A.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file Atom.hpp
 * @author    tlin
 * @date  10/22/2004
 * @version 1.0
 */ 
 
#ifndef PRIMITIVES_ATOM_HPP
#define PRIMITIVES_ATOM_HPP
 
#include "primitives/StuntDouble.hpp"
#include "types/AtomType.hpp"
 
namespace OpenMD{
  class Atom : public StuntDouble {
 
    typedef enum {
      UNSPECIFIED = 0,  //!< hybridization that hasn't been specified
      s,
      sp,
      sp2,
      sp3,
      sp3d,
      sp3d2,
      OTHER  //!< unrecognized hybridization
    } HybridizationType;
    
  public:
    Atom(AtomType* at);
    
    virtual std::string getType() {return atomType_->getName();}
    
    /**
     * Returns the inertia tensor of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     */ 
    virtual Mat3x3d getI();
    
    /**
     * Returns the gradient of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     */ 
    virtual std::vector<RealType> getGrad();
    
    virtual void accept(BaseVisitor* v);
    
    /** 
     * Returns the AtomType of this Atom.
     * @return the atom type of this atom
     */
    AtomType* getAtomType() {
      return atomType_;
    }
    
    //forward  functions of AtomType class
    bool isCharge()  {
      return atomType_->isCharge(); 
    }
    
    bool isDirectional() {
      return atomType_->isDirectional(); 
    }
    
    bool isDipole()  { 
      return atomType_->isDipole(); 
    }
    
    bool isMultipole()  { 
      return atomType_->isMultipole(); 
    }
    
    bool isGayBerne()  {
      return atomType_->isGayBerne(); 
    }
            
    bool isSticky()  { 
      return atomType_->isSticky(); 
    }
 
    bool isShape()  { 
      return atomType_->isShape(); 
    }            
    
    bool isMetal() {
      return atomType_->isMetal();
    }
 
    bool isFluctuatingCharge() {
      return atomType_->isFluctuatingCharge();
    }
 
    int getIdent() {
      return atomType_->getIdent();
    }
    
    RealType getChargeMass() {
      return chargeMass_;
    }
 
    void setChargeMass(RealType cm) {
      chargeMass_ = cm;
    }
 
    //! sets our hybridization
    void setHybridization(HybridizationType what) { hyb_ = what; };
    //! returns our hybridization
    HybridizationType getHybridization() const {
      return static_cast<HybridizationType>(hyb_);
    };
    
  protected:
    AtomType* atomType_;
    RealType chargeMass_;
    unsigned int hyb_;
  };
  
}//namespace OpenMD
 
#endif //PRIMITIVES_ATOM_HPP