Changeset c95b69 for molecuilder

Timestamp:

Jul 10, 2009, 9:19:23 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

a048fa

Parents:

88b936

Message:

BUGFIX: Due to stupid mistake, first atom was overlooked in periodic translation

• molecule::TranslatePeriodically() is fixed (while is ptr != end) and next pointer moved to its end

File:

• molecuilder/src/molecules.cpp (modified) (2 diffs)

molecuilder/src/molecules.cpp

@@ -853 +853 @@
   // go through all atoms
   ptr = start->next;  // start at first in list
-  if (ptr != end) {  //list not empty?
-    while (ptr->next != end) {  // continue with second if present
-      ptr = ptr->next;
-      //ptr->Output(1,1,out);
-      // multiply its vector with matrix inverse
-      x.CopyVector(&ptr->x);
+  while (ptr != end) {  // continue with second if present
+    //ptr->Output(1,1,out);
+    // multiply its vector with matrix inverse
+    x.CopyVector(&ptr->x);
+    x.Translate(trans);
+    x.MatrixMultiplication(Minv);
+    // truncate to [0,1] for each axis
+    for (int i=0;i<NDIM;i++) {
+      value = floor(fabs(x.x[i]));  // next lower integer
+      if (x.x[i] >=0) {
+        x.x[i] -= value;
+      } else {
+        x.x[i] += value+1;
+      }
+    }
+    // matrix multiply
+    x.MatrixMultiplication(M);
+    ptr->x.CopyVector(&x);
+    for (int j=0;j<MDSteps;j++) {
+      x.CopyVector(&Trajectories[ptr].R.at(j));
       x.Translate(trans);
       x.MatrixMultiplication(Minv);
       // truncate to [0,1] for each axis
       for (int i=0;i<NDIM;i++) {
-        value = floor(fabs(x.x[i]));  // next lower integer
+        value = floor(x.x[i]);  // next lower integer
         if (x.x[i] >=0) {
           x.x[i] -= value;
@@ -872 +886 @@
       // matrix multiply
       x.MatrixMultiplication(M);
-      ptr->x.CopyVector(&x);
-      for (int j=0;j<MDSteps;j++) {
-        x.CopyVector(&Trajectories[ptr].R.at(j));
-        x.Translate(trans);
-        x.MatrixMultiplication(Minv);
-        // truncate to [0,1] for each axis
-        for (int i=0;i<NDIM;i++) {
-          value = floor(x.x[i]);  // next lower integer
-          if (x.x[i] >=0) {
-            x.x[i] -= value;
-          } else {
-            x.x[i] += value+1;
-          }
-        }
-        // matrix multiply
-        x.MatrixMultiplication(M);
-        Trajectories[ptr].R.at(j).CopyVector(&x);
-      }
+      Trajectories[ptr].R.at(j).CopyVector(&x);
     }
+    ptr = ptr->next;
   }
   delete(M);