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Comparing trunk/mdtools/headers/Atom.hpp (file contents):
Revision 117 by mmeineke, Tue Sep 24 22:10:55 2002 UTC vs.
Revision 189 by mmeineke, Tue Nov 26 21:04:43 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 +    offset = 3 * index;
16    }
17    virtual ~Atom() {}
18 +
19 +  static void createArrays (int nElements) {
20 +    pos = new double[nElements*3];
21 +    vel = new double[nElements*3];
22 +    frc = new double[nElements*3];
23 +    trq = new double[nElements*3];
24 +  }
25 +  static void destroyArrays(void) {
26 +    delete[] pos;
27 +    delete[] vel;
28 +    delete[] frc;
29 +    delete[] trq;
30 +  }
31    
32 <  double getX() const {return c_x;}
33 <  double getY() const {return c_y;}
34 <  double getZ() const {return c_z;}
35 <  void setX(double x) {c_x = x;}
36 <  void setY(double y) {c_y = y;}
37 <  void setZ(double z) {c_z = z;}
32 >  double getX() const {return pos[offset];}
33 >  double getY() const {return pos[offset+1];}
34 >  double getZ() const {return pos[offset+2];}
35 >  void setX(double x) {pos[offset]   = x;}
36 >  void setY(double y) {pos[offset+1] = y;}
37 >  void setZ(double z) {pos[offset+2] = z;}
38    
39 <  double get_vx() const {return c_vx;}
40 <  double get_vy() const {return c_vy;}
41 <  double get_vz() const {return c_vz;}
42 <  void set_vx(double vx) {c_vx = vx;}
43 <  void set_vy(double vy) {c_vy = vy;}
44 <  void set_vz(double vz) {c_vz = vz;}
39 >  double get_vx() const  {return vel[offset];}
40 >  double get_vy() const  {return vel[offset+1];}
41 >  double get_vz() const  {return vel[offset+2];}
42 >  void set_vx(double vx) {vel[offset]   = vx;}
43 >  void set_vy(double vy) {vel[offset+1] = vy;}
44 >  void set_vz(double vz) {vel[offset+2] = vz;}
45    
46 <  double getFx() const {return c_Fx;}
47 <  double getFy() const {return c_Fy;}
48 <  double getFz() const {return c_Fz;}
49 <  void addFx(double add) {c_Fx += add;}
50 <  void addFy(double add) {c_Fy += add;}
51 <  void addFz(double add) {c_Fz += add;}
46 >  double getFx() const   {return frc[offset];}
47 >  double getFy() const   {return frc[offset+1];}
48 >  double getFz() const   {return frc[offset+2];}
49 >  void addFx(double add) {frc[offset]   += add;}
50 >  void addFy(double add) {frc[offset+1] += add;}
51 >  void addFz(double add) {frc[offset+2] += add;}
52    virtual void zeroForces() = 0;
53  
54    double getMass() const {return c_mass;}
# Line 48 | Line 63 | class Atom{ (public)
63    double getCovalent() const {return c_covalent;}
64    void setCovalent(double covalent) {c_covalent = covalent;}
65    
66 <  int getIndex() const {return c_index;}
67 <  void setIndex(int index) {c_index = index;}
66 >  int getIndex() const {return index;}
67 >  void setIndex(int theIndex) {index = theIndex; offset = index*3;}
68    
69    char *getType() {return c_name;}
70    void setType(char * name) {strcpy(c_name,name);}
# Line 58 | Line 73 | class Atom{ (public)
73    int get_n_hydrogens() const {return c_n_hyd;}
74  
75    void setHasDipole( int value ) { has_dipole = value; }
76 <  short int hasDipole( void ) { return has_dipole; }
76 >  int hasDipole( void ) { return has_dipole; }
77  
78    void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
79 <  short int isLJ( void )    { return is_LJ; }
79 >  int isLJ( void )    { return is_LJ; }
80  
81    void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
82 <  short int isVDW( void )    { return is_VDW; }
82 >  int isVDW( void )    { return is_VDW; }
83  
84    virtual int isDirectional( void ) = 0;
85  
86 +  static double* pos; // the position array
87 +  static double* vel; // the velocity array
88 +  static double* frc; // the forc array
89 +  static double* trq; // the torque vector  ( space fixed )
90 +
91   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;
92    
93    double c_mass; /* the mass of the atom in amu */
94    double c_sigma; /* the sigma parameter for van der walls interactions */
95    double c_epslon; /* the esplon parameter for VDW interactions */
96    double c_covalent; // The covalent radius of the atom.
97  
98 <  int c_index; /* set the atom's index */
98 >  int index; /* set the atom's index */
99 >  int offset; // the atom's offset in the storage array
100  
101    char c_name[100]; /* it's name */
102  
103    int c_n_hyd; // the number of hydrogens bonded to the atom
104    
105 <  short int has_dipole; // dipole boolean
106 <  short int is_VDW;    // VDW boolean
107 <  short int is_LJ;    // LJ boolean
105 >  int has_dipole; // dipole boolean
106 >  int is_VDW;    // VDW boolean
107 >  int is_LJ;    // LJ boolean
108    
109   };
110  
111 +
112 +
113   class GeneralAtom : public Atom{
114  
115   public:
116 <  GeneralAtom(){}
116 >  GeneralAtom(int theIndex): Atom(theIndex){}
117    virtual ~GeneralAtom(){}
118  
119    int isDirectional( void ){ return 0; }
120    void zeroForces() {
121 <    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
121 >    frc[offset]   = 0.0;
122 >    frc[offset+1] = 0.0;
123 >    frc[offset+2] = 0.0;
124    }
125   };
126  
127   class DirectionalAtom : public Atom {
128    
129   public:
130 <  DirectionalAtom() { ssdIdentity = 0; }
130 >  DirectionalAtom(int theIndex) : Atom(theIndex)
131 >  {
132 >    ssdIdentity = 0;
133 >  }
134    virtual ~DirectionalAtom() {}
135  
136 +  static void createDArrays(int nElements){
137 +    trq = new double[nElements*3];
138 +  }
139 +  static void destroyDArrays(void){
140 +    delete[] trq;
141 +  }
142 +
143    int isDirectional(void) { return 1; }
144    
145    void setSSD( int value) { ssdIdentity = value; }
# Line 137 | Line 161 | class DirectionalAtom : public Atom { (public)
161    void setJy( double the_jy ) { jy = the_jy; }
162    void setJz( double the_jz ) { jz = the_jz; }
163      
164 <  void addTx( double the_tx ) { tx += the_tx;}
165 <  void addTy( double the_ty ) { ty += the_ty;}
166 <  void addTz( double the_tz ) { tz += the_tz;}
164 >  void addTx( double the_tx ) { trq[offset]   += the_tx;}
165 >  void addTy( double the_ty ) { trq[offset+1] += the_ty;}
166 >  void addTz( double the_tz ) { trq[offset+2] += the_tz;}
167  
168    void setMu( double the_mu ) { mu = the_mu; }
169  
170    void zeroForces() {
171 <    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
172 <    tx = 0.0; ty = 0.0; tz = 0.0;
171 >    frc[offset]   = 0.0;
172 >    frc[offset+1] = 0.0;
173 >    frc[offset+2] = 0.0;
174 >
175 >    trq[offset]   = 0.0;
176 >    trq[offset+1] = 0.0;
177 >    trq[offset+2] = 0.0;
178    }
179  
180    double getAxx( void ) { return Axx; }
# Line 173 | Line 202 | class DirectionalAtom : public Atom { (public)
202    double getJy( void ) { return jy; }
203    double getJz( void ) { return jz; }
204  
205 <  double getTx( void ) { return tx; }
206 <  double getTy( void ) { return ty; }
207 <  double getTz( void ) { return tz; }
205 >  double getTx( void ) { return trq[offset];}
206 >  double getTy( void ) { return trq[offset+1]; }
207 >  double getTz( void ) { return trq[offset+2]; }
208  
209    double getIxx( void ) { return Ixx; }
210    double getIxy( void ) { return Ixy; }
# Line 195 | Line 224 | class DirectionalAtom : public Atom { (public)
224    void body2Lab( double r[3] );
225  
226   private:
227 +  int dIndex;
228  
229 <  double Axx, Axy, Axz;; // the rotational matrix
229 >  double Axx, Axy, Axz; // the rotational matrix
230    double Ayx, Ayy, Ayz;
231    double Azx, Azy, Azz;
232  
233 <  double sux, suy, suz; // the standard unit vector ( body fixed )
234 <  double jx, jy, jz; // the angular momentum vector ( body fixed )
205 <  double tx, ty, tz; // the torque vector           ( space fixed )
233 >  double sux, suy, suz; // the standard unit vector    ( body fixed )
234 >  double jx, jy, jz;    // the angular momentum vector ( body fixed )
235    
236 <  double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
236 >  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
237    double Iyx, Iyy, Iyz;
238    double Izx, Izy, Izz;
239  

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