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trunk/src/brains/SimCreator.cpp (file contents), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 55 | Line 56
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
59	<	#include "UseTheForce/ForceFieldFactory.hpp"
59	>	#include "brains/ForceField.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 76
76		#include "antlr/NoViableAltForCharException.hpp"
77		#include "antlr/NoViableAltException.hpp"
78
79	+	#include "types/DirectionalAdapter.hpp"
80	+	#include "types/MultipoleAdapter.hpp"
81	+	#include "types/EAMAdapter.hpp"
82	+	#include "types/SuttonChenAdapter.hpp"
83	+	#include "types/PolarizableAdapter.hpp"
84	+	#include "types/FixedChargeAdapter.hpp"
85	+	#include "types/FluctuatingChargeAdapter.hpp"
86	+
87		#ifdef IS_MPI
88	+	#include "mpi.h"
89		#include "math/ParallelRandNumGen.hpp"
90		#endif
91
92	<	namespace oopse {
92	>	namespace OpenMD {
93
94	<	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
94	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95		Globals* simParams = NULL;
96		try {
97
#	Line 92 | Line 102 | namespace oopse {
102		const int masterNode = 0;
103		int commStatus;
104		if (worldRank == masterNode) {
105	<	#endif
106	<
105	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
106	>	#endif
107		SimplePreprocessor preprocessor;
108		preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
109
#	Line 106 | Line 116 | namespace oopse {
116
117
118		} else {
119	+
120	+	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121	+
122		//get stream size
123		commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124	<
124	>
125		char* buf = new char[streamSize];
126		assert(buf);
127
#	Line 116 | Line 129 | namespace oopse {
129		commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
130
131		ppStream.str(buf);
132	<	delete buf;
132	>	delete [] buf;
133
134		}
135		#endif
#	Line 145 | Line 158 | namespace oopse {
158		treeParser.initializeASTFactory(factory);
159		treeParser.setASTFactory(&factory);
160		simParams = treeParser.walkTree(parser.getAST());
148	–
161		}
162
163
#	Line 215 | Line 227 | namespace oopse {
227		painCave.isFatal = 1;
228		simError();
229		}
230	<	catch (OOPSEException& e) {
230	>	catch (OpenMDException& e) {
231		sprintf(painCave.errMsg,
232		"%s\n",
233		e.getMessage().c_str());
#	Line 230 | Line 242 | namespace oopse {
242		simError();
243		}
244
245	+	simParams->setMDfileVersion(mdFileVersion);
246		return simParams;
247		}
248
249		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250		bool loadInitCoords) {
251	<
251	>
252		const int bufferSize = 65535;
253		char buffer[bufferSize];
254		int lineNo = 0;
#	Line 243 | Line 256 | namespace oopse {
256		int metaDataBlockStart = -1;
257		int metaDataBlockEnd = -1;
258		int i;
259	<	int mdOffset;
259	>	streamoff mdOffset;
260	>	int mdFileVersion;
261
262	+
263		#ifdef IS_MPI
264		const int masterNode = 0;
265		if (worldRank == masterNode) {
266		#endif
267
268	<	std::ifstream mdFile_(mdFileName.c_str());
268	>	std::ifstream mdFile_;
269	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
270
271		if (mdFile_.fail()) {
272		sprintf(painCave.errMsg,
#	Line 263 | Line 279 | namespace oopse {
279		mdFile_.getline(buffer, bufferSize);
280		++lineNo;
281		std::string line = trimLeftCopy(buffer);
282	<	i = CaseInsensitiveFind(line, "<OOPSE");
283	<	if (i == string::npos) {
282	>	i = CaseInsensitiveFind(line, "<OpenMD");
283	>	if (static_cast<size_t>(i) == string::npos) {
284	>	// try the older file strings to see if that works:
285	>	i = CaseInsensitiveFind(line, "<OOPSE");
286	>	}
287	>
288	>	if (static_cast<size_t>(i) == string::npos) {
289	>	// still no luck!
290		sprintf(painCave.errMsg,
291	<	"SimCreator: File: %s is not an OOPSE file!\n",
291	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
292		mdFileName.c_str());
293		painCave.isFatal = 1;
294		simError();
295		}
296	+
297	+	// found the correct opening string, now try to get the file
298	+	// format version number.
299
300	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
301	+	std::string fileType = tokenizer.nextToken();
302	+	toUpper(fileType);
303	+
304	+	mdFileVersion = 0;
305	+
306	+	if (fileType == "OPENMD") {
307	+	while (tokenizer.hasMoreTokens()) {
308	+	std::string token(tokenizer.nextToken());
309	+	toUpper(token);
310	+	if (token == "VERSION") {
311	+	mdFileVersion = tokenizer.nextTokenAsInt();
312	+	break;
313	+	}
314	+	}
315	+	}
316	+
317		//scan through the input stream and find MetaData tag
318		while(mdFile_.getline(buffer, bufferSize)) {
319		++lineNo;
#	Line 327 | Line 369 | namespace oopse {
369		std::stringstream rawMetaDataStream(mdRawData);
370
371		//parse meta-data file
372	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
372	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373	>	metaDataBlockStart + 1);
374
375		//create the force field
376	<	ForceField * ff = ForceFieldFactory::getInstance()
377	<	->createForceField(simParams->getForceField());
335	<
376	>	ForceField * ff = new ForceField(simParams->getForceField());
377	>
378		if (ff == NULL) {
379		sprintf(painCave.errMsg,
380		"ForceField Factory can not create %s force field\n",
#	Line 365 | Line 407 | namespace oopse {
407		}
408
409		ff->parse(forcefieldFileName);
368	–	ff->setFortranForceOptions();
410		//create SimInfo
411		SimInfo * info = new SimInfo(ff, simParams);
412
#	Line 383 | Line 424 | namespace oopse {
424		//create the molecules
425		createMolecules(info);
426
427	<
427	>	//find the storage layout
428	>
429	>	int storageLayout = computeStorageLayout(info);
430	>
431		//allocate memory for DataStorage(circular reference, need to
432		//break it)
433	<	info->setSnapshotManager(new SimSnapshotManager(info));
433	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435		//set the global index of atoms, rigidbodies and cutoffgroups
436		//(only need to be set once, the global index will never change
#	Line 395 | Line 439 | namespace oopse {
439		//responsibility to LocalIndexManager.
440		setGlobalIndex(info);
441
442	<	//Although addExcludePairs is called inside SimInfo's addMolecule
442	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
443		//method, at that point atoms don't have the global index yet
444		//(their global index are all initialized to -1).  Therefore we
445	<	//have to call addExcludePairs explicitly here. A way to work
445	>	//have to call addInteractionPairs explicitly here. A way to work
446		//around is that we can determine the beginning global indices of
447		//atoms before they get created.
448		SimInfo::MoleculeIterator mi;
449		Molecule* mol;
450		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
451	<	info->addExcludePairs(mol);
451	>	info->addInteractionPairs(mol);
452		}
453
454		if (loadInitCoords)
455		loadCoordinates(info, mdFileName);
412	–
456		return info;
457		}
458
#	Line 464 | Line 507 | namespace oopse {
507		int nGlobalMols = info->getNGlobalMolecules();
508		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
509
510	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
510	>	nProcessors = MPI::COMM_WORLD.Get_size();
511
512		if (nProcessors > nGlobalMols) {
513		sprintf(painCave.errMsg,
#	Line 473 | Line 516 | namespace oopse {
516		"\tthe number of molecules.  This will not result in a \n"
517		"\tusable division of atoms for force decomposition.\n"
518		"\tEither try a smaller number of processors, or run the\n"
519	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
519	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
520
521		painCave.isFatal = 1;
522		simError();
#	Line 502 | Line 545 | namespace oopse {
545		nTarget = (int)(precast + 0.5);
546
547		for(i = 0; i < nGlobalMols; i++) {
548	+
549		done = 0;
550		loops = 0;
551
#	Line 526 | Line 570 | namespace oopse {
570		// and be done with it.
571
572		if (loops > 100) {
573	+
574		sprintf(painCave.errMsg,
575	<	"I've tried 100 times to assign molecule %d to a "
576	<	" processor, but can't find a good spot.\n"
577	<	"I'm assigning it at random to processor %d.\n",
575	>	"There have been 100 attempts to assign molecule %d to an\n"
576	>	"\tunderworked processor, but there's no good place to\n"
577	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
578		i, which_proc);
579	<
579	>
580		painCave.isFatal = 0;
581	+	painCave.severity = OPENMD_INFO;
582		simError();
583
584		molToProcMap[i] = which_proc;
#	Line 577 | Line 623 | namespace oopse {
623		}
624
625		delete myRandom;
626	<
626	>
627		// Spray out this nonsense to all other processors:
628	<
583	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
628	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
629		} else {
630
631		// Listen to your marching orders from processor 0:
632	<
633	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
632	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
633	>
634		}
635
636		info->setMolToProcMap(molToProcMap);
637		sprintf(checkPointMsg,
638		"Successfully divided the molecules among the processors.\n");
639	<	MPIcheckPoint();
639	>	errorCheckPoint();
640		}
641
642		#endif
#	Line 608 | Line 653 | namespace oopse {
653		#endif
654
655		stampId = info->getMoleculeStampId(i);
656	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
657	<	stampId, i, info->getLocalIndexManager());
656	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
657	>	info->getMoleculeStamp(stampId),
658	>	stampId, i,
659	>	info->getLocalIndexManager());
660
661		info->addMolecule(mol);
662
#	Line 621 | Line 668 | namespace oopse {
668
669		} //end for(int i=0)
670		}
671	+
672	+	int SimCreator::computeStorageLayout(SimInfo* info) {
673	+
674	+	Globals* simParams = info->getSimParams();
675	+	int nRigidBodies = info->getNGlobalRigidBodies();
676	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
677	+	set<AtomType*>::iterator i;
678	+	bool hasDirectionalAtoms = false;
679	+	bool hasFixedCharge = false;
680	+	bool hasDipoles = false;
681	+	bool hasQuadrupoles = false;
682	+	bool hasPolarizable = false;
683	+	bool hasFluctuatingCharge = false;
684	+	bool hasMetallic = false;
685	+	int storageLayout = 0;
686	+	storageLayout |= DataStorage::dslPosition;
687	+	storageLayout |= DataStorage::dslVelocity;
688	+	storageLayout |= DataStorage::dslForce;
689	+
690	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
691	+
692	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
693	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
694	+	EAMAdapter ea = EAMAdapter( (*i) );
695	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
696	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
697	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
698	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
699	+
700	+	if (da.isDirectional()){
701	+	hasDirectionalAtoms = true;
702	+	}
703	+	if (ma.isDipole()){
704	+	hasDipoles = true;
705	+	}
706	+	if (ma.isQuadrupole()){
707	+	hasQuadrupoles = true;
708	+	}
709	+	if (ea.isEAM() || sca.isSuttonChen()){
710	+	hasMetallic = true;
711	+	}
712	+	if ( fca.isFixedCharge() ){
713	+	hasFixedCharge = true;
714	+	}
715	+	if ( fqa.isFluctuatingCharge() ){
716	+	hasFluctuatingCharge = true;
717	+	}
718	+	if ( pa.isPolarizable() ){
719	+	hasPolarizable = true;
720	+	}
721	+	}
722	+
723	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
724	+	storageLayout |= DataStorage::dslAmat;
725	+	if(storageLayout & DataStorage::dslVelocity) {
726	+	storageLayout |= DataStorage::dslAngularMomentum;
727	+	}
728	+	if (storageLayout & DataStorage::dslForce) {
729	+	storageLayout |= DataStorage::dslTorque;
730	+	}
731	+	}
732	+	if (hasDipoles) {
733	+	storageLayout |= DataStorage::dslDipole;
734	+	}
735	+	if (hasQuadrupoles) {
736	+	storageLayout |= DataStorage::dslQuadrupole;
737	+	}
738	+	if (hasFixedCharge || hasFluctuatingCharge) {
739	+	storageLayout |= DataStorage::dslSkippedCharge;
740	+	}
741	+	if (hasMetallic) {
742	+	storageLayout |= DataStorage::dslDensity;
743	+	storageLayout |= DataStorage::dslFunctional;
744	+	storageLayout |= DataStorage::dslFunctionalDerivative;
745	+	}
746	+	if (hasPolarizable) {
747	+	storageLayout |= DataStorage::dslElectricField;
748	+	}
749	+	if (hasFluctuatingCharge){
750	+	storageLayout |= DataStorage::dslFlucQPosition;
751	+	if(storageLayout & DataStorage::dslVelocity) {
752	+	storageLayout |= DataStorage::dslFlucQVelocity;
753	+	}
754	+	if (storageLayout & DataStorage::dslForce) {
755	+	storageLayout |= DataStorage::dslFlucQForce;
756	+	}
757	+	}
758
759	+	// if the user has asked for them, make sure we've got the memory for the
760	+	// objects defined.
761	+
762	+	if (simParams->getOutputParticlePotential()) {
763	+	storageLayout |= DataStorage::dslParticlePot;
764	+	}
765	+
766	+	if (simParams->havePrintHeatFlux()) {
767	+	if (simParams->getPrintHeatFlux()) {
768	+	storageLayout |= DataStorage::dslParticlePot;
769	+	}
770	+	}
771	+
772	+	if (simParams->getOutputElectricField()) {
773	+	storageLayout |= DataStorage::dslElectricField;
774	+	}
775	+
776	+	if (simParams->getOutputFluctuatingCharges()) {
777	+	storageLayout |= DataStorage::dslFlucQPosition;
778	+	storageLayout |= DataStorage::dslFlucQVelocity;
779	+	storageLayout |= DataStorage::dslFlucQForce;
780	+	}
781	+
782	+	return storageLayout;
783	+	}
784	+
785		void SimCreator::setGlobalIndex(SimInfo *info) {
786		SimInfo::MoleculeIterator mi;
787		Molecule::AtomIterator ai;
#	Line 636 | Line 796 | namespace oopse {
796		int beginRigidBodyIndex;
797		int beginCutoffGroupIndex;
798		int nGlobalAtoms = info->getNGlobalAtoms();
799	<
640	<	/**@todo fixme */
641	<	#ifndef IS_MPI
799	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
800
801		beginAtomIndex = 0;
644	–	beginRigidBodyIndex = 0;
645	–	beginCutoffGroupIndex = 0;
646	–
647	–	#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	–
802		//rigidbody's index begins right after atom's
803	<	beginRigidBodyIndex += info->getNGlobalAtoms();
804	<
805	<	for(mol = info->beginMolecule(mi); mol != NULL;
806	<	mol = info->nextMolecule(mi)) {
803	>	beginRigidBodyIndex = info->getNGlobalAtoms();
804	>	beginCutoffGroupIndex = 0;
805	>
806	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
807
808	<	//local index(index in DataStorge) of atom is important
809	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
810	<	atom->setGlobalIndex(beginAtomIndex++);
808	>	#ifdef IS_MPI
809	>	if (info->getMolToProc(i) == worldRank) {
810	>	#endif
811	>	// stuff to do if I own this molecule
812	>	mol = info->getMoleculeByGlobalIndex(i);
813	>
814	>	//local index(index in DataStorge) of atom is important
815	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
816	>	atom->setGlobalIndex(beginAtomIndex++);
817	>	}
818	>
819	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
820	>	rb = mol->nextRigidBody(ri)) {
821	>	rb->setGlobalIndex(beginRigidBodyIndex++);
822	>	}
823	>
824	>	//local index of cutoff group is trivial, it only depends on
825	>	//the order of travesing
826	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
827	>	cg = mol->nextCutoffGroup(ci)) {
828	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
829	>	}
830	>
831	>	#ifdef IS_MPI
832	>	}  else {
833	>
834	>	// stuff to do if I don't own this molecule
835	>
836	>	int stampId = info->getMoleculeStampId(i);
837	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
838	>
839	>	beginAtomIndex += stamp->getNAtoms();
840	>	beginRigidBodyIndex += stamp->getNRigidBodies();
841	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
842		}
843	<
844	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
845	<	rb = mol->nextRigidBody(ri)) {
846	<	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	<
843	>	#endif
844	>
845	>	} //end for(int i=0)
846	>
847		//fill globalGroupMembership
848		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
849		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 717 | Line 855 | namespace oopse {
855
856		}
857		}
858	<
858	>
859		#ifdef IS_MPI
860		// Since the globalGroupMembership has been zero filled and we've only
861		// poked values into the atoms we know, we can do an Allreduce
862		// to get the full globalGroupMembership array (We think).
863		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
864		// docs said we could.
865	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
866	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
867	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
865	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
866	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
867	>	&tmpGroupMembership[0], nGlobalAtoms,
868	>	MPI::INT, MPI::SUM);
869		info->setGlobalGroupMembership(tmpGroupMembership);
870		#else
871		info->setGlobalGroupMembership(globalGroupMembership);
872		#endif
873
874		//fill molMembership
875	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
875	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
876	>	info->getNGlobalRigidBodies(), 0);
877
878	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
879	<
878	>	for(mol = info->beginMolecule(mi); mol != NULL;
879	>	mol = info->nextMolecule(mi)) {
880		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
882		}
883	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
884	+	rb = mol->nextRigidBody(ri)) {
885	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
886	+	}
887		}
888
889		#ifdef IS_MPI
890	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
890	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
891	>	info->getNGlobalRigidBodies(), 0);
892	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
893	>	nGlobalAtoms + nGlobalRigidBodies,
894	>	MPI::INT, MPI::SUM);
895
748	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
749	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
750	–
896		info->setGlobalMolMembership(tmpMolMembership);
897		#else
898		info->setGlobalMolMembership(globalMolMembership);
#	Line 757 | Line 902 | namespace oopse {
902		// here the molecules are listed by their global indices.
903
904		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
905	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
905	>	for (mol = info->beginMolecule(mi); mol != NULL;
906	>	mol = info->nextMolecule(mi)) {
907		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
908		}
909
910		#ifdef IS_MPI
911		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
912	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
913	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
912	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
913	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
914		#else
915		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
916		#endif
917
918	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
919	<
920	<	int startingIndex = 0;
921	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
922	<	startingIOIndexForMol[i] = startingIndex;
923	<	startingIndex += numIntegrableObjectsPerMol[i];
924	<	}
925	<
926	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
927	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
918	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
919	>
920	>	int startingIndex = 0;
921	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
922	>	startingIOIndexForMol[i] = startingIndex;
923	>	startingIndex += numIntegrableObjectsPerMol[i];
924	>	}
925	>
926	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
927	>	for (mol = info->beginMolecule(mi); mol != NULL;
928	>	mol = info->nextMolecule(mi)) {
929		int myGlobalIndex = mol->getGlobalIndex();
930		int globalIO = startingIOIndexForMol[myGlobalIndex];
931	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
932	<	integrableObject = mol->nextIntegrableObject(ioi)) {
933	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
934	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
935	<	globalIO++;
931	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
932	>	sd = mol->nextIntegrableObject(ioi)) {
933	>	sd->setGlobalIntegrableObjectIndex(globalIO);
934	>	IOIndexToIntegrableObject[globalIO] = sd;
935	>	globalIO++;
936		}
937		}
938	<
939	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
940	<
938	>
939	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
940	>
941		}
942
943		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
944		Globals* simParams;
945	+
946		simParams = info->getSimParams();
947
800	–
948		DumpReader reader(info, mdFileName);
949		int nframes = reader.getNFrames();
950	<
950	>
951		if (nframes > 0) {
952		reader.readFrame(nframes - 1);
953		} else {
#	Line 811 | Line 958 | int startingIndex = 0;
958		painCave.isFatal = 1;
959		simError();
960		}
814	–
961		//copy the current snapshot to previous snapshot
962		info->getSnapshotManager()->advance();
963		}
964
965	<	} //end namespace oopse
965	>	} //end namespace OpenMD
966
967

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

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