Astrochem C API reference

This document gives a comprehensive list of the types and functions that are defined in Astrochem C API. These types and functions are defined in the libastrochem.h header file. For an example of how to use the C API, see calling Astrochem from C.

Warning

Astrochem C API is recent and it is subject to change in future releases.

Types

type species_name_t

Character array containing the species name

type astrochem_mem_t

Astrochem memory structure

type cell_t

Structure containing the parameters of a gas cell

double av

Visual extinction in the cell, in magnitudes

double nh

H nuclei density in the cell, in \(\mathrm{cm^{-3}}\)

double tgas

Gas temperature in the cell, in K

double tdust

Dust temperature in the cell, in K

type net_t

Structure containing a chemical network

int n_species

Number of species in the network

int n_alloc_species

Number of allocated species in the network structure

species_t *species

Structure containing the species in the network

int n_reactions

Number of reactions

react_t *reactions

Structure containing the reactions in the network

type phys_t

Structure containing the physical parameters

double chi

External UV radiation field, in Draine units

double cosmic

Cosmic ray ionization rate of molecular hydrogen, in \(\mathrm{s^{-1}}\)

double grain_size

The grain radius, in micron

double grain_abundance

The grain abundance

double grain_gas_mass_ratio

The grain-to-gas mass ratio

double grain_mass_density

The grain mass density in \(\mathrm{kg \, m^{-3}}\)

Functions

int alloc_abundances(const net_t *network, double **abundances)

Allocate an array to store the abundances for all species in a network

Parameters:

• network (net_t*) – Network structure

• abundances (double**) – Pointer on the abundance array

Returns:

EXIT_SUCCESS if the allocation was successful, EXIT_FAILURE otherwise

void free_abundances(double *abundances)

Free the array containing the abundances

Parameters:

• abundances (double**) – Pointer on the abundance array

int find_species(const species_name_t specie, const net_t *network)

Find the index of a species

Parameters:

• species (const species_name_t) – The species name

• network (const net_t) – The network

Returns:

-1 if the species is “”, -2 if the species is not found, or the species index.

int set_initial_abundances(const char **species, int n_initialized_abundances, const double *initial_abundances, const net_t *network, double *abundances)

Set the initial abundances

Parameters:

• species (char**) – Array containing the species name

• n_initialized_abundances (int) – Number of initial abundances

• initial_abundances (double*) – Array containing the initial abundances

• network (net_t*) – Network structure

• abundances (double*) – Array containing the abundances of all species

Returns:

0

int solver_init(const cell_t *cell, const net_t *network, const phys_t *phys, const double *abundances, double density, double abs_err, double rel_err, astrochem_mem_t *astrochem_mem)

Initialize the solver

Parameters:

• cell (cell_t*) – Cell structure

• network (net_t*) – Network structure

• phys (phys_t*) – Physical parameters structure

• abundances (double*) – Array containing the abundances of all species

• density (double) – Initial density, in \(\mathrm{cm^{-3}}\)

• abs_err (double) – Solver absolute error on the abundances

• rel_err (double) – Solver relative error on the abundances

• astrochem_mem (astrochem_mem_t*) – Astrochem memory structure

Returns:

0 if the initialization was successful, -1 otherwise.

int solve(astrochem_mem_t *astrochem_mem, const net_t *network, double *abundances, double time, const cell_t *new_cell, int verbose)

Solve the system of ODE

This function solve the system of ODE up to a given time, and update the abundance array. If the physical parameters in the gas cell have changed since the last call, a pointer to cell structure must be passed to the function; if not, a null pointer must be passed instead.

Parameters:

• astrochem_mem (astrochem_mem_t*) – Astrochem memory structure

• network (net_t*) – Network structure

• abundances (double*) – Array containing the abundances of all species

• time (double) – Time, in seconds

• new_cell (cell_t*) – New cell structure if the physical parameters have changed since the last call

• verbose (int) – Verbosity (0 for quiet, 1 for verbose)

Returns:

0

void solver_close(astrochem_mem_t *astrochem_mem)

Close the solver

Parameters:

• astrochem_mem (astrochem_mem_t*) – Astrochem memory structure

int read_network(const char *chem_file, net_t *network, const int verbose)

Read a chemical network

This function reads a chemical network in Astrochem format (.chm) and creates a network structure containing all the reactions.

Parameters:

• chem_file (char*) – Network filename

• network (net_t*) – Network structure

• verbose (int) – Verbosity (0 for quiet, 1 for verbose)

Returns:

EXIT_SUCCESS after a successful call, EXIT_FAILURE otherwise

void free_network(net_t *network)

Free a chemical network structure

Parameters:

• network (net_t*) – Network structure