1 |
mmeineke |
377 |
#ifndef _ATOM_H_ |
2 |
|
|
#define _ATOM_H_ |
3 |
|
|
|
4 |
gezelter |
829 |
#include <string.h> |
5 |
|
|
#include <stdlib.h> |
6 |
mmeineke |
377 |
#include <iostream> |
7 |
|
|
|
8 |
mmeineke |
670 |
#include "SimState.hpp" |
9 |
|
|
|
10 |
mmeineke |
377 |
class Atom{ |
11 |
|
|
public: |
12 |
|
|
|
13 |
mmeineke |
670 |
Atom(int theIndex, SimState* theConfig ); |
14 |
gezelter |
409 |
virtual ~Atom() {} |
15 |
mmeineke |
377 |
|
16 |
tim |
689 |
virtual void setCoords(void); |
17 |
mmeineke |
377 |
|
18 |
mmeineke |
599 |
void getPos( double theP[3] ); |
19 |
|
|
void setPos( double theP[3] ); |
20 |
|
|
|
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 |
mmeineke |
377 |
virtual void zeroForces() = 0; |
28 |
|
|
|
29 |
|
|
double getMass() const {return c_mass;} |
30 |
|
|
void setMass(double mass) {c_mass = mass;} |
31 |
chuckv |
669 |
|
32 |
|
|
double getEamRcut() const {return myEamRcut;} |
33 |
|
|
void setEamRcut(double eamRcut) {myEamRcut = eamRcut;} |
34 |
mmeineke |
377 |
|
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 |
|
|
|
44 |
|
|
int getIndex() const {return index;} |
45 |
gezelter |
409 |
void setIndex(int theIndex); |
46 |
mmeineke |
377 |
char *getType() {return c_name;} |
47 |
|
|
void setType(char * name) {strcpy(c_name,name);} |
48 |
|
|
|
49 |
|
|
int getIdent( void ) { return ident; } |
50 |
|
|
void setIdent( int info ) { ident = info; } |
51 |
|
|
|
52 |
|
|
#ifdef IS_MPI |
53 |
|
|
int getGlobalIndex( void ) { return myGlobalIndex; } |
54 |
|
|
void setGlobalIndex( int info ) { myGlobalIndex = info; } |
55 |
|
|
#endif // is_mpi |
56 |
|
|
|
57 |
|
|
void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;} |
58 |
|
|
int get_n_hydrogens() const {return c_n_hyd;} |
59 |
|
|
|
60 |
|
|
void setHasDipole( int value ) { has_dipole = value; } |
61 |
|
|
int hasDipole( void ) { return has_dipole; } |
62 |
|
|
|
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; } |
67 |
|
|
int isVDW( void ) { return is_VDW; } |
68 |
|
|
|
69 |
chuckv |
631 |
void setEAM( void ) { is_EAM = 1; } |
70 |
|
|
int isEAM( void ) { return is_EAM; } |
71 |
|
|
|
72 |
mmeineke |
377 |
virtual int isDirectional( void ) = 0; |
73 |
|
|
|
74 |
|
|
|
75 |
|
|
protected: |
76 |
|
|
|
77 |
mmeineke |
670 |
SimState* myConfig; |
78 |
|
|
|
79 |
|
|
double* pos; // the position array |
80 |
|
|
double* vel; // the velocity array |
81 |
|
|
double* frc; // the forc array |
82 |
|
|
double* trq; // the torque vector ( space fixed ) |
83 |
|
|
double* Amat; // the rotation matrix |
84 |
|
|
double* mu; // the array of dipole moments |
85 |
|
|
double* ul; // the lab frame unit directional vector |
86 |
|
|
|
87 |
mmeineke |
377 |
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. |
91 |
|
|
|
92 |
chuckv |
669 |
double myEamRcut; // Atom rcut for eam defined by the forcefield. |
93 |
|
|
|
94 |
mmeineke |
377 |
int index; /* set the atom's index */ |
95 |
|
|
int offset; // the atom's offset in the storage array |
96 |
|
|
int offsetX, offsetY, offsetZ; |
97 |
|
|
|
98 |
|
|
int Axx, Axy, Axz; // the rotational matrix indices |
99 |
|
|
int Ayx, Ayy, Ayz; |
100 |
|
|
int Azx, Azy, Azz; |
101 |
|
|
|
102 |
|
|
char c_name[100]; /* it's name */ |
103 |
|
|
int ident; // it's unique numeric identity. |
104 |
|
|
|
105 |
|
|
int c_n_hyd; // the number of hydrogens bonded to the atom |
106 |
|
|
|
107 |
|
|
int has_dipole; // dipole boolean |
108 |
|
|
int is_VDW; // VDW boolean |
109 |
|
|
int is_LJ; // LJ boolean |
110 |
chuckv |
631 |
int is_EAM; //EAM boolean |
111 |
mmeineke |
377 |
|
112 |
mmeineke |
670 |
bool hasCoords; |
113 |
|
|
|
114 |
mmeineke |
377 |
#ifdef IS_MPI |
115 |
|
|
int myGlobalIndex; |
116 |
|
|
#endif |
117 |
|
|
|
118 |
|
|
}; |
119 |
|
|
|
120 |
|
|
class GeneralAtom : public Atom{ |
121 |
|
|
|
122 |
|
|
public: |
123 |
mmeineke |
670 |
GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){} |
124 |
mmeineke |
377 |
virtual ~GeneralAtom(){} |
125 |
|
|
|
126 |
|
|
int isDirectional( void ){ return 0; } |
127 |
mmeineke |
670 |
void zeroForces( void ); |
128 |
mmeineke |
377 |
}; |
129 |
|
|
|
130 |
|
|
class DirectionalAtom : public Atom { |
131 |
|
|
|
132 |
|
|
public: |
133 |
mmeineke |
670 |
DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex, |
134 |
|
|
theConfig) |
135 |
mmeineke |
377 |
{ |
136 |
|
|
ssdIdentity = 0; |
137 |
|
|
sux = 0.0; |
138 |
|
|
suy = 0.0; |
139 |
|
|
suz = 0.0; |
140 |
tim |
689 |
myMu = 0.0; |
141 |
mmeineke |
377 |
} |
142 |
|
|
virtual ~DirectionalAtom() {} |
143 |
|
|
|
144 |
tim |
689 |
virtual void setCoords(void); |
145 |
|
|
|
146 |
mmeineke |
597 |
void printAmatIndex( void ); |
147 |
|
|
|
148 |
mmeineke |
377 |
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 |
mmeineke |
599 |
|
156 |
|
|
double getSUx( void ) { return sux; } |
157 |
|
|
double getSUy( void ) { return suy; } |
158 |
|
|
double getSUz( void ) { return suz; } |
159 |
mmeineke |
377 |
|
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 |
mmeineke |
670 |
void zeroForces(); |
165 |
mmeineke |
377 |
|
166 |
|
|
void getA( double the_A[3][3] ); // get the full rotation matrix |
167 |
mmeineke |
599 |
void setA( double the_A[3][3] ); |
168 |
mmeineke |
377 |
|
169 |
mmeineke |
599 |
void getU( double the_u[3] ); // get the unit vetor |
170 |
|
|
void updateU( void ); |
171 |
mmeineke |
377 |
|
172 |
|
|
void getQ( double the_q[4] ); // get the quanternions |
173 |
mmeineke |
599 |
void setQ( double the_q[4] ); |
174 |
mmeineke |
377 |
|
175 |
mmeineke |
599 |
void getJ( double theJ[3] ); |
176 |
|
|
void setJ( double theJ[3] ); |
177 |
|
|
|
178 |
mmeineke |
377 |
double getJx( void ) { return jx; } |
179 |
|
|
double getJy( void ) { return jy; } |
180 |
|
|
double getJz( void ) { return jz; } |
181 |
|
|
|
182 |
mmeineke |
599 |
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 |
gezelter |
611 |
// double getTx( void ) { return trq[offsetX];} |
190 |
|
|
// double getTy( void ) { return trq[offsetY]; } |
191 |
|
|
// double getTz( void ) { return trq[offsetZ]; } |
192 |
mmeineke |
377 |
|
193 |
mmeineke |
599 |
void setI( double the_I[3][3] ); |
194 |
|
|
void getI( double the_I[3][3] ); |
195 |
|
|
|
196 |
mmeineke |
377 |
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 |
mmeineke |
670 |
double getMu( void ); |
209 |
|
|
void setMu( double the_mu ); |
210 |
mmeineke |
377 |
|
211 |
|
|
void lab2Body( double r[3] ); |
212 |
|
|
void body2Lab( double r[3] ); |
213 |
|
|
|
214 |
mmeineke |
599 |
|
215 |
mmeineke |
377 |
private: |
216 |
|
|
int dIndex; |
217 |
|
|
|
218 |
tim |
689 |
double myMu; |
219 |
|
|
|
220 |
mmeineke |
377 |
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 |
|
|
|
231 |
|
|
#endif |