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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 1793 by gezelter, Fri Aug 31 21:16:10 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 612 | Line 650 | namespace OpenMD {
650		#endif
651
652		stampId = info->getMoleculeStampId(i);
653	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
654	<	stampId, i, info->getLocalIndexManager());
653	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
654	>	info->getMoleculeStamp(stampId),
655	>	stampId, i,
656	>	info->getLocalIndexManager());
657
658		info->addMolecule(mol);
659
#	Line 625 | Line 665 | namespace OpenMD {
665
666		} //end for(int i=0)
667		}
668	+
669	+	int SimCreator::computeStorageLayout(SimInfo* info) {
670	+
671	+	Globals* simParams = info->getSimParams();
672	+	int nRigidBodies = info->getNGlobalRigidBodies();
673	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
674	+	set<AtomType*>::iterator i;
675	+	bool hasDirectionalAtoms = false;
676	+	bool hasFixedCharge = false;
677	+	bool hasMultipoles = false;
678	+	bool hasPolarizable = false;
679	+	bool hasFluctuatingCharge = false;
680	+	bool hasMetallic = false;
681	+	int storageLayout = 0;
682	+	storageLayout |= DataStorage::dslPosition;
683	+	storageLayout |= DataStorage::dslVelocity;
684	+	storageLayout |= DataStorage::dslForce;
685	+
686	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
687	+
688	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
689	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
690	+	EAMAdapter ea = EAMAdapter( (*i) );
691	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
692	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
693	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
694	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
695	+
696	+	if (da.isDirectional()){
697	+	hasDirectionalAtoms = true;
698	+	}
699	+	if (ma.isMultipole()){
700	+	hasMultipoles = true;
701	+	}
702	+	if (ea.isEAM() || sca.isSuttonChen()){
703	+	hasMetallic = true;
704	+	}
705	+	if ( fca.isFixedCharge() ){
706	+	hasFixedCharge = true;
707	+	}
708	+	if ( fqa.isFluctuatingCharge() ){
709	+	hasFluctuatingCharge = true;
710	+	}
711	+	if ( pa.isPolarizable() ){
712	+	hasPolarizable = true;
713	+	}
714	+	}
715	+
716	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
717	+	storageLayout |= DataStorage::dslAmat;
718	+	if(storageLayout & DataStorage::dslVelocity) {
719	+	storageLayout |= DataStorage::dslAngularMomentum;
720	+	}
721	+	if (storageLayout & DataStorage::dslForce) {
722	+	storageLayout |= DataStorage::dslTorque;
723	+	}
724	+	}
725	+	if (hasMultipoles) {
726	+	storageLayout |= DataStorage::dslElectroFrame;
727	+	}
728	+	if (hasFixedCharge || hasFluctuatingCharge) {
729	+	storageLayout |= DataStorage::dslSkippedCharge;
730	+	}
731	+	if (hasMetallic) {
732	+	storageLayout |= DataStorage::dslDensity;
733	+	storageLayout |= DataStorage::dslFunctional;
734	+	storageLayout |= DataStorage::dslFunctionalDerivative;
735	+	}
736	+	if (hasPolarizable) {
737	+	storageLayout |= DataStorage::dslElectricField;
738	+	}
739	+	if (hasFluctuatingCharge){
740	+	storageLayout |= DataStorage::dslFlucQPosition;
741	+	if(storageLayout & DataStorage::dslVelocity) {
742	+	storageLayout |= DataStorage::dslFlucQVelocity;
743	+	}
744	+	if (storageLayout & DataStorage::dslForce) {
745	+	storageLayout |= DataStorage::dslFlucQForce;
746	+	}
747	+	}
748
749	+	// if the user has asked for them, make sure we've got the memory for the
750	+	// objects defined.
751	+
752	+	if (simParams->getOutputParticlePotential()) {
753	+	storageLayout |= DataStorage::dslParticlePot;
754	+	}
755	+
756	+	if (simParams->havePrintHeatFlux()) {
757	+	if (simParams->getPrintHeatFlux()) {
758	+	storageLayout |= DataStorage::dslParticlePot;
759	+	}
760	+	}
761	+
762	+	if (simParams->getOutputElectricField()) {
763	+	storageLayout |= DataStorage::dslElectricField;
764	+	}
765	+	if (simParams->getOutputFluctuatingCharges()) {
766	+	storageLayout |= DataStorage::dslFlucQPosition;
767	+	storageLayout |= DataStorage::dslFlucQVelocity;
768	+	storageLayout |= DataStorage::dslFlucQForce;
769	+	}
770	+
771	+	return storageLayout;
772	+	}
773	+
774		void SimCreator::setGlobalIndex(SimInfo *info) {
775		SimInfo::MoleculeIterator mi;
776		Molecule::AtomIterator ai;
#	Line 640 | Line 785 | namespace OpenMD {
785		int beginRigidBodyIndex;
786		int beginCutoffGroupIndex;
787		int nGlobalAtoms = info->getNGlobalAtoms();
643	–
644	–	/**@todo fixme */
645	–	#ifndef IS_MPI
788
789		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	–
790		//rigidbody's index begins right after atom's
791	<	beginRigidBodyIndex += info->getNGlobalAtoms();
792	<
793	<	for(mol = info->beginMolecule(mi); mol != NULL;
794	<	mol = info->nextMolecule(mi)) {
791	>	beginRigidBodyIndex = info->getNGlobalAtoms();
792	>	beginCutoffGroupIndex = 0;
793	>
794	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
795
796	<	//local index(index in DataStorge) of atom is important
797	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
798	<	atom->setGlobalIndex(beginAtomIndex++);
796	>	#ifdef IS_MPI
797	>	if (info->getMolToProc(i) == worldRank) {
798	>	#endif
799	>	// stuff to do if I own this molecule
800	>	mol = info->getMoleculeByGlobalIndex(i);
801	>
802	>	//local index(index in DataStorge) of atom is important
803	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
804	>	atom->setGlobalIndex(beginAtomIndex++);
805	>	}
806	>
807	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
808	>	rb = mol->nextRigidBody(ri)) {
809	>	rb->setGlobalIndex(beginRigidBodyIndex++);
810	>	}
811	>
812	>	//local index of cutoff group is trivial, it only depends on
813	>	//the order of travesing
814	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
815	>	cg = mol->nextCutoffGroup(ci)) {
816	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
817	>	}
818	>
819	>	#ifdef IS_MPI
820	>	}  else {
821	>
822	>	// stuff to do if I don't own this molecule
823	>
824	>	int stampId = info->getMoleculeStampId(i);
825	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
826	>
827	>	beginAtomIndex += stamp->getNAtoms();
828	>	beginRigidBodyIndex += stamp->getNRigidBodies();
829	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
830		}
831	<
832	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
833	<	rb = mol->nextRigidBody(ri)) {
834	<	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	<
831	>	#endif
832	>
833	>	} //end for(int i=0)
834	>
835		//fill globalGroupMembership
836		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
837		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 721 | Line 843 | namespace OpenMD {
843
844		}
845		}
846	<
846	>
847		#ifdef IS_MPI
848		// Since the globalGroupMembership has been zero filled and we've only
849		// poked values into the atoms we know, we can do an Allreduce
#	Line 784 | Line 906 | namespace OpenMD {
906		for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
907		int myGlobalIndex = mol->getGlobalIndex();
908		int globalIO = startingIOIndexForMol[myGlobalIndex];
909	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
910	<	integrableObject = mol->nextIntegrableObject(ioi)) {
911	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
912	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
909	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
910	>	sd = mol->nextIntegrableObject(ioi)) {
911	>	sd->setGlobalIntegrableObjectIndex(globalIO);
912	>	IOIndexToIntegrableObject[globalIO] = sd;
913		globalIO++;
914		}
915		}
916	<
916	>
917		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
918
919		}
920
921		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
922	<	Globals* simParams;
801	<	simParams = info->getSimParams();
802	<
803	<
922	>
923		DumpReader reader(info, mdFileName);
924		int nframes = reader.getNFrames();
925	<
925	>
926		if (nframes > 0) {
927		reader.readFrame(nframes - 1);
928		} else {
#	Line 814 | Line 933 | namespace OpenMD {
933		painCave.isFatal = 1;
934		simError();
935		}
817	–
936		//copy the current snapshot to previous snapshot
937		info->getSnapshotManager()->advance();
938		}

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

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

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