| 1 |
#ifndef _ATOM_H_ |
| 2 |
#define _ATOM_H_ |
| 3 |
|
| 4 |
#include <cstring> |
| 5 |
#include <cstdlib> |
| 6 |
#include <iostream> |
| 7 |
|
| 8 |
class Atom{ |
| 9 |
public: |
| 10 |
|
| 11 |
Atom(int theIndex); |
| 12 |
virtual ~Atom() {} |
| 13 |
|
| 14 |
static double* pos; // the position array |
| 15 |
static double* vel; // the velocity array |
| 16 |
static double* frc; // the forc array |
| 17 |
static double* trq; // the torque vector ( space fixed ) |
| 18 |
static double* Amat; // the rotation matrix |
| 19 |
static double* mu; // the dipole moment array |
| 20 |
static double* ul; // the lab frame unit directional vector |
| 21 |
static int nElements; |
| 22 |
|
| 23 |
static void createArrays (int the_nElements); |
| 24 |
static void destroyArrays(void); |
| 25 |
void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, |
| 26 |
double* Atrq, double* AAmat, double* Amu, |
| 27 |
double* Aul); |
| 28 |
void deleteAtom(int theIndex); |
| 29 |
void deleteRange(int startIndex, int stopIndex); |
| 30 |
|
| 31 |
static double* getPosArray( void ) { return pos; } |
| 32 |
static double* getVelArray( void ) { return vel; } |
| 33 |
static double* getFrcArray( void ) { return frc; } |
| 34 |
static double* getTrqArray( void ) { return trq; } |
| 35 |
static double* getAmatArray( void ) { return Amat; } |
| 36 |
static double* getMuArray( void ) { return mu; } |
| 37 |
static double* getUlArray( void ) { return ul; } |
| 38 |
|
| 39 |
void getPos( double theP[3] ); |
| 40 |
void setPos( double theP[3] ); |
| 41 |
|
| 42 |
double getX() const {return pos[offsetX];} |
| 43 |
double getY() const {return pos[offsetY];} |
| 44 |
double getZ() const {return pos[offsetZ];} |
| 45 |
void setX(double x) {pos[offsetX] = x;} |
| 46 |
void setY(double y) {pos[offsetY] = y;} |
| 47 |
void setZ(double z) {pos[offsetZ] = z;} |
| 48 |
|
| 49 |
void getVel( double theV[3] ); |
| 50 |
void setVel( double theV[3] ); |
| 51 |
|
| 52 |
double get_vx() const {return vel[offsetX];} |
| 53 |
double get_vy() const {return vel[offsetY];} |
| 54 |
double get_vz() const {return vel[offsetZ];} |
| 55 |
void set_vx(double vx) {vel[offsetX] = vx;} |
| 56 |
void set_vy(double vy) {vel[offsetY] = vy;} |
| 57 |
void set_vz(double vz) {vel[offsetZ] = vz;} |
| 58 |
|
| 59 |
|
| 60 |
void getFrc( double theF[3] ); |
| 61 |
void addFrc( double theF[3] ); |
| 62 |
|
| 63 |
double getFx() const {return frc[offsetX];} |
| 64 |
double getFy() const {return frc[offsetY];} |
| 65 |
double getFz() const {return frc[offsetZ];} |
| 66 |
void addFx(double add) {frc[offsetX] += add;} |
| 67 |
void addFy(double add) {frc[offsetY] += add;} |
| 68 |
void addFz(double add) {frc[offsetZ] += add;} |
| 69 |
virtual void zeroForces() = 0; |
| 70 |
|
| 71 |
double getMass() const {return c_mass;} |
| 72 |
void setMass(double mass) {c_mass = mass;} |
| 73 |
|
| 74 |
double getSigma() const {return c_sigma;} |
| 75 |
void setSigma(double sigma) {c_sigma = sigma;} |
| 76 |
|
| 77 |
double getEpslon() const {return c_epslon;} |
| 78 |
void setEpslon(double epslon) {c_epslon = epslon;} |
| 79 |
|
| 80 |
double getCovalent() const {return c_covalent;} |
| 81 |
void setCovalent(double covalent) {c_covalent = covalent;} |
| 82 |
|
| 83 |
int getIndex() const {return index;} |
| 84 |
void setIndex(int theIndex); |
| 85 |
char *getType() {return c_name;} |
| 86 |
void setType(char * name) {strcpy(c_name,name);} |
| 87 |
|
| 88 |
int getIdent( void ) { return ident; } |
| 89 |
void setIdent( int info ) { ident = info; } |
| 90 |
|
| 91 |
#ifdef IS_MPI |
| 92 |
int getGlobalIndex( void ) { return myGlobalIndex; } |
| 93 |
void setGlobalIndex( int info ) { myGlobalIndex = info; } |
| 94 |
#endif // is_mpi |
| 95 |
|
| 96 |
void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;} |
| 97 |
int get_n_hydrogens() const {return c_n_hyd;} |
| 98 |
|
| 99 |
void setHasDipole( int value ) { has_dipole = value; } |
| 100 |
int hasDipole( void ) { return has_dipole; } |
| 101 |
|
| 102 |
void setLJ( void ) { is_LJ = 1; is_VDW = 0; } |
| 103 |
int isLJ( void ) { return is_LJ; } |
| 104 |
|
| 105 |
void seVDW( void ) { is_VDW = 1; is_LJ = 0; } |
| 106 |
int isVDW( void ) { return is_VDW; } |
| 107 |
|
| 108 |
virtual int isDirectional( void ) = 0; |
| 109 |
|
| 110 |
|
| 111 |
protected: |
| 112 |
|
| 113 |
double c_mass; /* the mass of the atom in amu */ |
| 114 |
double c_sigma; /* the sigma parameter for van der walls interactions */ |
| 115 |
double c_epslon; /* the esplon parameter for VDW interactions */ |
| 116 |
double c_covalent; // The covalent radius of the atom. |
| 117 |
|
| 118 |
int index; /* set the atom's index */ |
| 119 |
int offset; // the atom's offset in the storage array |
| 120 |
int offsetX, offsetY, offsetZ; |
| 121 |
|
| 122 |
int Axx, Axy, Axz; // the rotational matrix indices |
| 123 |
int Ayx, Ayy, Ayz; |
| 124 |
int Azx, Azy, Azz; |
| 125 |
|
| 126 |
char c_name[100]; /* it's name */ |
| 127 |
int ident; // it's unique numeric identity. |
| 128 |
|
| 129 |
int c_n_hyd; // the number of hydrogens bonded to the atom |
| 130 |
|
| 131 |
int has_dipole; // dipole boolean |
| 132 |
int is_VDW; // VDW boolean |
| 133 |
int is_LJ; // LJ boolean |
| 134 |
|
| 135 |
#ifdef IS_MPI |
| 136 |
int myGlobalIndex; |
| 137 |
#endif |
| 138 |
|
| 139 |
}; |
| 140 |
|
| 141 |
class GeneralAtom : public Atom{ |
| 142 |
|
| 143 |
public: |
| 144 |
GeneralAtom(int theIndex): Atom(theIndex){} |
| 145 |
virtual ~GeneralAtom(){} |
| 146 |
|
| 147 |
int isDirectional( void ){ return 0; } |
| 148 |
void zeroForces() { |
| 149 |
frc[offsetX] = 0.0; |
| 150 |
frc[offsetY] = 0.0; |
| 151 |
frc[offsetZ] = 0.0; |
| 152 |
} |
| 153 |
}; |
| 154 |
|
| 155 |
class DirectionalAtom : public Atom { |
| 156 |
|
| 157 |
public: |
| 158 |
DirectionalAtom(int theIndex) : Atom(theIndex) |
| 159 |
{ |
| 160 |
ssdIdentity = 0; |
| 161 |
sux = 0.0; |
| 162 |
suy = 0.0; |
| 163 |
suz = 0.0; |
| 164 |
} |
| 165 |
virtual ~DirectionalAtom() {} |
| 166 |
|
| 167 |
void printAmatIndex( void ); |
| 168 |
|
| 169 |
int isDirectional(void) { return 1; } |
| 170 |
|
| 171 |
void setSSD( int value) { ssdIdentity = value; } |
| 172 |
int isSSD(void) {return ssdIdentity; } |
| 173 |
|
| 174 |
|
| 175 |
void setEuler( double phi, double theta, double psi ); |
| 176 |
|
| 177 |
double getSUx( void ) { return sux; } |
| 178 |
double getSUy( void ) { return suy; } |
| 179 |
double getSUz( void ) { return suz; } |
| 180 |
|
| 181 |
void setSUx( double the_sux ) { sux = the_sux; } |
| 182 |
void setSUy( double the_suy ) { suy = the_suy; } |
| 183 |
void setSUz( double the_suz ) { suz = the_suz; } |
| 184 |
|
| 185 |
void zeroForces() { |
| 186 |
frc[offsetX] = 0.0; |
| 187 |
frc[offsetY] = 0.0; |
| 188 |
frc[offsetZ] = 0.0; |
| 189 |
|
| 190 |
trq[offsetX] = 0.0; |
| 191 |
trq[offsetY] = 0.0; |
| 192 |
trq[offsetZ] = 0.0; |
| 193 |
} |
| 194 |
|
| 195 |
void getA( double the_A[3][3] ); // get the full rotation matrix |
| 196 |
void setA( double the_A[3][3] ); |
| 197 |
|
| 198 |
void getU( double the_u[3] ); // get the unit vetor |
| 199 |
void updateU( void ); |
| 200 |
|
| 201 |
void getQ( double the_q[4] ); // get the quanternions |
| 202 |
void setQ( double the_q[4] ); |
| 203 |
|
| 204 |
void getJ( double theJ[3] ); |
| 205 |
void setJ( double theJ[3] ); |
| 206 |
|
| 207 |
double getJx( void ) { return jx; } |
| 208 |
double getJy( void ) { return jy; } |
| 209 |
double getJz( void ) { return jz; } |
| 210 |
|
| 211 |
void setJx( double the_jx ) { jx = the_jx; } |
| 212 |
void setJy( double the_jy ) { jy = the_jy; } |
| 213 |
void setJz( double the_jz ) { jz = the_jz; } |
| 214 |
|
| 215 |
void getTrq( double theT[3] ); |
| 216 |
void addTrq( double theT[3] ); |
| 217 |
|
| 218 |
// double getTx( void ) { return trq[offsetX];} |
| 219 |
// double getTy( void ) { return trq[offsetY]; } |
| 220 |
// double getTz( void ) { return trq[offsetZ]; } |
| 221 |
|
| 222 |
void addTx( double the_tx ) { trq[offsetX] += the_tx;} |
| 223 |
void addTy( double the_ty ) { trq[offsetY] += the_ty;} |
| 224 |
void addTz( double the_tz ) { trq[offsetZ] += the_tz;} |
| 225 |
|
| 226 |
void setI( double the_I[3][3] ); |
| 227 |
void getI( double the_I[3][3] ); |
| 228 |
|
| 229 |
double getIxx( void ) { return Ixx; } |
| 230 |
double getIxy( void ) { return Ixy; } |
| 231 |
double getIxz( void ) { return Ixz; } |
| 232 |
|
| 233 |
double getIyx( void ) { return Iyx; } |
| 234 |
double getIyy( void ) { return Iyy; } |
| 235 |
double getIyz( void ) { return Iyz; } |
| 236 |
|
| 237 |
double getIzx( void ) { return Izx; } |
| 238 |
double getIzy( void ) { return Izy; } |
| 239 |
double getIzz( void ) { return Izz; } |
| 240 |
|
| 241 |
|
| 242 |
double getMu( void ) { return mu[index]; } |
| 243 |
void setMu( double the_mu ) { mu[index] = the_mu; } |
| 244 |
|
| 245 |
void lab2Body( double r[3] ); |
| 246 |
void body2Lab( double r[3] ); |
| 247 |
|
| 248 |
|
| 249 |
private: |
| 250 |
int dIndex; |
| 251 |
|
| 252 |
double sux, suy, suz; // the standard unit vector ( body fixed ) |
| 253 |
double jx, jy, jz; // the angular momentum vector ( body fixed ) |
| 254 |
|
| 255 |
double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed ) |
| 256 |
double Iyx, Iyy, Iyz; |
| 257 |
double Izx, Izy, Izz; |
| 258 |
|
| 259 |
int ssdIdentity; // boolean of whether atom is ssd |
| 260 |
|
| 261 |
}; |
| 262 |
|
| 263 |
#endif |
