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Added old syntax for HbondMatrix into code which appeared to have bee…
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…n deleted by accident
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Gareth Aneurin Tribello committed Oct 3, 2024
1 parent fa180a5 commit 473fe65
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2 changes: 2 additions & 0 deletions src/adjmat/AdjacencyMatrixBase.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 2 additions & 0 deletions src/adjmat/HbondMatrix.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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");
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Found broken examples in automatic/ANGLES.tmp
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