Changes in / [47548d:f39735]

Files:

• molecuilder/src/builder.cpp (modified) (5 diffs)
• molecuilder/src/molecules.cpp (modified) (7 diffs)
• util/src/CalculateDensity.sh.in (modified) (1 diff)
• util/src/CalculateMass.sh.in (modified) (2 diffs)

molecuilder/src/builder.cpp

@@ -463 +463 @@
       cin >> tmp1;
       first = mol->start;
-      second = first->next;
-      while(second != mol->end) {
-        first = second;
-        second = first->next;
+      while(first->next != mol->end) {
+        first = first->next;
         if (first->x.DistanceSquared((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
           mol->RemoveAtom(first);
@@ -474 +472 @@
       cout << Verbose(0) << "Which axis is it: ";
       cin >> axis;
-      cout << Verbose(0) << "Lower boundary: ";
+      cout << Verbose(0) << "Left inward boundary: ";
       cin >> tmp1;
-      cout << Verbose(0) << "Upper boundary: ";
+      cout << Verbose(0) << "Right inward boundary: ";
       cin >> tmp2;
       first = mol->start;
-      second = first->next;
-      while(second != mol->end) {
-        first = second;
-        second = first->next;
-        if ((first->x.x[axis] < tmp1) || (first->x.x[axis] > tmp2)) {// out of boundary ...
-          //cout << "Atom " << *first << " with " << first->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
+      while(first->next != mol->end) {
+        first = first->next;
+        if ((first->x.x[axis] > tmp2) || (first->x.x[axis] < tmp1)) // out of boundary ...
           mol->RemoveAtom(first);
-        }
       }
       break;
@@ -1355 +1349 @@
             cout << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
             cout << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl;
-            cout << "\t-N <radius> <file>\tGet non-convex-envelope." << endl;
+            cout << "\t-N\tGet non-convex-envelope." << endl;
             cout << "\t-o <out>\tGet volume of the convex envelope (and store to tecplot file)." << endl;
             cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
@@ -1361 +1355 @@
             cout << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl; 
             cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
-            cout << "\t-R\t\tRemove all atoms out of sphere around a given one." << endl;
             cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
             cout << "\t-T <file> Store temperatures from the config file in <file>." << endl;
@@ -1628 +1621 @@
                   cout << Verbose(2) << "File found and parsed." << endl;
                 argptr+=1;
-              }
-              break;
-            case 'R':
-              ExitFlag = 1;
-              if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])))  {
-                ExitFlag = 255;
-                cerr << "Not enough or invalid arguments given for removing atoms: -R <id> <distance>" << endl;
-              } else {
-                SaveFlag = true;
-                cout << Verbose(1) << "Removing atoms around " << argv[argptr] << " with radius " << argv[argptr+1] << "." << endl;
-                double tmp1 = atof(argv[argptr+1]);
-                atom *third = mol->FindAtom(atoi(argv[argptr]));
-                atom *first = mol->start;
-                if ((third != NULL) && (first != mol->end)) {
-                  atom *second = first->next;
-                  while(second != mol->end) {
-                    first = second;
-                    second = first->next;
-                    if (first->x.DistanceSquared((const Vector *)&third->x) > tmp1*tmp1) // distance to first above radius ...
-                      mol->RemoveAtom(first);
-                  }
-                } else {
-                  cerr << "Removal failed due to missing atoms on molecule or wrong id." << endl;
-                }
-                argptr+=2;
               }
               break;

molecuilder/src/molecules.cpp

@@ -1860 +1860 @@
 bool molecule::RemoveAtom(atom *pointer)
 {
-  if (ElementsInMolecule[pointer->type->Z] != 0)  { // this would indicate an error
+  if (ElementsInMolecule[pointer->type->Z] != 0)  // this would indicate an error
     ElementsInMolecule[pointer->type->Z]--;  // decrease number of atom of this element
-    AtomCount--;
-  } else
+  else
     cerr << "ERROR: Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl;
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
@@ -2846 +2845 @@
     ColorList[i] = white;
   }
-
+  
   *out << Verbose(1) << "Back edge list - ";
   BackEdgeStack->Output(out);
@@ -3853 +3852 @@
         OtherAtom = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
         if (OtherAtom == ListOfLocalAtoms[Binder->rightatom->nr]) { // found the bond
-          LocalStack->Push(ListOfBondsPerAtom[Walker->nr][i]);
-          *out << Verbose(3) << "Found local edge " << *(ListOfBondsPerAtom[Walker->nr][i]) << "." << endl;
+            LocalStack->Push(ListOfBondsPerAtom[Walker->nr][i]);
+                *out << Verbose(3) << "Found local edge " << *(ListOfBondsPerAtom[Walker->nr][i]) << "." << endl;
           break;
         }
@@ -3862 +3861 @@
     ReferenceStack->Push(Binder);
   } while (FirstBond != Binder);
-
+  
   return status;
 };
@@ -4007 +4006 @@
   Walker = start;
   while (Walker->next != end) {
-    Walker = Walker->next;
+    Walker = Walker->next; 
     *out << Verbose(4) << "Atom " << Walker->Name << "/" << Walker->nr << " with " << NumberOfBondsPerAtom[Walker->nr] << " bonds: ";
     TotalDegree = 0;
@@ -4366 +4365 @@
 #ifdef ADDHYDROGEN
    && (Walker->type->Z == 1)
+#endif
+                        ) { // search for first non-hydrogen atom
+    *out << Verbose(4) << "Current Root candidate is " << Walker->Name << "." << endl;
+    Walker = Walker->next;
+  }
+  if (Walker != end)
+    RootStack->Push(Walker);
+  else
+    *out << Verbose(0) << "ERROR: Could not find an appropriate Root atom!" << endl;
+  *out << Verbose(3) << "Root " << Walker->Name << " is on AtomStack, beginning loop through all vertices ..." << endl;
+
+  ///// OUTER LOOP ////////////
+  while (!RootStack->IsEmpty()) {
+    // get new root vertex from atom stack
+    Root = RootStack->PopFirst();
+    ShortestPathList[Root->nr] = 0;
+    if (Labels[Root->nr] == -1)
+      Labels[Root->nr] = RunningIndex++; // prevent it from getting again on AtomStack
+    PredecessorList[Root->nr] = Root;
+    TouchedStack->Push(Root);
+    *out << Verbose(0) << "Root for this loop is: " << Root->Name << ".\n";
+
+    // clear snake stack
+    SnakeStack->ClearStack();
+    //SnakeStack->TestImplementation(out, start->next);
+
+    ///// INNER LOOP ////////////
+    // Problems:
+    // - what about cyclic bonds?
+    Walker = Root;
+    do {
+      *out << Verbose(1) << "Current Walker is: " << Walker->Name;
+      // initial setting of the new Walker: label, color, shortest path and put on stacks
+      if (Labels[Walker->nr] == -1)  {  // give atom a unique, monotonely increasing number
+        Labels[Walker->nr] = RunningIndex++;
+        RootStack->Push(Walker);
+      }
+      *out << ", has label " << Labels[Walker->nr];
+      if ((ColorVertexList[Walker->nr] == white) || ((Binder != NULL) && (ColorEdgeList[Binder->nr] == white))) {  // color it if newly discovered and push on stacks (and if within reach!)
+        if ((Binder != NULL) && (ColorEdgeList[Binder->nr] == white)) {
+          // Binder ought to be set still from last neighbour search
+          *out << ", coloring bond " << *Binder << " black";
+          ColorEdgeList[Binder->nr] = black; // mark this bond as used
+        }
+        if (ShortestPathList[Walker->nr] == -1) {
+          ShortestPathList[Walker->nr] = ShortestPathList[PredecessorList[Walker->nr]->nr]+1;
+          TouchedStack->Push(Walker); // mark every atom for lists cleanup later, whose shortest path has been changed
+        }
+        if ((ShortestPathList[Walker->nr] < Order) && (ColorVertexList[Walker->nr] != darkgray)) {  // if not already on snake stack
+          SnakeStack->Push(Walker);
+          ColorVertexList[Walker->nr] = darkgray; // mark as dark gray of on snake stack
         }
       }
@@ -4402 +4452 @@
             } else { // otherwise check its colour and element
               if (
+#ifdef ADDHYDROGEN
               (OtherAtom->type->Z != 1) &&
 #endif

util/src/CalculateDensity.sh.in

@@ -3 +3 @@
 # calculates the density of a molecule contained in a espack config file
 
-exec_prefix=@prefix@
 MOLECUILDER="@bindir@/molecuilder"
 

util/src/CalculateMass.sh.in

@@ -3 +3 @@
 # calculates mass of a molecule in a XYZ file
 
-exec_prefix=@prefix@
 ELEMENTSDB="@bindir@/elements.db"
 
@@ -34 +33 @@
 done
 
-echo "Totalmass is $totalmass atomicmassunit"
+echo "Totalmass is $totalmass atomicunits"
 exit 0