Controller.h

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#ifndef CONTROLLER_H
#define CONTROLLER_H

#include "converse.h"
#include "Node.h"
#include "common.h"
#include <fstream>

class ControllerBroadcasts;
class NamdState;
class SimParameters;
class RequireReduction;

#ifdef MEM_OPT_VERSION
class CollectionMasterHandler;
#else
class CollectionMaster;
#endif

class Random;
class PressureProfileReduction;

class Controller
{
public:
    Controller(NamdState *s);
    virtual ~Controller(void);
    void run(void);             // spawn thread, etc.
    void awaken(void) { CthAwaken(thread); };

protected:
    friend class ScriptTcl;
    virtual void algorithm(void);       // subclasses redefine this method

    void integrate(); // Verlet integrator
    void minimize(); // CG minimizer

    void receivePressure(int step, int minimize = 0);
      Tensor pressure_normal;
      Tensor pressure_nbond;
      Tensor pressure_slow;
      Tensor groupPressure_normal;
      Tensor groupPressure_nbond;
      Tensor groupPressure_slow;
      Tensor controlPressure_normal;
      Tensor controlPressure_nbond;
      Tensor controlPressure_slow;
      int nbondFreq;
      int slowFreq;
      BigReal temp_avg;
      BigReal pressure_avg;
      BigReal groupPressure_avg;
      int avg_count;
      Tensor pressure_tavg;
      Tensor groupPressure_tavg;
      int tavg_count;
    void compareChecksums(int,int=0);
      int computeChecksum;
      int marginViolations;
      int pairlistWarnings;
    void printTiming(int);
    void printMinimizeEnergies(int);
      BigReal min_energy;
      BigReal min_f_dot_f;
      BigReal min_f_dot_v;
      BigReal min_v_dot_v;
      int min_huge_count;
    void printDynamicsEnergies(int);
    void printEnergies(int step, int minimize);
      int numDegFreedom;
      BigReal totalEnergy;
      BigReal electEnergy;
      BigReal electEnergySlow;
      BigReal ljEnergy;
//fepb
      BigReal electEnergy_f;
      BigReal electEnergySlow_f;
      BigReal ljEnergy_f;
      BigReal exp_dE_ByRT;
      BigReal net_dE;
      BigReal dG;
      int FepNo;
      void printFepMessage(int);
      BigReal fepSum;
//fepe

      BigReal electEnergy_ti_1;
      BigReal electEnergySlow_ti_1;
      BigReal ljEnergy_ti_1;
      BigReal electEnergy_ti_2;
      BigReal electEnergySlow_ti_2;
      BigReal ljEnergy_ti_2;
      BigReal net_dEdl_elec_1;
      BigReal net_dEdl_elec_2;
      BigReal net_dEdl_lj_1;
      BigReal net_dEdl_lj_2;
      BigReal electEnergyPME_ti_1;
      BigReal electEnergyPME_ti_2;
      int TiNo;
      BigReal recent_dEdl_elec_1;
      BigReal recent_dEdl_elec_2;
      BigReal recent_dEdl_lj_1;
      BigReal recent_dEdl_lj_2;
      int recent_TiNo;
      void printTiMessage(int);

      BigReal drudeComTemp;  // temperature of Drude centers of mass
      BigReal drudeBondTemp; // temperature of Drude bonds
      BigReal drudeComTempAvg;
      BigReal drudeBondTempAvg;

      BigReal kineticEnergy;
      BigReal kineticEnergyHalfstep;
      BigReal kineticEnergyCentered;
      BigReal temperature;
      BigReal smooth2_avg;
      BigReal smooth2_avg2;  // avoid internal compiler error
      Tensor pressure;
      Tensor groupPressure;
      int controlNumDegFreedom;
      Tensor controlPressure;
    void enqueueCollections(int);
    void correctMomentum(int step);
    void rescaleVelocities(int);
      BigReal rescaleVelocities_sumTemps;
      int rescaleVelocities_numTemps;
    void reassignVelocities(int);
    void tcoupleVelocities(int);
    void berendsenPressure(int);
      Tensor berendsenPressure_avg;
      int berendsenPressure_count;
    void langevinPiston1(int);
    void langevinPiston2(int);
      Tensor langevinPiston_strainRate;

    int ldbSteps;
    void rebalanceLoad(int);
      int fflush_count;
    void cycleBarrier(int,int);

    // void suspend(void) { CthSuspend(); };
    void terminate(void);

    Random *random;
    SimParameters *const simParams;     // for convenience
    NamdState *const state;             // access data in state
    RequireReduction *reduction;

    // data for pressure profile reductions and output
    PressureProfileReduction *ppbonded;
    PressureProfileReduction *ppnonbonded;
    PressureProfileReduction *ppint;
    int pressureProfileSlabs;
    int pressureProfileCount;
    BigReal *pressureProfileAverage;

    #ifdef MEM_OPT_VERSION
    CollectionMasterHandler *const collection;
    #else
    CollectionMaster *const collection;
    #endif
    ControllerBroadcasts * broadcast;
    std::ofstream xstFile;
    void outputExtendedSystem(int step);
    void writeExtendedSystemLabels(std::ofstream &file);
    void writeExtendedSystemData(int step, std::ofstream &file);

//fepb
    std::ofstream fepFile;
    void outputFepEnergy(int step);
    void writeFepEnergyData(int step, std::ofstream &file);
//fepe
    std::ofstream tiFile;
    void outputTiEnergy(int step);
    void writeTiEnergyData(int step, std::ofstream &file);

    // for checkpoint/revert
    int checkpoint_stored;
    Lattice checkpoint_lattice;
    Tensor checkpoint_langevinPiston_strainRate;
    Tensor checkpoint_berendsenPressure_avg;
    int checkpoint_berendsenPressure_count;

private:
    CthThread thread;
    static void threadRun(Controller*);

    double startCTime;
    double startWTime;
    double firstCTime;
    double firstWTime;
    double startBenchTime;

};

#endif // CONTROLLER_H

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