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root/OpenMD/branches/development/src/brains/SimCreator.cpp

Comparing:
trunk/src/brains/SimCreator.cpp (file contents), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

#	Line 6 | Line 6
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.
#	Line 37 | Line 28
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		/**
#	Line 79 | Line 79
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 ){
84	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
85		Globals* simParams = NULL;
86		try {
87
#	Line 92 | Line 92 | namespace oopse {
92		const int masterNode = 0;
93		int commStatus;
94		if (worldRank == masterNode) {
95	<	#endif
96	<
95	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
96	>	#endif
97		SimplePreprocessor preprocessor;
98		preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
99
#	Line 106 | Line 106 | namespace oopse {
106
107
108		} else {
109	+
110	+	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
111	+
112		//get stream size
113		commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
114	<
114	>
115		char* buf = new char[streamSize];
116		assert(buf);
117
#	Line 116 | Line 119 | namespace oopse {
119		commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
120
121		ppStream.str(buf);
122	<	delete buf;
122	>	delete [] buf;
123
124		}
125		#endif
#	Line 145 | Line 148 | namespace oopse {
148		treeParser.initializeASTFactory(factory);
149		treeParser.setASTFactory(&factory);
150		simParams = treeParser.walkTree(parser.getAST());
148	–
151		}
152
153
#	Line 215 | Line 217 | namespace oopse {
217		painCave.isFatal = 1;
218		simError();
219		}
220	<	catch (OOPSEException& e) {
220	>	catch (OpenMDException& e) {
221		sprintf(painCave.errMsg,
222		"%s\n",
223		e.getMessage().c_str());
#	Line 230 | Line 232 | namespace oopse {
232		simError();
233		}
234
235	+	simParams->setMDfileVersion(mdFileVersion);
236		return simParams;
237		}
238
239		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
240		bool loadInitCoords) {
241	<
241	>
242		const int bufferSize = 65535;
243		char buffer[bufferSize];
244		int lineNo = 0;
#	Line 244 | Line 247 | namespace oopse {
247		int metaDataBlockEnd = -1;
248		int i;
249		int mdOffset;
250	+	int mdFileVersion;
251
252		#ifdef IS_MPI
253		const int masterNode = 0;
#	Line 263 | Line 267 | namespace oopse {
267		mdFile_.getline(buffer, bufferSize);
268		++lineNo;
269		std::string line = trimLeftCopy(buffer);
270	<	i = CaseInsensitiveFind(line, "<OOPSE");
271	<	if (i == string::npos) {
270	>	i = CaseInsensitiveFind(line, "<OpenMD");
271	>	if (static_cast<size_t>(i) == string::npos) {
272	>	// try the older file strings to see if that works:
273	>	i = CaseInsensitiveFind(line, "<OOPSE");
274	>	}
275	>
276	>	if (static_cast<size_t>(i) == string::npos) {
277	>	// still no luck!
278		sprintf(painCave.errMsg,
279	<	"SimCreator: File: %s is not an OOPSE file!\n",
279	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
280		mdFileName.c_str());
281		painCave.isFatal = 1;
282		simError();
283		}
284	+
285	+	// found the correct opening string, now try to get the file
286	+	// format version number.
287
288	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
289	+	std::string fileType = tokenizer.nextToken();
290	+	toUpper(fileType);
291	+
292	+	mdFileVersion = 0;
293	+
294	+	if (fileType == "OPENMD") {
295	+	while (tokenizer.hasMoreTokens()) {
296	+	std::string token(tokenizer.nextToken());
297	+	toUpper(token);
298	+	if (token == "VERSION") {
299	+	mdFileVersion = tokenizer.nextTokenAsInt();
300	+	break;
301	+	}
302	+	}
303	+	}
304	+
305		//scan through the input stream and find MetaData tag
306		while(mdFile_.getline(buffer, bufferSize)) {
307		++lineNo;
#	Line 327 | Line 357 | namespace oopse {
357		std::stringstream rawMetaDataStream(mdRawData);
358
359		//parse meta-data file
360	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
360	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
361	>	metaDataBlockStart + 1);
362
363		//create the force field
364	<	ForceField * ff = ForceFieldFactory::getInstance()
365	<	->createForceField(simParams->getForceField());
335	<
364	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
365	>
366		if (ff == NULL) {
367		sprintf(painCave.errMsg,
368		"ForceField Factory can not create %s force field\n",
#	Line 365 | Line 395 | namespace oopse {
395		}
396
397		ff->parse(forcefieldFileName);
368	–	ff->setFortranForceOptions();
398		//create SimInfo
399		SimInfo * info = new SimInfo(ff, simParams);
400
#	Line 383 | Line 412 | namespace oopse {
412		//create the molecules
413		createMolecules(info);
414
386	–
415		//allocate memory for DataStorage(circular reference, need to
416		//break it)
417		info->setSnapshotManager(new SimSnapshotManager(info));
#	Line 395 | Line 423 | namespace oopse {
423		//responsibility to LocalIndexManager.
424		setGlobalIndex(info);
425
426	<	//Although addExcludePairs is called inside SimInfo's addMolecule
426	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
427		//method, at that point atoms don't have the global index yet
428		//(their global index are all initialized to -1).  Therefore we
429	<	//have to call addExcludePairs explicitly here. A way to work
429	>	//have to call addInteractionPairs explicitly here. A way to work
430		//around is that we can determine the beginning global indices of
431		//atoms before they get created.
432		SimInfo::MoleculeIterator mi;
433		Molecule* mol;
434		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
435	<	info->addExcludePairs(mol);
435	>	info->addInteractionPairs(mol);
436		}
437
438		if (loadInitCoords)
439		loadCoordinates(info, mdFileName);
412	–
440		return info;
441		}
442
#	Line 473 | Line 500 | namespace oopse {
500		"\tthe number of molecules.  This will not result in a \n"
501		"\tusable division of atoms for force decomposition.\n"
502		"\tEither try a smaller number of processors, or run the\n"
503	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
503	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
504
505		painCave.isFatal = 1;
506		simError();
#	Line 608 | Line 635 | namespace oopse {
635		#endif
636
637		stampId = info->getMoleculeStampId(i);
638	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
639	<	stampId, i, info->getLocalIndexManager());
638	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
639	>	info->getMoleculeStamp(stampId),
640	>	stampId, i,
641	>	info->getLocalIndexManager());
642
643		info->addMolecule(mol);
644
#	Line 636 | Line 665 | namespace oopse {
665		int beginRigidBodyIndex;
666		int beginCutoffGroupIndex;
667		int nGlobalAtoms = info->getNGlobalAtoms();
639	–
640	–	/**@todo fixme */
641	–	#ifndef IS_MPI
668
669		beginAtomIndex = 0;
670		beginRigidBodyIndex = 0;
671		beginCutoffGroupIndex = 0;
672	<
673	<	#else
648	<
649	<	int nproc;
650	<	int myNode;
651	<
652	<	myNode = worldRank;
653	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
654	<
655	<	std::vector < int > tmpAtomsInProc(nproc, 0);
656	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
657	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
658	<	std::vector < int > NumAtomsInProc(nproc, 0);
659	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
660	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
661	<
662	<	tmpAtomsInProc[myNode] = info->getNAtoms();
663	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
664	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
665	<
666	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
667	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
668	<	MPI_SUM, MPI_COMM_WORLD);
669	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
670	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
671	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
672	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
673	<
674	<	beginAtomIndex = 0;
675	<	beginRigidBodyIndex = 0;
676	<	beginCutoffGroupIndex = 0;
677	<
678	<	for(int i = 0; i < myNode; i++) {
679	<	beginAtomIndex += NumAtomsInProc[i];
680	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
681	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
682	<	}
683	<
684	<	#endif
685	<
686	<	//rigidbody's index begins right after atom's
687	<	beginRigidBodyIndex += info->getNGlobalAtoms();
688	<
689	<	for(mol = info->beginMolecule(mi); mol != NULL;
690	<	mol = info->nextMolecule(mi)) {
672	>
673	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
674
675	<	//local index(index in DataStorge) of atom is important
676	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
677	<	atom->setGlobalIndex(beginAtomIndex++);
675	>	#ifdef IS_MPI
676	>	if (info->getMolToProc(i) == worldRank) {
677	>	#endif
678	>	// stuff to do if I own this molecule
679	>	mol = info->getMoleculeByGlobalIndex(i);
680	>
681	>	//local index(index in DataStorge) of atom is important
682	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
683	>	atom->setGlobalIndex(beginAtomIndex++);
684	>	}
685	>
686	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
687	>	rb = mol->nextRigidBody(ri)) {
688	>	rb->setGlobalIndex(beginRigidBodyIndex++);
689	>	}
690	>
691	>	//local index of cutoff group is trivial, it only depends on
692	>	//the order of travesing
693	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
694	>	cg = mol->nextCutoffGroup(ci)) {
695	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
696	>	}
697	>
698	>	#ifdef IS_MPI
699	>	}  else {
700	>
701	>	// stuff to do if I don't own this molecule
702	>
703	>	int stampId = info->getMoleculeStampId(i);
704	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
705	>
706	>	beginAtomIndex += stamp->getNAtoms();
707	>	beginRigidBodyIndex += stamp->getNRigidBodies();
708	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
709		}
710	<
711	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
712	<	rb = mol->nextRigidBody(ri)) {
713	<	rb->setGlobalIndex(beginRigidBodyIndex++);
700	<	}
701	<
702	<	//local index of cutoff group is trivial, it only depends on the order of travesing
703	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
704	<	cg = mol->nextCutoffGroup(ci)) {
705	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
706	<	}
707	<	}
708	<
710	>	#endif
711	>
712	>	} //end for(int i=0)
713	>
714		//fill globalGroupMembership
715		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
716		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 717 | Line 722 | namespace oopse {
722
723		}
724		}
725	<
725	>
726		#ifdef IS_MPI
727		// Since the globalGroupMembership has been zero filled and we've only
728		// poked values into the atoms we know, we can do an Allreduce
729		// to get the full globalGroupMembership array (We think).
730		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
731		// docs said we could.
732	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
732	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
733		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
734		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
735		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 736 | Line 741 | namespace oopse {
741		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
742
743		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
739	–
744		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
745		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
746		}
747		}
748
749		#ifdef IS_MPI
750	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
750	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
751
752		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
753		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 769 | Line 773 | namespace oopse {
773		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
774		#endif
775
776	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
777	<
778	<	int startingIndex = 0;
779	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
780	<	startingIOIndexForMol[i] = startingIndex;
781	<	startingIndex += numIntegrableObjectsPerMol[i];
782	<	}
783	<
784	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
785	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
776	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
777	>
778	>	int startingIndex = 0;
779	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
780	>	startingIOIndexForMol[i] = startingIndex;
781	>	startingIndex += numIntegrableObjectsPerMol[i];
782	>	}
783	>
784	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
785	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
786		int myGlobalIndex = mol->getGlobalIndex();
787		int globalIO = startingIOIndexForMol[myGlobalIndex];
788		for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
789		integrableObject = mol->nextIntegrableObject(ioi)) {
790	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
791	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
792	<	globalIO++;
790	>	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
791	>	IOIndexToIntegrableObject[globalIO] = integrableObject;
792	>	globalIO++;
793		}
794		}
795	<
796	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
797	<
795	>
796	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
797	>
798		}
799
800		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
801		Globals* simParams;
802	+
803		simParams = info->getSimParams();
804
800	–
805		DumpReader reader(info, mdFileName);
806		int nframes = reader.getNFrames();
807	<
807	>
808		if (nframes > 0) {
809		reader.readFrame(nframes - 1);
810		} else {
#	Line 811 | Line 815 | int startingIndex = 0;
815		painCave.isFatal = 1;
816		simError();
817		}
814	–
818		//copy the current snapshot to previous snapshot
819		info->getSnapshotManager()->advance();
820		}
821
822	<	} //end namespace oopse
822	>	} //end namespace OpenMD
823
824

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

#	Line 0 | Line 1
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