| 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; |
| 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"); |
| 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(); |
| 369 |
|
} |
| 370 |
|
|
| 371 |
|
ff->parse(forcefieldFileName); |
| 366 |
– |
ff->setFortranForceOptions(); |
| 372 |
|
//create SimInfo |
| 373 |
|
SimInfo * info = new SimInfo(ff, simParams); |
| 374 |
|
|
| 386 |
|
//create the molecules |
| 387 |
|
createMolecules(info); |
| 388 |
|
|
| 384 |
– |
|
| 389 |
|
//allocate memory for DataStorage(circular reference, need to |
| 390 |
|
//break it) |
| 391 |
|
info->setSnapshotManager(new SimSnapshotManager(info)); |
| 411 |
|
|
| 412 |
|
if (loadInitCoords) |
| 413 |
|
loadCoordinates(info, mdFileName); |
| 410 |
– |
|
| 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(); |
| 708 |
|
} |
| 709 |
|
|
| 710 |
|
//fill globalGroupMembership |
| 711 |
< |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 711 |
> |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), -1); |
| 712 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 713 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 714 |
|
|
| 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 |
| 727 |
|
// docs said we could. |
| 728 |
|
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 729 |
|
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 730 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 730 |
> |
MPI_INT, MPI_MAX, MPI_COMM_WORLD); |
| 731 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 732 |
+ |
|
| 733 |
+ |
cerr << "ggm:\n"; |
| 734 |
+ |
for (int i = 0; i < tmpGroupMembership.size(); i++) |
| 735 |
+ |
cerr << "i = " << i << "\t ggm(i) = " << tmpGroupMembership[i] << "\n"; |
| 736 |
+ |
|
| 737 |
|
#else |
| 738 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
| 739 |
|
#endif |
| 800 |
|
|
| 801 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 802 |
|
Globals* simParams; |
| 803 |
+ |
|
| 804 |
|
simParams = info->getSimParams(); |
| 805 |
|
|
| 797 |
– |
|
| 806 |
|
DumpReader reader(info, mdFileName); |
| 807 |
|
int nframes = reader.getNFrames(); |
| 808 |
< |
|
| 808 |
> |
|
| 809 |
|
if (nframes > 0) { |
| 810 |
|
reader.readFrame(nframes - 1); |
| 811 |
|
} else { |
| 816 |
|
painCave.isFatal = 1; |
| 817 |
|
simError(); |
| 818 |
|
} |
| 811 |
– |
|
| 819 |
|
//copy the current snapshot to previous snapshot |
| 820 |
|
info->getSnapshotManager()->advance(); |
| 821 |
|
} |
| 822 |
|
|
| 823 |
< |
} //end namespace oopse |
| 823 |
> |
} //end namespace OpenMD |
| 824 |
|
|
| 825 |
|
|
