Merge remote-tracking branch 'origin/master' into emst-makewhole

# Conflicts:
#	src/core/ActionAtomistic.cpp
#	src/generic/WholeMolecules.cpp
#	src/tools/Tree.cpp

.astyle.options

@@ -1 +1,13 @@
--n --indent=spaces=2 --keep-one-line-statements --keep-one-line-blocks
+# long options can be written without the preceding '--'
+suffix=none #equivalent to "-n"
+style=attach
+add-braces
+indent=spaces=2
+break-one-line-headers
+
+# old options
+#suffix=none
+#indent=spaces=2
+#keep-one-line-statements
+#keep-one-line-blocks
+# end old options

.ci/install.boost

@@ -12,8 +12,9 @@ version_=${version//./_}
 
 echo $version $version_
 
-wget https://boostorg.jfrog.io/artifactory/main/release/$version/source/boost_${version_}.tar.gz > /dev/null 2> /dev/null
-tar xzf boost_${version_}.tar.gz
+#wget https://boostorg.jfrog.io/artifactory/main/release/$version/source/boost_${version_}.tar.gz > /dev/null 2> /dev/null
+wget https://sourceforge.net/projects/boost/files/boost/$version/boost_${version_}.tar.bz2 > /dev/null 2> /dev/null
+tar xjf boost_${version_}.tar.bz2
 
 cd boost_${version_}
 

.git-blame-ignore-revs

@@ -0,0 +1,9 @@
+# .git-blame-ignore-revs
+# https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
+# please comment the hashes that you add to this
+# new astyle applied to v2.9.3
+2cd41d16623b7a062b2a716eaf5c91a741cc19ea
+# new astyle applied to v2.10
+df781b48652d8cdde2994dae1197cdb623f3f3fa
+# new astyle applied to v2.11
+380bb46eea1bc2a38fba94f3f72af2d8d6e41669

.github/workflows/codeql.yml

@@ -37,15 +37,15 @@ jobs:
         run: ./configure --enable-modules=all --disable-asmjit
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/condaWF.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04 , macos-12 , macos-14 ]
+        os: [ubuntu-20.04 , macos-13 , macos-14 ]
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4

.github/workflows/linuxWF.yml

@@ -28,6 +28,8 @@ jobs:
 # see https://github.com/plumed/plumed2/issues/976
         - -intel-
         - -pycv-mpi-
+#this does not install mpi but uses the internal one
+        - -nvhpc-mpi-
     steps:
     - uses: actions/checkout@v4
     - uses: actions/cache@v4
@@ -136,6 +138,18 @@ jobs:
         echo "CXX=icpx" >> $GITHUB_ENV
         echo "CC=icx" >> $GITHUB_ENV
         echo "FC=ifx" >> $GITHUB_ENV
+    - name: Install NVHPC compiler
+      if: contains( matrix.variant, '-nvhpc-' )
+      # use this if it does not work
+      # wget https://developer.download.nvidia.com/hpc-sdk/24.3/nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz
+      # tar xpzf nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz
+      # nvhpc_2024_243_Linux_x86_64_cuda_12.3/install
+      run: |
+        curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg
+        echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
+        sudo apt-get update -y
+        sudo apt-get install -y nvhpc-24-3
+      # nvhpcinstalls his own mpi compilers
     - name: Install MPI
       # install MPI at last since it modifies CC and CXX
       if: contains( matrix.variant, '-mpi-' )
@@ -198,8 +212,7 @@ jobs:
       if: contains( matrix.variant, '-pycv-' )
       working-directory: ./plugins/pycv/
       run: |
-            pip install --user -r requirements.txt
             source ../../sourceme.sh
             ln -s $(realpath ../../regtest/scripts) ./regtest/scripts
-            ./prepareMakeForDevelop.sh
             make check
+            

.github/workflows/macWF.yml

@@ -21,7 +21,10 @@ jobs:
       matrix:
         variant: [ "" , "+allmodules" ]
         # this is to test both intel and arm64 macs
-        os: [ macos-12 , macos-14 ]
+        # note: macos-14 has a problem in fetching the git repository of plumed, namely a
+        # "fatal: detected dubious ownership in repository" error
+        # I didn't find any solution, so for the moment I keep macos-14 off
+        os: [ macos-13 ]
         exclude:
         # many tests on contributed modules are still failing for numerical reasons on arm64, see https://github.com/plumed/plumed2/pull/950
         # once fixed we could introduce this back:
@@ -68,7 +71,7 @@ jobs:
       fail-fast: false
       matrix:
         # this is to test both intel and arm64 macs
-        os: [ macos-12 , macos-14 ]
+        os: [ macos-13 , macos-14 ]
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4

CHANGES/v2.10.md

@@ -40,7 +40,6 @@ Before switching to version 2.10, users are invited to carefully read the follow
   - In \ref ANGLES you can no longer use the GROUP, GROUPA/GROUPB/GROUPC keywords.  Explicitly list all the distances you want to compute using ATOMS1,ATOMS2,ATOMS3...
   - Action NBONDS no longer exists.  The same effect can be achieved through a more transparent implementation that you can read about here: https://plumed-school.github.io/lessons/23/001/data/Steinhardt.html
   - Action CENTER_OF_MULTICOLVAR no longer exists.  You now simply use \ref CENTER with the PHASES option and a vector as input for the weights.
-  - The rational switching function when used with MM!=2*MM now returns a more correct derivative around `dist~=R0`
   - Dimensionality reduction methods and landmark selection actions have a new syntax. A good introduction that explains how to use these actions can be found in [this tutorial](https://plumed-school.github.io/lessons/21/006/data/DIMENSIONALITY.html)
   - When using \ref MOLINFO with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb.
 
@@ -73,3 +72,4 @@ Before switching to version 2.10, users are invited to carefully read the follow
   - You can use ActionShortcut to create complex inputs from a simpler initial input.  The nest will then allow users to explore these more complex inputs.
   - You can use \ref show_graph to create diagrams showing how values and forces are passed between the various actions in your input files.
   - Complete refactor of SwitchingFunction.cpp and SwitchingFunction.h, now adding new switching function is more straightforward and all the "book-keeping" can be done within a single class
+  - Python (cython) wrappers now use `nogil`. This should facilitate integration with Python. See https://github.com/plumed/plumed2/pull/1129#issuecomment-2410867829 (thanks to Guillaume Fraux).

CHANGES/v2.8.md

@@ -102,7 +102,10 @@ Changes from version 2.7 which are relevant for users:
 - Small fixes in the test suite to make sure `plumed` is always invoked with `--no-mpi` when testing for features. This avoids
   problems that were appearing when testing with some specific versions of OpenMPI.
 
-## Version 2.8.4
+## Version 2.8.4 (Jun 3, 2024)
+
+\plumednotmaintained
+
 - Added the possibility to disable `RTLD_DEEPBIND` (see \issue{952}).
 - Fixed a bug in `switchingfunction` mode `Q` thanks to @nm3787, (see #951)
 - Improved error reporting in CUSTOM switching function: an error is thrown if one uses `x` and `x2` arguments simultaneously (reported by Olivier Languin-Cattoen).
@@ -111,4 +114,8 @@ Changes from version 2.7 which are relevant for users:
 - Addressed numerical instabilities in the calculation of the derivative of the SwitchingFunction RATIONAL without simplification (where `NN!=2*MM`) around `d=R_0`.
 - Fixed an error in checking array shapes in the interface. Arrays with shape (N,4) should not be accepted for positions or forces.
 - Small fix in Python, where we do not assume anymore that strings are null terminated.
+- Environment variables such as `PLUMED_INCLUDEDIR` and similar are sanitized before they are used for running commands.
+- Fixed a bug leading to a crash when using python selectors (e.g., `@mda:` or `@mdt:`) and multiple MPI processes per replica.
+- Fixed leaks in Subprocess, potentially givin problems with a large number (>250) of sequentially created plumed objects all of them using `@mda:` or `@mdt:` selectors.
+- Quantum Espresso patches have been fixed for a bug leading to incorrect masses passed to PLUMED and for a missing string terminator.
 

CHANGES/v2.9.md

@@ -54,8 +54,18 @@ Changes from version 2.8 which are relevant for users:
   - Python (cython) wrappers now only use plain C instead of C++. Plumed exceptions are mapped to python exceptions.
   - Step number is now stored as a `long long int`. Might facilitate Windows compatibility.
 
-## Version 2.9.1 (to be released)
+## Version 2.9.1 (Jun 3, 2024)
 - Includes all fixes up to 2.8.4
-- Plumed now fetches the massses correctly from QEspresso 7.0
 - Fixed a size check in python interface when passing native arrays.
 
+## Version 2.9.2 (Sep 3, 2024)
+  - Patch for GROMACS 2023 updated to the latest version
+  - new patch for GROMACS 2024 
+  - Small optimization of \ref COORDINATION and related collective variables (\issue{1096}).
+
+## Version 2.9.3 (Jan 15, 2025)
+  - Patch for GROMACS 2024 was updated to fix a big issue preventing its use
+
+## Version 2.9.4 (in progress)
+  - Fixed an issue that might lead to a crash when using multicolvars implemented with linked cells and no PBCs, apparently
+    only showing up with Intel Mac. See \issue{1181}.

README.md

@@ -45,16 +45,17 @@ Below you find the status on [GitHub Actions](https://github.com/plumed/plumed2/
 
 | Branch   |      Status   | First stable release (year) | Still supported |
 |:--------:|:-------------:|:--------:|:------:|
-| master   | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=master)](https://github.com/plumed/plumed2/actions) | 2024 (expected) | / |
-| v2.9     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.9)](https://github.com/plumed/plumed2/actions)   | 2023 | yes |
-| v2.8     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.8)](https://github.com/plumed/plumed2/actions)   | 2022 | yes |
-| v2.7     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.7)](https://github.com/plumed/plumed2/actions)   | 2020 | no |
-| v2.6     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.6)](https://github.com/plumed/plumed2/actions)   | 2019 | no |
-| v2.5     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.5)](https://github.com/plumed/plumed2/actions)   | 2018 | no |
-| v2.4     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.4)](https://github.com/plumed/plumed2/actions)   | 2017 | no |
-| v2.3     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.3)](https://travis-ci.org/plumed/plumed2)   | 2016 | no |
-| v2.2     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.2)](https://travis-ci.org/plumed/plumed2)   | 2015 | no |
-| v2.1     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.1)](https://travis-ci.org/plumed/plumed2)   | 2014 | no |
+| master   | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=master)](https://github.com/plumed/plumed2/actions) | 2025 (expected) | / |
+| v2.10b   | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.10)](https://github.com/plumed/plumed2/actions) | 2024 (expected) | yes |
+| v2.9     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.9)](https://github.com/plumed/plumed2/actions) | 2023 | yes |
+| v2.8     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.8)](https://github.com/plumed/plumed2/actions) | 2022 | no |
+| v2.7     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.7)](https://github.com/plumed/plumed2/actions) | 2020 | no |
+| v2.6     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.6)](https://github.com/plumed/plumed2/actions) | 2019 | no |
+| v2.5     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.5)](https://github.com/plumed/plumed2/actions) | 2018 | no |
+| v2.4     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.4)](https://github.com/plumed/plumed2/actions) | 2017 | no |
+| v2.3     | Not available | 2016 | no |
+| v2.2     | Not available | 2015 | no |
+| v2.1     | Not available | 2014 | no |
 | v2.0     | Not available | 2013 | no |
 
 Content

VERSION.txt

@@ -5,4 +5,4 @@
 # (this is same as gromacs)
 # Notice that "plumed info --version" will return only 2.X
 # and "plumed info --long-version" will return the full string
-2.10.0-dev
+2.11.0-dev

conda/plumed/build.sh

@@ -19,6 +19,10 @@ export CXXFLAGS="${CXXFLAGS//-O2/-O3}"
 if [[ $(uname) == "Darwin" ]]; then
 # see https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
   CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+
+# for some unexpected reason, when building on MacOS plumed 2.10 (likely because of C++17) # we need to pass the arguments below.
+# if we do not do so, linking plumed-runtime fails because the destructor of std::bad_function_call is not found
+  export STATIC_LIBS="-Wl,-rpath,$PREFIX/lib -L$PREFIX/lib"
 fi
 
 # libraries are explicitly listed here due to --disable-libsearch

conda/plumed/conda_build_config.yaml

@@ -1,3 +1,3 @@
 CONDA_BUILD_SYSROOT:
-  - /opt/MacOSX10.9.sdk   # [osx and x86_64]
+  - /opt/MacOSX10.13.sdk   # [osx and x86_64]
   - /opt/MacOSX11.0.sdk   # [osx and arm64]

conda/py-plumed/conda_build_config.yaml

@@ -1,5 +1,5 @@
 CONDA_BUILD_SYSROOT:
-  - /opt/MacOSX10.9.sdk   # [osx and x86_64]
+  - /opt/MacOSX10.13.sdk   # [osx and x86_64]
   - /opt/MacOSX11.0.sdk   # [osx and arm64]
 python:
     - 3.8