Merge branch 'master' into torchann

.github/workflows/backend-template.yml

@@ -181,7 +181,8 @@ jobs:
           path: ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.diff
 
       - name: Run regression tests for library code with ${{ inputs.backend_name }} (binary restarts)
-        if: ${{ inputs.test_lib_directory }}
+        # Skipping GROMACS, because its restarts are always binary anyway
+        if: inputs.test_lib_directory != '' && inputs.backend_name != 'GROMACS-main'
         shell: bash
         working-directory: ${{ inputs.test_lib_directory }}
         env:

.github/workflows/test-backends.yml

@@ -72,18 +72,6 @@ jobs:
       private_key: ${{ secrets.PULL_VMD_KEY }}
       private_key_vmd_plugins: ${{ secrets.PULL_VMD_PLUGINS_KEY }}
 
-  gromacs-2022:
-    name: GROMACS (release-2022)
-    uses: ./.github/workflows/backend-template.yml
-    with:
-      backend_name: GROMACS-2022
-      backend_repo: gromacs/gromacs
-      backend_repo_ref: release-2022
-      container_name: CentOS9-devel
-      path_compile_script: devel-tools/compile-gromacs.sh
-      test_lib_directory: gromacs/tests/library
-      rpath_exe: install/bin/gmx_d
-
   gromacs-2023:
     name: GROMACS (release-2023)
     uses: ./.github/workflows/backend-template.yml
@@ -94,7 +82,7 @@ jobs:
       container_name: CentOS9-devel
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
-      rpath_exe: install/bin/gmx_d
+      rpath_exe: install/bin/gmx_mpi_d
 
   gromacs-main:
     name: GROMACS (main)
@@ -106,4 +94,5 @@ jobs:
       container_name: CentOS9-devel
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
-      rpath_exe: install/bin/gmx_d
+      test_interface_directory: gromacs/tests/interface
+      rpath_exe: install/bin/gmx_mpi_d

.github/workflows/test-library.yml

@@ -246,10 +246,6 @@ jobs:
           key: ${{ runner.os }}-build-asan-${{ github.sha }}
           restore-keys: ${{ runner.os }}-build-asan-
 
-      - name: Install build dependencies for library
-        run: |
-          sudo apt -y install tcl8.6-dev clang-14 clang-tools-14
-
       - name: Checkout OpenMM (for Lepton library)
         uses: actions/checkout@v4
         with:
@@ -430,6 +426,17 @@ jobs:
           scl enable gcc-toolset-12 -- \
           cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake
 
+      - name: GCC 13, C++20 (CentOS 9)
+        env:
+          CXX_STANDARD: 20
+          CXX: g++
+          CXX_VERSION: 13
+          CC: gcc
+        run: |
+          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
+          scl enable gcc-toolset-13 -- \
+          cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake
+
       - name: Clang 16, C++11 (CentOS 9)
         env:
           CXX_STANDARD: 11

README.md

@@ -1,28 +1,27 @@
 # Collective variables module (Colvars)
 
-A software module for molecular simulation and analysis that provides a high-performance implementation of sampling algorithms defined on a reduced space of continuously differentiable functions (aka collective variables).
+A software library for molecular simulation and analysis that provides a high-performance implementation of sampling algorithms defined on a reduced space of continuously differentiable functions (aka collective variables).
 
 First released in 2008 as part of the standard distribution of [NAMD](https://www.ks.uiuc.edu/Research/namd/) version 2.7b1, Colvars has also been integrated in [LAMMPS](https://lammps.sandia.gov/download.html), [VMD](https://www.ks.uiuc.edu/Research/vmd/), [GROMACS](http://www.gromacs.org/), and [Tinker-HP](https://tinker-hp.org/).  In VMD, interactive use is possible both from the command line and through the [Dashboard](vmd/cv_dashboard/README.md) graphical user interface.
 
-The functionality provided to those packages by the Colvars library includes a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.
+The functionality provided to those packages by Colvars includes a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.
 
 ## Obtaining and using
 
-The easiest way to obtain pre-compiled versions of Colvars is via one of following:
-- the molecular simulation program [LAMMPS](https://lammps.sandia.gov/download.html);
-- the molecular simulation program [NAMD](https://www.ks.uiuc.edu/Research/namd/);
-- the molecular simulation program [Tinker-HP](https://tinker-hp.org/);
-- the molecular visualization program [VMD](https://www.ks.uiuc.edu/Research/vmd/).
+The easiest way to obtain pre-compiled versions of Colvars is via one of the following software packages:
+- [GROMACS](https://manual.gromacs.org/)
+- [LAMMPS](https://lammps.sandia.gov/download.html)
+- [NAMD](https://www.ks.uiuc.edu/Research/namd/)
+- [Tinker-HP](https://tinker-hp.org/)
+- [VMD](https://www.ks.uiuc.edu/Research/vmd/)
 
 Please check [here](https://github.com/Colvars/colvars/wiki/List-of-Colvars-versions-included-in-simulation-and-analysis-packages) to see which version of Colvars is included with the round-number or "stable" versions of each code.
 
-For the molecular simulation program [GROMACS](http://www.gromacs.org/), code may be compiled via our Colvars-patched [releases](#gromacs-colvars-releases).
-
 ## Documentation
 
 The [Colvars webpage](https://colvars.github.io/) includes user documentation for all codes, as well as a Doxygen-based [developer documentation](https://colvars.github.io/doxygen/html/).
 
-To reflect the different availability of features in each engine, the Colvars reference manual comes in several flavors: [GROMACS](https://colvars.github.io/colvars-refman-gromacs/colvars-refman-gromacs.html) [LAMMPS](https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html) [NAMD](https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html) [Tinker-HP](https://colvars.github.io/colvars-refman-tinkerhp/colvars-refman-tinkerhp.html) [VMD](https://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html)
+To reflect the different availability of features in each engine, the Colvars reference manual comes in several flavors: [GROMACS](https://colvars.github.io/master/colvars-refman-gromacs.html) [LAMMPS](https://colvars.github.io/master/colvars-refman-lammps.html) [NAMD](https://colvars.github.io/master/colvars-refman-namd.html) [Tinker-HP](https://colvars.github.io/master/colvars-refman-tinkerhp.html) [VMD](https://colvars.github.io/master/colvars-refman-vmd.html)
 
 ## Citing
 
@@ -87,7 +86,7 @@ The [tests](https://github.com/Colvars/colvars/tree/master/tests?raw=true) folde
 
 ## Updating to the latest version
 
-To recompile each program with the most recent version of the module, [download](https://github.com/Colvars/colvars/archive/master.zip) the `master` branch of this repository, or clone it via git:
+To recompile each program with the most recent version of the library, [download](https://github.com/Colvars/colvars/archive/master.zip) the `master` branch of this repository, or clone it via git:
 ```
 git clone https://github.com/Colvars/colvars.git
 ```
@@ -109,45 +108,37 @@ The `update-colvars-code.sh` script support patching the latest development vers
 
 All of the above MD engine versions are automatically tested as part of GitHub Actions [workflows](https://github.com/Colvars/colvars/actions?query=branch%3Amaster).
 
-## GROMACS-Colvars releases
-
-Colvars can interface to GROMACS in two ways, depending on the version of GROMACS:
-1. Using a customized `mdrun` command line (GROMACS releases up to 2023); source code is available as patched versions of past GROMACS releases [here](https://github.com/Colvars/gromacs/tags).
-2. Using a standard `mdrun` command line (supported in the 2024-beta release); source code is available directly from the [GROMACS repository](https://github.com/gromacs/gromacs).
-
-The standard GROMACS installation procedure is supported in either case.
+## Legacy GROMACS-Colvars patched releases
 
-To update the version of Colvars to GROMACS in a given release, the Colvars [patching procedure](#updating-to-the-latest-version) can be used.  This procedure is generally compatible with all GROMACS versions from the same release years as those listed above.  Please use the latest revision of each release series whenever possible.
+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**".
 
-When posting a message to the [Gromacs forum](https://gromacs.bioexcel.eu/) please use the [`colvars` tag](https://gromacs.bioexcel.eu/tag/colvars) and please salso specify "GROMACS modification: **Yes**" unless you are using a standard GROMACS.
-
-If using a patched release, please also reference the Colvars version: this is included in the version string that is reported by the patched GROMACS (right after the GROMACS version), for example:
-```
-   :-) GROMACS - gmx_d, 2021.5-Colvars-2022-02-20-dev (double precision) (-:
-```
 
 ## Which version of Colvars is recommended?
 
-The Git `master` branch is to be considered the "*stable*" release at any given time; any bugfixes are released through `master` first.  The input syntax is near-completely *backward-compatible* and output files are *forward-compatible*.  Feel free to download Colvars and update NAMD, VMD, LAMMPS, GROMACS, or Tinker-HP as needed.
+The Git `master` branch is to be considered the "*stable*" release at any given time; any bugfixes are released through `master` first.  The input syntax is near-completely *backward-compatible* and output files are *forward-compatible*.  Feel free to download Colvars and update GROMACS, LAMMPS, NAMD, Tinker-HP or VMD as needed.
 
 Other branches are dedicated to the development of specific features: please use them at your own discretion.
 
+
 ## Which version of Colvars is included in package XX version YY?
 
 The specific version of Colvars is identified both in the code and in the documentation by the date of the most recent code revision (e.g. `2021-01-19`). 
 This date is printed to the standard output or log file as soon as Colvars is activated.
 
 A table mapping software package release versions to Colvars versions is given [here](https://github.com/Colvars/colvars/wiki/List-of-Colvars-versions-included-in-simulation-and-analysis-packages).
 
-
 If you are using a stable release of any of the codes mentioned above, feel free to use the version number of that code when asking questions.
 
+
 ## Feedback
 
-Please use the "[Issues](https://github.com/Colvars/colvars/issues)" tab of this page to submit new bug reports or to suggest new features.
+For usage questions, please start a new [Discussion](https://github.com/Colvars/colvars/discussions/new?category=q-a).
+
+For bug reports or feature requests, use the "[Issues](https://github.com/Colvars/colvars/issues)" tab.
+
 
 ## License
 
-This software is distributed under the GNU Lesser General Public License (LGPL), version 3.  See COPYING.LESSER for complete licensing terms.
+This software is distributed under the GNU Lesser General Public License version 3 (LGPLv3); see the file COPYING.LESSER for complete licensing terms.
 
-In the interest of broad distribution, copies of this code are also distributed together with LAMMPS (LGPL version 2), NAMD and VMD (UIUC license).  However, the terms of the LGPLv3 license still apply to code originating from this repository.
+In the interest of broad distribution, copies of this code are also included in GROMACS (LGPLv2), LAMMPS (LGPLv2), NAMD and VMD (UIUC license); however, the terms of the LGPLv3 still apply to code originating from this repository.

colvartools/plot_colvars_traj.py

@@ -3,7 +3,7 @@
 # Invoke this script with --help for documentation.
 
 # Download link: https://github.com/Colvars/colvars/blob/master/colvartools/plot_colvars_traj.py?raw=true
-# This version was modified on: 2023-07-13
+# This version was modified on: 2024-01-16
 # Contact: [email protected]
 
 from __future__ import print_function
@@ -314,10 +314,10 @@ def as_pandas(self, keys=None):
 
     parser.add_argument('--output-file',
                         type=str,
-                        help='Write the selected variables to a text file.  '
-                        'The step number is always included as the first '
-                        'column, and all variables '
-                        'must be defined on the same trajectory segments.',
+                        help="Write the selected variables to a file in NumPy format "
+                        " (if the extension is .npz) or in text format otherwise.  "
+                        "The step number is included as the first column, and all variables "
+                        "must be defined on the same trajectory segments.",
                         default=None)
 
     parser.add_argument('--plot-file',
@@ -388,24 +388,36 @@ def as_pandas(self, keys=None):
     plot_keys = dict(zip(variables, variables))
 
 
-    if (args.output_file):
+    if args.output_file:
 
-        fmt = " %12d"
-        columns = [colvars_traj[variables[0]].steps]
+        output_file = args.output_file
+        numpy_format = False
+        if output_file.endswith(".npz"):
+            numpy_format = True
+        if output_file == '-':
+            output_file = sys.stdout
+
+        text_fmt_string = " %12d"
+        if numpy_format:
+            columns = { 'step' : colvars_traj[variables[0]].steps }
+        else:
+            columns = [colvars_traj[variables[0]].steps]
         for var in variables:
             cv = colvars_traj[var]
             for ic in range(cv.num_dimensions):
                 y = cv.values
-                if (cv.num_dimensions > 1):
+                if cv.num_dimensions > 1 and not numpy_format:
                     y = cv.values[:,ic]
-                columns += [y]
-                fmt += " %21.14f"
-        columns = tuple(columns)
-        output_file = args.output_file
-        if (output_file == '-'): output_file = sys.stdout
-        np.savetxt(fname=output_file,
-                   X=list(zip(*columns)),
-                   fmt=str(fmt))
+                if numpy_format:
+                    columns[var] = y
+                else:
+                    columns += [y]
+                text_fmt_string += " %21.14f"
+
+        if numpy_format:
+            np.savez(output_file, **columns)
+        else:
+            np.savetxt(fname=output_file, X=np.column_stack(columns), fmt=str(text_fmt_string))
 
     else:
 

devel-tools/build_test_library.cmake

@@ -55,7 +55,14 @@ if(COLVARS_LEPTON)
   if(NOT DEFINED LEPTON_DIR)
     set(LEPTON_DIR "${COLVARS_SOURCE_DIR}/openmm-source/libraries/lepton")
     if(NOT EXISTS ${LEPTON_DIR})
+      # Try the parent folder
+      get_filename_component(LEPTON_DIR ${COLVARS_SOURCE_DIR} DIRECTORY)
+      set(LEPTON_DIR "${LEPTON_DIR}/openmm-source/libraries/lepton")
+    endif()
+    if(NOT EXISTS ${LEPTON_DIR})
+      # Giving up, cloning OpenMM into a sub-folder
       execute_process(COMMAND git clone --depth=1 https://github.com/openmm/openmm.git "${COLVARS_SOURCE_DIR}/openmm-source")
+      set(LEPTON_DIR "${COLVARS_SOURCE_DIR}/openmm-source/libraries/lepton")
     endif()
     message(STATUS "Using Lepton library from: ${LEPTON_DIR}")
   endif()

devel-tools/compile-gromacs.sh

@@ -4,6 +4,8 @@ source $(dirname $0)/load-recent-git.sh
 
 source $(dirname $0)/load-recent-gcc.sh
 
+source $(dirname $0)/load-openmpi.sh
+
 source $(dirname $0)/set-ccache.sh
 
 

devel-tools/compile-namd.sh

@@ -11,8 +11,9 @@ if [ -n "${CCACHE_HOME}" ] ; then
     export PATH=${CCACHE_HOME}:${PATH}
 fi
 
-# Save path to be used later
-devel_tools_folder=$(realpath $(dirname $0))
+if [ -e /opt/tcl/8.6/include/tcl.h ] ; then
+    export TCL_HOME=/opt/tcl/8.6
+fi
 
 
 compile_namd_target() {
@@ -77,18 +78,6 @@ EOF
         cmd+=(--charm-arch netlrts-linux-x86_64)
     fi
 
-    if grep -q -- -ltcl8.6 arch/Linux-x86_64.tcl ; then
-        if [ -d ${devel_tools_folder}/packages/tcl8.6.13-linux-x86_64-threaded ] ; then
-            export TCL_HOME=${devel_tools_folder}/packages/tcl8.6.13-linux-x86_64-threaded
-        fi
-    else
-        # Amend NAMD 2.x arch file for recent Tcl versions under RH and Debian paths
-        if [ -f /usr/lib64/libtcl8.6.so ] || \
-               [ -f /usr/lib/x86_64-linux-gnu/libtcl8.6.so ] ; then
-            sed -i 's/-ltcl8.5/-ltcl8.6/' arch/Linux-x86_64.tcl
-        fi
-    fi
-
     if [ -z "${TCL_HOME}" ] ; then
         if [ -f /usr/local/include/tcl.h ] ; then
             export TCL_HOME=/usr/local