RNEMD.hpp

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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef OPENMD_RNEMD_RNEMD_HPP
#define OPENMD_RNEMD_RNEMD_HPP
 
#include <bitset>
#include <fstream>
#include <map>
#include <memory>
#include <string>
#include <vector>
 
#include "brains/ForceManager.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Snapshot.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "types/AtomType.hpp"
#include "utils/Accumulator.hpp"
#include "utils/BaseAccumulator.hpp"
 
namespace OpenMD::RNEMD {
 
  class RNEMD {
  public:
    RNEMD(SimInfo* info, ForceManager*);
    virtual ~RNEMD();
 
    void getStarted();
    void doRNEMD();
    void collectData();
    void writeOutputFile();
 
  protected:
    enum RNEMDPrivilegedAxis { rnemdX = 0, rnemdY = 1, rnemdZ = 2 };
 
    enum RNEMDFluxType {
      rnemdKE,              // translational kinetic energy flux
      rnemdRotKE,           // rotational kinetic energy flux
      rnemdFullKE,          // full kinetic energy flux
      rnemdPx,              // flux of momentum along x axis
      rnemdPy,              // flux of momentum along y axis
      rnemdPz,              // flux of momentum along z axis
      rnemdPvector,         // flux of momentum vector
      rnemdLx,              // flux of angular momentum along x axis
      rnemdLy,              // flux of angular momentum along y axis
      rnemdLz,              // flux of angular momentum along z axis
      rnemdLvector,         // flux of angular momentum vector
      rnemdParticle,        // flux of particles
      rnemdParticleKE,      // flux of particles and total kinetic energy
      rnemdCurrentDensity,  // flux of electrons/charge
      rnemdKePx,            // flux of translational KE and x-momentum
      rnemdKePy,            // flux of translational KE and y-momentum
      rnemdKePvector,       // full combo flying platter
      rnemdKeLx,            // flux of translational KE and x-angular momentum
      rnemdKeLy,            // flux of translational KE and y-angular momentum
      rnemdKeLz,            // flux of translational KE and z-angular momentum
      rnemdKeLvector,       // full combo spinning platter
      rnemdUnknownFluxType
    };
 
    SimInfo* info_ {nullptr};
    Snapshot* currentSnap_ {nullptr};
    Mat3x3d hmat_;
    RealType slabWidth_;
 
    std::string rnemdObjectSelection_;
    std::vector<MoleculeStamp*> objectTypes_;
 
    SelectionManager commonA_;
    SelectionManager commonB_;
    RealType slabACenter_;
    RealType slabBCenter_;
 
    RNEMDPrivilegedAxis rnemdPrivilegedAxis_;
    RNEMDFluxType rnemdFluxType_;
 
    std::string rnemdFluxTypeLabel_;
    std::string rnemdMethodLabel_;
 
    bool doRNEMD_ {false};
    bool usePeriodicBoundaryConditions_ {false};
    bool useChargedSPF_ {false};
 
    Vector3d coordinateOrigin_;
 
    // target or desired one-time exchanges
    RealType kineticTarget_ {0.0};
    RealType particleTarget_ {0.0};
    Vector3d momentumTarget_ {V3Zero};
    Vector3d angularMomentumTarget_ {V3Zero};
 
    // actual exchanges (running total)
    RealType kineticExchange_ {0.0};
    RealType particleExchange_ {0.0};
    Vector3d momentumExchange_ {V3Zero};
    Vector3d angularMomentumExchange_ {V3Zero};
 
    unsigned int trialCount_ {0};
    unsigned int failTrialCount_ {0};
    unsigned int failRootCount_ {0};
 
    void setKineticFlux(RealType kineticFlux);
    void setParticleFlux(RealType particleFlux);
    void setMomentumFluxVector(const std::vector<RealType>& momentumFluxVector);
    void setAngularMomentumFluxVector(
        const std::vector<RealType>& angularMomentumFluxVector);
 
  private:
    enum OutputFields {
      BEGININDEX = 0,
      Z          = BEGININDEX,
      R,
      TEMPERATURE,
      VELOCITY,
      ANGULARVELOCITY,
      DENSITY,
      ACTIVITY,
      ELECTRICFIELD,
      ELECTROSTATICPOTENTIAL,
      ENDINDEX
    };
 
    struct OutputData {
      std::string title;
      std::string units;
      std::vector<std::unique_ptr<Utils::BaseAccumulator>> accumulator;
    };
 
    using OutputBitSet  = std::bitset<ENDINDEX - BEGININDEX>;
    using OutputMapType = std::map<std::string, OutputFields>;
 
    std::string rnemdAxisLabel_;
 
    // Object selection for specifying a particular species:
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
 
    // Geometric selections for the two regions for the exchange:
    std::string selectionA_;
    std::string selectionB_;
    SelectionEvaluator evaluatorA_;
    SelectionEvaluator evaluatorB_;
    SelectionManager seleManA_;
    SelectionManager seleManB_;
    bool hasSelectionA_ {false};
    bool hasSelectionB_ {false};
 
    // Output selection for collecting data about a particular species:
    std::string outputSelection_;
    SelectionEvaluator outputEvaluator_;
    SelectionManager outputSeleMan_;
 
    unsigned int nBins_ {0};
 
    RealType binWidth_;
 
    RealType sphereARadius_;
    RealType sphereBRadius_;
    RealType areaA_;
    RealType areaB_;
    RealType volumeA_;
    RealType volumeB_;
 
    bool hasData_ {false};
    bool hasDividingArea_ {false};
 
    RealType dividingArea_;
 
    // target or desired *flux*
    RealType kineticFlux_ {0.0};
    RealType particleFlux_ {0.0};
    Vector3d momentumFluxVector_ {V3Zero};
    Vector3d angularMomentumFluxVector_ {V3Zero};
 
    RealType exchangeTime_ {}, runTime_ {}, statusTime_ {};
 
    std::string rnemdFileName_;
    std::ofstream rnemdFile_ {};
 
    OutputBitSet outputMask_;
    OutputMapType outputMap_;
    std::vector<OutputData> data_;
    std::vector<AtomType*> outputTypes_;
 
    Utils::RealAccumulator areaAccumulator_ {};
 
    void parseOutputFileFormat(const std::string& format);
    std::string setSelection(RealType& slabCenter);
    RealType getDefaultDividingArea();
    int getBin(Vector3d pos);
 
    virtual void doRNEMDImpl(SelectionManager& smanA,
                             SelectionManager& smanB) = 0;
  };
}  // namespace OpenMD::RNEMD
 
#endif  // OPENMD_RNEMD_RNEMD_HPP