| 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(); |
| 167 |
|
double currSample; |
| 168 |
|
double currThermal; |
| 169 |
|
double currStatus; |
| 178 |
– |
double currTime; |
| 170 |
|
|
| 171 |
|
int calcPot, calcStress; |
| 172 |
|
int isError; |
| 190 |
|
tStats->velocitize(); |
| 191 |
|
} |
| 192 |
|
|
| 202 |
– |
dumpOut->writeDump( 0.0 ); |
| 203 |
– |
statOut->writeStat( 0.0 ); |
| 204 |
– |
|
| 193 |
|
calcPot = 0; |
| 194 |
|
calcStress = 0; |
| 195 |
|
currSample = sampleTime; |
| 196 |
|
currThermal = thermalTime; |
| 197 |
|
currStatus = statusTime; |
| 210 |
– |
currTime = 0.0;; |
| 198 |
|
|
| 199 |
+ |
dumpOut->writeDump( info->getTime() ); |
| 200 |
+ |
statOut->writeStat( info->getTime() ); |
| 201 |
|
|
| 202 |
|
readyCheck(); |
| 203 |
|
|
| 207 |
|
MPIcheckPoint(); |
| 208 |
|
#endif // is_mpi |
| 209 |
|
|
| 210 |
< |
while( currTime < runTime ){ |
| 210 |
> |
while( info->getTime() < runTime ){ |
| 211 |
|
|
| 212 |
< |
if( (currTime+dt) >= currStatus ){ |
| 212 |
> |
if( (info->getTime()+dt) >= currStatus ){ |
| 213 |
|
calcPot = 1; |
| 214 |
|
calcStress = 1; |
| 215 |
|
} |
| 216 |
|
|
| 228 |
– |
std::cerr << currTime << "\n"; |
| 229 |
– |
|
| 217 |
|
integrateStep( calcPot, calcStress ); |
| 218 |
|
|
| 219 |
< |
currTime += dt; |
| 219 |
> |
info->incrTime(dt); |
| 220 |
|
|
| 221 |
|
if( info->setTemp ){ |
| 222 |
< |
if( currTime >= currThermal ){ |
| 222 |
> |
if( info->getTime() >= currThermal ){ |
| 223 |
|
tStats->velocitize(); |
| 224 |
|
currThermal += thermalTime; |
| 225 |
|
} |
| 226 |
|
} |
| 227 |
|
|
| 228 |
< |
if( currTime >= currSample ){ |
| 229 |
< |
dumpOut->writeDump( currTime ); |
| 228 |
> |
if( info->getTime() >= currSample ){ |
| 229 |
> |
dumpOut->writeDump( info->getTime() ); |
| 230 |
|
currSample += sampleTime; |
| 231 |
|
} |
| 232 |
|
|
| 233 |
< |
if( currTime >= currStatus ){ |
| 234 |
< |
statOut->writeStat( currTime ); |
| 233 |
> |
if( info->getTime() >= currStatus ){ |
| 234 |
> |
statOut->writeStat( info->getTime() ); |
| 235 |
|
calcPot = 0; |
| 236 |
|
calcStress = 0; |
| 237 |
|
currStatus += statusTime; |
| 245 |
|
|
| 246 |
|
} |
| 247 |
|
|
| 248 |
< |
dumpOut->writeFinal(currTime); |
| 248 |
> |
dumpOut->writeFinal(info->getTime()); |
| 249 |
|
|
| 250 |
|
delete dumpOut; |
| 251 |
|
delete statOut; |
| 261 |
|
moveA(); |
| 262 |
|
if( nConstrained ) constrainA(); |
| 263 |
|
|
| 264 |
+ |
|
| 265 |
+ |
#ifdef IS_MPI |
| 266 |
+ |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
| 267 |
+ |
MPIcheckPoint(); |
| 268 |
+ |
#endif // is_mpi |
| 269 |
+ |
|
| 270 |
+ |
|
| 271 |
|
// calc forces |
| 272 |
|
|
| 273 |
|
myFF->doForces(calcPot,calcStress); |
| 274 |
|
|
| 275 |
+ |
#ifdef IS_MPI |
| 276 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
| 277 |
+ |
MPIcheckPoint(); |
| 278 |
+ |
#endif // is_mpi |
| 279 |
+ |
|
| 280 |
+ |
|
| 281 |
|
// finish the velocity half step |
| 282 |
|
|
| 283 |
|
moveB(); |
| 284 |
|
if( nConstrained ) constrainB(); |
| 285 |
< |
|
| 285 |
> |
|
| 286 |
> |
#ifdef IS_MPI |
| 287 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
| 288 |
> |
MPIcheckPoint(); |
| 289 |
> |
#endif // is_mpi |
| 290 |
> |
|
| 291 |
> |
|
| 292 |
|
} |
| 293 |
|
|
| 294 |
|
|
