Introduction

Objectives and State-Of-The-Art

What we will call the PeleSuite is currently composed of 3 separate codes:

  • PelePhysics is a repository of physics databases and implementation code for use within the other Pele codes. In particular, the choice of chemistry and transport models as well as associated functions and capabilities are managed in PelePhysics.

  • PeleLM is an adaptive-mesh Low-Mach number hydrodynamics code for reacting flows. It has a sibling, PeleLMeX, that solves for the same type of flow using a subtly different numerical approach.

  • PeleC is an adaptive-mesh compressible hydrodynamics code for reacting flows.

All three codes rely on AMReX, which is a software frameworks that provides the data structure and enable massive parallelization.

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PelePhysics (as well as the ChemDriver object of PeleLM ) used to rely upon DVODE [VODE1989] to perform the chemistry integration, no matter the problem at hand. DVODE is a very robust, but slightly outdated, variable-coefficient Ordinary Differential Equation (ODE) solver written in Fortran 77. At its core, it uses a direct dense linear solver. DVODE is very efficient in the resolution of small stiff systems of equations but can become prohibitively expensive when dealing with bigger systems of equations, such as those frequently encountered in combustion systems.

In recent years, the Sundials team at LLNL [LLNL2005] has been involved in the active development of a modern, C++ version, of DVODE called CVODE. CVODE implements the same functionalities as those available in DVODE, but offers much more flexibility through its user-friendly set of interface routines. Additionally, other linear solvers are available, such as iterative or sparse solvers which can prove to be very efficient in handling “larger” systems of equations.

The objective of this user-guide is to document the CVODE-based chemistry integration implemented in PelePhysics. Although it is possible to use CVODE in PeleC, the following is mainly intended for PeleLM users. This user-guide will cover:

  • ODE equations (reactor type)

  • Default settings (tolerances/order/…)

  • Linear solvers available –along with examples of performance

  • Setting-up a PelePhysics test case

  • …

How to naviguate this documentation

This section provides a short overview of the chemistry-related features of PelePhysics. For an in-depth discussion, relevant references to specific sections of this manuscript are given.

  • In PelePhysics, the user can select between two different reactor types. The first type is a constant volume reactor, were the choice of fixed variables are the internal energy and the density, to comply with PeleC transported variables. This reproduces what was originally implemented with DVODE in PelePhysics. A second reactor type formulated in terms of enthalpy and density has been put in place, to comply with PeleLM. Both reactors are available in DVODE (in fortran 90) and CVODE (in cpp). See sections The different reactors for additional details, and Activating the different CVODE solver options via the input files to see how to activate one or the other via the input files.

  • With both reactors, it is possible to use an Analytical Jacobian (depending upon the choice of linear solver, see section Linear Algebra.)

  • Three different types of linear solvers are implemented, see section Linear Algebra for additional details, and Activating the different CVODE solver options via the input files to see how to make a selection:

    • a dense direct solver – with or without Analytical Jacobian

    • a sparse direct solver (requires the KLU library) – always requires an Analytical Jacobian

    • a couple of sparse iterative solvers from the GMRES family – preconditioned or not

  • Regression testings have been put in place in PelePhysics to test the CVODE integration. See section Validation of the CV reactor implementation in CVODE (with CANTERA) for validations, and section The ReactEval_C test case with CVODE in details for a step-by-step example.

  • A CVODE version running on GPU is also technically available but the documentation is a WIP. The interested user can contact code developers for additional information

  • PelePhysics uses an automatic chemistry-related routine generator: CEPTR. CEPTR is part of the sources of PelePhysics. With CEPTR, a unique chemistry file is generated for a specific kinetic scheme. Instructions to generate your own chemistry files (all you need are chemistry files in the famous Cantera yaml format) are discussed in section CEPTR: Chemistry Evaluation for Pele Through Recasting. Note that PelePhysics already offers a large choice of more than 20 different kinetic schemes.