| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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 |
|
/** |
| 79 |
|
#include "math/ParallelRandNumGen.hpp" |
| 80 |
|
#endif |
| 81 |
|
|
| 82 |
< |
namespace oopse { |
| 82 |
> |
namespace OpenMD { |
| 83 |
|
|
| 84 |
|
Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){ |
| 85 |
|
Globals* simParams = NULL; |
| 108 |
|
} else { |
| 109 |
|
//get stream size |
| 110 |
|
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 111 |
< |
|
| 111 |
> |
|
| 112 |
|
char* buf = new char[streamSize]; |
| 113 |
|
assert(buf); |
| 114 |
|
|
| 116 |
|
commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 117 |
|
|
| 118 |
|
ppStream.str(buf); |
| 119 |
< |
delete buf; |
| 119 |
> |
delete [] buf; |
| 120 |
|
|
| 121 |
|
} |
| 122 |
|
#endif |
| 145 |
|
treeParser.initializeASTFactory(factory); |
| 146 |
|
treeParser.setASTFactory(&factory); |
| 147 |
|
simParams = treeParser.walkTree(parser.getAST()); |
| 148 |
– |
|
| 148 |
|
} |
| 149 |
|
|
| 150 |
|
|
| 214 |
|
painCave.isFatal = 1; |
| 215 |
|
simError(); |
| 216 |
|
} |
| 217 |
< |
catch (OOPSEException& e) { |
| 217 |
> |
catch (OpenMDException& e) { |
| 218 |
|
sprintf(painCave.errMsg, |
| 219 |
|
"%s\n", |
| 220 |
|
e.getMessage().c_str()); |
| 234 |
|
|
| 235 |
|
SimInfo* SimCreator::createSim(const std::string & mdFileName, |
| 236 |
|
bool loadInitCoords) { |
| 237 |
< |
|
| 237 |
> |
|
| 238 |
|
const int bufferSize = 65535; |
| 239 |
|
char buffer[bufferSize]; |
| 240 |
|
int lineNo = 0; |
| 262 |
|
mdFile_.getline(buffer, bufferSize); |
| 263 |
|
++lineNo; |
| 264 |
|
std::string line = trimLeftCopy(buffer); |
| 265 |
< |
i = CaseInsensitiveFind(line, "<OOPSE"); |
| 266 |
< |
if (i == string::npos) { |
| 265 |
> |
i = CaseInsensitiveFind(line, "<OpenMD"); |
| 266 |
> |
if (static_cast<size_t>(i) == string::npos) { |
| 267 |
> |
// try the older file strings to see if that works: |
| 268 |
> |
i = CaseInsensitiveFind(line, "<OOPSE"); |
| 269 |
> |
} |
| 270 |
> |
|
| 271 |
> |
if (static_cast<size_t>(i) == string::npos) { |
| 272 |
> |
// still no luck! |
| 273 |
|
sprintf(painCave.errMsg, |
| 274 |
< |
"SimCreator: File: %s is not an OOPSE file!\n", |
| 274 |
> |
"SimCreator: File: %s is not a valid OpenMD file!\n", |
| 275 |
|
mdFileName.c_str()); |
| 276 |
|
painCave.isFatal = 1; |
| 277 |
|
simError(); |
| 335 |
|
Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1); |
| 336 |
|
|
| 337 |
|
//create the force field |
| 338 |
< |
ForceField * ff = ForceFieldFactory::getInstance() |
| 339 |
< |
->createForceField(simParams->getForceField()); |
| 335 |
< |
|
| 338 |
> |
ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField()); |
| 339 |
> |
|
| 340 |
|
if (ff == NULL) { |
| 341 |
|
sprintf(painCave.errMsg, |
| 342 |
|
"ForceField Factory can not create %s force field\n", |
| 369 |
|
} |
| 370 |
|
|
| 371 |
|
ff->parse(forcefieldFileName); |
| 368 |
– |
ff->setFortranForceOptions(); |
| 372 |
|
//create SimInfo |
| 373 |
|
SimInfo * info = new SimInfo(ff, simParams); |
| 374 |
|
|
| 386 |
|
//create the molecules |
| 387 |
|
createMolecules(info); |
| 388 |
|
|
| 386 |
– |
|
| 389 |
|
//allocate memory for DataStorage(circular reference, need to |
| 390 |
|
//break it) |
| 391 |
|
info->setSnapshotManager(new SimSnapshotManager(info)); |
| 397 |
|
//responsibility to LocalIndexManager. |
| 398 |
|
setGlobalIndex(info); |
| 399 |
|
|
| 400 |
< |
//Although addExcludePairs is called inside SimInfo's addMolecule |
| 400 |
> |
//Although addInteractionPairs is called inside SimInfo's addMolecule |
| 401 |
|
//method, at that point atoms don't have the global index yet |
| 402 |
|
//(their global index are all initialized to -1). Therefore we |
| 403 |
< |
//have to call addExcludePairs explicitly here. A way to work |
| 403 |
> |
//have to call addInteractionPairs explicitly here. A way to work |
| 404 |
|
//around is that we can determine the beginning global indices of |
| 405 |
|
//atoms before they get created. |
| 406 |
|
SimInfo::MoleculeIterator mi; |
| 407 |
|
Molecule* mol; |
| 408 |
|
for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 409 |
< |
info->addExcludePairs(mol); |
| 409 |
> |
info->addInteractionPairs(mol); |
| 410 |
|
} |
| 411 |
|
|
| 412 |
|
if (loadInitCoords) |
| 413 |
|
loadCoordinates(info, mdFileName); |
| 412 |
– |
|
| 414 |
|
return info; |
| 415 |
|
} |
| 416 |
|
|
| 474 |
|
"\tthe number of molecules. This will not result in a \n" |
| 475 |
|
"\tusable division of atoms for force decomposition.\n" |
| 476 |
|
"\tEither try a smaller number of processors, or run the\n" |
| 477 |
< |
"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
| 477 |
> |
"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
| 478 |
|
|
| 479 |
|
painCave.isFatal = 1; |
| 480 |
|
simError(); |
| 718 |
|
|
| 719 |
|
} |
| 720 |
|
} |
| 721 |
< |
|
| 721 |
> |
|
| 722 |
|
#ifdef IS_MPI |
| 723 |
|
// Since the globalGroupMembership has been zero filled and we've only |
| 724 |
|
// poked values into the atoms we know, we can do an Allreduce |
| 725 |
|
// to get the full globalGroupMembership array (We think). |
| 726 |
|
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 727 |
|
// docs said we could. |
| 728 |
< |
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
| 728 |
> |
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 729 |
|
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 730 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 731 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 737 |
|
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 738 |
|
|
| 739 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 739 |
– |
|
| 740 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 741 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 742 |
|
} |
| 743 |
|
} |
| 744 |
|
|
| 745 |
|
#ifdef IS_MPI |
| 746 |
< |
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
| 746 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 747 |
|
|
| 748 |
|
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 749 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 769 |
|
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 770 |
|
#endif |
| 771 |
|
|
| 772 |
< |
std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules()); |
| 773 |
< |
|
| 774 |
< |
int startingIndex = 0; |
| 775 |
< |
for (int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 776 |
< |
startingIOIndexForMol[i] = startingIndex; |
| 777 |
< |
startingIndex += numIntegrableObjectsPerMol[i]; |
| 778 |
< |
} |
| 779 |
< |
|
| 780 |
< |
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 781 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 772 |
> |
std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules()); |
| 773 |
> |
|
| 774 |
> |
int startingIndex = 0; |
| 775 |
> |
for (int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 776 |
> |
startingIOIndexForMol[i] = startingIndex; |
| 777 |
> |
startingIndex += numIntegrableObjectsPerMol[i]; |
| 778 |
> |
} |
| 779 |
> |
|
| 780 |
> |
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 781 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 782 |
|
int myGlobalIndex = mol->getGlobalIndex(); |
| 783 |
|
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 784 |
|
for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL; |
| 785 |
|
integrableObject = mol->nextIntegrableObject(ioi)) { |
| 786 |
< |
integrableObject->setGlobalIntegrableObjectIndex(globalIO); |
| 787 |
< |
IOIndexToIntegrableObject[globalIO] = integrableObject; |
| 788 |
< |
globalIO++; |
| 786 |
> |
integrableObject->setGlobalIntegrableObjectIndex(globalIO); |
| 787 |
> |
IOIndexToIntegrableObject[globalIO] = integrableObject; |
| 788 |
> |
globalIO++; |
| 789 |
|
} |
| 790 |
|
} |
| 791 |
< |
|
| 792 |
< |
info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); |
| 793 |
< |
|
| 791 |
> |
|
| 792 |
> |
info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); |
| 793 |
> |
|
| 794 |
|
} |
| 795 |
|
|
| 796 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 797 |
|
Globals* simParams; |
| 798 |
+ |
|
| 799 |
|
simParams = info->getSimParams(); |
| 800 |
|
|
| 800 |
– |
|
| 801 |
|
DumpReader reader(info, mdFileName); |
| 802 |
|
int nframes = reader.getNFrames(); |
| 803 |
< |
|
| 803 |
> |
|
| 804 |
|
if (nframes > 0) { |
| 805 |
|
reader.readFrame(nframes - 1); |
| 806 |
|
} else { |
| 811 |
|
painCave.isFatal = 1; |
| 812 |
|
simError(); |
| 813 |
|
} |
| 814 |
– |
|
| 814 |
|
//copy the current snapshot to previous snapshot |
| 815 |
|
info->getSnapshotManager()->advance(); |
| 816 |
|
} |
| 817 |
|
|
| 818 |
< |
} //end namespace oopse |
| 818 |
> |
} //end namespace OpenMD |
| 819 |
|
|
| 820 |
|
|
