chemreac.core

In chemreac.core you will find ReactionDiffusion which is the class describing the system of ODEs.

class chemreac.core.ReactionDiffusion

Object representing the numerical model, with callbacks for evaluating derivatives and jacobian.

The instance provides methods:

• f(t, y, fout)
• dense_jac_rmaj(t, y, jout)
• dense_jac_cmaj(t, y, jout)
• banded_jac_cmaj(t, y, jout)
• banded_packed_jac_cmaj(t, y, jout)

some of which are used by chemreac.integrate.integrate_scipy

Additional convenience attributes (not used by underlying C++ class):

• substance_names
• substance_tex_names

Parameters:

n: integer

number of species

stoich_active: list of lists of integer indices

reactant index lists per reaction.

stoich_prod: list of lists of integer indices

product index lists per reaction.

k: 1-dimensional array

reaction rate coefficients

N: integer

number of compartments (default: 1 if x==None else len(x)-1)

D: sequence of floats

diffusion coefficients (of length n)

z_chg: sequence of integers

1-dimensional array ion charges

mobility: sequence of floats

mobility of ions

x: sequence of floats or pair of flats or float, optional

compartment boundaries (of length N+1), default: linspace(0, 1, N+1) if x is a pair of floats it is expanded into linspace(x[0], x[1], N+1). if x is a float it is expanded into linspace(0, x, N+1)

stoich_inactv: list of lists of integer indices

list of inactive reactant index lists per reaction.n, default: []

geom: integer

any of (FLAT, SPHERICAL, CYLINDRICAL)

logy: bool

f and *_jac_* routines operate on log(concentration)

logt: bool

f and *_jac_* routines operate on log(time)

logx: bool

f and *_jac_* routines operate on log(space)

nstencil: integer

number of points used in finite difference scheme

lrefl: bool

reflective left boundary (default: True)

rrefl: bool

reflective right boundary (default: True)

auto_efield: bool

calculate electric field from concentrations (default: False)

surf_chg: pair of floats

total charge of surface (defaut: (0.0, 0.0))

eps_rel: float

relative permitivity of medium (dielectric constant)

g_values: sequence of sequences of floats

per specie yields (amount / energy) per field type

g_value_parents: sequence of integers (optional)

indices of parents for each g_value. -1 denotes no concentration dependence of g_values. default: [-1]*len(g_values)

fields: sequence of sequence of floats

per bin field strength (energy / (volume time)) per field type. May be calculated as product between density and doserate

modulated_rxns: sequence of integers

Indicies of reactions subject to per bin modulation

modulation: sequence of sequences of floats

Per bin modulation vectors for each index in modulated_rxns

units: dict (optional)

default: None, see chemreac.units.SI_base for an example.

Attributes

units: dict