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root/group/trunk/mdtools/headers/Atom.hpp
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Comparing trunk/mdtools/headers/Atom.hpp (file contents):
Revision 134 by chuckv, Fri Oct 11 15:09:09 2002 UTC vs.
Revision 143 by mmeineke, Thu Oct 17 21:58:55 2002 UTC

# Line 6 | Line 6 | class Atom{ (public)
6  
7   class Atom{
8   public:
9 <  Atom() {
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 c_x;}
32 <  double getY() const {return c_y;}
33 <  double getZ() const {return c_z;}
34 <  void setX(double x) {c_x = x;}
35 <  void setY(double y) {c_y = y;}
36 <  void setZ(double z) {c_z = z;}
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 c_vx;}
39 <  double get_vy() const {return c_vy;}
40 <  double get_vz() const {return c_vz;}
41 <  void set_vx(double vx) {c_vx = vx;}
42 <  void set_vy(double vy) {c_vy = vy;}
43 <  void set_vz(double vz) {c_vz = vz;}
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 c_Fx;}
46 <  double getFy() const {return c_Fy;}
47 <  double getFz() const {return c_Fz;}
48 <  void addFx(double add) {c_Fx += add;}
49 <  void addFy(double add) {c_Fy += add;}
50 <  void addFz(double add) {c_Fz += add;}
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;}
# Line 48 | Line 62 | class Atom{ (public)
62    double getCovalent() const {return c_covalent;}
63    void setCovalent(double covalent) {c_covalent = covalent;}
64    
65 <  int getIndex() const {return c_index;}
66 <  void setIndex(int index) {c_index = index;}
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);}
# Line 69 | Line 83 | class Atom{ (public)
83    virtual int isDirectional( void ) = 0;
84  
85   protected:
72 –  double c_x; /*the atom's position */
73 –  double c_y;
74 –  double c_z;
75 –            
76 –  double c_vx; /*the atom's velocity */
77 –  double c_vy;
78 –  double c_vz;
79 –            
80 –  double c_Fx; /* the atom's forces */
81 –  double c_Fy;
82 –  double c_Fz;
86    
87 +  static double* pos; // the position array
88 +  static double* vel; // the velocity array
89 +  static double* frc; // the forc array
90 +  static double* trq; // the torque vector  ( space fixed )
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 c_index; /* set the atom's index */
97 >  int index; /* set the atom's index */
98  
99    char c_name[100]; /* it's name */
100  
# Line 101 | Line 109 | class GeneralAtom : public Atom{ (public)
109   class GeneralAtom : public Atom{
110  
111   public:
112 <  GeneralAtom(){}
112 >  GeneralAtom(int theIndex): Atom(theIndex){}
113    virtual ~GeneralAtom(){}
114  
115    int isDirectional( void ){ return 0; }
116    void zeroForces() {
117 <    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
117 >    frc[3*index]   = 0.0;
118 >    frc[3*index+1] = 0.0;
119 >    frc[3*index+2] = 0.0;
120    }
121   };
122  
123   class DirectionalAtom : public Atom {
124    
125   public:
126 <  DirectionalAtom() { ssdIdentity = 0; }
126 >  DirectionalAtom(int theIndex) : Atom(theIndex)
127 >  {
128 >    ssdIdentity = 0;
129 >  }
130    virtual ~DirectionalAtom() {}
131  
132 +  static void createDArrays(int nElements){
133 +    trq = new double[nElements*3];
134 +  }
135 +  static void destroyDArrays(void){
136 +    delete[] trq;
137 +  }
138 +
139    int isDirectional(void) { return 1; }
140    
141    void setSSD( int value) { ssdIdentity = value; }
# Line 137 | Line 157 | class DirectionalAtom : public Atom { (public)
157    void setJy( double the_jy ) { jy = the_jy; }
158    void setJz( double the_jz ) { jz = the_jz; }
159      
160 <  void addTx( double the_tx ) { tx += the_tx;}
161 <  void addTy( double the_ty ) { ty += the_ty;}
162 <  void addTz( double the_tz ) { tz += the_tz;}
160 >  void addTx( double the_tx ) { trq[3*index]   += the_tx;}
161 >  void addTy( double the_ty ) { trq[3*index+1] += the_ty;}
162 >  void addTz( double the_tz ) { trq[3*index+2] += the_tz;}
163  
164    void setMu( double the_mu ) { mu = the_mu; }
165  
166    void zeroForces() {
167 <    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
168 <    tx = 0.0; ty = 0.0; tz = 0.0;
167 >    frc[3*index]   = 0.0;
168 >    frc[3*index+1] = 0.0;
169 >    frc[3*index+2] = 0.0;
170 >
171 >    trq[3*index]   = 0.0;
172 >    trq[3*index+1] = 0.0;
173 >    trq[3*index+2] = 0.0;
174    }
175  
176    double getAxx( void ) { return Axx; }
# Line 173 | Line 198 | class DirectionalAtom : public Atom { (public)
198    double getJy( void ) { return jy; }
199    double getJz( void ) { return jz; }
200  
201 <  double getTx( void ) { return tx; }
202 <  double getTy( void ) { return ty; }
203 <  double getTz( void ) { return tz; }
201 >  double getTx( void ) { return trq[3*index];}
202 >  double getTy( void ) { return trq[3*index+1]; }
203 >  double getTz( void ) { return trq[3*index+2]; }
204  
205    double getIxx( void ) { return Ixx; }
206    double getIxy( void ) { return Ixy; }
# Line 195 | Line 220 | class DirectionalAtom : public Atom { (public)
220    void body2Lab( double r[3] );
221  
222   private:
223 +  int dIndex;
224  
225    double Axx, Axy, Axz; // the rotational matrix
226    double Ayx, Ayy, Ayz;
227    double Azx, Azy, Azz;
228  
229 <  double sux, suy, suz; // the standard unit vector ( body fixed )
230 <  double jx, jy, jz; // the angular momentum vector ( body fixed )
205 <  double tx, ty, tz; // the torque vector           ( space fixed )
229 >  double sux, suy, suz; // the standard unit vector    ( body fixed )
230 >  double jx, jy, jz;    // the angular momentum vector ( body fixed )
231    
232 <  double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
232 >  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
233    double Iyx, Iyy, Iyz;
234    double Izx, Izy, Izz;
235  

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