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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC vs.
Revision 1452 by tim, Mon Aug 23 15:11:36 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   #include "SimState.hpp"
9 + #include "StuntDouble.hpp"
10 + #include "BaseVisitor.hpp"
11  
12 < class Atom{
12 > class Atom : public StuntDouble {
13   public:
14  
15    Atom(int theIndex, SimState* theConfig );
# Line 15 | Line 17 | class Atom{ (public)
17  
18    virtual void setCoords(void);
19  
18 – //   void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
19 – //                 double* Atrq, double* AAmat, double* Amu,
20 – //                 double* Aul);
21 – //   void deleteAtom(int theIndex);
22 – //   void deleteRange(int startIndex, int stopIndex);
23 –
20    void getPos( double theP[3] );
21    void setPos( double theP[3] );
22  
# Line 28 | Line 24 | class Atom{ (public)
24    void setVel( double theV[3] );
25  
26    void getFrc( double theF[3] );
27 +  void setFrc( double theF[3] );  
28    void addFrc( double theF[3] );
29  
30 <  virtual void zeroForces() = 0;
30 >  virtual void zeroForces();
31  
32 <  double getMass() const {return c_mass;}
32 >  double getMass() {return c_mass;}
33    void setMass(double mass) {c_mass = mass;}
37 –
38 –  double getEamRcut() const {return myEamRcut;}
39 –  void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
34    
41 –  double getSigma() const {return c_sigma;}
42 –  void setSigma(double sigma) {c_sigma = sigma;}
43 –
44 –  double getEpslon() const {return c_epslon;}
45 –  void setEpslon(double epslon) {c_epslon = epslon;}
46 –  
47 –  double getCovalent() const {return c_covalent;}
48 –  void setCovalent(double covalent) {c_covalent = covalent;}
49 –  
35    int getIndex() const {return index;}
36    void setIndex(int theIndex);
37 +
38    char *getType() {return c_name;}
39    void setType(char * name) {strcpy(c_name,name);}
40    
# Line 60 | Line 46 | class Atom{ (public)
46    void setGlobalIndex( int info ) { myGlobalIndex = info; }
47   #endif // is_mpi
48  
63 –  void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
64 –  int get_n_hydrogens() const {return c_n_hyd;}
65 –
49    void setHasDipole( int value ) { has_dipole = value; }
50    int hasDipole( void ) { return has_dipole; }
51  
52 <  void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
53 <  int isLJ( void )    { return is_LJ; }
52 >  void setHasCharge(int value) {has_charge = value;}
53 >  int hasCharge(void) {return has_charge;}
54  
72 –  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
73 –  int isVDW( void )    { return is_VDW; }
55  
56 <  void setEAM( void ) { is_EAM = 1; }
57 <  int  isEAM( void ) { return is_EAM; }
77 <
78 <  virtual int isDirectional( void ) = 0;
79 <
80 <
56 >  virtual void accept(BaseVisitor* v) {v->visit(this);}
57 >  
58   protected:
59    
60    SimState* myConfig;
# Line 89 | Line 66 | class Atom{ (public)
66    double* Amat; // the rotation matrix
67    double* mu;   // the array of dipole moments
68    double* ul;   // the lab frame unit directional vector
69 +  double* quat; // the quaternion array
70  
71 +  double zAngle; // the rotation about the z-axis ( body-fixed )
72 +
73    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.
74  
98 –  double myEamRcut; // Atom rcut for eam defined by the forcefield.
99 –
75    int index; /* set the atom's index */
76    int offset; // the atom's offset in the storage array
77    int offsetX, offsetY, offsetZ;
# Line 107 | Line 82 | class Atom{ (public)
82  
83    char c_name[100]; /* it's name */
84    int ident;  // it's unique numeric identity.
110 –
111 –  int c_n_hyd; // the number of hydrogens bonded to the atom
85    
86    int has_dipole; // dipole boolean
87 <  int is_VDW;    // VDW boolean
115 <  int is_LJ;    // LJ boolean
116 <  int is_EAM; //EAM boolean
87 >  int has_charge; // charge boolean
88  
89    bool hasCoords;
90  
# Line 123 | Line 94 | class Atom{ (public)
94    
95   };
96  
126 – class GeneralAtom : public Atom{
127 –
128 – public:
129 –  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
130 –  virtual ~GeneralAtom(){}
131 –
132 –  int isDirectional( void ){ return 0; }
133 –  void zeroForces( void );
134 – };
135 –
136 – class DirectionalAtom : public Atom {
137 –  
138 – public:
139 –  DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex,
140 –                                                            theConfig)
141 –  {
142 –    ssdIdentity = 0;
143 –    sux = 0.0;
144 –    suy = 0.0;
145 –    suz = 0.0;
146 –    myMu = 0.0;
147 –  }
148 –  virtual ~DirectionalAtom() {}
149 –
150 –  virtual void setCoords(void);
151 –
152 –  void printAmatIndex( void );
153 –
154 –  int isDirectional(void) { return 1; }
155 –  
156 –  void setSSD( int value) { ssdIdentity = value; }
157 –  int isSSD(void) {return ssdIdentity; }
158 –
159 –  
160 –  void setEuler( double phi, double theta, double psi );
161 –
162 –  double getSUx( void ) { return sux; }
163 –  double getSUy( void ) { return suy; }
164 –  double getSUz( void ) { return suz; }
165 –  
166 –  void setSUx( double the_sux ) { sux = the_sux; }
167 –  void setSUy( double the_suy ) { suy = the_suy; }
168 –  void setSUz( double the_suz ) { suz = the_suz; }
169 –
170 –  void zeroForces();
171 –
172 –  void getA( double the_A[3][3] ); // get the full rotation matrix
173 –  void setA( double the_A[3][3] );
174 –
175 –  void getU( double the_u[3] ); // get the unit vetor
176 –  void updateU( void );
177 –
178 –  void getQ( double the_q[4] ); // get the quanternions
179 –  void setQ( double the_q[4] );
180 –
181 –  void getJ( double theJ[3] );
182 –  void setJ( double theJ[3] );
183 –
184 –  double getJx( void ) { return jx; }
185 –  double getJy( void ) { return jy; }
186 –  double getJz( void ) { return jz; }
187 –
188 –  void setJx( double the_jx ) { jx = the_jx; }
189 –  void setJy( double the_jy ) { jy = the_jy; }
190 –  void setJz( double the_jz ) { jz = the_jz; }
191 –
192 –  void getTrq( double theT[3] );
193 –  void addTrq( double theT[3] );
194 –
195 –  //  double getTx( void ) { return trq[offsetX];}
196 –  //  double getTy( void ) { return trq[offsetY]; }
197 –  //  double getTz( void ) { return trq[offsetZ]; }
198 –
199 –  void setI( double the_I[3][3] );
200 –  void getI( double the_I[3][3] );
201 –  
202 –  double getIxx( void ) { return Ixx; }
203 –  double getIxy( void ) { return Ixy; }
204 –  double getIxz( void ) { return Ixz; }
205 –  
206 –  double getIyx( void ) { return Iyx; }
207 –  double getIyy( void ) { return Iyy; }
208 –  double getIyz( void ) { return Iyz; }
209 –  
210 –  double getIzx( void ) { return Izx; }
211 –  double getIzy( void ) { return Izy; }
212 –  double getIzz( void ) { return Izz; }
213 –
214 –  double getMu( void );
215 –  void setMu( double the_mu );
216 –
217 –  void lab2Body( double r[3] );
218 –  void body2Lab( double r[3] );
219 –
220 –
221 – private:
222 –  int dIndex;
223 –
224 –  double myMu;
225 –
226 –  double sux, suy, suz; // the standard unit vector    ( body fixed )
227 –  double jx, jy, jz;    // the angular momentum vector ( body fixed )
228 –  
229 –  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
230 –  double Iyx, Iyy, Iyz;
231 –  double Izx, Izy, Izz;
232 –
233 –  int ssdIdentity; // boolean of whether atom is ssd
234 –
235 – };
236 –
97   #endif

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