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#ifndef _ATOM_H_ |
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#define _ATOM_H_ |
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#include <cstring> |
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#include <cstdlib> |
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#include <iostream> |
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class Atom{ |
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public: |
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|
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Atom(int theIndex); |
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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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|
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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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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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void setMass(double mass) {c_mass = mass;} |
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double getEamRcut() const {return myEamRcut;} |
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void setEamRcut(double eamRcut) {myEamRcut = eamRcut;} |
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double getSigma() const {return c_sigma;} |
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void setSigma(double sigma) {c_sigma = sigma;} |
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double getEpslon() const {return c_epslon;} |
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void setEpslon(double epslon) {c_epslon = epslon;} |
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double getCovalent() const {return c_covalent;} |
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void setCovalent(double covalent) {c_covalent = covalent;} |
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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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#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 set_n_hydrogens( int n_h ) {c_n_hyd = n_h;} |
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int get_n_hydrogens() const {return c_n_hyd;} |
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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 setLJ( void ) { is_LJ = 1; is_VDW = 0; } |
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int isLJ( void ) { return is_LJ; } |
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void seVDW( void ) { is_VDW = 1; is_LJ = 0; } |
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int isVDW( void ) { return is_VDW; } |
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void setEAM( void ) { is_EAM = 1; } |
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int isEAM( void ) { return is_EAM; } |
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virtual int isDirectional( void ) = 0; |
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protected: |
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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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double c_covalent; // The covalent radius of the atom. |
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double myEamRcut; // Atom rcut for eam defined by the forcefield. |
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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 c_n_hyd; // the number of hydrogens bonded to the atom |
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int has_dipole; // dipole boolean |
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int is_VDW; // VDW boolean |
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int is_LJ; // LJ boolean |
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int is_EAM; //EAM boolean |
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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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class GeneralAtom : public Atom{ |
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public: |
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GeneralAtom(int theIndex): Atom(theIndex){} |
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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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}; |
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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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{ |
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ssdIdentity = 0; |
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sux = 0.0; |
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suy = 0.0; |
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suz = 0.0; |
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} |
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virtual ~DirectionalAtom() {} |
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void printAmatIndex( void ); |
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int isDirectional(void) { return 1; } |
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void setSSD( int value) { ssdIdentity = value; } |
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int isSSD(void) {return ssdIdentity; } |
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void setEuler( double phi, double theta, double psi ); |
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double getSUx( void ) { return sux; } |
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double getSUy( void ) { return suy; } |
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double getSUz( void ) { return suz; } |
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void setSUx( double the_sux ) { sux = the_sux; } |
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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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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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void getU( double the_u[3] ); // get the unit vetor |
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void updateU( void ); |
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void getQ( double the_q[4] ); // get the quanternions |
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void setQ( double the_q[4] ); |
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void getJ( double theJ[3] ); |
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void setJ( double theJ[3] ); |
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double getJx( void ) { return jx; } |
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double getJy( void ) { return jy; } |
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double getJz( void ) { return jz; } |
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void setJx( double the_jx ) { jx = the_jx; } |
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void setJy( double the_jy ) { jy = the_jy; } |
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void setJz( double the_jz ) { jz = the_jz; } |
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void getTrq( double theT[3] ); |
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void addTrq( double theT[3] ); |
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// double getTx( void ) { return trq[offsetX];} |
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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 getIxx( void ) { return Ixx; } |
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double getIxy( void ) { return Ixy; } |
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double getIxz( void ) { return Ixz; } |
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double getIyx( void ) { return Iyx; } |
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double getIyy( void ) { return Iyy; } |
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double getIyz( void ) { return Iyz; } |
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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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void lab2Body( double r[3] ); |
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void body2Lab( double r[3] ); |
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private: |
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int dIndex; |
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double sux, suy, suz; // the standard unit vector ( body fixed ) |
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double jx, jy, jz; // the angular momentum vector ( body fixed ) |
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double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed ) |
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double Iyx, Iyy, Iyz; |
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double Izx, Izy, Izz; |
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int ssdIdentity; // boolean of whether atom is ssd |
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}; |
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#endif |
