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root/group/trunk/OOPSE/libmdtools/Atom.hpp
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Comparing trunk/OOPSE/libmdtools/Atom.hpp (file contents):
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC vs.
Revision 999 by chrisfen, Fri Jan 30 15:01:09 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 +
10   class Atom{
11   public:
12  
13 <  Atom(int theIndex);
13 >  Atom(int theIndex, SimState* theConfig );
14    virtual ~Atom() {}
15  
16 <  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;
16 >  virtual void setCoords(void);
17  
18 <  static void createArrays (int the_nElements);
19 <  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);
18 >  void getPos( double theP[3] );
19 >  void setPos( double theP[3] );
20  
21 <  static double* getPosArray( void ) { return pos; }
22 <  static double* getVelArray( void ) { return vel; }
23 <  static double* getFrcArray( void ) { return frc; }
24 <  static double* getTrqArray( void ) { return trq; }
25 <  static double* getAmatArray( void ) { return Amat; }
26 <  static double* getMuArray( void ) { return mu; }
37 <  static double* getUlArray( void ) { return ul; }
38 <  
39 <  double getX() const {return pos[offsetX];}
40 <  double getY() const {return pos[offsetY];}
41 <  double getZ() const {return pos[offsetZ];}
42 <  void setX(double x) {pos[offsetX] = x;}
43 <  void setY(double y) {pos[offsetY] = y;}
44 <  void setZ(double z) {pos[offsetZ] = z;}
45 <  
46 <  double get_vx() const  {return vel[offsetX];}
47 <  double get_vy() const  {return vel[offsetY];}
48 <  double get_vz() const  {return vel[offsetZ];}
49 <  void set_vx(double vx) {vel[offsetX] = vx;}
50 <  void set_vy(double vy) {vel[offsetY] = vy;}
51 <  void set_vz(double vz) {vel[offsetZ] = vz;}
52 <  
53 <  double getFx() const   {return frc[offsetX];}
54 <  double getFy() const   {return frc[offsetY];}
55 <  double getFz() const   {return frc[offsetZ];}
56 <  void addFx(double add) {frc[offsetX] += add;}
57 <  void addFy(double add) {frc[offsetY] += add;}
58 <  void addFz(double add) {frc[offsetZ] += add;}
21 >  void getVel( double theV[3] );
22 >  void setVel( double theV[3] );
23 >
24 >  void getFrc( double theF[3] );
25 >  void addFrc( double theF[3] );
26 >
27    virtual void zeroForces() = 0;
28  
29    double getMass() const {return c_mass;}
30    void setMass(double mass) {c_mass = mass;}
31 +
32 +  double getEamRcut() const {return myEamRcut;}
33 +  void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
34    
35    double getSigma() const {return c_sigma;}
36    void setSigma(double sigma) {c_sigma = sigma;}
# Line 92 | Line 63 | class Atom{ (public)
63    void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
64    int isLJ( void )    { return is_LJ; }
65  
66 <  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
66 >  void setVDW( void )        { is_VDW = 1; is_LJ = 0; }
67    int isVDW( void )    { return is_VDW; }
68  
69 +  void setEAM( void ) { is_EAM = 1; }
70 +  int  isEAM( void ) { return is_EAM; }
71 +
72 +  void setCharged( void ) { is_charged = 1; }
73 +  int isCharged( void ) { return is_charged; }
74 +
75    virtual int isDirectional( void ) = 0;
76  
77  
78   protected:
79    
80 +  SimState* myConfig;
81 +
82 +  double* pos; // the position array
83 +  double* vel; // the velocity array
84 +  double* frc; // the forc array
85 +  double* trq; // the torque vector  ( space fixed )
86 +  double* Amat; // the rotation matrix
87 +  double* mu;   // the array of dipole moments
88 +  double* ul;   // the lab frame unit directional vector
89 +
90    double c_mass; /* the mass of the atom in amu */
91    double c_sigma; /* the sigma parameter for van der walls interactions */
92    double c_epslon; /* the esplon parameter for VDW interactions */
93    double c_covalent; // The covalent radius of the atom.
94  
95 +  double myEamRcut; // Atom rcut for eam defined by the forcefield.
96 +
97    int index; /* set the atom's index */
98    int offset; // the atom's offset in the storage array
99    int offsetX, offsetY, offsetZ;
# Line 119 | Line 108 | class Atom{ (public)
108    int c_n_hyd; // the number of hydrogens bonded to the atom
109    
110    int has_dipole; // dipole boolean
111 <  int is_VDW;    // VDW boolean
112 <  int is_LJ;    // LJ boolean
111 >  int is_VDW;     // VDW boolean
112 >  int is_LJ;      // LJ boolean
113 >  int is_EAM;     // EAM boolean
114 >  int is_charged;   // isCharge boolean
115  
116 +  bool hasCoords;
117 +
118   #ifdef IS_MPI
119    int myGlobalIndex;
120   #endif
# Line 131 | Line 124 | class GeneralAtom : public Atom{ (public)
124   class GeneralAtom : public Atom{
125  
126   public:
127 <  GeneralAtom(int theIndex): Atom(theIndex){}
127 >  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
128    virtual ~GeneralAtom(){}
129  
130    int isDirectional( void ){ return 0; }
131 <  void zeroForces() {
139 <    frc[offsetX] = 0.0;
140 <    frc[offsetY] = 0.0;
141 <    frc[offsetZ] = 0.0;
142 <  }
131 >  void zeroForces( void );
132   };
133  
134   class DirectionalAtom : public Atom {
135    
136   public:
137 <  DirectionalAtom(int theIndex) : Atom(theIndex)
137 >  DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex,
138 >                                                            theConfig)
139    {
140      ssdIdentity = 0;
141      sux = 0.0;
142      suy = 0.0;
143      suz = 0.0;
144 +    myMu = 0.0;
145    }
146    virtual ~DirectionalAtom() {}
147  
148 +  virtual void setCoords(void);
149 +
150    void printAmatIndex( void );
151  
152    int isDirectional(void) { return 1; }
# Line 161 | Line 154 | class DirectionalAtom : public Atom { (public)
154    void setSSD( int value) { ssdIdentity = value; }
155    int isSSD(void) {return ssdIdentity; }
156  
164 –  void setA( double the_A[3][3] );
165 –
166 –  void setI( double the_I[3][3] );
167 –
168 –  void setQ( double the_q[4] );
157    
158    void setEuler( double phi, double theta, double psi );
159 +
160 +  double getSUx( void ) { return sux; }
161 +  double getSUy( void ) { return suy; }
162 +  double getSUz( void ) { return suz; }
163    
164    void setSUx( double the_sux ) { sux = the_sux; }
165    void setSUy( double the_suy ) { suy = the_suy; }
166    void setSUz( double the_suz ) { suz = the_suz; }
167  
168 <  void setJx( double the_jx ) { jx = the_jx; }
177 <  void setJy( double the_jy ) { jy = the_jy; }
178 <  void setJz( double the_jz ) { jz = the_jz; }
179 <    
180 <  void addTx( double the_tx ) { trq[offsetX] += the_tx;}
181 <  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
182 <  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
168 >  void zeroForces();
169  
184 –  void zeroForces() {
185 –    frc[offsetX] = 0.0;
186 –    frc[offsetY] = 0.0;
187 –    frc[offsetZ] = 0.0;
188 –
189 –    trq[offsetX] = 0.0;
190 –    trq[offsetY] = 0.0;
191 –    trq[offsetZ] = 0.0;
192 –  }
193 –
170    void getA( double the_A[3][3] ); // get the full rotation matrix
171 +  void setA( double the_A[3][3] );
172  
196 –  double getSUx( void ) { return sux; }
197 –  double getSUy( void ) { return suy; }
198 –  double getSUz( void ) { return suz; }
199 –
173    void getU( double the_u[3] ); // get the unit vetor
174 +  void updateU( void );
175 +
176    void getQ( double the_q[4] ); // get the quanternions
177 +  void setQ( double the_q[4] );
178  
179 +  void getJ( double theJ[3] );
180 +  void setJ( double theJ[3] );
181 +
182    double getJx( void ) { return jx; }
183    double getJy( void ) { return jy; }
184    double getJz( void ) { return jz; }
185  
186 <  double getTx( void ) { return trq[offsetX];}
187 <  double getTy( void ) { return trq[offsetY]; }
188 <  double getTz( void ) { return trq[offsetZ]; }
186 >  void setJx( double the_jx ) { jx = the_jx; }
187 >  void setJy( double the_jy ) { jy = the_jy; }
188 >  void setJz( double the_jz ) { jz = the_jz; }
189  
190 +  void getTrq( double theT[3] );
191 +  void addTrq( double theT[3] );
192 +
193 +  //  double getTx( void ) { return trq[offsetX];}
194 +  //  double getTy( void ) { return trq[offsetY]; }
195 +  //  double getTz( void ) { return trq[offsetZ]; }
196 +
197 +  void setI( double the_I[3][3] );
198 +  void getI( double the_I[3][3] );
199 +  
200    double getIxx( void ) { return Ixx; }
201    double getIxy( void ) { return Ixy; }
202    double getIxz( void ) { return Ixz; }
# Line 220 | Line 209 | class DirectionalAtom : public Atom { (public)
209    double getIzy( void ) { return Izy; }
210    double getIzz( void ) { return Izz; }
211  
212 <  double getMu( void ) { return mu[index]; }
213 <  void setMu( double the_mu ) { mu[index] = the_mu; }
212 >  double getMu( void );
213 >  void setMu( double the_mu );
214  
215    void lab2Body( double r[3] );
216    void body2Lab( double r[3] );
228 –  void updateU( void );
217  
218 +
219 +  // Four functions added for derivatives with respect to Euler Angles:
220 +  // (Needed for minimization routines):
221 +
222 +  void getGrad(double gradient[6] );
223 +  void getEulerAngles( double myEuler[3] );
224 +
225 +  double max(double x, double y);
226 +  double min(double x, double y);
227 +  
228 +
229   private:
230    int dIndex;
231  
232 +  double myMu;
233 +
234    double sux, suy, suz; // the standard unit vector    ( body fixed )
235    double jx, jy, jz;    // the angular momentum vector ( body fixed )
236    

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