# | Line 7 | Line 7 | |
---|---|---|
7 | #include <unistd.h> | |
8 | #endif //is_mpi | |
9 | ||
10 | + | #ifdef PROFILE |
11 | + | #include "mdProfile.hpp" |
12 | + | #endif // profile |
13 | + | |
14 | #include "Integrator.hpp" | |
15 | #include "simError.h" | |
16 | ||
# | Line 25 | Line 29 | template<typename T> Integrator<T>::Integrator(SimInfo | |
29 | if (info->the_integrator != NULL){ | |
30 | delete info->the_integrator; | |
31 | } | |
32 | < | |
32 | > | |
33 | nAtoms = info->n_atoms; | |
34 | ||
35 | // check for constraints | |
# | Line 158 | Line 162 | template<typename T> void Integrator<T>::integrate(voi | |
162 | double currThermal; | |
163 | double currStatus; | |
164 | double currReset; | |
165 | < | |
165 | > | |
166 | int calcPot, calcStress; | |
167 | ||
168 | tStats = new Thermo(info); | |
# | Line 179 | Line 183 | template<typename T> void Integrator<T>::integrate(voi | |
183 | if (nConstrained){ | |
184 | preMove(); | |
185 | constrainA(); | |
186 | < | calcForce(1, 1); |
186 | > | calcForce(1, 1); |
187 | constrainB(); | |
188 | } | |
189 | ||
# | Line 198 | Line 202 | template<typename T> void Integrator<T>::integrate(voi | |
202 | statOut->writeStat(info->getTime()); | |
203 | ||
204 | ||
201 | – | |
205 | #ifdef IS_MPI | |
206 | strcpy(checkPointMsg, "The integrator is ready to go."); | |
207 | MPIcheckPoint(); | |
# | Line 210 | Line 213 | template<typename T> void Integrator<T>::integrate(voi | |
213 | calcStress = 1; | |
214 | } | |
215 | ||
216 | + | #ifdef PROFILE |
217 | + | startProfile( pro1 ); |
218 | + | #endif |
219 | + | |
220 | integrateStep(calcPot, calcStress); | |
221 | ||
222 | + | #ifdef PROFILE |
223 | + | endProfile( pro1 ); |
224 | + | |
225 | + | startProfile( pro2 ); |
226 | + | #endif // profile |
227 | + | |
228 | info->incrTime(dt); | |
229 | ||
230 | if (info->setTemp){ | |
# | Line 227 | Line 240 | template<typename T> void Integrator<T>::integrate(voi | |
240 | } | |
241 | ||
242 | if (info->getTime() >= currStatus){ | |
243 | < | statOut->writeStat(info->getTime()); |
244 | < | calcPot = 0; |
243 | > | statOut->writeStat(info->getTime()); |
244 | > | calcPot = 0; |
245 | calcStress = 0; | |
246 | currStatus += statusTime; | |
247 | < | } |
247 | > | } |
248 | ||
249 | if (info->resetIntegrator){ | |
250 | if (info->getTime() >= currReset){ | |
# | Line 239 | Line 252 | template<typename T> void Integrator<T>::integrate(voi | |
252 | currReset += resetTime; | |
253 | } | |
254 | } | |
255 | + | |
256 | + | #ifdef PROFILE |
257 | + | endProfile( pro2 ); |
258 | + | #endif //profile |
259 | ||
260 | #ifdef IS_MPI | |
261 | strcpy(checkPointMsg, "successfully took a time step."); | |
# | Line 257 | Line 274 | template<typename T> void Integrator<T>::integrateStep | |
274 | template<typename T> void Integrator<T>::integrateStep(int calcPot, | |
275 | int calcStress){ | |
276 | // Position full step, and velocity half step | |
277 | + | |
278 | + | #ifdef PROFILE |
279 | + | startProfile(pro3); |
280 | + | #endif //profile |
281 | + | |
282 | preMove(); | |
283 | ||
284 | < | moveA(); |
284 | > | #ifdef PROFILE |
285 | > | endProfile(pro3); |
286 | ||
287 | + | startProfile(pro4); |
288 | + | #endif // profile |
289 | ||
290 | + | moveA(); |
291 | ||
292 | + | #ifdef PROFILE |
293 | + | endProfile(pro4); |
294 | + | |
295 | + | startProfile(pro5); |
296 | + | #endif//profile |
297 | ||
298 | + | |
299 | #ifdef IS_MPI | |
300 | strcpy(checkPointMsg, "Succesful moveA\n"); | |
301 | MPIcheckPoint(); | |
# | Line 279 | Line 311 | template<typename T> void Integrator<T>::integrateStep | |
311 | MPIcheckPoint(); | |
312 | #endif // is_mpi | |
313 | ||
314 | + | #ifdef PROFILE |
315 | + | endProfile( pro5 ); |
316 | ||
317 | + | startProfile( pro6 ); |
318 | + | #endif //profile |
319 | + | |
320 | // finish the velocity half step | |
321 | ||
322 | moveB(); | |
286 | – | |
323 | ||
324 | + | #ifdef PROFILE |
325 | + | endProfile(pro6); |
326 | + | #endif // profile |
327 | ||
328 | #ifdef IS_MPI | |
329 | strcpy(checkPointMsg, "Succesful moveB\n"); | |
# | Line 366 | Line 405 | template<typename T> void Integrator<T>::moveB(void){ | |
405 | if (atoms[i]->isDirectional()){ | |
406 | dAtom = (DirectionalAtom *) atoms[i]; | |
407 | ||
408 | < | // get and convert the torque to body frame |
408 | > | // get and convert the torque to body frame |
409 | ||
410 | dAtom->getTrq(Tb); | |
411 | dAtom->lab2Body(Tb); | |
# | Line 658 | Line 697 | template<typename T> void Integrator<T>::rotationPropa | |
697 | ||
698 | dAtom->getA(A); | |
699 | dAtom->getI(I); | |
700 | < | |
701 | < | // rotate about the x-axis |
700 | > | |
701 | > | // rotate about the x-axis |
702 | angle = dt2 * ji[0] / I[0][0]; | |
703 | < | this->rotate( 1, 2, angle, ji, A ); |
704 | < | |
703 | > | this->rotate( 1, 2, angle, ji, A ); |
704 | > | |
705 | // rotate about the y-axis | |
706 | angle = dt2 * ji[1] / I[1][1]; | |
707 | this->rotate( 2, 0, angle, ji, A ); | |
708 | < | |
708 | > | |
709 | // rotate about the z-axis | |
710 | angle = dt * ji[2] / I[2][2]; | |
711 | this->rotate( 0, 1, angle, ji, A); | |
712 | < | |
712 | > | |
713 | // rotate about the y-axis | |
714 | angle = dt2 * ji[1] / I[1][1]; | |
715 | this->rotate( 2, 0, angle, ji, A ); | |
716 | < | |
716 | > | |
717 | // rotate about the x-axis | |
718 | angle = dt2 * ji[0] / I[0][0]; | |
719 | this->rotate( 1, 2, angle, ji, A ); | |
720 | < | |
721 | < | dAtom->setA( A ); |
720 | > | |
721 | > | dAtom->setA( A ); |
722 | } | |
723 | ||
724 | template<typename T> void Integrator<T>::rotate(int axes1, int axes2, | |
# | Line 747 | Line 786 | template<typename T> void Integrator<T>::rotate(int ax | |
786 | } | |
787 | } | |
788 | ||
789 | < | // rotate the Rotation matrix acording to: |
789 | > | // rotate the Rotation matrix acording to: |
790 | // A[][] = A[][] * transpose(rot[][]) | |
791 | ||
792 | ||
# | Line 776 | Line 815 | template<typename T> double Integrator<T>::getConserve | |
815 | template<typename T> double Integrator<T>::getConservedQuantity(void){ | |
816 | return tStats->getTotalE(); | |
817 | } | |
818 | + | template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
819 | + | //By default, return a null string |
820 | + | //The reason we use string instead of char* is that if we use char*, we will |
821 | + | //return a pointer point to local variable which might cause problem |
822 | + | return string(); |
823 | + | } |
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