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root/group/trunk/mdtools/headers/Atom.hpp
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Comparing trunk/mdtools/headers/Atom.hpp (file contents):
Revision 143 by mmeineke, Thu Oct 17 21:58:55 2002 UTC vs.
Revision 213 by mmeineke, Mon Dec 16 21:42:11 2002 UTC

# Line 12 | Line 12 | class Atom{ (public)
12      is_VDW = 0;
13      is_LJ = 0;
14      index = theIndex;
15 +    offset = 3 * index;
16 +    offsetX = offset;
17 +    offsetY = offset+1;
18 +    offsetZ = offset+2;
19    }
20    virtual ~Atom() {}
21  
# Line 28 | Line 32 | class Atom{ (public)
32      delete[] trq;
33    }
34    
35 <  double getX() const {return pos[3*index];}
36 <  double getY() const {return pos[3*index+1];}
37 <  double getZ() const {return pos[3*index+2];}
38 <  void setX(double x) {pos[3*index]   = x;}
39 <  void setY(double y) {pos[3*index+1] = y;}
40 <  void setZ(double z) {pos[3*index+2] = z;}
35 >  double getX() const {return pos[offsetX];}
36 >  double getY() const {return pos[offsetY];}
37 >  double getZ() const {return pos[offsetZ];}
38 >  void setX(double x) {pos[offsetX]   = x;}
39 >  void setY(double y) {pos[offsetY] = y;}
40 >  void setZ(double z) {pos[offsetZ] = z;}
41    
42 <  double get_vx() const  {return vel[3*index];}
43 <  double get_vy() const  {return vel[3*index+1];}
44 <  double get_vz() const  {return vel[3*index+2];}
45 <  void set_vx(double vx) {vel[3*index]   = vx;}
46 <  void set_vy(double vy) {vel[3*index+1] = vy;}
47 <  void set_vz(double vz) {vel[3*index+2] = vz;}
42 >  double get_vx() const  {return vel[offsetX];}
43 >  double get_vy() const  {return vel[offsetY];}
44 >  double get_vz() const  {return vel[offsetZ];}
45 >  void set_vx(double vx) {vel[offsetX]   = vx;}
46 >  void set_vy(double vy) {vel[offsetY] = vy;}
47 >  void set_vz(double vz) {vel[offsetZ] = vz;}
48    
49 <  double getFx() const   {return frc[3*index];}
50 <  double getFy() const   {return frc[3*index+1];}
51 <  double getFz() const   {return frc[3*index+2];}
52 <  void addFx(double add) {frc[3*index]   += add;}
53 <  void addFy(double add) {frc[3*index+1] += add;}
54 <  void addFz(double add) {frc[3*index+2] += add;}
49 >  double getFx() const   {return frc[offsetX];}
50 >  double getFy() const   {return frc[offsetY];}
51 >  double getFz() const   {return frc[offsetZ];}
52 >  void addFx(double add) {frc[offsetX]   += add;}
53 >  void addFy(double add) {frc[offsetY] += add;}
54 >  void addFz(double add) {frc[offsetZ] += add;}
55    virtual void zeroForces() = 0;
56  
57    double getMass() const {return c_mass;}
# Line 63 | Line 67 | class Atom{ (public)
67    void setCovalent(double covalent) {c_covalent = covalent;}
68    
69    int getIndex() const {return index;}
70 <  void setIndex(int theIndex) {index = theIndex;}
71 <  
70 >  void setIndex(int theIndex) {
71 >    index = theIndex;
72 >    offset = index*3;
73 >    offsetX = offset;
74 >    offsetY = offset+1;
75 >    offsetZ = offset+2;
76 >  }
77 >
78    char *getType() {return c_name;}
79    void setType(char * name) {strcpy(c_name,name);}
80  
# Line 82 | Line 92 | class Atom{ (public)
92  
93    virtual int isDirectional( void ) = 0;
94  
85 – protected:
86 –  
95    static double* pos; // the position array
96    static double* vel; // the velocity array
97    static double* frc; // the forc array
98    static double* trq; // the torque vector  ( space fixed )
99  
100 + protected:
101 +  
102    double c_mass; /* the mass of the atom in amu */
103    double c_sigma; /* the sigma parameter for van der walls interactions */
104    double c_epslon; /* the esplon parameter for VDW interactions */
105    double c_covalent; // The covalent radius of the atom.
106  
107    int index; /* set the atom's index */
108 +  int offset; // the atom's offset in the storage array
109 +  int offsetX, offsetY, offsetZ;
110  
111    char c_name[100]; /* it's name */
112  
# Line 106 | Line 118 | class Atom{ (public)
118    
119   };
120  
121 +
122 +
123   class GeneralAtom : public Atom{
124  
125   public:
# Line 114 | Line 128 | class GeneralAtom : public Atom{ (public)
128  
129    int isDirectional( void ){ return 0; }
130    void zeroForces() {
131 <    frc[3*index]   = 0.0;
132 <    frc[3*index+1] = 0.0;
133 <    frc[3*index+2] = 0.0;
131 >    frc[offsetX]   = 0.0;
132 >    frc[offsetY] = 0.0;
133 >    frc[offsetZ] = 0.0;
134    }
135   };
136  
# Line 157 | Line 171 | class DirectionalAtom : public Atom { (public)
171    void setJy( double the_jy ) { jy = the_jy; }
172    void setJz( double the_jz ) { jz = the_jz; }
173      
174 <  void addTx( double the_tx ) { trq[3*index]   += the_tx;}
175 <  void addTy( double the_ty ) { trq[3*index+1] += the_ty;}
176 <  void addTz( double the_tz ) { trq[3*index+2] += the_tz;}
174 >  void addTx( double the_tx ) { trq[offsetX]   += the_tx;}
175 >  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
176 >  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
177  
178    void setMu( double the_mu ) { mu = the_mu; }
179  
180    void zeroForces() {
181 <    frc[3*index]   = 0.0;
182 <    frc[3*index+1] = 0.0;
183 <    frc[3*index+2] = 0.0;
181 >    frc[offsetX]   = 0.0;
182 >    frc[offsetY] = 0.0;
183 >    frc[offsetZ] = 0.0;
184  
185 <    trq[3*index]   = 0.0;
186 <    trq[3*index+1] = 0.0;
187 <    trq[3*index+2] = 0.0;
185 >    trq[offsetX]   = 0.0;
186 >    trq[offsetY] = 0.0;
187 >    trq[offsetZ] = 0.0;
188    }
189  
190    double getAxx( void ) { return Axx; }
# Line 198 | Line 212 | class DirectionalAtom : public Atom { (public)
212    double getJy( void ) { return jy; }
213    double getJz( void ) { return jz; }
214  
215 <  double getTx( void ) { return trq[3*index];}
216 <  double getTy( void ) { return trq[3*index+1]; }
217 <  double getTz( void ) { return trq[3*index+2]; }
215 >  double getTx( void ) { return trq[offsetX];}
216 >  double getTy( void ) { return trq[offsetY]; }
217 >  double getTz( void ) { return trq[offsetZ]; }
218  
219    double getIxx( void ) { return Ixx; }
220    double getIxy( void ) { return Ixy; }

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