AMReX-Combustion · jrood-nrel · Sep 19, 2023 · Sep 19, 2023 · Sep 19, 2023 · Sep 19, 2023
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -394,12 +394,12 @@ jobs:
         run: |
           curl -O https://repo.radeon.com/rocm/rocm.gpg.key
           sudo apt-key add rocm.gpg.key
-          echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
+          echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.6.1 ubuntu main' \
               | sudo tee /etc/apt/sources.list.d/rocm.list
           echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
               | sudo tee -a /etc/profile.d/rocm.sh
           sudo apt-get update
-          export TMPDIR=${{runner.workspace}}/.tmp && mkdir -p $TMPDIR && sudo apt-get install -y rocm-dev rocrand-dev rocprim-dev rocm-libs
+          sudo apt-get install -y rocm-dev rocrand-dev rocprim-dev
       - name: Install Ccache
         run: |
           wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz

diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -12,209 +12,8 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  #Build and run the 3D FlameSheet RegTest with GNU9.3 and no MPI support
-  F32D_NoMPI:
-    name: GNU@9.3 NOMPI Comp [FS3D]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      run: |
-        cd Exec/RegTests/FlameSheet/
-        make help
-        make TPL DIM=3 COMP=gnu USE_MPI=FALSE
-        make -j 2 DIM=3 COMP=gnu USE_MPI=FALSE
-    - name: Run
-      working-directory: ./Exec/RegTests/FlameSheet/
-      run: |
-        ./PeleLMeX3d.gnu.ex input.3d-regt peleLM.num_init_iter=1 amr.max_step=1 amr.plot_int=-1 amr.check_int=-1
-
-  # Build and Run the 2D FlameSheet RegTest with GNU9.3 and MPI support
-  FS2D_MPI:
-    name: GNU@9.3 MPI Comp [FS2D]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      run: |
-        cd Exec/RegTests/FlameSheet/
-        make TPL COMP=gnu
-        make -j 2 COMP=gnu
-    - name: RunBase
-      working-directory: ./Exec/RegTests/FlameSheet/
-      run: |
-        ./PeleLMeX2d.gnu.MPI.ex input.2d-regt amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
-    - name: RunSoret
-      working-directory: ./Exec/RegTests/FlameSheet/
-      run: |
-        ./PeleLMeX2d.gnu.MPI.ex input.2d-regt transport.use_soret=1 amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
-    - name: RunUnityLe
-      working-directory: ./Exec/RegTests/FlameSheet/
-      run: |
-        ./PeleLMeX2d.gnu.MPI.ex input.2d-regt peleLM.unity_Le=1 peleLM.Prandtl=0.75 amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
-
-  # Build the 2D FlameSheet RegTest with GNU9.3 and MPI+OMP support
-  FS2D_MPIOMP:
-    name: GNU@9.3 MPI OMP Comp [FS2D]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      run: |
-        cd Exec/RegTests/FlameSheet/
-        make TPL COMP=gnu USE_OMP=TRUE
-        make -j 2 COMP=gnu USE_OMP=TRUE
-
-  # Build and Run the CoVo RegTest with GNU9.3 and no MPI support
-  COVO2D_NoMPIRun:
-    name: GNU@9.3 NOMPI Run [COVO2D]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      working-directory: ./Exec/RegTests/PeriodicCases/
-      run: |
-        make TPL COMP=gnu USE_MPI=FALSE
-        make -j 2 COMP=gnu USE_MPI=FALSE
-    - name: Run
-      working-directory: ./Exec/RegTests/PeriodicCases/
-      run: |
-        ./PeleLMeX2d.gnu.ex input.2d_CoVo amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
-
-  # Build and Run the HoBubble RegTest with GNU9.3 and MPI support
-  HB2D_MPIRun:
-    name: GNU@9.3 MPI Run [HB2D]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      working-directory: ./Exec/RegTests/HotBubble/
-      run: |
-        make TPL COMP=gnu USE_MPI=TRUE
-        make -j 2 COMP=gnu USE_MPI=TRUE
-    - name: Run
-      working-directory: ./Exec/RegTests/HotBubble/
-      run: |
-        ./PeleLMeX2d.gnu.MPI.ex input.2d-regt amr.max_step=20 amr.plot_int=-1 amr.check_int=-1
-
-  # Build and Run the HotBubble RegTest with GNU9.3 in DEBUG
-  HB2D_DBGRun:
-    name: GNU@9.3 DEBUG Run [HB2DDBG]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      working-directory: ./Exec/RegTests/HotBubble/
-      run: |
-        make TPL COMP=gnu DEBUG=TRUE USE_MPI=FALSE
-        make -j 2 COMP=gnu DEBUG=TRUE USE_MPI=FALSE
-    - name: Run
-      working-directory: ./Exec/RegTests/HotBubble/
-      run: |
-        ./PeleLMeX2d.gnu.DEBUG.ex input.2d-regt amr.max_step=20 amr.plot_int=-1 amr.check_int=-1
-
-  # Build and Run the EnclosedFlame RegTest with GNU9.3 and MPI support
-  EF2D_MPIRun:
-    name: GNU@9.3 MPI Run [EF2D]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      working-directory: ./Exec/RegTests/EnclosedFlame/
-      run: |
-        make TPL COMP=gnu USE_MPI=TRUE
-        make -j 2 COMP=gnu USE_MPI=TRUE
-    - name: Run
-      working-directory: ./Exec/RegTests/EnclosedFlame/
-      run: |
-        ./PeleLMeX2d.gnu.MPI.ex input.2d-regt amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
-
   # Build and Run the EB_FlowPastCylinder RegTest with GNU9.3 and MPI support
-  FPC2D_MPIRun:
+  FPC2D:
     name: GNU@9.3 MPI Run [FPC2DDBG]
     runs-on: ubuntu-latest
     env:
@@ -242,28 +41,6 @@ jobs:
         ./PeleLMeX2d.gnu.DEBUG.MPI.ex input.2d-regt amr.max_step=2 amr.plot_int=-1 amr.check_int=-1 amrex.fpe_trap_invalid=1 amrex.fpe_trap_zero=1 amrex.fpe_trap_overflow=1
         ./PeleLMeX2d.gnu.DEBUG.MPI.ex input.2d-regt_WallBump amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
 
-  # Build and Run the HIT RegTest with GNU9.3 and MPI support
-  HIT3D_MPIRun:
-    name: GNU@9.3 MPI Run [HIT3D]
-    runs-on: ubuntu-latest
-    env:
-      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
-    steps:
-    - uses: actions/checkout@v3
-    - name: System Dependencies
-      run: .github/workflows/dependencies/dependencies_gcc10.sh
-    - name: Repo Dependencies
-      run: Utils/CloneDeps.sh
-    - name: Build
-      env:
-         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
-         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-         PELELMEX_HOME: ${GITHUB_WORKSPACE}
-         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
-         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
-      working-directory: ./Exec/RegTests/HITDecay/
-      run: |
-        make TPL COMP=gnu USE_MPI=TRUE
         make -j 2 COMP=gnu USE_MPI=TRUE
     - name: RunDNS
       working-directory: ./Exec/RegTests/HITDecay/
@@ -278,9 +55,8 @@ jobs:
       run: |
         ./PeleLMeX3d.gnu.MPI.ex input.3d_les peleLM.les_model="WALE" amr.max_step=10 amr.plot_int=-1 amr.check_int=-1
 
-
   # Build and Run the EB_PipeFlow RegTest with GNU9.3 and MPI support
-  EBPF3D_MPIRun:
+  EBPF3D:
     name: GNU@9.3 MPI Run [EBPF3D]
     runs-on: ubuntu-latest
     env:
@@ -308,7 +84,7 @@ jobs:
         mpirun -n 2 ./PeleLMeX3d.gnu.MPI.ex input.3d-regt amr.max_step=2 amr.plot_int=-1 amr.check_int=-1 amr.n_cell=128 32 32
 
   # Build and Run the TurbInflow RegTest in DEBUG with GNU9.3 and MPI support
-  TI3D_MPIRun:
+  TI3D:
     name: GNU@9.3 MPI Run [TI3DDBG]
     runs-on: ubuntu-latest
     env:
@@ -350,7 +126,7 @@ jobs:
         mpirun -n 2 ./PeleLMeX3d.gnu.DEBUG.MPI.ex input.3d_BoxLoZ peleLM.num_init_iter=1 amr.n_cell=32 32 32 amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
 
   # Build and Run the SprayTest RegTest with GNU9.3 and MPI support
-  SPRAY_MPIRun:
+  SPRAY:
     name: GNU@9.3 MPI Run [SPRAY]
     runs-on: ubuntu-latest
     env:

diff --git a/Exec/RegTests/EnclosedFlame/enclosedflame-2d.inp b/Exec/RegTests/EnclosedFlame/enclosedflame-2d.inp
@@ -0,0 +1,86 @@
+#----------------------DOMAIN DEFINITION------------------------
+geometry.is_periodic = 0 0               # For each dir, 0: non-perio, 1: periodic
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
+geometry.prob_lo     = -0.02 -0.02 0.0        # x_lo y_lo (z_lo)
+geometry.prob_hi     =  0.02  0.02 0.016        # x_hi y_hi (z_hi)
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# Interior, Inflow, Outflow, Symmetry,
+# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
+peleLM.lo_bc = NoSlipWallAdiab NoSlipWallAdiab
+peleLM.hi_bc = NoSlipWallAdiab NoSlipWallAdiab
+
+
+#-------------------------AMR CONTROL----------------------------
+amr.n_cell          = 128 128 32      # Level 0 number of cells in each direction   
+amr.v               = 1                # AMR verbose
+amr.max_level       = 2                # maximum level number allowed
+amr.ref_ratio       = 2 2 2 2 2         # refinement ratio
+amr.regrid_int      = 5                # how often to regrid
+amr.n_error_buf     = 2 2 2 2          # number of buffer cells in error est
+amr.grid_eff        = 0.7              # what constitutes an efficient grid
+amr.blocking_factor = 16               # block factor in grid generation (min box size)
+amr.max_grid_size   = 128               # max box size
+
+
+#--------------------------- Problem -------------------------------
+prob.P_mean = 101325.0
+prob.standoff = -0.002
+prob.pertmag = 0.0002
+pmf.datafile = "drm19_pmf.dat"
+pmf.do_cellAverage = 0
+
+#-------------------------PeleLM CONTROL----------------------------
+peleLM.v = 1
+peleLM.incompressible = 0
+peleLM.rho = 1.17
+peleLM.mu = 0.0
+peleLM.use_wbar = 1
+peleLM.sdc_iterMax = 2
+peleLM.floor_species = 0
+peleLM.num_divu_iter = 1
+peleLM.num_init_iter = 3
+
+peleLM.do_temporals = 1
+peleLM.do_mass_balance = 1
+
+#amr.restart = chk00005
+amr.check_int = 100
+amr.plot_int = 100
+amr.max_step = 10
+amr.dt_shrink = 0.0001
+amr.stop_time = 1.0
+#amr.stop_time = 1.00
+amr.cfl = 0.15
+amr.derive_plot_vars = avg_pressure mag_vort mass_fractions
+
+# --------------- INPUTS TO CHEMISTRY REACTOR ---------------
+peleLM.chem_integrator = "ReactorCvode"
+peleLM.use_typ_vals_chem = 1          # Use species/temp typical values in CVODE
+ode.rtol = 1.0e-6                     # Relative tolerance of the chemical solve
+ode.atol = 1.0e-5                     # Absolute tolerance factor applied on typical values
+cvode.solve_type = denseAJ_direct     # CVODE Linear solve type (for Newton direction) 
+cvode.max_order  = 4                  # CVODE max BDF order. 
+
+#--------------------REFINEMENT CONTROL------------------------
+#amr.refinement_indicators = temp
+#amr.temp.max_level     = 1
+#amr.temp.value_greater = 305
+#amr.temp.field_name    = temp
+
+#amr.refinement_indicators = magVort
+#amr.magVort.max_level     = 1
+#amr.magVort.value_greater = 500.0
+#amr.magVort.field_name    = mag_vort
+
+amr.refinement_indicators = yH
+amr.yH.max_level     = 5
+amr.yH.value_greater = 3.0e-7
+amr.yH.field_name    = Y(H)
+
+#--------------------LINEAR SOLVER CONTROL------------------------
+nodal_proj.verbose = 2
+nodal_proj.rtol = 2.0e-11
+amrex.fpe_trap_invalid = 1
+amrex.fpe_trap_zero = 1
+amrex.fpe_trap_overflow = 1