| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 44 |
|
* @file SimCreator.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/03/2004 |
| 47 |
– |
* @time 13:51am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
#include <exception> |
| 111 |
|
//brocasting the stream size |
| 112 |
|
streamSize = ppStream.str().size() +1; |
| 113 |
|
MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
| 114 |
< |
MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), |
| 115 |
< |
streamSize, MPI::CHAR, masterNode); |
| 117 |
< |
|
| 114 |
> |
MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode); |
| 115 |
> |
|
| 116 |
|
} else { |
| 119 |
– |
|
| 117 |
|
MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
| 118 |
|
|
| 119 |
|
//get stream size |
| 127 |
|
|
| 128 |
|
ppStream.str(buf); |
| 129 |
|
delete [] buf; |
| 133 |
– |
|
| 130 |
|
} |
| 131 |
|
#endif |
| 132 |
|
// Create a scanner that reads from the input stream |
| 251 |
|
std::string mdRawData; |
| 252 |
|
int metaDataBlockStart = -1; |
| 253 |
|
int metaDataBlockEnd = -1; |
| 254 |
< |
int i; |
| 255 |
< |
streamoff mdOffset(0); |
| 254 |
> |
int i, j; |
| 255 |
> |
streamoff mdOffset; |
| 256 |
|
int mdFileVersion; |
| 257 |
|
|
| 258 |
+ |
// Create a string for embedding the version information in the MetaData |
| 259 |
+ |
std::string version; |
| 260 |
+ |
version.assign("## Last run using OpenMD Version: "); |
| 261 |
+ |
version.append(OPENMD_VERSION_MAJOR); |
| 262 |
+ |
version.append("."); |
| 263 |
+ |
version.append(OPENMD_VERSION_MINOR); |
| 264 |
|
|
| 265 |
+ |
std::string svnrev; |
| 266 |
+ |
//convert a macro from compiler to a string in c++ |
| 267 |
+ |
STR_DEFINE(svnrev, SVN_REV ); |
| 268 |
+ |
version.append(" Revision: "); |
| 269 |
+ |
// If there's no SVN revision, just call this the RELEASE revision. |
| 270 |
+ |
if (!svnrev.empty()) { |
| 271 |
+ |
version.append(svnrev); |
| 272 |
+ |
} else { |
| 273 |
+ |
version.append("RELEASE"); |
| 274 |
+ |
} |
| 275 |
+ |
|
| 276 |
|
#ifdef IS_MPI |
| 277 |
|
const int masterNode = 0; |
| 278 |
|
if (worldRank == masterNode) { |
| 366 |
|
mdFile_.seekg(mdOffset); |
| 367 |
|
|
| 368 |
|
mdRawData.clear(); |
| 369 |
+ |
|
| 370 |
+ |
bool foundVersion = false; |
| 371 |
|
|
| 372 |
|
for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
| 373 |
|
mdFile_.getline(buffer, bufferSize); |
| 374 |
< |
mdRawData += buffer; |
| 374 |
> |
std::string line = trimLeftCopy(buffer); |
| 375 |
> |
j = CaseInsensitiveFind(line, "## Last run using OpenMD Version"); |
| 376 |
> |
if (static_cast<size_t>(j) != string::npos) { |
| 377 |
> |
foundVersion = true; |
| 378 |
> |
mdRawData += version; |
| 379 |
> |
} else { |
| 380 |
> |
mdRawData += buffer; |
| 381 |
> |
} |
| 382 |
|
mdRawData += "\n"; |
| 383 |
|
} |
| 384 |
< |
|
| 384 |
> |
|
| 385 |
> |
if (!foundVersion) mdRawData += version + "\n"; |
| 386 |
> |
|
| 387 |
|
mdFile_.close(); |
| 388 |
|
|
| 389 |
|
#ifdef IS_MPI |
| 511 |
|
|
| 512 |
|
#ifdef IS_MPI |
| 513 |
|
void SimCreator::divideMolecules(SimInfo *info) { |
| 490 |
– |
RealType numerator; |
| 491 |
– |
RealType denominator; |
| 492 |
– |
RealType precast; |
| 493 |
– |
RealType x; |
| 494 |
– |
RealType y; |
| 514 |
|
RealType a; |
| 496 |
– |
int old_atoms; |
| 497 |
– |
int add_atoms; |
| 498 |
– |
int new_atoms; |
| 499 |
– |
int nTarget; |
| 500 |
– |
int done; |
| 501 |
– |
int i; |
| 502 |
– |
int loops; |
| 503 |
– |
int which_proc; |
| 515 |
|
int nProcessors; |
| 516 |
|
std::vector<int> atomsPerProc; |
| 517 |
|
int nGlobalMols = info->getNGlobalMolecules(); |
| 518 |
< |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
| 518 |
> |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an |
| 519 |
> |
// error |
| 520 |
> |
// condition: |
| 521 |
|
|
| 522 |
|
nProcessors = MPI::COMM_WORLD.Get_size(); |
| 523 |
|
|
| 528 |
|
"\tthe number of molecules. This will not result in a \n" |
| 529 |
|
"\tusable division of atoms for force decomposition.\n" |
| 530 |
|
"\tEither try a smaller number of processors, or run the\n" |
| 531 |
< |
"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
| 531 |
> |
"\tsingle-processor version of OpenMD.\n", nProcessors, |
| 532 |
> |
nGlobalMols); |
| 533 |
|
|
| 534 |
|
painCave.isFatal = 1; |
| 535 |
|
simError(); |
| 536 |
|
} |
| 537 |
|
|
| 524 |
– |
int seedValue; |
| 538 |
|
Globals * simParams = info->getSimParams(); |
| 539 |
< |
SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
| 539 |
> |
SeqRandNumGen* myRandom; //divide labor does not need Parallel |
| 540 |
> |
//random number generator |
| 541 |
|
if (simParams->haveSeed()) { |
| 542 |
< |
seedValue = simParams->getSeed(); |
| 542 |
> |
int seedValue = simParams->getSeed(); |
| 543 |
|
myRandom = new SeqRandNumGen(seedValue); |
| 544 |
|
}else { |
| 545 |
|
myRandom = new SeqRandNumGen(); |
| 552 |
|
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
| 553 |
|
|
| 554 |
|
if (worldRank == 0) { |
| 555 |
< |
numerator = info->getNGlobalAtoms(); |
| 556 |
< |
denominator = nProcessors; |
| 557 |
< |
precast = numerator / denominator; |
| 558 |
< |
nTarget = (int)(precast + 0.5); |
| 555 |
> |
RealType numerator = info->getNGlobalAtoms(); |
| 556 |
> |
RealType denominator = nProcessors; |
| 557 |
> |
RealType precast = numerator / denominator; |
| 558 |
> |
int nTarget = (int)(precast + 0.5); |
| 559 |
|
|
| 560 |
< |
for(i = 0; i < nGlobalMols; i++) { |
| 560 |
> |
for(int i = 0; i < nGlobalMols; i++) { |
| 561 |
|
|
| 562 |
< |
done = 0; |
| 563 |
< |
loops = 0; |
| 562 |
> |
int done = 0; |
| 563 |
> |
int loops = 0; |
| 564 |
|
|
| 565 |
|
while (!done) { |
| 566 |
|
loops++; |
| 567 |
|
|
| 568 |
|
// Pick a processor at random |
| 569 |
|
|
| 570 |
< |
which_proc = (int) (myRandom->rand() * nProcessors); |
| 570 |
> |
int which_proc = (int) (myRandom->rand() * nProcessors); |
| 571 |
|
|
| 572 |
|
//get the molecule stamp first |
| 573 |
|
int stampId = info->getMoleculeStampId(i); |
| 574 |
|
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
| 575 |
|
|
| 576 |
|
// How many atoms does this processor have so far? |
| 577 |
< |
old_atoms = atomsPerProc[which_proc]; |
| 578 |
< |
add_atoms = moleculeStamp->getNAtoms(); |
| 579 |
< |
new_atoms = old_atoms + add_atoms; |
| 577 |
> |
int old_atoms = atomsPerProc[which_proc]; |
| 578 |
> |
int add_atoms = moleculeStamp->getNAtoms(); |
| 579 |
> |
int new_atoms = old_atoms + add_atoms; |
| 580 |
|
|
| 581 |
|
// If we've been through this loop too many times, we need |
| 582 |
|
// to just give up and assign the molecule to this processor |
| 620 |
|
// Pacc(x) = exp(- a * x) |
| 621 |
|
// where a = penalty / (average atoms per molecule) |
| 622 |
|
|
| 623 |
< |
x = (RealType)(new_atoms - nTarget); |
| 624 |
< |
y = myRandom->rand(); |
| 623 |
> |
RealType x = (RealType)(new_atoms - nTarget); |
| 624 |
> |
RealType y = myRandom->rand(); |
| 625 |
|
|
| 626 |
|
if (y < exp(- a * x)) { |
| 627 |
|
molToProcMap[i] = which_proc; |
| 690 |
|
set<AtomType*>::iterator i; |
| 691 |
|
bool hasDirectionalAtoms = false; |
| 692 |
|
bool hasFixedCharge = false; |
| 693 |
< |
bool hasMultipoles = false; |
| 693 |
> |
bool hasDipoles = false; |
| 694 |
> |
bool hasQuadrupoles = false; |
| 695 |
|
bool hasPolarizable = false; |
| 696 |
|
bool hasFluctuatingCharge = false; |
| 697 |
|
bool hasMetallic = false; |
| 713 |
|
if (da.isDirectional()){ |
| 714 |
|
hasDirectionalAtoms = true; |
| 715 |
|
} |
| 716 |
< |
if (ma.isMultipole()){ |
| 717 |
< |
hasMultipoles = true; |
| 716 |
> |
if (ma.isDipole()){ |
| 717 |
> |
hasDipoles = true; |
| 718 |
|
} |
| 719 |
+ |
if (ma.isQuadrupole()){ |
| 720 |
+ |
hasQuadrupoles = true; |
| 721 |
+ |
} |
| 722 |
|
if (ea.isEAM() || sca.isSuttonChen()){ |
| 723 |
|
hasMetallic = true; |
| 724 |
|
} |
| 742 |
|
storageLayout |= DataStorage::dslTorque; |
| 743 |
|
} |
| 744 |
|
} |
| 745 |
< |
if (hasMultipoles) { |
| 746 |
< |
storageLayout |= DataStorage::dslElectroFrame; |
| 745 |
> |
if (hasDipoles) { |
| 746 |
> |
storageLayout |= DataStorage::dslDipole; |
| 747 |
|
} |
| 748 |
+ |
if (hasQuadrupoles) { |
| 749 |
+ |
storageLayout |= DataStorage::dslQuadrupole; |
| 750 |
+ |
} |
| 751 |
|
if (hasFixedCharge || hasFluctuatingCharge) { |
| 752 |
|
storageLayout |= DataStorage::dslSkippedCharge; |
| 753 |
|
} |
| 782 |
|
} |
| 783 |
|
} |
| 784 |
|
|
| 785 |
< |
if (simParams->getOutputElectricField()) { |
| 785 |
> |
if (simParams->getOutputElectricField() | simParams->haveElectricField()) { |
| 786 |
|
storageLayout |= DataStorage::dslElectricField; |
| 787 |
|
} |
| 788 |
+ |
|
| 789 |
|
if (simParams->getOutputFluctuatingCharges()) { |
| 790 |
|
storageLayout |= DataStorage::dslFlucQPosition; |
| 791 |
|
storageLayout |= DataStorage::dslFlucQVelocity; |
| 792 |
|
storageLayout |= DataStorage::dslFlucQForce; |
| 793 |
|
} |
| 794 |
|
|
| 795 |
+ |
info->setStorageLayout(storageLayout); |
| 796 |
+ |
|
| 797 |
|
return storageLayout; |
| 798 |
|
} |
| 799 |
|
|
| 956 |
|
} |
| 957 |
|
|
| 958 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 959 |
< |
|
| 959 |
> |
|
| 960 |
|
DumpReader reader(info, mdFileName); |
| 961 |
|
int nframes = reader.getNFrames(); |
| 962 |
< |
|
| 962 |
> |
|
| 963 |
|
if (nframes > 0) { |
| 964 |
|
reader.readFrame(nframes - 1); |
| 965 |
|
} else { |
