Merge branch 'development' into nse_test_cleaning

AMReX-Astro · Dec 26, 2023 · 51b2328 · 51b2328
2 parents a151e25 + c3509d4
commit 51b2328
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diff --git a/.github/workflows/dependencies_hip.sh b/.github/workflows/dependencies_hip.sh
@@ -1,17 +1,26 @@
 #!/usr/bin/env bash
 #
-# Copyright 2020-2022 The AMReX Community
+# Copyright 2020 The AMReX Community
 #
 # License: BSD-3-Clause-LBNL
 # Authors: Axel Huebl
 
+# search recursive inside a folder if a file contains tabs
+#
+# @result 0 if no files are found, else 1
+#
+
 set -eu -o pipefail
 
+# `man apt.conf`:
+#   Number of retries to perform. If this is non-zero APT will retry
+#   failed files the given number of times.
+echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
 
 # Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
 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/${1-debian}/ ubuntu main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
@@ -34,12 +43,14 @@ sudo apt-get install -y --no-install-recommends \
     roctracer-dev   \
     rocprofiler-dev \
     rocrand-dev     \
-    rocprim-dev
+    rocprim-dev     \
+    hiprand-dev
 
 # activate
 #
 source /etc/profile.d/rocm.sh
 hipcc --version
+hipconfig --full
 which clang
 which clang++
 which flang
diff --git a/.github/workflows/model_parser.yml b/.github/workflows/model_parser.yml
@@ -0,0 +1,34 @@
+name: model parser
+
+on: [pull_request]
+jobs:
+  model_parser:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          cd ../amrex
+          git fetch; git checkout development
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
+
+      - name: Compile model_parser test
+        run: |
+          cd Util/model_parser/test
+          make -j 4
+
+      - name: Run model_parser test
+        run: |
+          cd Util/model_parser/test
+          ./Castro3d.gnu.ex
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,7 @@
+# 23.12
+
+  * The radiation solver port to C++ has been completed (#2638, #2648)
+
 # 23.11
 
   * Problem GNUmakefiles have been standardized and now allow for the

diff --git a/Docs/source/io.rst b/Docs/source/io.rst
@@ -562,7 +562,15 @@ By default, 4 output files are created:
 
        The species masses are given in units of solar masses.
 
-Some problems have custom versions of the diagnostics with additional information.
+``Castro/Util/scripts/diag_parser.py`` contains Python code for parsing
+these output files into Numpy arrays.  Usage instructions are included
+in the file, along with an example script at
+``Castro/Util/scripts/plot_species.py``.  This reads a
+``species_diag.out`` file provided on the command line and makes a plot
+of the total mass fractions over time.
+
+Some problems have custom versions of the diagnostics with additional
+information.  These are not currently supported by the Python parser.
 
 
 .. _sec:parallel_io:

diff --git a/Exec/Make.Castro b/Exec/Make.Castro
@@ -270,6 +270,10 @@ ifeq ($(USE_ROTATION), TRUE)
   DEFINES += -DROTATION
 endif
 
+ifeq ($(USE_SPECIES_SOURCES), TRUE)
+  DEFINES += -DCONS_SPECIES_HAVE_SOURCES
+endif
+
 ifeq ($(USE_PARTICLES), TRUE)
   Bdirs += Source/particles
 endif

diff --git a/Exec/radiation_tests/Rad2Tshock/ci-benchmarks/Rad2TShock-1d.out b/Exec/radiation_tests/Rad2Tshock/ci-benchmarks/Rad2TShock-1d.out
@@ -37,5 +37,5 @@
  magmom                       1.2327065163e-07       1.4587103381e-07
  angular_momentum_x                          0                      0
  angular_momentum_y                          0                      0
- angular_momentum_z                          0                      0
+ angular_momentum_z                         -0                     -0
 
diff --git a/Exec/reacting_tests/nse_test/create_pretty_tables.py b/Exec/reacting_tests/nse_test/create_pretty_tables.py
@@ -112,10 +112,9 @@ def read_convergence(file_lo, file_hi):
                  "rho_E": r"$\rho E$",
                  "rho_e": r"$\rho e$",
                  "Temp": r"$T$",
-                 "rho_H1": r"$\rho X(\isotm{H}{1})$",
+                 "rho_n": r"$\rho X(\mathrm{n})$",
+                 "rho_p": r"$\rho X(\mathrm{p})$",
                  "rho_He4": r"$\rho X(\isotm{He}{4})$",
-                 "rho_C12": r"$\rho X(\isotm{C}{12})$",
-                 "rho_O16": r"$\rho X(\isotm{O}{16})$",
                  "rho_Cr48": r"$\rho X(\isotm{Cr}{48})$",
                  "rho_Fe52": r"$\rho X(\isotm{Fe}{52})$",
                  "rho_Fe54": r"$\rho X(\isotm{Fe}{54})$",

diff --git a/Exec/reacting_tests/nse_test/problem_initialize_state_data.H b/Exec/reacting_tests/nse_test/problem_initialize_state_data.H
@@ -5,6 +5,7 @@
 #include <eos.H>
 #include <network.H>
 #if defined(NSE_TABLE)
+#include <nse_table_type.H>
 #include <nse_table.H>
 #elif defined(NSE_NET)
 #include <nse_solver.H>
@@ -63,14 +64,15 @@ void problem_initialize_state_data (int i, int j, int k,
     burn_state.y_e = ye;
 
 #if defined(NSE_TABLE)
-    Real abar;
-    Real dq;
-    Real dyedt;
-    Real dabardt;
-    Real dbeadt;
-    Real e_nu;
-
-    nse_interp(T, problem::rho0, ye, abar, dq, dyedt, dabardt, dbeadt, e_nu, burn_state.xn);
+    nse_table_t nse_state;
+    nse_state.T = T;
+    nse_state.rho = problem::rho0;
+    nse_state.Ye = ye;
+    nse_interp(nse_state);
+
+    for (int n = 0; n < NumSpec; ++n) {
+        burn_state.xn[n] = nse_state.X[n];
+    }
 #elif defined(NSE_NET)
     Real eps = 1.e-10_rt;
     bool input_ye_is_valid = true;
@@ -112,8 +114,8 @@ void problem_initialize_state_data (int i, int j, int k,
 
 #ifdef AUX_THERMO
     burn_state.aux[AuxZero::iye] = ye;
-    burn_state.aux[AuxZero::iabar] = abar;
-    burn_state.aux[AuxZero::ibea] = dq;
+    burn_state.aux[AuxZero::iabar] = nse_state.abar;
+    burn_state.aux[AuxZero::ibea] = nse_state.bea;
 #endif
 
     eos(eos_input_rt, burn_state);

diff --git a/Exec/science/Detonation/problem_initialize.H b/Exec/science/Detonation/problem_initialize.H
@@ -16,7 +16,7 @@ void problem_initialize ()
     problem::in14 = network_spec_index("nitrogen-14");
     problem::io16 = network_spec_index("oxygen-16");
 
-    if (problem::ihe4 < 0 || problem::ic12 < 0 || problem::in14 < 0 || problem::io16 < 0) {
+    if (problem::ihe4 < 0 || problem::ic12 < 0 || problem::io16 < 0) {
         amrex::Error("ERROR: species indices not found");
     }
 
@@ -51,9 +51,15 @@ void problem_initialize ()
     }
 
     problem::xn[problem::ic12] = amrex::max(problem::cfrac, problem::smallx);
-    problem::xn[problem::in14] = amrex::max(problem::nfrac, problem::smallx);
     problem::xn[problem::io16] = amrex::max(problem::ofrac, problem::smallx);
-    problem::xn[problem::ihe4] = 1.0_rt - problem::cfrac - problem::nfrac - problem::ofrac - (NumSpec - 3) * problem::smallx;
+
+    if (problem::in14 >= 0) {
+       problem::xn[problem::in14] = amrex::max(problem::nfrac, problem::smallx);
+       problem::xn[problem::ihe4] = 1.0_rt - problem::cfrac - problem::nfrac - problem::ofrac - (NumSpec - 3) * problem::smallx;
+    }
+    else {
+       problem::xn[problem::ihe4] = 1.0_rt - problem::cfrac - problem::ofrac - (NumSpec - 2) * problem::smallx;
+    }
 
     // Set the ambient material
 

diff --git a/Exec/science/flame_wave/ci-benchmarks/grid_diag.out b/Exec/science/flame_wave/ci-benchmarks/grid_diag.out
@@ -1,5 +1,5 @@
 #   COLUMN 1                        2                        3                        4                        5                        6                        7                        8                        9                       10                       11                       12                       13                       14                       15                       16                       17                       18                       19                       20                       21                       22                       23
 #   TIMESTEP                     TIME                     MASS                     XMOM                     YMOM                     ZMOM              ANG. MOM. X              ANG. MOM. Y              ANG. MOM. Z              KIN. ENERGY              INT. ENERGY               GAS ENERGY             GRAV. ENERGY             TOTAL ENERGY     CENTER OF MASS X-LOC     CENTER OF MASS Y-LOC     CENTER OF MASS Z-LOC     CENTER OF MASS X-VEL     CENTER OF MASS Y-VEL     CENTER OF MASS Z-VEL      MAXIMUM TEMPERATURE          MAXIMUM DENSITY        MAXIMUM T_S / T_E
            0       0.0000000000000000   1.4902024346464787e+20   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   2.9583337617665660e+37   2.9583337617665660e+37   0.0000000000000000e+00   2.9583337617665660e+37   2.7306640614148750e+04   6.8067773166795473e+02   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   0.0000000000000000e+00   1.0000000000156899e+08   3.1017131702472486e+07   0.0000000000000000e+00
-           1   5.9694928185132600e-08   1.4902038799260451e+20  -9.8852813993167483e+18   7.0758681407801181e+23  -3.7077151117729030e+15  -7.8559831399077499e+18   7.9789428545426686e+19   1.9321854546506737e+28   2.7622571688141327e+29   2.9583392229687520e+37   2.9583392505913144e+37   0.0000000000000000e+00   2.9583392505913144e+37   2.7306640614147251e+04   6.8067725884159722e+02   0.0000000000000000e+00  -6.6335093690719216e-02   4.7482550784469004e+03  -2.4880589573803199e-05   1.0000972452748042e+08   3.1017431302318867e+07   1.9852339015703824e-12
-           2   1.2535934918877847e-07   1.4902056479398973e+20  -2.0759055840781603e+19   1.4862415462814482e+24  -1.6351019859135748e+16  -3.4644556495600996e+19   3.5187152213757382e+20   4.0584338401784393e+28   5.5823502529134965e+29   2.9583452181108320e+37   2.9583452739343134e+37   0.0000000000000000e+00   2.9583452739343134e+37   2.7306640614140473e+04   6.8067697458181988e+02   0.0000000000000000e+00  -1.3930329595435043e-01   9.9733989623249036e+03  -1.0972324445112568e-04   1.0003863648020169e+08   3.1017667549506564e+07   1.9917944188178796e-12
+           1   5.9694928185132600e-08   1.4902038799260451e+20  -9.8852814000373391e+18   7.0758681407801342e+23  -3.7077151119947915e+15  -7.8559831403383900e+18   7.9789428550115738e+19   1.9321854546506743e+28   2.7622571688115688e+29   2.9583392229687520e+37   2.9583392505913144e+37   0.0000000000000000e+00   2.9583392505913144e+37   2.7306640614147251e+04   6.8067725884159722e+02   0.0000000000000000e+00  -6.6335093695554737e-02   4.7482550784469113e+03  -2.4880589575292177e-05   1.0000972452758998e+08   3.1017431302318867e+07   2.1834522208251888e-12
+           2   1.2535934918877847e-07   1.4902056479398969e+20  -2.0759055857352421e+19   1.4862415462814437e+24  -1.6351019861504854e+16  -3.4644556500407476e+19   3.5187152219157529e+20   4.0584338401784253e+28   5.5823502529036681e+29   2.9583452181108315e+37   2.9583452739343125e+37   0.0000000000000000e+00   2.9583452739343125e+37   2.7306640614140484e+04   6.8067697458182033e+02   0.0000000000000000e+00  -1.3930329606554864e-01   9.9733989623248763e+03  -1.0972324446702355e-04   1.0003863648118678e+08   3.1017667549506564e+07   1.8217100523183610e-12
diff --git a/Exec/science/flame_wave/ci-benchmarks/species_diag.out b/Exec/science/flame_wave/ci-benchmarks/species_diag.out
@@ -2,4 +2,4 @@
 #   TIMESTEP                     TIME                 Mass He4                 Mass C12                 Mass O16                Mass Ne20                Mass Mg24                Mass Si28                 Mass S32                Mass Ar36                Mass Ca40                Mass Ti44                Mass Cr48                Mass Fe52                Mass Ni56
            0       0.0000000000000000   3.5899765861250859e-15   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.4944801491560746e-24   7.1354824912929246e-14
            1   5.9694928185132600e-08   3.5899765861251656e-15   7.4944874211898590e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.4944874177116286e-24   7.1354897598484802e-14
-           2   1.2535934918877847e-07   3.5899765861253060e-15   7.4944963166333664e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.1354986514892610e-14
+           2   1.2535934918877847e-07   3.5899765861253060e-15   7.4944963166333664e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.4944963093524191e-24   7.1354986514892597e-14