Merge branch 'v2.0'

src/colvar/CS2Backbone.cpp

@@ -141,7 +141,7 @@ case 2:
 
 \verbatim
 WHOLEMOLECULES ENTITY0=1-174
-cs: CS2BACKBONE ATOMS=1-174 DATA=data/ FF=a03_gromacs.mdb FLAT=1.0 NRES=13 TERMINI=DEFAULT,NONE CYS-DISU PRINT=1000
+cs: CS2BACKBONE ATOMS=1-174 DATA=data/ FF=a03_gromacs.mdb FLAT=1.0 NRES=13 TERMINI=DEFAULT,NONE CYS-DISU WRITE_CS=1000
 PRINT ARG=cs
 \endverbatim
 
@@ -179,7 +179,7 @@ void CS2Backbone::registerKeywords( Keywords& keys ){
   keys.add("compulsory","FF","a03_gromacs.mdb","The ALMOST force-field to map the atoms' names.");
   keys.add("compulsory","FLAT","1.0","Flat region in the scoring function.");
   keys.add("compulsory","NEIGH_FREQ","10","Period in step for neighbour list update.");
-  keys.add("compulsory","WRITE_CS","0","Write chemical shifts period.");
+  keys.add("compulsory","WRITE_CS","0","Write the back-calculated chemical shifts every # steps.");
   keys.add("compulsory","NRES","Number of residues, corresponding to the number of chemical shifts.");
   keys.add("optional","TERMINI","Defines the protonation states of the chain-termini.");
   keys.addFlag("CYS-DISU",false,"Set to TRUE if your system has disulphide bridges.");  
@@ -385,6 +385,8 @@ void CS2Backbone::calculate()
   if(printout) {
     string csfile;
     char tmps1[21], tmps2[21];
+    // add to the name the label of the cv in such a way to have different files
+    // when there is more than one defined variable
     sprintf(tmps1, "%li", getStep());
     if(ensemble) {
       sprintf(tmps2, "%i", multi_sim_comm.Get_rank());

src/core/CLTool.cpp

@@ -38,7 +38,7 @@ keys(k)
 }
 
 void CLTool::registerKeywords( Keywords& keys ){
-  keys.addFlag("--help",false,"print this help");
+  keys.addFlag("--help/-h",false,"print this help");
 }
 
 CLTool::CLTool(const CLToolOptions& co ): 
@@ -106,6 +106,9 @@ bool CLTool::readCommandLineArgs( int argc, char**argv, FILE*out ){
          }
          if(!found){
             fprintf(stderr,"ERROR in input for command line tool %s : %s option is unknown \n\n", name.c_str(), a.c_str() );
+            fprintf(out,"Usage: %s < inputFile \n", name.c_str() );
+            fprintf(out,"inputFile should contain one directive per line.  The directives should come from amongst the following\n\n");
+            keywords.print( out ); 
             printhelp=true;
          }
       }
@@ -160,7 +163,10 @@ bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ){
   if(argc==2){
     mystdin=fopen(argv[1],"r");
     if(!mystdin){
-      fprintf(stderr,"ERROR: cannot open file %s\n",argv[1]);
+      fprintf(stderr,"ERROR: cannot open file %s\n\n",argv[1]);
+      fprintf(out,"Usage: %s < inputFile \n", name.c_str() );
+      fprintf(out,"inputFile should contain one directive per line.  The directives should come from amongst the following\n\n");
+      keywords.print( out );
       return false;
     }
   }
@@ -183,7 +189,10 @@ bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ){
          }
      }
      if(!found){
-        fprintf(stderr,"ERROR in input for command line tool %s : unknown keyword %s found in input file\n",name.c_str(),keyword.c_str());
+        fprintf(stderr,"ERROR in input for command line tool %s : unknown keyword %s found in input file\n\n",name.c_str(),keyword.c_str());
+        fprintf(out,"Usage: %s < inputFile \n", name.c_str() );
+        fprintf(out,"inputFile should contain one directive per line.  The directives should come from amongst the following\n\n");
+        keywords.print( out );
         if(mystdin) fclose(mystdin);
         return false;
      }

src/core/CLToolMain.cpp

@@ -183,7 +183,7 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc){
  if(printhelp){
     string msg=
         "Usage: plumed [options] [command] [command options]\n"
-        "  plumed [command] -h       : to print help for a specific command\n"
+        "  plumed [command] -h|--help: to print help for a specific command\n"
         "Options:\n"
         "  [help|-h|--help]          : to print this help\n"
         "  [--is-installed]          : fails if plumed is not installed\n"