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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 599 by mmeineke, Mon Jul 14 21:48:43 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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 >
11 > class Atom : public StuntDouble {
12   public:
13  
14 <  Atom(int theIndex);
14 >  Atom(int theIndex, SimState* theConfig );
15    virtual ~Atom() {}
16  
17 <  static double* pos; // the position array
15 <  static double* vel; // the velocity array
16 <  static double* frc; // the forc array
17 <  static double* trq; // the torque vector  ( space fixed )
18 <  static double* Amat; // the rotation matrix
19 <  static double* mu; // the dipole moment array
20 <  static double* ul; // the lab frame unit directional vector
21 <  static int nElements;
17 >  virtual void setCoords(void);
18  
23 –  static void createArrays (int the_nElements);
24 –  static void destroyArrays(void);
25 –  void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
26 –                double* Atrq, double* AAmat, double* Amu,
27 –                double* Aul);
28 –  void deleteAtom(int theIndex);
29 –  void deleteRange(int startIndex, int stopIndex);
30 –
31 –  static double* getPosArray( void ) { return pos; }
32 –  static double* getVelArray( void ) { return vel; }
33 –  static double* getFrcArray( void ) { return frc; }
34 –  static double* getTrqArray( void ) { return trq; }
35 –  static double* getAmatArray( void ) { return Amat; }
36 –  static double* getMuArray( void ) { return mu; }
37 –  static double* getUlArray( void ) { return ul; }
38 –  
19    void getPos( double theP[3] );
20    void setPos( double theP[3] );
21  
42 –  double getX() const {return pos[offsetX];}
43 –  double getY() const {return pos[offsetY];}
44 –  double getZ() const {return pos[offsetZ];}
45 –  void setX(double x) {pos[offsetX] = x;}
46 –  void setY(double y) {pos[offsetY] = y;}
47 –  void setZ(double z) {pos[offsetZ] = z;}
48 –  
22    void getVel( double theV[3] );
23    void setVel( double theV[3] );
24  
52 –  double get_vx() const  {return vel[offsetX];}
53 –  double get_vy() const  {return vel[offsetY];}
54 –  double get_vz() const  {return vel[offsetZ];}
55 –  void set_vx(double vx) {vel[offsetX] = vx;}
56 –  void set_vy(double vy) {vel[offsetY] = vy;}
57 –  void set_vz(double vz) {vel[offsetZ] = vz;}
58 –  
59 –
25    void getFrc( double theF[3] );
26    void addFrc( double theF[3] );
27  
28 <  double getFx() const   {return frc[offsetX];}
64 <  double getFy() const   {return frc[offsetY];}
65 <  double getFz() const   {return frc[offsetZ];}
66 <  void addFx(double add) {frc[offsetX] += add;}
67 <  void addFy(double add) {frc[offsetY] += add;}
68 <  void addFz(double add) {frc[offsetZ] += add;}
69 <  virtual void zeroForces() = 0;
28 >  virtual void zeroForces();
29  
30 <  double getMass() const {return c_mass;}
30 >  double getMass() {return c_mass;}
31    void setMass(double mass) {c_mass = mass;}
32    
74 –  double getSigma() const {return c_sigma;}
75 –  void setSigma(double sigma) {c_sigma = sigma;}
76 –
77 –  double getEpslon() const {return c_epslon;}
78 –  void setEpslon(double epslon) {c_epslon = epslon;}
79 –  
80 –  double getCovalent() const {return c_covalent;}
81 –  void setCovalent(double covalent) {c_covalent = covalent;}
82 –  
33    int getIndex() const {return index;}
34    void setIndex(int theIndex);
35 +
36    char *getType() {return c_name;}
37    void setType(char * name) {strcpy(c_name,name);}
38    
# Line 93 | Line 44 | class Atom{ (public)
44    void setGlobalIndex( int info ) { myGlobalIndex = info; }
45   #endif // is_mpi
46  
96 –  void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
97 –  int get_n_hydrogens() const {return c_n_hyd;}
98 –
47    void setHasDipole( int value ) { has_dipole = value; }
48    int hasDipole( void ) { return has_dipole; }
49  
102 –  void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
103 –  int isLJ( void )    { return is_LJ; }
104 –
105 –  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
106 –  int isVDW( void )    { return is_VDW; }
107 –
108 –  virtual int isDirectional( void ) = 0;
109 –
110 –
50   protected:
51    
52 +  SimState* myConfig;
53 +
54 +  double* pos; // the position array
55 +  double* vel; // the velocity array
56 +  double* frc; // the forc array
57 +  double* trq; // the torque vector  ( space fixed )
58 +  double* Amat; // the rotation matrix
59 +  double* mu;   // the array of dipole moments
60 +  double* ul;   // the lab frame unit directional vector
61 +
62    double c_mass; /* the mass of the atom in amu */
114 –  double c_sigma; /* the sigma parameter for van der walls interactions */
115 –  double c_epslon; /* the esplon parameter for VDW interactions */
116 –  double c_covalent; // The covalent radius of the atom.
63  
64    int index; /* set the atom's index */
65    int offset; // the atom's offset in the storage array
# Line 125 | Line 71 | class Atom{ (public)
71  
72    char c_name[100]; /* it's name */
73    int ident;  // it's unique numeric identity.
128 –
129 –  int c_n_hyd; // the number of hydrogens bonded to the atom
74    
75    int has_dipole; // dipole boolean
132 –  int is_VDW;    // VDW boolean
133 –  int is_LJ;    // LJ boolean
76  
77 +  bool hasCoords;
78 +
79   #ifdef IS_MPI
80    int myGlobalIndex;
81   #endif
82    
83   };
84  
141 – class GeneralAtom : public Atom{
142 –
143 – public:
144 –  GeneralAtom(int theIndex): Atom(theIndex){}
145 –  virtual ~GeneralAtom(){}
146 –
147 –  int isDirectional( void ){ return 0; }
148 –  void zeroForces() {
149 –    frc[offsetX] = 0.0;
150 –    frc[offsetY] = 0.0;
151 –    frc[offsetZ] = 0.0;
152 –  }
153 – };
154 –
155 – class DirectionalAtom : public Atom {
156 –  
157 – public:
158 –  DirectionalAtom(int theIndex) : Atom(theIndex)
159 –  {
160 –    ssdIdentity = 0;
161 –    sux = 0.0;
162 –    suy = 0.0;
163 –    suz = 0.0;
164 –  }
165 –  virtual ~DirectionalAtom() {}
166 –
167 –  void printAmatIndex( void );
168 –
169 –  int isDirectional(void) { return 1; }
170 –  
171 –  void setSSD( int value) { ssdIdentity = value; }
172 –  int isSSD(void) {return ssdIdentity; }
173 –
174 –  
175 –  void setEuler( double phi, double theta, double psi );
176 –
177 –  double getSUx( void ) { return sux; }
178 –  double getSUy( void ) { return suy; }
179 –  double getSUz( void ) { return suz; }
180 –  
181 –  void setSUx( double the_sux ) { sux = the_sux; }
182 –  void setSUy( double the_suy ) { suy = the_suy; }
183 –  void setSUz( double the_suz ) { suz = the_suz; }
184 –
185 –  void zeroForces() {
186 –    frc[offsetX] = 0.0;
187 –    frc[offsetY] = 0.0;
188 –    frc[offsetZ] = 0.0;
189 –
190 –    trq[offsetX] = 0.0;
191 –    trq[offsetY] = 0.0;
192 –    trq[offsetZ] = 0.0;
193 –  }
194 –
195 –  void getA( double the_A[3][3] ); // get the full rotation matrix
196 –  void setA( double the_A[3][3] );
197 –
198 –  void getU( double the_u[3] ); // get the unit vetor
199 –  void updateU( void );
200 –
201 –  void getQ( double the_q[4] ); // get the quanternions
202 –  void setQ( double the_q[4] );
203 –
204 –  void getJ( double theJ[3] );
205 –  void setJ( double theJ[3] );
206 –
207 –  double getJx( void ) { return jx; }
208 –  double getJy( void ) { return jy; }
209 –  double getJz( void ) { return jz; }
210 –
211 –  void setJx( double the_jx ) { jx = the_jx; }
212 –  void setJy( double the_jy ) { jy = the_jy; }
213 –  void setJz( double the_jz ) { jz = the_jz; }
214 –
215 –  void getTrq( double theT[3] );
216 –  void addTrq( double theT[3] );
217 –
218 –  double getTx( void ) { return trq[offsetX];}
219 –  double getTy( void ) { return trq[offsetY]; }
220 –  double getTz( void ) { return trq[offsetZ]; }
221 –
222 –  void addTx( double the_tx ) { trq[offsetX] += the_tx;}
223 –  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
224 –  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
225 –
226 –  void setI( double the_I[3][3] );
227 –  void getI( double the_I[3][3] );
228 –  
229 –  double getIxx( void ) { return Ixx; }
230 –  double getIxy( void ) { return Ixy; }
231 –  double getIxz( void ) { return Ixz; }
232 –  
233 –  double getIyx( void ) { return Iyx; }
234 –  double getIyy( void ) { return Iyy; }
235 –  double getIyz( void ) { return Iyz; }
236 –  
237 –  double getIzx( void ) { return Izx; }
238 –  double getIzy( void ) { return Izy; }
239 –  double getIzz( void ) { return Izz; }
240 –  
241 –
242 –  double getMu( void ) { return mu[index]; }
243 –  void setMu( double the_mu ) { mu[index] = the_mu; }
244 –
245 –  void lab2Body( double r[3] );
246 –  void body2Lab( double r[3] );
247 –
248 –
249 – private:
250 –  int dIndex;
251 –
252 –  double sux, suy, suz; // the standard unit vector    ( body fixed )
253 –  double jx, jy, jz;    // the angular momentum vector ( body fixed )
254 –  
255 –  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
256 –  double Iyx, Iyy, Iyz;
257 –  double Izx, Izy, Izz;
258 –
259 –  int ssdIdentity; // boolean of whether atom is ssd
260 –
261 – };
262 –
85   #endif

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