Pass state Array4 in initdata instead of separate Array4 for each ent…

…ry. (#54) * Update the Case/* pelelm_initdata to take in state Array4 instead of separate entries. * Update call to pelelm_initdata to take in state_arr instead of separate entries. * Update Efield folder. * Update UnitTest folder. * Update RegTest/EB* cases. * Update the remainder of the tests. * Activate fpe in HotBubble regtest 2D. * Add a couple of HoBubble regtests. * Need to keep the aux Array4. * Update submods. * Missing change to state Array4 * Remove deprecated include of pmf.H
AMReX-Combustion · Feb 22, 2022 · 0e49e06 · 0e49e06
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commit 0e49e06
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diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -120,6 +120,68 @@ jobs:
       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 GNU7.5 and MPI support
+  HB2D_MPIRun:
+    name: GNU@7.5 MPI Run [HB2D]
+    runs-on: ubuntu-latest
+    env: 
+      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
+    steps:
+    - name: Cancel previous runs
+      uses: styfle/cancel-workflow-action@0.6.0
+      with:
+        access_token: ${{github.token}}
+    - uses: actions/checkout@v2
+    - name: System Dependencies
+      run: .github/workflows/dependencies/dependencies.sh
+    - name: Repo Dependencies
+      run: Utils/CloneDeps.sh
+    - name: Build
+      env:
+         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
+         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
+         PELELM_HOME: ${GITHUB_WORKSPACE}
+         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
+      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 HoBubble RegTest with GNU7.5 in DEBUG
+  HB2D_DBGRun:
+    name: GNU@7.5 DEBUG Run [HB2DDBG]
+    runs-on: ubuntu-latest
+    env: 
+      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
+    steps:
+    - name: Cancel previous runs
+      uses: styfle/cancel-workflow-action@0.6.0
+      with:
+        access_token: ${{github.token}}
+    - uses: actions/checkout@v2
+    - name: System Dependencies
+      run: .github/workflows/dependencies/dependencies.sh
+    - name: Repo Dependencies
+      run: Utils/CloneDeps.sh
+    - name: Build
+      env:
+         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
+         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
+         PELELM_HOME: ${GITHUB_WORKSPACE}
+         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
+      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 GNU7.5 and MPI support
   EF2D_MPIRun:
     name: GNU@7.5 MPI Run [EF2D]

diff --git a/Exec/Cases/CounterFlow/pelelm_prob.H b/Exec/Cases/CounterFlow/pelelm_prob.H
@@ -14,11 +14,7 @@ AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
 void pelelm_initdata(int i, int j, int k,
                      int is_incompressible,
-                     amrex::Array4<amrex::Real> const& vel,
-                     amrex::Array4<amrex::Real> const& rho,
-                     amrex::Array4<amrex::Real> const& rhoY,
-                     amrex::Array4<amrex::Real> const& rhoH,
-                     amrex::Array4<amrex::Real> const& temp,
+                     amrex::Array4<amrex::Real> const& state,
                      amrex::Array4<amrex::Real> const& aux,
                      amrex::GeometryData const& geomdata,
                      ProbParm const& prob_parm,
@@ -43,17 +39,12 @@ void pelelm_initdata(int i, int j, int k,
     constexpr amrex::Real Pi = 3.14159265358979323846264338327950288;
 
     auto eos = pele::physics::PhysicsType::eos();
-    amrex::GpuArray<amrex::Real, NUM_SPECIES + 4> pmf_vals = {0.0};
-    amrex::Real u[3] = {0.0};
-    amrex::Real molefrac[NUM_SPECIES] = {0.0};
     amrex::Real massfrac[NUM_SPECIES] = {0.0};
-    amrex::Real y1, y2;
-    amrex::Real splitx = prob_lo[0] + 0.5 * Lx;
 
     massfrac[N2_ID] = 0.767;
     massfrac[O2_ID] = 0.233;
 
-    temp(i,j,k) = 298.0;
+    state(i,j,k,TEMP) = 298.0;
 
     if (prob_parm.do_ignit) {
        amrex::Real radiusSq = AMREX_D_TERM(  (x-xc) * (x-xc),
@@ -62,31 +53,31 @@ void pelelm_initdata(int i, int j, int k,
        amrex::Real radius = std::sqrt(radiusSq);
        amrex::Real mixingWidth = 0.1*prob_parm.ignitSphereRad;
        amrex::Real mixingFunction = 0.5 * ( 1.0 + std::tanh((prob_parm.ignitSphereRad - radius)/mixingWidth));
-       temp(i,j,k) = mixingFunction * prob_parm.ignitT + (1.0 - mixingFunction) * 298.0;
+       state(i,j,k,TEMP) = mixingFunction * prob_parm.ignitT + (1.0 - mixingFunction) * 298.0;
        massfrac[CH4_ID] = 0.02;
        massfrac[O2_ID] = 0.233 * (1.0 - massfrac[CH4_ID]);
        massfrac[N2_ID] = 1.0 - massfrac[CH4_ID] - massfrac[O2_ID];
     }
 
-    AMREX_D_TERM(vel(i,j,k,0) = 0.0;,
-                 vel(i,j,k,1) = 0.1;,
-                 vel(i,j,k,2) = 0.0);
+    AMREX_D_TERM(state(i,j,k,VELX) = 0.0;,
+                 state(i,j,k,VELY) = 0.1;,
+                 state(i,j,k,VELZ) = 0.0);
 
     amrex::Real P_cgs = prob_parm.P_mean * 10.0;
 
     // Density
     amrex::Real rho_cgs = 0.0;
-    eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
-    rho(i,j,k) = rho_cgs * 1.0e3;
+    eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
+    state(i,j,k,DENSITY) = rho_cgs * 1.0e3;
 
     // Enthalpy
     amrex::Real h_cgs = 0.0;
-    eos.TY2H(temp(i,j,k), massfrac, h_cgs);
-    rhoH(i,j,k) = h_cgs * 1.0e-4 * rho(i,j,k);
+    eos.TY2H(state(i,j,k,TEMP), massfrac, h_cgs);
+    state(i,j,k,RHOH) = h_cgs * 1.0e-4 * state(i,j,k,DENSITY);
 
     // Species mass
     for (int n = 0; n < NUM_SPECIES; n++) {
-       rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
+       state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
     }
 }
 

diff --git a/Exec/Cases/NormalJet_OpenDomain/pelelm_prob.H b/Exec/Cases/NormalJet_OpenDomain/pelelm_prob.H
@@ -16,11 +16,7 @@ AMREX_FORCE_INLINE
 void
 pelelm_initdata (int i, int j, int k,
                  int is_incompressible,
-                 amrex::Array4<amrex::Real> const& vel,
-                 amrex::Array4<amrex::Real> const& rho,
-                 amrex::Array4<amrex::Real> const& rhoY,
-                 amrex::Array4<amrex::Real> const& rhoH,
-                 amrex::Array4<amrex::Real> const& temp,
+                 amrex::Array4<amrex::Real> const& state,
                  amrex::Array4<amrex::Real> const& aux,
                  amrex::GeometryData const& geomdata,
                  ProbParm const& prob_parm,
@@ -30,28 +26,28 @@ pelelm_initdata (int i, int j, int k,
 
     amrex::Real massfrac[NUM_SPECIES] = {0.0};
 
-    temp(i,j,k) = prob_parm.T_ox;
+    state(i,j,k,TEMP) = prob_parm.T_ox;
 
     for (int n = 0; n < NUM_SPECIES; n++)
     {
         massfrac[n] = prob_parm.Y_ox[n];
     }
 
-    vel(i,j,k,0) = 0.0;
-    vel(i,j,k,1) = 0.0;
-    vel(i,j,k,2) = 1.0;
+    state(i,j,k,VELX) = 0.0;
+    state(i,j,k,VELY) = 0.0;
+    state(i,j,k,VELZ) = 1.0;
 
     amrex::Real rho_cgs, P_cgs;
     P_cgs = prob_parm.P_mean * 10.0;
 
-    eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
-    rho(i,j,k) = rho_cgs * 1.0e3;            // CGS -> MKS conversion
+    eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
+    state(i,j,k,DENSITY) = rho_cgs * 1.0e3;            // CGS -> MKS conversion
 
-    eos.TY2H(temp(i,j,k), massfrac, rhoH(i,j,k));
-    rhoH(i,j,k) *= 1.0e-4 * rho(i,j,k);   // CGS -> MKS conversion
+    eos.TY2H(state(i,j,k,TEMP), massfrac, state(i,j,k,RHOH));
+    state(i,j,k,RHOH) *= 1.0e-4 * state(i,j,k,DENSITY);   // CGS -> MKS conversion
 
     for (int n = 0; n < NUM_SPECIES; n++) {
-      rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
+      state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
     }
 }
 

diff --git a/Exec/Cases/PremBunsen2D/pelelm_prob.H b/Exec/Cases/PremBunsen2D/pelelm_prob.H
@@ -15,11 +15,7 @@ AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
 void pelelm_initdata(int i, int j, int k,
                      int is_incompressible,
-                     amrex::Array4<amrex::Real> const& vel,
-                     amrex::Array4<amrex::Real> const& rho,
-                     amrex::Array4<amrex::Real> const& rhoY,
-                     amrex::Array4<amrex::Real> const& rhoH,
-                     amrex::Array4<amrex::Real> const& temp,
+                     amrex::Array4<amrex::Real> const& state,
                      amrex::Array4<amrex::Real> const& aux,
                      amrex::GeometryData const& geomdata,
                      ProbParm const& prob_parm,
@@ -50,7 +46,7 @@ void pelelm_initdata(int i, int j, int k,
     massfrac[N2_ID] = 0.767;
     massfrac[O2_ID] = 0.233;
 
-    temp(i,j,k) = 298.0;
+    state(i,j,k,TEMP) = 298.0;
 
     if ( x >= splitx ) {
        if ( (x-splitx) < ( std::sqrt((y+0.0009) / 0.01))/100.0) {
@@ -61,7 +57,7 @@ void pelelm_initdata(int i, int j, int k,
           y2 += prob_parm.standoff;
 
           pele::physics::PMF::pmf(pmf_data,y2, y2, pmf_vals);
-          temp(i,j,k) = pmf_vals[0];
+          state(i,j,k,TEMP) = pmf_vals[0];
           for (int n = 0; n < NUM_SPECIES; n++){
             massfrac[n] = pmf_vals[3 + n];
           }
@@ -76,33 +72,33 @@ void pelelm_initdata(int i, int j, int k,
           y2 += prob_parm.standoff;
 
           pele::physics::PMF::pmf(pmf_data, y2, y2, pmf_vals);
-          temp(i,j,k) = pmf_vals[0];
+          state(i,j,k,TEMP) = pmf_vals[0];
           for (int n = 0; n < NUM_SPECIES; n++){
             massfrac[n] = pmf_vals[3 + n];
           }
           //eos.X2Y(molefrac, massfrac);
        }
     }
 
-    AMREX_D_TERM(vel(i,j,k,0) = 0.0;,
-                 vel(i,j,k,1) = 0.1;,
-                 vel(i,j,k,2) = 0.0);
+    AMREX_D_TERM(state(i,j,k,VELX) = 0.0;,
+                 state(i,j,k,VELX) = 0.1;,
+                 state(i,j,k,VELX) = 0.0);
 
     amrex::Real P_cgs = prob_parm.P_mean * 10.0;
 
     // Density
     amrex::Real rho_cgs = 0.0;
-    eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
-    rho(i,j,k) = rho_cgs * 1.0e3;
+    eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
+    state(i,j,k,DENSITY) = rho_cgs * 1.0e3;
 
     // Enthalpy
     amrex::Real h_cgs = 0.0;
-    eos.TY2H(temp(i,j,k), massfrac, h_cgs);
-    rhoH(i,j,k) = h_cgs * 1.0e-4 * rho(i,j,k);
+    eos.TY2H(state(i,j,k,TEMP), massfrac, h_cgs);
+    state(i,j,k,RHOH) = h_cgs * 1.0e-4 * state(i,j,k,DENSITY);
 
     // Species mass
     for (int n = 0; n < NUM_SPECIES; n++) {
-       rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
+       state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
     }
 }
 

diff --git a/Exec/Cases/PremBunsen3D/pelelm_prob.H b/Exec/Cases/PremBunsen3D/pelelm_prob.H
@@ -15,11 +15,7 @@ AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
 void pelelm_initdata(int i, int j, int k,
                      int is_incompressible,
-                     amrex::Array4<amrex::Real> const& vel,
-                     amrex::Array4<amrex::Real> const& rho,
-                     amrex::Array4<amrex::Real> const& rhoY,
-                     amrex::Array4<amrex::Real> const& rhoH,
-                     amrex::Array4<amrex::Real> const& temp,
+                     amrex::Array4<amrex::Real> const& state,
                      amrex::Array4<amrex::Real> const& aux,
                      amrex::GeometryData const& geomdata,
                      ProbParm const& prob_parm,
@@ -52,7 +48,7 @@ void pelelm_initdata(int i, int j, int k,
     massfrac[N2_ID] = 0.767;
     massfrac[O2_ID] = 0.233;
 
-    temp(i,j,k) = 298.0;
+    state(i,j,k,TEMP) = 298.0;
 
     if ( (rad_xy) < ( std::sqrt((z+0.0009) / 0.01))/100.0) {
        amrex::Real pl1_angle = std::atan(0.01/prob_parm.slot_width);
@@ -62,32 +58,32 @@ void pelelm_initdata(int i, int j, int k,
        y2 += prob_parm.standoff;
 
        pele::physics::PMF::pmf(pmf_data,y2, y2, pmf_vals);
-       temp(i,j,k) = pmf_vals[0];
+       state(i,j,k,TEMP) = pmf_vals[0];
        for (int n = 0; n < NUM_SPECIES; n++){
          massfrac[n] = pmf_vals[3 + n];
        }
        //eos.X2Y(molefrac, massfrac);
     }
 
-    AMREX_D_TERM(vel(i,j,k,0) = 0.0;,
-                 vel(i,j,k,1) = 0.1;,
-                 vel(i,j,k,2) = 0.0);
+    AMREX_D_TERM(state(i,j,k,VELX) = 0.0;,
+                 state(i,j,k,VELY) = 0.1;,
+                 state(i,j,k,VELZ) = 0.0);
 
     amrex::Real P_cgs = prob_parm.P_mean * 10.0;
 
     // Density
     amrex::Real rho_cgs = 0.0;
-    eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
-    rho(i,j,k) = rho_cgs * 1.0e3;
+    eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
+    state(i,j,k,DENSITY) = rho_cgs * 1.0e3;
 
     // Enthalpy
     amrex::Real h_cgs = 0.0;
-    eos.TY2H(temp(i,j,k), massfrac, h_cgs);
-    rhoH(i,j,k) = h_cgs * 1.0e-4 * rho(i,j,k);
+    eos.TY2H(state(i,j,k,TEMP), massfrac, h_cgs);
+    state(i,j,k,RHOH) = h_cgs * 1.0e-4 * state(i,j,k,DENSITY);
 
     // Species mass
     for (int n = 0; n < NUM_SPECIES; n++) {
-       rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
+       state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
     }
 }
 

diff --git a/Exec/Cases/TripleFlame/pelelm_prob.H b/Exec/Cases/TripleFlame/pelelm_prob.H
@@ -49,11 +49,7 @@ AMREX_FORCE_INLINE
 void
 pelelm_initdata (int i, int j, int k, 
                  int is_incompressible,
-                 amrex::Array4<amrex::Real> const& vel,
-                 amrex::Array4<amrex::Real> const& rho,
-                 amrex::Array4<amrex::Real> const& rhoY,
-                 amrex::Array4<amrex::Real> const& rhoH,
-                 amrex::Array4<amrex::Real> const& temp,
+                 amrex::Array4<amrex::Real> const& state,
                  amrex::Array4<amrex::Real> const& aux,
                  amrex::GeometryData const& geomdata,
                  ProbParm const& prob_parm,
@@ -94,28 +90,28 @@ pelelm_initdata (int i, int j, int k,
 
     amrex::Real Gaussian_T = std::exp( - (rad*rad) / (2.0 * ( Gauss_T_width * ( 1.0 + (y - y_lo) / 0.03)) 
                                                           * ( Gauss_T_width * ( 1.0 + (y - y_lo) / 0.03)) ));  
-    temp(i,j,k) = prob_parm.T_in + (Gauss_maxT-prob_parm.T_in) * Gaussian_T;
+    state(i,j,k,TEMP) = prob_parm.T_in + (Gauss_maxT-prob_parm.T_in) * Gaussian_T;
 
     amrex::Real Gaussian_spec = std::exp( - (rad*rad) / (2.0 * ( Gauss_Spec_width * ( 1.0 + (y - y_lo) / 0.03)) 
                                                           * ( Gauss_Spec_width * ( 1.0 + (y - y_lo) / 0.03)) ));  
     for (int n = 0; n < NUM_SPECIES; ++n) {  
        massfrac[n] = (1.0 - Gaussian_spec) * massfrac[n] + Gaussian_spec * air_Y[n];
     }     
 
-    vel(i,j,k,0) = 0.0;
-    vel(i,j,k,1) = prob_parm.V_in;
+    state(i,j,k,VELX) = 0.0;
+    state(i,j,k,VELY) = prob_parm.V_in;
 
     amrex::Real rho_cgs, P_cgs;
     P_cgs = prob_parm.P_mean * 10.0;
 
-    eos.PYT2R(P_cgs, massfrac, temp(i,j,k), rho_cgs);
-    rho(i,j,k) = rho_cgs * 1.0e3;            // CGS -> MKS conversion
+    eos.PYT2R(P_cgs, massfrac, state(i,j,k,TEMP), rho_cgs);
+    state(i,j,k,DENSITY) = rho_cgs * 1.0e3;               // CGS -> MKS conversion
 
-    eos.TY2H(temp(i,j,k), massfrac, rhoH(i,j,k));
-    rhoH(i,j,k) = rhoH(i,j,k) * 1.0e-4 * rho(i,j,k);   // CGS -> MKS conversion
+    eos.TY2H(state(i,j,k,TEMP), massfrac, state(i,j,k,RHOH));
+    state(i,j,k,RHOH) *= 1.0e-4 * state(i,j,k,DENSITY);   // CGS -> MKS conversion
 
     for (int n = 0; n < NUM_SPECIES; n++) {
-      rhoY(i,j,k,n) = massfrac[n] * rho(i,j,k);
+      state(i,j,k,FIRSTSPEC+n) = massfrac[n] * state(i,j,k,DENSITY);
     }
 }