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