Changeset 104cf4 for molecuilder/src/molecule.hpp

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/molecule.hpp (modified) (2 diffs)

molecuilder/src/molecule.hpp

@@ -56 +56 @@
 /************************************* Class definitions ****************************************/
 
-
+/** Structure to contain parameters needed for evaluation of constraint potential.
+ */
+struct EvaluatePotential
+{
+  int startstep;              //!< start configuration (MDStep in atom::trajectory)
+  int endstep;                //!< end configuration (MDStep in atom::trajectory)
+  atom **PermutationMap;      //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
+  DistanceMap **DistanceList; //!< distance list of each atom to each atom
+  DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
+  int *DoubleList;            //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
+  DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
+  bool IsAngstroem;           //!< whether coordinates are in angstroem (true) or bohrradius (false)
+  double *PenaltyConstants;   //!<  penalty constant in front of each term
+};
 
 #define MaxThermostats 6      //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented 
@@ -216 +229 @@
 
 
-  double ConstrainedPotential(ofstream *out, atom **permutation, int start, int end, double *constants, bool IsAngstroem);
+  double ConstrainedPotential(ofstream *out, struct EvaluatePotential &Params);
   double MinimiseConstrainedPotential(ofstream *out, atom **&permutation, int startstep, int endstep, bool IsAngstroem);
   void EvaluateConstrainedForces(ofstream *out, int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);