v2023.10 (#40)

New features - New 2D Cylindrical propagation grid option (for direct mapping of 2D input models) - Added test models for various combinations of 1D/2D input models and 1D/2D/3D propagation grids. - EXPERIMENTAL: Allow hybrid NLTE mode with some elements in full Non-LTE and other elements in either LTE or photoionisation equilibrium (classic quasi NLTE). Set with artisoptions.h LEVEL_IS_NLTE() - EXPERIMENTAL: Enforce Saha ionisation balance (allowing NLTE level pops) with artisoptions.h FORCE_SAHA_ION_BALANCE() function. - EXPERIMENTAL: FORCE_SPHERICAL_ESCAPE_SURFACE to remove the corners of a 2D or 3D model to create a spherical escape surface (allowing for increased velocity per axis cutoff). Cells with v_r_mid > vmax are set to empty, and packets found in cells with vel_r_inner > vmax are set to escaped. Fixes - Fix virtual packets (storage of bound-free departure coeff in cell history had introduced a dependence on the not-updated cell history) - Fix for bug in 1D spherical grid mode that caused a some packets to get out of their correct cells. Now ready for production use. Mapping of 1D and 2D models to a 3D Cartesian grid is still possible, but no longer recommended for new models. - Fix adiabatic cooling rate with NLTE populations on, replacing nnetot (free and bound electron density) with nntot (ion plus free electron density). No change to W7 nebular spectrum.
artis-mcrt · Oct 21, 2023 · 00661cf · 00661cf
1 parent 240684a
commit 00661cf
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diff --git a/.clang-tidy b/.clang-tidy
@@ -14,13 +14,15 @@ Checks: >
     -llvmlibc-*,
     -cert-err33-c,
     -cert-err34-c,
+    -cert-err58-cpp,
     -cppcoreguidelines-avoid-magic-numbers,
     -cppcoreguidelines-avoid-non-const-global-variables,
     -cppcoreguidelines-no-malloc,
     -cppcoreguidelines-owning-memory,
     -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
     -cppcoreguidelines-pro-bounds-constant-array-index,
     -cppcoreguidelines-pro-bounds-pointer-arithmetic,
+    -cppcoreguidelines-pro-type-reinterpret-cast,
     -cppcoreguidelines-pro-type-vararg,
     -clang-diagnostic-error,
     -fuchsia-*,
@@ -32,6 +34,7 @@ Checks: >
     -hicpp-signed-bitwise,
     -misc-use-anonymous-namespace,
     -misc-no-recursion,
+    -misc-non-private-member-variables-in-classes,
     -readability-identifier-length,
     -readability-function-cognitive-complexity,
     -readability-magic-numbers,
@@ -46,7 +49,7 @@ CheckOptions:
     - key: cppcoreguidelines-init-variables.MathHeader
       value: <cmath>
     - key: cppcoreguidelines-narrowing-conversions.IgnoreConversionFromTypes
-      value: size_t;ptrdiff_t;size_type;difference_type;time_t
+      value: size_t;ptrdiff_t;size_type;difference_type;time_t;MPI_Aint;unsigned long
     - key: cppcoreguidelines-narrowing-conversions.WarnOnFloatingPointNarrowingConversion
       value: 'false'
     - key: cppcoreguidelines-narrowing-conversions.WarnOnIntegerToFloatingPointNarrowingConversion

diff --git a/.github/workflows/ci-checks.yml b/.github/workflows/ci-checks.yml
@@ -11,23 +11,26 @@ on:
 
 jobs:
     cppcheck:
-        runs-on: ubuntu-22.04
+        runs-on: macos-latest
 
         steps:
             - uses: actions/checkout@v3
 
             - name: install dependencies
               run: |
-                  # git status
-                  # sudo apt-get update
-                  # sudo apt-get install libgsl-dev
-                  # sudo apt install -y openmpi-bin libopenmpi-dev
-                  sudo apt-get -y install cppcheck
+                  brew update
+                  brew install gsl openmpi cppcheck
+                  cp artisoptions_nltenebular.h artisoptions.h
 
-            - name: run cppcheck
+            - name: run cppcheck and check for errors
               run: |
-                  cp artisoptions_nltenebular.h artisoptions.h
-                  cppcheck --force --language=c++ --std=c++20 .
+                  cppcheck --version
+                  cppcheck --force --error-exitcode=1 --language=c++ --std=c++20 --enable=warning,performance,portability .
+
+            - name: show cppcheck style suggestions
+              run: |
+                  cppcheck --version
+                  cppcheck --force --language=c++ --std=c++20 --enable=style --suppress=knownConditionTrueFalse .
 
     clang-format:
         runs-on: ubuntu-22.04
@@ -45,12 +48,23 @@ jobs:
         runs-on: ubuntu-22.04
         strategy:
             matrix:
-                compiler: [{name: gcc, ver: 11}, {name: gcc, ver: 12}, {name: clang, ver: 14}, {name: clang, ver: 15}]
+                compiler: [{name: gcc, ver: 11}, {name: gcc, ver: 12}, {name: gcc, ver: 13}, {name: clang, ver: 14}, {name: clang, ver: 15}]
                 mpi: [ON, OFF]
+                openmp: [ON, OFF]
                 artisoptionsfile: [artisoptions_classic.h, artisoptions_nltenebular.h]
+                exclude:
+                    - compiler: {name: gcc, ver: 11}
+                      openmp: ON
+                    - compiler: {name: gcc, ver: 12}
+                      openmp: ON
+                    - compiler: {name: gcc, ver: 13}
+                      openmp: ON
+                    - compiler: {name: clang, ver: 15}
+                      openmp: ON
             fail-fast: false
 
-        name: ${{ matrix.compiler.name }}-${{ matrix.compiler.ver }}${{ matrix.mpi == 'ON' && ' MPI' || ''}} ${{ matrix.artisoptionsfile }}
+        name: ${{ matrix.compiler.name }}-${{ matrix.compiler.ver }}${{ matrix.mpi == 'ON' && ' MPI' || ''}}${{ matrix.openmp == 'ON' && ' OpenMP' || ''}}
+            ${{ matrix.artisoptionsfile }}
         steps:
             - uses: actions/checkout@v3
 
@@ -61,29 +75,38 @@ jobs:
                   # echo "count=$(python3 -c 'import psutil; print(int(psutil.cpu_count(logical=False)))')" >> $GITHUB_OUTPUT
                   echo "count=$(python3 -c 'import multiprocessing; print(multiprocessing.cpu_count())')" >> $GITHUB_OUTPUT
 
-            - name: apt-get update
+            - name: apt update
               run: |
+                  sudo add-apt-repository main
+                  sudo add-apt-repository universe
+                  sudo add-apt-repository restricted
+                  sudo add-apt-repository multiverse
                   sudo apt-get update
 
             - name: Install gcc-${{ matrix.compiler.ver }}
               if: matrix.compiler.name == 'gcc'
               run: |
-                  sudo apt-get install -y gcc-${{ matrix.compiler.ver }} g++-${{ matrix.compiler.ver }}
+                  sudo apt install -y gcc-${{ matrix.compiler.ver }} g++-${{ matrix.compiler.ver }}
                   echo "CXX=g++-${{ matrix.compiler.ver }}" >> $GITHUB_ENV
 
             - name: Install clang-${{ matrix.compiler.ver }}
               if: matrix.compiler.name == 'clang'
               run: |
-                  sudo apt-get install -y clang-${{ matrix.compiler.ver }} --install-suggests
+                  sudo apt install -y clang-${{ matrix.compiler.ver }} --install-suggests
                   echo "CXX=clang++-${{ matrix.compiler.ver }}" >> $GITHUB_ENV
 
             - name: install openmpi
               if: matrix.mpi == 'ON'
               run: |
                   sudo apt install -y openmpi-bin libopenmpi-dev
 
+            - name: install OpenMP
+              if: matrix.openmp == 'ON'
+              run: |
+                  sudo apt-get install -y libomp5-14 libomp-dev
+
             - name: install gsl
-              run: sudo apt-get install libgsl-dev
+              run: sudo apt install libgsl-dev
 
       # - name: Set compiler environment variables (MPI off)
       #   if: matrix.mpi == 'OFF'
@@ -103,4 +126,4 @@ jobs:
             - name: Compile
               run: |
                   cp -v -p ${{ matrix.artisoptionsfile }} artisoptions.h
-                  make MPI=${{matrix.mpi}} -j${{ steps.cpu-count.outputs.count}} sn3d exspec
+                  make MPI=${{matrix.mpi}} OPENMP=${{matrix.openmp}} -j${{ steps.cpu-count.outputs.count}} sn3d exspec
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -19,15 +19,15 @@ jobs:
                 # os: ['ubuntu-latest', 'self-hosted']
                 os: [ubuntu-22.04]
                 testmode: [OFF, ON]
-                testname: [classicmode, classicmode_3d, kilonova, nebularonezone]
+                testname: [classicmode_1d_3dgrid, classicmode_3d, kilonova_1d_1dgrid, kilonova_1d_3dgrid, kilonova_2d_2dgrid, kilonova_2d_3dgrid, nebularonezone_1d_3dgrid]
                 exclude:
                     - os: self-hosted
                       testmode: ON
             fail-fast: false
 
         runs-on: ${{ matrix.os }}
         timeout-minutes: 45
-        name: ${{ matrix.testname }} ${{ matrix.testmode == 'ON' && ' testmode ON' || ''}}
+        name: ${{ matrix.testname }}${{ matrix.testmode == 'ON' && ' testmode ON' || ''}}
 
         steps:
             - uses: actions/checkout@v3
@@ -38,11 +38,11 @@ jobs:
               if: matrix.os != 'selfhosted'
               run: |
                   git status
-                  sudo apt-get update
-                  sudo apt-get install -y gcc-12 g++-12
-                  sudo apt-get install -y libgsl-dev
+                  sudo apt update
+                  sudo apt install -y gcc-13 g++-13
+                  sudo apt install -y libgsl-dev
                   sudo apt install -y openmpi-bin libopenmpi-dev
-                  echo "OMPI_CXX=g++-12" >> $GITHUB_ENV
+                  echo "OMPI_CXX=g++-13" >> $GITHUB_ENV
 
             - name: CPU type and core count
               id: cpu-count
@@ -52,8 +52,7 @@ jobs:
 
             # cache this for classic options because the super low integration tolerance makes generation of the file very slow
             - name: Cache ratecoeff.dat
-              if: matrix.testname == 'classicmode' || matrix.testname == 'classicmode_3d'
-              # if: matrix.testname == 'classicmode' && matrix.testmode != 'ON'
+              if: matrix.testname == 'classicmode_1d_3dgrid' || matrix.testname == 'classicmode_3d'
               uses: actions/cache@v3
               with:
                   path: tests/${{ matrix.testname }}_testrun/ratecoeff.dat
@@ -62,15 +61,15 @@ jobs:
                       tests/${{ matrix.testname }}_testrun/ratecoeff.dat-
 
             - name: Cache test atomic data
-              if: matrix.testname != 'classicmode'
+              if: ${{ !startsWith(matrix.testname, 'classicmode_1d') }}
               uses: actions/cache@v3
               id: cache-testatomicdata
               with:
                   path: tests/atomicdata_feconi.tar.xz
                   key: tests/atomicdata_feconi.tar.xz
 
             - name: Cache test atomic data classic
-              if: matrix.testname == 'classicmode'
+              if: ${{ startsWith(matrix.testname, 'classicmode_1d') }}
               uses: actions/cache@v3
               id: cache-testatomicdata-classic
               with:
@@ -124,8 +123,7 @@ jobs:
               if: always() && matrix.os != 'selfhosted' && matrix.testmode == 'OFF'
               working-directory: tests/${{ matrix.testname }}_testrun
               run: |
-                  md5sum *.out job0/*.out
-
+                  md5sum *.out job0/*.out | tee ../${{ matrix.testname }}_inputfiles/results_md5_job0.txt
                   if [ -f results_md5_job0.txt ]; then md5sum -c results_md5_job0.txt; else echo "results_md5_job0.txt not found"; fi
 
             - name: Run test job1 resume
@@ -152,6 +150,11 @@ jobs:
               working-directory: tests/${{ matrix.testname }}_testrun/
               run: cat job1/output_0-0.txt
 
+            - name: cat job1 deposition.out
+              if: always()
+              working-directory: tests/${{ matrix.testname }}_testrun/
+              run: cat deposition.out
+
             - name: Run exspec
               if: always()
               working-directory: tests/${{ matrix.testname }}_testrun/
@@ -174,7 +177,7 @@ jobs:
               if: always() && matrix.os != 'selfhosted' && matrix.testmode == 'OFF'
               working-directory: tests/${{ matrix.testname }}_testrun
               run: |
-                  md5sum *.out job1/*.out
+                  md5sum *.out job1/*.out | tee ../${{ matrix.testname }}_inputfiles/results_md5_final.txt
                   if [ -f results_md5_final.txt ]; then md5sum -c results_md5_final.txt; else echo "results_md5_final.txt not found"; fi
 
             - name: Prepare for next steps
@@ -192,6 +195,13 @@ jobs:
                   name: test-${{ matrix.testname }}-output
                   path: tests/${{ matrix.testname }}_testrun/output
 
+            - name: Upload checksum files
+              uses: actions/upload-artifact@v3
+              if: always() && matrix.os != 'selfhosted' && matrix.testmode == 'OFF'
+              with:
+                  name: ${{ matrix.testname }}_inputfiles
+                  path: tests/${{ matrix.testname }}_inputfiles/results_md5*
+
             - name: Set up Python
               if: always() && matrix.os != 'selfhosted' && matrix.testmode == 'OFF'
               uses: actions/setup-python@v4
@@ -252,3 +262,21 @@ jobs:
     #       cp input-newrun.txt input.txt
     #       touch output_0-0.txt
     #       time mpirun -np 2 ./sn3d
+
+    combine_checksums:
+        needs: testmodels
+        if: always()
+        runs-on: ubuntu-latest
+        steps:
+            - name: Download test output
+              uses: actions/download-artifact@v3
+
+            - name: List all files
+              if: always()
+              run: find .
+
+            - name: Upload bundled checksum files
+              uses: actions/upload-artifact@v3
+              with:
+                  name: checksums
+                  path: '*_inputfiles/results_md5*.txt'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 fail_fast: false
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: check-added-large-files
             args: [--maxkb=800]

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.9)
+cmake_minimum_required(VERSION 3.26)
 project(artis)
 
 set(default_build_type "Release")
@@ -11,16 +11,18 @@ set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR})
 include_directories("${PROJECT_SOURCE_DIR}")
 
 set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
 
-set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+#set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
 
-set(SN3D_SOURCES sn3d.cc atomic.cc boundary.cc emissivities.cc gamma.cc globals.cc grey_emissivities.cc grid.cc input.cc kpkt.cc light_curve.cc ltepop.cc macroatom.cc nltepop.cc nonthermal.cc decay.cc packets.cc photo_electric.cc polarization.cc radfield.cc ratecoeff.cc rpkt.cc stats.cc thermalbalance.cc update_grid.cc update_packets.cc vectors.cc vpkt.cc md5.cc
+set(SN3D_SOURCES sn3d.cc atomic.cc boundary.cc gammapkt.cc globals.cc grid.cc input.cc kpkt.cc light_curve.cc ltepop.cc macroatom.cc nltepop.cc nonthermal.cc decay.cc packet.cc radfield.cc ratecoeff.cc rpkt.cc spectrum.cc stats.cc thermalbalance.cc update_grid.cc update_packets.cc vectors.cc vpkt.cc md5.cc)
 add_executable(sn3d ${SN3D_SOURCES})
 
-set(EXSPEC_SOURCES exspec.cc grid.cc globals.cc input.cc vectors.cc packets.cc update_grid.cc update_packets.cc gamma.cc boundary.cc macroatom.cc decay.cc rpkt.cc kpkt.cc photo_electric.cc emissivities.cc grey_emissivities.cc ltepop.cc atomic.cc ratecoeff.cc thermalbalance.cc light_curve.cc spectrum.cc polarization.cc nltepop.cc nonthermal.cc radfield.cc stats.cc vpkt.cc md5.cc)
+set(EXSPEC_SOURCES exspec.cc grid.cc globals.cc input.cc vectors.cc packet.cc update_grid.cc update_packets.cc gammapkt.cc boundary.cc macroatom.cc decay.cc rpkt.cc kpkt.cc ltepop.cc atomic.cc ratecoeff.cc thermalbalance.cc light_curve.cc spectrum.cc nltepop.cc nonthermal.cc radfield.cc stats.cc vpkt.cc md5.cc)
 
 add_executable(exspec ${EXSPEC_SOURCES})
 
+#if(UNIX AND NOT APPLE)
 if(UNIX AND NOT APPLE)
   find_package(MPI)
   include_directories(SYSTEM ${MPI_INCLUDE_PATH})
@@ -32,7 +34,7 @@ add_compile_options("-Wall" "-Wextra")
 string(APPEND CMAKE_CXX_FLAGS_DEBUG "-g")
 string(APPEND CMAKE_CXX_FLAGS_RELEASE "-O3")
 
-set(CMAKE_CXX_FLAGS "${CMAKE_C_FLAGS} -march=native")
+#set(CMAKE_CXX_FLAGS "${CMAKE_C_FLAGS} -march=native")
 
 add_compile_definitions(HAVE_INLINE)
 add_compile_definitions(GSL_RANGE_CHECK_OFF)

diff --git a/Makefile b/Makefile
@@ -3,8 +3,8 @@
 # place in architecture folder, e.g. build/arm64
 BUILD_DIR = build/$(shell uname -m)
 
-CXXFLAGS += -std=c++20 -fstrict-aliasing -ftree-vectorize -g -flto=auto -Werror -Werror=undef
-# CXXFLAGS += -Wpedantic -Wextra -Wall
+CXXFLAGS += -std=c++20 -fstrict-aliasing -ftree-vectorize -flto=auto
+
 # CXXFLAGS += -Wunreachable-code
 
 ifeq ($(shell uname -s),Darwin)
@@ -18,6 +18,7 @@ ifeq ($(shell uname -s),Darwin)
 		CXXFLAGS += -march=native
 	endif
 
+	CXXFLAGS += -fno-omit-frame-pointer
 #	CXXFLAGS += -Rpass=loop-vectorize
 #	CXXFLAGS += -Rpass-missed=loop-vectorize
 #	CXXFLAGS += -Rpass-analysis=loop-vectorize
@@ -77,20 +78,24 @@ ifeq ($(TESTMODE),ON)
 	CXXFLAGS += -DTESTMODE=true -O3 -DLIBCXX_ENABLE_DEBUG_MODE
 	# makes GitHub actions classic test run forever?
 	# CXXFLAGS += -D_GLIBCXX_DEBUG
-	CXXFLAGS += -fsanitize=address -fno-omit-frame-pointer -fno-common
+	CXXFLAGS += -fsanitize=address,undefined -fno-omit-frame-pointer -fno-common
 	BUILD_DIR := $(BUILD_DIR)_testmode
 else
 	# skip array range checking for better performance and use optimizations
 	CXXFLAGS += -DTESTMODE=false -DGSL_RANGE_CHECK_OFF -O3
 endif
 
-CXXFLAGS += -Winline -Wall -Wpedantic -Wredundant-decls -Wundef -Wno-unused-parameter -Wno-unused-function -Wstrict-aliasing -Wno-inline
+CXXFLAGS += -Werror -Werror=undef -Winline -Wall -Wpedantic -Wredundant-decls -Wundef -Wno-unused-parameter -Wno-unused-function -Wstrict-aliasing -Wno-inline
 
-ifeq ($(MPI),ON)
-else ifeq ($(MPI),OFF)
-else ifeq ($(MPI),)
+ifeq ($(MPI),)
 	# MPI option not specified. set to true by default
 	MPI := ON
+endif
+ifeq ($(MPI),ON)
+	CXX = mpicxx
+	CXXFLAGS += -DMPI_ON=true
+	BUILD_DIR := $(BUILD_DIR)_mpi
+else ifeq ($(MPI),OFF)
 else
 $(error bad value for MPI option. Should be ON or OFF)
 endif
@@ -102,17 +107,14 @@ else
 $(error bad value for testmode option. Should be ON or OFF)
 endif
 
-ifeq ($(MPI),ON)
-	CXX = mpicxx
-	CXXFLAGS += -DMPI_ON=true
-	BUILD_DIR := $(BUILD_DIR)_mpi
-endif
-
 ifeq ($(OPENMP),ON)
-	CXXFLAGS += -Xpreprocessor
-	CXXFLAGS += -fopenmp
+	CXXFLAGS += -Xpreprocessor -fopenmp
 	LDFLAGS += -lomp
 	BUILD_DIR := $(BUILD_DIR)_openmp
+else ifeq ($(OPENMP),OFF)
+else ifeq ($(OPENMP),)
+else
+$(error bad value for testmode option. Should be ON or OFF)
 endif
 
 ### use pg when you want to use gprof profiler
@@ -137,7 +139,7 @@ sn3d: $(sn3d_objects)
 -include $(sn3d_dep)
 
 sn3dwhole: version.h
-	$(CXX) $(CXXFLAGS) $(sn3d_files) $(LDFLAGS) -o sn3d
+	$(CXX) $(CXXFLAGS) -g $(sn3d_files) $(LDFLAGS) -o sn3d
 
 $(BUILD_DIR)/%.o: %.cc artisoptions.h Makefile
 	@mkdir -p $(@D)