Merge branch 'v2.10'

plumed · Oct 3, 2024 · 085483b · 085483b · PlumedBot · Oct 3, 2024
2 parents 5eabea9 + 473fe65
commit 085483b
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diff --git a/src/adjmat/AdjacencyMatrixBase.cpp b/src/adjmat/AdjacencyMatrixBase.cpp
@@ -63,7 +63,9 @@ AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao):
 
   if( t.size()==0 ) {
     std::vector<AtomNumber> ta; parseAtomList("GROUPA",ta);
+    if( ta.size()==0 && getName()=="HBOND_MATRIX") parseAtomList("DONORS",ta);
     std::vector<AtomNumber> tb; parseAtomList("GROUPB",tb);
+    if( tb.size()==0 && getName()=="HBOND_MATRIX") parseAtomList("ACCEPTORS",tb);
     if( ta.size()==0 || tb.size()==0 ) error("no atoms have been specified in input");
 
     // Create list of tasks

diff --git a/src/adjmat/HbondMatrix.cpp b/src/adjmat/HbondMatrix.cpp
@@ -96,6 +96,8 @@ PLUMED_REGISTER_ACTION(HbondMatrix,"HBOND_MATRIX")
 
 void HbondMatrix::registerKeywords( Keywords& keys ) {
   AdjacencyMatrixBase::registerKeywords( keys );
+  keys.add("atoms-2","DONORS","The list of atoms which can donate a hydrogen bond");
+  keys.add("atoms-2","ACCEPTORS","The list of atoms which can accept a hydrogen bond");
   keys.add("atoms","HYDROGENS","The list of atoms that can form the bridge between the two interesting parts "
            "of the structure.");
   keys.add("numbered","SWITCH","The switchingfunction that specifies how close a pair of atoms must be together for there to be a hydrogen bond between them");