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#include <cstdlib> |
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#include <iostream> |
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#include "SimState.hpp" |
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class Atom{ |
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public: |
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Atom(int theIndex); |
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Atom(int theIndex, SimState* theConfig ); |
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virtual ~Atom() {} |
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static double* pos; // the position array |
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static double* vel; // the velocity array |
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static double* frc; // the forc array |
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static double* trq; // the torque vector ( space fixed ) |
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static double* Amat; // the rotation matrix |
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static double* mu; // the dipole moment array |
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static double* ul; // the lab frame unit directional vector |
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static int nElements; |
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void setCoords(void); |
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static void createArrays (int the_nElements); |
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static void destroyArrays(void); |
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void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, |
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double* Atrq, double* AAmat, double* Amu, |
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double* Aul); |
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void deleteAtom(int theIndex); |
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void deleteRange(int startIndex, int stopIndex); |
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// void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, |
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// double* Atrq, double* AAmat, double* Amu, |
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// double* Aul); |
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// void deleteAtom(int theIndex); |
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// void deleteRange(int startIndex, int stopIndex); |
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static double* getPosArray( void ) { return pos; } |
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static double* getVelArray( void ) { return vel; } |
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static double* getFrcArray( void ) { return frc; } |
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static double* getTrqArray( void ) { return trq; } |
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static double* getAmatArray( void ) { return Amat; } |
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static double* getMuArray( void ) { return mu; } |
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static double* getUlArray( void ) { return ul; } |
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void getPos( double theP[3] ); |
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void setPos( double theP[3] ); |
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double getX() const {return pos[offsetX];} |
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double getY() const {return pos[offsetY];} |
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double getZ() const {return pos[offsetZ];} |
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void setX(double x) {pos[offsetX] = x;} |
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void setY(double y) {pos[offsetY] = y;} |
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void setZ(double z) {pos[offsetZ] = z;} |
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void getVel( double theV[3] ); |
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void setVel( double theV[3] ); |
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double get_vx() const {return vel[offsetX];} |
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double get_vy() const {return vel[offsetY];} |
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double get_vz() const {return vel[offsetZ];} |
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void set_vx(double vx) {vel[offsetX] = vx;} |
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void set_vy(double vy) {vel[offsetY] = vy;} |
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void set_vz(double vz) {vel[offsetZ] = vz;} |
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void getFrc( double theF[3] ); |
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void addFrc( double theF[3] ); |
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double getFx() const {return frc[offsetX];} |
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double getFy() const {return frc[offsetY];} |
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double getFz() const {return frc[offsetZ];} |
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void addFx(double add) {frc[offsetX] += add;} |
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void addFy(double add) {frc[offsetY] += add;} |
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void addFz(double add) {frc[offsetZ] += add;} |
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virtual void zeroForces() = 0; |
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double getMass() const {return c_mass;} |
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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 c_mass; /* the mass of the atom in amu */ |
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double c_sigma; /* the sigma parameter for van der walls interactions */ |
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double c_epslon; /* the esplon parameter for VDW interactions */ |
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int is_LJ; // LJ boolean |
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int is_EAM; //EAM 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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class GeneralAtom : public Atom{ |
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public: |
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GeneralAtom(int theIndex): Atom(theIndex){} |
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GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){} |
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virtual ~GeneralAtom(){} |
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int isDirectional( void ){ return 0; } |
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void zeroForces() { |
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frc[offsetX] = 0.0; |
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frc[offsetY] = 0.0; |
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frc[offsetZ] = 0.0; |
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} |
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void zeroForces( void ); |
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}; |
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class DirectionalAtom : public Atom { |
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public: |
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DirectionalAtom(int theIndex) : Atom(theIndex) |
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DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex, |
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theConfig) |
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{ |
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ssdIdentity = 0; |
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sux = 0.0; |
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void setSUy( double the_suy ) { suy = the_suy; } |
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void setSUz( double the_suz ) { suz = the_suz; } |
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void zeroForces() { |
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frc[offsetX] = 0.0; |
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frc[offsetY] = 0.0; |
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frc[offsetZ] = 0.0; |
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void zeroForces(); |
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trq[offsetX] = 0.0; |
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trq[offsetY] = 0.0; |
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trq[offsetZ] = 0.0; |
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} |
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void getA( double the_A[3][3] ); // get the full rotation matrix |
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void setA( double the_A[3][3] ); |
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// double getTy( void ) { return trq[offsetY]; } |
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// double getTz( void ) { return trq[offsetZ]; } |
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void addTx( double the_tx ) { trq[offsetX] += the_tx;} |
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void addTy( double the_ty ) { trq[offsetY] += the_ty;} |
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void addTz( double the_tz ) { trq[offsetZ] += the_tz;} |
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void setI( double the_I[3][3] ); |
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void getI( double the_I[3][3] ); |
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double getIzx( void ) { return Izx; } |
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double getIzy( void ) { return Izy; } |
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double getIzz( void ) { return Izz; } |
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double getMu( void ) { return mu[index]; } |
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void setMu( double the_mu ) { mu[index] = the_mu; } |
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double getMu( void ); |
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void setMu( double the_mu ); |
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void lab2Body( double r[3] ); |
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void body2Lab( double r[3] ); |