From 92cad719e5d9671a373c7fdc04810d47f4c6c88e Mon Sep 17 00:00:00 2001
From: Andy Nonaka <AJNonaka@lbl.gov>
Date: Thu, 22 Aug 2024 10:43:47 -0700
Subject: [PATCH] namelist

---
 exec/reactDiff/GNUmakefile            | 14 +++++++++++---
 src_reactDiff/Make.package            |  3 +++
 src_reactDiff/reactDiff_functions.H   | 16 ++++++++++++++++
 src_reactDiff/reactDiff_functions.cpp | 22 ++++++++++++++++++++++
 src_reactDiff/reactDiff_namespace.H   |  4 ++++
 5 files changed, 56 insertions(+), 3 deletions(-)
 create mode 100644 src_reactDiff/Make.package
 create mode 100644 src_reactDiff/reactDiff_functions.H
 create mode 100644 src_reactDiff/reactDiff_functions.cpp
 create mode 100644 src_reactDiff/reactDiff_namespace.H

diff --git a/exec/reactDiff/GNUmakefile b/exec/reactDiff/GNUmakefile
index 16102b88..24812ca7 100644
--- a/exec/reactDiff/GNUmakefile
+++ b/exec/reactDiff/GNUmakefile
@@ -9,6 +9,7 @@ USE_CUDA  = FALSE
 COMP      = gnu
 DIM       = 2
 MAX_SPEC  = 8
+MAX_REAC  = 5
 
 TINY_PROFILE = FALSE
 
@@ -19,9 +20,13 @@ include $(AMREX_HOME)/Tools/GNUMake/Make.defs
 #VPATH_LOCATIONS   += .
 #INCLUDE_LOCATIONS += .
 
-#include ../../src_reactDiff/Make.package
-#VPATH_LOCATIONS   += ../../src_reactDiff/
-#INCLUDE_LOCATIONS += ../../src_reactDiff/
+include ../../src_reactDiff/Make.package
+VPATH_LOCATIONS   += ../../src_reactDiff/
+INCLUDE_LOCATIONS += ../../src_reactDiff/
+
+include ../../src_chemistry/Make.package
+VPATH_LOCATIONS   += ../../src_chemistry/
+INCLUDE_LOCATIONS += ../../src_chemistry/
 
 include ../../src_analysis/Make.package
 VPATH_LOCATIONS   += ../../src_analysis/
@@ -54,3 +59,6 @@ endif
 MAXSPECIES := $(strip $(MAX_SPEC))
 DEFINES += -DMAX_SPECIES=$(MAXSPECIES)
 
+MAXREACTION := $(strip $(MAX_REAC))
+DEFINES += -DMAX_REACTION=$(MAXREACTION)
+
diff --git a/src_reactDiff/Make.package b/src_reactDiff/Make.package
new file mode 100644
index 00000000..a2258eb7
--- /dev/null
+++ b/src_reactDiff/Make.package
@@ -0,0 +1,3 @@
+CEXE_sources   += reactDiff_functions.cpp
+CEXE_headers   += reactDiff_functions.H
+CEXE_headers   += reactDiff_namespace.H
diff --git a/src_reactDiff/reactDiff_functions.H b/src_reactDiff/reactDiff_functions.H
new file mode 100644
index 00000000..1c63e846
--- /dev/null
+++ b/src_reactDiff/reactDiff_functions.H
@@ -0,0 +1,16 @@
+#ifndef _reactdiff_functions_H_
+#define _reactdiff_functions_H_
+
+#include <AMReX.H>
+
+#include "common_functions.H"
+#include "common_namespace.H"
+#include "reactDiff_namespace.H"
+
+using namespace reactDiff;
+using namespace amrex;
+using namespace common;
+
+void InitializeReactDiffNamespace();
+
+#endif
diff --git a/src_reactDiff/reactDiff_functions.cpp b/src_reactDiff/reactDiff_functions.cpp
new file mode 100644
index 00000000..20f91086
--- /dev/null
+++ b/src_reactDiff/reactDiff_functions.cpp
@@ -0,0 +1,22 @@
+#include "reactDiff_functions.H"
+#include "AMReX_ParmParse.H"
+
+// only used for split schemes (temporal_integrator>=0)
+// 0=explicit trapezoidal predictor/corrector
+// 1=Crank-Nicolson semi-implicit
+// 2=explicit midpoint
+// 3=multinomial diffusion
+// 4=forward Euler  
+
+AMREX_GPU_MANAGED int reactDiff::diffusion_type;
+
+void InitializeReactDiffNamespace()
+{
+    // extract inputs parameters
+    ParmParse pp;
+
+    diffusion_type = 0;
+    pp.query("diffusion_type",diffusion_type);
+    
+    return;
+}
diff --git a/src_reactDiff/reactDiff_namespace.H b/src_reactDiff/reactDiff_namespace.H
new file mode 100644
index 00000000..83fa5db0
--- /dev/null
+++ b/src_reactDiff/reactDiff_namespace.H
@@ -0,0 +1,4 @@
+namespace reactDiff {
+
+    extern AMREX_GPU_MANAGED int diffusion_type;
+}