| 1 |
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/* |
| 2 |
< |
* copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
| 5 |
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* non-exclusive, royalty free, license to use, modify and |
| 35 |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [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). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 44 |
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* @file SimCreator.cpp |
| 45 |
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* @author tlin |
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* @date 11/03/2004 |
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– |
* @time 13:51am |
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* @version 1.0 |
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*/ |
| 49 |
+ |
|
| 50 |
+ |
#ifdef IS_MPI |
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+ |
#include "mpi.h" |
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+ |
#include "math/ParallelRandNumGen.hpp" |
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+ |
#endif |
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+ |
|
| 55 |
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#include <exception> |
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#include <iostream> |
| 57 |
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#include <sstream> |
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#include "brains/ForceField.hpp" |
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#include "utils/simError.h" |
| 66 |
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#include "utils/StringUtils.hpp" |
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+ |
#include "utils/Revision.hpp" |
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#include "math/SeqRandNumGen.hpp" |
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#include "mdParser/MDLexer.hpp" |
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#include "mdParser/MDParser.hpp" |
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#include "types/FixedChargeAdapter.hpp" |
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#include "types/FluctuatingChargeAdapter.hpp" |
| 92 |
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|
| 87 |
– |
#ifdef IS_MPI |
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– |
#include "mpi.h" |
| 89 |
– |
#include "math/ParallelRandNumGen.hpp" |
| 90 |
– |
#endif |
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|
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namespace OpenMD { |
| 95 |
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|
| 104 |
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const int masterNode = 0; |
| 105 |
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|
| 106 |
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if (worldRank == masterNode) { |
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< |
MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
| 107 |
> |
MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
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#endif |
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SimplePreprocessor preprocessor; |
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< |
preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, |
| 111 |
< |
ppStream); |
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> |
preprocessor.preprocess(rawMetaDataStream, filename, |
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> |
startOfMetaDataBlock, ppStream); |
| 112 |
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|
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#ifdef IS_MPI |
| 114 |
< |
//brocasting the stream size |
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> |
//broadcasting the stream size |
| 115 |
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streamSize = ppStream.str().size() +1; |
| 116 |
< |
MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
| 117 |
< |
MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), |
| 118 |
< |
streamSize, MPI::CHAR, masterNode); |
| 117 |
< |
|
| 116 |
> |
MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 117 |
> |
MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), |
| 118 |
> |
streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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} else { |
| 120 |
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|
| 121 |
< |
MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
| 121 |
> |
MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 122 |
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|
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//get stream size |
| 124 |
< |
MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
| 124 |
< |
|
| 124 |
> |
MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 125 |
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char* buf = new char[streamSize]; |
| 126 |
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assert(buf); |
| 127 |
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|
| 128 |
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//receive file content |
| 129 |
< |
MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode); |
| 130 |
< |
|
| 129 |
> |
MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 130 |
> |
|
| 131 |
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ppStream.str(buf); |
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delete [] buf; |
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– |
|
| 133 |
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} |
| 134 |
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#endif |
| 135 |
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// Create a scanner that reads from the input stream |
| 151 |
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parser.initializeASTFactory(factory); |
| 152 |
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parser.setASTFactory(&factory); |
| 153 |
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parser.mdfile(); |
| 155 |
– |
|
| 154 |
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// Create a tree parser that reads information into Globals |
| 155 |
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MDTreeParser treeParser; |
| 156 |
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treeParser.initializeASTFactory(factory); |
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catch (OpenMDException& e) { |
| 229 |
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sprintf(painCave.errMsg, |
| 230 |
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"%s\n", |
| 231 |
< |
e.getMessage().c_str()); |
| 231 |
> |
e.what()); |
| 232 |
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painCave.isFatal = 1; |
| 233 |
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simError(); |
| 234 |
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} |
| 253 |
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std::string mdRawData; |
| 254 |
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int metaDataBlockStart = -1; |
| 255 |
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int metaDataBlockEnd = -1; |
| 256 |
< |
int i; |
| 259 |
< |
streamoff mdOffset(0); |
| 256 |
> |
streamoff mdOffset; |
| 257 |
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int mdFileVersion; |
| 258 |
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|
| 259 |
+ |
// Create a string for embedding the version information in the MetaData |
| 260 |
+ |
std::string version; |
| 261 |
+ |
version.assign("## Last run using OpenMD Version: "); |
| 262 |
+ |
version.append(OPENMD_VERSION_MAJOR); |
| 263 |
+ |
version.append("."); |
| 264 |
+ |
version.append(OPENMD_VERSION_MINOR); |
| 265 |
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|
| 266 |
+ |
std::string svnrev(g_REVISION, strnlen(g_REVISION, 20)); |
| 267 |
+ |
//convert a macro from compiler to a string in c++ |
| 268 |
+ |
// STR_DEFINE(svnrev, SVN_REV ); |
| 269 |
+ |
version.append(" Revision: "); |
| 270 |
+ |
// If there's no SVN revision, just call this the RELEASE revision. |
| 271 |
+ |
if (!svnrev.empty()) { |
| 272 |
+ |
version.append(svnrev); |
| 273 |
+ |
} else { |
| 274 |
+ |
version.append("RELEASE"); |
| 275 |
+ |
} |
| 276 |
+ |
|
| 277 |
|
#ifdef IS_MPI |
| 278 |
|
const int masterNode = 0; |
| 279 |
|
if (worldRank == masterNode) { |
| 293 |
|
mdFile_.getline(buffer, bufferSize); |
| 294 |
|
++lineNo; |
| 295 |
|
std::string line = trimLeftCopy(buffer); |
| 296 |
< |
i = CaseInsensitiveFind(line, "<OpenMD"); |
| 297 |
< |
if (static_cast<size_t>(i) == string::npos) { |
| 296 |
> |
std::size_t i = CaseInsensitiveFind(line, "<OpenMD"); |
| 297 |
> |
if (i == string::npos) { |
| 298 |
|
// try the older file strings to see if that works: |
| 299 |
|
i = CaseInsensitiveFind(line, "<OOPSE"); |
| 300 |
|
} |
| 301 |
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|
| 302 |
< |
if (static_cast<size_t>(i) == string::npos) { |
| 302 |
> |
if (i == string::npos) { |
| 303 |
|
// still no luck! |
| 304 |
|
sprintf(painCave.errMsg, |
| 305 |
|
"SimCreator: File: %s is not a valid OpenMD file!\n", |
| 334 |
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|
| 335 |
|
std::string line = trimLeftCopy(buffer); |
| 336 |
|
if (metaDataBlockStart == -1) { |
| 337 |
< |
i = CaseInsensitiveFind(line, "<MetaData>"); |
| 337 |
> |
std::size_t i = CaseInsensitiveFind(line, "<MetaData>"); |
| 338 |
|
if (i != string::npos) { |
| 339 |
|
metaDataBlockStart = lineNo; |
| 340 |
|
mdOffset = mdFile_.tellg(); |
| 341 |
|
} |
| 342 |
|
} else { |
| 343 |
< |
i = CaseInsensitiveFind(line, "</MetaData>"); |
| 343 |
> |
std::size_t i = CaseInsensitiveFind(line, "</MetaData>"); |
| 344 |
|
if (i != string::npos) { |
| 345 |
|
metaDataBlockEnd = lineNo; |
| 346 |
|
} |
| 368 |
|
|
| 369 |
|
mdRawData.clear(); |
| 370 |
|
|
| 371 |
+ |
bool foundVersion = false; |
| 372 |
+ |
|
| 373 |
|
for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
| 374 |
|
mdFile_.getline(buffer, bufferSize); |
| 375 |
< |
mdRawData += buffer; |
| 375 |
> |
std::string line = trimLeftCopy(buffer); |
| 376 |
> |
std::size_t j = CaseInsensitiveFind(line, |
| 377 |
> |
"## Last run using OpenMD Version"); |
| 378 |
> |
if (j != string::npos) { |
| 379 |
> |
foundVersion = true; |
| 380 |
> |
mdRawData += version; |
| 381 |
> |
} else { |
| 382 |
> |
mdRawData += buffer; |
| 383 |
> |
} |
| 384 |
|
mdRawData += "\n"; |
| 385 |
|
} |
| 386 |
< |
|
| 386 |
> |
|
| 387 |
> |
if (!foundVersion) mdRawData += version + "\n"; |
| 388 |
> |
|
| 389 |
|
mdFile_.close(); |
| 390 |
|
|
| 391 |
|
#ifdef IS_MPI |
| 513 |
|
|
| 514 |
|
#ifdef IS_MPI |
| 515 |
|
void SimCreator::divideMolecules(SimInfo *info) { |
| 490 |
– |
RealType numerator; |
| 491 |
– |
RealType denominator; |
| 492 |
– |
RealType precast; |
| 493 |
– |
RealType x; |
| 494 |
– |
RealType y; |
| 516 |
|
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; |
| 517 |
|
int nProcessors; |
| 518 |
|
std::vector<int> atomsPerProc; |
| 519 |
|
int nGlobalMols = info->getNGlobalMolecules(); |
| 520 |
< |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
| 520 |
> |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an |
| 521 |
> |
// error |
| 522 |
> |
// condition: |
| 523 |
|
|
| 524 |
< |
nProcessors = MPI::COMM_WORLD.Get_size(); |
| 524 |
> |
MPI_Comm_size( MPI_COMM_WORLD, &nProcessors); |
| 525 |
|
|
| 526 |
|
if (nProcessors > nGlobalMols) { |
| 527 |
|
sprintf(painCave.errMsg, |
| 530 |
|
"\tthe number of molecules. This will not result in a \n" |
| 531 |
|
"\tusable division of atoms for force decomposition.\n" |
| 532 |
|
"\tEither try a smaller number of processors, or run the\n" |
| 533 |
< |
"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
| 533 |
> |
"\tsingle-processor version of OpenMD.\n", nProcessors, |
| 534 |
> |
nGlobalMols); |
| 535 |
|
|
| 536 |
|
painCave.isFatal = 1; |
| 537 |
|
simError(); |
| 538 |
|
} |
| 539 |
|
|
| 524 |
– |
int seedValue; |
| 540 |
|
Globals * simParams = info->getSimParams(); |
| 541 |
< |
SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
| 541 |
> |
SeqRandNumGen* myRandom; //divide labor does not need Parallel |
| 542 |
> |
//random number generator |
| 543 |
|
if (simParams->haveSeed()) { |
| 544 |
< |
seedValue = simParams->getSeed(); |
| 544 |
> |
int seedValue = simParams->getSeed(); |
| 545 |
|
myRandom = new SeqRandNumGen(seedValue); |
| 546 |
|
}else { |
| 547 |
|
myRandom = new SeqRandNumGen(); |
| 554 |
|
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
| 555 |
|
|
| 556 |
|
if (worldRank == 0) { |
| 557 |
< |
numerator = info->getNGlobalAtoms(); |
| 558 |
< |
denominator = nProcessors; |
| 559 |
< |
precast = numerator / denominator; |
| 560 |
< |
nTarget = (int)(precast + 0.5); |
| 557 |
> |
RealType numerator = info->getNGlobalAtoms(); |
| 558 |
> |
RealType denominator = nProcessors; |
| 559 |
> |
RealType precast = numerator / denominator; |
| 560 |
> |
int nTarget = (int)(precast + 0.5); |
| 561 |
|
|
| 562 |
< |
for(i = 0; i < nGlobalMols; i++) { |
| 563 |
< |
done = 0; |
| 564 |
< |
loops = 0; |
| 562 |
> |
for(int i = 0; i < nGlobalMols; i++) { |
| 563 |
> |
|
| 564 |
> |
int done = 0; |
| 565 |
> |
int loops = 0; |
| 566 |
|
|
| 567 |
|
while (!done) { |
| 568 |
|
loops++; |
| 569 |
|
|
| 570 |
|
// Pick a processor at random |
| 571 |
|
|
| 572 |
< |
which_proc = (int) (myRandom->rand() * nProcessors); |
| 572 |
> |
int which_proc = (int) (myRandom->rand() * nProcessors); |
| 573 |
|
|
| 574 |
|
//get the molecule stamp first |
| 575 |
|
int stampId = info->getMoleculeStampId(i); |
| 576 |
|
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
| 577 |
|
|
| 578 |
|
// How many atoms does this processor have so far? |
| 579 |
< |
old_atoms = atomsPerProc[which_proc]; |
| 580 |
< |
add_atoms = moleculeStamp->getNAtoms(); |
| 581 |
< |
new_atoms = old_atoms + add_atoms; |
| 579 |
> |
int old_atoms = atomsPerProc[which_proc]; |
| 580 |
> |
int add_atoms = moleculeStamp->getNAtoms(); |
| 581 |
> |
int new_atoms = old_atoms + add_atoms; |
| 582 |
|
|
| 583 |
|
// If we've been through this loop too many times, we need |
| 584 |
|
// to just give up and assign the molecule to this processor |
| 585 |
|
// and be done with it. |
| 586 |
|
|
| 587 |
|
if (loops > 100) { |
| 588 |
+ |
|
| 589 |
|
sprintf(painCave.errMsg, |
| 590 |
< |
"I've tried 100 times to assign molecule %d to a " |
| 591 |
< |
" processor, but can't find a good spot.\n" |
| 592 |
< |
"I'm assigning it at random to processor %d.\n", |
| 590 |
> |
"There have been 100 attempts to assign molecule %d to an\n" |
| 591 |
> |
"\tunderworked processor, but there's no good place to\n" |
| 592 |
> |
"\tleave it. OpenMD is assigning it at random to processor %d.\n", |
| 593 |
|
i, which_proc); |
| 594 |
< |
|
| 594 |
> |
|
| 595 |
|
painCave.isFatal = 0; |
| 596 |
+ |
painCave.severity = OPENMD_INFO; |
| 597 |
|
simError(); |
| 598 |
|
|
| 599 |
|
molToProcMap[i] = which_proc; |
| 622 |
|
// Pacc(x) = exp(- a * x) |
| 623 |
|
// where a = penalty / (average atoms per molecule) |
| 624 |
|
|
| 625 |
< |
x = (RealType)(new_atoms - nTarget); |
| 626 |
< |
y = myRandom->rand(); |
| 625 |
> |
RealType x = (RealType)(new_atoms - nTarget); |
| 626 |
> |
RealType y = myRandom->rand(); |
| 627 |
|
|
| 628 |
|
if (y < exp(- a * x)) { |
| 629 |
|
molToProcMap[i] = which_proc; |
| 638 |
|
} |
| 639 |
|
|
| 640 |
|
delete myRandom; |
| 641 |
< |
|
| 641 |
> |
|
| 642 |
|
// Spray out this nonsense to all other processors: |
| 643 |
< |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 643 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 644 |
> |
|
| 645 |
|
} else { |
| 646 |
|
|
| 647 |
|
// Listen to your marching orders from processor 0: |
| 648 |
< |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 648 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 649 |
> |
|
| 650 |
|
} |
| 651 |
|
|
| 652 |
|
info->setMolToProcMap(molToProcMap); |
| 693 |
|
set<AtomType*>::iterator i; |
| 694 |
|
bool hasDirectionalAtoms = false; |
| 695 |
|
bool hasFixedCharge = false; |
| 696 |
< |
bool hasMultipoles = false; |
| 696 |
> |
bool hasDipoles = false; |
| 697 |
> |
bool hasQuadrupoles = false; |
| 698 |
|
bool hasPolarizable = false; |
| 699 |
|
bool hasFluctuatingCharge = false; |
| 700 |
|
bool hasMetallic = false; |
| 716 |
|
if (da.isDirectional()){ |
| 717 |
|
hasDirectionalAtoms = true; |
| 718 |
|
} |
| 719 |
< |
if (ma.isMultipole()){ |
| 720 |
< |
hasMultipoles = true; |
| 719 |
> |
if (ma.isDipole()){ |
| 720 |
> |
hasDipoles = true; |
| 721 |
|
} |
| 722 |
+ |
if (ma.isQuadrupole()){ |
| 723 |
+ |
hasQuadrupoles = true; |
| 724 |
+ |
} |
| 725 |
|
if (ea.isEAM() || sca.isSuttonChen()){ |
| 726 |
|
hasMetallic = true; |
| 727 |
|
} |
| 745 |
|
storageLayout |= DataStorage::dslTorque; |
| 746 |
|
} |
| 747 |
|
} |
| 748 |
< |
if (hasMultipoles) { |
| 749 |
< |
storageLayout |= DataStorage::dslElectroFrame; |
| 748 |
> |
if (hasDipoles) { |
| 749 |
> |
storageLayout |= DataStorage::dslDipole; |
| 750 |
|
} |
| 751 |
+ |
if (hasQuadrupoles) { |
| 752 |
+ |
storageLayout |= DataStorage::dslQuadrupole; |
| 753 |
+ |
} |
| 754 |
|
if (hasFixedCharge || hasFluctuatingCharge) { |
| 755 |
|
storageLayout |= DataStorage::dslSkippedCharge; |
| 756 |
|
} |
| 785 |
|
} |
| 786 |
|
} |
| 787 |
|
|
| 788 |
< |
if (simParams->getOutputElectricField()) { |
| 788 |
> |
if (simParams->getOutputElectricField() | |
| 789 |
> |
simParams->haveElectricField() | simParams->haveUniformField() | |
| 790 |
> |
simParams->haveUniformGradientStrength() | |
| 791 |
> |
simParams->haveUniformGradientDirection1() | |
| 792 |
> |
simParams->haveUniformGradientDirection2() ) { |
| 793 |
|
storageLayout |= DataStorage::dslElectricField; |
| 794 |
|
} |
| 795 |
+ |
|
| 796 |
+ |
if (simParams->getOutputSitePotential() ) { |
| 797 |
+ |
storageLayout |= DataStorage::dslSitePotential; |
| 798 |
+ |
} |
| 799 |
+ |
|
| 800 |
|
if (simParams->getOutputFluctuatingCharges()) { |
| 801 |
|
storageLayout |= DataStorage::dslFlucQPosition; |
| 802 |
|
storageLayout |= DataStorage::dslFlucQVelocity; |
| 803 |
|
storageLayout |= DataStorage::dslFlucQForce; |
| 804 |
|
} |
| 805 |
|
|
| 806 |
+ |
info->setStorageLayout(storageLayout); |
| 807 |
+ |
|
| 808 |
|
return storageLayout; |
| 809 |
|
} |
| 810 |
|
|
| 813 |
|
Molecule::AtomIterator ai; |
| 814 |
|
Molecule::RigidBodyIterator ri; |
| 815 |
|
Molecule::CutoffGroupIterator ci; |
| 816 |
+ |
Molecule::BondIterator boi; |
| 817 |
+ |
Molecule::BendIterator bei; |
| 818 |
+ |
Molecule::TorsionIterator ti; |
| 819 |
+ |
Molecule::InversionIterator ii; |
| 820 |
|
Molecule::IntegrableObjectIterator ioi; |
| 821 |
< |
Molecule * mol; |
| 822 |
< |
Atom * atom; |
| 823 |
< |
RigidBody * rb; |
| 824 |
< |
CutoffGroup * cg; |
| 821 |
> |
Molecule* mol; |
| 822 |
> |
Atom* atom; |
| 823 |
> |
RigidBody* rb; |
| 824 |
> |
CutoffGroup* cg; |
| 825 |
> |
Bond* bond; |
| 826 |
> |
Bend* bend; |
| 827 |
> |
Torsion* torsion; |
| 828 |
> |
Inversion* inversion; |
| 829 |
|
int beginAtomIndex; |
| 830 |
|
int beginRigidBodyIndex; |
| 831 |
|
int beginCutoffGroupIndex; |
| 832 |
+ |
int beginBondIndex; |
| 833 |
+ |
int beginBendIndex; |
| 834 |
+ |
int beginTorsionIndex; |
| 835 |
+ |
int beginInversionIndex; |
| 836 |
+ |
#ifdef IS_MPI |
| 837 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 838 |
+ |
int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
| 839 |
+ |
#endif |
| 840 |
|
|
| 841 |
|
beginAtomIndex = 0; |
| 842 |
< |
//rigidbody's index begins right after atom's |
| 842 |
> |
// The rigid body indices begin immediately after the atom indices: |
| 843 |
|
beginRigidBodyIndex = info->getNGlobalAtoms(); |
| 844 |
|
beginCutoffGroupIndex = 0; |
| 845 |
< |
|
| 845 |
> |
beginBondIndex = 0; |
| 846 |
> |
beginBendIndex = 0; |
| 847 |
> |
beginTorsionIndex = 0; |
| 848 |
> |
beginInversionIndex = 0; |
| 849 |
> |
|
| 850 |
|
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 851 |
|
|
| 852 |
|
#ifdef IS_MPI |
| 855 |
|
// stuff to do if I own this molecule |
| 856 |
|
mol = info->getMoleculeByGlobalIndex(i); |
| 857 |
|
|
| 858 |
< |
//local index(index in DataStorge) of atom is important |
| 859 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 858 |
> |
// The local index(index in DataStorge) of the atom is important: |
| 859 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 860 |
> |
atom = mol->nextAtom(ai)) { |
| 861 |
|
atom->setGlobalIndex(beginAtomIndex++); |
| 862 |
|
} |
| 863 |
|
|
| 866 |
|
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 867 |
|
} |
| 868 |
|
|
| 869 |
< |
//local index of cutoff group is trivial, it only depends on |
| 870 |
< |
//the order of travesing |
| 869 |
> |
// The local index of other objects only depends on the order |
| 870 |
> |
// of traversal: |
| 871 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 872 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 873 |
|
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 874 |
|
} |
| 875 |
+ |
for(bond = mol->beginBond(boi); bond != NULL; |
| 876 |
+ |
bond = mol->nextBond(boi)) { |
| 877 |
+ |
bond->setGlobalIndex(beginBondIndex++); |
| 878 |
+ |
} |
| 879 |
+ |
for(bend = mol->beginBend(bei); bend != NULL; |
| 880 |
+ |
bend = mol->nextBend(bei)) { |
| 881 |
+ |
bend->setGlobalIndex(beginBendIndex++); |
| 882 |
+ |
} |
| 883 |
+ |
for(torsion = mol->beginTorsion(ti); torsion != NULL; |
| 884 |
+ |
torsion = mol->nextTorsion(ti)) { |
| 885 |
+ |
torsion->setGlobalIndex(beginTorsionIndex++); |
| 886 |
+ |
} |
| 887 |
+ |
for(inversion = mol->beginInversion(ii); inversion != NULL; |
| 888 |
+ |
inversion = mol->nextInversion(ii)) { |
| 889 |
+ |
inversion->setGlobalIndex(beginInversionIndex++); |
| 890 |
+ |
} |
| 891 |
|
|
| 892 |
|
#ifdef IS_MPI |
| 893 |
|
} else { |
| 900 |
|
beginAtomIndex += stamp->getNAtoms(); |
| 901 |
|
beginRigidBodyIndex += stamp->getNRigidBodies(); |
| 902 |
|
beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms(); |
| 903 |
+ |
beginBondIndex += stamp->getNBonds(); |
| 904 |
+ |
beginBendIndex += stamp->getNBends(); |
| 905 |
+ |
beginTorsionIndex += stamp->getNTorsions(); |
| 906 |
+ |
beginInversionIndex += stamp->getNInversions(); |
| 907 |
|
} |
| 908 |
|
#endif |
| 909 |
|
|
| 911 |
|
|
| 912 |
|
//fill globalGroupMembership |
| 913 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 914 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 915 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 916 |
< |
|
| 914 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 915 |
> |
mol = info->nextMolecule(mi)) { |
| 916 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 917 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 918 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 919 |
|
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
| 920 |
|
} |
| 929 |
|
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 930 |
|
// docs said we could. |
| 931 |
|
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 932 |
< |
MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], |
| 933 |
< |
&tmpGroupMembership[0], nGlobalAtoms, |
| 934 |
< |
MPI::INT, MPI::SUM); |
| 932 |
> |
MPI_Allreduce(&globalGroupMembership[0], |
| 933 |
> |
&tmpGroupMembership[0], nGlobalAtoms, |
| 934 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 935 |
> |
|
| 936 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 937 |
|
#else |
| 938 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
| 939 |
|
#endif |
| 940 |
|
|
| 941 |
|
//fill molMembership |
| 942 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 942 |
> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms() + |
| 943 |
> |
info->getNGlobalRigidBodies(), 0); |
| 944 |
|
|
| 945 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 945 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 946 |
> |
mol = info->nextMolecule(mi)) { |
| 947 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 948 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 949 |
|
} |
| 950 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; |
| 951 |
+ |
rb = mol->nextRigidBody(ri)) { |
| 952 |
+ |
globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex(); |
| 953 |
+ |
} |
| 954 |
|
} |
| 955 |
|
|
| 956 |
|
#ifdef IS_MPI |
| 957 |
< |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 958 |
< |
MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 959 |
< |
nGlobalAtoms, |
| 960 |
< |
MPI::INT, MPI::SUM); |
| 957 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + |
| 958 |
> |
info->getNGlobalRigidBodies(), 0); |
| 959 |
> |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 960 |
> |
nGlobalAtoms + nGlobalRigidBodies, |
| 961 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 962 |
|
|
| 963 |
|
info->setGlobalMolMembership(tmpMolMembership); |
| 964 |
|
#else |
| 969 |
|
// here the molecules are listed by their global indices. |
| 970 |
|
|
| 971 |
|
std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
| 972 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 972 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 973 |
> |
mol = info->nextMolecule(mi)) { |
| 974 |
|
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
| 975 |
|
} |
| 976 |
|
|
| 977 |
|
#ifdef IS_MPI |
| 978 |
|
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
| 979 |
< |
MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 980 |
< |
info->getNGlobalMolecules(), MPI::INT, MPI::SUM); |
| 979 |
> |
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 980 |
> |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 981 |
|
#else |
| 982 |
|
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 983 |
|
#endif |
| 991 |
|
} |
| 992 |
|
|
| 993 |
|
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 994 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 994 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 995 |
> |
mol = info->nextMolecule(mi)) { |
| 996 |
|
int myGlobalIndex = mol->getGlobalIndex(); |
| 997 |
|
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 998 |
|
for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; |
| 1008 |
|
} |
| 1009 |
|
|
| 1010 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 1011 |
< |
|
| 1011 |
> |
|
| 1012 |
|
DumpReader reader(info, mdFileName); |
| 1013 |
|
int nframes = reader.getNFrames(); |
| 1014 |
< |
|
| 1014 |
> |
|
| 1015 |
|
if (nframes > 0) { |
| 1016 |
|
reader.readFrame(nframes - 1); |
| 1017 |
|
} else { |
