Merge branch 'development' into ROCK4

.codespell-ignore-words

@@ -1,3 +1,4 @@
+aprox
 blocs
 bloc
 inout
@@ -15,3 +16,6 @@ crate
 vie
 rock4
 rock2
+hep
+ine
+

.github/workflows/cuda.yml

@@ -41,8 +41,8 @@ jobs:
           make realclean
           make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4
 
-      - name: compile test_nse_net (ase)
+      - name: compile nse_net_cell (ase)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
-          cd unit_test/test_nse_net
+          cd unit_test/nse_net_cell
           make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4

.github/workflows/jac_cell.yml

@@ -34,7 +34,7 @@ jobs:
       - name: Run jac_cell
         run: |
           cd unit_test/jac_cell
-          ./main3d.gnu.ex inputs_aprox13 > test.out
+          ./main3d.gnu.ex inputs > test.out
 
       - name: Compare to stored output
         run: |

.github/workflows/nse_net.yml

@@ -26,42 +26,42 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
-      - name: Compile, test_nse_net (NSE_NET, ase)
+      - name: Compile, nse_net_cell (NSE_NET, ase)
         run: |
-          cd unit_test/test_nse_net
+          cd unit_test/nse_net_cell
           make realclean
           make -j 4
 
-      - name: Run test_nse_net (NSE_NET, ase)
+      - name: Run nse_net_cell (NSE_NET, ase)
         run: |
-          cd unit_test/test_nse_net
+          cd unit_test/nse_net_cell
           ./main3d.gnu.ex inputs_ase amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Print backtrace
-        if: ${{ failure() && hashFiles('unit_test/test_nse_net/Backtrace.0') != '' }}
-        run: cat unit_test/test_nse_net/Backtrace.0
+        if: ${{ failure() && hashFiles('unit_test/nse_net_cell/Backtrace.0') != '' }}
+        run: cat unit_test/nse_net_cell/Backtrace.0
 
       - name: Compare to stored output (NSE_NET, ase)
         run: |
-          cd unit_test/test_nse_net
+          cd unit_test/nse_net_cell
           diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/nse_net_unit_test.out
 
-      - name: Compile, test_nse_net/make_table (NSE_NET, ase, make_table)
+      - name: Compile, nse_net_cell/make_table (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_nse_net/make_table
+          cd unit_test/nse_net_cell/make_table
           make realclean
           make -j 4
 
-      - name: Run, test_nse_net/make_table (NSE_NET, ase, make_table)
+      - name: Run, nse_net_cell/make_table (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_nse_net/make_table
+          cd unit_test/nse_net_cell/make_table
           ./main3d.gnu.ex amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Print backtrace
-        if: ${{ failure() && hashFiles('unit_test/test_nse_net/make_table/Backtrace.0') != '' }}
-        run: cat unit_test/test_nse_net/make_table/Backtrace.0
+        if: ${{ failure() && hashFiles('unit_test/nse_net_cell/make_table/Backtrace.0') != '' }}
+        run: cat unit_test/nse_net_cell/make_table/Backtrace.0
 
       - name: Compare to stored output (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_nse_net/make_table
+          cd unit_test/nse_net_cell/make_table
           diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/nse_net_make_table_unit_test.out

.github/workflows/test_partition_functions.yml

@@ -28,17 +28,17 @@ jobs:
 
       - name: Compile
         run: |
-          cd unit_test/test_part_func
+          cd unit_test/part_func_cell
           make clean
           make -j 4
 
-      - name: Run test_part_func
+      - name: Run part_func_cell
         run: |
-          cd unit_test/test_part_func
+          cd unit_test/part_func_cell
           ./main3d.gnu.ex > test.out
 
       - name: Compare to stored output
         run: |
-          cd unit_test/test_part_func
+          cd unit_test/part_func_cell
           diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/part_func.out
 

.gitignore

@@ -12,6 +12,7 @@
 *.ind
 Docs/*/*.pdf
 Docs/*/*.ps
+Docs/source/runtime_parameters.rst
 MaestroUsersGuide.out
 MaestroUsersGuide.old
 
@@ -79,7 +80,7 @@ extern.f90
 build/
 doxy_files
 Docs/source/runtime_parameters.rst
-
+Docs/source/changelog.md
 
 # C++ parameters
 extern_parameters.H