Merge changes due to pulling updates from the main Phantom repo. N.B.…

… options for the EOS and cooling method have changed numbers.
alisonkyoung1 · Sep 19, 2024 · b6b62b4 · b6b62b4
2 parents 952a540 + 4e3c1b1
commit b6b62b4
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -11,8 +11,6 @@ on:
     paths-ignore:
       - 'docs/**'
       - 'README.md'
-#  schedule:
-#    - cron: "0 0 * * *"
 
 env:
   OMP_STACKSIZE: 512M
@@ -22,20 +20,17 @@ env:
   WEB_SERVER: data.phantom.cloud.edu.au
   WEB_HTML_DIR: /var/www/html
   BUILD_LOG_DIR: /ci/build/logs
-  RSYNC_RSH: ssh -o "StrictHostKeyChecking=no" -o "UserKnownHostsFile=/dev/null"
   NPARALLEL: 32
 
 jobs:
   matrix_prep:
-    # Skip scheduled runs on forks
-    if: ${{ github.event_name != 'schedule' || github.repository == 'danieljprice/phantom' }}
     runs-on: ubuntu-latest
     outputs:
       batch: ${{ steps.set-sequence.outputs.batch }}
       nbatch: ${{ steps.set-sequence.outputs.nbatch }}
     steps:
     - name: Check out repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Generate sequence of batch numbers for normal tests, or run sequentially for scheduled tests
       id: set-sequence
       run: |
@@ -67,51 +62,25 @@ jobs:
     - name: "Nuke the github workspace before doing anything"
       run: rm -r ${{ github.workspace }} && mkdir ${{ github.workspace }}
 
-    - name: Setup Intel repo
-      if: matrix.system == 'ifort'
-      id: intel-repo
-      run: |
-        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
-        sudo apt-get update
-        INTELVERSION=$(apt-cache show intel-oneapi-compiler-fortran | grep Version | head -1)
-        echo "::set-output name=intelversion::$INTELVERSION"
-
-    - name: Cache intel installation
-      if: matrix.system == 'ifort'
-      id: cache-intel
-      uses: actions/cache@v3
-      with:
-        path: |
-          /opt/intel
-        key: ${{ steps.intel-repo.outputs.intelversion }}
-
-    - name: Install Intel compilers
-      if: ${{ steps.cache-intel.outputs.cache-hit != 'true' && matrix.system == 'ifort' }}
-      run: |
-        sudo apt-get install -y intel-oneapi-common-vars
-        sudo apt-get install -y intel-oneapi-compiler-fortran
-        sudo apt-get install -y intel-oneapi-mpi
-        sudo apt-get install -y intel-oneapi-mpi-devel
+    - name: Update package list
+      run: sudo apt-get update
 
-    - name: Setup Intel oneAPI environment
+    - name: Setup Intel compiler
       if: matrix.system == 'ifort'
-      run: |
-        source /opt/intel/oneapi/setvars.sh
-        printenv >> $GITHUB_ENV
+      uses: fortran-lang/setup-fortran@v1
+      with:
+          compiler: intel-classic
 
     - name: Install numpy and matplotlib for analysis unit tests
       run: |
         sudo apt-get install -y python3-numpy
         sudo apt-get install -y python3-matplotlib
 
     - name: "Clone phantom"
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: "Grab a copy of splash source code"
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: danieljprice/splash
         path: splash
@@ -120,36 +89,13 @@ jobs:
       if: github.event_name == 'schedule'
       run: mkdir logs
 
-#    - name: "Grab previous build logs from web server"
-#      if: github.event_name == 'schedule'
-#      env:
-#        WGET: wget --recursive --no-parent --reject "index.html*" --cut-dirs=2 --no-host-directories
-#      run: ${WGET} -A '*${{ matrix.system[1] }}.txt' http://${WEB_SERVER}${BUILD_LOG_DIR}/ || true
-
     - name: "Run buildbot.sh"
       run: ./buildbot.sh --maxdim 17000000 --url http://${WEB_SERVER}/${BUILD_LOG_DIR} --parallel ${{ matrix.batch }} ${{ env.NPARALLEL }}
       working-directory: scripts
       env:
         SYSTEM: ${{ matrix.system }}
         RETURN_ERR: yes
 
-#    - name: "Install SSH Key"
-#      if: github.event_name == 'schedule'
-#      uses: webfactory/[email protected]
-#      with:
-#        ssh-private-key: ${{ secrets.RUNNER_PRIVATE_KEY }}
-
-#    - name: "Copy new build logs to web server"
-#      if: ${{ (success() || failure()) && github.event_name == 'schedule' }}
-#      run: rsync -vau logs/*.txt ${WEB_USER}@${WEB_SERVER}:${WEB_HTML_DIR}/${BUILD_LOG_DIR}
-
-#    - name: "Copy HTML files to web server"
-#      if: ${{ (success() || failure()) && github.event_name == 'schedule' }}
-#      run: |
-#        export WEB_BUILD_DIR=${WEB_HTML_DIR}/nightly/build/$(date "+%Y%m%d")
-#        ssh -o "StrictHostKeyChecking=no" -o "UserKnownHostsFile=/dev/null" ${WEB_USER}@${WEB_SERVER} -- mkdir -p ${WEB_BUILD_DIR}
-#        rsync -vau logs/*.html ${WEB_USER}@${WEB_SERVER}:${WEB_BUILD_DIR}/
-
     - name: logs/build-failures-${{ matrix.system }}.txt
       if: always()
       run: cat logs/build-failures-${{ matrix.system }}.txt || true

diff --git a/.github/workflows/krome.yml b/.github/workflows/krome.yml
@@ -0,0 +1,55 @@
+name: krome
+
+# Trigger on pull request, but only for the master branch
+on:
+  pull_request:
+    branches: [ master ]
+    paths-ignore:
+      - 'docs/**'
+      - 'README.md'
+
+env:
+  PREFIX: /usr/local/
+  PHANTOM_DIR: ${{ github.workspace }}
+  KROMEPATH: ${{ github.workspace }}/krome
+  FC: gfortran  # default if not overwritten by matrix
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        toolchain: [{compiler: gcc}, {compiler: intel-classic}]
+        exclude:
+          - os: macos-latest
+            toolchain: {compiler: intel-classic}
+
+    steps:
+      - name: "Install gfortran compiler"
+        uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: ${{ matrix.toolchain.compiler }}
+
+      - name: "Clone phantom"
+        uses: actions/checkout@v4
+
+      - name: "Clone krome"
+        run: git clone https://bitbucket.org/tgrassi/krome.git krome
+
+      - name: "make krome.setup"
+        run: echo -e "-n=networks/react_AGBwind_nucleation\n-cooling=ATOMIC,CHEM,H2,CIE,Z,CI,CII,OI,OII,CO,OH,H2O,HCN\n-heating=CHEM,CR\n-H2opacity=RIPAMONTI\n-gamma=EXACT\n-noSinkCheck\n-noRecCheck\n-noTlimits\n-useX\n-conserveLin\n-useTabs\n-unsafe\n-iRHS" > krome.setup && cat krome.setup
+
+      - name: "Compile phantom and link with krome"
+        run: make SYSTEM=${{ env.FC }} SETUP=wind KROME=krome KROMEPATH=${KROMEPATH} PREFIX=${PREFIX} RUNDIR=${{ github.workspace }}
+
+      - name: "Compile phantomsetup and link with krome"
+        run: make SYSTEM=${{ env.FC }} SETUP=wind KROME=krome KROMEPATH=${KROMEPATH} PREFIX=${PREFIX} RUNDIR=${PREFIX} setup
+
+      - name: "Compile phantomanalysis and link with krome"
+        run: make SYSTEM=${{ env.FC }} SETUP=wind KROME=krome KROMEPATH=${KROMEPATH} PREFIX=${PREFIX} RUNDIR=${PREFIX} analysis
+
+      - name: "Compile phantommoddump and link with krome"
+        run: make SYSTEM=${{ env.FC }} SETUP=wind KROME=krome KROMEPATH=${KROMEPATH} PREFIX=${PREFIX} RUNDIR=${PREFIX} moddump
diff --git a/.github/workflows/mcfost.yml b/.github/workflows/mcfost.yml
@@ -9,7 +9,7 @@ on:
       - 'README.md'
 
 env:
-  PREFIX: /usr/local/
+  PREFIX: /opt/homebrew
   MCFOST_GIT: 1
   SYSTEM: gfortran
   HOMEBREW_NO_INSTALL_CLEANUP: 1
@@ -23,13 +23,13 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-    - name: install gfortran
-      run: brew install gfortran
+    - name: install gfortran compiler
+      uses: fortran-lang/setup-fortran@v1
+      with:
+         compiler: gcc
 
-    - name: soft link gfortran and check version
-      run: |
-        ln -s `ls $PREFIX/bin/gfortran-* | tail -1` $PREFIX/bin/gfortran
-        gfortran -v
+    - name: Check gfortran version
+      run: gfortran --version
 
     - name: tap the homebrew repo
       run: brew tap danieljprice/all
@@ -38,7 +38,7 @@ jobs:
       run: brew install mcfost
 
     - name: "Clone phantom"
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: "Compile phantom and link with mcfost"
       run: make SETUP=disc MCFOST=yes PREFIX=${PREFIX} LIBCXX=-lc++

diff --git a/.github/workflows/mpi.yml b/.github/workflows/mpi.yml
@@ -19,7 +19,7 @@ jobs:
           - yes
         ntasks:
           - 1
-          - 4
+          - 2
         input: # [SETUP, phantom_tests]
           - ['test', '']
           - ['testkd', '']
@@ -43,7 +43,7 @@ jobs:
 
     env:
       OMP_STACKSIZE: 512M
-      OMP_NUM_THREADS: 4
+      OMP_NUM_THREADS: 2
 
     steps:
 
@@ -53,7 +53,7 @@ jobs:
         sudo apt-get --yes install gfortran openmpi-bin openmpi-common libopenmpi-dev
 
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Compile with MPI
       run: make SETUP=${{ matrix.input[0] }} MPI=yes DEBUG=${{ matrix.debug }} OPENMP=${{ matrix.openmp }}  phantomtest

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -20,7 +20,7 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     - name: checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: recursive
 

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -53,41 +53,12 @@ jobs:
 
     - name: Setup Intel repo
       if: matrix.system == 'ifort'
-      id: intel-repo
-      run: |
-        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
-        sudo apt-get update
-        INTELVERSION=$(apt-cache show intel-oneapi-compiler-fortran | grep Version | head -1)
-        echo "::set-output name=intelversion::$INTELVERSION"
-
-    - name: Cache intel installation
-      if: matrix.system == 'ifort'
-      id: cache-intel
-      uses: actions/cache@v3
+      uses: fortran-lang/setup-fortran@v1
       with:
-        path: |
-          /opt/intel
-        key: ${{ steps.intel-repo.outputs.intelversion }}
-
-    - name: Install Intel compilers
-      if: ${{ steps.cache-intel.outputs.cache-hit != 'true' && matrix.system == 'ifort' }}
-      run: |
-        sudo apt-get install -y intel-oneapi-common-vars
-        sudo apt-get install -y intel-oneapi-compiler-fortran
-        sudo apt-get install -y intel-oneapi-mpi
-        sudo apt-get install -y intel-oneapi-mpi-devel
-
-    - name: Setup Intel oneAPI environment
-      if: matrix.system == 'ifort'
-      run: |
-        source /opt/intel/oneapi/setvars.sh
-        printenv >> $GITHUB_ENV
+          compiler: intel-classic
 
     - name: "Clone phantom"
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: "Compile phantom"
       run: make SETUP=${{ matrix.input[0] }} DEBUG=${{ matrix.debug }} phantomtest

diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,9 @@ build/phantom-version.h
 *~
 */*~
 */*/*~
+eos_binary_table.dat
+helm_data.tab
+forcing.dat
 *.bindata
 *.pyc
 #*
@@ -23,3 +26,7 @@ build/phantom-version.h
 *.tar
 .DS_Store
 _build
+*.cmdx
+*.cmod
+*.ilm
+*.stb