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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 802 by mmeineke, Thu Oct 9 22:09:52 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   #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 24 | Line 26 | class Atom{ (public)
26    void getFrc( double theF[3] );
27    void addFrc( double theF[3] );
28  
29 <  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;}
31 –
32 –  double getEamRcut() const {return myEamRcut;}
33 –  void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
33    
35 –  double getSigma() const {return c_sigma;}
36 –  void setSigma(double sigma) {c_sigma = sigma;}
37 –
38 –  double getEpslon() const {return c_epslon;}
39 –  void setEpslon(double epslon) {c_epslon = epslon;}
40 –  
41 –  double getCovalent() const {return c_covalent;}
42 –  void setCovalent(double covalent) {c_covalent = covalent;}
43 –  
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  
57 –  void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
58 –  int get_n_hydrogens() const {return c_n_hyd;}
59 –
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  
66 –  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
67 –  int isVDW( void )    { return is_VDW; }
60  
61 <  void setEAM( void ) { is_EAM = 1; }
62 <  int  isEAM( void ) { return is_EAM; }
71 <
72 <  virtual int isDirectional( void ) = 0;
73 <
74 <
61 >  virtual void accept(BaseVisitor* v) {v->visit(this);}
62 >  
63   protected:
64    
65    SimState* myConfig;
# Line 83 | Line 71 | class Atom{ (public)
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 */
88 –  double c_sigma; /* the sigma parameter for van der walls interactions */
89 –  double c_epslon; /* the esplon parameter for VDW interactions */
90 –  double c_covalent; // The covalent radius of the atom.
78  
92 –  double myEamRcut; // Atom rcut for eam defined by the forcefield.
93 –
79    int index; /* set the atom's index */
80    int offset; // the atom's offset in the storage array
81    int offsetX, offsetY, offsetZ;
# Line 101 | Line 86 | class Atom{ (public)
86  
87    char c_name[100]; /* it's name */
88    int ident;  // it's unique numeric identity.
104 –
105 –  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
109 <  int is_LJ;    // LJ boolean
110 <  int is_EAM; //EAM boolean
91 >  int has_charge; // charge boolean
92  
93    bool hasCoords;
94  
# Line 117 | Line 98 | class Atom{ (public)
98    
99   };
100  
120 – class GeneralAtom : public Atom{
121 –
122 – public:
123 –  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
124 –  virtual ~GeneralAtom(){}
125 –
126 –  int isDirectional( void ){ return 0; }
127 –  void zeroForces( void );
128 – };
129 –
130 – class DirectionalAtom : public Atom {
131 –  
132 – public:
133 –  DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex,
134 –                                                            theConfig)
135 –  {
136 –    ssdIdentity = 0;
137 –    sux = 0.0;
138 –    suy = 0.0;
139 –    suz = 0.0;
140 –    myMu = 0.0;
141 –  }
142 –  virtual ~DirectionalAtom() {}
143 –
144 –  virtual void setCoords(void);
145 –
146 –  void printAmatIndex( void );
147 –
148 –  int isDirectional(void) { return 1; }
149 –  
150 –  void setSSD( int value) { ssdIdentity = value; }
151 –  int isSSD(void) {return ssdIdentity; }
152 –
153 –  
154 –  void setEuler( double phi, double theta, double psi );
155 –
156 –  double getSUx( void ) { return sux; }
157 –  double getSUy( void ) { return suy; }
158 –  double getSUz( void ) { return suz; }
159 –  
160 –  void setSUx( double the_sux ) { sux = the_sux; }
161 –  void setSUy( double the_suy ) { suy = the_suy; }
162 –  void setSUz( double the_suz ) { suz = the_suz; }
163 –
164 –  void zeroForces();
165 –
166 –  void getA( double the_A[3][3] ); // get the full rotation matrix
167 –  void setA( double the_A[3][3] );
168 –
169 –  void getU( double the_u[3] ); // get the unit vetor
170 –  void updateU( void );
171 –
172 –  void getQ( double the_q[4] ); // get the quanternions
173 –  void setQ( double the_q[4] );
174 –
175 –  void getJ( double theJ[3] );
176 –  void setJ( double theJ[3] );
177 –
178 –  double getJx( void ) { return jx; }
179 –  double getJy( void ) { return jy; }
180 –  double getJz( void ) { return jz; }
181 –
182 –  void setJx( double the_jx ) { jx = the_jx; }
183 –  void setJy( double the_jy ) { jy = the_jy; }
184 –  void setJz( double the_jz ) { jz = the_jz; }
185 –
186 –  void getTrq( double theT[3] );
187 –  void addTrq( double theT[3] );
188 –
189 –  //  double getTx( void ) { return trq[offsetX];}
190 –  //  double getTy( void ) { return trq[offsetY]; }
191 –  //  double getTz( void ) { return trq[offsetZ]; }
192 –
193 –  void setI( double the_I[3][3] );
194 –  void getI( double the_I[3][3] );
195 –  
196 –  double getIxx( void ) { return Ixx; }
197 –  double getIxy( void ) { return Ixy; }
198 –  double getIxz( void ) { return Ixz; }
199 –  
200 –  double getIyx( void ) { return Iyx; }
201 –  double getIyy( void ) { return Iyy; }
202 –  double getIyz( void ) { return Iyz; }
203 –  
204 –  double getIzx( void ) { return Izx; }
205 –  double getIzy( void ) { return Izy; }
206 –  double getIzz( void ) { return Izz; }
207 –
208 –  double getMu( void );
209 –  void setMu( double the_mu );
210 –
211 –  void lab2Body( double r[3] );
212 –  void body2Lab( double r[3] );
213 –
214 –
215 – private:
216 –  int dIndex;
217 –
218 –  double myMu;
219 –
220 –  double sux, suy, suz; // the standard unit vector    ( body fixed )
221 –  double jx, jy, jz;    // the angular momentum vector ( body fixed )
222 –  
223 –  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
224 –  double Iyx, Iyy, Iyz;
225 –  double Izx, Izy, Izz;
226 –
227 –  int ssdIdentity; // boolean of whether atom is ssd
228 –
229 – };
230 –
101   #endif

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