| 27 |
|
|
| 28 |
|
nAtoms = info->n_atoms; |
| 29 |
|
|
| 30 |
– |
std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
| 31 |
– |
|
| 30 |
|
// check for constraints |
| 31 |
|
|
| 32 |
|
constrainedA = NULL; |
| 73 |
|
|
| 74 |
|
constrained = theArray[j]->is_constrained(); |
| 75 |
|
|
| 78 |
– |
std::cerr << "Is the folowing bond constrained \n"; |
| 79 |
– |
theArray[j]->printMe(); |
| 80 |
– |
|
| 76 |
|
if(constrained){ |
| 82 |
– |
|
| 83 |
– |
std::cerr << "Yes\n"; |
| 77 |
|
|
| 78 |
|
dummy_plug = theArray[j]->get_constraint(); |
| 79 |
|
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
| 83 |
|
nConstrained++; |
| 84 |
|
constrained = 0; |
| 85 |
|
} |
| 93 |
– |
else std::cerr << "No.\n"; |
| 86 |
|
} |
| 87 |
|
|
| 88 |
|
theArray = (SRI**) molecules[i].getMyBends(); |
| 217 |
|
calcStress = 1; |
| 218 |
|
} |
| 219 |
|
|
| 228 |
– |
std::cerr << currTime << "\n"; |
| 229 |
– |
|
| 220 |
|
integrateStep( calcPot, calcStress ); |
| 221 |
|
|
| 222 |
|
currTime += dt; |
| 264 |
|
moveA(); |
| 265 |
|
if( nConstrained ) constrainA(); |
| 266 |
|
|
| 267 |
+ |
|
| 268 |
+ |
#ifdef IS_MPI |
| 269 |
+ |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
| 270 |
+ |
MPIcheckPoint(); |
| 271 |
+ |
#endif // is_mpi |
| 272 |
+ |
|
| 273 |
+ |
|
| 274 |
|
// calc forces |
| 275 |
|
|
| 276 |
|
myFF->doForces(calcPot,calcStress); |
| 277 |
|
|
| 278 |
+ |
#ifdef IS_MPI |
| 279 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
| 280 |
+ |
MPIcheckPoint(); |
| 281 |
+ |
#endif // is_mpi |
| 282 |
+ |
|
| 283 |
+ |
|
| 284 |
|
// finish the velocity half step |
| 285 |
|
|
| 286 |
|
moveB(); |
| 287 |
|
if( nConstrained ) constrainB(); |
| 288 |
< |
|
| 288 |
> |
|
| 289 |
> |
#ifdef IS_MPI |
| 290 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
| 291 |
> |
MPIcheckPoint(); |
| 292 |
> |
#endif // is_mpi |
| 293 |
> |
|
| 294 |
> |
|
| 295 |
|
} |
| 296 |
|
|
| 297 |
|
|
