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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Atom.hpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Atom.hpp (file contents), Revision 1187 by chrisfen, Sat May 22 18:16:18 2004 UTC

# Line 1 | Line 1
1   #ifndef _ATOM_H_
2   #define _ATOM_H_
3  
4 < #include <cstring>
5 < #include <cstdlib>
4 > #include <string.h>
5 > #include <stdlib.h>
6   #include <iostream>
7  
8 < class Atom{
8 > #include "SimState.hpp"
9 > #include "StuntDouble.hpp"
10 > #include "BaseVisitor.hpp"
11 >
12 > class Atom : public StuntDouble {
13   public:
10 –  Atom(int theIndex) {
11 –    c_n_hyd = 0;
12 –    has_dipole = 0;
13 –    is_VDW = 0;
14 –    is_LJ = 0;
14  
15 <    index = theIndex;
16 <    offset = 3 * index;
18 <    offsetX = offset;
19 <    offsetY = offset+1;
20 <    offsetZ = offset+2;
15 >  Atom(int theIndex, SimState* theConfig );
16 >  virtual ~Atom() {}
17  
18 <    Axx = index*9;
23 <    Axy = Axx+1;
24 <    Axz = Axx+2;
25 <    
26 <    Ayx = Axx+3;
27 <    Ayy = Axx+4;
28 <    Ayz = Axx+5;
18 >  virtual void setCoords(void);
19  
20 <    Azx = Axx+6;
21 <    Azy = Axx+7;
32 <    Azz = Axx+8;
33 <  }
34 <  virtual ~Atom() {}
20 >  void getPos( double theP[3] );
21 >  void setPos( double theP[3] );
22  
23 <  static void createArrays (int nElements) {
24 <    int i;
38 <    
39 <    pos = new double[nElements*3];
40 <    vel = new double[nElements*3];
41 <    frc = new double[nElements*3];
42 <    trq = new double[nElements*3];
43 <    Amat = new double[nElements*9];
44 <    mu = new double[nElements];
45 <    ul = new double[nElements*3];
23 >  void getVel( double theV[3] );
24 >  void setVel( double theV[3] );
25  
26 <    // init directional values to zero
27 <    
49 <    for( i=0; i<nElements; i++){
50 <      trq[i] = 0.0;
51 <      trq[i+1] = 0.0;
52 <      trq[i+2] = 0.0;
53 <      
54 <      Amat[i] = 1.0;
55 <      Amat[i+1] = 0.0;
56 <      Amat[i+2] = 0.0;
57 <      
58 <      Amat[i+3] = 0.0;
59 <      Amat[i+4] = 1.0;
60 <      Amat[i+5] = 0.0;
61 <      
62 <      Amat[i+6] = 0.0;
63 <      Amat[i+7] = 0.0;
64 <      Amat[i+8] = 1.0;
65 <      
66 <      mu[i] = 0.0;    
67 <      
68 <      ul[i] = 0.0;
69 <      ul[i+1] = 0.0;
70 <      ul[i+2] = 0.0;
71 <    }
72 <  }
73 <  static void destroyArrays(void) {
74 <    delete[] pos;
75 <    delete[] vel;
76 <    delete[] frc;
77 <    delete[] trq;
78 <    delete[] Amat;
79 <    delete[] mu;
80 <  }
26 >  void getFrc( double theF[3] );
27 >  void addFrc( double theF[3] );
28  
29 <  static double* getPosArray( void ) { return pos; }
83 <  static double* getVelArray( void ) { return vel; }
84 <  static double* getFrcArray( void ) { return frc; }
85 <  static double* getTrqArray( void ) { return trq; }
86 <  static double* getAmatArray( void ) { return Amat; }
87 <  static double* getMuArray( void ) { return mu; }
88 <  static double* getUlArray( void ) { return ul; }
89 <  
90 <  double getX() const {return pos[offsetX];}
91 <  double getY() const {return pos[offsetY];}
92 <  double getZ() const {return pos[offsetZ];}
93 <  void setX(double x) {pos[offsetX] = x;}
94 <  void setY(double y) {pos[offsetY] = y;}
95 <  void setZ(double z) {pos[offsetZ] = z;}
96 <  
97 <  double get_vx() const  {return vel[offsetX];}
98 <  double get_vy() const  {return vel[offsetY];}
99 <  double get_vz() const  {return vel[offsetZ];}
100 <  void set_vx(double vx) {vel[offsetX] = vx;}
101 <  void set_vy(double vy) {vel[offsetY] = vy;}
102 <  void set_vz(double vz) {vel[offsetZ] = vz;}
103 <  
104 <  double getFx() const   {return frc[offsetX];}
105 <  double getFy() const   {return frc[offsetY];}
106 <  double getFz() const   {return frc[offsetZ];}
107 <  void addFx(double add) {frc[offsetX] += add;}
108 <  void addFy(double add) {frc[offsetY] += add;}
109 <  void addFz(double add) {frc[offsetZ] += add;}
110 <  virtual void zeroForces() = 0;
29 >  virtual void zeroForces();
30  
31 <  double getMass() const {return c_mass;}
31 >  double getMass() {return c_mass;}
32    void setMass(double mass) {c_mass = mass;}
33    
115 –  double getSigma() const {return c_sigma;}
116 –  void setSigma(double sigma) {c_sigma = sigma;}
117 –
118 –  double getEpslon() const {return c_epslon;}
119 –  void setEpslon(double epslon) {c_epslon = epslon;}
120 –  
121 –  double getCovalent() const {return c_covalent;}
122 –  void setCovalent(double covalent) {c_covalent = covalent;}
123 –  
34    int getIndex() const {return index;}
35 <  void setIndex(int theIndex) {
126 <    index = theIndex;
127 <    offset = index*3;
128 <    offsetX = offset;
129 <    offsetY = offset+1;
130 <    offsetZ = offset+2;
35 >  void setIndex(int theIndex);
36  
132 –    Axx = index*9;
133 –    Axy = Axx+1;
134 –    Axz = Axx+2;
135 –    
136 –    Ayx = Axx+3;
137 –    Ayy = Axx+4;
138 –    Ayz = Axx+5;
139 –
140 –    Azx = Axx+6;
141 –    Azy = Axx+7;
142 –    Azz = Axx+8;
143 –  }
144 –
37    char *getType() {return c_name;}
38    void setType(char * name) {strcpy(c_name,name);}
39    
# Line 153 | Line 45 | class Atom{ (public)
45    void setGlobalIndex( int info ) { myGlobalIndex = info; }
46   #endif // is_mpi
47  
156 –  void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
157 –  int get_n_hydrogens() const {return c_n_hyd;}
158 –
48    void setHasDipole( int value ) { has_dipole = value; }
49    int hasDipole( void ) { return has_dipole; }
50  
51 <  void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
52 <  int isLJ( void )    { return is_LJ; }
51 >  void setHasCharge(int value) {has_charge = value;}
52 >  int hasCharge(void) {return has_charge;}
53  
165 –  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
166 –  int isVDW( void )    { return is_VDW; }
54  
55 <  virtual int isDirectional( void ) = 0;
56 <
170 <  static double* pos; // the position array
171 <  static double* vel; // the velocity array
172 <  static double* frc; // the forc array
173 <  static double* trq; // the torque vector  ( space fixed )
174 <  static double* Amat; // the rotation matrix
175 <  static double* mu; // the dipole moment array
176 <  static double* ul; // the lab frame unit directional vector
177 <
55 >  virtual void accept(BaseVisitor* v) {v->visit(this);}
56 >  
57   protected:
58    
59 +  SimState* myConfig;
60 +
61 +  double* pos; // the position array
62 +  double* vel; // the velocity array
63 +  double* frc; // the forc array
64 +  double* trq; // the torque vector  ( space fixed )
65 +  double* Amat; // the rotation matrix
66 +  double* mu;   // the array of dipole moments
67 +  double* ul;   // the lab frame unit directional vector
68 +
69 +  double zAngle; // the rotation about the z-axis ( body-fixed )
70 +
71    double c_mass; /* the mass of the atom in amu */
181 –  double c_sigma; /* the sigma parameter for van der walls interactions */
182 –  double c_epslon; /* the esplon parameter for VDW interactions */
183 –  double c_covalent; // The covalent radius of the atom.
72  
73    int index; /* set the atom's index */
74    int offset; // the atom's offset in the storage array
# Line 192 | Line 80 | class Atom{ (public)
80  
81    char c_name[100]; /* it's name */
82    int ident;  // it's unique numeric identity.
195 –
196 –  int c_n_hyd; // the number of hydrogens bonded to the atom
83    
84    int has_dipole; // dipole boolean
85 <  int is_VDW;    // VDW boolean
200 <  int is_LJ;    // LJ boolean
85 >  int has_charge; // charge boolean
86  
87 +  bool hasCoords;
88 +
89   #ifdef IS_MPI
90    int myGlobalIndex;
91   #endif
92    
93   };
94  
208 –
209 –
210 – class GeneralAtom : public Atom{
211 –
212 – public:
213 –  GeneralAtom(int theIndex): Atom(theIndex){}
214 –  virtual ~GeneralAtom(){}
215 –
216 –  int isDirectional( void ){ return 0; }
217 –  void zeroForces() {
218 –    frc[offsetX] = 0.0;
219 –    frc[offsetY] = 0.0;
220 –    frc[offsetZ] = 0.0;
221 –  }
222 – };
223 –
224 – class DirectionalAtom : public Atom {
225 –  
226 – public:
227 –  DirectionalAtom(int theIndex) : Atom(theIndex)
228 –  {
229 –    ssdIdentity = 0;
230 –    sux = 0.0;
231 –    suy = 0.0;
232 –    suz = 0.0;
233 –  }
234 –  virtual ~DirectionalAtom() {}
235 –
236 –  int isDirectional(void) { return 1; }
237 –  
238 –  void setSSD( int value) { ssdIdentity = value; }
239 –  int isSSD(void) {return ssdIdentity; }
240 –
241 –  void setA( double the_A[3][3] );
242 –
243 –  void setI( double the_I[3][3] );
244 –
245 –  void setQ( double the_q[4] );
246 –  
247 –  void setEuler( double phi, double theta, double psi );
248 –  
249 –  void setSUx( double the_sux ) { sux = the_sux; }
250 –  void setSUy( double the_suy ) { suy = the_suy; }
251 –  void setSUz( double the_suz ) { suz = the_suz; }
252 –
253 –  void setJx( double the_jx ) { jx = the_jx; }
254 –  void setJy( double the_jy ) { jy = the_jy; }
255 –  void setJz( double the_jz ) { jz = the_jz; }
256 –    
257 –  void addTx( double the_tx ) { trq[offsetX] += the_tx;}
258 –  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
259 –  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
260 –
261 –  void zeroForces() {
262 –    frc[offsetX] = 0.0;
263 –    frc[offsetY] = 0.0;
264 –    frc[offsetZ] = 0.0;
265 –
266 –    trq[offsetX] = 0.0;
267 –    trq[offsetY] = 0.0;
268 –    trq[offsetZ] = 0.0;
269 –  }
270 –
271 –  double getAxx( void ) { return Amat[Axx]; }
272 –  double getAxy( void ) { return Amat[Axy]; }
273 –  double getAxz( void ) { return Amat[Axz]; }
274 –  
275 –  double getAyx( void ) { return Amat[Ayx]; }
276 –  double getAyy( void ) { return Amat[Ayy]; }
277 –  double getAyz( void ) { return Amat[Ayz]; }
278 –  
279 –  double getAzx( void ) { return Amat[Azx]; }
280 –  double getAzy( void ) { return Amat[Azy]; }
281 –  double getAzz( void ) { return Amat[Azz]; }
282 –
283 –  void getA( double the_A[3][3] ); // get the full rotation matrix
284 –
285 –  double getSUx( void ) { return sux; }
286 –  double getSUy( void ) { return suy; }
287 –  double getSUz( void ) { return suz; }
288 –
289 –  void getU( double the_u[3] ); // get the unit vetor
290 –  void getQ( double the_q[4] ); // get the quanternions
291 –
292 –  double getJx( void ) { return jx; }
293 –  double getJy( void ) { return jy; }
294 –  double getJz( void ) { return jz; }
295 –
296 –  double getTx( void ) { return trq[offsetX];}
297 –  double getTy( void ) { return trq[offsetY]; }
298 –  double getTz( void ) { return trq[offsetZ]; }
299 –
300 –  double getIxx( void ) { return Ixx; }
301 –  double getIxy( void ) { return Ixy; }
302 –  double getIxz( void ) { return Ixz; }
303 –  
304 –  double getIyx( void ) { return Iyx; }
305 –  double getIyy( void ) { return Iyy; }
306 –  double getIyz( void ) { return Iyz; }
307 –  
308 –  double getIzx( void ) { return Izx; }
309 –  double getIzy( void ) { return Izy; }
310 –  double getIzz( void ) { return Izz; }
311 –
312 –  double getMu( void ) { return mu[index]; }
313 –  void setMu( double the_mu ) { mu[index] = the_mu; }
314 –
315 –  void lab2Body( double r[3] );
316 –  void body2Lab( double r[3] );
317 –  void updateU( void );
318 –
319 – private:
320 –  int dIndex;
321 –
322 –  double sux, suy, suz; // the standard unit vector    ( body fixed )
323 –  double jx, jy, jz;    // the angular momentum vector ( body fixed )
324 –  
325 –  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
326 –  double Iyx, Iyy, Iyz;
327 –  double Izx, Izy, Izz;
328 –
329 –  int ssdIdentity; // boolean of whether atom is ssd
330 –
331 – };
332 –
95   #endif

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