merge with master

.github/workflows/backend-template.yml

@@ -86,7 +86,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2023-07-20
+          key: Linux-x86_64-containers-build-2023-09-05
 
       - name: Checkout OpenMM (for Lepton library)
         uses: actions/checkout@v3
@@ -137,15 +137,11 @@ jobs:
           apptainer pull CentOS7-devel.sif library://giacomofiorin/default/colvars_development:centos7
           apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9
 
-      - name : Get spiff
-        shell: bash
-        working-directory: devel-tools
-        run: sudo cp -f $(apptainer exec ${{ inputs.container_name }}.sif ./get_spiff) /usr/local/bin
-
       - name: Update and build ${{ inputs.backend_name }}
         shell: bash
         env:
           OPENMM_SOURCE: ${{ github.workspace }}/openmm-source
+          CMAKE_GENERATOR: Ninja
         run: |
           apptainer exec devel-tools/${{ inputs.container_name }}.sif ./update-colvars-code.sh -f ${{ inputs.backend_name }}-source
           CCACHE_DIR=~/ccache_${{ inputs.container_name }} \

.github/workflows/test-backends.yml

@@ -138,3 +138,16 @@ jobs:
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
       rpath_exe: install/bin/gmx_d
+
+  gromacs-2023:
+    name: GROMACS 2023
+    if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-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_d

.github/workflows/test-library.yml

@@ -165,6 +165,7 @@ jobs:
     if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
     env:
       CCACHE: ccache
+      CMAKE_GENERATOR: Ninja
 
     steps:
       - uses: actions/checkout@v3
@@ -182,7 +183,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2023-07-20
+          key: Linux-x86_64-containers-build-2023-09-05
 
       - name: Get small downloadable packages
         uses: actions/checkout@v3
@@ -387,7 +388,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2023-07-20
+          key: Linux-x86_64-containers-build-2023-09-05
 
       - name: Checkout Sun compiler (Oracle Developer Studio)
         uses: actions/checkout@v3

devel-tools/compile-gromacs.sh

@@ -21,7 +21,7 @@ compile_gromacs_target() {
     fi
 
     local GMX_SRC_DIR=""
-    if [ -f "${1}/src/gromacs/commandline.h" ] ; then
+    if [ -d "${1}/src/gromacs" ] ; then
         GMX_SRC_DIR=$(realpath "${1}")
         shift
     else

devel-tools/containers/CentOS7-devel.def

@@ -14,7 +14,7 @@ From: centos:7
         ncurses which bc man-db vim emacs screen tmux \
         gcc gcc-c++ gcc-gfortran glibc-static libstdc++-static clang cppcheck \
         autoconf automake  cvs git git-cvs cvsps subversion mercurial \
-        rh-git227 devtoolset-{7..11} llvm-toolset-7 cmake3 ccache ninja \
+        rh-git227 devtoolset-{7..11} llvm-toolset-7 cmake3 ccache ninja-build \
         doxygen \
         openmpi-devel fftw-devel tcl-devel \
         python-{devel,virtualenv} numpy scipy tkinter \
@@ -34,11 +34,14 @@ From: centos:7
 
     # Build Charm++
     umask 022
-    git clone --single-branch --depth=1 -b v7.0.0 https://github.com/UIUC-PPL/charm.git /opt/charm && \
-        cd /opt/charm && \
-        ./build charm++ mpi-linux-x86_64 -j\$(nproc) --with-production && \
-        ./build charm++ multicore-linux-x86_64 -j\$(nproc) --with-production && \
-        ./build charm++ netlrts-linux-x86_64 -j\$(nproc) --with-production
+    source /etc/profile
+    module load mpi
+    git clone --single-branch --depth=1 -b v7.0.0 https://github.com/UIUC-PPL/charm.git /opt/charm
+    cd /opt/charm
+    export CCACHE_DIR=/tmp
+    ./build charm++ mpi-linux-x86_64 -j16 --with-production && \
+    ./build charm++ multicore-linux-x86_64 -j16 --with-production && \
+    ./build charm++ netlrts-linux-x86_64 -j16 --with-production
 
     # Load Git 2.27
     cat > /etc/profile.d/git.sh <<EOF
@@ -47,3 +50,8 @@ if [ \$(id -u) != 0 ] && [ -d /opt/rh/rh-git227 ] ; then
 fi
 EOF
 
+    # Build and install spiff
+    rm -fr /tmp/spiff
+    git clone https://github.com/jhenin/spiff /tmp/spiff && \
+        make -C /tmp/spiff && \
+        install /tmp/spiff/spiff /usr/local/bin/

devel-tools/containers/CentOS9-devel.def

@@ -21,7 +21,7 @@ From: quay.io/centos/centos:stream9
         gcc gcc-c++ gcc-gfortran cppcheck \
         gcc-toolset-{12,13} \
         autoconf automake cvs git subversion mercurial \
-        cmake ccache \
+        cmake ccache ninja-build \
         openmpi-devel tbb-devel fftw-devel tcl-devel \
         python3-{devel,tkinter,virtualenv,numpy,scipy} \
         ncurses-devel \
@@ -40,9 +40,17 @@ From: quay.io/centos/centos:stream9
 
     # Build Charm++
     umask 022
+    source /etc/profile
+    module load mpi
     git clone --single-branch --depth=1 -b v7.0.0 https://github.com/UIUC-PPL/charm.git /opt/charm
     cd /opt/charm
     export CCACHE_DIR=/tmp
-    ./build charm++ mpi-linux-x86_64 -j\$(nproc) --with-production
-    ./build charm++ netlrts-linux-x86_64 -j\$(nproc) --with-production
-    ./build charm++ multicore-linux-x86_64 -j\$(nproc) --with-production
+    ./build charm++ mpi-linux-x86_64 -j16 --with-production && \
+    ./build charm++ multicore-linux-x86_64 -j16 --with-production && \
+    ./build charm++ netlrts-linux-x86_64 -j16 --with-production
+
+    # Build and install spiff
+    rm -fr /tmp/spiff
+    git clone https://github.com/jhenin/spiff /tmp/spiff && \
+        make -C /tmp/spiff && \
+        install /tmp/spiff/spiff /usr/local/bin/

doc/colvars-refman-main.tex

@@ -2968,7 +2968,7 @@
 \item %
   \key
     {fittingAtoms}{%
-    \texttt{gspath} and \texttt{gspath}}{%
+    \texttt{gspath} and \texttt{gzpath}}{%
     The atoms that are used for alignment}{%
     Group of atoms}{%
 		Before calculating $\mathbf{v}_1$, $\mathbf{v}_2$, $\mathbf{v}_3$ and $\mathbf{v}_4$, the current frame need to be aligned to the corresponding reference frames. This option specifies which atoms are used to do alignment.
@@ -3297,6 +3297,98 @@
 All distances are calculated every \texttt{freq} timesteps to update the list of nearby images.
 }\fi
 
+\cvsubsubsec{\texttt{aspath}: progress along a path defined in atomic Cartesian coordinate space.}{sec:cvc_aspath}
+\labelkey{colvar|aspath}
+
+This CV computes a special case of Eq. \ref{eq:apath_s}, where $x_j$ is the
+$j$-th atomic position, $x_{i,j}$ is the $j$-th atomic position of the $i$-th
+reference frame. The subtraction $x_j - x_{i,j}$ is actually calculated as
+$\mathbf{x}_j - R_i\mathbf{x}_{i,j}$, where $\mathrm{R}_i$ is a 3x3 rotation
+matrix that minimizes the RMSD between the current atomic positions of
+simulation and the $i$-th reference frame. Bold $\mathbf{x}_j$ is used since
+an atomic position is a vector.
+
+\ifdefined\cvvmdornamd{
+For NAMD and VMD users, this component can be regarded as an improved C++
+implementation of the PCV progress component of the Tcl-scripted version
+(see \ref{sec:apath_scripted}).
+}\fi
+
+\begin{cvcoptions}
+\item %
+  \key
+    {atoms}{%
+    \texttt{aspath} and \texttt{azpath}}{%
+    Group of atoms}{%
+    Block \texttt{atoms \{...\}}}{%
+    Defines the atoms whose coordinates make up the value of the component.}
+
+\item %
+  \key
+    {refPositionsCol}{%
+    \texttt{aspath} and \texttt{azpath}}{%
+    PDB column containing atom flags}{%
+    \texttt{O}, \texttt{B}, \texttt{X}, \texttt{Y}, or \texttt{Z}}{%
+    If \texttt{refPositionsFileN} is a PDB file that contains all the atoms in the topology, this option may be provided to set which PDB field is used to flag the reference coordinates for \texttt{atoms}.}
+
+\item %
+  \key
+    {refPositionsFileN}{%
+    \texttt{aspath} and \texttt{azpath}}{%
+    File containing the reference positions for fitting}{%
+    UNIX filename}{%
+		The path is defined by multiple \texttt{refPositionsFile}s which are similiar to \texttt{refPositionsFile} in the \texttt{rmsd} CV. If your path consists of $10$ nodes, you can list the coordinate file (in PDB or XYZ format) from \texttt{refPositionsFile1} to \texttt{refPositionsFile10}.
+    }
+
+\item %
+  \key
+    {fittingAtoms}{%
+    \texttt{aspath} and \texttt{azpath}}{%
+    The atoms that are used for alignment}{%
+    Group of atoms}{%
+		Before calculating $\mathbf{v}_1$, $\mathbf{v}_2$, $\mathbf{v}_3$ and $\mathbf{v}_4$, the current frame need to be aligned to the corresponding reference frames. This option specifies which atoms are used to do alignment.
+    }
+
+\end{cvcoptions}
+
+\cvsubsubsec{\texttt{azpath}: distance from a path defined in atomic Cartesian coordinate space.}{sec:cvc_azpath}
+\labelkey{colvar|azpath}
+
+Similar to \refkey{aspath}{colvar|aspath}, this CV computes a special case of Eq.
+\ref{eq:apath_z}, and shares the same options as \refkey{aspath}{colvar|aspath}.
+
+The usage of \texttt{azpath} and \texttt{aspath} is illustrated below:
+
+\begin{cvexampleinput}
+colvar \{\\
+\-~~\# Progress along the path\\
+\-~~name as\\
+\-~~\# The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)\\
+\-~~\# Use atomic coordinate from atoms 1, 2 and 3 to compute the path\\
+\-~~aspath \{\\
+\-~~~~atoms \{atomnumbers \{ 1 2 3 \}\}\\
+\-~~~~refPositionsFile1 string-00.pdb\\
+\-~~~~refPositionsFile2 string-01.pdb\\
+\-~~~~refPositionsFile3 string-02.pdb\\
+\-~~~~refPositionsFile4 string-03.pdb\\
+\-~~~~refPositionsFile5 string-04.pdb\\
+\-~~\}\\
+\}\\
+\noindent\ttfamily colvar \{\\
+\-~~\# Distance from the path\\
+\-~~name az\\
+\-~~\# The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)\\
+\-~~\# Use atomic coordinate from atoms 1, 2 and 3 to compute the path\\
+\-~~azpath \{\\
+\-~~~~atoms \{atomnumbers \{ 1 2 3 \}\}\\
+\-~~~~refPositionsFile1 string-00.pdb\\
+\-~~~~refPositionsFile2 string-01.pdb\\
+\-~~~~refPositionsFile3 string-02.pdb\\
+\-~~~~refPositionsFile4 string-03.pdb\\
+\-~~~~refPositionsFile5 string-04.pdb\\
+\-~~\}\\
+\}
+\end{cvexampleinput}
 
 \cvsubsec{Dense neural network in CV space (MLCV)}{sec:cvc_neuralNetwork}
 \labelkey{colvar|NeuralNetwork}

doc/cv_version.tex

@@ -1 +1 @@
-\newcommand{\cvversion}{2023-08-21}
+\newcommand{\cvversion}{2023-09-05}