Index

A

ABS_Species (class in HTMACat.model.Species) add_adsorbate() (HTMACat.catkit.gen.adsorption.Builder method) add_adsorbates() (HTMACat.catkit.gen.adsorption.Builder method) add_sites() (HTMACat.model.Ads.Adsorption method) add_species() (HTMACat.model.Ads.Adsorption method) adj (HTMACat.catkit.Gratoms property) (HTMACat.catkit.gratoms.Gratoms property)

ads() (in module HTMACat.command) ads_from_input() (in module HTMACat.model.Ads) Adsorption (class in HTMACat.model.Ads) adsorption_sites() (HTMACat.catkit.gen.surface.SlabGenerator method) AdsorptionSites (class in HTMACat.catkit.gen.adsorption) align_crystal() (HTMACat.catkit.gen.surface.SlabGenerator method) atoms (HTMACat.model.Species.File_Species property)

B

Builder (class in HTMACat.catkit.gen.adsorption)

Bulk (class in HTMACat.model.Substrate) bulk() (in module HTMACat.catkit.build)

C

cal_adE_coad() (in module HTMACat.Extract_info) (in module HTMACat.post.cal_adsE) cal_Eads() (in module HTMACat.Extract_info) (in module HTMACat.post.cal_adsE) cal_Erad() (in module HTMACat.Extract_info) (in module HTMACat.post.cal_adsE) cal_Erad_atom() (in module HTMACat.Extract_info) (in module HTMACat.post.cal_adsE) cal_Eslab() (in module HTMACat.Extract_info) (in module HTMACat.post.cal_adsE) calE_neb() (in module HTMACat.NEB.post_neb) Coadsorption (class in HTMACat.model.Ads) complete() (in module HTMACat.command) connectivity (HTMACat.catkit.Gratoms property) (HTMACat.catkit.gratoms.Gratoms property) connectivity_to_edges() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.graph) construct() (HTMACat.model.Ads.Adsorption method) (HTMACat.model.Ads.Coadsorption method) (HTMACat.model.Structure.Structure method) (HTMACat.model.Substrate.Bulk method) (HTMACat.model.Substrate.FileSlab method) (HTMACat.model.Substrate.Slab method)

Construct_1stLayer_slab() (HTMACat.model.Substrate.Slab method) Construct_adsorption_yaml() (in module HTMACat.model.Construct_adsorption_yaml) Construct_coadsorption_11() (HTMACat.model.Ads.Coadsorption method) Construct_coadsorption_12() (HTMACat.model.Ads.Coadsorption method) Construct_coadsorption_22() (HTMACat.model.Ads.Coadsorption method) Construct_des_module() (in module HTMACat.descriptor.Construct_descriptor_surface) (in module HTMACat.descriptor.Construct_descriptor_surface_single) Construct_des_module_2() (in module HTMACat.descriptor.Construct_descriptor_surface_single) Construct_descriptor() (in module HTMACat.descriptor.Construct_descriptor) (in module HTMACat.descriptor.Construct_descriptor_surface) (in module HTMACat.descriptor.Construct_descriptor_surface_single) Construct_descriptor_coad() (in module HTMACat.descriptor.Construct_descriptor_coad) Construct_descriptor_info() (in module HTMACat.Extract_info) Construct_descriptor_info_E() (in module HTMACat.descriptor.Construct_descriptor_surface_single) Construct_doped_slab() (HTMACat.model.Substrate.Slab method) Construct_double_adsorption() (HTMACat.model.Ads.Adsorption method) Construct_neb() (in module HTMACat.NEB.Construct_neb) Construct_single_adsorption() (HTMACat.model.Ads.Adsorption method) Construct_slab() (HTMACat.model.Substrate.Slab method) convert_miller_index() (in module HTMACat.catkit.gen.surface) copy() (HTMACat.catkit.Gratoms method) (HTMACat.catkit.gratoms.Gratoms method) crn() (in module HTMACat.command) crngen() (in module HTMACat.command)

D

degree (HTMACat.catkit.Gratoms property) (HTMACat.catkit.gratoms.Gratoms property) dict2object() (in module HTMACat.IO)

Dismove() (in module HTMACat.NEB.Dismove) distinguish_atom_binding() (in module HTMACat.Extract_info) dop_bulk() (HTMACat.model.Substrate.Bulk method) dope_slab() (HTMACat.model.Substrate.Slab method)

E

edges (HTMACat.catkit.Gratoms property) (HTMACat.catkit.gratoms.Gratoms property) edges_list (HTMACat.model.Species.File_Species property) ex_sites() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) expand_cell() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.coordinates) ext_gcd() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utilities)

Extract_adsE() (in module HTMACat.Extract_info) Extract_atomic_info() (in module HTMACat.Extract_info) Extract_energy() (in module HTMACat.Extract_info) Extract_energy_single() (in module HTMACat.Extract_info) Extract_reaction() (in module HTMACat.Extract_info) Extract_slab_info_1() (in module HTMACat.Extract_info) Extract_slab_info_2() (in module HTMACat.Extract_info)

F

File_Species (class in HTMACat.model.Species) FileSlab (class in HTMACat.model.Substrate) find_surface_atoms() (HTMACat.model.Substrate.FileSlab method)

from_input() (HTMACat.model.Ads.Adsorption class method) (HTMACat.model.Ads.Coadsorption class method) (HTMACat.model.Species.ABS_Species class method) from_input_dict() (HTMACat.model.Species.ABS_Species class method)

G

generate_indices() (in module HTMACat.catkit.gen.surface) generate_unique_filename() (in module HTMACat.IO) get_ads_dict() (in module HTMACat.IO) get_adsorbate_info() (in module HTMACat.descriptor.Construct_descriptor_NEB) get_adsorption_edges() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) get_adsorption_energy_stable() (in module HTMACat.Extract_info) get_adsorption_sites() (in module HTMACat.catkit.gen.adsorption) get_adsorption_vectors() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) get_adspecie_dir() (in module HTMACat.post.Extract_cal_fre) get_atom_neigh() (in module HTMACat.Extract_info) get_atomic_numbers() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utilities) get_basis_vectors() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.vectors) get_binding_adatom() (in module HTMACat.Extract_info) get_chemical_tags() (HTMACat.catkit.Gratoms method) (HTMACat.catkit.gratoms.Gratoms method) get_connectivity() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) get_coordinates() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) get_cutoff_neighbors() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.connectivity) get_degenerate_indices() (in module HTMACat.catkit.gen.surface) get_dis_inter() (HTMACat.model.Substrate.FileSlab method) (HTMACat.model.Substrate.Slab method) get_distance_adatoms() (in module HTMACat.Extract_info) get_dop_element() (HTMACat.model.Substrate.Bulk method) get_ele_dop() (HTMACat.model.Substrate.Bulk method) get_facet() (HTMACat.model.Substrate.Slab method) get_file_name() (in module HTMACat.descriptor.Construct_descriptor_NEB) (in module HTMACat.Extract_info) (in module HTMACat.post.Extract_cal_fre) get_formular() (HTMACat.model.Species.ABS_Species method) get_integer_enumeration() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.coordinates) get_lattice_name() (HTMACat.catkit.gen.symmetry.Symmetry method) get_layers() (HTMACat.model.Substrate.Slab method) get_main_element() (HTMACat.model.Substrate.Bulk method) get_miller_index() (HTMACat.model.Substrate.Slab method) get_min_distance_group() (in module HTMACat.Extract_info) get_modified_spin_symbols() (in module HTMACat.catkit.gen.symmetry) get_molecule() (HTMACat.model.Species.ABS_Species method) (HTMACat.model.Species.File_Species method) (HTMACat.model.Species.Sim_Species method) (HTMACat.model.Species.Sml_Species method) get_natom_dop() (HTMACat.model.Substrate.Bulk method)

get_neighbor_symbols() (HTMACat.catkit.Gratoms method) (HTMACat.catkit.gratoms.Gratoms method) get_new_dict() (in module HTMACat.Base_tools) get_periodic_sites() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) get_pointgroup() (HTMACat.catkit.gen.symmetry.Symmetry method) get_potcar() (in module HTMACat.Extract_info) get_reaction_info() (in module HTMACat.descriptor.Construct_descriptor_NEB) get_reciprocal_vectors() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.vectors) get_reference_energies() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utilities) get_site() (in module HTMACat.Extract_info) get_site_info() (in module HTMACat.descriptor.Construct_descriptor_NEB) get_site_stable() (in module HTMACat.Extract_info) get_site_stable_energy() (in module HTMACat.Extract_info) get_sites() (HTMACat.model.Ads.Adsorption method) get_slab() (HTMACat.catkit.gen.surface.SlabGenerator method) get_slab_basis() (HTMACat.catkit.gen.surface.SlabGenerator method) get_species_dict() (in module HTMACat.IO) get_standardized_cell() (in module HTMACat.catkit.gen.symmetry) get_substrate_dict() (in module HTMACat.IO) get_supercell() (HTMACat.model.Substrate.Bulk method) get_surface_atoms() (HTMACat.catkit.Gratoms method) (HTMACat.catkit.gratoms.Gratoms method) get_surface_info() (in module HTMACat.descriptor.Construct_descriptor_NEB) get_symmetric_sites() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) get_symmetry_operations() (HTMACat.catkit.gen.symmetry.Symmetry method) get_symmetry_surfatoms() (in module HTMACat.Extract_info) get_templator() (in module HTMACat.IO) get_topology() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) get_unique_coordinates() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.coordinates) get_unique_indices() (in module HTMACat.catkit.gen.surface) get_unique_terminations() (HTMACat.catkit.gen.surface.SlabGenerator method) get_unique_xy() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.coordinates) get_unmodified_spin_symbols() (in module HTMACat.catkit.gen.symmetry) get_unsaturated_nodes() (HTMACat.catkit.Gratoms method) (HTMACat.catkit.gratoms.Gratoms method) get_voronoi_neighbors() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.connectivity) graph (HTMACat.catkit.Gratoms property) (HTMACat.catkit.gratoms.Gratoms property) Gratoms (class in HTMACat.catkit) (class in HTMACat.catkit.gratoms)

H

HTMACat module HTMACat.Base_tools module HTMACat.catkit module HTMACat.catkit.build module HTMACat.catkit.data module HTMACat.catkit.gen module HTMACat.catkit.gen.adsorption module HTMACat.catkit.gen.surface module HTMACat.catkit.gen.symmetry module HTMACat.catkit.gen.utils module HTMACat.catkit.gen.utils.connectivity module HTMACat.catkit.gen.utils.coordinates module HTMACat.catkit.gen.utils.graph module HTMACat.catkit.gen.utils.utilities module HTMACat.catkit.gen.utils.utils_mdnm module HTMACat.catkit.gen.utils.vectors module HTMACat.catkit.gratoms module HTMACat.command module HTMACat.configuration module HTMACat.descriptor module HTMACat.descriptor.Construct_descriptor module HTMACat.descriptor.Construct_descriptor_coad module

HTMACat.descriptor.Construct_descriptor_NEB module HTMACat.descriptor.Construct_descriptor_surface module HTMACat.descriptor.Construct_descriptor_surface_single module HTMACat.Extract_info module HTMACat.IO module HTMACat.model module HTMACat.model.Ads module HTMACat.model.Construct_adsorption_yaml module HTMACat.model.Species module HTMACat.model.Structure module HTMACat.model.Substrate module HTMACat.NEB module HTMACat.NEB.Construct_neb module HTMACat.NEB.Dismove module HTMACat.NEB.post_neb module HTMACat.post module HTMACat.post.cal_adsE module HTMACat.post.Extract_adener module HTMACat.post.Extract_adener_alloy module HTMACat.post.Extract_adener_site module HTMACat.post.Extract_cal_fre module

I

init_all_slab() (HTMACat.model.Substrate.FileSlab class method) (HTMACat.model.Substrate.Slab class method) init_from_ads() (in module HTMACat.model.Species) init_one_slab() (HTMACat.model.Substrate.Slab class method) is_dope() (HTMACat.model.Substrate.FileSlab method) (HTMACat.model.Substrate.Slab method)

is_isomorph() (HTMACat.catkit.Gratoms method) (HTMACat.catkit.gratoms.Gratoms method) isequal() (in module HTMACat.Base_tools) isinclude() (in module HTMACat.Base_tools) isomorphic_molecules() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.graph)

L

list_gcd() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utilities)

M

main() (in module HTMACat.command) main_command() (in module HTMACat.command) make_symmetric() (HTMACat.catkit.gen.surface.SlabGenerator method) matching_coordinates() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.coordinates) matching_sites() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.coordinates) module HTMACat HTMACat.Base_tools HTMACat.catkit HTMACat.catkit.build HTMACat.catkit.data HTMACat.catkit.gen HTMACat.catkit.gen.adsorption HTMACat.catkit.gen.surface HTMACat.catkit.gen.symmetry HTMACat.catkit.gen.utils HTMACat.catkit.gen.utils.connectivity HTMACat.catkit.gen.utils.coordinates HTMACat.catkit.gen.utils.graph HTMACat.catkit.gen.utils.utilities HTMACat.catkit.gen.utils.utils_mdnm HTMACat.catkit.gen.utils.vectors HTMACat.catkit.gratoms HTMACat.command HTMACat.configuration HTMACat.descriptor HTMACat.descriptor.Construct_descriptor HTMACat.descriptor.Construct_descriptor_coad HTMACat.descriptor.Construct_descriptor_NEB HTMACat.descriptor.Construct_descriptor_surface HTMACat.descriptor.Construct_descriptor_surface_single HTMACat.Extract_info HTMACat.IO HTMACat.model HTMACat.model.Ads HTMACat.model.Construct_adsorption_yaml HTMACat.model.Species HTMACat.model.Structure HTMACat.model.Substrate HTMACat.NEB HTMACat.NEB.Construct_neb HTMACat.NEB.Dismove HTMACat.NEB.post_neb HTMACat.post HTMACat.post.cal_adsE HTMACat.post.Extract_adener HTMACat.post.Extract_adener_alloy HTMACat.post.Extract_adener_site HTMACat.post.Extract_cal_fre

mol_to_graph() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utils_mdnm) molecule() (in module HTMACat.catkit.build)

N

nodes (HTMACat.catkit.Gratoms property) (HTMACat.catkit.gratoms.Gratoms property)

O

out_file_name() (HTMACat.model.Ads.Adsorption method) (HTMACat.model.Ads.Coadsorption method) (HTMACat.model.Species.ABS_Species method) (HTMACat.model.Species.File_Species method) (HTMACat.model.Species.Sml_Species method) (HTMACat.model.Structure.Structure method) (HTMACat.model.Substrate.FileSlab method) (HTMACat.model.Substrate.Slab method)

out_print() (HTMACat.model.Ads.Adsorption method) (HTMACat.model.Species.ABS_Species method) (HTMACat.model.Structure.Structure method) (HTMACat.model.Substrate.FileSlab method) (HTMACat.model.Substrate.Slab method) out_templator_file() (in module HTMACat.IO)

P

parse_slice() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utilities) plane_normal() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.vectors)

plot() (HTMACat.catkit.gen.adsorption.AdsorptionSites method) plt_neb() (in module HTMACat.NEB.post_neb) print_templator() (in module HTMACat.IO)

R

read() (in module HTMACat.IO) remove_same() (HTMACat.model.Ads.Adsorption method) (HTMACat.model.Ads.Coadsorption method)

running_mean() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utilities)

S

set_filetype() (HTMACat.model.Species.File_Species method) set_lattice_constant() (HTMACat.model.Substrate.Bulk method) set_size() (HTMACat.catkit.gen.surface.SlabGenerator method) set_species() (HTMACat.model.Ads.Adsorption method) set_surface_atoms() (HTMACat.catkit.Gratoms method) (HTMACat.catkit.gratoms.Gratoms method) Sim_Species (class in HTMACat.model.Species) Slab (class in HTMACat.model.Substrate) SlabGenerator (class in HTMACat.catkit.gen.surface)

Sml_Species (class in HTMACat.model.Species) solve_normal_vector_linearsvc() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utils_mdnm) species_from_input() (in module HTMACat.model.Species) Structure (class in HTMACat.model.Structure) substrate_from_input() (in module HTMACat.model.Substrate) surface() (in module HTMACat.catkit.build) Symmetry (class in HTMACat.catkit.gen.symmetry) symmetry_equivalent_points() (in module HTMACat.catkit.gen.adsorption)

T

templator() (in module HTMACat.command) to_gratoms() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.utilities)

transform_ab() (in module HTMACat.catkit.gen.surface) trilaterate() (in module HTMACat.catkit.gen.utils) (in module HTMACat.catkit.gen.utils.coordinates)

W

write() (in module HTMACat.IO)

Y

yaml2dict() (in module HTMACat.IO)