ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/development/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.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1600 by gezelter, Wed Aug 3 20:20:37 2011 UTC

#	Line 234 | Line 234 | namespace OpenMD {
234
235		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236		bool loadInitCoords) {
237	<
237	>
238		const int bufferSize = 65535;
239		char buffer[bufferSize];
240		int lineNo = 0;
#	Line 369 | Line 369 | namespace OpenMD {
369		}
370
371		ff->parse(forcefieldFileName);
372	–	ff->setFortranForceOptions();
372		//create SimInfo
373		SimInfo * info = new SimInfo(ff, simParams);
374
#	Line 387 | Line 386 | namespace OpenMD {
386		//create the molecules
387		createMolecules(info);
388
390	–
389		//allocate memory for DataStorage(circular reference, need to
390		//break it)
391		info->setSnapshotManager(new SimSnapshotManager(info));
#	Line 413 | Line 411 | namespace OpenMD {
411
412		if (loadInitCoords)
413		loadCoordinates(info, mdFileName);
416	–
414		return info;
415		}
416
#	Line 592 | Line 589 | namespace OpenMD {
589		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
590		}
591
592	+	cerr << "molToProcMap:\n";
593	+	for (int i = 0; i < molToProcMap.size(); i++) {
594	+	cerr << "m = " << i << " mtpr[m] = " << molToProcMap[i] <<"\n";
595	+	}
596	+
597		info->setMolToProcMap(molToProcMap);
598		sprintf(checkPointMsg,
599		"Successfully divided the molecules among the processors.\n");
#	Line 612 | Line 614 | namespace OpenMD {
614		#endif
615
616		stampId = info->getMoleculeStampId(i);
617	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
618	<	stampId, i, info->getLocalIndexManager());
617	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
618	>	info->getMoleculeStamp(stampId),
619	>	stampId, i,
620	>	info->getLocalIndexManager());
621
622		info->addMolecule(mol);
623
#	Line 640 | Line 644 | namespace OpenMD {
644		int beginRigidBodyIndex;
645		int beginCutoffGroupIndex;
646		int nGlobalAtoms = info->getNGlobalAtoms();
643	–
644	–	/**@todo fixme */
645	–	#ifndef IS_MPI
646	–
647	–	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);
647
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	–
648		beginAtomIndex = 0;
649		beginRigidBodyIndex = 0;
650		beginCutoffGroupIndex = 0;
651	<
652	<	for(int i = 0; i < myNode; i++) {
683	<	beginAtomIndex += NumAtomsInProc[i];
684	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
685	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
686	<	}
687	<
688	<	#endif
689	<
690	<	//rigidbody's index begins right after atom's
691	<	beginRigidBodyIndex += info->getNGlobalAtoms();
692	<
693	<	for(mol = info->beginMolecule(mi); mol != NULL;
694	<	mol = info->nextMolecule(mi)) {
651	>
652	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
653
654	<	//local index(index in DataStorge) of atom is important
655	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
656	<	atom->setGlobalIndex(beginAtomIndex++);
654	>	#ifdef IS_MPI
655	>	if (info->getMolToProc(i) == worldRank) {
656	>	#endif
657	>	// stuff to do if I own this molecule
658	>	mol = info->getMoleculeByGlobalIndex(i);
659	>
660	>	//local index(index in DataStorge) of atom is important
661	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
662	>	atom->setGlobalIndex(beginAtomIndex++);
663	>	}
664	>
665	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
666	>	rb = mol->nextRigidBody(ri)) {
667	>	rb->setGlobalIndex(beginRigidBodyIndex++);
668	>	}
669	>
670	>	//local index of cutoff group is trivial, it only depends on
671	>	//the order of travesing
672	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
673	>	cg = mol->nextCutoffGroup(ci)) {
674	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
675	>	}
676	>
677	>	#ifdef IS_MPI
678	>	}  else {
679	>
680	>	// stuff to do if I don't own this molecule
681	>
682	>	int stampId = info->getMoleculeStampId(i);
683	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
684	>
685	>	beginAtomIndex += stamp->getNAtoms();
686	>	beginRigidBodyIndex += stamp->getNRigidBodies();
687	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
688		}
689	<
690	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
691	<	rb = mol->nextRigidBody(ri)) {
692	<	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	<
689	>	#endif
690	>
691	>	} //end for(int i=0)
692	>
693		//fill globalGroupMembership
694		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
695		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 721 | Line 701 | namespace OpenMD {
701
702		}
703		}
704	<
704	>
705		#ifdef IS_MPI
706		// Since the globalGroupMembership has been zero filled and we've only
707		// poked values into the atoms we know, we can do an Allreduce
#	Line 732 | Line 712 | namespace OpenMD {
712		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
713		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
714		info->setGlobalGroupMembership(tmpGroupMembership);
715	+
716	+	cerr << "ggm:\n";
717	+	for (int i = 0; i < tmpGroupMembership.size(); i++)
718	+	cerr << "i = " << i << "\t ggm(i) = " << tmpGroupMembership[i] << "\n";
719	+
720		#else
721		info->setGlobalGroupMembership(globalGroupMembership);
722		#endif
#	Line 791 | Line 776 | namespace OpenMD {
776		globalIO++;
777		}
778		}
779	<
779	>	cerr << "ioi2io:\n";
780	>	for (int i = 0; i < IOIndexToIntegrableObject.size(); i++) {
781	>	if (IOIndexToIntegrableObject[i] != NULL) {
782	>	cerr << "i = " << i << "globalIOindex = " << IOIndexToIntegrableObject[i]->getGlobalIntegrableObjectIndex() << "\n";
783	>	}
784	>	}
785	>
786		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
787
788		}
789
790		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
791		Globals* simParams;
792	+
793		simParams = info->getSimParams();
794
803	–
795		DumpReader reader(info, mdFileName);
796		int nframes = reader.getNFrames();
797	<
797	>
798		if (nframes > 0) {
799		reader.readFrame(nframes - 1);
800		} else {
#	Line 814 | Line 805 | namespace OpenMD {
805		painCave.isFatal = 1;
806		simError();
807		}
817	–
808		//copy the current snapshot to previous snapshot
809		info->getSnapshotManager()->advance();
810		}

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 1600 by gezelter, Wed Aug 3 20:20:37 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines