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#include <unistd.h> |
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#endif //is_mpi |
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|
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#ifdef PROFILE |
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#include "mdProfile.hpp" |
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#endif // profile |
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|
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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if (info->the_integrator != NULL){ |
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delete info->the_integrator; |
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} |
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< |
|
32 |
> |
|
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nAtoms = info->n_atoms; |
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|
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// check for constraints |
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double currThermal; |
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double currStatus; |
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double currReset; |
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< |
|
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> |
|
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int calcPot, calcStress; |
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|
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tStats = new Thermo(info); |
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if (nConstrained){ |
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preMove(); |
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constrainA(); |
186 |
< |
calcForce(1, 1); |
186 |
> |
calcForce(1, 1); |
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constrainB(); |
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} |
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|
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statOut->writeStat(info->getTime()); |
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|
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|
201 |
– |
|
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "The integrator is ready to go."); |
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MPIcheckPoint(); |
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calcStress = 1; |
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} |
215 |
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|
216 |
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#ifdef PROFILE |
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startProfile( pro1 ); |
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#endif |
219 |
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|
220 |
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integrateStep(calcPot, calcStress); |
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|
222 |
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#ifdef PROFILE |
223 |
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endProfile( pro1 ); |
224 |
+ |
|
225 |
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startProfile( pro2 ); |
226 |
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#endif // profile |
227 |
+ |
|
228 |
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info->incrTime(dt); |
229 |
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|
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if (info->setTemp){ |
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} |
241 |
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|
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if (info->getTime() >= currStatus){ |
243 |
< |
statOut->writeStat(info->getTime()); |
244 |
< |
calcPot = 0; |
243 |
> |
statOut->writeStat(info->getTime()); |
244 |
> |
calcPot = 0; |
245 |
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calcStress = 0; |
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currStatus += statusTime; |
247 |
< |
} |
247 |
> |
} |
248 |
|
|
249 |
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if (info->resetIntegrator){ |
250 |
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if (info->getTime() >= currReset){ |
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currReset += resetTime; |
253 |
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} |
254 |
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} |
255 |
+ |
|
256 |
+ |
#ifdef PROFILE |
257 |
+ |
endProfile( pro2 ); |
258 |
+ |
#endif //profile |
259 |
|
|
260 |
|
#ifdef IS_MPI |
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strcpy(checkPointMsg, "successfully took a time step."); |
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template<typename T> void Integrator<T>::integrateStep(int calcPot, |
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int calcStress){ |
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// Position full step, and velocity half step |
277 |
+ |
|
278 |
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#ifdef PROFILE |
279 |
+ |
startProfile(pro3); |
280 |
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#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(); |
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"); |
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); |
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, |
786 |
|
} |
787 |
|
} |
788 |
|
|
789 |
< |
// rotate the Rotation matrix acording to: |
789 |
> |
// rotate the Rotation matrix acording to: |
790 |
|
// A[][] = A[][] * transpose(rot[][]) |
791 |
|
|
792 |
|
|
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 |
+ |
} |