Merge branch 'v2.0' of github.com:plumed/plumed2 into 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/CLToolMain.cpp

@@ -181,7 +181,7 @@ 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"
         "  [--has-mpi]               : fails if plumed is running without MPI\n"