get_number_of_atoms() (in module catkit.hub.ase_tools)
get_numbers_from_formula() (in module catkit.hub.ase_tools)
get_parameters() (catkit.db.FingerprintDB method)
get_pbc() (in module catkit.hub.ase_tools)
get_pdos() (in module catkit.flow.fwespresso)
get_periodic_sites() (catkit.gen.adsorption.AdsorptionSites method)
get_point_group() (in module catkit.gen.utils)
get_potential_energy() (in module catkit.flow.fwespresso)
get_publications() (in module catkit.hub.query)
get_reaction_atoms() (in module catkit.hub.ase_tools)
get_reaction_energy() (in module catkit.hub.ase_tools)
get_reaction_from_folder() (in module catkit.hub.ase_tools)
get_reaction_routes() (in module catkit.gen.route)
get_reactions() (in module catkit.hub.query)
get_reciprocal_vectors() (in module catkit.gen.utils)
get_reference() (in module catkit.hub.ase_tools)
get_reference_energies() (in module catkit.gen.utils)
get_relaxed_calculation() (in module catkit.flow.fwespresso)
get_response_reactions() (in module catkit.gen.route)
get_server() (in module catkit.flow.hpcio)
get_slab() (catkit.gen.surface.SlabGenerator method)
get_slab_basis() (catkit.gen.surface.SlabGenerator method)
get_spglib_cell() (in module catkit.gen.utils)
get_state() (in module catkit.hub.ase_tools)
get_stoichiometry_factors() (in module catkit.hub.ase_tools.gas_phase_references)
get_surface_atoms() (catkit.gratoms.Gratoms method)
get_surface_composition() (in module catkit.hub.ase_tools)
get_symmetric_sites() (catkit.gen.adsorption.AdsorptionSites method)
get_symmetry() (in module catkit.gen.utils)
get_topologies() (in module catkit.gen.molecules)
get_topology() (catkit.gen.adsorption.AdsorptionSites method)
get_total_potential() (in module catkit.flow.fwespresso)
get_traj_str() (in module catkit.hub.ase_tools)
get_unique_coordinates() (in module catkit.gen.utils)
get_unique_indices() (in module catkit.gen.surface)
get_unique_terminations() (catkit.gen.surface.SlabGenerator method)
get_unique_xy() (in module catkit.gen.utils)
get_unsaturated_nodes() (catkit.gratoms.Gratoms method)
get_value_strlist() (in module catkit.hub.cathubsqlite)
get_voronoi_neighbors() (in module catkit.gen.utils)
graph (catkit.gratoms.Gratoms attribute)
graphql_query() (in module catkit.hub.query)
Gratoms (class in catkit.gratoms)
H
hydrogenate() (in module catkit.gen.molecules)
I
id (catkit.db.Atom attribute)
(catkit.db.Atom_Result attribute)
(catkit.db.Calculator attribute)
(catkit.db.Element attribute)
(catkit.db.Entry attribute)
(catkit.db.Structure attribute)
(catkit.db.Structure_Result attribute)
(catkit.db.Trajectories attribute)
id_adsorbate_atoms() (catkit.gen.analysis.Classifier method)
(catkit.gen.analysis.classifier.Classifier method)
id_adsorbates() (catkit.gen.analysis.Classifier method)
(catkit.gen.analysis.classifier.Classifier method)
id_reconstruction() (in module catkit.gen.analysis.reconfiguration)
id_slab_atoms() (catkit.gen.analysis.Classifier method)
(catkit.gen.analysis.classifier.Classifier method)
id_surface_atoms() (catkit.gen.analysis.Classifier method)
(catkit.gen.analysis.classifier.Classifier method)
image_entry() (catkit.db.FingerprintDB method)
is_isomorph() (catkit.gratoms.Gratoms method)
isomorphic_molecules() (in module catkit.gen.utils)
L
list_gcd() (in module catkit.gen.utils)
load_3d_structures() (catkit.gen.pathways.ReactionNetwork method)
load_molecules() (catkit.gen.pathways.ReactionNetwork method)
load_pathways() (catkit.gen.pathways.ReactionNetwork method)
log_to_atoms() (in module catkit.flow.qeio)
M
magmom (catkit.db.Atom attribute)
main() (in module catkit.hub.ase_connect)
(in module catkit.hub.convert_traj)
(in module catkit.hub.create_user)
(in module catkit.hub.db2server)
(in module catkit.hub.folder2db)
(in module catkit.hub.folder_check)
(in module catkit.hub.organize)
(in module catkit.hub.psql_server_connect)
MaintainPostgres (class in catkit.hub.maintain_server)
make_symmetric() (catkit.gen.surface.SlabGenerator method)
map_column_names() (in module catkit.hub.query)
mass (catkit.db.Element attribute)
matching_coordinates() (in module catkit.gen.utils)
matching_sites() (in module catkit.gen.utils)
molecule() (in module catkit.build)
molecule_search() (catkit.gen.pathways.ReactionNetwork method)
molecules2symbols() (in module catkit.hub.ase_tools.gas_phase_references)
N
name (catkit.db.Calculator attribute)
natoms (catkit.db.Entry attribute)
nodes (catkit.gratoms.Gratoms attribute)
O
online_learning() (in module catkit.learn)
optimizer() (in module catkit.learn)
P
parameter_entry() (catkit.db.FingerprintDB method)
parameters (catkit.db.Calculator attribute)
parse_slice() (in module catkit.gen.utils)
path_search() (catkit.gen.pathways.ReactionNetwork method)
pbc (catkit.db.Structure attribute)
periodic_convolution() (in module catkit.pawprint.operations)
plane_normal() (in module catkit.gen.utils)
plot() (catkit.gen.adsorption.AdsorptionSites method)
plot_reaction_network() (catkit.gen.pathways.ReactionNetwork method)
publication_status() (catkit.hub.postgresql.CathubPostgreSQL method)
Q
query() (in module catkit.hub.query)
R
raw_properties() (in module catkit.pawprint.operations)
reactant_indices() (in module catkit.gen.analysis.matching)
ReactionNetwork (class in catkit.gen.pathways)
read() (catkit.hub.cathubsqlite.CathubSQLite method)
(catkit.hub.folderreader.FolderReader method)
(catkit.hub.postgresql.CathubPostgreSQL method)
read_ase() (in module catkit.hub.ase_tools)
read_bulk() (catkit.hub.folderreader.FolderReader method)
read_energies() (catkit.hub.folderreader.FolderReader method)
read_gas() (catkit.hub.folderreader.FolderReader method)
read_name_from_folder() (in module catkit.hub.folderreader)
read_pub() (catkit.hub.folderreader.FolderReader method)
read_reaction() (catkit.hub.folderreader.FolderReader method)
read_slab() (catkit.hub.folderreader.FolderReader method)
remove_user() (catkit.hub.postgresql.CathubPostgreSQL method)
running_mean() (in module catkit.gen.utils)
S
save_3d_structure() (catkit.gen.pathways.ReactionNetwork method)
save_molecules() (catkit.gen.pathways.ReactionNetwork method)
save_pathways() (catkit.gen.pathways.ReactionNetwork method)
search_keys (catkit.db.Entry attribute)
set_size() (catkit.gen.surface.SlabGenerator method)
set_surface_atoms() (catkit.gratoms.Gratoms method)
slab_indices() (in module catkit.gen.analysis.matching)
SlabGenerator (class in catkit.gen.surface)
smax (catkit.db.Entry attribute)
status() (catkit.hub.postgresql.CathubPostgreSQL method)
structure (catkit.db.Atom attribute)
(catkit.db.Entry attribute)
(catkit.db.Structure_Result attribute)
Structure (class in catkit.db)
structure_id (catkit.db.Atom attribute)
(catkit.db.Entry attribute)
(catkit.db.Structure_Result attribute)
(catkit.db.Trajectories attribute)
structure_result (catkit.db.Calculator attribute)
(catkit.db.Structure attribute)
Structure_Result (class in catkit.db)
surface() (in module catkit.build)
surfaces() (in module catkit.enumeration)
symbol (catkit.db.Element attribute)
symbols() (in module catkit.hub.organize)
T
tag_atoms() (in module catkit.hub.ase_tools)
to_gratoms() (in module catkit.gen.utils)
Trajectories (class in catkit.db)
trajectory (catkit.db.Entry attribute)
transfer() (catkit.hub.postgresql.CathubPostgreSQL method)
transform_ab() (in module catkit.gen.surface)
trilaterate() (in module catkit.gen.utils)
U
update() (catkit.hub.cathubsqlite.CathubSQLite method)
(catkit.hub.postgresql.CathubPostgreSQL method)
update_ase() (in module catkit.hub.ase_tools)
update_publication() (catkit.hub.postgresql.CathubPostgreSQL method)
W
write() (catkit.hub.cathubsqlite.CathubSQLite method)
(catkit.hub.folderreader.FolderReader method)
(catkit.hub.postgresql.CathubPostgreSQL method)
write_ase() (in module catkit.hub.ase_tools)
write_publication() (catkit.hub.cathubsqlite.CathubSQLite method)
(catkit.hub.folderreader.FolderReader method)
(catkit.hub.postgresql.CathubPostgreSQL method)
write_to_db() (in module catkit.flow.qeio)
X
x1_cell (catkit.db.Structure attribute)
x2_cell (catkit.db.Structure attribute)
x3_cell (catkit.db.Structure attribute)
x_coordinate (catkit.db.Atom attribute)
x_fixed (catkit.db.Atom attribute)
x_force (catkit.db.Atom_Result attribute)
x_kpoints (catkit.db.Calculator attribute)
xc (catkit.db.Calculator attribute)
xx_stress (catkit.db.Structure_Result attribute)
xy_stress (catkit.db.Structure_Result attribute)
xz_stress (catkit.db.Structure_Result attribute)
Y
y1_cell (catkit.db.Structure attribute)
y2_cell (catkit.db.Structure attribute)
y3_cell (catkit.db.Structure attribute)
y_coordinate (catkit.db.Atom attribute)
y_fixed (catkit.db.Atom attribute)
y_force (catkit.db.Atom_Result attribute)
y_kpoints (catkit.db.Calculator attribute)
yy_stress (catkit.db.Structure_Result attribute)
yz_stress (catkit.db.Structure_Result attribute)
Z
z1_cell (catkit.db.Structure attribute)
z2_cell (catkit.db.Structure attribute)
z3_cell (catkit.db.Structure attribute)
z_coordinate (catkit.db.Atom attribute)
z_fixed (catkit.db.Atom attribute)
z_force (catkit.db.Atom_Result attribute)
z_kpoints (catkit.db.Calculator attribute)
zz_stress (catkit.db.Structure_Result attribute)
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