DataStorage.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).
 */
 
/**
 * @file Vector.hpp
 * @author Teng Lin
 * @date 09/14/2004
 * @version 1.0
 */
 
#ifndef BRAINS_DATASTORAGE_HPP
#define BRAINS_DATASTORAGE_HPP
 
#include <vector>
 
#include <math/SquareMatrix3.hpp>
#include <math/Vector3.hpp>
 
using namespace std;
namespace OpenMD {
  /**
   * @class DataStorage
   * @warning do not try to insert element into (or ease element from) private
   * member data of DataStorage directly.
   * @todo DataStorage may need refactoring. Every vector can inherit from the
   * same base class which will make it easy to maintain
   */
  class DataStorage {
  public:
    enum {
      dslPosition             = 1,
      dslVelocity             = 2,
      dslForce                = 4,
      dslAmat                 = 8,
      dslAngularMomentum      = 16,
      dslTorque               = 32,
      dslParticlePot          = 64,
      dslDensity              = 128,
      dslFunctional           = 256,
      dslFunctionalDerivative = 512,
      dslDipole               = 1024,
      dslQuadrupole           = 2048,
      dslElectricField        = 4096,
      dslSkippedCharge        = 8192,
      dslFlucQPosition        = 16384,
      dslFlucQVelocity        = 32768,
      dslFlucQForce           = 65536,
      dslSitePotential        = 131072
    };
 
    DataStorage();
    DataStorage(std::size_t size, int storageLayout = 0);
    /** return the size of this DataStorage. */
    std::size_t getSize();
    /**
     * Changes the size of this DataStorage.
     * @param newSize new size of this DataStorage
     */
    void resize(std::size_t newSize);
    /**
     * Reallocates memory manually.
     *
     * The main reason for using reserve() is efficiency if you know
     * the capacity to which your vector must eventually grow,
     * then it is usually more efficient to allocate that memory all
     * at once.
     */
    void reserve(std::size_t size);
    /**
     * Copies data inside DataStorage class.
     *
     * Copy function actually calls copy for every vector in
     * DataStorage class.  One Precondition of copy is that
     * target is not within the range [source, soruce + num]
     *
     * @param source
     * @param num number of element to be moved
     * @param target
     */
    void copy(int source, std::size_t num, std::size_t target);
    /** Returns the storage layout  */
    int getStorageLayout();
    /** Sets the storage layout  */
    void setStorageLayout(int layout);
    /** Returns the pointer of internal array */
    RealType* getArrayPointer(int whichArray);
 
    vector<Vector3d> position;        /** position array */
    vector<Vector3d> velocity;        /** velocity array */
    vector<Vector3d> force;           /** force array */
    vector<RotMat3x3d> aMat;          /** rotation matrix array */
    vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
    vector<Vector3d> torque;          /** torque array */
    vector<RealType> particlePot;     /** particle potential arrray */
    vector<RealType> density;         /** electron density */
    vector<RealType> functional;      /** density functional */
    vector<RealType> functionalDerivative; /** derivative of functional */
    vector<Vector3d> dipole;               /** space-frame dipole vector */
    vector<Mat3x3d> quadrupole;            /** space-frame quadrupole tensor */
    vector<Vector3d> electricField;        /** local electric field */
    vector<RealType>
        skippedCharge; /** charge skipped during normal pairwise calculation */
    vector<RealType> flucQPos;      /** fluctuating charges */
    vector<RealType> flucQVel;      /** fluctuating charge velocities */
    vector<RealType> flucQFrc;      /** fluctuating charge forces */
    vector<RealType> sitePotential; /** electrostatic site potentials */
 
    static std::size_t getBytesPerStuntDouble(int layout);
 
  private:
    RealType* internalGetArrayPointer(vector<Vector3d>& v);
    RealType* internalGetArrayPointer(vector<Mat3x3d>& v);
    RealType* internalGetArrayPointer(vector<RealType>& v);
 
    template<typename T>
    void internalResize(std::vector<T>& v, std::size_t newSize);
 
    template<typename T>
    void internalCopy(std::vector<T>& v, int source, std::size_t num,
                      std::size_t target);
 
    std::size_t size_;
    int storageLayout_;
  };
}  // namespace OpenMD
 
#endif  // BRAINS_DATASTORAGE_HPP