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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1810 by gezelter, Thu Nov 8 14:23:43 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
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 90 | Line 100 | namespace oopse {
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);
124	<
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;
132	>	delete [] buf;
133
134		}
135		#endif
#	Line 145 | Line 158 | namespace oopse {
158		treeParser.initializeASTFactory(factory);
159		treeParser.setASTFactory(&factory);
160		simParams = treeParser.walkTree(parser.getAST());
148	–
161		}
162
163
#	Line 215 | 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 230 | 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;
255		std::string mdRawData;
256		int metaDataBlockStart = -1;
257		int metaDataBlockEnd = -1;
258	<	int i;
259	<	int mdOffset;
258	>	int i, j;
259	>	streamoff mdOffset(0);
260	>	int mdFileVersion;
261
262	+	// Create a string for embedding the version information in the MetaData
263	+	std::string version;
264	+	version.assign("## Last run using OpenMD Version: ");
265	+	version.append(OPENMD_VERSION_MAJOR);
266	+	version.append(".");
267	+	version.append(OPENMD_VERSION_MINOR);
268	+
269	+	std::string svnrev;
270	+	//convert a macro from compiler to a string in c++
271	+	STR_DEFINE(svnrev, SVN_REV );
272	+	version.append(" Revision: ");
273	+	// If there's no SVN revision, just call this the RELEASE revision.
274	+	if (!svnrev.empty()) {
275	+	version.append(svnrev);
276	+	} else {
277	+	version.append("RELEASE");
278	+	}
279	+
280		#ifdef IS_MPI
281		const int masterNode = 0;
282		if (worldRank == masterNode) {
283		#endif
284
285	<	std::ifstream mdFile_(mdFileName.c_str());
285	>	std::ifstream mdFile_;
286	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
287
288		if (mdFile_.fail()) {
289		sprintf(painCave.errMsg,
#	Line 263 | Line 296 | namespace oopse {
296		mdFile_.getline(buffer, bufferSize);
297		++lineNo;
298		std::string line = trimLeftCopy(buffer);
299	<	i = CaseInsensitiveFind(line, "<OOPSE");
300	<	if (i == string::npos) {
299	>	i = CaseInsensitiveFind(line, "<OpenMD");
300	>	if (static_cast<size_t>(i) == string::npos) {
301	>	// try the older file strings to see if that works:
302	>	i = CaseInsensitiveFind(line, "<OOPSE");
303	>	}
304	>
305	>	if (static_cast<size_t>(i) == string::npos) {
306	>	// still no luck!
307		sprintf(painCave.errMsg,
308	<	"SimCreator: File: %s is not an OOPSE file!\n",
308	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
309		mdFileName.c_str());
310		painCave.isFatal = 1;
311		simError();
312		}
313	+
314	+	// found the correct opening string, now try to get the file
315	+	// format version number.
316
317	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
318	+	std::string fileType = tokenizer.nextToken();
319	+	toUpper(fileType);
320	+
321	+	mdFileVersion = 0;
322	+
323	+	if (fileType == "OPENMD") {
324	+	while (tokenizer.hasMoreTokens()) {
325	+	std::string token(tokenizer.nextToken());
326	+	toUpper(token);
327	+	if (token == "VERSION") {
328	+	mdFileVersion = tokenizer.nextTokenAsInt();
329	+	break;
330	+	}
331	+	}
332	+	}
333	+
334		//scan through the input stream and find MetaData tag
335		while(mdFile_.getline(buffer, bufferSize)) {
336		++lineNo;
#	Line 312 | Line 371 | namespace oopse {
371
372		mdRawData.clear();
373
374	+	bool foundVersion = false;
375	+
376		for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
377		mdFile_.getline(buffer, bufferSize);
378	<	mdRawData += buffer;
378	>	std::string line = trimLeftCopy(buffer);
379	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
380	>	if (static_cast<size_t>(j) != string::npos) {
381	>	foundVersion = true;
382	>	mdRawData += version;
383	>	} else {
384	>	mdRawData += buffer;
385	>	}
386		mdRawData += "\n";
387		}
388	<
388	>
389	>	if (!foundVersion) mdRawData += version + "\n";
390	>
391		mdFile_.close();
392
393		#ifdef IS_MPI
#	Line 327 | Line 397 | namespace oopse {
397		std::stringstream rawMetaDataStream(mdRawData);
398
399		//parse meta-data file
400	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
400	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
401	>	metaDataBlockStart + 1);
402
403		//create the force field
404	<	ForceField * ff = ForceFieldFactory::getInstance()
405	<	->createForceField(simParams->getForceField());
335	<
404	>	ForceField * ff = new ForceField(simParams->getForceField());
405	>
406		if (ff == NULL) {
407		sprintf(painCave.errMsg,
408		"ForceField Factory can not create %s force field\n",
#	Line 365 | Line 435 | namespace oopse {
435		}
436
437		ff->parse(forcefieldFileName);
368	–	ff->setFortranForceOptions();
438		//create SimInfo
439		SimInfo * info = new SimInfo(ff, simParams);
440
#	Line 383 | Line 452 | namespace oopse {
452		//create the molecules
453		createMolecules(info);
454
455	<
455	>	//find the storage layout
456	>
457	>	int storageLayout = computeStorageLayout(info);
458	>
459		//allocate memory for DataStorage(circular reference, need to
460		//break it)
461	<	info->setSnapshotManager(new SimSnapshotManager(info));
461	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
462
463		//set the global index of atoms, rigidbodies and cutoffgroups
464		//(only need to be set once, the global index will never change
#	Line 395 | Line 467 | namespace oopse {
467		//responsibility to LocalIndexManager.
468		setGlobalIndex(info);
469
470	<	//Although addExcludePairs is called inside SimInfo's addMolecule
470	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
471		//method, at that point atoms don't have the global index yet
472		//(their global index are all initialized to -1).  Therefore we
473	<	//have to call addExcludePairs explicitly here. A way to work
473	>	//have to call addInteractionPairs explicitly here. A way to work
474		//around is that we can determine the beginning global indices of
475		//atoms before they get created.
476		SimInfo::MoleculeIterator mi;
477		Molecule* mol;
478		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
479	<	info->addExcludePairs(mol);
479	>	info->addInteractionPairs(mol);
480		}
481
482		if (loadInitCoords)
483		loadCoordinates(info, mdFileName);
412	–
484		return info;
485		}
486
#	Line 456 | Line 527 | namespace oopse {
527		int nTarget;
528		int done;
529		int i;
459	–	int j;
530		int loops;
531		int which_proc;
532		int nProcessors;
#	Line 464 | Line 534 | namespace oopse {
534		int nGlobalMols = info->getNGlobalMolecules();
535		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
536
537	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
537	>	nProcessors = MPI::COMM_WORLD.Get_size();
538
539		if (nProcessors > nGlobalMols) {
540		sprintf(painCave.errMsg,
#	Line 473 | Line 543 | namespace oopse {
543		"\tthe number of molecules.  This will not result in a \n"
544		"\tusable division of atoms for force decomposition.\n"
545		"\tEither try a smaller number of processors, or run the\n"
546	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
546	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
547
548		painCave.isFatal = 1;
549		simError();
#	Line 502 | Line 572 | namespace oopse {
572		nTarget = (int)(precast + 0.5);
573
574		for(i = 0; i < nGlobalMols; i++) {
575	+
576		done = 0;
577		loops = 0;
578
#	Line 526 | Line 597 | namespace oopse {
597		// and be done with it.
598
599		if (loops > 100) {
600	+
601		sprintf(painCave.errMsg,
602	<	"I've tried 100 times to assign molecule %d to a "
603	<	" processor, but can't find a good spot.\n"
604	<	"I'm assigning it at random to processor %d.\n",
602	>	"There have been 100 attempts to assign molecule %d to an\n"
603	>	"\tunderworked processor, but there's no good place to\n"
604	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
605		i, which_proc);
606	<
606	>
607		painCave.isFatal = 0;
608	+	painCave.severity = OPENMD_INFO;
609		simError();
610
611		molToProcMap[i] = which_proc;
#	Line 577 | Line 650 | namespace oopse {
650		}
651
652		delete myRandom;
653	<
653	>
654		// Spray out this nonsense to all other processors:
655	<
583	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
655	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
656		} else {
657
658		// Listen to your marching orders from processor 0:
659	<
660	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
659	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
660	>
661		}
662
663		info->setMolToProcMap(molToProcMap);
664		sprintf(checkPointMsg,
665		"Successfully divided the molecules among the processors.\n");
666	<	MPIcheckPoint();
666	>	errorCheckPoint();
667		}
668
669		#endif
#	Line 608 | Line 680 | namespace oopse {
680		#endif
681
682		stampId = info->getMoleculeStampId(i);
683	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
684	<	stampId, i, info->getLocalIndexManager());
683	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
684	>	info->getMoleculeStamp(stampId),
685	>	stampId, i,
686	>	info->getLocalIndexManager());
687
688		info->addMolecule(mol);
689
#	Line 621 | Line 695 | namespace oopse {
695
696		} //end for(int i=0)
697		}
698	+
699	+	int SimCreator::computeStorageLayout(SimInfo* info) {
700	+
701	+	Globals* simParams = info->getSimParams();
702	+	int nRigidBodies = info->getNGlobalRigidBodies();
703	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
704	+	set<AtomType*>::iterator i;
705	+	bool hasDirectionalAtoms = false;
706	+	bool hasFixedCharge = false;
707	+	bool hasMultipoles = 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.isMultipole()){
730	+	hasMultipoles = true;
731	+	}
732	+	if (ea.isEAM() || sca.isSuttonChen()){
733	+	hasMetallic = true;
734	+	}
735	+	if ( fca.isFixedCharge() ){
736	+	hasFixedCharge = true;
737	+	}
738	+	if ( fqa.isFluctuatingCharge() ){
739	+	hasFluctuatingCharge = true;
740	+	}
741	+	if ( pa.isPolarizable() ){
742	+	hasPolarizable = true;
743	+	}
744	+	}
745	+
746	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
747	+	storageLayout |= DataStorage::dslAmat;
748	+	if(storageLayout & DataStorage::dslVelocity) {
749	+	storageLayout |= DataStorage::dslAngularMomentum;
750	+	}
751	+	if (storageLayout & DataStorage::dslForce) {
752	+	storageLayout |= DataStorage::dslTorque;
753	+	}
754	+	}
755	+	if (hasMultipoles) {
756	+	storageLayout |= DataStorage::dslElectroFrame;
757	+	}
758	+	if (hasFixedCharge || hasFluctuatingCharge) {
759	+	storageLayout |= DataStorage::dslSkippedCharge;
760	+	}
761	+	if (hasMetallic) {
762	+	storageLayout |= DataStorage::dslDensity;
763	+	storageLayout |= DataStorage::dslFunctional;
764	+	storageLayout |= DataStorage::dslFunctionalDerivative;
765	+	}
766	+	if (hasPolarizable) {
767	+	storageLayout |= DataStorage::dslElectricField;
768	+	}
769	+	if (hasFluctuatingCharge){
770	+	storageLayout |= DataStorage::dslFlucQPosition;
771	+	if(storageLayout & DataStorage::dslVelocity) {
772	+	storageLayout |= DataStorage::dslFlucQVelocity;
773	+	}
774	+	if (storageLayout & DataStorage::dslForce) {
775	+	storageLayout |= DataStorage::dslFlucQForce;
776	+	}
777	+	}
778
779	+	// if the user has asked for them, make sure we've got the memory for the
780	+	// objects defined.
781	+
782	+	if (simParams->getOutputParticlePotential()) {
783	+	storageLayout |= DataStorage::dslParticlePot;
784	+	}
785	+
786	+	if (simParams->havePrintHeatFlux()) {
787	+	if (simParams->getPrintHeatFlux()) {
788	+	storageLayout |= DataStorage::dslParticlePot;
789	+	}
790	+	}
791	+
792	+	if (simParams->getOutputElectricField()) {
793	+	storageLayout |= DataStorage::dslElectricField;
794	+	}
795	+	if (simParams->getOutputFluctuatingCharges()) {
796	+	storageLayout |= DataStorage::dslFlucQPosition;
797	+	storageLayout |= DataStorage::dslFlucQVelocity;
798	+	storageLayout |= DataStorage::dslFlucQForce;
799	+	}
800	+
801	+	return storageLayout;
802	+	}
803	+
804		void SimCreator::setGlobalIndex(SimInfo *info) {
805		SimInfo::MoleculeIterator mi;
806		Molecule::AtomIterator ai;
#	Line 636 | Line 815 | namespace oopse {
815		int beginRigidBodyIndex;
816		int beginCutoffGroupIndex;
817		int nGlobalAtoms = info->getNGlobalAtoms();
818	<
640	<	/**@todo fixme */
641	<	#ifndef IS_MPI
818	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
819
820		beginAtomIndex = 0;
644	–	beginRigidBodyIndex = 0;
645	–	beginCutoffGroupIndex = 0;
646	–
647	–	#else
648	–
649	–	int nproc;
650	–	int myNode;
651	–
652	–	myNode = worldRank;
653	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
654	–
655	–	std::vector < int > tmpAtomsInProc(nproc, 0);
656	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
657	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
658	–	std::vector < int > NumAtomsInProc(nproc, 0);
659	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
660	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
661	–
662	–	tmpAtomsInProc[myNode] = info->getNAtoms();
663	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
664	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
665	–
666	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
667	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
668	–	MPI_SUM, MPI_COMM_WORLD);
669	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
670	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
671	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
672	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
673	–
674	–	beginAtomIndex = 0;
675	–	beginRigidBodyIndex = 0;
676	–	beginCutoffGroupIndex = 0;
677	–
678	–	for(int i = 0; i < myNode; i++) {
679	–	beginAtomIndex += NumAtomsInProc[i];
680	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
681	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
682	–	}
683	–
684	–	#endif
685	–
821		//rigidbody's index begins right after atom's
822	<	beginRigidBodyIndex += info->getNGlobalAtoms();
823	<
824	<	for(mol = info->beginMolecule(mi); mol != NULL;
825	<	mol = info->nextMolecule(mi)) {
822	>	beginRigidBodyIndex = info->getNGlobalAtoms();
823	>	beginCutoffGroupIndex = 0;
824	>
825	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
826
827	<	//local index(index in DataStorge) of atom is important
828	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
829	<	atom->setGlobalIndex(beginAtomIndex++);
827	>	#ifdef IS_MPI
828	>	if (info->getMolToProc(i) == worldRank) {
829	>	#endif
830	>	// stuff to do if I own this molecule
831	>	mol = info->getMoleculeByGlobalIndex(i);
832	>
833	>	//local index(index in DataStorge) of atom is important
834	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
835	>	atom->setGlobalIndex(beginAtomIndex++);
836	>	}
837	>
838	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
839	>	rb = mol->nextRigidBody(ri)) {
840	>	rb->setGlobalIndex(beginRigidBodyIndex++);
841	>	}
842	>
843	>	//local index of cutoff group is trivial, it only depends on
844	>	//the order of travesing
845	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
846	>	cg = mol->nextCutoffGroup(ci)) {
847	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
848	>	}
849	>
850	>	#ifdef IS_MPI
851	>	}  else {
852	>
853	>	// stuff to do if I don't own this molecule
854	>
855	>	int stampId = info->getMoleculeStampId(i);
856	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
857	>
858	>	beginAtomIndex += stamp->getNAtoms();
859	>	beginRigidBodyIndex += stamp->getNRigidBodies();
860	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
861		}
862	<
863	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
864	<	rb = mol->nextRigidBody(ri)) {
865	<	rb->setGlobalIndex(beginRigidBodyIndex++);
700	<	}
701	<
702	<	//local index of cutoff group is trivial, it only depends on the order of travesing
703	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
704	<	cg = mol->nextCutoffGroup(ci)) {
705	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
706	<	}
707	<	}
708	<
862	>	#endif
863	>
864	>	} //end for(int i=0)
865	>
866		//fill globalGroupMembership
867		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
868		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 717 | Line 874 | namespace oopse {
874
875		}
876		}
877	<
877	>
878		#ifdef IS_MPI
879		// Since the globalGroupMembership has been zero filled and we've only
880		// poked values into the atoms we know, we can do an Allreduce
881		// to get the full globalGroupMembership array (We think).
882		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
883		// docs said we could.
884	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
885	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
886	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
884	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
885	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
886	>	&tmpGroupMembership[0], nGlobalAtoms,
887	>	MPI::INT, MPI::SUM);
888		info->setGlobalGroupMembership(tmpGroupMembership);
889		#else
890		info->setGlobalGroupMembership(globalGroupMembership);
891		#endif
892
893		//fill molMembership
894	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
894	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
895	>	info->getNGlobalRigidBodies(), 0);
896
897	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
898	<
897	>	for(mol = info->beginMolecule(mi); mol != NULL;
898	>	mol = info->nextMolecule(mi)) {
899		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
900		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
901		}
902	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
903	+	rb = mol->nextRigidBody(ri)) {
904	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
905	+	}
906		}
907
908		#ifdef IS_MPI
909	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
909	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
910	>	info->getNGlobalRigidBodies(), 0);
911	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
912	>	nGlobalAtoms + nGlobalRigidBodies,
913	>	MPI::INT, MPI::SUM);
914
748	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
749	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
750	–
915		info->setGlobalMolMembership(tmpMolMembership);
916		#else
917		info->setGlobalMolMembership(globalMolMembership);
#	Line 757 | Line 921 | namespace oopse {
921		// here the molecules are listed by their global indices.
922
923		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
924	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
924	>	for (mol = info->beginMolecule(mi); mol != NULL;
925	>	mol = info->nextMolecule(mi)) {
926		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
927		}
928
929		#ifdef IS_MPI
930		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
931	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
932	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
931	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
932	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
933		#else
934		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
935		#endif
936
937	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
938	<
939	<	int startingIndex = 0;
940	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
941	<	startingIOIndexForMol[i] = startingIndex;
942	<	startingIndex += numIntegrableObjectsPerMol[i];
943	<	}
944	<
945	<	std::cerr << "nGIO = " << info->getNGlobalIntegrableObjects() << "\n";
946	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
947	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
937	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
938	>
939	>	int startingIndex = 0;
940	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
941	>	startingIOIndexForMol[i] = startingIndex;
942	>	startingIndex += numIntegrableObjectsPerMol[i];
943	>	}
944	>
945	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
946	>	for (mol = info->beginMolecule(mi); mol != NULL;
947	>	mol = info->nextMolecule(mi)) {
948		int myGlobalIndex = mol->getGlobalIndex();
949		int globalIO = startingIOIndexForMol[myGlobalIndex];
950	<	std::cerr << "myGlobalIndex = " << myGlobalIndex << " globalIO = " << globalIO << "\n";
951	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
952	<	integrableObject = mol->nextIntegrableObject(ioi)) {
953	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
954	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
790	<	globalIO++;
950	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
951	>	sd = mol->nextIntegrableObject(ioi)) {
952	>	sd->setGlobalIntegrableObjectIndex(globalIO);
953	>	IOIndexToIntegrableObject[globalIO] = sd;
954	>	globalIO++;
955		}
956		}
957	<
958	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
959	<
957	>
958	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
959	>
960		}
961
962		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
963	<	Globals* simParams;
800	<	simParams = info->getSimParams();
801	<
802	<
963	>
964		DumpReader reader(info, mdFileName);
965		int nframes = reader.getNFrames();
966	<
966	>
967		if (nframes > 0) {
968		reader.readFrame(nframes - 1);
969		} else {
#	Line 813 | Line 974 | int startingIndex = 0;
974		painCave.isFatal = 1;
975		simError();
976		}
816	–
977		//copy the current snapshot to previous snapshot
978		info->getSnapshotManager()->advance();
979		}
980
981	<	} //end namespace oopse
981	>	} //end namespace OpenMD
982
983

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1810 by gezelter, Thu Nov 8 14:23:43 2012 UTC

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