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Dengo Documentation

Dengo Documentation

class dengo.chemical_network.ChemicalNetwork(write_intermediate=False, stop_time=31557000000000.0)[source]

A chemical network that gathers all the species and reactions.

reactions

the dictionary that holds the reactions added through self.add_reaction

Type

dict

cooling_actions

the dictionary that tracks the cooling tracked by the ChemicalNetwork

Type

dict

required_species

the set of chemical species tracked by ChemicalNetwork

add_cooling(cooling_term, auto_add=True)[source]

Add cooling to the ChemicalNetwork

Parameters

term (cooling) – the string that corresponds to the cooling that are previously registered in cooling_registry

Return type

None

add_reaction(reaction, auto_add=True)[source]

Add reaction to the ChemicalNetwork

Parameters

reaction – the string of the reactions that are previously registered in reaction_registry

Return type

None

property chemical_species

helper function for code generation

init_redshift(z_bounds=(0.0, 10.0), n_z_bins=100)[source]

Initialize the range of redshift over which the rate tables are generated

Parameters

  • z_bounds (List[Float, Float], optional (default=(0.0,10.0))) – the range over which the rates table is interpolated

  • n_bins (int, optional (default=1024)) –

init_temperature(T_bounds=(1, 100000000.0), n_bins=1024)[source]

Initialize the range of temperature over which the rate tables are generated

Parameters

  • T_bounds (List[Float, Float], optional (default=(1,1e8))) – the range over which the rates table is interpolated

  • n_bins (int, optional (default=1024)) –

print_JacTimesVec_component(s1, assign_to=None)[source]

Compute the product of Jacobian * Vec for a given Vec Might be useful when we use the CVSpils solver

print_conserved_species(s, assign_to, is_mass_density=True)[source]

Calculate the total {H, He, …} atoms locked in species considered

solve_equilibrium_abundance(species)[source]

write the equilibrium abundance of species sp

species_total(species)[source]

Output the RHS function of the given species

Parameters

species (str,) –

Returns

eq – the dydt (RHS function) in sympy expressions

Return type

Sympy.symbols

update_ode_species()[source]

this refers to the set of species that our ODE solver solves

write_solver(solver_name, solver_template='rates_and_rate_tables', ode_solver_source='BE_chem_solve.C', output_dir='.', init_values=None, main_name='main', input_is_number=False)[source]

Write the chemistry solver, based on the specified solver templates

Parameters

  • solver_name (str) – the name of the solver

  • solver_template (str, default = rate_and_rate_tables) – the jinja2 template the ChemicalNetwork populates, read dengo/templates for examples

  • ode_solver_source (str, default = BE_chem_solve.C) – the ODE solver used

  • output_dir (str, deafault = .) – the directory at which these files would be generated

class dengo.reaction_classes.AtomicSpecies(atom_name, free_electrons)[source]

Initialize the atomic species

Parameters

  • atom_name (str) – name of the atom

  • free_electrons (int) – number of free electron

Note

since it is an atom, the weight is taken directly from the periodic table.

class dengo.reaction_classes.ChemicalSpecies(name, weight, free_electrons=0.0, pretty_name=None)[source]

initialize chemical species object

Parameters

  • name (str) – name of the chemical species

  • weight (float) – the weight of the species in terms of atomic mass unit

  • free_electrons (int) – the number of free electrons of the species

find_constituent()[source]

find elements based on its name return: total weight

class dengo.reaction_classes.MolecularSpecies(molecule_name, weight, free_electrons, original_name=None)[source]

Initialize molecular species

Parameters

  • molecule_name (str) – the name of the molecules

  • weight (float) – weight of the molecule in amu

  • free_electrons (int) – free electron in molecules

class dengo.reaction_classes.ReactionCoefficient(name, **assumptions)[source]
property free_symbols

Return from the atoms of self those which are free symbols.

For most expressions, all symbols are free symbols. For some classes this is not true. e.g. Integrals use Symbols for the dummy variables which are bound variables, so Integral has a method to return all symbols except those. Derivative keeps track of symbols with respect to which it will perform a derivative; those are bound variables, too, so it has its own free_symbols method.

Any other method that uses bound variables should implement a free_symbols method.

dengo.reaction_classes.reaction(name, left_side, right_side)

Initialize Reaction, the chemical reactions between species

Parameters

  • name (str) – name of the reaction

  • left_side – left hand side of the chemical reaction

  • right_side – right hand side of the chemical reaction

  • f – a function that takes state, and returns the reaction coefficient

dengo.reaction_classes.registry_setup(func)[source]

a decorator function register unseen species, cooling and reactions into the registry

Indices and tables

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