Changes in molecuilder/src/builder.cpp [48cd93:66ce7a]

File:

• molecuilder/src/builder.cpp (modified) (14 diffs)

molecuilder/src/builder.cpp

@@ -188 +188 @@
           // remove the projection onto the rotation plane of the second angle
           n.CopyVector(&y);
-          n.Scale(first->x.Projection(&y));
+          n.Scale(first->x.ScalarProduct(&y));
           cout << "N1: ",
           n.Output((ofstream *)&cout);
@@ -197 +197 @@
           cout << endl;
           n.CopyVector(&z);
-          n.Scale(first->x.Projection(&z));
+          n.Scale(first->x.ScalarProduct(&z));
           cout << "N2: ",
           n.Output((ofstream *)&cout);
@@ -584 +584 @@
         LinkedCell LCList(mol, 10.);
         class Tesselation *TesselStruct = NULL;
-        FindConvexBorder((ofstream *)&cout, mol, &LCList, NULL);
+        Find_convex_border((ofstream *)&cout, mol, &LCList, NULL);
         double clustervolume = VolumeOfConvexEnvelope((ofstream *)&cout, TesselStruct, configuration);
         cout << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;
@@ -644 +644 @@
   Vector x,y,z,n; // coordinates for absolute point in cell volume
   double *factor; // unit factor if desired
-  double bond, minBond;
+  double bond, min_bond;
   char choice;  // menu choice char
   bool valid;
@@ -683 +683 @@
         first = mol->AskAtom("Enter first (fixed) atom: ");
         second = mol->AskAtom("Enter second (shifting) atom: ");
-        minBond = 0.;
+        min_bond = 0.;
         for (int i=NDIM;i--;)
-          minBond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
-        minBond = sqrt(minBond);
-        cout << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << minBond << " a.u." << endl;
+          min_bond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
+        min_bond = sqrt(min_bond);
+        cout << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << min_bond << " a.u." << endl;
         cout << Verbose(0) << "Enter new bond length [a.u.]: ";
         cin >> bond;
         for (int i=NDIM;i--;) {
-          second->x.x[i] -= (second->x.x[i]-first->x.x[i])/minBond*(minBond-bond);
+          second->x.x[i] -= (second->x.x[i]-first->x.x[i])/min_bond*(min_bond-bond);
         }
         //cout << Verbose(0) << "New coordinates of Atom " << second->nr << " are: ";
@@ -1325 +1325 @@
   int j;
   double volume = 0.;
-  enum ConfigStatus configPresent = absent;
+  enum ConfigStatus config_present = absent;
   clock_t start,end;
   int argptr;
@@ -1425 +1425 @@
         if (output == NULL) {
           cout << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl;
-          configPresent = absent;
+          config_present = absent;
         } else {
           cout << "Empty configuration file." << endl;
           ConfigFileName = argv[1];
-          configPresent = empty;
+          config_present = empty;
           output.close();
         }
@@ -1440 +1440 @@
             cout << "new syntax." << endl;
             configuration.Load(ConfigFileName, periode, mol);
-            configPresent = present;
+            config_present = present;
             break;
           case 0:
             cout << "old syntax." << endl;
             configuration.LoadOld(ConfigFileName, periode, mol);
-            configPresent = present;
+            config_present = present;
             break;
           default:
             cout << "Unknown syntax or empty, yet present file." << endl;
-            configPresent = empty;
+            config_present = empty;
        }
       }
     } else
-      configPresent = absent;
+      config_present = absent;
     // 4. parse again through options, now for those depending on elements db and config presence
     argptr = 1;
@@ -1460 +1460 @@
       if (argv[argptr][0] == '-') {
         argptr++;
-        if ((configPresent == present) || (configPresent == empty)) {
+        if ((config_present == present) || (config_present == empty)) {
           switch(argv[argptr-1][1]) {
             case 'p':
@@ -1474 +1474 @@
                 else {
                   cout << Verbose(2) << "File found and parsed." << endl;
-                  configPresent = present;
+                  config_present = present;
                 }
               }
@@ -1494 +1494 @@
                 if (first->type != NULL) {
                   mol->AddAtom(first);  // add to molecule
-                  if ((configPresent == empty) && (mol->AtomCount != 0))
-                    configPresent = present;
+                  if ((config_present == empty) && (mol->AtomCount != 0))
+                    config_present = present;
                 } else
                   cerr << Verbose(1) << "Could not find the specified element." << endl;
@@ -1505 +1505 @@
           }
         }
-        if (configPresent == present) {
+        if (config_present == present) {
           switch(argv[argptr-1][1]) {
             case 'M':
@@ -1627 +1627 @@
                 start = clock();
                 LinkedCell LCList(mol, atof(argv[argptr])*2.);
-                FindNonConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr+1], atof(argv[argptr]));
+                Find_non_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr+1], atof(argv[argptr]));
                 //FindDistributionOfEllipsoids((ofstream *)&cout, &T, &LCList, N, number, filename.c_str());
                 end = clock();
@@ -1871 +1871 @@
                 cout << Verbose(1) << "Storing tecplot data in " << argv[argptr] << "." << endl;
                 LinkedCell LCList(mol, 10.);
-                //FindConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr]);
-                FindNonConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr], 10.);
+                //Find_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr]);
+                Find_non_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr], 10.);
 
                 double volumedifference = ConvexizeNonconvexEnvelope((ofstream *)&cout, mol->TesselStruct, mol, argv[argptr]);