| 1 |
#ifndef _ATOM_H_ |
| 2 |
#define _ATOM_H_ |
| 3 |
|
| 4 |
#include <string.h> |
| 5 |
#include <stdlib.h> |
| 6 |
#include <iostream> |
| 7 |
|
| 8 |
#include "SimState.hpp" |
| 9 |
#include "StuntDouble.hpp" |
| 10 |
#include "BaseVisitor.hpp" |
| 11 |
|
| 12 |
class Atom : public StuntDouble { |
| 13 |
public: |
| 14 |
|
| 15 |
Atom(int theIndex, SimState* theConfig ); |
| 16 |
virtual ~Atom() {} |
| 17 |
|
| 18 |
virtual void setCoords(void); |
| 19 |
|
| 20 |
void getPos( double theP[3] ); |
| 21 |
void setPos( double theP[3] ); |
| 22 |
|
| 23 |
void getVel( double theV[3] ); |
| 24 |
void setVel( double theV[3] ); |
| 25 |
|
| 26 |
void getFrc( double theF[3] ); |
| 27 |
void setFrc( double theF[3] ); |
| 28 |
void addFrc( double theF[3] ); |
| 29 |
|
| 30 |
virtual void zeroForces(); |
| 31 |
|
| 32 |
double getMass() {return c_mass;} |
| 33 |
void setMass(double mass) {c_mass = mass;} |
| 34 |
|
| 35 |
int getIndex() const {return index;} |
| 36 |
void setIndex(int theIndex); |
| 37 |
|
| 38 |
char *getType() {return c_name;} |
| 39 |
void setType(char * name) {strcpy(c_name,name);} |
| 40 |
|
| 41 |
int getIdent( void ) { return ident; } |
| 42 |
void setIdent( int info ) { ident = info; } |
| 43 |
|
| 44 |
#ifdef IS_MPI |
| 45 |
int getGlobalIndex( void ) { return myGlobalIndex; } |
| 46 |
void setGlobalIndex( int info ) { myGlobalIndex = info; } |
| 47 |
#endif // is_mpi |
| 48 |
|
| 49 |
void setHasDipole( int value ) { has_dipole = value; } |
| 50 |
int hasDipole( void ) { return has_dipole; } |
| 51 |
|
| 52 |
void setHasCharge(int value) {has_charge = value;} |
| 53 |
int hasCharge(void) {return has_charge;} |
| 54 |
|
| 55 |
|
| 56 |
virtual void accept(BaseVisitor* v) {v->visit(this);} |
| 57 |
|
| 58 |
protected: |
| 59 |
|
| 60 |
SimState* myConfig; |
| 61 |
|
| 62 |
double* pos; // the position array |
| 63 |
double* vel; // the velocity array |
| 64 |
double* frc; // the forc array |
| 65 |
double* trq; // the torque vector ( space fixed ) |
| 66 |
double* Amat; // the rotation matrix |
| 67 |
double* mu; // the array of dipole moments |
| 68 |
double* ul; // the lab frame unit directional vector |
| 69 |
double* quat; // the quaternion array |
| 70 |
|
| 71 |
double zAngle; // the rotation about the z-axis ( body-fixed ) |
| 72 |
|
| 73 |
double c_mass; /* the mass of the atom in amu */ |
| 74 |
|
| 75 |
int index; /* set the atom's index */ |
| 76 |
int offset; // the atom's offset in the storage array |
| 77 |
int offsetX, offsetY, offsetZ; |
| 78 |
|
| 79 |
int Axx, Axy, Axz; // the rotational matrix indices |
| 80 |
int Ayx, Ayy, Ayz; |
| 81 |
int Azx, Azy, Azz; |
| 82 |
|
| 83 |
char c_name[100]; /* it's name */ |
| 84 |
int ident; // it's unique numeric identity. |
| 85 |
|
| 86 |
int has_dipole; // dipole boolean |
| 87 |
int has_charge; // charge boolean |
| 88 |
|
| 89 |
bool hasCoords; |
| 90 |
|
| 91 |
#ifdef IS_MPI |
| 92 |
int myGlobalIndex; |
| 93 |
#endif |
| 94 |
|
| 95 |
}; |
| 96 |
|
| 97 |
#endif |
