36 |
|
static double* getMuArray( void ) { return mu; } |
37 |
|
static double* getUlArray( void ) { return ul; } |
38 |
|
|
39 |
+ |
void getPos( double theP[3] ); |
40 |
+ |
void setPos( double theP[3] ); |
41 |
+ |
|
42 |
|
double getX() const {return pos[offsetX];} |
43 |
|
double getY() const {return pos[offsetY];} |
44 |
|
double getZ() const {return pos[offsetZ];} |
46 |
|
void setY(double y) {pos[offsetY] = y;} |
47 |
|
void setZ(double z) {pos[offsetZ] = z;} |
48 |
|
|
49 |
+ |
void getVel( double theV[3] ); |
50 |
+ |
void setVel( double theV[3] ); |
51 |
+ |
|
52 |
|
double get_vx() const {return vel[offsetX];} |
53 |
|
double get_vy() const {return vel[offsetY];} |
54 |
|
double get_vz() const {return vel[offsetZ];} |
56 |
|
void set_vy(double vy) {vel[offsetY] = vy;} |
57 |
|
void set_vz(double vz) {vel[offsetZ] = vz;} |
58 |
|
|
59 |
+ |
|
60 |
+ |
void getFrc( double theF[3] ); |
61 |
+ |
void addFrc( double theF[3] ); |
62 |
+ |
|
63 |
|
double getFx() const {return frc[offsetX];} |
64 |
|
double getFy() const {return frc[offsetY];} |
65 |
|
double getFz() const {return frc[offsetZ];} |
70 |
|
|
71 |
|
double getMass() const {return c_mass;} |
72 |
|
void setMass(double mass) {c_mass = mass;} |
73 |
+ |
|
74 |
+ |
double getEamRcut() const {return myEamRcut;} |
75 |
+ |
void setEamRcut(double eamRcut) {myEamRcut = eamRcut;} |
76 |
|
|
77 |
|
double getSigma() const {return c_sigma;} |
78 |
|
void setSigma(double sigma) {c_sigma = sigma;} |
108 |
|
void seVDW( void ) { is_VDW = 1; is_LJ = 0; } |
109 |
|
int isVDW( void ) { return is_VDW; } |
110 |
|
|
111 |
+ |
void setEAM( void ) { is_EAM = 1; } |
112 |
+ |
int isEAM( void ) { return is_EAM; } |
113 |
+ |
|
114 |
|
virtual int isDirectional( void ) = 0; |
115 |
|
|
116 |
|
|
121 |
|
double c_epslon; /* the esplon parameter for VDW interactions */ |
122 |
|
double c_covalent; // The covalent radius of the atom. |
123 |
|
|
124 |
+ |
double myEamRcut; // Atom rcut for eam defined by the forcefield. |
125 |
+ |
|
126 |
|
int index; /* set the atom's index */ |
127 |
|
int offset; // the atom's offset in the storage array |
128 |
|
int offsetX, offsetY, offsetZ; |
139 |
|
int has_dipole; // dipole boolean |
140 |
|
int is_VDW; // VDW boolean |
141 |
|
int is_LJ; // LJ boolean |
142 |
+ |
int is_EAM; //EAM boolean |
143 |
|
|
144 |
|
#ifdef IS_MPI |
145 |
|
int myGlobalIndex; |
173 |
|
} |
174 |
|
virtual ~DirectionalAtom() {} |
175 |
|
|
176 |
+ |
void printAmatIndex( void ); |
177 |
+ |
|
178 |
|
int isDirectional(void) { return 1; } |
179 |
|
|
180 |
|
void setSSD( int value) { ssdIdentity = value; } |
181 |
|
int isSSD(void) {return ssdIdentity; } |
182 |
|
|
162 |
– |
void setA( double the_A[3][3] ); |
163 |
– |
|
164 |
– |
void setI( double the_I[3][3] ); |
165 |
– |
|
166 |
– |
void setQ( double the_q[4] ); |
183 |
|
|
184 |
|
void setEuler( double phi, double theta, double psi ); |
185 |
+ |
|
186 |
+ |
double getSUx( void ) { return sux; } |
187 |
+ |
double getSUy( void ) { return suy; } |
188 |
+ |
double getSUz( void ) { return suz; } |
189 |
|
|
190 |
|
void setSUx( double the_sux ) { sux = the_sux; } |
191 |
|
void setSUy( double the_suy ) { suy = the_suy; } |
192 |
|
void setSUz( double the_suz ) { suz = the_suz; } |
193 |
|
|
174 |
– |
void setJx( double the_jx ) { jx = the_jx; } |
175 |
– |
void setJy( double the_jy ) { jy = the_jy; } |
176 |
– |
void setJz( double the_jz ) { jz = the_jz; } |
177 |
– |
|
178 |
– |
void addTx( double the_tx ) { trq[offsetX] += the_tx;} |
179 |
– |
void addTy( double the_ty ) { trq[offsetY] += the_ty;} |
180 |
– |
void addTz( double the_tz ) { trq[offsetZ] += the_tz;} |
181 |
– |
|
194 |
|
void zeroForces() { |
195 |
|
frc[offsetX] = 0.0; |
196 |
|
frc[offsetY] = 0.0; |
200 |
|
trq[offsetY] = 0.0; |
201 |
|
trq[offsetZ] = 0.0; |
202 |
|
} |
191 |
– |
|
192 |
– |
double getAxx( void ) { return Amat[Axx]; } |
193 |
– |
double getAxy( void ) { return Amat[Axy]; } |
194 |
– |
double getAxz( void ) { return Amat[Axz]; } |
195 |
– |
|
196 |
– |
double getAyx( void ) { return Amat[Ayx]; } |
197 |
– |
double getAyy( void ) { return Amat[Ayy]; } |
198 |
– |
double getAyz( void ) { return Amat[Ayz]; } |
199 |
– |
|
200 |
– |
double getAzx( void ) { return Amat[Azx]; } |
201 |
– |
double getAzy( void ) { return Amat[Azy]; } |
202 |
– |
double getAzz( void ) { return Amat[Azz]; } |
203 |
|
|
204 |
|
void getA( double the_A[3][3] ); // get the full rotation matrix |
205 |
+ |
void setA( double the_A[3][3] ); |
206 |
|
|
206 |
– |
double getSUx( void ) { return sux; } |
207 |
– |
double getSUy( void ) { return suy; } |
208 |
– |
double getSUz( void ) { return suz; } |
209 |
– |
|
207 |
|
void getU( double the_u[3] ); // get the unit vetor |
208 |
+ |
void updateU( void ); |
209 |
+ |
|
210 |
|
void getQ( double the_q[4] ); // get the quanternions |
211 |
+ |
void setQ( double the_q[4] ); |
212 |
|
|
213 |
+ |
void getJ( double theJ[3] ); |
214 |
+ |
void setJ( double theJ[3] ); |
215 |
+ |
|
216 |
|
double getJx( void ) { return jx; } |
217 |
|
double getJy( void ) { return jy; } |
218 |
|
double getJz( void ) { return jz; } |
219 |
|
|
220 |
< |
double getTx( void ) { return trq[offsetX];} |
221 |
< |
double getTy( void ) { return trq[offsetY]; } |
222 |
< |
double getTz( void ) { return trq[offsetZ]; } |
220 |
> |
void setJx( double the_jx ) { jx = the_jx; } |
221 |
> |
void setJy( double the_jy ) { jy = the_jy; } |
222 |
> |
void setJz( double the_jz ) { jz = the_jz; } |
223 |
|
|
224 |
+ |
void getTrq( double theT[3] ); |
225 |
+ |
void addTrq( double theT[3] ); |
226 |
+ |
|
227 |
+ |
// double getTx( void ) { return trq[offsetX];} |
228 |
+ |
// double getTy( void ) { return trq[offsetY]; } |
229 |
+ |
// double getTz( void ) { return trq[offsetZ]; } |
230 |
+ |
|
231 |
+ |
void addTx( double the_tx ) { trq[offsetX] += the_tx;} |
232 |
+ |
void addTy( double the_ty ) { trq[offsetY] += the_ty;} |
233 |
+ |
void addTz( double the_tz ) { trq[offsetZ] += the_tz;} |
234 |
+ |
|
235 |
+ |
void setI( double the_I[3][3] ); |
236 |
+ |
void getI( double the_I[3][3] ); |
237 |
+ |
|
238 |
|
double getIxx( void ) { return Ixx; } |
239 |
|
double getIxy( void ) { return Ixy; } |
240 |
|
double getIxz( void ) { return Ixz; } |
246 |
|
double getIzx( void ) { return Izx; } |
247 |
|
double getIzy( void ) { return Izy; } |
248 |
|
double getIzz( void ) { return Izz; } |
249 |
+ |
|
250 |
|
|
251 |
|
double getMu( void ) { return mu[index]; } |
252 |
|
void setMu( double the_mu ) { mu[index] = the_mu; } |
253 |
|
|
254 |
|
void lab2Body( double r[3] ); |
255 |
|
void body2Lab( double r[3] ); |
238 |
– |
void updateU( void ); |
256 |
|
|
257 |
+ |
|
258 |
|
private: |
259 |
|
int dIndex; |
260 |
|
|