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#ifndef _ATOM_H_ |
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#define _ATOM_H_ |
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#include <string.h> |
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#include <stdlib.h> |
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#include <iostream> |
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#include "SimState.hpp" |
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#include "StuntDouble.hpp" |
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#include "BaseVisitor.hpp" |
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class Atom : public StuntDouble { |
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public: |
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Atom(int theIndex, SimState* theConfig ); |
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virtual ~Atom() {} |
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virtual void setCoords(void); |
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void getPos( double theP[3] ); |
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void setPos( double theP[3] ); |
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void getVel( double theV[3] ); |
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void setVel( double theV[3] ); |
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void getFrc( double theF[3] ); |
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void addFrc( double theF[3] ); |
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virtual void zeroForces(); |
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double getMass() {return c_mass;} |
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void setMass(double mass) {c_mass = mass;} |
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int getIndex() const {return index;} |
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void setIndex(int theIndex); |
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char *getType() {return c_name;} |
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void setType(char * name) {strcpy(c_name,name);} |
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int getIdent( void ) { return ident; } |
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void setIdent( int info ) { ident = info; } |
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void getRc(double theRc[3]); |
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void setRc(double theRc[3]); |
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double getMassRatio() { return *massRatio;} |
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void setMassRatio(double theMassRatio) { *massRatio = theMassRatio;} |
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#ifdef IS_MPI |
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int getGlobalIndex( void ) { return myGlobalIndex; } |
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void setGlobalIndex( int info ) { myGlobalIndex = info; } |
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#endif // is_mpi |
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void setHasDipole( int value ) { has_dipole = value; } |
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int hasDipole( void ) { return has_dipole; } |
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void setHasCharge(int value) {has_charge = value;} |
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int hasCharge(void) {return has_charge;} |
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virtual void accept(BaseVisitor* v) {v->visit(this);} |
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protected: |
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SimState* myConfig; |
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double* pos; // the position array |
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double* vel; // the velocity array |
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double* frc; // the forc array |
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double* trq; // the torque vector ( space fixed ) |
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double* Amat; // the rotation matrix |
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double* mu; // the array of dipole moments |
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double* ul; // the lab frame unit directional vector |
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double* rc; //the center of mass of the molecule |
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double* massRatio; //the ratio of this atom to the total mass of the molecule |
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double c_mass; /* the mass of the atom in amu */ |
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int index; /* set the atom's index */ |
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int offset; // the atom's offset in the storage array |
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int offsetX, offsetY, offsetZ; |
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int Axx, Axy, Axz; // the rotational matrix indices |
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int Ayx, Ayy, Ayz; |
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int Azx, Azy, Azz; |
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char c_name[100]; /* it's name */ |
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int ident; // it's unique numeric identity. |
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int has_dipole; // dipole boolean |
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int has_charge; // charge boolean |
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bool hasCoords; |
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#ifdef IS_MPI |
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int myGlobalIndex; |
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#endif |
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}; |
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#endif |
