diff --git a/regtest/adjmat/rt-dfg-wcsurf/Makefile b/regtest/adjmat/rt-dfg-wcsurf/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/adjmat/rt-dfg-wcsurf/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/adjmat/rt-dfg-wcsurf/config b/regtest/adjmat/rt-dfg-wcsurf/config
new file mode 100644
index 0000000000000000000000000000000000000000..999b209af907e501185cf7868b3f2b41de44141d
--- /dev/null
+++ b/regtest/adjmat/rt-dfg-wcsurf/config
@@ -0,0 +1,4 @@
+mpiprocs=1
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz traj.xyz --length-units A --box 28.66,28.66,28.66"
diff --git a/regtest/adjmat/rt-dfg-wcsurf/plumed.dat b/regtest/adjmat/rt-dfg-wcsurf/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..8a89ab0b372e37bd51cc7d94ce3646acfeece19f
--- /dev/null
+++ b/regtest/adjmat/rt-dfg-wcsurf/plumed.dat
@@ -0,0 +1,9 @@
+c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
+cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
+mat: CONTACT_MATRIX ATOMS=cf WTOL=0.01 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
+dfs: DFSCLUSTERING MATRIX=mat
+clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1
+
+# DUMPMULTICOLVAR DATA=clust1 ORIGIN=1 UNITS=A FILE=atoms.xyz
+# MULTICOLVARDENS DATA=clust1 ORIGIN=1 DIR=xyz NBINS=30,30,30 BANDWIDTH=1.0,1.0,1.0 RUN=1 OFILE=dens.cube
+WCSURFACE DATA=clust1 ORIGIN=1 FILE=surface.xyz NBINS=30,30,30 BANDWIDTH=1.0,1.0,1.0 UNITS=A CONTOUR=250.0 PRECISION=4
diff --git a/regtest/adjmat/rt-dfg-wcsurf/surface.xyz.reference b/regtest/adjmat/rt-dfg-wcsurf/surface.xyz.reference
new file mode 100644
index 0000000000000000000000000000000000000000..289eb8fb36a612575e1dd8bd32b81d23da808586
--- /dev/null
+++ b/regtest/adjmat/rt-dfg-wcsurf/surface.xyz.reference
@@ -0,0 +1,678 @@
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diff --git a/src/adjmat/ClusterAnalysisBase.cpp b/src/adjmat/ClusterAnalysisBase.cpp
index 1b92aca9d32000f25200d859237f9c97fb947778..d6a2decbf8fe94539150121328eedc21bda95c27 100644
--- a/src/adjmat/ClusterAnalysisBase.cpp
+++ b/src/adjmat/ClusterAnalysisBase.cpp
@@ -35,6 +35,8 @@ Action(ao),
MultiColvarFunction(ao),
myclusters(NULL)
{
+ // This makes these colvars behave appropriately with dump and analysis
+ usespecies=true;
// Find what action we are taking the clusters from
std::vector<std::string> matname(1); parse("CLUSTERS",matname[0]);
bool found_cluster=interpretInputMultiColvars(matname,0.0);
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index 1b95ea8b2335ae4073874712db41c0a4d0304dda..a5f75c5731535f86813e42c3b9f884c9b42aaa6a 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -145,7 +145,7 @@ DumpMultiColvar::DumpMultiColvar(const ActionOptions&ao):
}
void DumpMultiColvar::update(){
- of.printf("%u\n",mycolv->getFullNumberOfTasks());
+ of.printf("%u\n",mycolv->getCurrentNumberOfActiveTasks());
const Tensor & t(mycolv->getPbc().getBox());
if(mycolv->getPbc().isOrthorombic()){
of.printf((" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));
@@ -162,6 +162,7 @@ void DumpMultiColvar::update(){
for(unsigned i=0;i<mycolv->getFullNumberOfTasks();++i){
const char* defname="X";
const char* name=defname;
+ if( !mycolv->taskIsCurrentlyActive(i) ) continue;
Vector apos = mycolv->getCentralAtomPos( mycolv->getTaskCode(i) );
if( getNumberOfAtoms()>0 ) apos=pbcDistance( apos, getPosition(0) );
diff --git a/src/multicolvar/MultiColvarDensity.cpp b/src/multicolvar/MultiColvarDensity.cpp
index 1a9bb94f30bd77e11fb4431158c675e3fa79e7a2..369960a46d4a45f93b65aa3e3e3e9b3ea92ca8f9 100644
--- a/src/multicolvar/MultiColvarDensity.cpp
+++ b/src/multicolvar/MultiColvarDensity.cpp
@@ -219,6 +219,9 @@ void MultiColvarDensity::update(){
plumed_dbg_assert( stash ); std::vector<double> cvals( mycolv->getNumberOfQuantities() );
Vector origin = getPosition(0); std::vector<double> pp( directions.size() ); Vector fpos;
for(unsigned i=0;i<mycolv->getFullNumberOfTasks();++i){
+ // Skip if task was not active on last run through
+ if( !mycolv->taskIsCurrentlyActive(i) ) continue ;
+
stash->retrieveValue( i, false, cvals );
Vector apos = pbcDistance( mycolv->getCentralAtomPos( mycolv->getTaskCode(i) ), origin );
if( fractional ){ fpos = getPbc().realToScaled( apos ); } else { fpos=apos; }
@@ -239,7 +242,7 @@ void MultiColvarDensity::update(){
// Cube files are in au so I convert from "Angstrom" to AU so that when
// VMD converts this number back to Angstroms (from AU) it looks right
if( plumed.getAtoms().usingNaturalUnits() ) gg->writeCubeFile( gridfile, 1.0/0.5292 );
- else gg->writeCubeFile( gridfile, plumed.getAtoms().getUnits().getLength()/5.929 );
+ else gg->writeCubeFile( gridfile, plumed.getAtoms().getUnits().getLength()/.05929 );
} else gg->writeToFile( gridfile );
gridfile.close();
diff --git a/src/multicolvar/WillardChandlerSurface.cpp b/src/multicolvar/WillardChandlerSurface.cpp
index 96bea6080bd8e1f044eb60cc1cfd12e47375762b..01fd4f7aa95106928e5620bfdae7ec84625f5847 100644
--- a/src/multicolvar/WillardChandlerSurface.cpp
+++ b/src/multicolvar/WillardChandlerSurface.cpp
@@ -179,6 +179,9 @@ void WillardChandlerSurface::update(){
unsigned rank=comm.Get_rank(), size=comm.Get_size();
for(unsigned i=rank;i<mycolv->getFullNumberOfTasks();i+=size){
+ // Skip if task was not active on last run through
+ if( !mycolv->taskIsCurrentlyActive(i) ) continue ;
+
stash->retrieveValue( i, false, cvals );
Vector apos = pbcDistance( mycolv->getCentralAtomPos( mycolv->getTaskCode(i) ), origin );
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index e7fc0af4b1dba896146d5b5efa72005f4e0f897f..c0e50420a4f62994f054f625b3548592d52dcca0 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -131,12 +131,8 @@ protected:
bool usingLowMem() const ;
/// Set that we are using low memory
void setLowMemOption(const bool& );
-/// Get the number of tasks that are currently active
- unsigned getCurrentNumberOfActiveTasks() const ;
/// Get the ith of the currently active tasks
unsigned getActiveTask( const unsigned& ii ) const ;
-/// Check whether or not a particular task is currently active
- bool taskIsCurrentlyActive( const unsigned& index ) const ;
/// Deactivate all the tasks in the task list
void deactivateAllTasks();
/// Deactivate all tasks with i in lower \f$\le\f$ i < upper
@@ -151,6 +147,10 @@ public:
~ActionWithVessel();
void unlockContributors();
void lockContributors();
+/// Get the number of tasks that are currently active
+ unsigned getCurrentNumberOfActiveTasks() const ;
+/// Check whether or not a particular task is currently active
+ bool taskIsCurrentlyActive( const unsigned& index ) const ;
virtual void finishTaskListUpdate(){};
/// Activate the jth colvar
/// Deactivate the current task in future loops