Permittivity.h

/*
 * Permittivity.h
 *
 *  Created on: November 2019
 *      Author: Joshua Marx
 */
 
 // DESCRIPTION: Samples the relative permittivity of Stockmayer fluids in the NVT ensemble
 // Important: Permittivity may take a long time to converge, i.e. a few million steps with ~1000 particles. Reducing number of slabs for the thermostat can drastically improve results!
 
#ifndef SRC_PLUGINS_PERMITTIVITY_H_
#define SRC_PLUGINS_PERMITTIVITY_H_
 
#include "Domain.h"
#include "parallel/DomainDecompBase.h"
#include "particleContainer/ParticleContainer.h"
#include "plugins/PluginBase.h"
 
class Permittivity: public PluginBase {
public:
 
    void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override;
    void readXML(XMLfileUnits& xmlconfig) override;
    void record(ParticleContainer* particleContainer);
    void endStep(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain,
                 unsigned long simstep) override;
    void reset();
    void collect(DomainDecompBase* domainDecomp);
    void writeRunningAverage(unsigned long indexM, double tempMX, double tempMY, double tempMZ, double tempMSquared);
    void output(Domain* domain, unsigned long timestep);
    void finish(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override{};
    std::string getPluginName() override { return std::string("Permittivity"); }
    static PluginBase* createInstance() { return new Permittivity();}
    
    
    
private:
    bool _readStartingStep;             // Auxiliary bool variable to read the current time step during the first iteration of endStep
    unsigned long _writeFrequency;      // Write frequency for all profiles -> Length of recording frame before output
    unsigned long _initStatistics;      // Timesteps to skip at start of the simulation
    unsigned long _recordingTimesteps;  // Record every Nth timestep during recording frame
    unsigned long _accumulatedSteps;    // Number of steps in a block
    unsigned long _runningAverageSteps; // Timesteps for running average output
    unsigned long _totalNumTimeSteps;   // Total number of time steps
    unsigned long _startingStep;        // current time step at the start of simulation
    unsigned long _numParticlesLocal;   // Counts number of particles considered for each block locally
    unsigned long _RAVCounter;
    unsigned _numOutputs;               // Number of output values to be written
    unsigned _numComponents;            // Number of components
    unsigned _currentOutputNum;         // Number of current block
    std::map<unsigned,double> _myAbs;   // Dipole moment of component
    std::map<unsigned,unsigned long> _numParticles; // Counts number of particles considered for each block globally
    std::map<unsigned,double> _outputSquaredM; // Total average squared dipole moment for each block
    std::map<unsigned, std::map<unsigned, double>> _outputM; // Total average dipole moment for each block
    std::map<unsigned long, std::map<unsigned long, double >> _localM; // Total dipole moment local
    std::map<unsigned long, std::map<unsigned long, double >> _globalM; // Total dipole moment global
    std::array<double, 3> simBoxSize;
    double _totalAverageM[3]; // Total dipole moment averaged over whole production run
    double _totalAverageSquaredM; // Total squared dipole moment averaged over whole production run
    double _MRAV[3]; // Running average for M
    double _MSquaredRAV; // Running average for <M2>
    double _permRAV; // Running average for permittivity (without consideration of <M>2
    double _V; // Box volume
    double _T; // Target temperature
    std::ofstream _ravStream;
    std::string _outputPrefix;
};
 
#endif /*SRC_PLUGINS_PERMITTIVITY_H_*/