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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 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
#	Line 36 | Line 36
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).
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 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 OpenMD {
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);
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;
#	Line 229 | Line 242 | namespace OpenMD {
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 242 | Line 256 | namespace OpenMD {
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 276 | Line 293 | namespace OpenMD {
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 332 | Line 369 | namespace OpenMD {
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()->createForceField(simParams->getForceField());
376	>	ForceField * ff = new ForceField(simParams->getForceField());
377
378		if (ff == NULL) {
379		sprintf(painCave.errMsg,
#	Line 369 | Line 407 | namespace OpenMD {
407		}
408
409		ff->parse(forcefieldFileName);
372	–	ff->setFortranForceOptions();
410		//create SimInfo
411		SimInfo * info = new SimInfo(ff, simParams);
412
#	Line 387 | Line 424 | namespace OpenMD {
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 413 | Line 453 | namespace OpenMD {
453
454		if (loadInitCoords)
455		loadCoordinates(info, mdFileName);
416	–
456		return info;
457		}
458
#	Line 460 | Line 499 | namespace OpenMD {
499		int nTarget;
500		int done;
501		int i;
463	–	int j;
502		int loops;
503		int which_proc;
504		int nProcessors;
#	Line 468 | Line 506 | namespace OpenMD {
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 506 | Line 544 | namespace OpenMD {
544		nTarget = (int)(precast + 0.5);
545
546		for(i = 0; i < nGlobalMols; i++) {
547	+
548		done = 0;
549		loops = 0;
550
#	Line 530 | Line 569 | namespace OpenMD {
569		// and be done with it.
570
571		if (loops > 100) {
572	+
573		sprintf(painCave.errMsg,
574	<	"I've tried 100 times to assign molecule %d to a "
575	<	" processor, but can't find a good spot.\n"
576	<	"I'm assigning it at random to processor %d.\n",
574	>	"There have been 100 attempts to assign molecule %d to an\n"
575	>	"\tunderworked processor, but there's no good place to\n"
576	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
577		i, which_proc);
578	<
578	>
579		painCave.isFatal = 0;
580	+	painCave.severity = OPENMD_INFO;
581		simError();
582
583		molToProcMap[i] = which_proc;
#	Line 581 | Line 622 | namespace OpenMD {
622		}
623
624		delete myRandom;
625	<
625	>
626		// Spray out this nonsense to all other processors:
627	<
587	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
627	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
628		} else {
629
630		// Listen to your marching orders from processor 0:
631	<
632	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
631	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
632	>
633		}
634
635		info->setMolToProcMap(molToProcMap);
#	Line 612 | Line 652 | namespace OpenMD {
652		#endif
653
654		stampId = info->getMoleculeStampId(i);
655	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
656	<	stampId, i, info->getLocalIndexManager());
655	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
656	>	info->getMoleculeStamp(stampId),
657	>	stampId, i,
658	>	info->getLocalIndexManager());
659
660		info->addMolecule(mol);
661
#	Line 626 | Line 668 | namespace OpenMD {
668		} //end for(int i=0)
669		}
670
671	+	int SimCreator::computeStorageLayout(SimInfo* info) {
672	+
673	+	Globals* simParams = info->getSimParams();
674	+	int nRigidBodies = info->getNGlobalRigidBodies();
675	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
676	+	set<AtomType*>::iterator i;
677	+	bool hasDirectionalAtoms = false;
678	+	bool hasFixedCharge = false;
679	+	bool hasMultipoles = false;
680	+	bool hasPolarizable = false;
681	+	bool hasFluctuatingCharge = false;
682	+	bool hasMetallic = false;
683	+	int storageLayout = 0;
684	+	storageLayout |= DataStorage::dslPosition;
685	+	storageLayout |= DataStorage::dslVelocity;
686	+	storageLayout |= DataStorage::dslForce;
687	+
688	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
689	+
690	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
691	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
692	+	EAMAdapter ea = EAMAdapter( (*i) );
693	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
694	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
695	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
696	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
697	+
698	+	if (da.isDirectional()){
699	+	hasDirectionalAtoms = true;
700	+	}
701	+	if (ma.isMultipole()){
702	+	hasMultipoles = true;
703	+	}
704	+	if (ea.isEAM() || sca.isSuttonChen()){
705	+	hasMetallic = true;
706	+	}
707	+	if ( fca.isFixedCharge() ){
708	+	hasFixedCharge = true;
709	+	}
710	+	if ( fqa.isFluctuatingCharge() ){
711	+	hasFluctuatingCharge = true;
712	+	}
713	+	if ( pa.isPolarizable() ){
714	+	hasPolarizable = true;
715	+	}
716	+	}
717	+
718	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
719	+	storageLayout |= DataStorage::dslAmat;
720	+	if(storageLayout & DataStorage::dslVelocity) {
721	+	storageLayout |= DataStorage::dslAngularMomentum;
722	+	}
723	+	if (storageLayout & DataStorage::dslForce) {
724	+	storageLayout |= DataStorage::dslTorque;
725	+	}
726	+	}
727	+	if (hasMultipoles) {
728	+	storageLayout |= DataStorage::dslElectroFrame;
729	+	}
730	+	if (hasFixedCharge || hasFluctuatingCharge) {
731	+	storageLayout |= DataStorage::dslSkippedCharge;
732	+	}
733	+	if (hasMetallic) {
734	+	storageLayout |= DataStorage::dslDensity;
735	+	storageLayout |= DataStorage::dslFunctional;
736	+	storageLayout |= DataStorage::dslFunctionalDerivative;
737	+	}
738	+	if (hasPolarizable) {
739	+	storageLayout |= DataStorage::dslElectricField;
740	+	}
741	+	if (hasFluctuatingCharge){
742	+	storageLayout |= DataStorage::dslFlucQPosition;
743	+	if(storageLayout & DataStorage::dslVelocity) {
744	+	storageLayout |= DataStorage::dslFlucQVelocity;
745	+	}
746	+	if (storageLayout & DataStorage::dslForce) {
747	+	storageLayout |= DataStorage::dslFlucQForce;
748	+	}
749	+	}
750	+
751	+	// if the user has asked for them, make sure we've got the memory for the
752	+	// objects defined.
753	+
754	+	if (simParams->getOutputParticlePotential()) {
755	+	storageLayout |= DataStorage::dslParticlePot;
756	+	}
757	+
758	+	if (simParams->havePrintHeatFlux()) {
759	+	if (simParams->getPrintHeatFlux()) {
760	+	storageLayout |= DataStorage::dslParticlePot;
761	+	}
762	+	}
763	+
764	+	if (simParams->getOutputElectricField()) {
765	+	storageLayout |= DataStorage::dslElectricField;
766	+	}
767	+	if (simParams->getOutputFluctuatingCharges()) {
768	+	storageLayout |= DataStorage::dslFlucQPosition;
769	+	storageLayout |= DataStorage::dslFlucQVelocity;
770	+	storageLayout |= DataStorage::dslFlucQForce;
771	+	}
772	+
773	+	return storageLayout;
774	+	}
775	+
776		void SimCreator::setGlobalIndex(SimInfo *info) {
777		SimInfo::MoleculeIterator mi;
778		Molecule::AtomIterator ai;
#	Line 640 | Line 787 | namespace OpenMD {
787		int beginRigidBodyIndex;
788		int beginCutoffGroupIndex;
789		int nGlobalAtoms = info->getNGlobalAtoms();
643	–
644	–	/**@todo fixme */
645	–	#ifndef IS_MPI
790
791		beginAtomIndex = 0;
648	–	beginRigidBodyIndex = 0;
649	–	beginCutoffGroupIndex = 0;
650	–
651	–	#else
652	–
653	–	int nproc;
654	–	int myNode;
655	–
656	–	myNode = worldRank;
657	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
658	–
659	–	std::vector < int > tmpAtomsInProc(nproc, 0);
660	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
661	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
662	–	std::vector < int > NumAtomsInProc(nproc, 0);
663	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
664	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
665	–
666	–	tmpAtomsInProc[myNode] = info->getNAtoms();
667	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
668	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
669	–
670	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
671	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
672	–	MPI_SUM, MPI_COMM_WORLD);
673	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
674	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
675	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
676	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
677	–
678	–	beginAtomIndex = 0;
679	–	beginRigidBodyIndex = 0;
680	–	beginCutoffGroupIndex = 0;
681	–
682	–	for(int i = 0; i < myNode; i++) {
683	–	beginAtomIndex += NumAtomsInProc[i];
684	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
685	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
686	–	}
687	–
688	–	#endif
689	–
792		//rigidbody's index begins right after atom's
793	<	beginRigidBodyIndex += info->getNGlobalAtoms();
794	<
795	<	for(mol = info->beginMolecule(mi); mol != NULL;
796	<	mol = info->nextMolecule(mi)) {
793	>	beginRigidBodyIndex = info->getNGlobalAtoms();
794	>	beginCutoffGroupIndex = 0;
795	>
796	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
797
798	<	//local index(index in DataStorge) of atom is important
799	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
800	<	atom->setGlobalIndex(beginAtomIndex++);
798	>	#ifdef IS_MPI
799	>	if (info->getMolToProc(i) == worldRank) {
800	>	#endif
801	>	// stuff to do if I own this molecule
802	>	mol = info->getMoleculeByGlobalIndex(i);
803	>
804	>	//local index(index in DataStorge) of atom is important
805	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
806	>	atom->setGlobalIndex(beginAtomIndex++);
807	>	}
808	>
809	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
810	>	rb = mol->nextRigidBody(ri)) {
811	>	rb->setGlobalIndex(beginRigidBodyIndex++);
812	>	}
813	>
814	>	//local index of cutoff group is trivial, it only depends on
815	>	//the order of travesing
816	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
817	>	cg = mol->nextCutoffGroup(ci)) {
818	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
819	>	}
820	>
821	>	#ifdef IS_MPI
822	>	}  else {
823	>
824	>	// stuff to do if I don't own this molecule
825	>
826	>	int stampId = info->getMoleculeStampId(i);
827	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
828	>
829	>	beginAtomIndex += stamp->getNAtoms();
830	>	beginRigidBodyIndex += stamp->getNRigidBodies();
831	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
832		}
833	<
834	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
835	<	rb = mol->nextRigidBody(ri)) {
836	<	rb->setGlobalIndex(beginRigidBodyIndex++);
704	<	}
705	<
706	<	//local index of cutoff group is trivial, it only depends on the order of travesing
707	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
708	<	cg = mol->nextCutoffGroup(ci)) {
709	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
710	<	}
711	<	}
712	<
833	>	#endif
834	>
835	>	} //end for(int i=0)
836	>
837		//fill globalGroupMembership
838		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
839		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 721 | Line 845 | namespace OpenMD {
845
846		}
847		}
848	<
848	>
849		#ifdef IS_MPI
850		// Since the globalGroupMembership has been zero filled and we've only
851		// poked values into the atoms we know, we can do an Allreduce
#	Line 729 | Line 853 | namespace OpenMD {
853		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
854		// docs said we could.
855		std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
856	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
857	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
856	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
857	>	&tmpGroupMembership[0], nGlobalAtoms,
858	>	MPI::INT, MPI::SUM);
859		info->setGlobalGroupMembership(tmpGroupMembership);
860		#else
861		info->setGlobalGroupMembership(globalGroupMembership);
#	Line 747 | Line 872 | namespace OpenMD {
872
873		#ifdef IS_MPI
874		std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
875	+	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
876	+	nGlobalAtoms,
877	+	MPI::INT, MPI::SUM);
878
751	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
752	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
753	–
879		info->setGlobalMolMembership(tmpMolMembership);
880		#else
881		info->setGlobalMolMembership(globalMolMembership);
#	Line 766 | Line 891 | namespace OpenMD {
891
892		#ifdef IS_MPI
893		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
894	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
895	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
894	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
895	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
896		#else
897		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
898		#endif
#	Line 784 | Line 909 | namespace OpenMD {
909		for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
910		int myGlobalIndex = mol->getGlobalIndex();
911		int globalIO = startingIOIndexForMol[myGlobalIndex];
912	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
913	<	integrableObject = mol->nextIntegrableObject(ioi)) {
914	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
915	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
912	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
913	>	sd = mol->nextIntegrableObject(ioi)) {
914	>	sd->setGlobalIntegrableObjectIndex(globalIO);
915	>	IOIndexToIntegrableObject[globalIO] = sd;
916		globalIO++;
917		}
918		}
919	<
919	>
920		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
921
922		}
923
924		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
925	<	Globals* simParams;
801	<	simParams = info->getSimParams();
802	<
803	<
925	>
926		DumpReader reader(info, mdFileName);
927		int nframes = reader.getNFrames();
928	<
928	>
929		if (nframes > 0) {
930		reader.readFrame(nframes - 1);
931		} else {
#	Line 814 | Line 936 | namespace OpenMD {
936		painCave.isFatal = 1;
937		simError();
938		}
817	–
939		//copy the current snapshot to previous snapshot
940		info->getSnapshotManager()->advance();
941		}

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC

#	Line 0 | Line 1
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