Merge branch 'v2.8' into v2.9

src/cltools/pesmd.cpp

@@ -109,7 +109,7 @@ class PesMD  : public PLMD::CLTool {
     keys.add("compulsory","plumed","plumed.dat","the name of the plumed input file containing the potential");
     keys.add("compulsory","ipos","0.0","the initial position of the system");
     keys.add("compulsory","idum","0","The random number seed");
-    keys.addFlag("periodic","false","are your input coordinates periodic");
+    keys.addFlag("periodic",false,"are your input coordinates periodic");
     keys.add("optional","min","minimum value the coordinates can take for a periodic domain");
     keys.add("optional","max","maximum value the coordinates can take for a periodic domain");
   }

src/colvar/Template.cpp

@@ -61,7 +61,6 @@ PLUMED_REGISTER_ACTION(Template,"TEMPLATE")
 void Template::registerKeywords(Keywords& keys) {
   Colvar::registerKeywords(keys);
   keys.addFlag("TEMPLATE_DEFAULT_OFF_FLAG",false,"flags that are by default not performed should be specified like this");
-  keys.addFlag("TEMPLATE_DEFAULT_ON_FLAG",true,"flags that are by default performed should be specified like this");
   keys.add("compulsory","TEMPLATE_COMPULSORY","all compulsory keywords should be added like this with a description here");
   keys.add("optional","TEMPLATE_OPTIONAL","all optional keywords that have input should be added like a description here");
   keys.add("atoms","ATOMS","the keyword with which you specify what atoms to use should be added like this");

src/core/ActionWithValue.cpp

@@ -37,7 +37,7 @@ void ActionWithValue::registerKeywords(Keywords& keys) {
 
 void ActionWithValue::noAnalyticalDerivatives(Keywords& keys) {
   keys.remove("NUMERICAL_DERIVATIVES");
-  keys.addFlag("NUMERICAL_DERIVATIVES",true,"analytical derivatives are not implemented for this keyword so numerical derivatives are always used");
+  keys.addFlag("NUMERICAL_DERIVATIVES",false,"analytical derivatives are not implemented for this keyword so numerical derivatives are always used");
 }
 
 void ActionWithValue::componentsAreNotOptional(Keywords& keys) {

src/eds/EDS.cpp

@@ -301,8 +301,7 @@ void EDS::registerKeywords(Keywords &keys)
   keys.add("optional", "VIRIAL", "Add an update penalty for having non-zero virial contributions. Only makes sense with multiple correlated CVs.");
   keys.add("optional", "LOGWEIGHTS", "Add weights to use for computing statistics. For example, if biasing with metadynamics.");
   keys.addFlag("LM", false, "Use Levenberg-Marquadt algorithm along with simultaneous keyword. Otherwise use gradient descent.");
-  keys.addFlag("LM_MIXING", "1", "Initial mixing parameter when using Levenberg-Marquadt minimization.");
-
+  keys.add("compulsory", "LM_MIXING", "1", "Initial mixing parameter when using Levenberg-Marquadt minimization.");
   keys.add("optional", "RESTART_FMT", "the format that should be used to output real numbers in EDS restarts");
   keys.add("optional", "OUT_RESTART", "Output file for all information needed to continue EDS simulation. "
            "If you have the RESTART directive set (global or for EDS), this file will be appended to. "

src/function/FuncSumHills.cpp

@@ -215,7 +215,7 @@ void FuncSumHills::registerKeywords(Keywords& keys) {
   keys.add("optional","OUTHISTO"," output file for histogram ");
   keys.add("optional","INITSTRIDE"," stride if you want an initial dump ");
   keys.add("optional","STRIDE"," stride when you do it on the fly ");
-  keys.addFlag("ISCLTOOL",true,"use via plumed command line: calculate at read phase and then go");
+  keys.addFlag("ISCLTOOL",false,"use via plumed command line: calculate at read phase and then go");
   keys.addFlag("PARALLELREAD",false,"read parallel HILLS file");
   keys.addFlag("NEGBIAS",false,"dump  negative bias ( -bias )   instead of the free energy: needed in well tempered with flexible hills ");
   keys.addFlag("NOHISTORY",false,"to be used with INITSTRIDE:  it splits the bias/histogram in pieces without previous history  ");

src/maze/Optimizer.cpp

@@ -52,7 +52,7 @@ void Optimizer::registerKeywords(Keywords& keys) {
 
   keys.addFlag(
     "NLIST",
-    true,
+    false,
     "Use a neighbor list of ligand-protein atom pairs to speed up the "
     "calculating of the distances."
   );

src/tools/Keywords.cpp

@@ -207,8 +207,8 @@ void Keywords::add( const std::string & t, const std::string & k, const std::str
 
 void Keywords::addFlag( const std::string & k, const bool def, const std::string & d ) {
   plumed_massert( !exists(k) && !reserved(k), "keyword " + k + " has already been registered");
-  std::string defstr;
-  if( def ) { defstr="( default=on ) "; } else { defstr="( default=off ) "; }
+  std::string defstr; plumed_massert( !def, "the second argument to addFlag must be false " + k );
+  defstr="( default=off ) ";
   types.insert( std::pair<std::string,KeyType>(k,KeyType("flag")) );
   documentation.insert( std::pair<std::string,std::string>(k,defstr + d) );
   allowmultiple.insert( std::pair<std::string,bool>(k,false) );