Fixed bug with shortcuts and citation manager (plumed#1201)

When creating actions from shortcuts you need to use readInputWords rather than
readInputLine as readInputLine prints and clears the bibliography after creating
the action.  In contrast readInputWords keeps the bibliography and only prints it
at the end of the log one the whole plumed input is read

Co-authored-by: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local>

Author: gtribello

src/core/ActionShortcut.cpp

@@ -92,19 +92,18 @@ void ActionShortcut::readInputLine( const std::string& input, bool saveline ) {
     founds=true;
   }
   if( found ) {
-    std::string f_input = input;
     if( !founds && saveline ) {
       addToSavedInputLines( input );
     }
     if( keywords.exists("RESTART") ) {
       if( restart ) {
-        f_input += " RESTART=YES";
+        words.push_back("RESTART=YES");
       }
       if( !restart ) {
-        f_input += " RESTART=NO";
+        words.push_back("RESTART=NO");
       }
     }
-    plumed.readInputLine( f_input );
+    plumed.readInputWords( words, false);
     if( !founds ) {
       ActionWithValue* av=NULL;
       for(auto pp=plumed.getActionSet().rbegin(); pp!=plumed.getActionSet().rend(); ++pp) {

src/core/PlumedMain.cpp

@@ -1067,6 +1067,9 @@ void PlumedMain::readInputLine(const std::string & str, const bool& before_init)
     return;
   }
   std::vector<std::string> words=Tools::getWords(str);
+  if( before_init ) {
+    plumed_assert( citations.empty() );
+  }
   citations.clear();
   readInputWords(words,before_init);
   if(!citations.empty()) {
@@ -1729,7 +1732,7 @@ bool PlumedMain::DeprecatedAtoms::usingNaturalUnits() const {
 }
 
 void PlumedMain::DeprecatedAtoms::setCollectEnergy(bool b) const {
-  plumed.readInputLine( plumed.MDEngine + "_energy: ENERGY" );
+  plumed.readInputWords( Tools::getWords(plumed.MDEngine + "_energy: ENERGY"), false );
   plumed.setEnergyValue( plumed.MDEngine + "_energy" );
 }
 

src/gridtools/KDE.cpp

@@ -157,20 +157,20 @@ KDE::KDE(const ActionOptions&ao):
             band += "," + bwidths[i];
           }
         }
-        plumed.readInputLine( getLabel() + "_sigma: CONSTANT " + band );
-        plumed.readInputLine( getLabel() + "_cov: CUSTOM ARG=" + getLabel() + "_sigma FUNC=x*x PERIODIC=NO" );
-        plumed.readInputLine( getLabel() + "_icov: CUSTOM ARG=" + getLabel() + "_cov FUNC=1/x PERIODIC=NO" );
+        plumed.readInputWords( Tools::getWords(getLabel() + "_sigma: CONSTANT " + band), false );
+        plumed.readInputWords( Tools::getWords(getLabel() + "_cov: CUSTOM ARG=" + getLabel() + "_sigma FUNC=x*x PERIODIC=NO"), false );
+        plumed.readInputWords( Tools::getWords(getLabel() + "_icov: CUSTOM ARG=" + getLabel() + "_cov FUNC=1/x PERIODIC=NO"), false );
         bandwidth = getLabel() + "_icov";
 
         if( (kerneltype=="gaussian" || kerneltype=="GAUSSIAN") && weights_are_volumes ) {
           std::string pstr;
           Tools::convert( sqrt(pow(2*pi,bwidths.size())), pstr );
-          plumed.readInputLine( getLabel() + "_bwprod: PRODUCT ARG=" + getLabel() + "_cov");
-          plumed.readInputLine( getLabel() + "_vol: CUSTOM ARG=" + getLabel() + "_bwprod FUNC=(sqrt(x)*" + pstr + ") PERIODIC=NO");
+          plumed.readInputWords( Tools::getWords(getLabel() + "_bwprod: PRODUCT ARG=" + getLabel() + "_cov"), false );
+          plumed.readInputWords( Tools::getWords(getLabel() + "_vol: CUSTOM ARG=" + getLabel() + "_bwprod FUNC=(sqrt(x)*" + pstr + ") PERIODIC=NO"), false );
           if( hasheight ) {
-            plumed.readInputLine( getLabel() + "_height: CUSTOM ARG=" + weight_str[0] + "," + getLabel() + "_vol FUNC=x/y PERIODIC=NO");
+            plumed.readInputWords( Tools::getWords(getLabel() + "_height: CUSTOM ARG=" + weight_str[0] + "," + getLabel() + "_vol FUNC=x/y PERIODIC=NO"), false);
           } else {
-            plumed.readInputLine( getLabel() + "_height: CUSTOM ARG=" + getLabel() + "_vol FUNC=1/x PERIODIC=NO");
+            plumed.readInputWords( Tools::getWords(getLabel() + "_height: CUSTOM ARG=" + getLabel() + "_vol FUNC=1/x PERIODIC=NO"), false);
           }
           hasheight=true;
           weight_str.resize(1);

src/valtools/SelectWithMask.cpp

@@ -110,15 +110,15 @@ SelectWithMask::SelectWithMask(const ActionOptions& ao):
       for(unsigned i=1; i<getPntrToArgument(0)->getShape()[1]; ++i) {
         con += ",0";
       }
-      plumed.readInputLine( getLabel() + "_colmask: CONSTANT VALUES=" + con );
+      plumed.readInputWords( Tools::getWords(getLabel() + "_colmask: CONSTANT VALUES=" + con), false );
       std::vector<std::string> labs(1, getLabel() + "_colmask");
       ActionWithArguments::interpretArgumentList( labs, plumed.getActionSet(), this, cmask );
     } else if( rmask.size()==0 ) {
       std::string con="0";
       for(unsigned i=1; i<getPntrToArgument(0)->getShape()[0]; ++i) {
         con += ",0";
       }
-      plumed.readInputLine( getLabel() + "_rowmask: CONSTANT VALUES=" + con );
+      plumed.readInputWords( Tools::getWords(getLabel() + "_rowmask: CONSTANT VALUES=" + con), false );
       std::vector<std::string> labs(1, getLabel() + "_rowmask");
       ActionWithArguments::interpretArgumentList( labs, plumed.getActionSet(), this, rmask );
     }