HTMACat.model package

Submodules

HTMACat.model.Ads module

Created on Sat Mar 18 09:00:12 2023.

@author: YuxiaoLan

class HTMACat.model.Ads.Adsorption(species: list, sites: list, spec_ads_stable=None, substrate=<HTMACat.model.Substrate.Slab object>)[source]

Bases: Structure

Methods

Construct_double_adsorption

Construct_single_adsorption

add_sites

add_species

construct

from_input

get_sites

out_file_name

out_print

remove_same

set_species
Construct_double_adsorption()[source]
Construct_single_adsorption(ele=None)[source]
add_sites(sites)[source]
add_species(species)[source]
construct()[source]
classmethod from_input(init_list, substrates, species_dict=None)[source]
get_sites()[source]
out_file_name()[source]
out_print()[source]
remove_same(slabs_ads)[source]
set_species(species)[source]
class HTMACat.model.Ads.Coadsorption(species: list, sites: list, spec_ads_stable=None, substrate=<HTMACat.model.Substrate.Slab object>)[source]

Bases: Adsorption

Methods

Construct_coadsorption_11

Construct_coadsorption_12

Construct_coadsorption_22

Construct_double_adsorption

Construct_single_adsorption

add_sites

add_species

construct

from_input

get_sites

out_file_name

out_print

remove_same

set_species
Construct_coadsorption_11()[source]
Construct_coadsorption_12()[source]
Construct_coadsorption_22()[source]
construct()[source]
classmethod from_input(init_list, substrates, species_dict=None)[source]
out_file_name()[source]
remove_same(slabs_ads)[source]
HTMACat.model.Ads.ads_from_input(ads_model, substrate, species_dict=None)[source]

HTMACat.model.Construct_adsorption_yaml module

HTMACat.model.Construct_adsorption_yaml.Construct_adsorption_yaml(filename)[source]

HTMACat.model.Species module

class HTMACat.model.Species.ABS_Species(form, formtype='sim', alias_name=None)[source]

Bases: ABC

Methods

from_input

from_input_dict

get_formular

get_molecule

out_file_name

out_print
classmethod from_input(input_dict)[source]
classmethod from_input_dict(init_dict)[source]
get_formular()[source]
abstract get_molecule() → Gratoms[source]
out_file_name()[source]
out_print()[source]
class HTMACat.model.Species.File_Species(form, formtype='file', alias_name=None)[source]

Bases: ABS_Species

Attributes:
atoms
edges_list

Methods

from_input

from_input_dict

get_formular

get_molecule

out_file_name

out_print

set_filetype
property atoms: Atoms
property edges_list
get_molecule() → Gratoms[source]
out_file_name()[source]
set_filetype(typename)[source]
class HTMACat.model.Species.Sim_Species(form, formtype='sim', alias_name=None)[source]

Bases: ABS_Species

Methods

from_input

from_input_dict

get_formular

get_molecule

out_file_name

out_print
get_molecule()[source]
class HTMACat.model.Species.Sml_Species(form, formtype='sml', alias_name=None)[source]

Bases: ABS_Species

Methods

from_input

from_input_dict

get_formular

get_molecule

out_file_name

out_print
get_molecule() → Gratoms[source]
out_file_name()[source]
HTMACat.model.Species.init_from_ads(init_str, species_dict=None)[source]
HTMACat.model.Species.species_from_input(init_dict)[source]

HTMACat.model.Structure module

class HTMACat.model.Structure.Structure[source]

Bases: ABC

Methods

construct

out_file_name

out_print
abstract construct() → Atoms[source]
abstract out_file_name() → str[source]
abstract out_print() → str[source]

HTMACat.model.Substrate module

Created on Fri Mar 17 15:34:47 2023.

@author: YuxiaoLan

class HTMACat.model.Substrate.Bulk(element='Pt', lattice_type='fcc', lattice_constant=None, ele_dop='Cu', natom_dop='0', supercell=None)[source]

Bases: object

Methods

construct

dop_bulk

get_dop_element

get_ele_dop

get_main_element

get_natom_dop

get_supercell

set_lattice_constant
construct()[source]
dop_bulk(mbulk)[source]
get_dop_element()[source]
get_ele_dop()[source]
get_main_element()[source]
get_natom_dop()[source]
get_supercell()[source]
set_lattice_constant(latcont)[source]
class HTMACat.model.Substrate.FileSlab(filename)[source]

Bases: Structure

Methods

find_surface_atoms(atomstype[, tol_zdiff, ...])

Generate the list of surface atoms (top surface). Parameters ---------- atomstype: str 'top' means find the top surface of slab 'bottom' means find the bottom surface of slab tol_zdiff: number If the z_coord of an atom is higher than zmax-tol_zdiff, this atom is recognized as a "surface atom". Returns ---------- index_topsurf: list List of the indices of the surface atoms.

construct

get_dis_inter

init_all_slab

is_dope

out_file_name

out_print
construct()[source]
find_surface_atoms(atomstype, tol_zdiff=0.7, tol_zangle_min=0)[source]

Generate the list of surface atoms (top surface). Parameters ———- atomstype: str

‘top’ means find the top surface of slab ‘bottom’ means find the bottom surface of slab

tol_zdiff: number

If the z_coord of an atom is higher than zmax-tol_zdiff, this atom is recognized as a “surface atom”.

Returns

index_topsurf: list

List of the indices of the surface atoms.

get_dis_inter()[source]
classmethod init_all_slab(input_list: list)[source]
is_dope()[source]
out_file_name() → str[source]
out_print() → str[source]
class HTMACat.model.Substrate.Slab(in_bulk=<HTMACat.model.Substrate.Bulk object>, facet='100', layers=4)[source]

Bases: Structure

Methods

Construct_1stLayer_slab

Construct_doped_slab

Construct_slab

construct

dope_slab

get_dis_inter

get_facet

get_layers

get_miller_index

init_all_slab

init_one_slab

is_dope

out_file_name

out_print
Construct_1stLayer_slab()[source]
Construct_doped_slab()[source]
Construct_slab()[source]
construct()[source]
dope_slab(slab, atom_number_dop)[source]
get_dis_inter()[source]
get_facet()[source]
get_layers()[source]
get_miller_index()[source]
classmethod init_all_slab(struct_Info: dict)[source]
classmethod init_one_slab(init_dict)[source]
is_dope() → bool[source]
out_file_name()[source]
out_print()[source]
HTMACat.model.Substrate.substrate_from_input(init_dict)[source]

Module contents