Changeset 7c2f6b for molecuilder/src/atom.hpp

Timestamp:

Oct 12, 2009, 10:30:02 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

ff9879

Parents:

104cf4

Message:

Complete refactoring of molecule_dynamics.cpp

• new small functions: SumDistanceOfTrajectories(), PenalizeEqualTargets(), (), CreateInitialLists(), TryNextNearestNeighbourForInjectivePermutation(), MakeInjectivePermutation()
• Thermostat routines (case blocks) have been shifted to small functions in atom class (and soon to be extracted from there into its own class: ThermostatedParticle ?)
• old functions are a lot smaller now: MinimiseConstrainedPotential(), molecule::EvaluateConstrainedForces(), VerletForceIntegration(), also using ActOnAllAtoms
• atom class has a lot of new small functions:
  • trajectory: ResizeTrajectory(), CopyStepOnStep(), VelocityVerletUpdate(), VelocityVerletUpdate()
  • constraint potential: CorrectVelocity(), Thermostat_...()

File:

• molecuilder/src/atom.hpp (modified) (3 diffs)

molecuilder/src/atom.hpp

@@ -21 +21 @@
 #include <vector>
 
+#include <gsl/gsl_randist.h>
+
 #include "tesselation.hpp"
 
@@ -26 +28 @@
 
 class bond;
+class config;
 class element;
 class ForceMatrix;
@@ -80 +83 @@
   bool Compare(const atom &ptr);
 
+  // trajectory stuff
+  void ResizeTrajectory(int MaxSteps);
+  void CopyStepOnStep(int dest, int src);
+  void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force);
+  void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity );
+
   double DistanceToVector(Vector &origin);
   double DistanceSquaredToVector(Vector &origin);
 
+  bool IsInParallelepiped(Vector offset, double *parallelepiped);
+
+  // constraint potential and dynamics stuff
   void AddKineticToTemperature(double *temperature, int step) const;
   void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
+  void CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity);
 
-  bool IsInParallelepiped(Vector offset, double *parallelepiped);
+  // thermostats
+  void Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin);
+  void Thermostat_Gaussian_init(int Step, double *G, double *E);
+  void Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration);
+  void Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration);
+  void Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration);
+  void Thermostat_NoseHoover_init(int Step, double *delta_alpha);
+  void Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration);
+
 
   ostream & operator << (ostream &ost);