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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 1790 by gezelter, Thu Aug 30 17:18:22 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		/**
#	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 92 | Line 102 | namespace OpenMD {
102		const int masterNode = 0;
103		int commStatus;
104		if (worldRank == masterNode) {
105	<	#endif
106	<
105	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
106	>	#endif
107		SimplePreprocessor preprocessor;
108		preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
109
#	Line 106 | Line 116 | namespace OpenMD {
116
117
118		} else {
119	+
120	+	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121	+
122		//get stream size
123		commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124
#	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 612 | Line 651 | namespace OpenMD {
651		#endif
652
653		stampId = info->getMoleculeStampId(i);
654	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
655	<	stampId, i, info->getLocalIndexManager());
654	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
655	>	info->getMoleculeStamp(stampId),
656	>	stampId, i,
657	>	info->getLocalIndexManager());
658
659		info->addMolecule(mol);
660
#	Line 625 | Line 666 | namespace OpenMD {
666
667		} //end for(int i=0)
668		}
669	+
670	+	int SimCreator::computeStorageLayout(SimInfo* info) {
671	+
672	+	Globals* simParams = info->getSimParams();
673	+	int nRigidBodies = info->getNGlobalRigidBodies();
674	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
675	+	set<AtomType*>::iterator i;
676	+	bool hasDirectionalAtoms = false;
677	+	bool hasFixedCharge = false;
678	+	bool hasMultipoles = false;
679	+	bool hasPolarizable = false;
680	+	bool hasFluctuatingCharge = false;
681	+	bool hasMetallic = false;
682	+	int storageLayout = 0;
683	+	storageLayout |= DataStorage::dslPosition;
684	+	storageLayout |= DataStorage::dslVelocity;
685	+	storageLayout |= DataStorage::dslForce;
686	+
687	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
688	+
689	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
690	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
691	+	EAMAdapter ea = EAMAdapter( (*i) );
692	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
693	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
694	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
695	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
696	+
697	+	if (da.isDirectional()){
698	+	hasDirectionalAtoms = true;
699	+	}
700	+	if (ma.isMultipole()){
701	+	hasMultipoles = true;
702	+	}
703	+	if (ea.isEAM() || sca.isSuttonChen()){
704	+	hasMetallic = true;
705	+	}
706	+	if ( fca.isFixedCharge() ){
707	+	hasFixedCharge = true;
708	+	}
709	+	if ( fqa.isFluctuatingCharge() ){
710	+	hasFluctuatingCharge = true;
711	+	}
712	+	if ( pa.isPolarizable() ){
713	+	hasPolarizable = true;
714	+	}
715	+	}
716
717	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
718	+	storageLayout |= DataStorage::dslAmat;
719	+	if(storageLayout & DataStorage::dslVelocity) {
720	+	storageLayout |= DataStorage::dslAngularMomentum;
721	+	}
722	+	if (storageLayout & DataStorage::dslForce) {
723	+	storageLayout |= DataStorage::dslTorque;
724	+	}
725	+	}
726	+	if (hasMultipoles) {
727	+	storageLayout |= DataStorage::dslElectroFrame;
728	+	}
729	+	if (hasFixedCharge || hasFluctuatingCharge) {
730	+	storageLayout |= DataStorage::dslSkippedCharge;
731	+	}
732	+	if (hasMetallic) {
733	+	storageLayout |= DataStorage::dslDensity;
734	+	storageLayout |= DataStorage::dslFunctional;
735	+	storageLayout |= DataStorage::dslFunctionalDerivative;
736	+	}
737	+	if (hasPolarizable) {
738	+	storageLayout |= DataStorage::dslElectricField;
739	+	}
740	+	if (hasFluctuatingCharge){
741	+	storageLayout |= DataStorage::dslFlucQPosition;
742	+	if(storageLayout & DataStorage::dslVelocity) {
743	+	storageLayout |= DataStorage::dslFlucQVelocity;
744	+	}
745	+	if (storageLayout & DataStorage::dslForce) {
746	+	storageLayout |= DataStorage::dslFlucQForce;
747	+	}
748	+	}
749	+
750	+	// if the user has asked for them, make sure we've got the memory for the
751	+	// objects defined.
752	+
753	+	if (simParams->getOutputParticlePotential()) {
754	+	storageLayout |= DataStorage::dslParticlePot;
755	+	}
756	+
757	+	if (simParams->havePrintHeatFlux()) {
758	+	if (simParams->getPrintHeatFlux()) {
759	+	storageLayout |= DataStorage::dslParticlePot;
760	+	}
761	+	}
762	+
763	+	if (simParams->getOutputElectricField()) {
764	+	storageLayout |= DataStorage::dslElectricField;
765	+	}
766	+	if (simParams->getOutputFluctuatingCharges()) {
767	+	storageLayout |= DataStorage::dslFlucQPosition;
768	+	storageLayout |= DataStorage::dslFlucQVelocity;
769	+	storageLayout |= DataStorage::dslFlucQForce;
770	+	}
771	+
772	+	return storageLayout;
773	+	}
774	+
775		void SimCreator::setGlobalIndex(SimInfo *info) {
776		SimInfo::MoleculeIterator mi;
777		Molecule::AtomIterator ai;
#	Line 640 | Line 786 | namespace OpenMD {
786		int beginRigidBodyIndex;
787		int beginCutoffGroupIndex;
788		int nGlobalAtoms = info->getNGlobalAtoms();
643	–
644	–	/**@todo fixme */
645	–	#ifndef IS_MPI
789
790		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	–
791		//rigidbody's index begins right after atom's
792	<	beginRigidBodyIndex += info->getNGlobalAtoms();
793	<
794	<	for(mol = info->beginMolecule(mi); mol != NULL;
795	<	mol = info->nextMolecule(mi)) {
792	>	beginRigidBodyIndex = info->getNGlobalAtoms();
793	>	beginCutoffGroupIndex = 0;
794	>
795	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
796
797	<	//local index(index in DataStorge) of atom is important
798	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
799	<	atom->setGlobalIndex(beginAtomIndex++);
797	>	#ifdef IS_MPI
798	>	if (info->getMolToProc(i) == worldRank) {
799	>	#endif
800	>	// stuff to do if I own this molecule
801	>	mol = info->getMoleculeByGlobalIndex(i);
802	>
803	>	//local index(index in DataStorge) of atom is important
804	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
805	>	atom->setGlobalIndex(beginAtomIndex++);
806	>	}
807	>
808	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
809	>	rb = mol->nextRigidBody(ri)) {
810	>	rb->setGlobalIndex(beginRigidBodyIndex++);
811	>	}
812	>
813	>	//local index of cutoff group is trivial, it only depends on
814	>	//the order of travesing
815	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
816	>	cg = mol->nextCutoffGroup(ci)) {
817	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
818	>	}
819	>
820	>	#ifdef IS_MPI
821	>	}  else {
822	>
823	>	// stuff to do if I don't own this molecule
824	>
825	>	int stampId = info->getMoleculeStampId(i);
826	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
827	>
828	>	beginAtomIndex += stamp->getNAtoms();
829	>	beginRigidBodyIndex += stamp->getNRigidBodies();
830	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
831		}
832	<
833	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
834	<	rb = mol->nextRigidBody(ri)) {
835	<	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	<
832	>	#endif
833	>
834	>	} //end for(int i=0)
835	>
836		//fill globalGroupMembership
837		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
838		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 721 | Line 844 | namespace OpenMD {
844
845		}
846		}
847	<
847	>
848		#ifdef IS_MPI
849		// Since the globalGroupMembership has been zero filled and we've only
850		// poked values into the atoms we know, we can do an Allreduce
#	Line 784 | Line 907 | namespace OpenMD {
907		for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
908		int myGlobalIndex = mol->getGlobalIndex();
909		int globalIO = startingIOIndexForMol[myGlobalIndex];
910	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
911	<	integrableObject = mol->nextIntegrableObject(ioi)) {
912	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
913	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
910	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
911	>	sd = mol->nextIntegrableObject(ioi)) {
912	>	sd->setGlobalIntegrableObjectIndex(globalIO);
913	>	IOIndexToIntegrableObject[globalIO] = sd;
914		globalIO++;
915		}
916		}
917	<
917	>
918		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
919
920		}
921
922		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
923		Globals* simParams;
924	+
925		simParams = info->getSimParams();
926
803	–
927		DumpReader reader(info, mdFileName);
928		int nframes = reader.getNFrames();
929	<
929	>
930		if (nframes > 0) {
931		reader.readFrame(nframes - 1);
932		} else {
#	Line 814 | Line 937 | namespace OpenMD {
937		painCave.isFatal = 1;
938		simError();
939		}
817	–
940		//copy the current snapshot to previous snapshot
941		info->getSnapshotManager()->advance();
942		}

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

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

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