Changeset 104cf4 for molecuilder/src/atom.cpp

Timestamp:

Oct 9, 2009, 2:35:14 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

7c2f6b

Parents:

e71890

Message:

First half of molecule_dynamics.cpp is refactored into smaller parts.

• new function atom::EvaluateConstrainedForce() evaluating a constraint force
• molecule::EvaluateConstrainedForces() uses the above with ActOnAllatoms()
• new helper functions in molecule_dynamics.cpp: SumDistanceOfTrajectories(), SumDistanceOfTrajectories(), FillDistanceList(), CreateInitialLists(), TryNextNearestNeighbourForInjectivePermutation(), MakeInjectivePermutation()
• new struct EvaluatePotential in molecules.hpp to contain most of the values for the above functions

File:

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

molecuilder/src/atom.cpp

@@ -9 +9 @@
 #include "element.hpp"
 #include "memoryallocator.hpp"
+#include "parser.hpp"
 #include "vector.hpp"
 
@@ -297 +298 @@
 };
 
+/** Evaluates some constraint potential if atom moves from \a startstep at once to \endstep in trajectory.
+ * \param startstep trajectory begins at
+ * \param endstep trajectory ends at
+ * \param **PermutationMap if atom switches places with some other atom, there is no translation but a permutaton noted here (not in the trajectories of each).
+ * \param *Force Force matrix to store result in
+ */
+void atom::EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force)
+{
+  double constant = 10.;
+  atom *Sprinter = PermutationMap[nr];
+  // set forces
+  for (int i=NDIM;i++;)
+    Force->Matrix[0][nr][5+i] += 2.*constant*sqrt(Trajectory.R.at(startstep).Distance(&Sprinter->Trajectory.R.at(endstep)));
+};