Updates.

.github/workflows/ci.yml

@@ -69,7 +69,7 @@ jobs:
           du -hs ${HOME}/.cache/ccache
       - name: FlameSheet debug test
         working-directory: ./Exec/RegTests/FlameSheet
-        run: ./PeleLMeX3d.gnu.DEBUG.ex flamesheet-drm19.inp max_step=2 amr.plot_files_output=0 amr.checkpoint_files_output=0
+        run: ./PeleLMeX3d.gnu.DEBUG.ex flamesheet-drm19.inp amr.max_step=1 amr.plot_int=-1 amr.check_int=-1
       - name: FlameSheet debug report
         working-directory: ./Exec/RegTests/FlameSheet
         run: |

.github/workflows/docs.yml

@@ -1,31 +1,33 @@
 name: PeleLMeX-Docs
 
 on:
+  workflow_dispatch:
   push:
     branches: [development]
     paths:
        - 'Docs/**'
-       - 'README.md'
        - '.github/workflows/docs.yml'
   pull_request:
     branches: [development]
     paths:
        - 'Docs/**'
-       - 'README.md'
        - '.github/workflows/docs.yml'
 
 jobs:
   Docs:
     runs-on: ubuntu-latest
     steps:
-      - name: Clone
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v3
       - name: Python
         uses: actions/setup-python@v3
         with:
           python-version: '3.x'
       - name: Dependencies
         run: |
+          #Currently ignoring doxygen
+          #export DEBIAN_FRONTEND=noninteractive
+          #sudo apt-get update
+          #sudo apt-get install -y --no-install-recommends doxygen graphviz
           python -m pip install --upgrade pip
           pip install sphinx sphinx_rtd_theme
       - name: Configure
@@ -38,7 +40,7 @@ jobs:
            echo "::remove-matcher owner=sphinx-problem-matcher-loose-no-severity::"
            echo "::remove-matcher owner=sphinx-problem-matcher-loose::"
            echo "::remove-matcher owner=sphinx-problem-matcher::"
-           touch ${{runner.workspace}}/build-docs/html/.nojekyll
+           touch ${{runner.workspace}}/build-docs/html/manual/html/.nojekyll
       - name: Deploy
         if: github.event_name == 'push' && github.ref == 'refs/heads/development'
         uses: JamesIves/github-pages-deploy-action@releases/v4

CMake/SetAmrexOptions.cmake

@@ -2,7 +2,7 @@ set(USE_XSDK_DEFAULTS OFF)
 set(AMReX_SPACEDIM "${PELELMEX_DIM}" CACHE STRING "Number of physical dimensions" FORCE)
 set(AMReX_MPI ${PELELMEX_ENABLE_MPI})
 set(AMReX_OMP ${PELELMEX_ENABLE_OPENMP})
-set(AMReX_EB ON)
+set(AMReX_EB ${PELELMEX_ENABLE_EB})
 set(AMReX_PARTICLES ${PELELMEX_ENABLE_AMREX_PARTICLES})
 set(AMReX_PLOTFILE_TOOLS ${PELELMEX_ENABLE_FCOMPARE})
 set(AMReX_SUNDIALS OFF)

CMakeLists.txt

@@ -25,9 +25,10 @@ option(PELELMEX_ENABLE_HYPRE "Enable Offload to Hypre" OFF)
 set(PELELMEX_PRECISION "DOUBLE" CACHE STRING "Floating point precision SINGLE or DOUBLE")
 
 # Physics options
-option(PELELMEX_ENABLE_EB "Enable Embedded Boundary" ON)
+option(PELELMEX_ENABLE_EB "Enable Embedded Boundary" OFF)
 option(PELELMEX_ENABLE_EFIELD "Enable Electric field module" OFF)
 option(PELELMEX_ENABLE_SOOT "Enable Soot module" OFF)
+option(PELELMEX_ENABLE_PARTICLE "Enable particles" OFF)
 
 # HPC options
 option(PELELMEX_ENABLE_MPI "Enable MPI" OFF)

Exec/Cases/ChallengeProblem/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/CounterFlow/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/CounterFlowSpray/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/DiffBunsen2D/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/JetInCrossflow/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/NormalJet_OpenDomain/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/PremBunsen2D/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/PremBunsen3D/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/SwirlFlowWallInteractions/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/Cases/TripleFlame/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/Efield/FlameSheetIons/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/Efield/IonizedAirWave/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/Efield/PremBunsen3DKuhl/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/RegTests/EB_BackwardStepFlame/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/RegTests/EB_EnclosedFlame/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/RegTests/EB_EnclosedVortex/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/RegTests/EB_FlowPastCylinder/GNUmakefile

@@ -8,7 +8,6 @@ AMREX_HYDRO_HOME   ?= ${PELELMEX_HOME}/Submodules/AMReX-Hydro
 DIM             = 2
 DEBUG           = FALSE
 PRECISION       = DOUBLE
-VERBOSE         = FALSE
 TINY_PROFILE    = FALSE
 USE_EB		= TRUE
 USE_HYPRE	= FALSE

Exec/RegTests/EB_PipeFlow/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/RegTests/EnclosedFlame/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = TRUE
 USE_HYPRE = FALSE
 

Exec/RegTests/EnclosedInjection/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/RegTests/FlameSheet/CMakeLists.txt

@@ -1,4 +1,3 @@
-set(PELELMEX_ENABLE_PARTICLES OFF)
 set(PELELMEX_EOS_MODEL Fuego)
 set(PELELMEX_CHEMISTRY_MODEL drm19)
 set(PELELMEX_TRANSPORT_MODEL Simple)

Exec/RegTests/FlameSheet/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/RegTests/HITDecay/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 3
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/RegTests/HotBubble/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/RegTests/PeriodicCases/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE
 

Exec/RegTests/SprayTest/GNUmakefile

@@ -2,7 +2,6 @@
 DIM = 2
 COMP = clang
 PRECISION = DOUBLE
-VERBOSE = FALSE
 USE_EB = FALSE
 USE_HYPRE = FALSE