/PelePhysics

A collection of physics databases and implementation code for use with the Pele suite of of codes

Primary LanguageFortranOtherNOASSERTION

PelePhysics

A respository of physics databases and implementation code for use with the Pele suite of of codes

FUEGO

This PelePhysics repository contains the FUEGO source code generation tool in order to support the inclusion of chemical models specified in the CHEMKIN-II format. Fuego was originally created by Michael Aivazis at CalTech, and donated to CCSE in 2001. Originally, FUEGO was part of a larger Python-based set of workflow tools Michael developed for managing and publishing simulation-based studies. FUEGO itself was developed as a drop-in replacement for the CHEMKIN library, and provided "hand-coded" replacement routines for evaluation of EOS thermodynamic functions that are considerably more efficient than their CHEMKIN counterparts. Since 2001, CCSE has continued to modify FUEGO independently for its own use so that the current version here bears little resemblance to Michael's original code, or its intentions.

Typically, CHEMKIN-based mechanisms (combustion models) are transmitted via a set of ASCII files, which provide data for

  • Species - definition of chemical species, as composed by fundamental elements
  • Chemistry - modified Arrhenius reaction parameters, including third body efficiencies and pressure dependencies
  • Thermodynamics - NASA-formatted polynomial expressions, assuming a mixture of ideal gases
  • Transport - physical parameters for each of the chemical species required for the EGLib (or comparable) library for computing species- and temperature-dependent molecular transport coefficients

This information is read by the FUEGO tool, and source code files are generated that are to linked directly into an executable in the Pele code suite in order to provide data and functions necessary to evaluate chemistry, transport and thermodynamic relationships. PelePhysics supports the following in addition to standard CHEMKIN style models:

  • Soave-Redlich-Kwong real gas equation of state, implemented to be consistent with corresponding ideal gas model at suitable conditions
  • Gamma-law gas equation of state
  • Constant coefficient transport
  • Simple A simplified mixture-averaged transport model consistent with EGLib under suitable conditions
  • Inert Chemistry setting to ignore reactions
  • Utilization of auxiliary source files (C++,f90,c) that follow the CHEMKIN species production rate function interface (e.g., QSS approximations)

Note that the CHEMKIN-II specification assumes a mixture of ideal gases. If the Pele codes are built with Eos_dir = Fuego, the make system variable Chemistry_Model must be set to one of the models (subfolders) that exist in the ${PELE_PHYSICS_HOME}/Support/Fuego/Mechanism/Models folder. The repository currently provides (multiple) models for each of the following mixtures:

  • air
  • hydrogen
  • methane
  • ethane
  • n-dodecane
  • di-methyl ether
  • ... more can be added (see below)

NOTE: Non-ideal equations of state

PelePhysics currently supports a cubic EOS model: Soave-Redlich-Kwong. It is built on top of the ideal gas models, and is selected by specifying its name as the Eos_dir during the build (the make system requires that both Eos_dir and Chemistry_Model be specified). Any additional parameters required for the EOS (e.g., attractions, repulsions, critical states) are either included in the underlying FUEGO database used to generate the source file model implementation, or else are inferred from the input model data.

Model generation procedures

This repository provides the tools necessary for generating new Pele-compatible combustion mechanisms. To do this:

  1. Ensure that the environment variable PELE_PHYSICS_HOME is set to the root folder of your local PelePhysics clone

  2. Set up the required FUEGO variables by doing

    . ${PELE_PHYSICS_HOME}/Support/Fuego/Pythia/setup.sh` (for bash), or
source ${PELE_PHYSICS_HOME}/Support/Fuego/Pythia/setup.csh` (for C-shell)

  3. Check that all is setup correctly by reproducing one of the existing C++ model files. For example, to generate the LiDryer model for H2 combustion:

     cd ${PELE_PHYSICS_HOME}/Support/Fuego/Mechanism/Models/LiDryer  
     ./make-LiDryer.sh

That script generates a C++ source file. If this file "almost" matches the one in git, you're all set... By "almost" we mean minus reordering in the egtransetEPS, egtransetSIG, egtransetDIP, egtransetPOL, egtransetZROT and egtransetNLIN functions. If not, and there are no error messages, it might be that the git version needs to be updated. Contact MSDay@lbl.gov to verify the correct actions to take.

  1. To build and use a new CHEMKIN-II based model, make a new model folder in ${PELE_PHYSICS_HOME}/Support/Fuego/Mechanism/Models, say XXX, and copy your CHEMKIN input files there. Additionally copy make-LiDryer.sh from the LiDryer model folder there as a template, rename it to make-XXX.sh, and edit the filenames at the top.

  2. Next, modify the chemistry input file to include a transport section that is generated by one of our scripts:

     python ${PELE_PHYSICS_HOME}/Support/Fuego/Mechanism/Models script_trans.py chem.inp trans.dat

(chem.inp is your CHEMKIN chemistry file, and trans.dat is the data expected by CHEMKIN's tranfit function. This should generate a text file, TRANFILE_APPEND.txt. Insert the entire contents of this file into the chemistry input file, just above REACTION section. Next, run your newly created script file, make-XXX.sh. If all goes well, FUEGO will be called to generate a chem.cpp file that gets concatenated with a few others, into a result file, XXX.cpp, and cleans up its mess.

  1. Add a Make.package text file in that model folder that will be included by the AMReX make system. In most cases, this file will contain a single line, CEXE_sources+=YYY.cpp (see the other models for examples if there are auxiliary files in languages other than C++ to include in the build of this model).

  2. Finally, edit the GNUmakefile where you want to use this (in, e.g., PeleC/Exec) so that Chemistry_Model is XXX. In PeleC/Exec/Make.PeleC, the model is expected to be in the folder ${PELE_PHYSICS_HOME}/Support/Fuego/Mechanism/Models/$(Chemistry_Model), and it is expected that the folder contains a Make.package file to include, so make sure things are where they need to be.