PeleC

A compressible AMR combustion code

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

Getting Started

• To compile and run the Pele suite of codes, one needs a C++ compiler that supports the C++11 standard and a Fortran compiler that supports the 2003 standard. A hierarchical strategy for parallelism is supported, based MPI + OpenMP. The codes work with all major MPI and OpenMP implementations. The codes should build and run with no modifications to the make system if using a Linux system with the GNU compilers, version 4.8.4 and above.

To build PeleC and run a sample 2D flame problem:

1. Set the environment variable, AMREX_HOME, and clone a copy of AMReX there

   export AMREX_HOME=<location for AMReX>
   git clone git@github.com:AMReX-Codes/amrex.git ${AMREX_HOME}
   

1a. This version of PeleC has been tested against AMReX git hash 413193591ee6bef00b4f72ac2d5e39722ead7708 (9/26/2017)

2. Set the environment variable, PELE_PHYSICS_HOME, and clone a copy of PelePhysics there. You should be placed in the development branch

   export PELE_PHYSICS_HOME=<location for PelePhysics>
   git clone git@github.com:AMReX-Combustion/PelePhysics.git ${PELE_PHYSICS_HOME}
   

3. Set the environment variable, PELEC_HOME, and clone a copy of PeleC there. You should be placed in the development branch

   export PELEC_HOME=<location for PeleC>
   git clone git@github.com:AMReX-Combustion/PeleC.git ${PELEC_HOME}
   

4. Move to an example build folder, build an executable, run a test case

   cd ${PELEC_HOME}/Exec/PMF
   make
   ./Pele2d.xxx,yyy.ex inputs-2d-regt
   

• Notes

  1. In the exec line above, xxx.yyy is a tag identifying your compiler and various build options, and will vary across pltaform. (Note that GNU compilers must be at least 4.8.4, and MPI should be at least version 3).
  2. The example is 2D premixed flame, flowing vertically upward through the domain with no gravity. The lateral boundaries are periodic. A detailed hydrogen model is used. The solution is initialized with a wrinkled (perturbed) 1D steady flame solution computed using the PREMIX code. Two levels of solution-adaptive refinement are automatically triggered by the presence of the flame intermediate, HO2.
  3. In addition to informative output to the terminal, periodic plotfiles are written in the run folder. These may be viewed with CCSE's Amrvis (<https://ccse.lbl.gov/Downloads/downloadAmrvis.html>) or Vis-It (<http://vis.lbl.gov/NERSC/Software/visit/>):
     1. In Vis-It, direct the File->Open dialogue to select the file named "Header" that is inside each plotfile folder..
     2. With Amrvis, "amrvis2d plt00030", for example.
  4. The sample case is one of the PeleC regresion tests, and is therefore quite small/coarse and quick to run. For a more significant test, replace the input file above with inputs-2d-fiab.

Dependencies

PeleC was created as a renamed, stripped down version of Maui, and is built on the AMReX library. In the process, the Microphysics folder was extracted, and reorganized into a separate repository, PelePhysics.

Development model

To add a new feature to PeleC, the procedure is:

1. Create a branch for the new feature (locally)

   git checkout -b AmazingNewFeature
   

2. Develop the feature, merging changes often from the development branch into your AmazingNewFeature branch

   git commit -m "Developed AmazingNewFeature"
   git checkout development
   git pull                     [fix any identified conflicts between local and remote branches of "development"]
   git checkout AmazingNewFeature
   git merge development        [fix any identified conflicts between "development" and "AmazingNewFeature"]
   

3. Push feature branch to PeleC repository

   git push -u origin AmazingNewFeature [Note: -u option required only for the first push of new branch]
   

3a. Check the pipeline status and make sure the regression tests passed

4. Submit a merge request through git@github.com:AMReX-Combustion/PeleC.git - be sure you are requesting to merge your branch to the development branch.

Documentation

The full documentation for Pele exists in the Docs directory; at present this is maintained inline using Doxygen and Sphinx Sphinx. With Sphinx, documentation is written in Restructured Text. reST is a markup language similar to Markdown, but with somewhat greater capabilities (and idiosyncrasies). There are several primers available to get started. One gotcha is that indentation matters. To build the documentation, run Doxygen in the Docs directory then build the sphinx

doxygen Doxyfile
cd sphinx_doc
make html

Acknowledgment

This research was supported by the Exascale Computing Project (ECP), Project Number: 17-SC-20-SC, a collaborative effort of two DOE organizations -- the Office of Science and the National Nuclear Security Administration -- responsible for the planning and preparation of a capable exascale ecosystem -- including software, applications, hardware, advanced system engineering, and early testbed platforms -- to support the nation's exascale computing imperative.