Changeset b21e1f for molecuilder/src/molecules.cpp

Timestamp:

Sep 6, 2008, 4:21:31 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

03c204

Parents:

d473c3

Message:

BUGFIX: molecule::...Scale(),Translate(),Mirror() and Align() did only change vectors of atom struct, not in the Trajectories structure. RemoveAtom did not remove trajectories entry

This is fixed.
Also, fixed that RemoveAtom() did not remove the entry in Trajectories structure.

File:

• molecuilder/src/molecules.cpp (modified) (10 diffs)

molecuilder/src/molecules.cpp

@@ -644 +644 @@
   if (!status)
     *out << "WARNING: molecule is bigger than defined box!" << endl;
-  else {  // else center in box 
-    ptr = start;
-    while (ptr->next != end) {
-      ptr = ptr->next;
-      for (int i=NDIM;i--;)
-        ptr->x.x[i] += -(max->x[i] + min->x[i])/2. + BoxLengths->x[i]/2.; // first term centers molecule at (0,0,0), second shifts to center of new box
-    }
+  else {  // else center in box
+    max->AddVector(min);
+    max->Scale(-1.);
+    max->AddVector(BoxLengths);
+    max->Scale(0.5);
+    Translate(max);
   }
 
@@ -687 +686 @@
 //    min->Output(out);
 //    *out << endl;
-    
-    for (int i=NDIM;i--;) {
-      min->x[i] *= -1.;
-      max->x[i] += min->x[i];
-    } 
+    min->Scale(-1.);
+    max->AddVector(min);
     Translate(min);
   } 
@@ -772 +768 @@
     a->Scale(-1./Num); // divide through total mass (and sign for direction)
   }
-  *out << Verbose(1) << "Resulting center of gravity: ";
-  a->Output(out);
-  *out << endl;
+//  *out << Verbose(1) << "Resulting center of gravity: ";
+//  a->Output(out);
+//  *out << endl;
   return a;
 };
@@ -802 +798 @@
   while (ptr->next != end) {
     ptr = ptr->next;
+    for (int j=0;j<MDSteps;j++)
+      Trajectories[ptr].R.at(j).Scale(factor);
     ptr->x.Scale(factor);
   }      
@@ -815 +813 @@
   while (ptr->next != end) {
     ptr = ptr->next;
+    for (int j=0;j<MDSteps;j++)
+      Trajectories[ptr].R.at(j).Translate(trans);
     ptr->x.Translate(trans);
   }      
@@ -828 +828 @@
   while (ptr->next != end) {
     ptr = ptr->next;
+    for (int j=0;j<MDSteps;j++)
+      Trajectories[ptr].R.at(j).Mirror(n);
     ptr->x.Mirror(n);
   }      
@@ -961 +963 @@
           while (ptr->next != end) {
             ptr = ptr->next;
+            for (int j=0;j<MDSteps;j++)
+              Trajectories[ptr].R.at(j).MatrixMultiplication(evec->data);
             ptr->x.MatrixMultiplication(evec->data);
           }
@@ -1142 +1146 @@
     ptr->x.x[0] =  cos(alpha) * tmp + sin(alpha) * ptr->x.x[2]; 
     ptr->x.x[2] = -sin(alpha) * tmp + cos(alpha) * ptr->x.x[2];
+    for (int j=0;j<MDSteps;j++) {
+      tmp = Trajectories[ptr].R.at(j).x[0];
+      Trajectories[ptr].R.at(j).x[0] =  cos(alpha) * tmp + sin(alpha) * Trajectories[ptr].R.at(j).x[2]; 
+      Trajectories[ptr].R.at(j).x[2] = -sin(alpha) * tmp + cos(alpha) * Trajectories[ptr].R.at(j).x[2];
+    }
   }      
   // rotate n vector
@@ -1160 +1169 @@
     ptr->x.x[1] =  cos(alpha) * tmp + sin(alpha) * ptr->x.x[2]; 
     ptr->x.x[2] = -sin(alpha) * tmp + cos(alpha) * ptr->x.x[2];
+    for (int j=0;j<MDSteps;j++) {
+      tmp = Trajectories[ptr].R.at(j).x[1];
+      Trajectories[ptr].R.at(j).x[1] =  cos(alpha) * tmp + sin(alpha) * Trajectories[ptr].R.at(j).x[2]; 
+      Trajectories[ptr].R.at(j).x[2] = -sin(alpha) * tmp + cos(alpha) * Trajectories[ptr].R.at(j).x[2];
+    }
   }      
   // rotate n vector (for consistency check)
@@ -1184 +1198 @@
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
     ElementCount--;
+  Trajectories.erase(pointer);
   return remove(pointer, start, end);
 };