1 |
+ |
#include <iostream> |
2 |
+ |
|
3 |
+ |
using namespace std; |
4 |
+ |
|
5 |
|
#include "Atom.hpp" |
6 |
|
|
7 |
+ |
double* Atom::pos; // the position array |
8 |
+ |
double* Atom::vel; // the velocity array |
9 |
+ |
double* Atom::frc; // the forc array |
10 |
+ |
double* Atom::trq; // the torque vector ( space fixed ) |
11 |
+ |
double* Atom::Amat; // the rotation matrix |
12 |
+ |
double* Atom::mu; // the array of dipole moments |
13 |
+ |
double* Atom::ul; // the lab frame unit directional vector |
14 |
+ |
int Atom::nElements; |
15 |
+ |
|
16 |
|
Atom::Atom(int theIndex) { |
17 |
|
c_n_hyd = 0; |
18 |
|
has_dipole = 0; |
38 |
|
Azz = Axx+8; |
39 |
|
} |
40 |
|
|
41 |
< |
void Atom::createArrays (int nElements) { |
41 |
> |
void Atom::createArrays (int the_nElements) { |
42 |
|
int i; |
43 |
|
|
44 |
+ |
nElements = the_nElements; |
45 |
+ |
|
46 |
|
pos = new double[nElements*3]; |
47 |
|
vel = new double[nElements*3]; |
48 |
|
frc = new double[nElements*3]; |
132 |
|
|
133 |
|
for(i = 0; i < 3*nAdded; i++) { |
134 |
|
j = i + 3*nElements; |
135 |
< |
new_pos[j] = pos[i]; |
136 |
< |
new_vel[j] = vel[i]; |
137 |
< |
new_frc[j] = frc[i]; |
138 |
< |
new_trq[j] = trq[i]; |
139 |
< |
new_ul[j] = ul[i]; |
135 |
> |
new_pos[j] = Apos[i]; |
136 |
> |
new_vel[j] = Avel[i]; |
137 |
> |
new_frc[j] = Afrc[i]; |
138 |
> |
new_trq[j] = Atrq[i]; |
139 |
> |
new_ul[j] = Aul[i]; |
140 |
|
} |
141 |
|
|
142 |
|
for (i = 0; i < 9*nElements; i++) { |
145 |
|
|
146 |
|
for(i = 0; i < 9*nAdded; i++) { |
147 |
|
j = i + 9*nElements; |
148 |
< |
new_Amat[j] = Amat[i]; |
148 |
> |
new_Amat[j] = AAmat[i]; |
149 |
|
} |
150 |
|
|
151 |
|
for (i = 0; i < nElements; i++) { |
154 |
|
|
155 |
|
for(i = 0; i < nAdded; i++) { |
156 |
|
j = i + nElements; |
157 |
< |
new_mu[j] = mu[i]; |
157 |
> |
new_mu[j] = Amu[i]; |
158 |
|
} |
159 |
|
|
160 |
|
delete[] pos; |
243 |
|
mu = new_mu; |
244 |
|
|
245 |
|
nElements = nNew; |
246 |
+ |
} |
247 |
+ |
|
248 |
+ |
|
249 |
+ |
void Atom::getPos( double theP[3] ){ |
250 |
+ |
|
251 |
+ |
theP[0] = pos[offsetX]; |
252 |
+ |
theP[1] = pos[offsetY]; |
253 |
+ |
theP[2] = pos[offsetZ]; |
254 |
|
} |
255 |
+ |
|
256 |
+ |
void Atom::setPos( double theP[3] ){ |
257 |
+ |
|
258 |
+ |
pos[offsetX] = theP[0]; |
259 |
+ |
pos[offsetY] = theP[1]; |
260 |
+ |
pos[offsetZ] = theP[2]; |
261 |
+ |
} |
262 |
+ |
|
263 |
+ |
void Atom::getVel( double theV[3] ){ |
264 |
+ |
|
265 |
+ |
theV[0] = vel[offsetX]; |
266 |
+ |
theV[1] = vel[offsetY]; |
267 |
+ |
theV[2] = vel[offsetZ]; |
268 |
+ |
} |
269 |
+ |
|
270 |
+ |
void Atom::setVel( double theV[3] ){ |
271 |
+ |
|
272 |
+ |
vel[offsetX] = theV[0]; |
273 |
+ |
vel[offsetY] = theV[1]; |
274 |
+ |
vel[offsetZ] = theV[2]; |
275 |
+ |
} |
276 |
+ |
|
277 |
+ |
void Atom::getFrc( double theF[3] ){ |
278 |
+ |
|
279 |
+ |
theF[0] = frc[offsetX]; |
280 |
+ |
theF[1] = frc[offsetY]; |
281 |
+ |
theF[2] = frc[offsetZ]; |
282 |
+ |
} |
283 |
+ |
|
284 |
+ |
void Atom::addFrc( double theF[3] ){ |
285 |
+ |
|
286 |
+ |
frc[offsetX] += theF[0]; |
287 |
+ |
frc[offsetY] += theF[1]; |
288 |
+ |
frc[offsetZ] += theF[2]; |
289 |
+ |
} |