Species Handling

SpeciesSymbols

Tuple containing all chemical element symbols supported by KIM-API.

This includes all elements from the periodic table from hydrogen (H) to oganesson (Og), plus "electron" as a special particle type. The order corresponds to the atomic numbers, with "electron" at index 1.

Example

SpeciesSymbols[2]  # "H" (hydrogen)
SpeciesSymbols[15] # "Si" (silicon)

SpeciesToAtomicNumbers

Simple dict map between species symbol and atomic numbers

species.jl

KIM-API species management and utilities.

This module provides functions for handling chemical species in KIM-API, including species name lookup, validation, and mapping between string representations and integer codes used by KIM models.

Key Types

• SpeciesName: Type alias for species integer codes

Constants

• SpeciesSymbols: Tuple of all supported chemical element symbols

Key Functions

• get_species_number: Convert species string to integer code
• get_species_symbol: Convert species integer code to string
• get_species_codes_from_model: Map species strings to model-specific codes
• get_species_map_closure: Create efficient species mapping function

Model Integration

The module provides functions to check which species are supported by a specific KIM model and create efficient mappings for repeated use.

get_species_codes(model::Model, species_strings::Vector{String})

Check species support and return array of KIM species codes for each particle. Throws error if any species not supported. From mdstresslab++

get_static_species_map(model::Model, species_list::Vector{String}) -> Vector{Cint}
Get a static closure that maps species strings to their codes.

get_species_number(name::String) -> Cint

Get species name constant from string

get_species_support_and_code(model::Model, species::Cint) -> (supported, code)

Check if a species is supported and get its code.

get_species_number(species::Cint) -> String

Get species symbol constant from string (e.g., "Ar", "Si", etc.)

get_unique_species_map(model::Model, species_list::Vector{String})

Map all species strings to their codes from the model. TODO: Rename :symbol? It might gte confusing with actual Julia :Symbols

get_unique_species_map(model::Model, species_list::Vector{String})

Check unique species and return mapping dict. More efficient when many particles of same species.

species_name_equal(lhs::SpeciesName, rhs::SpeciesName) -> Bool

Check if two species names are equal.

species_name_known(species::SpeciesName) -> Bool

Check if species name is known/valid in KIM-API.

species_name_not_equal(lhs::SpeciesName, rhs::SpeciesName) -> Bool

Check if two species names are not equal.