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Comparing trunk/mdtools/headers/Atom.hpp (file contents):
Revision 30 by mmeineke, Tue Jul 16 21:10:49 2002 UTC vs.
Revision 253 by chuckv, Thu Jan 30 15:20:21 2003 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 +    offsetX = offset;
17 +    offsetY = offset+1;
18 +    offsetZ = offset+2;
19    }
20 <  ~Atom() {}
20 >  virtual ~Atom() {}
21 >
22 >  static void createArrays (int nElements) {
23 >    pos = new double[nElements*3];
24 >    vel = new double[nElements*3];
25 >    frc = new double[nElements*3];
26 >    trq = new double[nElements*3];
27 >  }
28 >  static void destroyArrays(void) {
29 >    delete[] pos;
30 >    delete[] vel;
31 >    delete[] frc;
32 >    delete[] trq;
33 >  }
34 >
35 >  static double* getPosArray( void ) { return pos; }
36 >  static double* getVelArray( void ) { return vel; }
37 >  static double* getFrcArray( void ) { return frc; }
38 >  static double* getTrqArray( void ) { return trq; }
39    
17 –  double getX() const {return c_x;}
18 –  double getY() const {return c_y;}
19 –  double getZ() const {return c_z;}
20 –  void setX(double x) {c_x = x;}
21 –  void setY(double y) {c_y = y;}
22 –  void setZ(double z) {c_z = z;}
40    
41 <  double get_vx() const {return c_vx;}
42 <  double get_vy() const {return c_vy;}
43 <  double get_vz() const {return c_vz;}
44 <  void set_vx(double vx) {c_vx = vx;}
45 <  void set_vy(double vy) {c_vy = vy;}
46 <  void set_vz(double vz) {c_vz = vz;}
41 >  double getX() const {return pos[offsetX];}
42 >  double getY() const {return pos[offsetY];}
43 >  double getZ() const {return pos[offsetZ];}
44 >  void setX(double x) {pos[offsetX] = x;}
45 >  void setY(double y) {pos[offsetY] = y;}
46 >  void setZ(double z) {pos[offsetZ] = z;}
47    
48 <  double getFx() const {return c_Fx;}
49 <  double getFy() const {return c_Fy;}
50 <  double getFz() const {return c_Fz;}
51 <  void addFx(double add) {c_Fx += add;}
52 <  void addFy(double add) {c_Fy += add;}
53 <  void addFz(double add) {c_Fz += add;}
48 >  double get_vx() const  {return vel[offsetX];}
49 >  double get_vy() const  {return vel[offsetY];}
50 >  double get_vz() const  {return vel[offsetZ];}
51 >  void set_vx(double vx) {vel[offsetX]   = vx;}
52 >  void set_vy(double vy) {vel[offsetY] = vy;}
53 >  void set_vz(double vz) {vel[offsetZ] = vz;}
54 >  
55 >  double getFx() const   {return frc[offsetX];}
56 >  double getFy() const   {return frc[offsetY];}
57 >  double getFz() const   {return frc[offsetZ];}
58 >  void addFx(double add) {frc[offsetX]   += add;}
59 >  void addFy(double add) {frc[offsetY] += add;}
60 >  void addFz(double add) {frc[offsetZ] += add;}
61    virtual void zeroForces() = 0;
62  
63    double getMass() const {return c_mass;}
# Line 48 | Line 72 | class Atom{ (public)
72    double getCovalent() const {return c_covalent;}
73    void setCovalent(double covalent) {c_covalent = covalent;}
74    
75 <  int getIndex() const {return c_index;}
76 <  void setIndex(int index) {c_index = index;}
77 <  
75 >  int getIndex() const {return index;}
76 >  void setIndex(int theIndex) {
77 >    index = theIndex;
78 >    offset = index*3;
79 >    offsetX = offset;
80 >    offsetY = offset+1;
81 >    offsetZ = offset+2;
82 >  }
83 >
84    char *getType() {return c_name;}
85    void setType(char * name) {strcpy(c_name,name);}
86 +  
87 +  int getIdent( void ) { return ident; }
88 +  void setIdent( int info ) { ident = info; }
89  
90 + #ifdef IS_MPI
91 +  int getGlobalIndex( void ) { return myGlobalIndex; }
92 +  void setGlobalIndex( int info ) { myGlobalIndex = info; }
93 + #endif // is_mpi
94 +
95    void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
96    int get_n_hydrogens() const {return c_n_hyd;}
97  
98    void setHasDipole( int value ) { has_dipole = value; }
99 <  short int hasDipole( void ) { return has_dipole; }
99 >  int hasDipole( void ) { return has_dipole; }
100  
101    void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
102 <  short int isLJ( void )    { return is_LJ; }
102 >  int isLJ( void )    { return is_LJ; }
103  
104    void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
105 <  short int isVDW( void )    { return is_VDW; }
105 >  int isVDW( void )    { return is_VDW; }
106  
107    virtual int isDirectional( void ) = 0;
108  
109 +  static double* pos; // the position array
110 +  static double* vel; // the velocity array
111 +  static double* frc; // the forc array
112 +  static double* trq; // the torque vector  ( space fixed )
113 +
114   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;
115    
116    double c_mass; /* the mass of the atom in amu */
117    double c_sigma; /* the sigma parameter for van der walls interactions */
118    double c_epslon; /* the esplon parameter for VDW interactions */
119    double c_covalent; // The covalent radius of the atom.
120  
121 <  int c_index; /* set the atom's index */
121 >  int index; /* set the atom's index */
122 >  int offset; // the atom's offset in the storage array
123 >  int offsetX, offsetY, offsetZ;
124  
125    char c_name[100]; /* it's name */
126 +  int ident;  // it's unique numeric identity.
127  
128    int c_n_hyd; // the number of hydrogens bonded to the atom
129    
130 <  short int has_dipole; // dipole boolean
131 <  short int is_VDW;    // VDW boolean
132 <  short int is_LJ;    // LJ boolean
130 >  int has_dipole; // dipole boolean
131 >  int is_VDW;    // VDW boolean
132 >  int is_LJ;    // LJ boolean
133 >
134 > #ifdef IS_MPI
135 >  int myGlobalIndex;
136 > #endif
137    
138   };
139  
140 +
141 +
142   class GeneralAtom : public Atom{
143  
144   public:
145 <  GeneralAtom(){}
146 <  ~GeneralAtom(){}
145 >  GeneralAtom(int theIndex): Atom(theIndex){}
146 >  virtual ~GeneralAtom(){}
147  
148    int isDirectional( void ){ return 0; }
149    void zeroForces() {
150 <    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
150 >    frc[offsetX]   = 0.0;
151 >    frc[offsetY] = 0.0;
152 >    frc[offsetZ] = 0.0;
153    }
154   };
155  
156   class DirectionalAtom : public Atom {
157    
158   public:
159 <  DirectionalAtom() { ssdIdentity = 0; }
160 <  ~DirectionalAtom() {}
159 >  DirectionalAtom(int theIndex) : Atom(theIndex)
160 >  {
161 >    ssdIdentity = 0;
162 >  }
163 >  virtual ~DirectionalAtom() {}
164  
165 +  static void createDArrays(int nElements){
166 +    trq = new double[nElements*3];
167 +  }
168 +  static void destroyDArrays(void){
169 +    delete[] trq;
170 +  }
171 +
172    int isDirectional(void) { return 1; }
173    
174    void setSSD( int value) { ssdIdentity = value; }
# Line 137 | Line 190 | class DirectionalAtom : public Atom { (public)
190    void setJy( double the_jy ) { jy = the_jy; }
191    void setJz( double the_jz ) { jz = the_jz; }
192      
193 <  void addTx( double the_tx ) { tx += the_tx;}
194 <  void addTy( double the_ty ) { ty += the_ty;}
195 <  void addTz( double the_tz ) { tz += the_tz;}
193 >  void addTx( double the_tx ) { trq[offsetX]   += the_tx;}
194 >  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
195 >  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
196  
197    void setMu( double the_mu ) { mu = the_mu; }
198  
199    void zeroForces() {
200 <    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
201 <    tx = 0.0; ty = 0.0; tz = 0.0;
200 >    frc[offsetX]   = 0.0;
201 >    frc[offsetY] = 0.0;
202 >    frc[offsetZ] = 0.0;
203 >
204 >    trq[offsetX]   = 0.0;
205 >    trq[offsetY] = 0.0;
206 >    trq[offsetZ] = 0.0;
207    }
208  
209    double getAxx( void ) { return Axx; }
# Line 173 | Line 231 | class DirectionalAtom : public Atom { (public)
231    double getJy( void ) { return jy; }
232    double getJz( void ) { return jz; }
233  
234 <  double getTx( void ) { return tx; }
235 <  double getTy( void ) { return ty; }
236 <  double getTz( void ) { return tz; }
234 >  double getTx( void ) { return trq[offsetX];}
235 >  double getTy( void ) { return trq[offsetY]; }
236 >  double getTz( void ) { return trq[offsetZ]; }
237  
238    double getIxx( void ) { return Ixx; }
239    double getIxy( void ) { return Ixy; }
# Line 195 | Line 253 | class DirectionalAtom : public Atom { (public)
253    void body2Lab( double r[3] );
254  
255   private:
256 +  int dIndex;
257  
258 <  double Axx, Axy, Axz;; // the rotational matrix
258 >  double Axx, Axy, Axz; // the rotational matrix
259    double Ayx, Ayy, Ayz;
260    double Azx, Azy, Azz;
261  
262 <  double sux, suy, suz; // the standard unit vector ( body fixed )
263 <  double jx, jy, jz; // the angular momentum vector ( body fixed )
205 <  double tx, ty, tz; // the torque vector           ( space fixed )
262 >  double sux, suy, suz; // the standard unit vector    ( body fixed )
263 >  double jx, jy, jz;    // the angular momentum vector ( body fixed )
264    
265 <  double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
265 >  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
266    double Iyx, Iyy, Iyz;
267    double Izx, Izy, Izz;
268  

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