Enable and test mwABF in GROMACS

I disabled an init-time check for mutliple replicas because the
info becomes available after the proxy construction in GMX.
The lack of mutliple-replica setup will then be caught when the
first communication attempt occurs.

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

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

@@ -0,0 +1,46 @@
+#!/bin/bash
+# -*- sh-basic-offset: 2; sh-indentation: 2; -*-
+
+# Script to launch the REMD regression tests
+# It's best to have Gromacs compiled in double precision
+# Reference files have been generated with Gromacs version 2024-dev
+
+echo -n "Running $(basename $PWD)..."
+
+#set -e
+
+# if script called from `run_tests.sh` in the parent folder, retrieve the correct command binary from the argument
+if [ -x "$1" ]
+then
+    BINARY=$1
+else
+    BINARY="gmx_mpi_d"
+fi
+
+mpirun -np 16 -oversubscribe $BINARY mdrun -multidir a b c d -s test.tpr -deffnm test -reseed 376 >& test.out
+
+labels=(a b c d)
+for number in $(seq 1 ${#labels[@]}) ; do
+  index=$((${number} - 1))
+  label=${labels[${index}]}
+  replica_msg=$(grep -s "colvars: Enabling multiple replicas: this is replica number" ${label}/test.log)
+  if [ -z "${replica_msg}" ] ; then
+    echo "Error: missing replica initialization message." >& 2
+    exit 1
+  fi
+  replica_num=$(echo ${replica_msg} | cut -d' ' -f 9)
+  replicas_count=$(echo ${replica_msg} | cut -d' ' -f 11)
+  replicas_count=${replicas_count%.}
+  if [ ${replicas_count} != 4 ] || [ ${replica_num} != ${number} ] ; then
+    echo -e "Error: wrong initialization for replica number ${number}; got the following message:\n\n${replica_msg}\n" >& 2
+    exit 1
+  fi
+done
+
+# Copy result files to be tested in the main folder
+cp a/test.colvars.traj a/test.colvars.state .
+cp a/test.log ./test.out
+cp a/test.all.czar.pmf ./test.all.czar.pmf
+
+echo " Done."
+

gromacs/tests/interface/run_tests.sh

@@ -6,11 +6,19 @@ if [ ! -d ${TOPDIR} ] ; then
     exit 1
 fi
 
+MPI_TESTS=[0-9][0-9][0-9]_MPI_*
+
 tests=([0-9][0-9][0-9]_*)
-tests=(${tests[@]/010_MPI_multi-sim})
+
+for DIR in $MPI_TESTS
+do
+  tests=(${tests[@]/$DIR})
+done
 
 ALL_SUCCESS=1
 
+echo "Running tests ${tests[@]}"
+
 ../library/run_tests.sh $1 ${tests[@]}
 
 if [ $? -ne 0 ]
@@ -20,14 +28,17 @@ fi
 
 # Run tests that depend on an MPI build
 if source ${TOPDIR}/devel-tools/load-openmpi.sh ; then
-    if pushd 010_MPI_multi-sim > /dev/null ; then
-        ./run.sh $1
-        if [ $? -ne 0 ]
-        then
-            ALL_SUCCESS=0
-        fi
-        popd > /dev/null
-    fi
+    for DIR in $MPI_TESTS
+    do
+      if pushd $DIR > /dev/null ; then
+          ./run.sh $1
+          if [ $? -ne 0 ]
+          then
+              ALL_SUCCESS=0
+          fi
+          popd > /dev/null
+      fi
+    done
 fi