source: src/Atom/atom_atominfo.hpp@ 6458e7

/*
 * atom_atominfo.hpp
 *
 *  Created on: Oct 19, 2009
 *      Author: heber
 */

#ifndef ATOM_ATOMINFO_HPP_
#define ATOM_ATOMINFO_HPP_


using namespace std;

/*********************************************** includes ***********************************/

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <boost/function.hpp>
#include <vector>

#include "atom_observable.hpp"

#include "types.hpp"

#include "LinearAlgebra/Vector.hpp"
#include "LinearAlgebra/VectorInterface.hpp"

/****************************************** forward declarations *****************************/

class AtomInfo;
class element;
class ForceMatrix;
class RealSpaceMatrix;

namespace MoleCuilder {
  void removeLastStep(const std::vector<atomId_t> &atoms);
};

/********************************************** declarations *******************************/

class AtomInfo : public VectorInterface, public virtual AtomObservable  {

public:
  AtomInfo();
  AtomInfo(const AtomInfo &_atom);
  AtomInfo(const VectorInterface &_v);
  virtual ~AtomInfo();

  /** Pushes back another step in all trajectory vectors.
   *
   * This allows to extend all trajectories contained in different classes
   * consistently. This is implemented by the topmost class which calls the
   * real functions, \sa AppendTrajectoryStep(), by all necessary subclasses.
   */
  virtual void UpdateStep(const unsigned int _step)=0;

  /** Pops all steps in the interval [\a _firststep, \a _laststep] in all trajectory vectors.
   *
   * This allows to decrease all trajectories contained in different classes
   * by one consistently. This is implemented by the topmost class which calls
   * the real functions, \sa removeTrajectorySteps(), by all necessary subclasses.
   *
   * \param _firststep first step in interval to be removed
   * \param _laststep last step in interval to be removed
   */
  virtual void removeSteps(const unsigned int _firststep, const unsigned int _laststep)=0;

  /** DEPRECATED: Getter for element indicated by AtomicElement.
   *
   * \deprecated This function is deprecated, use getElement() instead.
   *
   * @return constant pointer to element for AtomicElement
   */
  const element *getType() const;

  /** Getter for element indicated by AtomicElement.
   *
   * \note Looking up the element requires looking the World instance and is
   * thus significantly slower than instead just returning the internally
   * stored atomicNumber_t. So, if possible use getElementNo() instead and
   * check soundly whether you truely need access to all of element's member
   * variables.
   *
   * @return const reference to element indicated by AtomicElement
   */
  const element & getElement() const;

  /** Getter for AtomicElement.
   *
   * @return AtomicElement
   */
  atomicNumber_t getElementNo() const;

  /** Getter for the name of Particle this atom is associated with.
   *
   * \return name of Particle to use in lookup in ParticleRegistry
   */
  const std::string &getParticleName() const;

  /** Setter for the Particle name this atom is associated with.
   *
   * \param _name new name of atom's Particle
   */
  void setParticleName(const std::string & _name);

  /** Setter for AtomicElement.
   *
   * @param _type new element by pointer to set
   */
  void setType(const element *_type);
  /** Setter for AtomicElement.
   *
   * @param _typenr new element by index to set
   */
  void setType(const int _typenr);

  /** Getter for AtomicVelocity.
   *
   * Current time step is used.
   *
   * @return constant reference to AtomicVelocity
   */
//  Vector& getAtomicVelocity();
  /** Getter for AtomicVelocity.
   *
   * @param _step time step to return
   * @return constant reference to AtomicVelocity
   */
//  Vector& getAtomicVelocity(const int _step);
  /** Getter for AtomicVelocity.
   *
   * Current time step is used.
   *
   * @return constant reference to AtomicVelocity
   */
  const Vector& getAtomicVelocity() const;
  /** Getter for AtomicVelocity.
   *
   * @param _step time step to return
   * @return constant reference to AtomicVelocity
   */
  const Vector& getAtomicVelocityAtStep(const unsigned int _step) const;
  /** Setter for AtomicVelocity.
   *
   * Current time step is used.
   *
   * @param _newvelocity new velocity to set
   */
  void setAtomicVelocity(const Vector &_newvelocity);
  /** Setter for AtomicVelocity.
   *
   * @param _step time step to set
   * @param _newvelocity new velocity to set
   */
  void setAtomicVelocityAtStep(const unsigned int _step, const Vector &_newvelocity);

  /** Getter for AtomicForce.
   *
   * Current time step is used.
   *
   * @return constant reference to AtomicForce
   */
  const Vector& getAtomicForce() const;
  /** Getter for AtomicForce.
   *
   * @param _step time step to return
   * @return constant reference to AtomicForce
   */
  const Vector& getAtomicForceAtStep(const unsigned int _step) const;
  /** Setter for AtomicForce.
   *
   * Current time step is used.
   *
   * @param _newvelocity new force vector to set
   */
  void setAtomicForce(const Vector &_newforce);
  /** Setter for AtomicForce.
   *
   * @param _step time step to set
   * @param _newvelocity new force vector to set
   */
  void setAtomicForceAtStep(const unsigned int _step, const Vector &_newforce);

  /** Getter for FixedIon.
   *
   * @return constant reference to FixedIon
   */
  bool getFixedIon() const;
  /** Setter for FixedIon.
   *
   * @param _fixedion new state of FixedIon
   */
  void setFixedIon(const bool _fixedion);

  ///// manipulation of the atomic position

  // Accessors ussually come in pairs... and sometimes even more than that
  /** Getter for AtomicPosition.
   *
   * Current time step is used.
   *
   * @param i component of vector
   * @return i-th component of atomic position
   */
  const double& operator[](size_t i) const;
  /** Getter for AtomicPosition.
   *
   * Current time step is used.
   *
   * \sa operator[], this is if instance is a reference.
   *
   * @param i component of vector
   * @return i-th component of atomic position
   */
  const double& at(size_t i) const;
  /** Getter for AtomicPosition.
   *
   * \sa operator[], this is if instance is a reference.
   *
   * @param i index of component of AtomicPosition
   * @param _step time step to return
   * @return atomic position at time step _step
   */
  const double& atStep(size_t i, unsigned int _step) const;
  /** Setter for AtomicPosition.
   *
   * Current time step is used.
   *
   * @param i component to set
   * @param value value to set to
   */
  void set(size_t i, const double value);
  /** Setter for AtomicPosition.
   *
   * @param i component to set
   * @param _step time step to set
   * @param value value to set to
   */
  void setAtStep(size_t i, unsigned int _step, const double value);
  /** Getter for AtomicPosition.
   *
   * Current time step is used.
   *
   * @return atomic position
   */
  const Vector& getPosition() const;
  /** Getter for AtomicPosition.
   *
   * @param _step time step to return
   * @return atomic position at time step _step
   */
  const Vector& getPositionAtStep(unsigned int _step) const;

  // Assignment operator
  /** Setter for AtomicPosition.
   *
   * Current time step is used.
   *
   * @param _vector new position to set
   */
  void setPosition(const Vector& _vector);
  /** Setter for AtomicPosition.
   *
   * @param _step time step to set
   * @param _vector new position to set for time step _step
   */
  void setPositionAtStep(const unsigned int _step, const Vector& _vector);
  class VectorInterface &operator=(const Vector& _vector);

  // operators for mathematical operations
  const VectorInterface& operator+=(const Vector& b);
  const VectorInterface& operator-=(const Vector& b);
  Vector const operator+(const Vector& b) const;
  Vector const operator-(const Vector& b) const;

  void Zero();
  void One(const double one);
  void LinearCombinationOfVectors(const Vector &x1, const Vector &x2, const Vector &x3, const double * const factors);

  double distance(const Vector &point) const;
  double DistanceSquared(const Vector &y) const;
  double distance(const VectorInterface &_atom) const;
  double DistanceSquared(const VectorInterface &_atom) const;

  void ScaleAll(const double *factor);
  void ScaleAll(const Vector &factor);
  void Scale(const double factor);

  // operations for trajectories
  bool isStepPresent(const unsigned int _step) const;
  void ResizeTrajectory(size_t MaxSteps);
  size_t getTrajectorySize() const;
  void CopyStepOnStep(const unsigned int dest, const unsigned int src);
  void VelocityVerletUpdateX(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem);
  void VelocityVerletUpdateU(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem);
  double getKineticEnergy(const unsigned int step) const;
  Vector getMomentum(const unsigned int step) const;
  double getMass() const;
  double getCharge() const {
    return charge;
  }
  void setCharge(const double _charge) {
    charge = _charge;
  }

  std::ostream & operator << (std::ostream &ost) const;

protected:
  /** Function used by this and inheriting classes to extend the trajectory
   * vectors.
   */
  void AppendTrajectoryStep(const unsigned int _step);

  /** Function used by this and inheriting classes to decrease the trajectory
   * vectors by one.
   *
   * \param _firststep first step in interval to be removed
   * \param _laststep last step in interval to be removed
   */
  void removeTrajectorySteps(const unsigned int _firststep, const unsigned int _laststep);

  // make these protected only such that deriving atom class still has full
  // access needed for clone and alike

  //!> typedef for a vector of Vectors with inverse sorting to make lower_bound return present or last past step
  typedef std::map<unsigned int, Vector, std::greater<unsigned int> > VectorTrajectory_t;
  VectorTrajectory_t AtomicPosition;       //!< coordinate vector of atom, giving last position within cell
  VectorTrajectory_t AtomicVelocity;       //!< velocity vector of atom, giving last velocity within cell
  VectorTrajectory_t AtomicForce;       //!< Force vector of atom, giving last force within cell

  /** Helper function to avoid an interval of steps in VectorTrajectory_t.
   *
   * \param  _trajectory trajectory to remove in
   * \param _firststep first step in interval to be removed
   * \param _laststep last step in interval to be removed
   */
  static void eraseInTrajctory(
      VectorTrajectory_t &_trajectory,
      const unsigned int _firststep, const unsigned int _laststep);

private:
  atomicNumber_t AtomicElement;          //!< contains atomic number (i.e. Z of element) or "-1" if unset
  bool FixedIon;    //!< whether this nuclei is influenced by force integration or not
  double charge;    //!< charge of this nuclei
  std::string particlename; //!< name of associated Particle
};

std::ostream & operator << (std::ostream &ost, const AtomInfo &a);

//const AtomInfo& operator*=(AtomInfo& a, const double m);
//AtomInfo const operator*(const AtomInfo& a, const double m);
//AtomInfo const operator*(const double m, const AtomInfo& a);

#endif /* ATOM_ATOMINFO_HPP_ */