| 1 |
< |
/* |
| 2 |
< |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
< |
* |
| 4 |
< |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
< |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
< |
* redistribute this software in source and binary code form, provided |
| 7 |
< |
* that the following conditions are met: |
| 8 |
< |
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
< |
* notice, this list of conditions and the following disclaimer. |
| 20 |
< |
* |
| 21 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
< |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
< |
* documentation and/or other materials provided with the |
| 24 |
< |
* distribution. |
| 25 |
< |
* |
| 26 |
< |
* This software is provided "AS IS," without a warranty of any |
| 27 |
< |
* kind. All express or implied conditions, representations and |
| 28 |
< |
* warranties, including any implied warranty of merchantability, |
| 29 |
< |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
< |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
< |
* be liable for any damages suffered by licensee as a result of |
| 32 |
< |
* using, modifying or distributing the software or its |
| 33 |
< |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
< |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
< |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
< |
* damages, however caused and regardless of the theory of liability, |
| 37 |
< |
* arising out of the use of or inability to use software, even if the |
| 38 |
< |
* University of Notre Dame has been advised of the possibility of |
| 39 |
< |
* such damages. |
| 40 |
< |
*/ |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
> |
* notice, this list of conditions and the following disclaimer. |
| 11 |
> |
* |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
> |
* documentation and/or other materials provided with the |
| 15 |
> |
* distribution. |
| 16 |
> |
* |
| 17 |
> |
* This software is provided "AS IS," without a warranty of any |
| 18 |
> |
* kind. All express or implied conditions, representations and |
| 19 |
> |
* warranties, including any implied warranty of merchantability, |
| 20 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
> |
* be liable for any damages suffered by licensee as a result of |
| 23 |
> |
* using, modifying or distributing the software or its |
| 24 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
> |
* damages, however caused and regardless of the theory of liability, |
| 28 |
> |
* arising out of the use of or inability to use software, even if the |
| 29 |
> |
* University of Notre Dame has been advised of the possibility of |
| 30 |
> |
* such damages. |
| 31 |
> |
* |
| 32 |
> |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
> |
* research, please cite the appropriate papers when you publish your |
| 34 |
> |
* work. Good starting points are: |
| 35 |
> |
* |
| 36 |
> |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
> |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
> |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
> |
*/ |
| 41 |
|
|
| 42 |
|
#define _LARGEFILE_SOURCE64 |
| 43 |
|
#define _FILE_OFFSET_BITS 64 |
| 67 |
|
#endif // is_mpi |
| 68 |
|
|
| 69 |
|
|
| 70 |
< |
namespace oopse { |
| 70 |
> |
namespace OpenMD { |
| 71 |
|
|
| 72 |
|
DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
| 73 |
< |
: info_(info), filename_(filename), isScanned_(false), nframes_(0) { |
| 73 |
> |
: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) { |
| 74 |
|
|
| 75 |
|
#ifdef IS_MPI |
| 76 |
|
|
| 92 |
|
} |
| 93 |
|
|
| 94 |
|
strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
| 95 |
< |
MPIcheckPoint(); |
| 95 |
> |
errorCheckPoint(); |
| 96 |
|
|
| 97 |
|
#endif |
| 98 |
|
|
| 113 |
|
} |
| 114 |
|
|
| 115 |
|
strcpy(checkPointMsg, "Dump file closed successfully."); |
| 116 |
< |
MPIcheckPoint(); |
| 116 |
> |
errorCheckPoint(); |
| 117 |
|
|
| 118 |
|
#endif |
| 119 |
|
|
| 240 |
|
} |
| 241 |
|
|
| 242 |
|
readSet(whichFrame); |
| 243 |
+ |
|
| 244 |
+ |
if (needCOMprops_) { |
| 245 |
+ |
Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 246 |
+ |
Vector3d com; |
| 247 |
+ |
Vector3d comvel; |
| 248 |
+ |
Vector3d comw; |
| 249 |
+ |
if (needPos_ && needVel_){ |
| 250 |
+ |
info_->getComAll(com, comvel); |
| 251 |
+ |
comw = info_->getAngularMomentum(); |
| 252 |
+ |
}else{ |
| 253 |
+ |
com = info_->getCom(); |
| 254 |
+ |
comvel = 0.0; |
| 255 |
+ |
comw = 0.0; |
| 256 |
+ |
} |
| 257 |
+ |
s->setCOMprops(com, comvel, comw); |
| 258 |
+ |
} |
| 259 |
+ |
|
| 260 |
|
} |
| 261 |
|
|
| 262 |
|
void DumpReader::readSet(int whichFrame) { |
| 263 |
|
std::string line; |
| 264 |
|
|
| 265 |
|
#ifndef IS_MPI |
| 249 |
– |
|
| 266 |
|
inFile_->clear(); |
| 267 |
|
inFile_->seekg(framePos_[whichFrame]); |
| 268 |
|
|
| 296 |
|
int sendBufferSize; |
| 297 |
|
MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 298 |
|
char * recvBuffer = new char[sendBufferSize+1]; |
| 299 |
+ |
assert(recvBuffer); |
| 300 |
+ |
recvBuffer[sendBufferSize] = '\0'; |
| 301 |
|
MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 302 |
|
sstream.str(recvBuffer); |
| 303 |
+ |
delete [] recvBuffer; |
| 304 |
|
} |
| 305 |
|
|
| 306 |
|
std::istream& inputStream = sstream; |
| 341 |
|
|
| 342 |
|
nTokens = tokenizer.countTokens(); |
| 343 |
|
|
| 344 |
< |
if (nTokens < 2) { |
| 344 |
> |
if (nTokens < 2) { |
| 345 |
|
sprintf(painCave.errMsg, |
| 346 |
|
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 347 |
|
painCave.isFatal = 1; |
| 357 |
|
} |
| 358 |
|
std::string type = tokenizer.nextToken(); |
| 359 |
|
int size = type.size(); |
| 360 |
+ |
|
| 361 |
+ |
size_t found; |
| 362 |
+ |
|
| 363 |
+ |
if (needPos_) { |
| 364 |
+ |
found = type.find("p"); |
| 365 |
+ |
if (found == std::string::npos) { |
| 366 |
+ |
sprintf(painCave.errMsg, |
| 367 |
+ |
"DumpReader Error: StuntDouble %d has no Position\n" |
| 368 |
+ |
"\tField (\"p\") specified.\n%s\n", index, |
| 369 |
+ |
line.c_str()); |
| 370 |
+ |
painCave.isFatal = 1; |
| 371 |
+ |
simError(); |
| 372 |
+ |
} |
| 373 |
+ |
} |
| 374 |
+ |
|
| 375 |
+ |
if (integrableObject->isDirectional()) { |
| 376 |
+ |
if (needQuaternion_) { |
| 377 |
+ |
found = type.find("q"); |
| 378 |
+ |
if (found == std::string::npos) { |
| 379 |
+ |
sprintf(painCave.errMsg, |
| 380 |
+ |
"DumpReader Error: Directional StuntDouble %d has no\n" |
| 381 |
+ |
"\tQuaternion Field (\"q\") specified.\n%s\n", index, |
| 382 |
+ |
line.c_str()); |
| 383 |
+ |
painCave.isFatal = 1; |
| 384 |
+ |
simError(); |
| 385 |
+ |
} |
| 386 |
+ |
} |
| 387 |
+ |
} |
| 388 |
+ |
|
| 389 |
|
for(int i = 0; i < size; ++i) { |
| 390 |
|
switch(type[i]) { |
| 391 |
|
|
| 420 |
|
q[3] = tokenizer.nextTokenAsDouble(); |
| 421 |
|
|
| 422 |
|
RealType qlen = q.length(); |
| 423 |
< |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
| 423 |
> |
if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 |
| 424 |
|
|
| 425 |
|
sprintf(painCave.errMsg, |
| 426 |
|
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
| 446 |
|
integrableObject->setJ(ji); |
| 447 |
|
} |
| 448 |
|
} |
| 449 |
+ |
break; |
| 450 |
|
} |
| 451 |
|
case 'f': { |
| 452 |
|
|
| 466 |
|
integrableObject->setTrq(torque); |
| 467 |
|
break; |
| 468 |
|
} |
| 469 |
+ |
case 'u' : { |
| 470 |
+ |
|
| 471 |
+ |
RealType particlePot; |
| 472 |
+ |
particlePot = tokenizer.nextTokenAsDouble(); |
| 473 |
+ |
integrableObject->setParticlePot(particlePot); |
| 474 |
+ |
break; |
| 475 |
+ |
} |
| 476 |
|
default: { |
| 477 |
|
sprintf(painCave.errMsg, |
| 478 |
|
"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
| 584 |
|
} |
| 585 |
|
|
| 586 |
|
|
| 587 |
< |
}//end namespace oopse |
| 587 |
> |
}//end namespace OpenMD |
