Merge branch 'development' into pr-2435

zhichen3 · Nov 27, 2023 · 54e7fdd · 54e7fdd
2 parents d078ee0 + bc5fe8d
commit 54e7fdd
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Showing 23 changed files with 236 additions and 1,558 deletions.
diff --git a/Exec/reacting_tests/nse_test/problem_initialize_state_data.H b/Exec/reacting_tests/nse_test/problem_initialize_state_data.H
@@ -67,8 +67,11 @@ void problem_initialize_state_data (int i, int j, int k,
     Real abar;
     Real dq;
     Real dyedt;
+    Real dabardt;
+    Real dbeadt;
+    Real e_nu;
 
-    nse_interp(T, problem::rho0, ye, abar, dq, dyedt, burn_state.xn);
+    nse_interp(T, problem::rho0, ye, abar, dq, dyedt, dabardt, dbeadt, e_nu, burn_state.xn);
 #elif defined(NSE_NET)
     Real eps = 1.e-10_rt;
     bool input_ye_is_valid = true;

diff --git a/Exec/science/Detonation/problem_initialize.H b/Exec/science/Detonation/problem_initialize.H
@@ -16,7 +16,7 @@ void problem_initialize ()
     problem::in14 = network_spec_index("nitrogen-14");
     problem::io16 = network_spec_index("oxygen-16");
 
-    if (problem::ihe4 < 0 || problem::ic12 < 0 || problem::in14 < 0 || problem::io16 < 0) {
+    if (problem::ihe4 < 0 || problem::ic12 < 0 || problem::io16 < 0) {
         amrex::Error("ERROR: species indices not found");
     }
 
@@ -51,9 +51,15 @@ void problem_initialize ()
     }
 
     problem::xn[problem::ic12] = amrex::max(problem::cfrac, problem::smallx);
-    problem::xn[problem::in14] = amrex::max(problem::nfrac, problem::smallx);
     problem::xn[problem::io16] = amrex::max(problem::ofrac, problem::smallx);
-    problem::xn[problem::ihe4] = 1.0_rt - problem::cfrac - problem::nfrac - problem::ofrac - (NumSpec - 3) * problem::smallx;
+
+    if (problem::in14 >= 0) {
+       problem::xn[problem::in14] = amrex::max(problem::nfrac, problem::smallx);
+       problem::xn[problem::ihe4] = 1.0_rt - problem::cfrac - problem::nfrac - problem::ofrac - (NumSpec - 3) * problem::smallx;
+    }
+    else {
+       problem::xn[problem::ihe4] = 1.0_rt - problem::cfrac - problem::ofrac - (NumSpec - 2) * problem::smallx;
+    }
 
     // Set the ambient material
 

diff --git a/Exec/science/massive_star/problem_initialize_state_data.H b/Exec/science/massive_star/problem_initialize_state_data.H
@@ -82,10 +82,13 @@ void problem_initialize_state_data (int i, int j, int k,
         Real abar;
         Real dq;
         Real dyedt;
+        Real dabardt;
+        Real dbeadt;
+        Real e_nu;
         Real xn[NumSpec];
 
         nse_interp(state(i,j,k,UTEMP), state(i,j,k,URHO),
-                   state(i,j,k,UFX+AuxZero::iye), abar, dq, dyedt, xn);
+                   state(i,j,k,UFX+AuxZero::iye), abar, dq, dyedt, dabardt, dbeadt, e_nu, xn);
 
         state(i,j,k,UFX+AuxZero::iabar) = abar;
         state(i,j,k,UFX+AuxZero::ibea) = dq;

diff --git a/Source/driver/Castro.cpp b/Source/driver/Castro.cpp
@@ -24,7 +24,6 @@
 
 #ifdef RADIATION
 #include <Radiation.H>
-#include <RAD_F.H>
 #endif
 
 #ifdef AMREX_PARTICLES

diff --git a/Source/hydro/Castro_ctu_rad.cpp b/Source/hydro/Castro_ctu_rad.cpp
@@ -3,7 +3,6 @@
 
 #include "Radiation.H"
 #include "RadHydro.H"
-#include "RAD_F.H"
 #include "fluxlimiter.H"
 
 using namespace amrex;

diff --git a/Source/radiation/MGFLD.cpp b/Source/radiation/MGFLD.cpp
@@ -1,5 +1,4 @@
 #include <Radiation.H>
-#include <RAD_F.H>
 #include <rad_util.H>
 #include <filter.H>
 #include <blackbody.H>

diff --git a/Source/radiation/MGFLDRadSolver.cpp b/Source/radiation/MGFLDRadSolver.cpp
@@ -5,9 +5,6 @@
 #include <Radiation.H>
 #include <RadSolve.H>
 
-
-#include <RAD_F.H>
-
 #include <iostream>
 #include <iomanip>
 

diff --git a/Source/radiation/MGRadBndry.cpp b/Source/radiation/MGRadBndry.cpp
@@ -10,8 +10,6 @@
 #include <omp.h>
 #endif
 
-#include <RAD_F.H>
-
 using namespace amrex;
 
 int         MGRadBndry::ngroups = 1;

diff --git a/Source/radiation/Make.package b/Source/radiation/Make.package
@@ -29,8 +29,6 @@ CEXE_headers += HABEC.H
 CEXE_headers += filter.H
 CEXE_headers += filt_prim.H
 
-FEXE_headers += RAD_F.H
-
 CEXE_sources += trace_ppm_rad.cpp
 
 CEXE_headers += fluxlimiter.H

diff --git a/Source/radiation/RAD_F.H b/Source/radiation/RAD_F.H
diff --git a/Source/radiation/RadBndry.cpp b/Source/radiation/RadBndry.cpp
@@ -9,8 +9,6 @@
 #include <omp.h>
 #endif
 
-#include <RAD_F.H>
-
 using namespace amrex;
 
 int         RadBndry::first = 1;

diff --git a/Source/radiation/RadMultiGroup.cpp b/Source/radiation/RadMultiGroup.cpp
@@ -4,8 +4,6 @@
 
 #include <Radiation.H>
 
-#include <RAD_F.H>
-
 #include <AMReX_ParmParse.H>
 
 #include <iostream>

diff --git a/Source/radiation/RadPlotvar.cpp b/Source/radiation/RadPlotvar.cpp
@@ -2,8 +2,6 @@
 #include <Radiation.H>
 #include <fluxlimiter.H>
 
-#include <RAD_F.H>
-
 using namespace amrex;
 
 void Radiation::save_lambda_in_plotvar(int level, const Array<MultiFab,AMREX_SPACEDIM>& lambda)

diff --git a/Source/radiation/RadSolve.cpp b/Source/radiation/RadSolve.cpp
@@ -7,7 +7,6 @@
 #include <Radiation.H>  // for access to static physical constants only
 #include <rad_util.H>
 #include <problem_rad_source.H>
-#include <RAD_F.H>
 
 #include <iostream>
 

diff --git a/Source/radiation/Radiation.cpp b/Source/radiation/Radiation.cpp
@@ -5,7 +5,6 @@
 #include <rad_util.H>
 #include <filt_prim.H>
 
-#include <RAD_F.H>
 #include <AMReX_PROB_AMR_F.H>
 
 #include <opacity.H>

diff --git a/Source/radiation/SGRadSolver.cpp b/Source/radiation/SGRadSolver.cpp
@@ -5,9 +5,6 @@
 #include <Radiation.H>
 #include <RadSolve.H>
 
-
-#include <RAD_F.H>
-
 #include <iostream>
 
 #ifdef _OPENMP

diff --git a/Source/radiation/_interpbndry/Make.package b/Source/radiation/_interpbndry/Make.package
@@ -4,7 +4,3 @@ CA_BASE=EXE
 C$(CA_BASE)_sources += RadInterpBndryData.cpp RadBndryData.cpp
 
 C$(CA_BASE)_headers += RadInterpBndryData.H RadBndryData.H RadBoundCond.H
-
-ca_F90$(CA_BASE)_sources += RadInterpBndryData_$(DIM)d.F90
-
-ca_F$(CA_BASE)_headers += RADINTERPBNDRYDATA_F.H