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trunk/src/brains/SimCreator.cpp (file contents), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1825 by gezelter, Wed Jan 9 19:27:52 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	<
123	>
124		char* buf = new char[streamSize];
125		assert(buf);
126
#	Line 116 | Line 128 | namespace oopse {
128		commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129
130		ppStream.str(buf);
131	<	delete buf;
131	>	delete [] buf;
132
133		}
134		#endif
#	Line 145 | Line 157 | namespace oopse {
157		treeParser.initializeASTFactory(factory);
158		treeParser.setASTFactory(&factory);
159		simParams = treeParser.walkTree(parser.getAST());
148	–
160		}
161
162
#	Line 215 | 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 230 | 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 263 | Line 295 | namespace oopse {
295		mdFile_.getline(buffer, bufferSize);
296		++lineNo;
297		std::string line = trimLeftCopy(buffer);
298	<	i = CaseInsensitiveFind(line, "<OOPSE");
299	<	if (i == string::npos) {
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 312 | 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 327 | 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()
404	<	->createForceField(simParams->getForceField());
335	<
403	>	ForceField * ff = new ForceField(simParams->getForceField());
404	>
405		if (ff == NULL) {
406		sprintf(painCave.errMsg,
407		"ForceField Factory can not create %s force field\n",
#	Line 365 | Line 434 | namespace oopse {
434		}
435
436		ff->parse(forcefieldFileName);
368	–	ff->setFortranForceOptions();
437		//create SimInfo
438		SimInfo * info = new SimInfo(ff, simParams);
439
#	Line 383 | 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 395 | Line 466 | namespace oopse {
466		//responsibility to LocalIndexManager.
467		setGlobalIndex(info);
468
469	<	//Although addExcludePairs is called inside SimInfo's addMolecule
469	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
470		//method, at that point atoms don't have the global index yet
471		//(their global index are all initialized to -1).  Therefore we
472	<	//have to call addExcludePairs explicitly here. A way to work
472	>	//have to call addInteractionPairs explicitly here. A way to work
473		//around is that we can determine the beginning global indices of
474		//atoms before they get created.
475		SimInfo::MoleculeIterator mi;
476		Molecule* mol;
477		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
478	<	info->addExcludePairs(mol);
478	>	info->addInteractionPairs(mol);
479		}
480
481		if (loadInitCoords)
482		loadCoordinates(info, mdFileName);
412	–
483		return info;
484		}
485
#	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);
#	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 hasDipoles = false;
708	+	bool hasQuadrupoles = false;
709	+	bool hasPolarizable = false;
710	+	bool hasFluctuatingCharge = false;
711	+	bool hasMetallic = false;
712	+	int storageLayout = 0;
713	+	storageLayout |= DataStorage::dslPosition;
714	+	storageLayout |= DataStorage::dslVelocity;
715	+	storageLayout |= DataStorage::dslForce;
716	+
717	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
718	+
719	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
720	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
721	+	EAMAdapter ea = EAMAdapter( (*i) );
722	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
723	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
724	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
725	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
726	+
727	+	if (da.isDirectional()){
728	+	hasDirectionalAtoms = true;
729	+	}
730	+	if (ma.isDipole()){
731	+	hasDipoles = true;
732	+	}
733	+	if (ma.isQuadrupole()){
734	+	hasQuadrupoles = true;
735	+	}
736	+	if (ea.isEAM() || sca.isSuttonChen()){
737	+	hasMetallic = true;
738	+	}
739	+	if ( fca.isFixedCharge() ){
740	+	hasFixedCharge = true;
741	+	}
742	+	if ( fqa.isFluctuatingCharge() ){
743	+	hasFluctuatingCharge = true;
744	+	}
745	+	if ( pa.isPolarizable() ){
746	+	hasPolarizable = true;
747	+	}
748	+	}
749	+
750	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
751	+	storageLayout |= DataStorage::dslAmat;
752	+	if(storageLayout & DataStorage::dslVelocity) {
753	+	storageLayout |= DataStorage::dslAngularMomentum;
754	+	}
755	+	if (storageLayout & DataStorage::dslForce) {
756	+	storageLayout |= DataStorage::dslTorque;
757	+	}
758	+	}
759	+	if (hasDipoles) {
760	+	storageLayout |= DataStorage::dslDipole;
761	+	}
762	+	if (hasQuadrupoles) {
763	+	storageLayout |= DataStorage::dslQuadrupole;
764	+	}
765	+	if (hasFixedCharge || hasFluctuatingCharge) {
766	+	storageLayout |= DataStorage::dslSkippedCharge;
767	+	}
768	+	if (hasMetallic) {
769	+	storageLayout |= DataStorage::dslDensity;
770	+	storageLayout |= DataStorage::dslFunctional;
771	+	storageLayout |= DataStorage::dslFunctionalDerivative;
772	+	}
773	+	if (hasPolarizable) {
774	+	storageLayout |= DataStorage::dslElectricField;
775	+	}
776	+	if (hasFluctuatingCharge){
777	+	storageLayout |= DataStorage::dslFlucQPosition;
778	+	if(storageLayout & DataStorage::dslVelocity) {
779	+	storageLayout |= DataStorage::dslFlucQVelocity;
780	+	}
781	+	if (storageLayout & DataStorage::dslForce) {
782	+	storageLayout |= DataStorage::dslFlucQForce;
783	+	}
784	+	}
785
786	+	// if the user has asked for them, make sure we've got the memory for the
787	+	// objects defined.
788	+
789	+	if (simParams->getOutputParticlePotential()) {
790	+	storageLayout |= DataStorage::dslParticlePot;
791	+	}
792	+
793	+	if (simParams->havePrintHeatFlux()) {
794	+	if (simParams->getPrintHeatFlux()) {
795	+	storageLayout |= DataStorage::dslParticlePot;
796	+	}
797	+	}
798	+
799	+	if (simParams->getOutputElectricField()) {
800	+	storageLayout |= DataStorage::dslElectricField;
801	+	}
802	+
803	+	if (simParams->getOutputFluctuatingCharges()) {
804	+	storageLayout |= DataStorage::dslFlucQPosition;
805	+	storageLayout |= DataStorage::dslFlucQVelocity;
806	+	storageLayout |= DataStorage::dslFlucQForce;
807	+	}
808	+
809	+	return storageLayout;
810	+	}
811	+
812		void SimCreator::setGlobalIndex(SimInfo *info) {
813		SimInfo::MoleculeIterator mi;
814		Molecule::AtomIterator ai;
#	Line 636 | Line 823 | namespace oopse {
823		int beginRigidBodyIndex;
824		int beginCutoffGroupIndex;
825		int nGlobalAtoms = info->getNGlobalAtoms();
826	<
640	<	/**@todo fixme */
641	<	#ifndef IS_MPI
826	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
827
828		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	–
829		//rigidbody's index begins right after atom's
830	<	beginRigidBodyIndex += info->getNGlobalAtoms();
831	<
832	<	for(mol = info->beginMolecule(mi); mol != NULL;
833	<	mol = info->nextMolecule(mi)) {
830	>	beginRigidBodyIndex = info->getNGlobalAtoms();
831	>	beginCutoffGroupIndex = 0;
832	>
833	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
834
835	<	//local index(index in DataStorge) of atom is important
836	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
837	<	atom->setGlobalIndex(beginAtomIndex++);
835	>	#ifdef IS_MPI
836	>	if (info->getMolToProc(i) == worldRank) {
837	>	#endif
838	>	// stuff to do if I own this molecule
839	>	mol = info->getMoleculeByGlobalIndex(i);
840	>
841	>	//local index(index in DataStorge) of atom is important
842	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
843	>	atom->setGlobalIndex(beginAtomIndex++);
844	>	}
845	>
846	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
847	>	rb = mol->nextRigidBody(ri)) {
848	>	rb->setGlobalIndex(beginRigidBodyIndex++);
849	>	}
850	>
851	>	//local index of cutoff group is trivial, it only depends on
852	>	//the order of travesing
853	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
854	>	cg = mol->nextCutoffGroup(ci)) {
855	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
856	>	}
857	>
858	>	#ifdef IS_MPI
859	>	}  else {
860	>
861	>	// stuff to do if I don't own this molecule
862	>
863	>	int stampId = info->getMoleculeStampId(i);
864	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
865	>
866	>	beginAtomIndex += stamp->getNAtoms();
867	>	beginRigidBodyIndex += stamp->getNRigidBodies();
868	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
869		}
870	<
871	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
872	<	rb = mol->nextRigidBody(ri)) {
873	<	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	<
870	>	#endif
871	>
872	>	} //end for(int i=0)
873	>
874		//fill globalGroupMembership
875		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
876		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 717 | Line 882 | namespace oopse {
882
883		}
884		}
885	<
885	>
886		#ifdef IS_MPI
887		// Since the globalGroupMembership has been zero filled and we've only
888		// poked values into the atoms we know, we can do an Allreduce
889		// to get the full globalGroupMembership array (We think).
890		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
891		// docs said we could.
892	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
893	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
894	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
892	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
893	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
894	>	&tmpGroupMembership[0], nGlobalAtoms,
895	>	MPI::INT, MPI::SUM);
896		info->setGlobalGroupMembership(tmpGroupMembership);
897		#else
898		info->setGlobalGroupMembership(globalGroupMembership);
899		#endif
900
901		//fill molMembership
902	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
902	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
903	>	info->getNGlobalRigidBodies(), 0);
904
905	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
906	<
905	>	for(mol = info->beginMolecule(mi); mol != NULL;
906	>	mol = info->nextMolecule(mi)) {
907		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
908		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
909		}
910	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
911	+	rb = mol->nextRigidBody(ri)) {
912	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
913	+	}
914		}
915
916		#ifdef IS_MPI
917	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
917	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
918	>	info->getNGlobalRigidBodies(), 0);
919	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
920	>	nGlobalAtoms + nGlobalRigidBodies,
921	>	MPI::INT, MPI::SUM);
922
748	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
749	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
750	–
923		info->setGlobalMolMembership(tmpMolMembership);
924		#else
925		info->setGlobalMolMembership(globalMolMembership);
#	Line 757 | Line 929 | namespace oopse {
929		// here the molecules are listed by their global indices.
930
931		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
932	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
932	>	for (mol = info->beginMolecule(mi); mol != NULL;
933	>	mol = info->nextMolecule(mi)) {
934		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
935		}
936
937		#ifdef IS_MPI
938		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
939	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
940	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
939	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
940	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
941		#else
942		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
943		#endif
944
945	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
946	<
947	<	int startingIndex = 0;
948	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
949	<	startingIOIndexForMol[i] = startingIndex;
950	<	startingIndex += numIntegrableObjectsPerMol[i];
951	<	}
952	<
953	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
954	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
945	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
946	>
947	>	int startingIndex = 0;
948	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
949	>	startingIOIndexForMol[i] = startingIndex;
950	>	startingIndex += numIntegrableObjectsPerMol[i];
951	>	}
952	>
953	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
954	>	for (mol = info->beginMolecule(mi); mol != NULL;
955	>	mol = info->nextMolecule(mi)) {
956		int myGlobalIndex = mol->getGlobalIndex();
957		int globalIO = startingIOIndexForMol[myGlobalIndex];
958	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
959	<	integrableObject = mol->nextIntegrableObject(ioi)) {
960	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
961	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
962	<	globalIO++;
958	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
959	>	sd = mol->nextIntegrableObject(ioi)) {
960	>	sd->setGlobalIntegrableObjectIndex(globalIO);
961	>	IOIndexToIntegrableObject[globalIO] = sd;
962	>	globalIO++;
963		}
964		}
965	<
966	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
967	<
965	>
966	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
967	>
968		}
969
970		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
797	–	Globals* simParams;
798	–	simParams = info->getSimParams();
971
800	–
972		DumpReader reader(info, mdFileName);
973		int nframes = reader.getNFrames();
974
#	Line 811 | Line 982 | int startingIndex = 0;
982		painCave.isFatal = 1;
983		simError();
984		}
814	–
985		//copy the current snapshot to previous snapshot
986		info->getSnapshotManager()->advance();
987		}
988
989	<	} //end namespace oopse
989	>	} //end namespace OpenMD
990
991

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

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