Merge remote-tracking branch 'origin/fix-underscores' into v2.4

regtest/basic/rt-close-structure/plumed.dat

-p2: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 EPSILON=0.001 LOG-CLOSE=1 DEBUG-CLOSE=1
+# LOG_CLOSE and DEBUG_CLOSE are synonym of CLOSE and DEBUG-CLOSE
+p2: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 EPSILON=0.001 LOG_CLOSE=1 DEBUG_CLOSE=1
 p3: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5 EPSILON=0.001 LOG-CLOSE=1 DEBUG-CLOSE=1
 PRINT ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.2f
 DUMPDERIVATIVES ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=deriv FMT=%8.2f

regtest/basic/rt-multirmsd/plumed.dat

-rmsd0:   MULTI-RMSD TYPE=MULTI-OPTIMAL REFERENCE=test0.pdb
+# MULTI_RMSD is a synonym of MULTI-RMSD
+rmsd0:   MULTI_RMSD TYPE=MULTI-OPTIMAL REFERENCE=test0.pdb
 rmsds1:  MULTI-RMSD TYPE=MULTI-SIMPLE  REFERENCE=test1.pdb
 drmsd1:  MULTI-RMSD TYPE=MULTI-DRMSD REFERENCE=test2.pdb 
 

src/colvar/MultiRMSD.cpp

@@ -148,6 +148,28 @@ END
 
 PLUMED_REGISTER_ACTION(MultiRMSD,"MULTI-RMSD")
 
+//+PLUMEDOC DCOLVAR MULTI_RMSD
+/*
+An alias to the \ref MULTI-RMSD function.
+
+\par Examples
+
+Just replace \ref MULTI-RMSD with \ref MULTI_RMSD
+
+\plumedfile
+MULTI_RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
+\endplumedfile
+
+*/
+//+ENDPLUMEDOC
+
+class Multi_RMSD :
+  public MultiRMSD {
+};
+
+PLUMED_REGISTER_ACTION(MultiRMSD,"MULTI_RMSD")
+
+
 void MultiRMSD::registerKeywords(Keywords& keys) {
   Colvar::registerKeywords(keys);
   keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure and the atoms involved in the CV.");

src/colvar/PCARMSD.cpp

@@ -76,6 +76,7 @@ void PCARMSD::registerKeywords(Keywords& keys) {
   keys.addOutputComponent("eig","default","the projections on each eigenvalue are stored on values labeled eig-1, eig-2, ...");
   keys.addOutputComponent("residual","default","the distance of the present configuration from the configuration supplied as AVERAGE in terms of MSD after optimal alignment ");
   keys.addFlag("SQUARED-ROOT",false," This should be setted if you want RMSD instead of MSD ");
+  keys.addFlag("SQUARED_ROOT",false," Same as SQUARED-ROOT");
 }
 
 PCARMSD::PCARMSD(const ActionOptions&ao):
@@ -88,6 +89,7 @@ PCARMSD::PCARMSD(const ActionOptions&ao):
   string f_eigenvectors;
   parse("EIGENVECTORS",f_eigenvectors);
   bool sq;  parseFlag("SQUARED-ROOT",sq);
+  if(!sq) parseFlag("SQUARED_ROOT",sq);
   if (sq) { squared=false; }
   checkRead();
 

src/colvar/PathMSDBase.cpp

@@ -44,6 +44,8 @@ void PathMSDBase::registerKeywords(Keywords& keys) {
   keys.add("optional", "EPSILON", "(default=-1) the maximum distance between the close and the current structure, the positive value turn on the close structure method");
   keys.add("optional", "LOG-CLOSE", "(default=0) value 1 enables logging regarding the close structure");
   keys.add("optional", "DEBUG-CLOSE", "(default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower");
+  keys.add("optional", "LOG_CLOSE", "same as LOG-CLOSE");
+  keys.add("optional", "DEBUG_CLOSE", "same as DEBUG-CLOSE");
 }
 
 PathMSDBase::PathMSDBase(const ActionOptions&ao):
@@ -62,7 +64,9 @@ PathMSDBase::PathMSDBase(const ActionOptions&ao):
   parse("REFERENCE",reference);
   parse("EPSILON", epsilonClose);
   parse("LOG-CLOSE", logClose);
+  if(!logClose) parse("LOG_CLOSE", logClose);
   parse("DEBUG-CLOSE", debugClose);
+  if(!debugClose) parse("DEBUG_CLOSE",debugClose);
 
   // open the file
   FILE* fp=fopen(reference.c_str(),"r");