Merge branch 'compile-warnings' into 'master'

Compile warnings

See merge request !23

gromos++/programs/0index.doxy

@@ -44,6 +44,7 @@
  * - Drazen Petrov @anchor dp (dp)
  * - Anita de Ruiter @anchor adr (adr)
  * - Martina Setz @anchor ms (ms)
+ * - Stefan Bachmann @anchor sb (sb)
  * </p>
  *
  * <h2>Available Programs:</h2>
@@ -60,6 +61,8 @@
  * - @ref com_top combine molecular topology files into one
  * - @ref con_top convert topology to different force field version
  * - @ref copy_box repeats a simulation box in a given direction
+ * - @ref cos_dipole calculate molecular dipoles including COS charges
+ * - @ref cos_epsilon calculate relative permittivity and box dipole moment autocorrelations 
  * - @ref cry perform symmetry operations on molecules
  * - @ref cry_rms perform RMSD and RMSF calculations based on crystallographic symmetry.
  * - @ref dfmult calculates multiple free energy differences

gromos++/programs/Makefile.am

@@ -105,7 +105,9 @@ bin_PROGRAMS = rmsd\
     trs_ana\
     dGslv_pbsolv\
     dfgrid\
-    contactnum
+    contactnum\
+    cos_dipole\
+    cos_epsilon
 
 nhoparam_SOURCES = nhoparam.cc
 frameout_SOURCES = frameout.cc
@@ -207,6 +209,9 @@ trs_ana_SOURCES = trs_ana.cc
 dGslv_pbsolv_SOURCES = dGslv_pbsolv.cc
 dfgrid_SOURCES = dfgrid.cc
 contactnum_SOURCES = contactnum.cc
+cos_dipole_SOURCES = cos_dipole.cc
+cos_epsilon_SOURCES = cos_epsilon.cc
+
 
 LDADD = $(top_builddir)/src/libgromos.la
 

gromos++/programs/atominfo.cc

@@ -155,7 +155,7 @@ int main(int argc, char **argv){
 	 << setw(12) << "Atom Code"
 	 << endl;
 
-    for(int i=0; i < as.size(); ++i){
+    for(unsigned int i=0; i < as.size(); ++i){
       if(as.atom()[i]->type()==utils::spec_virtual){
 	utils::AtomSpecifier conf=as.atom()[i]->conf();
 	cout << "----------------------------------------"
@@ -202,7 +202,7 @@ int main(int argc, char **argv){
 
 	}
 
-	for(int j=0; j< conf.size(); ++j){
+	for(unsigned int j=0; j< conf.size(); ++j){
 	  cout << setw(13) << conf.toString(j)
 	       << setw(10) << conf.gromosAtom(j)+1
 	       << setw(10) << conf.resnum(j)+1

gromos++/programs/bilayer_dist.cc

@@ -197,7 +197,7 @@ int main(int argc, char** argv) {
         min_d = -sys.box().M().abs()/2; // before was: cm[2]-sys.box()[2]/2;
         max_d = sys.box().M().abs()/2;
 
-        for(int i = 0; i < selection.size(); i++) {
+        for(unsigned int i = 0; i < selection.size(); i++) {
           Vec & vector1 = selection.pos(i);
           Vec dist = vector1 - pbc->nearestImage(vector1, cm, sys.box());
           zcoord.push_back(dist[2]);

gromos++/programs/check_box.cc

@@ -149,7 +149,7 @@ int main(int argc, char **argv){
 
     //init variables
     double overall_min_dist2=1e4;
-    int limit = 1;
+    unsigned int limit = 1;
     double cutoff = 1.4;
     double cutoff2 = cutoff*cutoff;
     bool no_cutoff=false; //do not report all distances
@@ -359,12 +359,12 @@ int main(int argc, char **argv){
                     //if 2 neighbours have the same atoms (=there is only 1 cube total in this direction), only half of the distances must be calculated:
                     bool skip=cubes.same_cube(c);
 
-                    for(int i=0; i < cubes.cube_i_atomlist(c).size(); ++i ){
+                    for(unsigned int i=0; i < cubes.cube_i_atomlist(c).size(); ++i ){
 
                         int atom_i = cubes.cube_i_atomlist(c)[i];
                         Vec atom_i_pos = atoms.pos(atom_i);
 
-                        int j=0;
+                        unsigned int j=0;
                         if(skip)
                             j=i+1;
 
@@ -438,7 +438,7 @@ int main(int argc, char **argv){
     cout << "###" << endl;
     cout << "# Time     Distance [nm]     Atom A - Atom B      Mol:Residue Atom A -  Mol:Resiude Atom B" << endl;
     double itime=0;
-    for (int ii =0; ii < output.size(); ii++) {
+    for (unsigned int ii =0; ii < output.size(); ii++) {
       for(vec_it = output[ii].begin(); vec_it != output[ii].end(); ++vec_it){
 
         if (read_time) itime=vec_it->time;

gromos++/programs/close_pair.cc

@@ -148,10 +148,10 @@ int main(int argc, char **argv) {
       debug = atoi(args["debug"].c_str());
     }
     if (debug == 1) {
-      for (int i = 0; i < groupA.size(); ++i) {
+      for (unsigned int i = 0; i < groupA.size(); ++i) {
         cout << "# groupA mol " << groupA.mol(i) << " size " << groupA.size() << endl;
       }
-      for (int j = 0; j < groupB.size(); ++j) {
+      for (unsigned int j = 0; j < groupB.size(); ++j) {
         cout << "# groupB mol " << groupB.mol(j) << " size " << groupB.size() << endl;
       }
     }
@@ -224,7 +224,7 @@ int main(int argc, char **argv) {
 
         int pass = 1000;
 
-        for (int i = 0; i < groupA.size(); ++i) {
+        for (unsigned int i = 0; i < groupA.size(); ++i) {
           // skip hydrogen atoms
           int m = groupA.mol(i);
 
@@ -236,7 +236,7 @@ int main(int argc, char **argv) {
                   "atom name not specified properly.");
           if (m != pass && m > 0)
             if (groupA.mass(i) != 1.008) {
-              for (int j = 0; j < groupB.size(); ++j) {
+              for (unsigned int j = 0; j < groupB.size(); ++j) {
                 if (debug >= 3) {
                   cout << "# groupB size " << groupB.size() << endl;
                   cout << "# molA " << groupA.mol(i)

gromos++/programs/cog.cc

@@ -196,7 +196,7 @@ int main(int argc, char **argv){
       }
     }
 
-    for(int a=0; a<atomspec.size(); a++){
+    for(unsigned int a=0; a<atomspec.size(); a++){
 	  osys.addMolecule(mt_spec);
 	  osys.mol(molnum).initPos();
 	  molnum++;
@@ -266,10 +266,10 @@ int main(int argc, char **argv){
 	  }
 	  }
 
-	  for (int i=0; i < atomspec.size(); i++) {
+	  for (unsigned int i=0; i < atomspec.size(); i++) {
 	    Vec cog(0.0,0.0,0.0);
 	    double molmass=0;
-	    for (int a=0; a < atomspec[i].size(); a++) {
+	    for (unsigned int a=0; a < atomspec[i].size(); a++) {
 	      if(inc=="cog"){
 		cog+=atomspec[i].pos(a);
 	      }

gromos++/programs/contactnum.cc

@@ -91,7 +91,7 @@ double fastpow(double base, int exp);
 int main(int argc, char **argv){
   Argument_List knowns; 
   knowns << "topo" << "traj" << "atoms" << "cutoffs" << "pbc" << "exp"
-         << "time" << "debug" << "printpairs" << "excludemass";
+         << "time" << "printpairs" << "excludemass";
 
   string usage = "# " + string(argv[0]);
   usage += "\n\t@topo         <molecular topology file>\n";
@@ -120,10 +120,6 @@ int main(int argc, char **argv){
     InTopology it(args["topo"]);
     System sys(it.system());
 
-    int debug=0;
-    if(args.count("debug")>0)
-        debug=1;
-
     if (args.count("pbc") <=0) {
       cout << "# WARNING: no @pbc argument found - no gathering will be done!";
     }
@@ -189,15 +185,15 @@ int main(int argc, char **argv){
 
     // exclude atoms with given mass
     for (int i=atomgroup1.size()-1; i>=0 ; i--) {
-      for(int j=0; j<excludemass.size(); j++) {
+      for(unsigned int j=0; j<excludemass.size(); j++) {
         if (atomgroup1.mass(i)== excludemass[j]) {
           //cerr << "atom " << atomgroup1.atom(i) << " mass " << atomgroup1.mass(i)<<endl;
           atomgroup1.removeAtom(i);
         }
       }
     }
     for (int i=atomgroup2.size()-1; i>=0 ; i--) {
-      for(int j=0; j<excludemass.size(); j++) {
+      for(unsigned int j=0; j<excludemass.size(); j++) {
         if (atomgroup2.mass(i)== excludemass[j]){
           //cerr << "atom " << atomgroup2.atom(i) << " mass " << atomgroup2.mass(i) << endl;
           atomgroup2.removeAtom(i);
@@ -213,7 +209,7 @@ int main(int argc, char **argv){
     // Parse boundary conditions for sys
     Boundary *pbc = BoundaryParser::boundary(sys, args);
 
-	for (int cut=0; cut<cutoffs.size(); cut++) {
+	for (unsigned int cut=0; cut<cutoffs.size(); cut++) {
 	   cout <<setw(15) << cutoffs[cut];
 	}
 	cout << endl;
@@ -240,10 +236,10 @@ int main(int argc, char **argv){
 
         cout.precision(2);
         cout << time;
-	    for (int cut=0; cut<cutoffs.size(); cut++) {
+	    for (unsigned int cut=0; cut<cutoffs.size(); cut++) {
 	      double ct=0;
-          for (int i=0; i< atomgroup1.size(); i++) {
-            for (int j=0; j < atomgroup2.size(); j++) {
+          for (unsigned int i=0; i< atomgroup1.size(); i++) {
+            for (unsigned int j=0; j < atomgroup2.size(); j++) {
               double func;
               gmath::Vec v = atomgroup1.pos(i) - pbc->nearestImage(atomgroup1.pos(i), atomgroup2.pos(j), sys.box());
               double rdist=v.abs();
@@ -263,7 +259,7 @@ int main(int argc, char **argv){
       ic.close();
     }  
     cout <<"# averages     ";
-    for (int i=0; i<cutoffs.size(); i++) {
+    for (unsigned int i=0; i<cutoffs.size(); i++) {
       cout << setw(15) << ct_ave[i]/numFrames; 
     }
     cout << endl;