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trunk/src/brains/SimCreator.cpp (file contents), Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1826 by gezelter, Wed Jan 9 19:41:48 2013 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		/**
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 oopse {
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 oopse {
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 oopse {
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 214 | Line 226 | namespace oopse {
226		painCave.isFatal = 1;
227		simError();
228		}
229	<	catch (OOPSEException& e) {
229	>	catch (OpenMDException& e) {
230		sprintf(painCave.errMsg,
231		"%s\n",
232		e.getMessage().c_str());
#	Line 229 | Line 241 | namespace oopse {
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;
254		std::string mdRawData;
255		int metaDataBlockStart = -1;
256		int metaDataBlockEnd = -1;
257	<	int i;
258	<	int mdOffset;
257	>	int i, j;
258	>	streamoff mdOffset;
259	>	int mdFileVersion;
260
261	+	// Create a string for embedding the version information in the MetaData
262	+	std::string version;
263	+	version.assign("## Last run using OpenMD Version: ");
264	+	version.append(OPENMD_VERSION_MAJOR);
265	+	version.append(".");
266	+	version.append(OPENMD_VERSION_MINOR);
267	+
268	+	std::string svnrev;
269	+	//convert a macro from compiler to a string in c++
270	+	STR_DEFINE(svnrev, SVN_REV );
271	+	version.append(" Revision: ");
272	+	// If there's no SVN revision, just call this the RELEASE revision.
273	+	if (!svnrev.empty()) {
274	+	version.append(svnrev);
275	+	} else {
276	+	version.append("RELEASE");
277	+	}
278	+
279		#ifdef IS_MPI
280		const int masterNode = 0;
281		if (worldRank == masterNode) {
282		#endif
283
284	<	std::ifstream mdFile_(mdFileName.c_str());
284	>	std::ifstream mdFile_;
285	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
286
287		if (mdFile_.fail()) {
288		sprintf(painCave.errMsg,
#	Line 262 | Line 295 | namespace oopse {
295		mdFile_.getline(buffer, bufferSize);
296		++lineNo;
297		std::string line = trimLeftCopy(buffer);
298	<	i = CaseInsensitiveFind(line, "<OOPSE");
298	>	i = CaseInsensitiveFind(line, "<OpenMD");
299		if (static_cast<size_t>(i) == string::npos) {
300	+	// try the older file strings to see if that works:
301	+	i = CaseInsensitiveFind(line, "<OOPSE");
302	+	}
303	+
304	+	if (static_cast<size_t>(i) == string::npos) {
305	+	// still no luck!
306		sprintf(painCave.errMsg,
307	<	"SimCreator: File: %s is not an OOPSE file!\n",
307	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
308		mdFileName.c_str());
309		painCave.isFatal = 1;
310		simError();
311		}
312	+
313	+	// found the correct opening string, now try to get the file
314	+	// format version number.
315
316	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
317	+	std::string fileType = tokenizer.nextToken();
318	+	toUpper(fileType);
319	+
320	+	mdFileVersion = 0;
321	+
322	+	if (fileType == "OPENMD") {
323	+	while (tokenizer.hasMoreTokens()) {
324	+	std::string token(tokenizer.nextToken());
325	+	toUpper(token);
326	+	if (token == "VERSION") {
327	+	mdFileVersion = tokenizer.nextTokenAsInt();
328	+	break;
329	+	}
330	+	}
331	+	}
332	+
333		//scan through the input stream and find MetaData tag
334		while(mdFile_.getline(buffer, bufferSize)) {
335		++lineNo;
#	Line 311 | Line 370 | namespace oopse {
370
371		mdRawData.clear();
372
373	+	bool foundVersion = false;
374	+
375		for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
376		mdFile_.getline(buffer, bufferSize);
377	<	mdRawData += buffer;
377	>	std::string line = trimLeftCopy(buffer);
378	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
379	>	if (static_cast<size_t>(j) != string::npos) {
380	>	foundVersion = true;
381	>	mdRawData += version;
382	>	} else {
383	>	mdRawData += buffer;
384	>	}
385		mdRawData += "\n";
386		}
387	<
387	>
388	>	if (!foundVersion) mdRawData += version + "\n";
389	>
390		mdFile_.close();
391
392		#ifdef IS_MPI
#	Line 326 | Line 396 | namespace oopse {
396		std::stringstream rawMetaDataStream(mdRawData);
397
398		//parse meta-data file
399	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
399	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
400	>	metaDataBlockStart + 1);
401
402		//create the force field
403	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
403	>	ForceField * ff = new ForceField(simParams->getForceField());
404
405		if (ff == NULL) {
406		sprintf(painCave.errMsg,
#	Line 363 | Line 434 | namespace oopse {
434		}
435
436		ff->parse(forcefieldFileName);
366	–	ff->setFortranForceOptions();
437		//create SimInfo
438		SimInfo * info = new SimInfo(ff, simParams);
439
#	Line 381 | Line 451 | namespace oopse {
451		//create the molecules
452		createMolecules(info);
453
454	<
454	>	//find the storage layout
455	>
456	>	int storageLayout = computeStorageLayout(info);
457	>
458		//allocate memory for DataStorage(circular reference, need to
459		//break it)
460	<	info->setSnapshotManager(new SimSnapshotManager(info));
460	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
461
462		//set the global index of atoms, rigidbodies and cutoffgroups
463		//(only need to be set once, the global index will never change
#	Line 407 | Line 480 | namespace oopse {
480
481		if (loadInitCoords)
482		loadCoordinates(info, mdFileName);
410	–
483		return info;
484		}
485
#	Line 454 | Line 526 | namespace oopse {
526		int nTarget;
527		int done;
528		int i;
457	–	int j;
529		int loops;
530		int which_proc;
531		int nProcessors;
#	Line 462 | Line 533 | namespace oopse {
533		int nGlobalMols = info->getNGlobalMolecules();
534		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
535
536	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
536	>	nProcessors = MPI::COMM_WORLD.Get_size();
537
538		if (nProcessors > nGlobalMols) {
539		sprintf(painCave.errMsg,
#	Line 471 | Line 542 | namespace oopse {
542		"\tthe number of molecules.  This will not result in a \n"
543		"\tusable division of atoms for force decomposition.\n"
544		"\tEither try a smaller number of processors, or run the\n"
545	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
545	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
546
547		painCave.isFatal = 1;
548		simError();
#	Line 500 | Line 571 | namespace oopse {
571		nTarget = (int)(precast + 0.5);
572
573		for(i = 0; i < nGlobalMols; i++) {
574	+
575		done = 0;
576		loops = 0;
577
#	Line 524 | Line 596 | namespace oopse {
596		// and be done with it.
597
598		if (loops > 100) {
599	<	sprintf(painCave.errMsg,
600	<	"I've tried 100 times to assign molecule %d to a "
601	<	" processor, but can't find a good spot.\n"
602	<	"I'm assigning it at random to processor %d.\n",
599	>
600	>	sprintf(painCave.errMsg,
601	>	"There have been 100 attempts to assign molecule %d to an\n"
602	>	"\tunderworked processor, but there's no good place to\n"
603	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
604		i, which_proc);
605	<
605	>
606		painCave.isFatal = 0;
607	+	painCave.severity = OPENMD_INFO;
608		simError();
609
610		molToProcMap[i] = which_proc;
#	Line 575 | Line 649 | namespace oopse {
649		}
650
651		delete myRandom;
652	<
652	>
653		// Spray out this nonsense to all other processors:
654	<
581	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
654	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655		} else {
656
657		// Listen to your marching orders from processor 0:
658	<
659	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
658	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
659	>
660		}
661
662		info->setMolToProcMap(molToProcMap);
#	Line 606 | Line 679 | namespace oopse {
679		#endif
680
681		stampId = info->getMoleculeStampId(i);
682	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
683	<	stampId, i, info->getLocalIndexManager());
682	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
683	>	info->getMoleculeStamp(stampId),
684	>	stampId, i,
685	>	info->getLocalIndexManager());
686
687		info->addMolecule(mol);
688
#	Line 619 | Line 694 | namespace oopse {
694
695		} //end for(int i=0)
696		}
697	+
698	+	int SimCreator::computeStorageLayout(SimInfo* info) {
699	+
700	+	Globals* simParams = info->getSimParams();
701	+	int nRigidBodies = info->getNGlobalRigidBodies();
702	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
703	+	set<AtomType*>::iterator i;
704	+	bool hasDirectionalAtoms = false;
705	+	bool hasFixedCharge = false;
706	+	bool hasDipoles = false;
707	+	bool hasQuadrupoles = false;
708	+	bool hasPolarizable = false;
709	+	bool hasFluctuatingCharge = false;
710	+	bool hasMetallic = false;
711	+	int storageLayout = 0;
712	+	storageLayout |= DataStorage::dslPosition;
713	+	storageLayout |= DataStorage::dslVelocity;
714	+	storageLayout |= DataStorage::dslForce;
715	+
716	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717	+
718	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
719	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
720	+	EAMAdapter ea = EAMAdapter( (*i) );
721	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
722	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
723	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
724	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
725	+
726	+	if (da.isDirectional()){
727	+	hasDirectionalAtoms = true;
728	+	}
729	+	if (ma.isDipole()){
730	+	hasDipoles = true;
731	+	}
732	+	if (ma.isQuadrupole()){
733	+	hasQuadrupoles = true;
734	+	}
735	+	if (ea.isEAM() || sca.isSuttonChen()){
736	+	hasMetallic = true;
737	+	}
738	+	if ( fca.isFixedCharge() ){
739	+	hasFixedCharge = true;
740	+	}
741	+	if ( fqa.isFluctuatingCharge() ){
742	+	hasFluctuatingCharge = true;
743	+	}
744	+	if ( pa.isPolarizable() ){
745	+	hasPolarizable = true;
746	+	}
747	+	}
748	+
749	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
750	+	storageLayout |= DataStorage::dslAmat;
751	+	if(storageLayout & DataStorage::dslVelocity) {
752	+	storageLayout |= DataStorage::dslAngularMomentum;
753	+	}
754	+	if (storageLayout & DataStorage::dslForce) {
755	+	storageLayout |= DataStorage::dslTorque;
756	+	}
757	+	}
758	+	if (hasDipoles) {
759	+	storageLayout |= DataStorage::dslDipole;
760	+	}
761	+	if (hasQuadrupoles) {
762	+	storageLayout |= DataStorage::dslQuadrupole;
763	+	}
764	+	if (hasFixedCharge || hasFluctuatingCharge) {
765	+	storageLayout |= DataStorage::dslSkippedCharge;
766	+	}
767	+	if (hasMetallic) {
768	+	storageLayout |= DataStorage::dslDensity;
769	+	storageLayout |= DataStorage::dslFunctional;
770	+	storageLayout |= DataStorage::dslFunctionalDerivative;
771	+	}
772	+	if (hasPolarizable) {
773	+	storageLayout |= DataStorage::dslElectricField;
774	+	}
775	+	if (hasFluctuatingCharge){
776	+	storageLayout |= DataStorage::dslFlucQPosition;
777	+	if(storageLayout & DataStorage::dslVelocity) {
778	+	storageLayout |= DataStorage::dslFlucQVelocity;
779	+	}
780	+	if (storageLayout & DataStorage::dslForce) {
781	+	storageLayout |= DataStorage::dslFlucQForce;
782	+	}
783	+	}
784
785	+	// if the user has asked for them, make sure we've got the memory for the
786	+	// objects defined.
787	+
788	+	if (simParams->getOutputParticlePotential()) {
789	+	storageLayout |= DataStorage::dslParticlePot;
790	+	}
791	+
792	+	if (simParams->havePrintHeatFlux()) {
793	+	if (simParams->getPrintHeatFlux()) {
794	+	storageLayout |= DataStorage::dslParticlePot;
795	+	}
796	+	}
797	+
798	+	if (simParams->getOutputElectricField()) {
799	+	storageLayout |= DataStorage::dslElectricField;
800	+	}
801	+
802	+	if (simParams->getOutputFluctuatingCharges()) {
803	+	storageLayout |= DataStorage::dslFlucQPosition;
804	+	storageLayout |= DataStorage::dslFlucQVelocity;
805	+	storageLayout |= DataStorage::dslFlucQForce;
806	+	}
807	+
808	+	return storageLayout;
809	+	}
810	+
811		void SimCreator::setGlobalIndex(SimInfo *info) {
812		SimInfo::MoleculeIterator mi;
813		Molecule::AtomIterator ai;
#	Line 634 | Line 822 | namespace oopse {
822		int beginRigidBodyIndex;
823		int beginCutoffGroupIndex;
824		int nGlobalAtoms = info->getNGlobalAtoms();
825	<
638	<	/**@todo fixme */
639	<	#ifndef IS_MPI
825	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
826
827		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	–
828		//rigidbody's index begins right after atom's
829	<	beginRigidBodyIndex += info->getNGlobalAtoms();
830	<
831	<	for(mol = info->beginMolecule(mi); mol != NULL;
832	<	mol = info->nextMolecule(mi)) {
829	>	beginRigidBodyIndex = info->getNGlobalAtoms();
830	>	beginCutoffGroupIndex = 0;
831	>
832	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
833
834	<	//local index(index in DataStorge) of atom is important
835	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
836	<	atom->setGlobalIndex(beginAtomIndex++);
834	>	#ifdef IS_MPI
835	>	if (info->getMolToProc(i) == worldRank) {
836	>	#endif
837	>	// stuff to do if I own this molecule
838	>	mol = info->getMoleculeByGlobalIndex(i);
839	>
840	>	//local index(index in DataStorge) of atom is important
841	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	>	atom->setGlobalIndex(beginAtomIndex++);
843	>	}
844	>
845	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
846	>	rb = mol->nextRigidBody(ri)) {
847	>	rb->setGlobalIndex(beginRigidBodyIndex++);
848	>	}
849	>
850	>	//local index of cutoff group is trivial, it only depends on
851	>	//the order of travesing
852	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
853	>	cg = mol->nextCutoffGroup(ci)) {
854	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
855	>	}
856	>
857	>	#ifdef IS_MPI
858	>	}  else {
859	>
860	>	// stuff to do if I don't own this molecule
861	>
862	>	int stampId = info->getMoleculeStampId(i);
863	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
864	>
865	>	beginAtomIndex += stamp->getNAtoms();
866	>	beginRigidBodyIndex += stamp->getNRigidBodies();
867	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
868		}
869	<
870	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
871	<	rb = mol->nextRigidBody(ri)) {
872	<	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	<
869	>	#endif
870	>
871	>	} //end for(int i=0)
872	>
873		//fill globalGroupMembership
874		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
875		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 715 | Line 881 | namespace oopse {
881
882		}
883		}
884	<
884	>
885		#ifdef IS_MPI
886		// Since the globalGroupMembership has been zero filled and we've only
887		// poked values into the atoms we know, we can do an Allreduce
#	Line 723 | Line 889 | namespace oopse {
889		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
890		// docs said we could.
891		std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
892	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
893	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
892	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
893	>	&tmpGroupMembership[0], nGlobalAtoms,
894	>	MPI::INT, MPI::SUM);
895		info->setGlobalGroupMembership(tmpGroupMembership);
896		#else
897		info->setGlobalGroupMembership(globalGroupMembership);
898		#endif
899
900		//fill molMembership
901	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
901	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
902	>	info->getNGlobalRigidBodies(), 0);
903
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		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
908		}
909	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
910	+	rb = mol->nextRigidBody(ri)) {
911	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
912	+	}
913		}
914
915		#ifdef IS_MPI
916	<	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
916	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
917	>	info->getNGlobalRigidBodies(), 0);
918	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
919	>	nGlobalAtoms + nGlobalRigidBodies,
920	>	MPI::INT, MPI::SUM);
921
745	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
746	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
747	–
922		info->setGlobalMolMembership(tmpMolMembership);
923		#else
924		info->setGlobalMolMembership(globalMolMembership);
#	Line 754 | Line 928 | namespace oopse {
928		// here the molecules are listed by their global indices.
929
930		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
931	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
931	>	for (mol = info->beginMolecule(mi); mol != NULL;
932	>	mol = info->nextMolecule(mi)) {
933		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
934		}
935
936		#ifdef IS_MPI
937		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
938	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
939	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
938	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
939	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
940		#else
941		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
942		#endif
#	Line 775 | Line 950 | namespace oopse {
950		}
951
952		std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
953	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
953	>	for (mol = info->beginMolecule(mi); mol != NULL;
954	>	mol = info->nextMolecule(mi)) {
955		int myGlobalIndex = mol->getGlobalIndex();
956		int globalIO = startingIOIndexForMol[myGlobalIndex];
957	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
958	<	integrableObject = mol->nextIntegrableObject(ioi)) {
959	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
960	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
957	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
958	>	sd = mol->nextIntegrableObject(ioi)) {
959	>	sd->setGlobalIntegrableObjectIndex(globalIO);
960	>	IOIndexToIntegrableObject[globalIO] = sd;
961		globalIO++;
962		}
963		}
964	<
964	>
965		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
966
967		}
968
969		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
794	–	Globals* simParams;
795	–	simParams = info->getSimParams();
970
797	–
971		DumpReader reader(info, mdFileName);
972		int nframes = reader.getNFrames();
973
#	Line 808 | Line 981 | namespace oopse {
981		painCave.isFatal = 1;
982		simError();
983		}
811	–
984		//copy the current snapshot to previous snapshot
985		info->getSnapshotManager()->advance();
986		}
987
988	<	} //end namespace oopse
988	>	} //end namespace OpenMD
989
990

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1826 by gezelter, Wed Jan 9 19:41:48 2013 UTC

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