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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
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]  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 oopse {
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 oopse {
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 oopse {
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 214 | Line 227 | namespace oopse {
227		painCave.isFatal = 1;
228		simError();
229		}
230	<	catch (OOPSEException& e) {
230	>	catch (OpenMDException& e) {
231		sprintf(painCave.errMsg,
232		"%s\n",
233		e.getMessage().c_str());
#	Line 229 | Line 242 | namespace oopse {
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 oopse {
256		int metaDataBlockStart = -1;
257		int metaDataBlockEnd = -1;
258		int i;
259	<	int mdOffset;
259	>	streamoff mdOffset;
260	>	int mdFileVersion;
261
262		#ifdef IS_MPI
263		const int masterNode = 0;
#	Line 262 | Line 277 | namespace oopse {
277		mdFile_.getline(buffer, bufferSize);
278		++lineNo;
279		std::string line = trimLeftCopy(buffer);
280	<	i = CaseInsensitiveFind(line, "<OOPSE");
280	>	i = CaseInsensitiveFind(line, "<OpenMD");
281		if (static_cast<size_t>(i) == string::npos) {
282	+	// try the older file strings to see if that works:
283	+	i = CaseInsensitiveFind(line, "<OOPSE");
284	+	}
285	+
286	+	if (static_cast<size_t>(i) == string::npos) {
287	+	// still no luck!
288		sprintf(painCave.errMsg,
289	<	"SimCreator: File: %s is not an OOPSE file!\n",
289	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
290		mdFileName.c_str());
291		painCave.isFatal = 1;
292		simError();
293		}
294	+
295	+	// found the correct opening string, now try to get the file
296	+	// format version number.
297
298	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
299	+	std::string fileType = tokenizer.nextToken();
300	+	toUpper(fileType);
301	+
302	+	mdFileVersion = 0;
303	+
304	+	if (fileType == "OPENMD") {
305	+	while (tokenizer.hasMoreTokens()) {
306	+	std::string token(tokenizer.nextToken());
307	+	toUpper(token);
308	+	if (token == "VERSION") {
309	+	mdFileVersion = tokenizer.nextTokenAsInt();
310	+	break;
311	+	}
312	+	}
313	+	}
314	+
315		//scan through the input stream and find MetaData tag
316		while(mdFile_.getline(buffer, bufferSize)) {
317		++lineNo;
#	Line 326 | Line 367 | namespace oopse {
367		std::stringstream rawMetaDataStream(mdRawData);
368
369		//parse meta-data file
370	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
370	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
371	>	metaDataBlockStart + 1);
372
373		//create the force field
374	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
374	>	ForceField * ff = new ForceField(simParams->getForceField());
375
376		if (ff == NULL) {
377		sprintf(painCave.errMsg,
#	Line 363 | Line 405 | namespace oopse {
405		}
406
407		ff->parse(forcefieldFileName);
366	–	ff->setFortranForceOptions();
408		//create SimInfo
409		SimInfo * info = new SimInfo(ff, simParams);
410
#	Line 381 | Line 422 | namespace oopse {
422		//create the molecules
423		createMolecules(info);
424
425	<
425	>	//find the storage layout
426	>
427	>	int storageLayout = computeStorageLayout(info);
428	>
429		//allocate memory for DataStorage(circular reference, need to
430		//break it)
431	<	info->setSnapshotManager(new SimSnapshotManager(info));
431	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
432
433		//set the global index of atoms, rigidbodies and cutoffgroups
434		//(only need to be set once, the global index will never change
#	Line 407 | Line 451 | namespace oopse {
451
452		if (loadInitCoords)
453		loadCoordinates(info, mdFileName);
410	–
454		return info;
455		}
456
#	Line 471 | Line 514 | namespace oopse {
514		"\tthe number of molecules.  This will not result in a \n"
515		"\tusable division of atoms for force decomposition.\n"
516		"\tEither try a smaller number of processors, or run the\n"
517	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
517	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
518
519		painCave.isFatal = 1;
520		simError();
#	Line 606 | Line 649 | namespace oopse {
649		#endif
650
651		stampId = info->getMoleculeStampId(i);
652	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
653	<	stampId, i, info->getLocalIndexManager());
652	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
653	>	info->getMoleculeStamp(stampId),
654	>	stampId, i,
655	>	info->getLocalIndexManager());
656
657		info->addMolecule(mol);
658
#	Line 619 | Line 664 | namespace oopse {
664
665		} //end for(int i=0)
666		}
667	+
668	+	int SimCreator::computeStorageLayout(SimInfo* info) {
669	+
670	+	Globals* simParams = info->getSimParams();
671	+	int nRigidBodies = info->getNGlobalRigidBodies();
672	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
673	+	set<AtomType*>::iterator i;
674	+	bool hasDirectionalAtoms = false;
675	+	bool hasFixedCharge = false;
676	+	bool hasMultipoles = false;
677	+	bool hasPolarizable = false;
678	+	bool hasFluctuatingCharge = false;
679	+	bool hasMetallic = false;
680	+	int storageLayout = 0;
681	+	storageLayout |= DataStorage::dslPosition;
682	+	storageLayout |= DataStorage::dslVelocity;
683	+	storageLayout |= DataStorage::dslForce;
684	+
685	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
686	+
687	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
688	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
689	+	EAMAdapter ea = EAMAdapter( (*i) );
690	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
691	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
692	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
693	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
694	+
695	+	if (da.isDirectional()){
696	+	hasDirectionalAtoms = true;
697	+	}
698	+	if (ma.isMultipole()){
699	+	hasMultipoles = true;
700	+	}
701	+	if (ea.isEAM() || sca.isSuttonChen()){
702	+	hasMetallic = true;
703	+	}
704	+	if ( fca.isFixedCharge() ){
705	+	hasFixedCharge = true;
706	+	}
707	+	if ( fqa.isFluctuatingCharge() ){
708	+	hasFluctuatingCharge = true;
709	+	}
710	+	if ( pa.isPolarizable() ){
711	+	hasPolarizable = true;
712	+	}
713	+	}
714	+
715	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
716	+	storageLayout |= DataStorage::dslAmat;
717	+	if(storageLayout & DataStorage::dslVelocity) {
718	+	storageLayout |= DataStorage::dslAngularMomentum;
719	+	}
720	+	if (storageLayout & DataStorage::dslForce) {
721	+	storageLayout |= DataStorage::dslTorque;
722	+	}
723	+	}
724	+	if (hasMultipoles) {
725	+	storageLayout |= DataStorage::dslElectroFrame;
726	+	}
727	+	if (hasFixedCharge || hasFluctuatingCharge) {
728	+	storageLayout |= DataStorage::dslSkippedCharge;
729	+	}
730	+	if (hasMetallic) {
731	+	storageLayout |= DataStorage::dslDensity;
732	+	storageLayout |= DataStorage::dslFunctional;
733	+	storageLayout |= DataStorage::dslFunctionalDerivative;
734	+	}
735	+	if (hasPolarizable) {
736	+	storageLayout |= DataStorage::dslElectricField;
737	+	}
738	+	if (hasFluctuatingCharge){
739	+	storageLayout |= DataStorage::dslFlucQPosition;
740	+	if(storageLayout & DataStorage::dslVelocity) {
741	+	storageLayout |= DataStorage::dslFlucQVelocity;
742	+	}
743	+	if (storageLayout & DataStorage::dslForce) {
744	+	storageLayout |= DataStorage::dslFlucQForce;
745	+	}
746	+	}
747
748	+	// if the user has asked for them, make sure we've got the memory for the
749	+	// objects defined.
750	+
751	+	if (simParams->getOutputParticlePotential()) {
752	+	storageLayout |= DataStorage::dslParticlePot;
753	+	}
754	+
755	+	if (simParams->havePrintHeatFlux()) {
756	+	if (simParams->getPrintHeatFlux()) {
757	+	storageLayout |= DataStorage::dslParticlePot;
758	+	}
759	+	}
760	+
761	+	if (simParams->getOutputElectricField()) {
762	+	storageLayout |= DataStorage::dslElectricField;
763	+	}
764	+	if (simParams->getOutputFluctuatingCharges()) {
765	+	storageLayout |= DataStorage::dslFlucQPosition;
766	+	storageLayout |= DataStorage::dslFlucQVelocity;
767	+	storageLayout |= DataStorage::dslFlucQForce;
768	+	}
769	+
770	+	return storageLayout;
771	+	}
772	+
773		void SimCreator::setGlobalIndex(SimInfo *info) {
774		SimInfo::MoleculeIterator mi;
775		Molecule::AtomIterator ai;
#	Line 634 | Line 784 | namespace oopse {
784		int beginRigidBodyIndex;
785		int beginCutoffGroupIndex;
786		int nGlobalAtoms = info->getNGlobalAtoms();
637	–
638	–	/**@todo fixme */
639	–	#ifndef IS_MPI
787
788		beginAtomIndex = 0;
642	–	beginRigidBodyIndex = 0;
643	–	beginCutoffGroupIndex = 0;
644	–
645	–	#else
646	–
647	–	int nproc;
648	–	int myNode;
649	–
650	–	myNode = worldRank;
651	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
652	–
653	–	std::vector < int > tmpAtomsInProc(nproc, 0);
654	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
655	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
656	–	std::vector < int > NumAtomsInProc(nproc, 0);
657	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
658	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
659	–
660	–	tmpAtomsInProc[myNode] = info->getNAtoms();
661	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
662	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
663	–
664	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
665	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
666	–	MPI_SUM, MPI_COMM_WORLD);
667	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
668	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
669	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
670	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
671	–
672	–	beginAtomIndex = 0;
673	–	beginRigidBodyIndex = 0;
674	–	beginCutoffGroupIndex = 0;
675	–
676	–	for(int i = 0; i < myNode; i++) {
677	–	beginAtomIndex += NumAtomsInProc[i];
678	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
679	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
680	–	}
681	–
682	–	#endif
683	–
789		//rigidbody's index begins right after atom's
790	<	beginRigidBodyIndex += info->getNGlobalAtoms();
791	<
792	<	for(mol = info->beginMolecule(mi); mol != NULL;
793	<	mol = info->nextMolecule(mi)) {
790	>	beginRigidBodyIndex = info->getNGlobalAtoms();
791	>	beginCutoffGroupIndex = 0;
792	>
793	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
794
795	<	//local index(index in DataStorge) of atom is important
796	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
797	<	atom->setGlobalIndex(beginAtomIndex++);
795	>	#ifdef IS_MPI
796	>	if (info->getMolToProc(i) == worldRank) {
797	>	#endif
798	>	// stuff to do if I own this molecule
799	>	mol = info->getMoleculeByGlobalIndex(i);
800	>
801	>	//local index(index in DataStorge) of atom is important
802	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
803	>	atom->setGlobalIndex(beginAtomIndex++);
804	>	}
805	>
806	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
807	>	rb = mol->nextRigidBody(ri)) {
808	>	rb->setGlobalIndex(beginRigidBodyIndex++);
809	>	}
810	>
811	>	//local index of cutoff group is trivial, it only depends on
812	>	//the order of travesing
813	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
814	>	cg = mol->nextCutoffGroup(ci)) {
815	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
816	>	}
817	>
818	>	#ifdef IS_MPI
819	>	}  else {
820	>
821	>	// stuff to do if I don't own this molecule
822	>
823	>	int stampId = info->getMoleculeStampId(i);
824	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
825	>
826	>	beginAtomIndex += stamp->getNAtoms();
827	>	beginRigidBodyIndex += stamp->getNRigidBodies();
828	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
829		}
830	<
831	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
832	<	rb = mol->nextRigidBody(ri)) {
833	<	rb->setGlobalIndex(beginRigidBodyIndex++);
698	<	}
699	<
700	<	//local index of cutoff group is trivial, it only depends on the order of travesing
701	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
702	<	cg = mol->nextCutoffGroup(ci)) {
703	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
704	<	}
705	<	}
706	<
830	>	#endif
831	>
832	>	} //end for(int i=0)
833	>
834		//fill globalGroupMembership
835		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
836		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 715 | Line 842 | namespace oopse {
842
843		}
844		}
845	<
845	>
846		#ifdef IS_MPI
847		// Since the globalGroupMembership has been zero filled and we've only
848		// poked values into the atoms we know, we can do an Allreduce
#	Line 778 | Line 905 | namespace oopse {
905		for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
906		int myGlobalIndex = mol->getGlobalIndex();
907		int globalIO = startingIOIndexForMol[myGlobalIndex];
908	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
909	<	integrableObject = mol->nextIntegrableObject(ioi)) {
910	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
911	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
908	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
909	>	sd = mol->nextIntegrableObject(ioi)) {
910	>	sd->setGlobalIntegrableObjectIndex(globalIO);
911	>	IOIndexToIntegrableObject[globalIO] = sd;
912		globalIO++;
913		}
914		}
915	<
915	>
916		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
917
918		}
919
920		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
921		Globals* simParams;
922	+
923		simParams = info->getSimParams();
924
797	–
925		DumpReader reader(info, mdFileName);
926		int nframes = reader.getNFrames();
927	<
927	>
928		if (nframes > 0) {
929		reader.readFrame(nframes - 1);
930		} else {
#	Line 808 | Line 935 | namespace oopse {
935		painCave.isFatal = 1;
936		simError();
937		}
811	–
938		//copy the current snapshot to previous snapshot
939		info->getSnapshotManager()->advance();
940		}
941
942	<	} //end namespace oopse
942	>	} //end namespace OpenMD
943
944

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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+	Added lines
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