Simulating Mechanisms

Simulations

Defining a Phase

A phase in RMS defines how thermodynamic and kinetic parameters for individual species and reactions are calculated. For the IdealGas case defining a phase is quite simple:

ig = IdealGas(spcs,rxns,name="gas")

where spcs and rxns and lists of AbstractSpecies and AbstractReaction objects respectively.
For an IdealDiluteSolution it is slightly more complicated because some of these properties (currently primarily diffusion limitations) can be dependent on the solvent:

solv = Solvent("octane",RiedelViscosity(-98.805,3905.5,14.103,-2.5112e-5,2.0))
liq = IdealDiluteSolution(spcs,rxns,solv;name="phase",diffusionlimited=true)

Defining Initial Conditions

Initial conditions for the simulation are defined within a dictionary in SI units. The keys "T","P" and "V" correspond to thermodynamic values ("V" being the extensive volume) while species names correspond to numbers of moles (extensive).

For example, since the initial V can be calculated implicitly a valid IdealGas initial condition might be:

Dict(["T"=>1000.0,"P"=>1e5,"H2"=>0.67,"O2"=>0.33])

In the case of an IdealDiluteSolution where pressure is assumed to not affect the thermodynamic state it might look more like:

Dict(["T"=>450.0,"V"=>1.0e-6,"octane"=>6.154e-3,"oxygen"=>4.953e-6])

Defining a Domain

A domain in RMS is a homogeneous volume that contains a single phase. The AbstractDomain object defines how the thermodynamics of the volume evolve with respect to time. For example in a ConstantTPDomain the temperature and pressure are defined in the domain object and held constant over the simulation and the volume is integrated for while in a ConstantVDomain (a constant V adiabatic reactor) the volume is kept constant and the temperature is integrated for.

When constructing a Domain object constant concentration species can be defined (list of species names).
During integration the derivatives with respect to time of these species will be kept at zero.

Sensitivity analysis can also be requested on the Domain object.

IdealDiluteSolution example:

domain,y0 = ConstantTVDomain(phase=liq,initialconds=initialconds,constantspecies=["oxygen"])

IdealGas example:

domain,y0 = ConstantTPDomain(phase=ig,initialconds=initialconds;sensitivity=true)

Defining a Reactor object

The Reactor object exists primarily to automatically sets up the ODEProblem object for you to solve.
It takes the domain, the initial condition vector returned when constructing the domain and a time interval.

Example:

react = Reactor(domain,y0,(0.0,150.1))

Solving a Reactor object

RMS purposefully exposes the solver interface provide users with all the options available from Julia's DifferentialEquations package. The ODEProblem object is a field of the Reactor object react.ode and can be solved as the user desires.

Example:

sol = solve(react.ode,CVODE_BDF(),abstol=1e-20,reltol=1e-12)

In general CVODE_BDF tends to work well on these problems.

Saving a Solution Object

The user may wish to save the sol object from above or the bsol object obtained from:

bsol = Simulation(sol, domain)

Saving the data to a Julia data structure (JLD2) seems to work well. Once the JLD2 package has been downloaded, data can be saved using the following commands:

using JLD2, FileIO
save("<file_name>.jld2", "bsol_saved", bsol)

The data can be read back into Julia as a dictionary, and the desired data can be accessed using its corresponding key:

d = load("<file_name>.jld2")
bsol_loaded = d["bsol_saved"]

Since the data is saved in HDF5 format, it can also be read into Python as follows:

import h5py
f = h5py.File("<file_name", "r")