| 1 | /*
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| 2 | * atom_trajectoryparticle.hpp
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| 3 | *
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| 4 | * Created on: Oct 19, 2009
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | #ifndef ATOM_TRAJECTORYPARTICLE_HPP_
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| 9 | #define ATOM_TRAJECTORYPARTICLE_HPP_
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| 10 |
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| 11 | using namespace std;
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| 12 |
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| 13 | /*********************************************** includes ***********************************/
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| 14 |
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| 15 | // include config.h
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| 16 | #ifdef HAVE_CONFIG_H
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| 17 | #include <config.h>
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| 18 | #endif
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| 19 |
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| 20 | #include <fstream>
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| 21 |
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| 22 | #include <gsl/gsl_randist.h>
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| 23 |
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| 24 | #include "atom_atominfo.hpp"
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| 25 | #include "atom_particleinfo.hpp"
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| 26 | #include "atom_trajectoryparticleinfo.hpp"
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| 27 |
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| 28 | /****************************************** forward declarations *****************************/
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| 29 |
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| 30 | class atom;
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| 31 | class config;
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| 32 | class ForceMatrix;
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| 33 | class Vector;
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| 34 |
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| 35 | /********************************************** declarations *******************************/
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| 36 |
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| 37 |
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| 38 | class TrajectoryParticle : public TrajectoryParticleInfo, public virtual AtomInfo, public virtual ParticleInfo {
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| 39 | public:
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| 40 |
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| 41 | TrajectoryParticle();
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| 42 | virtual ~TrajectoryParticle();
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| 43 |
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| 44 | // constraint potential and dynamics stuff
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| 45 | void AddKineticToTemperature(double *temperature, int step) const;
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| 46 | void EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force) const;
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| 47 | void CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity);
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| 48 |
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| 49 | // trajectory stuff
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| 50 | void ResizeTrajectory(int MaxSteps);
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| 51 | void CopyStepOnStep(int dest, int src);
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| 52 | void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force);
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| 53 | void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const;
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| 54 |
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| 55 | // thermostats
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| 56 | void Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin);
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| 57 | void Thermostat_Gaussian_init(int Step, double *G, double *E);
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| 58 | void Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration);
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| 59 | void Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration);
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| 60 | void Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration);
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| 61 | void Thermostat_NoseHoover_init(int Step, double *delta_alpha);
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| 62 | void Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration);
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| 63 |
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| 64 | private:
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| 65 |
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| 66 | };
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| 67 |
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| 68 |
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| 69 | #endif /* ATOM_TRAJECTORYPARTICLE_HPP_ */
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