bug fixes in ran_solvation and ene_ana

biomos · Dec 9, 2013 · fb98a70 · fb98a70
1 parent 9fbd272
commit fb98a70
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/gromos++/programs/ene_ana.cc b/gromos++/programs/ene_ana.cc
@@ -118,6 +118,8 @@ int main(int argc, char **argv){
       if(iter!=args.upper_bound("time")){
         dt=atof(iter->second.c_str());
 	usertime=true;
+        // a bit ugly: as the time is increased by dt before the first printout: reduce t0
+	t0 -= dt;
       }
     }
 
@@ -281,7 +283,7 @@ void print(gmath::Stat<double> &p, string s, vector<double>& time)
        << setw(15) << s
        << endl;
   for(int i=0; i< p.n(); i++){
-    fout << setw(15) << time[i]
+    fout << setw(15) << time[i] << " "
 	 << setw(15) << p.val(i)
 	 << endl;
   }

diff --git a/gromos++/programs/ran_solvation.cc b/gromos++/programs/ran_solvation.cc
@@ -239,6 +239,7 @@ int main(int argc, char **argv) {
     // pbc:
     InTopology it(args["topo_u"]);
     System solu(it.system());
+    Box box;
     Boundary *pbc = BoundaryParser::boundary(solu, args);
     int truncoct = 0, rectbox = 0, cubic = 0;
     double size_corr = 1.0;
@@ -255,7 +256,8 @@ int main(int argc, char **argv) {
         if (minwall.size() == 0)
           if (boxsize[0] != boxsize[1] || boxsize[0] != boxsize[2])
             throw (gromos::Exception("ran_solvation",
-                  "For truncated octahedral boxes, the specified boxsize should be the same in all dimensions"));
+                 "For truncated octahedral boxes, the specified boxsize should be the same in all dimensions"));
+        box.setNtb(gcore::Box::truncoct);
         break;
       case('r'):
         truncoct = 0;
@@ -265,14 +267,15 @@ int main(int argc, char **argv) {
         else if (minwall.size() == 0 &&
                 (boxsize[0] == boxsize[1] && boxsize[0] == boxsize[2]))
           cubic = 1;
+        box.setNtb(gcore::Box::rectangular);
         break;
       case('v'):
         throw (gromos::Exception("ran_solvation",
                 "Why are you running this program if @pbc is vacuum?"));
         break;
       default:
         stringstream msg;
-        msg << "Periodic boundary condition " << 'v' << " is not supported.";
+        msg << "Periodic boundary condition " << pbc->type() << " is not supported.";
         throw gromos::Exception("ran_solvation", msg.str());
         break;
     }
@@ -297,6 +300,8 @@ int main(int argc, char **argv) {
     ic >> solu;
     ic.close();
 
+    solu.box() = box;
+
     // shift molecule to cog
     double radius_pro = calc_mol_radius(solu);
     Vec shiftcog = fit::PositionUtils::shiftToCog(&solu);
@@ -320,6 +325,7 @@ int main(int argc, char **argv) {
     solu.box().K()[0] = boxsize[0];
     solu.box().L()[1] = boxsize[1];
     solu.box().M()[2] = boxsize[2];
+
     Vec box_mid(solu.box().K()[0] / 2.0, solu.box().L()[1] / 2.0, solu.box().M()[2] / 2.0);
     fit::PositionUtils::translate(&solu, box_mid);
     double vol_cell = fac_vol * boxsize[0] * boxsize[1] * boxsize[2];