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root/OpenMD/trunk/src/brains/SimCreator.cpp

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1051 by gezelter, Mon Sep 25 22:08:33 2006 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
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 90 | Line 100 | namespace oopse {
100		#ifdef IS_MPI
101		int streamSize;
102		const int masterNode = 0;
103	<	int commStatus;
103	>
104		if (worldRank == masterNode) {
105	<	#endif
106	<
105	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
106	>	#endif
107		SimplePreprocessor preprocessor;
108	<	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock,
109	>	ppStream);
110
111		#ifdef IS_MPI
112		//brocasting the stream size
113		streamSize = ppStream.str().size() +1;
114	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
115	<
116	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106	<
114	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
115	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
116	>	streamSize, MPI::CHAR, masterNode);
117
118		} else {
119	+
120	+	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
121	+
122		//get stream size
123	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124	<
123	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
124	>
125		char* buf = new char[streamSize];
126		assert(buf);
127
128		//receive file content
129	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
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(0);
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 342 | Line 384 | namespace oopse {
384		}
385
386		if (simParams->haveForceFieldFileName()) {
345	–	std::cout<< simParams->getForceFieldFileName() << "\n";
387		ff->setForceFieldFileName(simParams->getForceFieldFileName());
388		}
389
#	Line 366 | Line 407 | namespace oopse {
407		}
408
409		ff->parse(forcefieldFileName);
369	–	ff->setFortranForceOptions();
410		//create SimInfo
411		SimInfo * info = new SimInfo(ff, simParams);
412
#	Line 384 | 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 396 | 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);
413	–
456		return info;
457		}
458
#	Line 457 | Line 499 | namespace oopse {
499		int nTarget;
500		int done;
501		int i;
460	–	int j;
502		int loops;
503		int which_proc;
504		int nProcessors;
#	Line 465 | Line 506 | namespace oopse {
506		int nGlobalMols = info->getNGlobalMolecules();
507		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
508
509	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
509	>	nProcessors = MPI::COMM_WORLD.Get_size();
510
511		if (nProcessors > nGlobalMols) {
512		sprintf(painCave.errMsg,
#	Line 474 | Line 515 | namespace oopse {
515		"\tthe number of molecules.  This will not result in a \n"
516		"\tusable division of atoms for force decomposition.\n"
517		"\tEither try a smaller number of processors, or run the\n"
518	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
518	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
519
520		painCave.isFatal = 1;
521		simError();
#	Line 580 | Line 621 | namespace oopse {
621		delete myRandom;
622
623		// Spray out this nonsense to all other processors:
624	<
584	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
624	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
625		} else {
626
627		// Listen to your marching orders from processor 0:
628	<
589	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
628	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
629		}
630
631		info->setMolToProcMap(molToProcMap);
632		sprintf(checkPointMsg,
633		"Successfully divided the molecules among the processors.\n");
634	<	MPIcheckPoint();
634	>	errorCheckPoint();
635		}
636
637		#endif
#	Line 609 | Line 648 | namespace oopse {
648		#endif
649
650		stampId = info->getMoleculeStampId(i);
651	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
652	<	stampId, i, info->getLocalIndexManager());
651	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
652	>	info->getMoleculeStamp(stampId),
653	>	stampId, i,
654	>	info->getLocalIndexManager());
655
656		info->addMolecule(mol);
657
#	Line 623 | Line 664 | namespace oopse {
664		} //end for(int i=0)
665		}
666
667	+	int SimCreator::computeStorageLayout(SimInfo* info) {
668	+
669	+	Globals* simParams = info->getSimParams();
670	+	int nRigidBodies = info->getNGlobalRigidBodies();
671	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
672	+	set<AtomType*>::iterator i;
673	+	bool hasDirectionalAtoms = false;
674	+	bool hasFixedCharge = false;
675	+	bool hasMultipoles = false;
676	+	bool hasPolarizable = false;
677	+	bool hasFluctuatingCharge = false;
678	+	bool hasMetallic = false;
679	+	int storageLayout = 0;
680	+	storageLayout |= DataStorage::dslPosition;
681	+	storageLayout |= DataStorage::dslVelocity;
682	+	storageLayout |= DataStorage::dslForce;
683	+
684	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
685	+
686	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
687	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
688	+	EAMAdapter ea = EAMAdapter( (*i) );
689	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
690	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
691	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
692	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
693	+
694	+	if (da.isDirectional()){
695	+	hasDirectionalAtoms = true;
696	+	}
697	+	if (ma.isMultipole()){
698	+	hasMultipoles = true;
699	+	}
700	+	if (ea.isEAM() || sca.isSuttonChen()){
701	+	hasMetallic = true;
702	+	}
703	+	if ( fca.isFixedCharge() ){
704	+	hasFixedCharge = true;
705	+	}
706	+	if ( fqa.isFluctuatingCharge() ){
707	+	hasFluctuatingCharge = true;
708	+	}
709	+	if ( pa.isPolarizable() ){
710	+	hasPolarizable = true;
711	+	}
712	+	}
713	+
714	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
715	+	storageLayout |= DataStorage::dslAmat;
716	+	if(storageLayout & DataStorage::dslVelocity) {
717	+	storageLayout |= DataStorage::dslAngularMomentum;
718	+	}
719	+	if (storageLayout & DataStorage::dslForce) {
720	+	storageLayout |= DataStorage::dslTorque;
721	+	}
722	+	}
723	+	if (hasMultipoles) {
724	+	storageLayout |= DataStorage::dslElectroFrame;
725	+	}
726	+	if (hasFixedCharge || hasFluctuatingCharge) {
727	+	storageLayout |= DataStorage::dslSkippedCharge;
728	+	}
729	+	if (hasMetallic) {
730	+	storageLayout |= DataStorage::dslDensity;
731	+	storageLayout |= DataStorage::dslFunctional;
732	+	storageLayout |= DataStorage::dslFunctionalDerivative;
733	+	}
734	+	if (hasPolarizable) {
735	+	storageLayout |= DataStorage::dslElectricField;
736	+	}
737	+	if (hasFluctuatingCharge){
738	+	storageLayout |= DataStorage::dslFlucQPosition;
739	+	if(storageLayout & DataStorage::dslVelocity) {
740	+	storageLayout |= DataStorage::dslFlucQVelocity;
741	+	}
742	+	if (storageLayout & DataStorage::dslForce) {
743	+	storageLayout |= DataStorage::dslFlucQForce;
744	+	}
745	+	}
746	+
747	+	// if the user has asked for them, make sure we've got the memory for the
748	+	// objects defined.
749	+
750	+	if (simParams->getOutputParticlePotential()) {
751	+	storageLayout |= DataStorage::dslParticlePot;
752	+	}
753	+
754	+	if (simParams->havePrintHeatFlux()) {
755	+	if (simParams->getPrintHeatFlux()) {
756	+	storageLayout |= DataStorage::dslParticlePot;
757	+	}
758	+	}
759	+
760	+	if (simParams->getOutputElectricField()) {
761	+	storageLayout |= DataStorage::dslElectricField;
762	+	}
763	+	if (simParams->getOutputFluctuatingCharges()) {
764	+	storageLayout |= DataStorage::dslFlucQPosition;
765	+	storageLayout |= DataStorage::dslFlucQVelocity;
766	+	storageLayout |= DataStorage::dslFlucQForce;
767	+	}
768	+
769	+	return storageLayout;
770	+	}
771	+
772		void SimCreator::setGlobalIndex(SimInfo *info) {
773		SimInfo::MoleculeIterator mi;
774		Molecule::AtomIterator ai;
#	Line 637 | Line 783 | namespace oopse {
783		int beginRigidBodyIndex;
784		int beginCutoffGroupIndex;
785		int nGlobalAtoms = info->getNGlobalAtoms();
640	–
641	–	/**@todo fixme */
642	–	#ifndef IS_MPI
786
787		beginAtomIndex = 0;
645	–	beginRigidBodyIndex = 0;
646	–	beginCutoffGroupIndex = 0;
647	–
648	–	#else
649	–
650	–	int nproc;
651	–	int myNode;
652	–
653	–	myNode = worldRank;
654	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
655	–
656	–	std::vector < int > tmpAtomsInProc(nproc, 0);
657	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
658	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
659	–	std::vector < int > NumAtomsInProc(nproc, 0);
660	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
661	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
662	–
663	–	tmpAtomsInProc[myNode] = info->getNAtoms();
664	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
665	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
666	–
667	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
668	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
669	–	MPI_SUM, MPI_COMM_WORLD);
670	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
671	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
672	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
673	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
674	–
675	–	beginAtomIndex = 0;
676	–	beginRigidBodyIndex = 0;
677	–	beginCutoffGroupIndex = 0;
678	–
679	–	for(int i = 0; i < myNode; i++) {
680	–	beginAtomIndex += NumAtomsInProc[i];
681	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
682	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
683	–	}
684	–
685	–	#endif
686	–
788		//rigidbody's index begins right after atom's
789	<	beginRigidBodyIndex += info->getNGlobalAtoms();
790	<
791	<	for(mol = info->beginMolecule(mi); mol != NULL;
792	<	mol = info->nextMolecule(mi)) {
789	>	beginRigidBodyIndex = info->getNGlobalAtoms();
790	>	beginCutoffGroupIndex = 0;
791	>
792	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
793
794	<	//local index(index in DataStorge) of atom is important
795	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
796	<	atom->setGlobalIndex(beginAtomIndex++);
794	>	#ifdef IS_MPI
795	>	if (info->getMolToProc(i) == worldRank) {
796	>	#endif
797	>	// stuff to do if I own this molecule
798	>	mol = info->getMoleculeByGlobalIndex(i);
799	>
800	>	//local index(index in DataStorge) of atom is important
801	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
802	>	atom->setGlobalIndex(beginAtomIndex++);
803	>	}
804	>
805	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
806	>	rb = mol->nextRigidBody(ri)) {
807	>	rb->setGlobalIndex(beginRigidBodyIndex++);
808	>	}
809	>
810	>	//local index of cutoff group is trivial, it only depends on
811	>	//the order of travesing
812	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
813	>	cg = mol->nextCutoffGroup(ci)) {
814	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
815	>	}
816	>
817	>	#ifdef IS_MPI
818	>	}  else {
819	>
820	>	// stuff to do if I don't own this molecule
821	>
822	>	int stampId = info->getMoleculeStampId(i);
823	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
824	>
825	>	beginAtomIndex += stamp->getNAtoms();
826	>	beginRigidBodyIndex += stamp->getNRigidBodies();
827	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
828		}
829	<
830	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
831	<	rb = mol->nextRigidBody(ri)) {
832	<	rb->setGlobalIndex(beginRigidBodyIndex++);
701	<	}
702	<
703	<	//local index of cutoff group is trivial, it only depends on the order of travesing
704	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
705	<	cg = mol->nextCutoffGroup(ci)) {
706	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
707	<	}
708	<	}
709	<
829	>	#endif
830	>
831	>	} //end for(int i=0)
832	>
833		//fill globalGroupMembership
834		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
835		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 718 | Line 841 | namespace oopse {
841
842		}
843		}
844	<
844	>
845		#ifdef IS_MPI
846		// Since the globalGroupMembership has been zero filled and we've only
847		// poked values into the atoms we know, we can do an Allreduce
848		// to get the full globalGroupMembership array (We think).
849		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
850		// docs said we could.
851	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
852	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
853	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
851	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
852	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
853	>	&tmpGroupMembership[0], nGlobalAtoms,
854	>	MPI::INT, MPI::SUM);
855		info->setGlobalGroupMembership(tmpGroupMembership);
856		#else
857		info->setGlobalGroupMembership(globalGroupMembership);
#	Line 737 | Line 861 | namespace oopse {
861		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
862
863		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
740	–
864		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
865		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
866		}
867		}
868
869		#ifdef IS_MPI
870	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
870	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
871	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
872	>	nGlobalAtoms,
873	>	MPI::INT, MPI::SUM);
874
749	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
750	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
751	–
875		info->setGlobalMolMembership(tmpMolMembership);
876		#else
877		info->setGlobalMolMembership(globalMolMembership);
#	Line 764 | Line 887 | namespace oopse {
887
888		#ifdef IS_MPI
889		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
890	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
891	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
890	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
891	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
892		#else
893		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
894		#endif
895
896	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
897	<
898	<	int startingIndex = 0;
899	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
900	<	startingIOIndexForMol[i] = startingIndex;
901	<	startingIndex += numIntegrableObjectsPerMol[i];
902	<	}
903	<
904	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
905	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
896	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
897	>
898	>	int startingIndex = 0;
899	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
900	>	startingIOIndexForMol[i] = startingIndex;
901	>	startingIndex += numIntegrableObjectsPerMol[i];
902	>	}
903	>
904	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
905	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
906		int myGlobalIndex = mol->getGlobalIndex();
907		int globalIO = startingIOIndexForMol[myGlobalIndex];
908	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
909	<	integrableObject = mol->nextIntegrableObject(ioi)) {
910	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
911	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
912	<	globalIO++;
908	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
909	>	sd = mol->nextIntegrableObject(ioi)) {
910	>	sd->setGlobalIntegrableObjectIndex(globalIO);
911	>	IOIndexToIntegrableObject[globalIO] = sd;
912	>	globalIO++;
913		}
914		}
915	<
916	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
917	<
915	>
916	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
917	>
918		}
919
920		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
921	<	Globals* simParams;
799	<	simParams = info->getSimParams();
800	<
801	<
921	>
922		DumpReader reader(info, mdFileName);
923		int nframes = reader.getNFrames();
924	<
924	>
925		if (nframes > 0) {
926		reader.readFrame(nframes - 1);
927		} else {
#	Line 812 | Line 932 | int startingIndex = 0;
932		painCave.isFatal = 1;
933		simError();
934		}
815	–
935		//copy the current snapshot to previous snapshot
936		info->getSnapshotManager()->advance();
937		}
938
939	<	} //end namespace oopse
939	>	} //end namespace OpenMD
940
941

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1051 by gezelter, Mon Sep 25 22:08:33 2006 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

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