enable use of CVs defined by PyTorch neural network models

.github/workflows/backend-template.yml

@@ -76,7 +76,8 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Load compiler cache
-        uses: actions/cache@v3
+        uses: actions/cache/restore@v4
+        id: compiler-cache-restore
         with:
           path: |
             ~/ccache_${{ inputs.container_name }}
@@ -141,6 +142,21 @@ jobs:
           apptainer exec devel-tools/${{ inputs.container_name }}.sif \
               bash ${{ inputs.path_compile_script }} ${{ inputs.backend_name }}-source
 
+      - name: Save compiler cache
+        uses: actions/cache/save@v4
+        id: compiler-cache-save
+        if: always() && steps.compiler-cache-restore.outputs.cache-hit != 'true'
+        with:
+          path: |
+            ~/ccache_${{ inputs.container_name }}
+          key: ${{ runner.os }}-build-${{ inputs.backend_name }}-${{ github.sha }}
+
+      - name: Keep only one cache besides the one from this job
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh ${{ runner.os }}-build-${{ inputs.backend_name }}-
 
       # 2 types of tests can be performed with the MD engine: library & interface
       # It depends on the working directory
@@ -158,10 +174,14 @@ jobs:
 
       - name: Save failed library test artifact
         if: ${{ failure() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: failed-library-test-diffs-${{ inputs.backend_name }}
-          path: ${{ github.workspace }}/${{ inputs.test_lib_directory }}/*/*.diff
+          name: failed-library-test-output-${{ inputs.backend_name }}
+          path: |
+            ${{ github.workspace }}/${{ inputs.test_lib_directory }}/*/*.diff
+            ${{ github.workspace }}/${{ inputs.test_lib_directory }}/*/*.err
+            ${{ github.workspace }}/${{ inputs.test_lib_directory }}/*/*.log
+            ${{ github.workspace }}/${{ inputs.test_lib_directory }}/*/*.out
 
       - name: Run regression tests for ${{ inputs.backend_name }} interface code
         if: ${{ inputs.test_interface_directory }}
@@ -175,10 +195,14 @@ jobs:
 
       - name: Save failed interface test artifact
         if: ${{ failure() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: failed-interface-test-diffs-${{ inputs.backend_name }}
-          path: ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.diff
+          name: failed-interface-test-output-${{ inputs.backend_name }}
+          path: |
+            ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.diff
+            ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.err
+            ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.log
+            ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.out
 
       - name: Run regression tests for library code with ${{ inputs.backend_name }} (binary restarts)
         # Skipping GROMACS, because its restarts are always binary anyway
@@ -190,10 +214,3 @@ jobs:
         run: |
           apptainer exec ${{github.workspace}}/devel-tools/${{ inputs.container_name }}.sif \
           ./run_tests.sh ${{github.workspace}}/${{ inputs.backend_name }}-source/${{ inputs.rpath_exe }} 0??_*
-
-      - name: Keep only one cache besides the one from this job
-        shell: bash
-        env:
-          GH_TOKEN: ${{ github.token }}
-        run: |
-          bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh ${{ runner.os }}-build-${{ inputs.backend_name }}-

.github/workflows/test-backends.yml

@@ -44,7 +44,7 @@ jobs:
       test_lib_directory: namd/tests/library
       test_interface_directory: namd/tests/interface
       rpath_exe: Linux-x86_64-g++.mpi/namd3
-      container_name: CentOS7-devel
+      container_name: CentOS9-devel
     secrets:
       # Choice of license by UIUC prevents sharing the code, hence the secret
       private_key: ${{ secrets.PULL_NAMD_KEY }}
@@ -56,7 +56,7 @@ jobs:
       backend_name: VMD
       backend_repo: Colvars/vmd
       backend_repo_ref: master
-      container_name: CentOS7-devel
+      container_name: CentOS9-devel
       # Special variable for VMD test case since it's the only one
       # which needs to checkout 2 repos
       vmd_plugins_repo: Colvars/vmd-plugins
@@ -68,18 +68,6 @@ jobs:
       private_key: ${{ secrets.PULL_VMD_KEY }}
       private_key_vmd_plugins: ${{ secrets.PULL_VMD_PLUGINS_KEY }}
 
-  gromacs-2023:
-    name: GROMACS (release-2023)
-    uses: ./.github/workflows/backend-template.yml
-    with:
-      backend_name: GROMACS-2023
-      backend_repo: gromacs/gromacs
-      backend_repo_ref: release-2023
-      container_name: CentOS9-devel
-      path_compile_script: devel-tools/compile-gromacs.sh
-      test_lib_directory: gromacs/tests/library
-      rpath_exe: install/bin/gmx_mpi_d
-
   gromacs-main:
     name: GROMACS (main)
     uses: ./.github/workflows/backend-template.yml

.github/workflows/test-library.yml

@@ -21,7 +21,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Load compiler cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ github.workspace }}/ccache
           key: ${{ runner.os }}-build-basic-${{ github.sha }}
@@ -51,7 +51,11 @@ jobs:
               exit 1
           fi
 
-      - name: Build and test library (GCC)
+      - name: Build and test library (Clang)
+        env:
+          CMAKE_BUILD_DIR: build
+          CXX: clang++
+          CC: clang
         run: cmake -P devel-tools/build_test_library.cmake
 
       - name: Check documentation of command-line scripting interface
@@ -64,11 +68,11 @@ jobs:
               exit 1
           fi
 
-      - name: Build and test library (Clang)
+      - name: Build and test library (GCC)
         env:
-          CMAKE_BUILD_DIR: build-clang
-          CXX: clang++
-          CC: clang
+          CMAKE_BUILD_DIR: build-gcc
+          CXX: g++
+          CC: gcc
         run: cmake -P devel-tools/build_test_library.cmake
 
       - name: Build library with debug code enabled (GCC)
@@ -221,7 +225,7 @@ jobs:
           fi
 
       - name: Archive warnings artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: warnings_clang_static_analyser
@@ -240,7 +244,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Load compiler ccache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ github.workspace }}/ccache
           key: ${{ runner.os }}-build-asan-${{ github.sha }}
@@ -276,7 +280,7 @@ jobs:
           cmake -P devel-tools/build_test_library.cmake
 
       - name: Archive warnings artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: Clang_address_sanitizer_output
@@ -303,7 +307,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Load compiler ccache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ github.workspace }}/ccache
           key: ${{ runner.os }}-build-multiple-${{ github.sha }}
@@ -511,6 +515,89 @@ jobs:
           cmake3 -D CMAKE_CXX_STANDARD=11 -P devel-tools/build_test_library.cmake
 
 
+  build-linux-x86_64-intel:
+    name: Linux x86_64 (Intel oneAPI)
+    runs-on: ubuntu-latest
+    needs: basicchecks
+    env:
+      CCACHE: ccache
+      CMAKE_GENERATOR: Ninja
+      CCACHE_DIR: ${{ github.workspace }}/ccache
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Load compiler ccache
+        uses: actions/cache@v4
+        with:
+          path: ${{ github.workspace }}/ccache
+          key: ${{ runner.os }}-build-oneapi-${{ github.sha }}
+          restore-keys: ${{ runner.os }}-build-oneapi-
+
+      - name: Get small downloadable packages
+        uses: actions/checkout@v4
+        with:
+          repository: 'Colvars/build-tools-packages'
+          ref: 'master'
+          path: 'devel-tools/packages'
+
+      - name: Install Apptainer
+        shell: bash
+        run: |
+          sudo add-apt-repository -y ppa:apptainer/ppa
+          sudo apt update
+          sudo apt install -y apptainer-suid
+
+      - name: Get container images for build dependencies
+        shell: bash
+        working-directory: devel-tools
+        run: |
+          apptainer pull CentOS9-devel-oneAPI.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel-oneAPI
+
+      - name: Intel oneAPI 2024.2, C++11
+        shell: bash
+        env:
+          CC: icx
+          CXX: icpx
+          CXX_STANDARD: 11
+          BASH_ENV: "/etc/profile.d/oneapi.sh"
+        run: |
+          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
+          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"
+
+      - name: Intel oneAPI 2024.2, C++14
+        shell: bash
+        env:
+          CC: icx
+          CXX: icpx
+          CXX_STANDARD: 14
+          BASH_ENV: "/etc/profile.d/oneapi.sh"
+        run: |
+          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
+          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"
+
+      - name: Intel oneAPI 2024.2, C++17
+        shell: bash
+        env:
+          CC: icx
+          CXX: icpx
+          CXX_STANDARD: 17
+          BASH_ENV: "/etc/profile.d/oneapi.sh"
+        run: |
+          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
+          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"
+
+      - name: Intel oneAPI 2024.2, C++20
+        shell: bash
+        env:
+          CC: icx
+          CXX: icpx
+          CXX_STANDARD: 20
+          BASH_ENV: "/etc/profile.d/oneapi.sh"
+        run: |
+          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
+          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"
+
+
   build-windows-x86_64-msvc:
     name: Windows x86_64 (MSVC)
     runs-on: windows-latest

.gitignore

@@ -46,3 +46,5 @@
 *.pmf
 !**/AutoDiff/*.pmf
 
+# macOS
+.DS_Store

README-versions.md

@@ -1,12 +1,21 @@
+[Versions included in GROMACS](#versions-included-in-GROMACS)
+
 [Versions included in LAMMPS](#versions-included-in-LAMMPS)
 
 [Versions included in NAMD](#versions-included-in-NAMD)
 
 [Versions included in VMD](#versions-included-in-VMD)
 
+### Versions included in GROMACS
+GROMACS version | Colvars version
+-------------- | ---------------
+2024 | [2023-12-05](https://github.com/Colvars/colvars/tree/gromacs-2024)
+
 ### Versions included in LAMMPS
 LAMMPS version | Colvars version
 -------------- | ---------------
+stable_29Aug2024 | [2024-06-04](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Aug2024)
+stable_2Aug2023 | [2023-05-01](https://github.com/Colvars/colvars/releases/tag/lammps-stable_2Aug2023)
 stable_23Jun2022 | [2022-05-24](https://github.com/Colvars/colvars/releases/tag/lammps-stable_23Jun2022)
 stable_29Sep2021 | [2021-09-13](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Sep2021)
 stable_29Oct2020 | [2020-09-17](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Oct2020)
@@ -27,6 +36,7 @@ stable_4Nov2016 | [2016-10-21](https://github.com/Colvars/colvars/releases/tag/l
 
 NAMD version | Colvars version
 -------------- | ---------------
+3.0 | [2024-06-04](https://github.com/Colvars/colvars/tree/namd-3.0)
 2.14 | [2020-07-07](https://github.com/Colvars/colvars/releases/tag/namd-2.14)
 2.13b2 | [2018-10-12](https://github.com/Colvars/colvars/releases/tag/namd-2.13b2)
 2.13b1 | [2018-09-07](https://github.com/Colvars/colvars/releases/tag/namd-2.13b1)
@@ -40,6 +50,7 @@ VMD version | Colvars version
 -------------- | ---------------
 1.9.4a58 | [2022-04-14](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a58)
 1.9.4a49 | [2020-10-22](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a49)
+1.9.4a12 | [2017-10-11](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a12)
 1.9.3 | [2016-10-26](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.3)
 1.9.2 | [2014-10-13](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.2)
 

README.md

@@ -110,7 +110,7 @@ All of the above MD engine versions are automatically tested as part of GitHub A
 
 ## Legacy GROMACS-Colvars patched releases
 
-Versions GROMACS prior to 2024 are supported through the use of a customized `mdrun` command line; source code of these patched releases is available [here](https://github.com/Colvars/gromacs).  When posting a message to the [Gromacs forum](https://gromacs.bioexcel.eu/) regarding the use of these patched releases, please specify "GROMACS modification: **Yes**".
+Versions of GROMACS prior to 2024 are no longer supported by the current version of Colvars: please use GROMACS 2024 or later.
 
 
 ## Which version of Colvars is recommended?