forgot this

src/generic/Debug.cpp

@@ -49,6 +49,7 @@ DEBUG logRequestedAtoms STRIDE=2
 class Debug:
   public ActionPilot
 {
+  OFile ofile;
   bool logActivity;
   bool logRequestedAtoms;
   bool novirial;
@@ -71,6 +72,7 @@ void Debug::registerKeywords( Keywords& keys ){
   keys.addFlag("logRequestedAtoms",false,"write in the log which atoms have been requested at a given time");
   keys.addFlag("NOVIRIAL",false,"switch off the virial contribution for the entirity of the simulation");
   keys.addFlag("DETAILED_TIMERS",false,"switch on detailed timers");
+  keys.add("optional","FILE","the name of the file on which to output these quantities");
 }
 
 Debug::Debug(const ActionOptions&ao):
@@ -89,6 +91,16 @@ novirial(false){
   parseFlag("DETAILED_TIMERS",detailedTimers);
   if(detailedTimers) log.printf("  Detailed timing on\n");
   plumed.detailedTimers=true;
+  ofile.link(*this);
+  std::string file;
+  parse("FILE",file);
+  if(file.length()>0){
+    ofile.open(file);
+    log.printf("  on file %s\n",file.c_str());
+  } else {
+    log.printf("  on plumed log file\n");
+    ofile.link(log);
+  }
   checkRead();
 }
 
@@ -101,23 +113,23 @@ void Debug::apply(){
       if((*p)->isActive()) a++;
     };
     if(a>0){
-      log.printf("activity at step %i: ",getStep());
+      ofile.printf("activity at step %i: ",getStep());
       for(ActionSet::const_iterator p=actionSet.begin();p!=actionSet.end();++p){
         if(dynamic_cast<Debug*>(*p))continue;
-        if((*p)->isActive()) log.printf("+");
-        else                 log.printf("-");
+        if((*p)->isActive()) ofile.printf("+");
+        else                 ofile.printf("-");
       };
-      log.printf("\n");
+      ofile.printf("\n");
     };
   };
   if(logRequestedAtoms){
-    log.printf("requested atoms at step %i: ",getStep());
+    ofile.printf("requested atoms at step %i: ",getStep());
     int* l;
     int n;
     plumed.cmd("createFullList",&n);
     plumed.cmd("getFullList",&l);
-    for(int i=0;i<n;i++) log.printf(" %d",l[i]);
-    log.printf("\n");
+    for(int i=0;i<n;i++) ofile.printf(" %d",l[i]);
+    ofile.printf("\n");
     plumed.cmd("clearFullList");
   }