Merge branch 'development' into new_rk2_sdc_and_eos

.github/workflows/castro-development.yml

@@ -0,0 +1,85 @@
+name: Castro development
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-apps-dev
+  cancel-in-progress: true
+
+jobs:
+  castro-development:
+    name: Castro development
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Download Castro
+      uses: actions/checkout@v4
+      with:
+        repository: 'AMReX-Astro/Castro'
+        ref: development
+        path: 'Castro'
+    - name: Download AMReX
+      uses: actions/checkout@v4
+      with:
+        repository: 'AMReX-Codes/amrex'
+        ref: development
+        path: 'amrex'
+    - name: Dependencies
+      run: |
+        .github/workflows/dependencies/dependencies.sh
+        .github/workflows/dependencies/dependencies_ccache.sh
+    - name: Set Up Cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/ccache
+        key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+        restore-keys: |
+             ccache-${{ github.workflow }}-${{ github.job }}-git-
+    - name: Build flame_wave
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=75M
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
+
+        export AMREX_HOME=${PWD}/amrex
+        export MICROPHYSICS_HOME=${PWD}
+
+        cd Castro/Exec/science/flame_wave/
+        make -j2 CCACHE=ccache USE_MPI=FALSE
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
+    - name: Build subchandra
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=75M
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
+
+        export AMREX_HOME=${PWD}/amrex
+        export MICROPHYSICS_HOME=${PWD}
+
+        cd Castro/Exec/science/subchandra/
+        make -j2 CCACHE=ccache USE_MPI=FALSE
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
+  save_pr_number:
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Save PR number
+        env:
+          PR_NUMBER: ${{ github.event.number }}
+        run: |
+          echo $PR_NUMBER > pr_number.txt
+      - uses: actions/upload-artifact@v3
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1

integration/VODE/actual_integrator.H

@@ -100,8 +100,9 @@ void actual_integrator (BurnT& state, Real dt)
     // need to sync the auxiliary data up with the new mass fractions
     set_aux_comp_from_X(state);
 #endif
-
-    eos(eos_input_re, state);
+    if (call_eos_in_rhs) {
+        eos(eos_input_re, state);
+    }
 
 #endif
 

interfaces/rhs_type.H

@@ -2,37 +2,13 @@
 #define rhs_type_H
 
 #include <AMReX_REAL.H>
+#include <AMReX_Loop.H>
 #include <network_properties.H>
 #ifdef SCREENING
 #include <screen.H>
 #endif
 #include <tfactors.H>
 
-// Implementation of "constexpr for" based on
-// https://artificial-mind.net/blog/2020/10/31/constexpr-for
-//
-// Approximates what one would get from a compile-time
-// unrolling of the loop
-// for (int i = 0; i < N; ++i) {
-//    f(i);
-// }
-//
-// The mechanism is recursive, we evaluate f(i) at the current
-// i and then call the for loop at i+1. f() is a lambda function
-// that provides the body of the loop and takes only an integer
-// i as its argument. It is assumed that at the loop call site
-// the lambda is declared [&] so that it can operate on whatever
-// data it needs.
-
-template<auto I, auto N, class F>
-AMREX_GPU_HOST_DEVICE AMREX_INLINE
-constexpr void constexpr_for (F&& f)
-{
-    if constexpr (I < N) {
-        f(std::integral_constant<decltype(I), I>());
-        constexpr_for<I+1, N>(f);
-    }
-}
 
 namespace RHS
 {

networks/rhs.H

@@ -4,6 +4,7 @@
 #include <AMReX.H>
 #include <AMReX_REAL.H>
 #include <AMReX_Print.H>
+#include <AMReX_Loop.H>
 
 #include <ArrayUtilities.H>
 #include <rhs_type.H>

nse_solver/nse_compatibility/GNUmakefile

@@ -0,0 +1,44 @@
+PRECISION  = DOUBLE
+PROFILE    = FALSE
+
+DEBUG      = FALSE
+
+DIM        = 3
+
+COMP	   = gnu
+
+USE_MPI    = FALSE
+USE_OMP    = FALSE
+
+USE_REACT = TRUE
+
+USE_NSE_NET = TRUE
+EBASE = main
+
+# define the location of the Microphysics top directory
+MICROPHYSICS_HOME ?= ../..
+
+# This sets the EOS directory
+EOS_DIR     := helmholtz
+
+# This sets the network directory
+NETWORK_DIR := subch_base
+
+SCREEN_METHOD = chabrier1998
+
+CONDUCTIVITY_DIR := stellar
+
+INTEGRATOR_DIR =  VODE
+
+ifeq ($(USE_CUDA), TRUE)
+  INTEGRATOR_DIR := VODE
+endif
+
+EXTERN_SEARCH += .
+
+Bpack   := ./Make.package
+Blocs   := .
+
+include $(MICROPHYSICS_HOME)/unit_test/Make.unit_test
+
+

nse_solver/nse_compatibility/Make.package

@@ -0,0 +1,2 @@
+CEXE_sources += main.cpp
+CEXE_headers += nse_network_compatibility.H

nse_solver/nse_compatibility/README.md

@@ -0,0 +1,14 @@
+# NSE Network Checking Script
+
+This is a script for checking whether integrated mass fractions of
+a reaction network will eventually match with the mass fractions
+calculated via NSE equations. Currently, this is only valid for networks
+that do not involve weak rates.
+
+* Note that the integration doesn't achieve NSE even though we have
+USE_NSE_NET=TRUE is due to the reference size of the cell. By setting
+nse.nse_dx_independet=1 will fix this.
+
+Script will print out all burn_state cases when nse_dx_independent is
+not enabled. It will only print out burn_state cases that didn't enter NSE
+when nse_dx_independent=1

nse_solver/nse_compatibility/_parameters

@@ -0,0 +1,22 @@
+@namespace: unit_test
+
+run_prefix    character  ""
+
+# the final time to integrate to
+tmax          real       1.e3
+
+# first output time -- we will output in nsteps logarithmically spaced steps between [tfirst, tmax]
+tfirst        real       0.0
+
+# number of steps (logarithmically spaced)
+nsteps        integer    100
+
+rho_min   real   1.e7
+rho_max   real   1.e9
+
+nrho      integer    4
+
+T_min     real   6.e9
+T_max     real   8.e9
+
+nT        integer    4

nse_solver/nse_compatibility/inputs_nse_compatibility

@@ -0,0 +1,26 @@
+# this inputs is used for checking the compatibility of networks with NSE_NET
+
+unit_test.run_prefix = "test_nse_network_compatibility_"
+
+integrator.burner_verbose = 0
+
+# Set which jacobian to use
+# 1 = analytic jacobian
+# 2 = numerical jacobian
+
+integrator.jacobian = 1
+
+integrator.renormalize_abundances = 0
+
+integrator.rtol_spec = 1.0e-6
+integrator.rtol_enuc = 1.0e-6
+integrator.atol_spec = 1.0e-10
+integrator.atol_enuc = 1.0e-6
+
+unit_test.tmax = 1.e3
+unit_test.tfirst = 1.e-10
+unit_test.nsteps = 100
+
+integrator.integrate_energy = 0
+integrator.call_eos_in_rhs = 0
+integrator.do_species_clip = 0

nse_solver/nse_compatibility/main.cpp

@@ -0,0 +1,34 @@
+#include <iostream>
+#include <cstring>
+#include <vector>
+
+#include <AMReX_ParmParse.H>
+#include <AMReX_MultiFab.H>
+using namespace amrex;
+
+#include <extern_parameters.H>
+#include <eos.H>
+#include <network.H>
+#include <nse_network_compatibility.H>
+#include <unit_test.H>
+
+int main(int argc, char *argv[]) {
+
+  amrex::Initialize(argc, argv);
+
+  std::cout << "starting the single zone burn..." << std::endl;
+
+  ParmParse ppa("amr");
+
+  init_unit_test();
+
+  // C++ EOS initialization (must be done after Fortran eos_init and init_extern_parameters)
+  eos_init();
+
+  // C++ Network, RHS, screening, rates initialization
+  network_init();
+
+  nse_network_compatibility();
+
+  amrex::Finalize();
+}