Add the README and building instructions (#21)

* add skeleton for README * using PeleLMeX clangformat * edit readme * add badges * add CI badge * fix badge * edit the README * add the build script * edit the example script * add the example keywords for input file * edit the README * edit the README * user specified path for the database
AMReX-Combustion · Nov 16, 2023 · eb76192 · eb76192
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diff --git a/.clang-format b/.clang-format
@@ -1,12 +1,94 @@
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-Language: Cpp
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-BreakConstructorInitializers: BeforeColon
-ColumnLimit: 80
-BreakBeforeBraces: Allman
-AlignConsecutiveAssignments: true
-AlignOperands: true
-AllowShortIfStatementsOnASingleLine: true
+# -*- mode: yaml -*-
+---
+Language:        Cpp
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 AlwaysBreakTemplateDeclarations: true
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+UseTab:          Never
+
diff --git a/README.md b/README.md
@@ -1,4 +1,38 @@
-PeleRad
-==========
+# PeleRad
+
+[![CI](https://github.com/AMReX-Combustion/PeleRad/actions/workflows/linux.yml/badge.svg)](https://github.com/AMReX-Combustion/PeleRad)
+[![AMReX Badge](https://img.shields.io/static/v1?label=%22powered%20by%22&message=%22AMReX%22&color=%22blue%22)](https://amrex-codes.github.io/amrex/)
+[![Exascale Computing Project](https://img.shields.io/badge/supported%20by-ECP-blue)](https://www.exascaleproject.org/research-project/combustion-pele/)
+
+## Table of Contents
+- [Description](#description)
+- [Installation](#installation)
+- [Usage](#usage)
+- [License](#license)
+
+## Description
+PeleRad is a module for modeling radiative transfer in reacting flows. It supports GPU performance portability and adaptive mesh refinement through AMReX and is coupled to PeleLMeX.
+
+## Installation
+1. Clone the repository: `git clone https://github.com/AMReX-Combustion/PeleRad.git`
+2. The example CMake scripts for Summit CUDA build and Frontier HIP build are in the '/scripts' folder.
+3. To enable the unit tests, PeleRad needs to build with the Boost library.
+
+To build with the PeleLMeX flow solver, GNUMake is prefered.
+One example script to build a test case on Frontier is provided in the '/scripts' folder.
+
+To run the script:
+'./build_PeleLMeX_Fontier.sh' 
+
+## Usage
+PeleRad is designed for modeling radiative transfer in reacting flows. To activate and use PeleRad in conjunction with PeleLMeX, follow these steps:
+1. Add 'USE_PELERAD = TRUE' in the GNUmakefile in the case folder.
+2. If using the clang compiler on Frontier, link the c++ file system by adding 'LIBRARIES += -lstdc++fs'.
+3. Add the pelerad input keywords to the amrex-style input file in the case folder. Example keywords can be found in '/inputs/inputs.egLMeX'
+4. Specify the path of the spectral database ($PELERAD_HOME/data/kpDB/) is needed for the 'pelerad.kppath' keywords in the input file.
+
+## License
+The license file is located at
+https://github.com/AMReX-Combustion/PeleMP/blob/master/license.txt
+
 
-PeleRad is a module for modeling radiative transfer in reacting flows. 
diff --git a/inputs/inputs.egforLMeX b/inputs/inputs.egforLMeX
@@ -0,0 +1,19 @@
+peleLM.do_rad_solve = 1
+pelerad.kppath = "path/data/kpDB/"
+pelerad.composite_solve = 1
+pelerad.use_hypre = 0
+pelerad.verbose = 0
+pelerad.max_iter = 200
+pelerad.max_coarsening_level = 10
+pelerad.reltol = 1.0e-4
+pelerad.abstol = 1.0e-4
+pelerad.bottom_reltol = 1.0e-6
+pelerad.bottom_abstol = 1.0e-6
+pelerad.agglomeration = 1
+pelerad.consolidation = 0
+pelerad.bottom_verbose = 0
+pelerad.maxorder = 2
+pelerad.linop_maxorder = 2
+pelerad.max_fmg_iter = 0
+pelerad.lo_bc = Robin Periodic Periodic
+pelerad.hi_bc = Robin Periodic Periodic
diff --git a/scripts/build_PeleLMeX_Frontier.sh b/scripts/build_PeleLMeX_Frontier.sh
@@ -0,0 +1,32 @@
+#!/bin/bash -l
+
+MYPWD=${PWD}
+
+module load PrgEnv-cray cmake rocm/5.2.0 craype-x86-trento craype-accel-amd-gfx90a cray-libsci/21.08.1.2
+
+# git clone --recursive --branch development https://github.com/AMReX-Combustion/PeleLMeX.git
+git clone --recursive --branch pr_rad https://github.com/wjge/PeleLMeX.git
+git clone --branch main https://github.com/AMReX-Combustion/PeleRad.git
+git clone --branch eb_robin https://github.com/WeiqunZhang/amrex.git
+git clone --branch pr_rad https://github.com/wjge/PeleMP.git
+
+export PELELMEX_HOME=${MYPWD}/PeleLMeX
+export AMREX_HOME=${MYPWD}/amrex
+export PELE_PHYSICS_HOME=${MYPWD}/PeleLMeX/Submodules/PelePhysics
+export PELEMP_HOME=${MYPWD}/PeleMP
+export AMREX_HYDRO_HOME=${MYPWD}/PeleLMeX/Submodules/AMReX-Hydro
+export PELERAD_HOME=${MYPWD}/PeleRad
+
+cd ${PELEMP_HOME}/Exec/SootTests/PeleLMeX/laminar_flame
+
+# Build LMeX laminar_flame case
+#Build SUNDIALS and MAGMA
+make -j8 COMP=clang USE_HIP=TRUE USE_MPI=TRUE TINY_PROFILE=TRUE PELE_USE_MAGMA=TRUE HOSTNAME=frontier TPLrealclean
+make -j8 COMP=clang USE_HIP=TRUE USE_MPI=TRUE TINY_PROFILE=TRUE PELE_USE_MAGMA=TRUE HOSTNAME=frontier TPL
+
+#Build PeleLMeX
+make -j8 COMP=clang USE_HIP=TRUE USE_MPI=TRUE TINY_PROFILE=TRUE PELE_USE_MAGMA=TRUE HOSTNAME=frontier realclean
+make -j8 COMP=clang USE_HIP=TRUE USE_MPI=TRUE TINY_PROFILE=TRUE PELE_USE_MAGMA=TRUE HOSTNAME=frontier
+
+echo "pelerad.kppath = "$PELERAD_HOME/data/kpDB/"" >> first-input
+./PeleLMeX2d.hip.x86-trento.TPROF.MPI.HIP.ex first-input
diff --git a/src/AMRParam.hpp b/src/AMRParam.hpp
@@ -5,32 +5,31 @@
 #include <AMReX_Vector.H>
 #include <string>
 
-namespace PeleRad
-{
+namespace PeleRad {
 
 struct AMRParam
 {
 public:
-    amrex::ParmParse pp_;
+  amrex::ParmParse pp_;
 
-    int max_level_;
-    int ref_ratio_;
-    int n_cell_;
-    int max_grid_size_;
-    int prob_type_;
-    std::string plot_file_name_;
+  int max_level_;
+  int ref_ratio_;
+  int n_cell_;
+  int max_grid_size_;
+  int prob_type_;
+  std::string plot_file_name_;
 
-    AMREX_GPU_HOST
-    AMRParam(amrex::ParmParse const& pp) : pp_(pp)
-    {
-        pp_.query("max_level", max_level_);
-        pp_.query("ref_ratio", ref_ratio_);
-        pp_.query("n_cell", n_cell_);
-        pp_.query("max_grid_size", max_grid_size_);
-        pp_.query("prob_type", prob_type_);
-        pp.query("plot_file_name", plot_file_name_);
-    }
+  AMREX_GPU_HOST
+  AMRParam(amrex::ParmParse const& pp) : pp_(pp)
+  {
+    pp_.query("max_level", max_level_);
+    pp_.query("ref_ratio", ref_ratio_);
+    pp_.query("n_cell", n_cell_);
+    pp_.query("max_grid_size", max_grid_size_);
+    pp_.query("prob_type", prob_type_);
+    pp.query("plot_file_name", plot_file_name_);
+  }
 };
 
-}
+} // namespace PeleRad
 #endif
diff --git a/src/Constants.hpp b/src/Constants.hpp
@@ -1,36 +1,35 @@
 #ifndef CONSTANTS_HPP
 #define CONSTANTS_HPP
 
-namespace PeleRad
-{
+namespace PeleRad {
 
 struct RadComps
 {
-    int co2Indx  = -1;
-    int h2oIndx  = -1;
-    int coIndx   = -1;
-    int ch4Indx  = -1;
-    int c2h4Indx = -1;
+  int co2Indx = -1;
+  int h2oIndx = -1;
+  int coIndx = -1;
+  int ch4Indx = -1;
+  int c2h4Indx = -1;
 
-    void checkIndices()
-    {
-        if (co2Indx > 0)
-            std::cout << " include radiative gas: CO2, the index is " << co2Indx
-                      << std::endl;
-        if (h2oIndx > 0)
-            std::cout << " include radiative gas: H2O, the index is " << h2oIndx
-                      << std::endl;
-        if (coIndx > 0)
-            std::cout << " include radiative gas: CO, the index is " << coIndx
-                      << std::endl;
-        if (ch4Indx > 0)
-            std::cout << " include radiative gas: CH4, the index is " << coIndx
-                      << std::endl;
-        if (c2h4Indx > 0)
-            std::cout << " include radiative gas: C2H4, the index is " << coIndx
-                      << std::endl;
-    }
+  void checkIndices()
+  {
+    if (co2Indx > 0)
+      std::cout << " include radiative gas: CO2, the index is " << co2Indx
+                << std::endl;
+    if (h2oIndx > 0)
+      std::cout << " include radiative gas: H2O, the index is " << h2oIndx
+                << std::endl;
+    if (coIndx > 0)
+      std::cout << " include radiative gas: CO, the index is " << coIndx
+                << std::endl;
+    if (ch4Indx > 0)
+      std::cout << " include radiative gas: CH4, the index is " << coIndx
+                << std::endl;
+    if (c2h4Indx > 0)
+      std::cout << " include radiative gas: C2H4, the index is " << coIndx
+                << std::endl;
+  }
 };
 
-}
+} // namespace PeleRad
 #endif