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trunk/src/brains/SimCreator.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	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		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49		#include <exception>
#	Line 55 | Line 55
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
58	<	#include "UseTheForce/ForceFieldFactory.hpp"
58	>	#include "brains/ForceField.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 75
75		#include "antlr/NoViableAltForCharException.hpp"
76		#include "antlr/NoViableAltException.hpp"
77
78	+	#include "types/DirectionalAdapter.hpp"
79	+	#include "types/MultipoleAdapter.hpp"
80	+	#include "types/EAMAdapter.hpp"
81	+	#include "types/SuttonChenAdapter.hpp"
82	+	#include "types/PolarizableAdapter.hpp"
83	+	#include "types/FixedChargeAdapter.hpp"
84	+	#include "types/FluctuatingChargeAdapter.hpp"
85	+
86		#ifdef IS_MPI
87	+	#include "mpi.h"
88		#include "math/ParallelRandNumGen.hpp"
89		#endif
90
91		namespace OpenMD {
92
93	<	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
93	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
94		Globals* simParams = NULL;
95		try {
96
#	Line 92 | Line 101 | namespace OpenMD {
101		const int masterNode = 0;
102		int commStatus;
103		if (worldRank == masterNode) {
104	<	#endif
105	<
104	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
105	>	#endif
106		SimplePreprocessor preprocessor;
107		preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108
#	Line 106 | Line 115 | namespace OpenMD {
115
116
117		} else {
118	+
119	+	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
120	+
121		//get stream size
122		commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
123
#	Line 229 | Line 241 | namespace OpenMD {
241		simError();
242		}
243
244	+	simParams->setMDfileVersion(mdFileVersion);
245		return simParams;
246		}
247
248		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
249		bool loadInitCoords) {
250	<
250	>
251		const int bufferSize = 65535;
252		char buffer[bufferSize];
253		int lineNo = 0;
#	Line 242 | Line 255 | namespace OpenMD {
255		int metaDataBlockStart = -1;
256		int metaDataBlockEnd = -1;
257		int i;
258	<	int mdOffset;
258	>	streamoff mdOffset;
259	>	int mdFileVersion;
260
261	+
262		#ifdef IS_MPI
263		const int masterNode = 0;
264		if (worldRank == masterNode) {
265		#endif
266
267	<	std::ifstream mdFile_(mdFileName.c_str());
267	>	std::ifstream mdFile_;
268	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
269
270		if (mdFile_.fail()) {
271		sprintf(painCave.errMsg,
#	Line 276 | Line 292 | namespace OpenMD {
292		painCave.isFatal = 1;
293		simError();
294		}
295	+
296	+	// found the correct opening string, now try to get the file
297	+	// format version number.
298
299	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
300	+	std::string fileType = tokenizer.nextToken();
301	+	toUpper(fileType);
302	+
303	+	mdFileVersion = 0;
304	+
305	+	if (fileType == "OPENMD") {
306	+	while (tokenizer.hasMoreTokens()) {
307	+	std::string token(tokenizer.nextToken());
308	+	toUpper(token);
309	+	if (token == "VERSION") {
310	+	mdFileVersion = tokenizer.nextTokenAsInt();
311	+	break;
312	+	}
313	+	}
314	+	}
315	+
316		//scan through the input stream and find MetaData tag
317		while(mdFile_.getline(buffer, bufferSize)) {
318		++lineNo;
#	Line 332 | Line 368 | namespace OpenMD {
368		std::stringstream rawMetaDataStream(mdRawData);
369
370		//parse meta-data file
371	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
371	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
372	>	metaDataBlockStart + 1);
373
374		//create the force field
375	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
375	>	ForceField * ff = new ForceField(simParams->getForceField());
376
377		if (ff == NULL) {
378		sprintf(painCave.errMsg,
#	Line 369 | Line 406 | namespace OpenMD {
406		}
407
408		ff->parse(forcefieldFileName);
372	–	ff->setFortranForceOptions();
409		//create SimInfo
410		SimInfo * info = new SimInfo(ff, simParams);
411
#	Line 387 | Line 423 | namespace OpenMD {
423		//create the molecules
424		createMolecules(info);
425
426	<
426	>	//find the storage layout
427	>
428	>	int storageLayout = computeStorageLayout(info);
429	>
430		//allocate memory for DataStorage(circular reference, need to
431		//break it)
432	<	info->setSnapshotManager(new SimSnapshotManager(info));
432	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
433
434		//set the global index of atoms, rigidbodies and cutoffgroups
435		//(only need to be set once, the global index will never change
#	Line 413 | Line 452 | namespace OpenMD {
452
453		if (loadInitCoords)
454		loadCoordinates(info, mdFileName);
416	–
455		return info;
456		}
457
#	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 hasDipoles = false;
680	+	bool hasQuadrupoles = false;
681	+	bool hasPolarizable = false;
682	+	bool hasFluctuatingCharge = false;
683	+	bool hasMetallic = false;
684	+	int storageLayout = 0;
685	+	storageLayout |= DataStorage::dslPosition;
686	+	storageLayout |= DataStorage::dslVelocity;
687	+	storageLayout |= DataStorage::dslForce;
688	+
689	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
690	+
691	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
692	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
693	+	EAMAdapter ea = EAMAdapter( (*i) );
694	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
695	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
696	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
697	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
698	+
699	+	if (da.isDirectional()){
700	+	hasDirectionalAtoms = true;
701	+	}
702	+	if (ma.isDipole()){
703	+	hasDipoles = true;
704	+	}
705	+	if (ma.isQuadrupole()){
706	+	hasQuadrupoles = true;
707	+	}
708	+	if (ea.isEAM() || sca.isSuttonChen()){
709	+	hasMetallic = true;
710	+	}
711	+	if ( fca.isFixedCharge() ){
712	+	hasFixedCharge = true;
713	+	}
714	+	if ( fqa.isFluctuatingCharge() ){
715	+	hasFluctuatingCharge = true;
716	+	}
717	+	if ( pa.isPolarizable() ){
718	+	hasPolarizable = true;
719	+	}
720	+	}
721	+
722	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
723	+	storageLayout |= DataStorage::dslAmat;
724	+	if(storageLayout & DataStorage::dslVelocity) {
725	+	storageLayout |= DataStorage::dslAngularMomentum;
726	+	}
727	+	if (storageLayout & DataStorage::dslForce) {
728	+	storageLayout |= DataStorage::dslTorque;
729	+	}
730	+	}
731	+	if (hasDipoles) {
732	+	storageLayout |= DataStorage::dslDipole;
733	+	}
734	+	if (hasQuadrupoles) {
735	+	storageLayout |= DataStorage::dslQuadrupole;
736	+	}
737	+	if (hasFixedCharge || hasFluctuatingCharge) {
738	+	storageLayout |= DataStorage::dslSkippedCharge;
739	+	}
740	+	if (hasMetallic) {
741	+	storageLayout |= DataStorage::dslDensity;
742	+	storageLayout |= DataStorage::dslFunctional;
743	+	storageLayout |= DataStorage::dslFunctionalDerivative;
744	+	}
745	+	if (hasPolarizable) {
746	+	storageLayout |= DataStorage::dslElectricField;
747	+	}
748	+	if (hasFluctuatingCharge){
749	+	storageLayout |= DataStorage::dslFlucQPosition;
750	+	if(storageLayout & DataStorage::dslVelocity) {
751	+	storageLayout |= DataStorage::dslFlucQVelocity;
752	+	}
753	+	if (storageLayout & DataStorage::dslForce) {
754	+	storageLayout |= DataStorage::dslFlucQForce;
755	+	}
756	+	}
757	+
758	+	// if the user has asked for them, make sure we've got the memory for the
759	+	// objects defined.
760	+
761	+	if (simParams->getOutputParticlePotential()) {
762	+	storageLayout |= DataStorage::dslParticlePot;
763	+	}
764	+
765	+	if (simParams->havePrintHeatFlux()) {
766	+	if (simParams->getPrintHeatFlux()) {
767	+	storageLayout |= DataStorage::dslParticlePot;
768	+	}
769	+	}
770	+
771	+	if (simParams->getOutputElectricField()) {
772	+	storageLayout |= DataStorage::dslElectricField;
773	+	}
774	+
775	+	if (simParams->getOutputFluctuatingCharges()) {
776	+	storageLayout |= DataStorage::dslFlucQPosition;
777	+	storageLayout |= DataStorage::dslFlucQVelocity;
778	+	storageLayout |= DataStorage::dslFlucQForce;
779	+	}
780	+
781	+	return storageLayout;
782	+	}
783	+
784		void SimCreator::setGlobalIndex(SimInfo *info) {
785		SimInfo::MoleculeIterator mi;
786		Molecule::AtomIterator ai;
#	Line 640 | Line 795 | namespace OpenMD {
795		int beginRigidBodyIndex;
796		int beginCutoffGroupIndex;
797		int nGlobalAtoms = info->getNGlobalAtoms();
798	<
644	<	/**@todo fixme */
645	<	#ifndef IS_MPI
798	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
799
800		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	–
801		//rigidbody's index begins right after atom's
802	<	beginRigidBodyIndex += info->getNGlobalAtoms();
803	<
804	<	for(mol = info->beginMolecule(mi); mol != NULL;
805	<	mol = info->nextMolecule(mi)) {
802	>	beginRigidBodyIndex = info->getNGlobalAtoms();
803	>	beginCutoffGroupIndex = 0;
804	>
805	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
806
807	<	//local index(index in DataStorge) of atom is important
808	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
809	<	atom->setGlobalIndex(beginAtomIndex++);
807	>	#ifdef IS_MPI
808	>	if (info->getMolToProc(i) == worldRank) {
809	>	#endif
810	>	// stuff to do if I own this molecule
811	>	mol = info->getMoleculeByGlobalIndex(i);
812	>
813	>	//local index(index in DataStorge) of atom is important
814	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
815	>	atom->setGlobalIndex(beginAtomIndex++);
816	>	}
817	>
818	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
819	>	rb = mol->nextRigidBody(ri)) {
820	>	rb->setGlobalIndex(beginRigidBodyIndex++);
821	>	}
822	>
823	>	//local index of cutoff group is trivial, it only depends on
824	>	//the order of travesing
825	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
826	>	cg = mol->nextCutoffGroup(ci)) {
827	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
828	>	}
829	>
830	>	#ifdef IS_MPI
831	>	}  else {
832	>
833	>	// stuff to do if I don't own this molecule
834	>
835	>	int stampId = info->getMoleculeStampId(i);
836	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
837	>
838	>	beginAtomIndex += stamp->getNAtoms();
839	>	beginRigidBodyIndex += stamp->getNRigidBodies();
840	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
841		}
842	<
843	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
844	<	rb = mol->nextRigidBody(ri)) {
845	<	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	<
842	>	#endif
843	>
844	>	} //end for(int i=0)
845	>
846		//fill globalGroupMembership
847		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
848		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 721 | Line 854 | namespace OpenMD {
854
855		}
856		}
857	<
857	>
858		#ifdef IS_MPI
859		// Since the globalGroupMembership has been zero filled and we've only
860		// poked values into the atoms we know, we can do an Allreduce
#	Line 729 | Line 862 | namespace OpenMD {
862		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
863		// docs said we could.
864		std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
865	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
866	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
865	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
866	>	&tmpGroupMembership[0], nGlobalAtoms,
867	>	MPI::INT, MPI::SUM);
868		info->setGlobalGroupMembership(tmpGroupMembership);
869		#else
870		info->setGlobalGroupMembership(globalGroupMembership);
871		#endif
872
873		//fill molMembership
874	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
874	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
875	>	info->getNGlobalRigidBodies(), 0);
876
877	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
877	>	for(mol = info->beginMolecule(mi); mol != NULL;
878	>	mol = info->nextMolecule(mi)) {
879		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
880		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
881		}
882	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
883	+	rb = mol->nextRigidBody(ri)) {
884	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
885	+	}
886		}
887
888		#ifdef IS_MPI
889	<	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
889	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
890	>	info->getNGlobalRigidBodies(), 0);
891	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
892	>	nGlobalAtoms + nGlobalRigidBodies,
893	>	MPI::INT, MPI::SUM);
894
751	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
752	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
753	–
895		info->setGlobalMolMembership(tmpMolMembership);
896		#else
897		info->setGlobalMolMembership(globalMolMembership);
#	Line 760 | Line 901 | namespace OpenMD {
901		// here the molecules are listed by their global indices.
902
903		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
904	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
904	>	for (mol = info->beginMolecule(mi); mol != NULL;
905	>	mol = info->nextMolecule(mi)) {
906		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
907		}
908
909		#ifdef IS_MPI
910		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
911	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
912	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
911	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
912	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
913		#else
914		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
915		#endif
#	Line 781 | Line 923 | namespace OpenMD {
923		}
924
925		std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
926	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
926	>	for (mol = info->beginMolecule(mi); mol != NULL;
927	>	mol = info->nextMolecule(mi)) {
928		int myGlobalIndex = mol->getGlobalIndex();
929		int globalIO = startingIOIndexForMol[myGlobalIndex];
930	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
931	<	integrableObject = mol->nextIntegrableObject(ioi)) {
932	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
933	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
930	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
931	>	sd = mol->nextIntegrableObject(ioi)) {
932	>	sd->setGlobalIntegrableObjectIndex(globalIO);
933	>	IOIndexToIntegrableObject[globalIO] = sd;
934		globalIO++;
935		}
936		}
937	<
937	>
938		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
939
940		}
941
942		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
943		Globals* simParams;
944	+
945		simParams = info->getSimParams();
946
803	–
947		DumpReader reader(info, mdFileName);
948		int nframes = reader.getNFrames();
949	<
949	>
950		if (nframes > 0) {
951		reader.readFrame(nframes - 1);
952		} else {
#	Line 814 | Line 957 | namespace OpenMD {
957		painCave.isFatal = 1;
958		simError();
959		}
817	–
960		//copy the current snapshot to previous snapshot
961		info->getSnapshotManager()->advance();
962		}

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	Line 0 | Line 1
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