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

Comparing:
trunk/src/brains/SimCreator.cpp (file contents), Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1601 by gezelter, Thu Aug 4 20:04:35 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 ){
85		Globals* simParams = NULL;
#	Line 108 | Line 108 | namespace oopse {
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
#	Line 116 | Line 116 | namespace oopse {
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
#	Line 214 | Line 214 | namespace oopse {
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());
#	Line 234 | Line 234 | namespace oopse {
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;
#	Line 262 | Line 262 | namespace oopse {
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();
#	Line 363 | Line 369 | namespace oopse {
369		}
370
371		ff->parse(forcefieldFileName);
366	–	ff->setFortranForceOptions();
372		//create SimInfo
373		SimInfo * info = new SimInfo(ff, simParams);
374
#	Line 381 | Line 386 | namespace oopse {
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));
#	Line 393 | Line 397 | namespace oopse {
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);
410	–
414		return info;
415		}
416
#	Line 471 | Line 474 | namespace oopse {
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();
#	Line 606 | Line 609 | namespace oopse {
609		#endif
610
611		stampId = info->getMoleculeStampId(i);
612	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
613	<	stampId, i, info->getLocalIndexManager());
612	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
613	>	info->getMoleculeStamp(stampId),
614	>	stampId, i,
615	>	info->getLocalIndexManager());
616
617		info->addMolecule(mol);
618
#	Line 634 | Line 639 | namespace oopse {
639		int beginRigidBodyIndex;
640		int beginCutoffGroupIndex;
641		int nGlobalAtoms = info->getNGlobalAtoms();
637	–
638	–	/**@todo fixme */
639	–	#ifndef IS_MPI
642
643		beginAtomIndex = 0;
644		beginRigidBodyIndex = 0;
645		beginCutoffGroupIndex = 0;
646	<
647	<	#else
646	<
647	<	int nproc;
648	<	int myNode;
649	<
650	<	myNode = worldRank;
651	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
652	<
653	<	std::vector < int > tmpAtomsInProc(nproc, 0);
654	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
655	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
656	<	std::vector < int > NumAtomsInProc(nproc, 0);
657	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
658	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
659	<
660	<	tmpAtomsInProc[myNode] = info->getNAtoms();
661	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
662	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
663	<
664	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
665	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
666	<	MPI_SUM, MPI_COMM_WORLD);
667	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
668	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
669	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
670	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
671	<
672	<	beginAtomIndex = 0;
673	<	beginRigidBodyIndex = 0;
674	<	beginCutoffGroupIndex = 0;
675	<
676	<	for(int i = 0; i < myNode; i++) {
677	<	beginAtomIndex += NumAtomsInProc[i];
678	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
679	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
680	<	}
681	<
682	<	#endif
683	<
684	<	//rigidbody's index begins right after atom's
685	<	beginRigidBodyIndex += info->getNGlobalAtoms();
686	<
687	<	for(mol = info->beginMolecule(mi); mol != NULL;
688	<	mol = info->nextMolecule(mi)) {
646	>
647	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
648
649	<	//local index(index in DataStorge) of atom is important
650	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
651	<	atom->setGlobalIndex(beginAtomIndex++);
649	>	#ifdef IS_MPI
650	>	if (info->getMolToProc(i) == worldRank) {
651	>	#endif
652	>	// stuff to do if I own this molecule
653	>	mol = info->getMoleculeByGlobalIndex(i);
654	>
655	>	//local index(index in DataStorge) of atom is important
656	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
657	>	atom->setGlobalIndex(beginAtomIndex++);
658	>	}
659	>
660	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
661	>	rb = mol->nextRigidBody(ri)) {
662	>	rb->setGlobalIndex(beginRigidBodyIndex++);
663	>	}
664	>
665	>	//local index of cutoff group is trivial, it only depends on
666	>	//the order of travesing
667	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
668	>	cg = mol->nextCutoffGroup(ci)) {
669	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
670	>	}
671	>
672	>	#ifdef IS_MPI
673	>	}  else {
674	>
675	>	// stuff to do if I don't own this molecule
676	>
677	>	int stampId = info->getMoleculeStampId(i);
678	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
679	>
680	>	beginAtomIndex += stamp->getNAtoms();
681	>	beginRigidBodyIndex += stamp->getNRigidBodies();
682	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
683		}
684	<
685	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
686	<	rb = mol->nextRigidBody(ri)) {
687	<	rb->setGlobalIndex(beginRigidBodyIndex++);
698	<	}
699	<
700	<	//local index of cutoff group is trivial, it only depends on the order of travesing
701	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
702	<	cg = mol->nextCutoffGroup(ci)) {
703	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
704	<	}
705	<	}
706	<
684	>	#endif
685	>
686	>	} //end for(int i=0)
687	>
688		//fill globalGroupMembership
689		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
690		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 715 | Line 696 | namespace oopse {
696
697		}
698		}
699	<
699	>
700		#ifdef IS_MPI
701		// Since the globalGroupMembership has been zero filled and we've only
702		// poked values into the atoms we know, we can do an Allreduce
703		// to get the full globalGroupMembership array (We think).
704		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
705		// docs said we could.
706	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
706	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
707		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
708		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
709		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 734 | Line 715 | namespace oopse {
715		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
716
717		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
737	–
718		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
720		}
721		}
722
723		#ifdef IS_MPI
724	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
724	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
725
726		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
727		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 767 | Line 747 | namespace oopse {
747		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
748		#endif
749
750	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
751	<
752	<	int startingIndex = 0;
753	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
754	<	startingIOIndexForMol[i] = startingIndex;
755	<	startingIndex += numIntegrableObjectsPerMol[i];
756	<	}
757	<
758	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
759	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
750	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
751	>
752	>	int startingIndex = 0;
753	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
754	>	startingIOIndexForMol[i] = startingIndex;
755	>	startingIndex += numIntegrableObjectsPerMol[i];
756	>	}
757	>
758	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
759	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
760		int myGlobalIndex = mol->getGlobalIndex();
761		int globalIO = startingIOIndexForMol[myGlobalIndex];
762		for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
763		integrableObject = mol->nextIntegrableObject(ioi)) {
764	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
765	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
766	<	globalIO++;
764	>	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
765	>	IOIndexToIntegrableObject[globalIO] = integrableObject;
766	>	globalIO++;
767		}
768		}
769	<
770	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
771	<
769	>
770	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
771	>
772		}
773
774		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
775		Globals* simParams;
776	+
777		simParams = info->getSimParams();
778
798	–
779		DumpReader reader(info, mdFileName);
780		int nframes = reader.getNFrames();
781	<
781	>
782		if (nframes > 0) {
783		reader.readFrame(nframes - 1);
784		} else {
#	Line 809 | Line 789 | int startingIndex = 0;
789		painCave.isFatal = 1;
790		simError();
791		}
812	–
792		//copy the current snapshot to previous snapshot
793		info->getSnapshotManager()->advance();
794		}
795
796	<	} //end namespace oopse
796	>	} //end namespace OpenMD
797
798

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

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