Added checks for manual construction

This is for vessels.  Basically you now can't create a FunctionVessel
without adding a description to the manual of the quantity it
calculates

regtest/mapping/rt39/colvar.reference

-#! FIELDS time p2.sss p2.zzz p3.sss p3.zzz
+#! FIELDS time p2.spath p2.zpath p3.sss p3.zzz
  0.000000   1.9434   0.0001   1.9434   0.0001
  0.250000   1.0090   0.0001   1.0090   0.0001
  0.500000   1.0579   0.0001   1.0579   0.0001

regtest/mapping/rt39/deriv.reference

-#! FIELDS time parameter p2.sss p2.zzz p3.sss p3.zzz
+#! FIELDS time parameter p2.spath p2.zpath p3.sss p3.zzz
  0.000000 0   2.9260   0.0007   2.9260   0.0007
  0.000000 1  -3.2521  -0.0011  -3.2521  -0.0011
  0.000000 2   4.2465  -0.0003   4.2465  -0.0003

regtest/mapping/rt39/plumed.dat

 p2: PATH REFERENCE=all.pdb LAMBDA=69087    
 p3: PATHMSD REFERENCE=all.pdb LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5
-PRINT ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-DUMPDERIVATIVES ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=deriv FMT=%8.4f
+PRINT ARG=p2.spath,p2.zpath,p3.sss,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=p2.spath,p2.zpath,p3.sss,p3.zzz STRIDE=1 FILE=deriv FMT=%8.4f

regtest/mapping/rt40/colvar.reference

-#! FIELDS time p2.X p2.Y p2.zzz p3.X p3.Y p3.zzz
+#! FIELDS time p2.X p2.Y p2.zpath p3.X p3.Y p3.zzz
  0.000000   1.9434   2.9434   0.0001   1.9434   2.9434   0.0001
  0.250000   1.0090   2.0090   0.0001   1.0090   2.0090   0.0001
  0.500000   1.0579   2.0579   0.0001   1.0579   2.0579   0.0001

regtest/mapping/rt40/deriv.reference

-#! FIELDS time parameter p2.X p2.Y p2.zzz p3.X p3.Y p3.zzz
+#! FIELDS time parameter p2.X p2.Y p2.zpath p3.X p3.Y p3.zzz
  0.000000 0   2.9260   2.9260   0.0007   2.9260   2.9260   0.0007
  0.000000 1  -3.2521  -3.2521  -0.0011  -3.2521  -3.2521  -0.0011
  0.000000 2   4.2465   4.2465  -0.0003   4.2465   4.2465  -0.0003

regtest/mapping/rt40/plumed.dat

 p2: GPROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087    
 p3: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5
-PRINT ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-DUMPDERIVATIVES ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=deriv FMT=%8.4f
+PRINT ARG=p2.X,p2.Y,p2.zpath,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=p2.X,p2.Y,p2.zpath,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=deriv FMT=%8.4f
 

src/mapping/Mapping.cpp

@@ -65,7 +65,7 @@ ActionWithVessel(ao)
      mymap->setPropertyNames( property, false );
   } else {
      std::vector<std::string> property(1); 
-     property[0]="sss";
+     property[0]="spath";
      mymap->setPropertyNames( property, true );
   }
 

src/mapping/Path.cpp

@@ -76,10 +76,10 @@ PathBase(ao)
 
   std::string empty;
   if(!nos){
-     if( getPropertyIndex("sss")!=0 || getNumberOfProperties()>1 ){
+     if( getPropertyIndex("spath")!=0 || getNumberOfProperties()>1 ){
         error("paths only work when there is a single property called sss being calculated"); 
      }
-     empty="LABEL=sss"; 
+     empty="LABEL=spath"; 
      addVessel("SPATH",empty,0);    
   }
   readVesselKeywords();

src/mapping/PathBase.cpp

@@ -41,7 +41,7 @@ Mapping(ao)
   // Create the list of tasks
   for(unsigned i=0;i<getNumberOfReferencePoints();++i) addTaskToList( i );
 
-  std::string empty="LABEL=zzz";
+  std::string empty="LABEL=zpath";
   if(!noz) addVessel("ZPATH",empty,0);
 }
 

src/mapping/SpathVessel.cpp

@@ -49,7 +49,7 @@ void SpathVessel::registerKeywords( Keywords& keys ){
 
 void SpathVessel::reserveKeyword( Keywords& keys ){
   keys.reserveFlag("SPATH",false,"docs should not appear",true);
-  keys.addOutputComponent("sss","SPATH","the position on the path");
+  keys.addOutputComponent("spath","SPATH","the position on the path");
 }
 
 SpathVessel::SpathVessel( const vesselbase::VesselOptions& da ):

src/mapping/ZpathVessel.cpp

@@ -46,7 +46,7 @@ void ZpathVessel::registerKeywords( Keywords& keys ){
 
 void ZpathVessel::reserveKeyword( Keywords& keys ){
   keys.reserveFlag("ZPATH",false,"calculate the distance from the low dimensionality manifold",true);
-  keys.addOutputComponent("zzz","ZPATH","the distance from the path");
+  keys.addOutputComponent("zpath","ZPATH","the distance from the path");
 }
 
 ZpathVessel::ZpathVessel( const vesselbase::VesselOptions& da ):

src/vesselbase/ActionWithVessel.cpp

@@ -26,6 +26,7 @@
 #include "StoreDataVessel.h"
 #include "VesselRegister.h"
 #include "BridgeVessel.h"
+#include "FunctionVessel.h"
 
 using namespace std;
 namespace PLMD{
@@ -80,7 +81,12 @@ ActionWithVessel::~ActionWithVessel(){
 
 void ActionWithVessel::addVessel( const std::string& name, const std::string& input, const int numlab ){
   VesselOptions da(name,"",numlab,input,this);
-  Vessel* vv=vesselRegister().create(name,da); 
+  Vessel* vv=vesselRegister().create(name,da);
+  FunctionVessel* fv=dynamic_cast<FunctionVessel*>(vv);
+  if( fv ){
+      std::string mylabel=Vessel::transformName( name );
+      plumed_massert( keywords.outputComponentExists(mylabel,false), "a description of the value calculated by vessel " + name + " has not been added to the manual"); 
+  } 
   addVessel(vv);
 }
 

src/vesselbase/Vessel.cpp

@@ -55,6 +55,19 @@ void Vessel::registerKeywords( Keywords& keys ){
   keys.add("optional","LABEL","the label used to reference this particular quantity");
 }
 
+std::string Vessel::transformName( const std::string& name ){
+   std::string tlabel=name; 
+   // Convert to lower case
+   std::transform( tlabel.begin(), tlabel.end(), tlabel.begin(), tolower );
+   // Remove any underscore characters (as these are reserved)
+   for(unsigned i=0;;++i){
+      std::size_t num=tlabel.find_first_of("_");
+      if( num==std::string::npos ) break;
+      tlabel.erase( tlabel.begin() + num, tlabel.begin() + num + 1 );
+   }
+   return tlabel;
+}
+
 Vessel::Vessel( const VesselOptions& da ):
 myname(da.myname),
 numlab(da.numlab),
@@ -70,15 +83,7 @@ log((da.action)->log)
   } else {
       if( keywords.exists("LABEL") ) parse("LABEL",mylabel);
       if( mylabel.length()==0 && numlab>=0 ){
-          mylabel=myname; std::string nn; 
-          // Convert to lower case
-          std::transform( mylabel.begin(), mylabel.end(), mylabel.begin(), tolower );
-          // Remove any underscore characters (as these are reserved)
-          for(unsigned i=0;;++i){
-             std::size_t num=mylabel.find_first_of("_");
-             if( num==std::string::npos ) break;
-             mylabel.erase( mylabel.begin() + num, mylabel.begin() + num + 1 ); 
-          }
+          mylabel=transformName( myname ); std::string nn; 
           if(numlab>0){ Tools::convert( numlab, nn ); mylabel =  mylabel + "-" + nn; }
           else { mylabel = mylabel; }
       } 

src/vesselbase/Vessel.h

@@ -129,6 +129,8 @@ public:
   Log& log;
 /// Reserve any keywords for this particular vessel  
   static void registerKeywords( Keywords& keys );
+/// Convert the name to the label of the component
+  static std::string transformName( const std::string& name );
 /// The constructor
   Vessel( const VesselOptions& da );
 /// Virtual destructor needed for proper inheritance