Changeset 0fc0b5 for molecuilder/src/molecules.cpp

Timestamp:

Aug 7, 2009, 9:13:21 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

ef5521

Parents:

8f9a8e

Message:

Test case of filling a simulation domain with water included.

File:

• molecuilder/src/molecules.cpp (modified) (1 diff)

molecuilder/src/molecules.cpp

@@ -741 +741 @@
   delete(Minv);
   delete(Center);
+  return status;
+};
+
+
+/** Bounds the molecule in the box whose lengths are defined by vector \a *BoxLengths.
+ * \param *out output stream for debugging
+ */
+bool molecule::BoundInBox(ofstream *out)
+{
+  bool status = true;
+  Vector x;
+  double *M = ReturnFullMatrixforSymmetric(cell_size);
+  double *Minv = x.InverseMatrix(M);
+
+  // go through all atoms
+  atom *ptr = start;  // start at first in list
+  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);
+    x.MatrixMultiplication(Minv);
+    // truncate to [0,1] for each axis
+    for (int i=0;i<NDIM;i++) {
+      while (x.x[i] >= 1.)
+        x.x[i] -= 1.;
+      while (x.x[i] < 0.)
+        x.x[i] += 1.;
+    }
+    x.MatrixMultiplication(M);
+    ptr->x.CopyVector(&x);
+  }
+  delete(M);
+  delete(Minv);
   return status;
 };