diff --git a/regtest/mapping/rt39/colvar.reference b/regtest/mapping/rt39/colvar.reference
index 9cc657c86ff75b992646c018ffeefb890ab9958d..a3a560c16ec02520514591a00957880f6e038fa6 100644
--- a/regtest/mapping/rt39/colvar.reference
+++ b/regtest/mapping/rt39/colvar.reference
@@ -1,4 +1,4 @@
-#! 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
diff --git a/regtest/mapping/rt39/deriv.reference b/regtest/mapping/rt39/deriv.reference
index 09999da95ca32564763086920e7e9da7cde81aa6..f44fb446f8bc62afac1ee62bd133c8289121d681 100644
--- a/regtest/mapping/rt39/deriv.reference
+++ b/regtest/mapping/rt39/deriv.reference
@@ -1,4 +1,4 @@
-#! 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
diff --git a/regtest/mapping/rt39/plumed.dat b/regtest/mapping/rt39/plumed.dat
index 004bef3835cda13e7012e4a899e933651d47abec..c16953f0a610a51a9f23c9eaafaa1ddd359cc595 100644
--- a/regtest/mapping/rt39/plumed.dat
+++ b/regtest/mapping/rt39/plumed.dat
@@ -1,4 +1,4 @@
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
diff --git a/regtest/mapping/rt40/colvar.reference b/regtest/mapping/rt40/colvar.reference
index ef73462540de059b3b2386f27004b324432705a6..4985a2543600b8171ec8b3457096aba2812c4a0f 100644
--- a/regtest/mapping/rt40/colvar.reference
+++ b/regtest/mapping/rt40/colvar.reference
@@ -1,4 +1,4 @@
-#! 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
diff --git a/regtest/mapping/rt40/deriv.reference b/regtest/mapping/rt40/deriv.reference
index 9e3e75d6c91867f420c9aaef93aad082caadb42e..b8f9d32a22db508a7786f332cebfc8804cd12cb5 100644
--- a/regtest/mapping/rt40/deriv.reference
+++ b/regtest/mapping/rt40/deriv.reference
@@ -1,4 +1,4 @@
-#! 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
diff --git a/regtest/mapping/rt40/plumed.dat b/regtest/mapping/rt40/plumed.dat
index b79c076e45d948e9198973cb4238116259b71829..669e21ee16361afebcb7d029feb0b488b6bf59f4 100644
--- a/regtest/mapping/rt40/plumed.dat
+++ b/regtest/mapping/rt40/plumed.dat
@@ -1,5 +1,5 @@
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
diff --git a/src/mapping/Mapping.cpp b/src/mapping/Mapping.cpp
index c4af16d7efdf26786a53bcc26f2cd5729e2806fc..906d9ffb413b51d71c6dc970adfab5b155c2a28a 100644
--- a/src/mapping/Mapping.cpp
+++ b/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 );
}
diff --git a/src/mapping/Path.cpp b/src/mapping/Path.cpp
index f3b3a77e6fe320885f8558ec3e3c1fd96fc2bb43..51fa4f81f8b638b06dce0f693c13c4119a66028a 100644
--- a/src/mapping/Path.cpp
+++ b/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();
diff --git a/src/mapping/PathBase.cpp b/src/mapping/PathBase.cpp
index c959ddcb5196c820ec0bf05782e0c424852d2c46..b30b2a2713544cde70ccdaa6052ba9d769a31062 100644
--- a/src/mapping/PathBase.cpp
+++ b/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);
}
diff --git a/src/mapping/SpathVessel.cpp b/src/mapping/SpathVessel.cpp
index f15cf13d8a06bbd6919104ecbc86a51fd5b3ccce..23c43cabf81d1adfda7e3f501c5558cc8223ddf6 100644
--- a/src/mapping/SpathVessel.cpp
+++ b/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 ):
diff --git a/src/mapping/ZpathVessel.cpp b/src/mapping/ZpathVessel.cpp
index 42e9fd11314ed473ebd53beb01d8708005d4e53d..9807baed33fe192292da398fa1014d8e84d1a7e2 100644
--- a/src/mapping/ZpathVessel.cpp
+++ b/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 ):
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index ead4d4312f26fc087bd3625ded569281759ddd9c..1476382990bae01b04cc982e2558dc7ebc15ea32 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/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);
}
diff --git a/src/vesselbase/Vessel.cpp b/src/vesselbase/Vessel.cpp
index 8fadfc5b5e2e7d45781c4b03d333ac8cc20f5ac0..8aae48d0a10809e316cdbf33c77e64fee24e3f64 100644
--- a/src/vesselbase/Vessel.cpp
+++ b/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; }
}
diff --git a/src/vesselbase/Vessel.h b/src/vesselbase/Vessel.h
index 29abac6f13dfa5cb745d4795d6f9672c958a6f87..1074f6b93d5bca8ae5a6e762bd7bccd27678e03e 100644
--- a/src/vesselbase/Vessel.h
+++ b/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