Merge branch 'master' into isdb

CHANGES/v2.3.txt

@@ -157,6 +157,7 @@ See branch \branch{v2.3} on git repository.
 - Fixed bug when using \ref MOVINGRESTRAINT with periodic variables such as \ref TORSION \issue{225}.
 - Fixed bug in \ref HBONDS that used to apear when you used DONORNS and ACCEPTORS with same numbers of atoms 
 - Fixed bug in \ref DISTANCES that appears when using BETWEEN and link cells.
+- Prevented users from causing segfaults by storing derivatives without LOWMEM flag.  In these caess PLUMED crashes with meaningful errors.
 
 For developers:
 - plumedcheck validation has been made stricter. All the checks are now described in the developer manual.

regtest/adjmat/rt-dfg-wcsurf/plumed.dat

@@ -5,7 +5,7 @@ cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
 # Build a contact matrix
 mat: CONTACT_MATRIX ATOMS=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} 
 # Find largest cluster
-dfs: DFSCLUSTERING MATRIX=mat
+dfs: DFSCLUSTERING MATRIX=mat LOWMEM
 clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 
 nat: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1
 

regtest/adjmat/rt-topolog-deriv/plumed.dat

@@ -8,7 +8,7 @@ TOPOLOGY_MATRIX ...
   LABEL=mat
 ... TOPOLOGY_MATRIX
 
-dfs: DFSCLUSTERING MATRIX=mat 
+dfs: DFSCLUSTERING LOWMEM MATRIX=mat 
 
 mm: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM
 

src/vesselbase/StoreDataVessel.cpp

@@ -51,6 +51,9 @@ void StoreDataVessel::resize(){
      nspace = 1;
      active_der.resize( max_lowmem_stash * ( 1 + getAction()->getNumberOfDerivatives() ) );
   } else {
+     if( getAction()->getNumberOfDerivatives()>getAction()->maxderivatives ){
+          error("not enough memory to store derivatives for action " + getAction()->getLabel() + " use LOWMEM option");
+     }
      nspace = 1 + getAction()->maxderivatives;
      active_der.resize( getNumberOfStoredValues() * ( 1 + getAction()->maxderivatives ) );
   }