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Fixed grids so that old style multicolvar still works.
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In old multicolvar label of argument containing less than is aa.lessthan.
This is changed now to aa_lessthan as aa_lessthan is from a different action than
aa multicolvar.  I added to grid something to check if there is a value called aa.lessthan
in the grid file if it finds a request for aa_lessthan.
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Gareth Aneurin Tribello authored and Gareth Aneurin Tribello committed Mar 25, 2024
1 parent 4ceefe1 commit cdb4e96
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Showing 4 changed files with 45 additions and 31 deletions.
4 changes: 2 additions & 2 deletions src/adjmat/AdjacencyMatrixBase.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,8 +55,8 @@ AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao):
{
std::vector<unsigned> shape(2); std::vector<AtomNumber> t; parseAtomList("GROUP", t );
if( t.size()==0 ) {
parseAtomList("ATOMS", t);
if( t.size()>0 ) warning("using depracated syntax for contact matrix. You are strongly recommended to use GROUP instead of ATOMS");
parseAtomList("ATOMS", t);
if( t.size()>0 ) warning("using depracated syntax for contact matrix. You are strongly recommended to use GROUP instead of ATOMS");
}

if( t.size()==0 ) {
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32 changes: 16 additions & 16 deletions src/adjmat/ContactMatrixShortcut.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -90,23 +90,23 @@ ContactMatrixShortcut::ContactMatrixShortcut(const ActionOptions& ao):
Action(ao),
ActionShortcut(ao)
{
std::vector<std::string> grp_str; std::string atomsstr="";
std::vector<std::string> atomsvec; parseVector("ATOMS",atomsvec);
std::vector<std::string> grp_str; std::string atomsstr="";
std::vector<std::string> atomsvec; parseVector("ATOMS",atomsvec);
if( atomsvec.size()>0 ) {
for(unsigned i=0; i<atomsvec.size(); ++i) {
Group* gg = plumed.getActionSet().selectWithLabel<Group*>( atomsvec[i] );
if( gg ) grp_str.push_back( atomsvec[i] );
}
if( grp_str.size()!=atomsvec.size() ) {
grp_str.resize(0);
atomsstr = " ATOMS=" + atomsvec[0]; for(unsigned i=1; i<atomsvec.size(); ++i) atomsstr += "," + atomsvec[i];
}
} else {
std::string grp_inpt;
for(unsigned i=1;; ++i) {
if( !parseNumbered("GROUP",i,grp_inpt) ) break;
grp_str.push_back( grp_inpt );
}
for(unsigned i=0; i<atomsvec.size(); ++i) {
Group* gg = plumed.getActionSet().selectWithLabel<Group*>( atomsvec[i] );
if( gg ) grp_str.push_back( atomsvec[i] );
}
if( grp_str.size()!=atomsvec.size() ) {
grp_str.resize(0);
atomsstr = " ATOMS=" + atomsvec[0]; for(unsigned i=1; i<atomsvec.size(); ++i) atomsstr += "," + atomsvec[i];
}
} else {
std::string grp_inpt;
for(unsigned i=1;; ++i) {
if( !parseNumbered("GROUP",i,grp_inpt) ) break;
grp_str.push_back( grp_inpt );
}
}
if( grp_str.size()>9 ) error("cannot handle more than 9 groups");
if( grp_str.size()==0 ) { readInputLine( getShortcutLabel() + ": CONTACT_MATRIX_PROPER " + atomsstr + " " + convertInputLineToString() ); return; }
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20 changes: 10 additions & 10 deletions src/adjmat/Sprint.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -103,17 +103,17 @@ Sprint::Sprint(const ActionOptions& ao):
Action(ao),
ActionShortcut(ao)
{
std::string matinp; parse("MATRIX",matinp);
std::string matinp; parse("MATRIX",matinp);
if( matinp.length()==0 ) {
readInputLine( getShortcutLabel() + "_jmat: CONTACT_MATRIX " + convertInputLineToString() );
matinp = getShortcutLabel() + "_jmat";
}
readInputLine( getShortcutLabel() + "_jmat: CONTACT_MATRIX " + convertInputLineToString() );
matinp = getShortcutLabel() + "_jmat";
}
std::vector<unsigned> nin_group; unsigned ntot_atoms=0;
for(unsigned i=1;; ++i) {
std::string inum; Tools::convert( i, inum );
ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( matinp + inum + inum );
if( !av ) break ;
unsigned natoms = (av->copyOutput(0))->getShape()[0]; nin_group.push_back( natoms ); ntot_atoms += natoms;
std::string inum; Tools::convert( i, inum );
ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( matinp + inum + inum );
if( !av ) break ;
unsigned natoms = (av->copyOutput(0))->getShape()[0]; nin_group.push_back( natoms ); ntot_atoms += natoms;
}

// Diagonalization
Expand All @@ -133,8 +133,8 @@ Sprint::Sprint(const ActionOptions& ao):
readInputLine( sort_act );
readInputLine( getShortcutLabel() + jnum + ": SORT ARG=" + getShortcutLabel() + "_selection" + jnum );
for(unsigned n=0; n<nin_group[j]; ++n) {
std::string knum, nnum; Tools::convert( kk, knum ); Tools::convert( n+1, nnum ); kk++;
readInputLine( getShortcutLabel() + "_coord-" + knum + ": COMBINE ARG=" + getShortcutLabel() + jnum + "." + nnum + " PERIODIC=NO" );
std::string knum, nnum; Tools::convert( kk, knum ); Tools::convert( n+1, nnum ); kk++;
readInputLine( getShortcutLabel() + "_coord-" + knum + ": COMBINE ARG=" + getShortcutLabel() + jnum + "." + nnum + " PERIODIC=NO" );
}
}
}
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20 changes: 17 additions & 3 deletions src/tools/Grid.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -527,8 +527,22 @@ std::unique_ptr<GridBase> GridBase::create(const std::string& funcl, const std::
std::vector<int> gbin1(nvar); std::vector<unsigned> gbin(nvar);
std::vector<std::string> labels(nvar),gmin(nvar),gmax(nvar);
std::vector<std::string> fieldnames; ifile.scanFieldList( fieldnames );

// Retrieve names for fields
for(unsigned i=0; i<args.size(); ++i) labels[i]=args[i]->getName();
for(unsigned i=0; i<args.size(); ++i) {
labels[i]=args[i]->getName(); bool found=false;
for(unsigned j=0; j<fieldnames.size(); ++j) {
if( labels[i]==fieldnames[j] ) { found=true; break; }
}
// This is a change to ensure that we can deal with old style names for multicolvars
std::size_t und = labels[i].find_first_of("_");
if( !found && und!=std::string::npos ) {
labels[i] = labels[i].substr(0,und) + "." + labels[i].substr(und+1);
for(unsigned j=0; j<fieldnames.size(); ++j) {
if( labels[i]==fieldnames[j] ) { found=true; break; }
}
}
}
// And read the stuff from the header
plumed_massert( ifile.FieldExist( funcl ), "no column labelled " + funcl + " in in grid input");
for(unsigned i=0; i<args.size(); ++i) {
Expand All @@ -546,7 +560,7 @@ std::unique_ptr<GridBase> GridBase::create(const std::string& funcl, const std::
gbin[i]=gbin1[i]-1; // Note header in grid file indicates one more bin that there should be when data is not periodic
plumed_massert( pstring=="false", "input value is not periodic but grid is");
}
hasder=ifile.FieldExist( "der_" + args[i]->getName() );
hasder=ifile.FieldExist( "der_" + labels[i] );
if( doder && !hasder ) plumed_merror("missing derivatives from grid file");
for(unsigned j=0; j<fieldnames.size(); ++j) {
for(unsigned k=i+1; k<args.size(); ++k) {
Expand All @@ -570,7 +584,7 @@ std::unique_ptr<GridBase> GridBase::create(const std::string& funcl, const std::
ifile.scanField( "nbins_" + labels[i], gbin1[i]);
ifile.scanField( "periodic_" + labels[i], pstring );
}
if(hasder) { for(unsigned i=0; i<nvar; ++i) { ifile.scanField( "der_" + args[i]->getName(), dder[i] ); } }
if(hasder) { for(unsigned i=0; i<nvar; ++i) { ifile.scanField( "der_" + labels[i], dder[i] ); } }
index_t index=grid->getIndex(xx);
if(doder) {grid->setValueAndDerivatives(index,f,dder);}
else {grid->setValue(index,f);}
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