Merge branch 'AMReX-Combustion:development' into null-deref

.github/workflows/ci.yml

@@ -271,9 +271,15 @@ jobs:
               pip install numpy
               ccache -z
               make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=dodecane_lu TINY_PROFILE=TRUE USE_CCACHE=TRUE ${{matrix.amrex_build_args}}
-              bash exec_ignDelay.sh
+              bash exec_ignDelay.sh firstpass
               python check_ignDelay.py
               if [ $? -ne 0 ]; then exit 1; fi; \
+              rm log PPreaction.txt inputs/inputs.0d_refine
+              make realclean
+              make -j ${{env.NPROCS}} Eos_Model=Manifold Transport_Model=Manifold Manifold_Dim=1 Chemistry_Model=Null TINY_PROFILE=TRUE USE_CCACHE=TRUE ${{matrix.amrex_build_args}}
+              bash exec_ignDelay.sh manifold
+              python check_ignDelay.py 0.0766 10
+              if [ $? -ne 0 ]; then exit 1; fi; \
           fi;
           make realclean
       - name: Ignition delay ccache report

.github/workflows/docs.yml

@@ -34,11 +34,16 @@ jobs:
         working-directory: ${{runner.workspace}}/build-docs
         run:  |
            echo "::add-matcher::.github/problem-matchers/sphinx.json"
-           cmake --build ${{runner.workspace}}/build-docs
-           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::"
+           cmake --build ${{runner.workspace}}/build-docs 2>&1 | tee -a build-output.txt
            touch ${{runner.workspace}}/build-docs/sphinx/html/.nojekyll
+      - name: Report
+        working-directory: ${{runner.workspace}}/build-docs
+        run: |
+          echo "::add-matcher::.github/problem-matchers/sphinx.json"
+          egrep "WARNING:|Warning:|warning:|ERROR:|Error:|error:" build-output.txt | sort | uniq | \
+            awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > build-output-warnings.txt
+          cat build-output-warnings.txt
+          exit $(tail -n 1 build-output-warnings.txt | awk '{print $2}')
       - name: Deploy
         if: github.event_name == 'push' && github.ref == 'refs/heads/development'
         uses: JamesIves/github-pages-deploy-action@releases/v3

Mechanisms/Null/mechanism.cpp

@@ -14,14 +14,14 @@ void
 CKSYME_STR(amrex::Vector<std::string>& ename)
 {
   ename.resize(1);
-  ename[0] = "XO";
+  ename[0] = "X0";
 }
 void
 CKSYMS_STR(amrex::Vector<std::string>& kname)
 {
   kname.resize(NUM_SPECIES);
   for (int i = 0; i < NUM_SPECIES; ++i) {
-    kname[0] = "X" + std::to_string(i);
+    kname[i] = "X" + std::to_string(i);
   }
 }
 

README.md

@@ -15,7 +15,7 @@ PelePhysics contains C++ source code for the following physics and other modules
 * *Reactions*: Routines for substepped integration of stiff chemical systems, including with CVODE
 * *Spray*: Lagrangian spray droplet library, formerly part of [PeleMP](https://github.com/AMReX-Combustion/PeleMP)
 * *Soot*: An implementation of the Hybrid Method of Moments soot model, formerly part of [PeleMP](https://github.com/AMReX-Combustion/PeleMP)
-* *Radiation*: Raidative heat transfer model based on the spherical harmonics method, formerly [PeleRad](https://github.com/AMReX-Combustion/PeleRad)
+* *Radiation*: Radiative heat transfer model based on the spherical harmonics method, formerly [PeleRad](https://github.com/AMReX-Combustion/PeleRad)
 * *Utility*: Several handy modules for data management across other Pele codes
 
 Additionally, PelePhysics contains a variety of stand-alone tools to aid in Pele simulation workflows, found in the `Support` directory.
@@ -50,8 +50,11 @@ imperative.
 
 ## Citation
 
-To cite PelePhysics as a whole and its use as part of the broader Pele suite, please use the following
-[SIAM Parallel Processing article](https://doi.org/10.1137/1.9781611977967.2):
+To cite PelePhysics as a whole and its use as part of the broader Pele
+suite, please use the following [SIAM Parallel
+Processing](https://doi.org/10.1137/1.9781611977967.2) and [Combustion
+and Flame](https://doi.org/10.1016/j.combustflame.2024.113740)
+articles:
 
 ```
 @article{PeleSoftware,
@@ -67,6 +70,18 @@ To cite PelePhysics as a whole and its use as part of the broader Pele suite, pl
   year = {2024},
   publisher = {Proceedings of the 2024 SIAM Conference on Parallel Processing for Scientific Computing}
 }
+
+@article{Hassanaly2024,
+  author = {Malik Hassanaly and Nicholas T. Wimer and Anne Felden and Lucas Esclapez and Julia Ream and Marc T. {Henry de Frahan} and Jon Rood and Marc Day},
+  title = {Symbolic construction of the chemical Jacobian of quasi-steady state (QSS) chemistries for Exascale computing platforms},
+  journal = {Combustion and Flame},
+  volume = {270},
+  pages = {113740},
+  year = {2024},
+  issn = {0010-2180},
+  doi = {https://doi.org/10.1016/j.combustflame.2024.113740},
+  url = {https://www.sciencedirect.com/science/article/pii/S0010218024004498},
+}
 ```
 
 To cite the multi-physics (soot, spray, radiation) capabilities in PelePhysics that were imported from
@@ -81,7 +96,7 @@ PeleMP and PeleRad, please use the following [Journal of Fluids Engineering arti
 }
 ```
 
-## Getting help, contributing
+## Getting help
 
 Do you have a question ? Found an issue ? Please use the [GitHub Discussions](https://github.com/AMReX-Combustion/PelePhysics/discussions) to engage
 with the development team or open a new [GitHub issue](https://github.com/AMReX-Combustion/PelePhysics/issues) to report a bug. The development team
@@ -93,7 +108,7 @@ New contributions to *PelePhysics* are welcome ! Contributing Guidelines are pro
 
 ## CEPTR
 
-This `PelePhysics` repository contains the CEPTR source code generation tool in order to support the inclusion of chemical models specified in the Cantera yaml format. CETPR derives from FUEGO, which was originally created by Michael Aivazis at CalTech, and donated to CCSE in 2001.  Originally, FUEGO was part of a larger Python-based set of workflow tools Michael developed for managing and publishing simulation-based studies.  FUEGO itself was developed as a drop-in replacement for the CHEMKIN library, and provided "hand-coded" replacement routines for evaluation of EOS thermodynamic functions that are considerably more efficient than their CHEMKIN counterparts.  Since 2001, CCSE has continued to modify FUEGO independently for its own use so that the current version here bears little resemblance to Michael's original code, or its intentions. CEPTR has adapted FUEGO code to use the Cantera yaml format and is now the preferred way of generating mechanism files.
+This `PelePhysics` repository contains the CEPTR source code generation tool in order to support the inclusion of chemical models specified in the Cantera yaml format. CETPR derives from FUEGO, which was originally created by Michael Aivazis at CalTech, and donated to CCSE in 2001.  Originally, FUEGO was part of a larger Python-based set of workflow tools Michael developed for managing and publishing simulation-based studies.  FUEGO itself was developed as a drop-in replacement for the CHEMKIN library, and provided "hand-coded" replacement routines for evaluation of EOS thermodynamic functions that are considerably more efficient than their CHEMKIN counterparts.  Since 2001, CCSE has continued to modify FUEGO independently for its own use so that the current version here bears little resemblance to Michael's original code, or its intentions. CEPTR has adapted FUEGO code to use the Cantera yaml format and is now the preferred way of generating mechanism files. If using CEPTR, please cite the above `Hassanaly2024` journal article.
 
 Typically, Cantera *mechanisms* (combustion models) are transmitted via a set of yaml files, which provide data for
 * *Species* - definition of chemical species, as composed by fundamental elements

Source/Eos/Manifold.H

@@ -92,7 +92,7 @@ struct Manifold
     const amrex::Real /*R*/,
     const amrex::Real /*T*/,
     const amrex::Real* /*Y[]*/,
-    amrex::Real* /*E*/)
+    amrex::Real /*E*/)
   {
     amrex::Error("RTY2E does not have significance for Manifold EOS");
   }

Source/Reactions/ReactorBase.H

@@ -81,11 +81,28 @@ public:
 
   void set_typ_vals_ode(const std::vector<amrex::Real>& ExtTypVals);
 
+  // Manifold EOS needs an eosparm - right now that is only propagated through
+  // the RK64 reactor
+  virtual void set_eos_parm(
+    const pele::physics::eos::EosParm<pele::physics::PhysicsType::eos_type>*
+      eosparm)
+  {
+    auto eos = pele::physics::PhysicsType::eos(eosparm);
+    if (eos.identifier() == "Manifold") {
+      amrex::Abort(
+        "Manifold EOS only supported with ReactorRK64 and ReactorNull for now");
+    } else {
+      m_eosparm = eosparm;
+    }
+  }
+
   ~ReactorBase() override = default;
 
 protected:
   int verbose{0};
   amrex::GpuArray<amrex::Real, NUM_SPECIES + 1> m_typ_vals = {0.0};
+  const pele::physics::eos::EosParm<pele::physics::PhysicsType::eos_type>*
+    m_eosparm;
 };
 } // namespace pele::physics::reactions
 #endif

Source/Reactions/ReactorNull.H

@@ -86,6 +86,13 @@ public:
       rhoE, frcEExt, FC_in, y_vect, vect_energy, FCunt, dt);
   }
 
+  void set_eos_parm(
+    const pele::physics::eos::EosParm<pele::physics::PhysicsType::eos_type>*
+      eosparm) override
+  {
+    m_eosparm = eosparm;
+  }
+
 private:
   utils::FlattenOps<Ordering> flatten_ops;
   int m_reactor_type{0};

Source/Reactions/ReactorNull.cpp

@@ -40,6 +40,7 @@ ReactorNull::react(
 #endif
 
   int captured_reactor_type = m_reactor_type;
+  const auto* leosparm = m_eosparm;
 
   ParallelFor(box, [=] AMREX_GPU_DEVICE(int i, int j, int k) noexcept {
     amrex::Real renergy_loc =
@@ -60,7 +61,7 @@ ReactorNull::react(
     }
     amrex::Real energy_loc = renergy_loc / rho_loc;
     amrex::Real T_loc = T_in(i, j, k, 0);
-    auto eos = pele::physics::PhysicsType::eos();
+    auto eos = pele::physics::PhysicsType::eos(leosparm);
     if (captured_reactor_type == ReactorTypes::e_reactor_type) {
       eos.REY2T(rho_loc, energy_loc, Y_loc, T_loc);
     } else if (captured_reactor_type == ReactorTypes::h_reactor_type) {

Source/Reactions/ReactorRK64.H

@@ -120,6 +120,13 @@ public:
       rhoE, frcEExt, FC_in, y_vect, vect_energy, FCunt, dt);
   }
 
+  void set_eos_parm(
+    const pele::physics::eos::EosParm<pele::physics::PhysicsType::eos_type>*
+      eosparm) override
+  {
+    m_eosparm = eosparm;
+  }
+
 private:
   amrex::Real absTol{1e-10};
   int rk64_nsubsteps_guess{10};

Source/Reactions/ReactorRK64.cpp

@@ -64,6 +64,7 @@ ReactorRK64::react(
   const int captured_nsubsteps_min = rk64_nsubsteps_min;
   const int captured_nsubsteps_max = rk64_nsubsteps_max;
   const amrex::Real captured_abstol = absTol;
+  const auto* leosparm = m_eosparm;
   RK64Params rkp;
 
   amrex::Gpu::DeviceVector<int> v_nsteps(ncells, 0);
@@ -103,7 +104,7 @@ ReactorRK64::react(
       for (int stage = 0; stage < rkp.nstages_rk64; stage++) {
         utils::fKernelSpec<Ordering>(
           0, 1, current_time - time_init, captured_reactor_type, soln_reg, ydot,
-          rhoe_init, rhoesrc_ext, rYsrc_ext);
+          rhoe_init, rhoesrc_ext, rYsrc_ext, leosparm);
 
         for (int sp = 0; sp < neq; sp++) {
           error_reg[sp] += rkp.err_rk64[stage] * dt_rk * ydot[sp];
@@ -131,9 +132,9 @@ ReactorRK64::react(
           rkp.betaerr_rk64 * pow((captured_abstol / max_err), rkp.exp2_rk64);
         dt_rk = amrex::max<amrex::Real>(dt_rk_min, dt_rk * change_factor);
       }
+      // Don't overstep the integration time
+      dt_rk = amrex::min<amrex::Real>(dt_rk, time_out - current_time);
     }
-    // Don't overstep the integration time
-    dt_rk = amrex::min<amrex::Real>(dt_rk, time_out - current_time);
     d_nsteps[icell] = nsteps;
     // copy data back
     for (int sp = 0; sp < neq; sp++) {
@@ -192,6 +193,7 @@ ReactorRK64::react(
   const int captured_nsubsteps_min = rk64_nsubsteps_min;
   const int captured_nsubsteps_max = rk64_nsubsteps_max;
   const amrex::Real captured_abstol = absTol;
+  const auto* leosparm = m_eosparm;
   RK64Params rkp;
 
   int ncells = static_cast<int>(box.numPts());
@@ -210,21 +212,18 @@ ReactorRK64::react(
     amrex::Real current_time = time_init;
     const int neq = (NUM_SPECIES + 1);
 
-    amrex::Real rho = 0.0;
+    auto eos = pele::physics::PhysicsType::eos(leosparm);
     for (int sp = 0; sp < NUM_SPECIES; sp++) {
       soln_reg[sp] = rY_in(i, j, k, sp);
       carryover_reg[sp] = soln_reg[sp];
-      rho += rY_in(i, j, k, sp);
     }
-    amrex::Real rho_inv = 1.0 / rho;
+    amrex::Real rho = 0.0, rho_inv = 0.0;
     amrex::Real mass_frac[NUM_SPECIES] = {0.0};
-    for (int sp = 0; sp < NUM_SPECIES; sp++) {
-      mass_frac[sp] = rY_in(i, j, k, sp) * rho_inv;
-    }
+    eos.RY2RRinvY(soln_reg, rho, rho_inv, mass_frac);
+
     amrex::Real temp = T_in(i, j, k, 0);
 
     amrex::Real Enrg_loc = rEner_in(i, j, k, 0) * rho_inv;
-    auto eos = pele::physics::PhysicsType::eos();
     if (captured_reactor_type == ReactorTypes::e_reactor_type) {
       eos.REY2T(rho, Enrg_loc, mass_frac, temp);
     } else if (captured_reactor_type == ReactorTypes::h_reactor_type) {
@@ -255,7 +254,7 @@ ReactorRK64::react(
       for (int stage = 0; stage < rkp.nstages_rk64; stage++) {
         utils::fKernelSpec<Ordering>(
           0, 1, current_time - time_init, captured_reactor_type, soln_reg, ydot,
-          rhoe_init, rhoesrc_ext, rYsrc_ext);
+          rhoe_init, rhoesrc_ext, rYsrc_ext, leosparm);
 
         for (int sp = 0; sp < neq; sp++) {
           error_reg[sp] += rkp.err_rk64[stage] * dt_rk * ydot[sp];
@@ -290,15 +289,11 @@ ReactorRK64::react(
     // copy data back
     int icell = (k - lo.z) * len.x * len.y + (j - lo.y) * len.x + (i - lo.x);
     d_nsteps[icell] = nsteps;
-    rho = 0.0;
     for (int sp = 0; sp < NUM_SPECIES; sp++) {
       rY_in(i, j, k, sp) = soln_reg[sp];
-      rho += rY_in(i, j, k, sp);
-    }
-    rho_inv = 1.0 / rho;
-    for (int sp = 0; sp < NUM_SPECIES; sp++) {
-      mass_frac[sp] = rY_in(i, j, k, sp) * rho_inv;
     }
+    eos.RY2RRinvY(soln_reg, rho, rho_inv, mass_frac);
+
     temp = soln_reg[NUM_SPECIES];
     rEner_in(i, j, k, 0) = rhoe_init[0] + dt_react * rhoesrc_ext[0];
     Enrg_loc = rEner_in(i, j, k, 0) * rho_inv;

Source/Reactions/ReactorUtils.H

@@ -369,29 +369,27 @@ fKernelSpec(
   amrex::Real* ydot_d, // NOLINT(readability-non-const-parameter)
   const amrex::Real* rhoe_init,
   const amrex::Real* rhoesrc_ext,
-  const amrex::Real* rYs)
+  const amrex::Real* rYs,
+  const pele::physics::eos::EosParm<pele::physics::PhysicsType::eos_type>*
+    eosparm = nullptr)
 {
-  amrex::Real rho_pt = 0.0;
-  amrex::GpuArray<amrex::Real, NUM_SPECIES> massfrac = {0.0};
+  auto eos = pele::physics::PhysicsType::eos(eosparm);
+  amrex::Real rho_pt = 0.0, rho_pt_inv = 0.0;
+  amrex::GpuArray<amrex::Real, NUM_SPECIES> massfrac = {0.0}, massdens = {0.0};
   for (int n = 0; n < NUM_SPECIES; n++) {
-    massfrac[n] = yvec_d[vec_index<OrderType>(n, icell, ncells)];
-    rho_pt += massfrac[n];
-  }
-  const amrex::Real rho_pt_inv = 1.0 / rho_pt;
-
-  for (int n = 0; n < NUM_SPECIES; n++) {
-    massfrac[n] *= rho_pt_inv;
+    massdens[n] = yvec_d[vec_index<OrderType>(n, icell, ncells)];
   }
+  eos.RY2RRinvY(massdens.data(), rho_pt, rho_pt_inv, massfrac.data());
 
   const amrex::Real nrg_pt =
     (rhoe_init[icell] + rhoesrc_ext[icell] * dt_save) * rho_pt_inv;
 
   amrex::Real temp_pt =
     yvec_d[vec_index<OrderType>(NUM_SPECIES, icell, ncells)];
 
-  amrex::Real Cv_pt = 0.0;
+  amrex::Real Cv_pt = 1.0;
   amrex::GpuArray<amrex::Real, NUM_SPECIES> ei_pt = {0.0};
-  auto eos = pele::physics::PhysicsType::eos();
+#ifndef USE_MANIFOLD_EOS
   if (reactor_type == ReactorTypes::e_reactor_type) {
     eos.REY2T(rho_pt, nrg_pt, massfrac.arr, temp_pt);
     eos.RTY2Ei(rho_pt, temp_pt, massfrac.arr, ei_pt.arr);
@@ -403,6 +401,7 @@ fKernelSpec(
   } else {
     amrex::Abort("Wrong reactor type. Choose between 1 (e) or 2 (h).");
   }
+#endif
 
   amrex::GpuArray<amrex::Real, NUM_SPECIES> cdots_pt = {0.0};
   eos.RTY2WDOT(rho_pt, temp_pt, massfrac.arr, cdots_pt.arr);

Testing/Exec/EosEval/main.cpp

@@ -190,6 +190,8 @@ main(int argc, char* argv[])
       amrex::WriteSingleLevelPlotfile(
         outfile, VarPlt, plt_VarsName, geom, 0.0, 0);
     }
+
+    eos_parms.deallocate();
   }
 
   amrex::Finalize();

Testing/Exec/IgnitionDelay/GPU_misc.H

@@ -23,7 +23,9 @@ initialize_data(
   amrex::Real t0,
   amrex::Real equiv_ratio,
   amrex::Real p,
-  amrex::GeometryData const& geomdata) noexcept
+  amrex::GeometryData const& geomdata,
+  const pele::physics::eos::EosParm<pele::physics::PhysicsType::eos_type>*
+    eosparm) noexcept
 {
   const amrex::Real* plo = geomdata.ProbLo();
   const amrex::Real* phi = geomdata.ProbHi();
@@ -50,26 +52,30 @@ initialize_data(
     P[n] = L[n] / 4.0;
   }
   // Y
+  auto eos = pele::physics::PhysicsType::eos(eosparm);
+
+#ifndef USE_MANIFOLD_EOS
   for (int n = 0; n < NUM_SPECIES; n++) {
     X[n] = 0.0;
   }
-  // X[O2_ID]   = 0.7;
-  // X[fuel_id] = 0.3;
+  // Assumes n-Dodecane
   X[O2_ID] = 1.0 / (equiv_ratio / 18.5 + 1 + 0.79 / 0.21);
   X[N2_ID] = 0.79 * X[O2_ID] / 0.21;
   X[fuel_id] = 1.0 - X[O2_ID] - X[N2_ID];
-
-  auto eos = pele::physics::PhysicsType::eos();
-
   eos.X2Y(&X[0], &Y[0]);
+#else
+  Y[0] = 0.0; // Progress variable
+  Y[1] = 1.0; // Density
+#endif
 
   // T
   temp = t0;
   // temp =  Temp_lo + (Temp_hi-Temp_lo)*y/L[1] + dTemp *
   // std::sin(2.0*pi*y/P[1]);
   if (energy_type == 1) {
     // get rho and E
-    eos.PYT2RE(pressure, &Y[0], temp, density, energy);
+    eos.PYT2R(pressure, &Y[0], temp, density);
+    eos.RTY2E(density, temp, &Y[0], energy);
   } else {
     // get rho and H
     eos.PYT2R(pressure, &Y[0], temp, density);