chemistry module

Methods related to the actual chemical processes used in EOM

chemistry.backwardEuler(density, PhotoDissRate, N, dt, iAlt)

Update the density using the backward euler method. Currently requires source and loss terms to be calculated and their derivatives.

chemistry.calcChemistry(u0, PhotoDissRate, N, temp, dt, chemsolver='simple', iAlt=None, usr=None)

Perform the chemistry update.

The #CHEMISTRY input flag determines the method to use, simple or explicit.

u0 : array

Input density at a single altitude for all species

PhotoDissRate : array

Input photo dissociation rates for all photo active species

N : float

Total number density at single altitude

temp : float

Temperature at single altitude

dt : float

Time step

chemsolver : char, optional

Specify which method to use to solve chemistry

iAlt : int, optional

Mainly used for debugging

chemistry.calcJacobian(density, PhotoDissRate, N)

Get jacobian maxtrix for backward euler.

chemistry.calcsourceterms(u, PhotoDissRate, N, dt, ialt)

Calculate the full time-dependent chemical sources and losses for the current time step explicitly.

chemistry.updateRates(temp)

Update chemical reaction rates given the temperature