Squashed merge of master branch

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 no longer supported by the current version of Colvars: please use GROMACS 2024 or later.
+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?

doc/colvars-code-refs.bib

@@ -144,6 +144,20 @@ @article{Fiorin2020
   url = {https://doi.org/10.1002/jcc.26075}
 }
 
+% Updated multiple-walker ABF implementation
+@article{Fiorin2024,
+  author = {Fiorin, Giacomo and Marinelli, Fabrizio and Forrest, Lucy R. and Chen, Haochuan and Chipot, Christophe and Kohlmeyer, Axel and Santuz, Hubert and H{\'e}nin, J{\'e}rôme},
+  title = {Expanded Functionality and Portability for the Colvars Library},
+  journal = {J. Phys. Chem. {B}},
+  volume = {0},
+  number = {0},
+  pages = {null},
+  year = {2024},
+  doi = {10.1021/acs.jpcb.4c05604},
+  pmid = 39501453,
+  url = { https://doi.org/10.1021/acs.jpcb.4c05604}
+}
+
 % Umbrella-integration eABF estimator
 @article{Fu2016,
   author = {Fu, Haohao and Shao, Xueguang and Chipot, Christophe and Cai, Wensheng},

doc/colvars-refman-main.tex

@@ -5616,13 +5616,12 @@
   }
 \end{itemize}
 
-\cvnamdonly{
 \cvsubsubsec{Multiple-walker ABF}{sec:colvarbias_abf_shared}
 \label{sec:mw-ABF}
 
-This implements the multiple-walker ABF scheme described in \cite{Minoukadeh2010}. The reference for this
-implementation is \cite{Comer2014c}.
-This feature requires that \MDENGINE be compiled and executed with multiple-replica
+This implements the multiple-walker ABF scheme described in \cite{Minoukadeh2010}. The references for this
+implementation are \cite{Comer2014c} and \cite{Fiorin2024}.
+This feature requires that \MDENGINE{} be compiled and executed with multiple-replica
 support.
 
 If \refkey{shared}{abf|shared} is enabled, the total force samples will be synchronized among all replicas
@@ -5632,14 +5631,15 @@
 Thus, it is as if total force samples among all replicas are gathered in a single shared buffer.
 Shared ABF allows all replicas to benefit from the sampling done by other replicas and can lead to faster convergence of the biasing force.
 
+\cvnamdonly{
 An implementation of the selection mechanism described in \cite{Comer2014c} is provided as a set of Tcl scripts in \texttt{colvartools/mwABF\_selection.tcl} in the Colvars repository.
 Compared with the initial implementation, the current implementation supports selection on sets of up to 3 colvars.
 To reduce noise, samples can be counted in a hybercube around the current bin (see Tcl script for details).
 A set of example NAMD inputs can be found in the \texttt{namd/tests/library/multiple\_walker\_abf} directory.
-
+} % end of \cvnamdonly
 
 \paragraph{Output files of multiple-walker ABF.}
-In multiple-walker ABF runs, each walker now outputs gradient and count files containing only data collected locally (this is a change in version 2024-01-06).
+In multiple-walker ABF runs, since Colvars version 2024-01-06, each walker outputs gradient and count files containing only data collected locally.
 In addition, the first walker outputs the collected data using the common prefix, with an additional \texttt{".all"} string (i.e. file names ending with \texttt{".all.count"}, \texttt{".all.grad"} etc.).
 
 
@@ -5665,7 +5665,6 @@
     Because this forces the replicas to synchronize, small values of this parameter may slightly reduce the overall throughput, especially on systems with unequal performance.
   }
 \end{itemize}
-}
 
 \cvsubsubsec{Output files}{sec:colvarbias_abf_output}
 

doc/cv_version.tex

@@ -1 +1 @@
-\newcommand{\cvversion}{2024-11-08}
+\newcommand{\cvversion}{2024-11-13}

doc/doxygen/Doxyfile

@@ -1420,7 +1420,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:

gromacs/tests/interface/010_MPI_multi-sim/run.sh

@@ -42,5 +42,5 @@ done
 # cp -f a/test.colvars.traj a/test.colvars.state .
 # cp -f a/test.log ./test.out
 
-echo " Success!"
+echo " Done."
 

gromacs/tests/interface/011_MPI_mwABF/README.md

@@ -0,0 +1,20 @@
+## Gromacs mwABF regression test
+
+This directory contains a test for multiple-walker ABF in Colvars/Gromacs.
+
+
+### Version tested
+
+The tests are valid against Gromacs version 2024.3 and following.
+
+
+### Files tested
+
+Only the traj files of the simulation **a** is being tested.
+
+
+### Scripts
+
+  - `create_tpr.sh` is used to generate the .tpr
+  - `run.sh` is called by a `run_tests.sh` script to run the REMD simulation
+  - `cleanup.sh` is called by a `run_tests.sh` to clean the simulations files in the subfolders.

gromacs/tests/interface/011_MPI_mwABF/a/system.mdp

@@ -0,0 +1,56 @@
+;Run control
+integrator               = md-vv
+;time step in picoseconds
+dt                       = 0.002
+;number of steps
+nsteps                   = 50
+;no trr
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+;frequency to write energies to log file
+nstlog                   = 1
+;frequency to write energies to energy file
+nstenergy                = 1
+nstcalcenergy            = 1
+;frequency to write coordinates to xtc trajectory
+nstxout-compressed     = 1
+
+cutoff-scheme            = verlet
+
+
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+
+; Bond parameters
+constraint_algorithm    = lincs
+constraints             = h-bonds
+
+
+
+;treatment of van der waals interactions
+vdwtype = cut-off
+vdw-modifier = Potential-switch
+rvdw = 1.2
+rvdw-switch = 1.0
+
+coulombtype              = PME
+rcoulomb                = 1.2
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+
+;Temperature coupling
+tcoupl                   = v-rescale
+tc-grps                  = System
+ref-t                    = 300
+tau-t                    = 1
+ld-seed                  = 1
+
+; pressure coupling
+pcoupl                   = no
+
+gen-vel                  = no
+
+colvars-active           = yes
+colvars-configfile       = test.colvars
+

gromacs/tests/interface/011_MPI_mwABF/a/test.colvars

@@ -0,0 +1 @@
+../test.colvars

gromacs/tests/interface/011_MPI_mwABF/b/system.mdp

@@ -0,0 +1,56 @@
+;Run control
+integrator               = md-vv
+;time step in picoseconds
+dt                       = 0.002
+;number of steps
+nsteps                   = 50
+;no trr
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+;frequency to write energies to log file
+nstlog                   = 1
+;frequency to write energies to energy file
+nstenergy                = 1
+nstcalcenergy            = 1
+;frequency to write coordinates to xtc trajectory
+nstxout-compressed     = 1
+
+cutoff-scheme            = verlet
+
+
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+
+; Bond parameters
+constraint_algorithm    = lincs
+constraints             = h-bonds
+
+
+
+;treatment of van der waals interactions
+vdwtype = cut-off
+vdw-modifier = Potential-switch
+rvdw = 1.2
+rvdw-switch = 1.0
+
+coulombtype              = PME
+rcoulomb                = 1.2
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+
+;Temperature coupling
+tcoupl                   = v-rescale
+tc-grps                  = System
+ref-t                    = 300
+tau-t                    = 1
+ld-seed                  = 2
+
+; pressure coupling
+pcoupl                   = no
+
+gen-vel                  = no
+
+colvars-active           = yes
+colvars-configfile       = test.colvars
+

gromacs/tests/interface/011_MPI_mwABF/b/test.colvars

@@ -0,0 +1 @@
+../test.colvars

gromacs/tests/interface/011_MPI_mwABF/c/system.mdp

@@ -0,0 +1,56 @@
+;Run control
+integrator               = md-vv
+;time step in picoseconds
+dt                       = 0.002
+;number of steps
+nsteps                   = 50
+;no trr
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+;frequency to write energies to log file
+nstlog                   = 1
+;frequency to write energies to energy file
+nstenergy                = 1
+nstcalcenergy            = 1
+;frequency to write coordinates to xtc trajectory
+nstxout-compressed     = 1
+
+cutoff-scheme            = verlet
+
+
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+
+; Bond parameters
+constraint_algorithm    = lincs
+constraints             = h-bonds
+
+
+
+;treatment of van der waals interactions
+vdwtype = cut-off
+vdw-modifier = Potential-switch
+rvdw = 1.2
+rvdw-switch = 1.0
+
+coulombtype              = PME
+rcoulomb                = 1.2
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+
+;Temperature coupling
+tcoupl                   = v-rescale
+tc-grps                  = System
+ref-t                    = 300
+tau-t                    = 1
+ld-seed                  = 3
+
+; pressure coupling
+pcoupl                   = no
+
+gen-vel                  = no
+
+colvars-active           = yes
+colvars-configfile       = test.colvars
+

gromacs/tests/interface/011_MPI_mwABF/c/test.colvars

@@ -0,0 +1 @@
+../test.colvars

gromacs/tests/interface/011_MPI_mwABF/cleanup.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+# -*- sh-basic-offset: 2; sh-indentation: 2; -*-
+
+# Script to remove simulations files
+# Called by `run_tests.sh` scripts
+
+echo "Cleaning up output files"
+for i in a b c d
+do
+    cd $i
+    rm -f *.xtc *.trr *.edr *.cpt *.gro *.log *~ \#*\# mdout.mdp
+    rm -f *.state *.old *.traj *.zcount
+    cd ..
+done

gromacs/tests/interface/011_MPI_mwABF/d/system.mdp

@@ -0,0 +1,56 @@
+;Run control
+integrator               = md-vv
+;time step in picoseconds
+dt                       = 0.002
+;number of steps
+nsteps                   = 50
+;no trr
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+;frequency to write energies to log file
+nstlog                   = 1
+;frequency to write energies to energy file
+nstenergy                = 1
+nstcalcenergy            = 1
+;frequency to write coordinates to xtc trajectory
+nstxout-compressed     = 1
+
+cutoff-scheme            = verlet
+
+
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+
+; Bond parameters
+constraint_algorithm    = lincs
+constraints             = h-bonds
+
+
+
+;treatment of van der waals interactions
+vdwtype = cut-off
+vdw-modifier = Potential-switch
+rvdw = 1.2
+rvdw-switch = 1.0
+
+coulombtype              = PME
+rcoulomb                = 1.2
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+
+;Temperature coupling
+tcoupl                   = v-rescale
+tc-grps                  = System
+ref-t                    = 300
+tau-t                    = 1
+ld-seed                  = 4
+
+; pressure coupling
+pcoupl                   = no
+
+gen-vel                  = no
+
+colvars-active           = yes
+colvars-configfile       = test.colvars
+

gromacs/tests/interface/011_MPI_mwABF/d/test.colvars

@@ -0,0 +1 @@
+../test.colvars