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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 631 by chuckv, Thu Jul 17 19:25:51 2003 UTC vs.
Revision 1136 by tim, Tue Apr 27 16:26:44 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:
14  
15 <  Atom(int theIndex);
15 >  Atom(int theIndex, SimState* theConfig );
16    virtual ~Atom() {}
17  
18 <  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;
18 >  virtual void setCoords(void);
19  
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 –  
20    void getPos( double theP[3] );
21    void setPos( double theP[3] );
22  
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 –  
23    void getVel( double theV[3] );
24    void setVel( double theV[3] );
25  
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 –
26    void getFrc( double theF[3] );
27    void addFrc( double theF[3] );
28  
29 <  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;
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    
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 –  
34    int getIndex() const {return index;}
35    void setIndex(int theIndex);
36 +
37    char *getType() {return c_name;}
38    void setType(char * name) {strcpy(c_name,name);}
39    
40    int getIdent( void ) { return ident; }
41    void setIdent( int info ) { ident = info; }
42  
43 +  void getRc(double theRc[3]);
44 +  void setRc(double theRc[3]);
45 +
46 +  double getMassRatio() { return *massRatio;}
47 +  void setMassRatio(double theMassRatio) { *massRatio = theMassRatio;}
48 +
49   #ifdef IS_MPI
50    int getGlobalIndex( void ) { return myGlobalIndex; }
51    void setGlobalIndex( int info ) { myGlobalIndex = info; }
52   #endif // is_mpi
53  
96 –  void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
97 –  int get_n_hydrogens() const {return c_n_hyd;}
98 –
54    void setHasDipole( int value ) { has_dipole = value; }
55    int hasDipole( void ) { return has_dipole; }
56  
57 <  void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
58 <  int isLJ( void )    { return is_LJ; }
57 >  void setHasCharge(int value) {has_charge = value;}
58 >  int hasCharge(void) {return has_charge;}
59  
105 –  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
106 –  int isVDW( void )    { return is_VDW; }
60  
61 <  void setEAM( void ) { is_EAM = 1; }
62 <  int  isEAM( void ) { return is_EAM; }
110 <
111 <  virtual int isDirectional( void ) = 0;
112 <
113 <
61 >  virtual void accept(BaseVisitor* v) {v->visit(this);}
62 >  
63   protected:
64    
65 +  SimState* myConfig;
66 +
67 +  double* pos; // the position array
68 +  double* vel; // the velocity array
69 +  double* frc; // the forc array
70 +  double* trq; // the torque vector  ( space fixed )
71 +  double* Amat; // the rotation matrix
72 +  double* mu;   // the array of dipole moments
73 +  double* ul;   // the lab frame unit directional vector
74 +  double* rc; //the center of mass of the molecule
75 +  double* massRatio; //the ratio of this atom to the total mass of the molecule
76 +
77    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.
78  
79    int index; /* set the atom's index */
80    int offset; // the atom's offset in the storage array
# Line 128 | Line 86 | class Atom{ (protected)
86  
87    char c_name[100]; /* it's name */
88    int ident;  // it's unique numeric identity.
131 –
132 –  int c_n_hyd; // the number of hydrogens bonded to the atom
89    
90    int has_dipole; // dipole boolean
91 <  int is_VDW;    // VDW boolean
136 <  int is_LJ;    // LJ boolean
137 <  int is_EAM; //EAM boolean
91 >  int has_charge; // charge boolean
92  
93 +  bool hasCoords;
94 +
95   #ifdef IS_MPI
96    int myGlobalIndex;
97   #endif
98    
99   };
100  
145 – class GeneralAtom : public Atom{
146 –
147 – public:
148 –  GeneralAtom(int theIndex): Atom(theIndex){}
149 –  virtual ~GeneralAtom(){}
150 –
151 –  int isDirectional( void ){ return 0; }
152 –  void zeroForces() {
153 –    frc[offsetX] = 0.0;
154 –    frc[offsetY] = 0.0;
155 –    frc[offsetZ] = 0.0;
156 –  }
157 – };
158 –
159 – class DirectionalAtom : public Atom {
160 –  
161 – public:
162 –  DirectionalAtom(int theIndex) : Atom(theIndex)
163 –  {
164 –    ssdIdentity = 0;
165 –    sux = 0.0;
166 –    suy = 0.0;
167 –    suz = 0.0;
168 –  }
169 –  virtual ~DirectionalAtom() {}
170 –
171 –  void printAmatIndex( void );
172 –
173 –  int isDirectional(void) { return 1; }
174 –  
175 –  void setSSD( int value) { ssdIdentity = value; }
176 –  int isSSD(void) {return ssdIdentity; }
177 –
178 –  
179 –  void setEuler( double phi, double theta, double psi );
180 –
181 –  double getSUx( void ) { return sux; }
182 –  double getSUy( void ) { return suy; }
183 –  double getSUz( void ) { return suz; }
184 –  
185 –  void setSUx( double the_sux ) { sux = the_sux; }
186 –  void setSUy( double the_suy ) { suy = the_suy; }
187 –  void setSUz( double the_suz ) { suz = the_suz; }
188 –
189 –  void zeroForces() {
190 –    frc[offsetX] = 0.0;
191 –    frc[offsetY] = 0.0;
192 –    frc[offsetZ] = 0.0;
193 –
194 –    trq[offsetX] = 0.0;
195 –    trq[offsetY] = 0.0;
196 –    trq[offsetZ] = 0.0;
197 –  }
198 –
199 –  void getA( double the_A[3][3] ); // get the full rotation matrix
200 –  void setA( double the_A[3][3] );
201 –
202 –  void getU( double the_u[3] ); // get the unit vetor
203 –  void updateU( void );
204 –
205 –  void getQ( double the_q[4] ); // get the quanternions
206 –  void setQ( double the_q[4] );
207 –
208 –  void getJ( double theJ[3] );
209 –  void setJ( double theJ[3] );
210 –
211 –  double getJx( void ) { return jx; }
212 –  double getJy( void ) { return jy; }
213 –  double getJz( void ) { return jz; }
214 –
215 –  void setJx( double the_jx ) { jx = the_jx; }
216 –  void setJy( double the_jy ) { jy = the_jy; }
217 –  void setJz( double the_jz ) { jz = the_jz; }
218 –
219 –  void getTrq( double theT[3] );
220 –  void addTrq( double theT[3] );
221 –
222 –  //  double getTx( void ) { return trq[offsetX];}
223 –  //  double getTy( void ) { return trq[offsetY]; }
224 –  //  double getTz( void ) { return trq[offsetZ]; }
225 –
226 –  void addTx( double the_tx ) { trq[offsetX] += the_tx;}
227 –  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
228 –  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
229 –
230 –  void setI( double the_I[3][3] );
231 –  void getI( double the_I[3][3] );
232 –  
233 –  double getIxx( void ) { return Ixx; }
234 –  double getIxy( void ) { return Ixy; }
235 –  double getIxz( void ) { return Ixz; }
236 –  
237 –  double getIyx( void ) { return Iyx; }
238 –  double getIyy( void ) { return Iyy; }
239 –  double getIyz( void ) { return Iyz; }
240 –  
241 –  double getIzx( void ) { return Izx; }
242 –  double getIzy( void ) { return Izy; }
243 –  double getIzz( void ) { return Izz; }
244 –  
245 –
246 –  double getMu( void ) { return mu[index]; }
247 –  void setMu( double the_mu ) { mu[index] = the_mu; }
248 –
249 –  void lab2Body( double r[3] );
250 –  void body2Lab( double r[3] );
251 –
252 –
253 – private:
254 –  int dIndex;
255 –
256 –  double sux, suy, suz; // the standard unit vector    ( body fixed )
257 –  double jx, jy, jz;    // the angular momentum vector ( body fixed )
258 –  
259 –  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
260 –  double Iyx, Iyy, Iyz;
261 –  double Izx, Izy, Izz;
262 –
263 –  int ssdIdentity; // boolean of whether atom is ssd
264 –
265 – };
266 –
101   #endif

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