Depracated action tracking

regtest/secondarystructure/rt-coverage-antibetarmsd/colvar.reference

@@ -1,4 +1,4 @@
-#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum
+#! FIELDS time b_lessthan brf_lessthan br_lessthan p_lessthan prf_lessthan pr_lessthan sum
  0.000000   0.0607   0.1654   0.1654   0.2681   0.1425   0.1425   0.3287
  0.050000   0.0000  42.5600  42.5600  14.6579   4.1424   4.1424  14.6579
  0.100000   0.0188  34.0262  34.0262  13.0049   3.2851   3.2851  13.0238

regtest/secondarystructure/rt-coverage-antibetarmsd/forces.reference

@@ -1,4 +1,4 @@
-#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum @8.bias @8.force2
+#! FIELDS time b_lessthan brf_lessthan br_lessthan p_lessthan prf_lessthan pr_lessthan sum r.bias r.force2
  0.000000   -0.3893763023   -0.1653910914   -0.1653910914   -0.5967893540   -0.1425260828   -0.1425260828   -0.3287218854    0.0000000000    0.0000000000
  0.050000  -14.6578542139  -42.5600014141  -42.5600014141  -29.3157084279   -4.1424316083   -4.1424316083  -14.6578542139    0.0000000000    0.0000000000
  0.100000  -13.0426114706  -34.0261914601  -34.0261914601  -26.0287209912   -3.2850812434   -3.2850812434  -13.0237774873    0.0000000000    0.0000000000

regtest/secondarystructure/rt-coverage-antibetarmsd/plumed.dat

@@ -7,9 +7,9 @@ PARABETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATION
 PARABETARMSD RESIDUES=all TYPE=OPTIMAL STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=pr
 COMBINE ARG=b.lessthan,p.lessthan PERIODIC=NO LABEL=sum 
 
-RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0
+r: RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0
 
-DUMPFORCES ARG=* FILE=forces STRIDE=1
+DUMPFORCES ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum,r.* FILE=forces STRIDE=1
 
 PRINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f
 

src/cltools/GenJson.cpp

@@ -123,6 +123,16 @@
     // Now output keyword information
     Keywords keys; actionRegister().getKeywords( action_names[i], keys );
     std::cout<<"    \"displayname\" : \""<<keys.getDisplayName()<<"\",\n";
+    // This is used for noting actions that have been deprecated
+    std::string replacement = keys.getReplacementAction();
+    if( replacement!="none" ) {
+      bool found=false;
+      for(unsigned j=0; j<action_names.size(); ++j) {
+        if( action_names[j]==replacement ) { found=true; break; }
+      }
+      if( !found ) error("could not find action named " + replacement + " that is supposed to be used to replace " + action_names[i] );
+    }
+    std::cout<<"    \"replacement\" : \""<<replacement<<"\",\n";
     std::cout<<"    \"syntax\" : {"<<std::endl;
     for(unsigned j=0; j<keys.size(); ++j) {
       std::string defa = "", desc = keys.getKeywordDescription( keys.getKeyword(j) );

src/core/ActionRegister.cpp

@@ -41,7 +41,7 @@ std::unique_ptr<Action> ActionRegister::create(const std::vector<void*> & images
 
   auto content=get(images,ao.line[0]);
   Keywords keys; keys.thisactname = ao.line[0];
-  content.keys(keys);
+  keys.replaceaction = "none"; content.keys(keys);
   ActionOptions nao( ao,keys );
   auto fullPath=getFullPath(images,ao.line[0]);
   nao.setFullPath(fullPath);
@@ -79,7 +79,7 @@ bool ActionRegister::printTemplate(const std::string& action, bool include_optio
   //no need to insert the try/catch block: check will ensure that action is known
   if( check(action) ) {
     Keywords keys; keys.thisactname = action;
-    get(action).keys(keys);
+    keys.replaceaction = "none"; get(action).keys(keys);
     keys.print_template(action, include_optional);
     return true;
   } else {
@@ -101,14 +101,15 @@ bool ActionRegister::getKeywords(const std::string& action, Keywords& keys) {
   //no need to insert the try/catch block: check will ensure that action is known
   if(check(action)) {
     keys.thisactname = action;
+    keys.replaceaction = "none";
     get(action).keys(keys);
     return true;
   }
   return false;
 }
 
 void ActionRegister::getKeywords(const std::vector<void*> & images, const std::string& action, Keywords& keys) {
-  auto content=get(images,action); keys.thisactname = action; content.keys(keys);
+  auto content=get(images,action); keys.thisactname = action; keys.replaceaction = "none"; content.keys(keys);
 }
 
 }

src/multicolvar/DumpMultiColvar.cpp

@@ -47,6 +47,7 @@ PLUMED_REGISTER_ACTION(DumpMultiColvar,"DUMPMULTICOLVAR")
 
 void DumpMultiColvar::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
+  keys.setDeprecated("DUMPATOMS");
   keys.add("compulsory","DATA","the vector you wish to transform");
   keys.add("compulsory","FILE","the file that you would like to output the data to");
   keys.remove("HAS_VALUES"); keys.needsAction("DUMPATOMS");

src/multicolvar/MFilterLess.cpp

@@ -47,6 +47,7 @@ PLUMED_REGISTER_ACTION(MFilterLess,"MFILTER_LESS")
 
 void MFilterLess::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
+  keys.setDeprecated("LESS_THAN");
   keys.add("compulsory","DATA","the vector you wish to transform");
   keys.add("compulsory","SWITCH","the switching function that transform");
   keys.setValueDescription("vector","a vector that has the same dimension as the input vector with elements equal to one if the corresponding component of the vector is less than a tolerance and zero otherwise");

src/multicolvar/MFilterMore.cpp

@@ -47,6 +47,7 @@ PLUMED_REGISTER_ACTION(MFilterMore,"MFILTER_MORE")
 
 void MFilterMore::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
+  keys.setDeprecated("MORE_THAN");
   keys.add("compulsory","DATA","the vector you wish to transform");
   keys.add("compulsory","SWITCH","the switching function that transform");
   keys.addFlag("LOWMEM",false,"this flag does nothing and is present only to ensure back-compatibility");

src/multicolvar/UWalls.cpp

@@ -48,6 +48,7 @@ PLUMED_REGISTER_ACTION(UWalls,"UWALLS")
 
 void UWalls::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
+  keys.setDeprecated("UPPER_WALLS");
   keys.add("compulsory","DATA","the values you want to restrain");
   keys.add("compulsory","AT","the radius of the sphere");
   keys.add("compulsory","KAPPA","the force constant for the wall.  The k_i in the expression for a wall.");

src/tools/Keywords.cpp

@@ -776,4 +776,13 @@ std::string Keywords::getDisplayName() const {
   return thisactname;
 }
 
+void Keywords::setDeprecated( const std::string& name ) {
+  replaceaction = name;
+}
+
+std::string Keywords::getReplacementAction() const {
+  return replaceaction;
+}
+
+
 }

src/tools/Keywords.h

@@ -66,6 +66,8 @@ class Keywords {
   bool isatoms;
 /// The name of the action that has this set of keywords
   std::string thisactname;
+/// The action to use in place of this deprecated action
+  std::string replaceaction;
 /// The names of the allowed keywords
   std::vector<std::string> keys;
 /// The names of the reserved keywords
@@ -217,6 +219,10 @@ class Keywords {
   std::string getDisplayName() const ;
 /// Set the display name
   void setDisplayName( const std::string& name );
+/// Get the action that should be used to replace this one if action has been deprecated
+  std::string getReplacementAction() const ;
+/// Note that this action has been deprecated
+  void setDeprecated( const std::string& name );
 };
 
 }