| 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 |
|
|
| 178 |
|
|
| 179 |
|
// initialize the forces before the first step |
| 180 |
|
|
| 177 |
– |
std::cerr << "Before initial Force calc\n"; |
| 178 |
– |
|
| 181 |
|
calcForce(1, 1); |
| 182 |
|
|
| 183 |
|
if (nConstrained){ |
| 185 |
|
constrainA(); |
| 186 |
|
calcForce(1, 1); |
| 187 |
|
constrainB(); |
| 186 |
– |
std::cerr << "premove done\n"; |
| 188 |
|
} |
| 189 |
< |
|
| 189 |
< |
|
| 190 |
< |
|
| 189 |
> |
|
| 190 |
|
if (info->setTemp){ |
| 191 |
|
thermalize(); |
| 192 |
|
} |
| 202 |
|
statOut->writeStat(info->getTime()); |
| 203 |
|
|
| 204 |
|
|
| 206 |
– |
|
| 205 |
|
#ifdef IS_MPI |
| 206 |
|
strcpy(checkPointMsg, "The integrator is ready to go."); |
| 207 |
|
MPIcheckPoint(); |
| 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){ |
| 252 |
|
currReset += resetTime; |
| 253 |
|
} |
| 254 |
|
} |
| 255 |
< |
|
| 256 |
< |
std::cerr << "done with time = " << info->getTime() << "\n"; |
| 255 |
> |
|
| 256 |
> |
#ifdef PROFILE |
| 257 |
> |
endProfile( pro2 ); |
| 258 |
> |
#endif //profile |
| 259 |
|
|
| 260 |
|
#ifdef IS_MPI |
| 261 |
|
strcpy(checkPointMsg, "successfully took a time step."); |
| 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 |
| 310 |
|
strcpy(checkPointMsg, "Succesful doForces\n"); |
| 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(); |
| 293 |
– |
|
| 323 |
|
|
| 324 |
+ |
#ifdef PROFILE |
| 325 |
+ |
endProfile(pro6); |
| 326 |
+ |
#endif // profile |
| 327 |
|
|
| 328 |
|
#ifdef IS_MPI |
| 329 |
|
strcpy(checkPointMsg, "Succesful moveB\n"); |
