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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (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 90 | Line 99 | namespace oopse {
99		#ifdef IS_MPI
100		int streamSize;
101		const int masterNode = 0;
102	<	int commStatus;
102	>
103		if (worldRank == masterNode) {
104	<	#endif
105	<
104	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
105	>	#endif
106		SimplePreprocessor preprocessor;
107	<	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock,
108	>	ppStream);
109
110		#ifdef IS_MPI
111		//brocasting the stream size
112		streamSize = ppStream.str().size() +1;
113	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
114	<
115	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106	<
107	<
113	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
114	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
115	>
116		} else {
117	+	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
118	+
119		//get stream size
120	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
121	<
120	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121	>
122		char* buf = new char[streamSize];
123		assert(buf);
124
125		//receive file content
126	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
126	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
127
128		ppStream.str(buf);
129	<	delete buf;
120	<
129	>	delete [] buf;
130		}
131		#endif
132		// Create a scanner that reads from the input stream
#	Line 145 | Line 154 | namespace oopse {
154		treeParser.initializeASTFactory(factory);
155		treeParser.setASTFactory(&factory);
156		simParams = treeParser.walkTree(parser.getAST());
148	–
157		}
158
159
#	Line 215 | Line 223 | namespace oopse {
223		painCave.isFatal = 1;
224		simError();
225		}
226	<	catch (OOPSEException& e) {
226	>	catch (OpenMDException& e) {
227		sprintf(painCave.errMsg,
228		"%s\n",
229		e.getMessage().c_str());
#	Line 230 | Line 238 | namespace oopse {
238		simError();
239		}
240
241	+	simParams->setMDfileVersion(mdFileVersion);
242		return simParams;
243		}
244
245		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
246		bool loadInitCoords) {
247	<
247	>
248		const int bufferSize = 65535;
249		char buffer[bufferSize];
250		int lineNo = 0;
251		std::string mdRawData;
252		int metaDataBlockStart = -1;
253		int metaDataBlockEnd = -1;
254	<	int i;
255	<	int mdOffset;
254	>	int i, j;
255	>	streamoff mdOffset;
256	>	int mdFileVersion;
257
258	+	// Create a string for embedding the version information in the MetaData
259	+	std::string version;
260	+	version.assign("## Last run using OpenMD Version: ");
261	+	version.append(OPENMD_VERSION_MAJOR);
262	+	version.append(".");
263	+	version.append(OPENMD_VERSION_MINOR);
264	+
265	+	std::string svnrev;
266	+	//convert a macro from compiler to a string in c++
267	+	STR_DEFINE(svnrev, SVN_REV );
268	+	version.append(" Revision: ");
269	+	// If there's no SVN revision, just call this the RELEASE revision.
270	+	if (!svnrev.empty()) {
271	+	version.append(svnrev);
272	+	} else {
273	+	version.append("RELEASE");
274	+	}
275	+
276		#ifdef IS_MPI
277		const int masterNode = 0;
278		if (worldRank == masterNode) {
279		#endif
280
281	<	std::ifstream mdFile_(mdFileName.c_str());
281	>	std::ifstream mdFile_;
282	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
283
284		if (mdFile_.fail()) {
285		sprintf(painCave.errMsg,
#	Line 263 | Line 292 | namespace oopse {
292		mdFile_.getline(buffer, bufferSize);
293		++lineNo;
294		std::string line = trimLeftCopy(buffer);
295	<	i = CaseInsensitiveFind(line, "<OOPSE");
296	<	if (i == string::npos) {
295	>	i = CaseInsensitiveFind(line, "<OpenMD");
296	>	if (static_cast<size_t>(i) == string::npos) {
297	>	// try the older file strings to see if that works:
298	>	i = CaseInsensitiveFind(line, "<OOPSE");
299	>	}
300	>
301	>	if (static_cast<size_t>(i) == string::npos) {
302	>	// still no luck!
303		sprintf(painCave.errMsg,
304	<	"SimCreator: File: %s is not an OOPSE file!\n",
304	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
305		mdFileName.c_str());
306		painCave.isFatal = 1;
307		simError();
308		}
309	+
310	+	// found the correct opening string, now try to get the file
311	+	// format version number.
312
313	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
314	+	std::string fileType = tokenizer.nextToken();
315	+	toUpper(fileType);
316	+
317	+	mdFileVersion = 0;
318	+
319	+	if (fileType == "OPENMD") {
320	+	while (tokenizer.hasMoreTokens()) {
321	+	std::string token(tokenizer.nextToken());
322	+	toUpper(token);
323	+	if (token == "VERSION") {
324	+	mdFileVersion = tokenizer.nextTokenAsInt();
325	+	break;
326	+	}
327	+	}
328	+	}
329	+
330		//scan through the input stream and find MetaData tag
331		while(mdFile_.getline(buffer, bufferSize)) {
332		++lineNo;
#	Line 312 | Line 367 | namespace oopse {
367
368		mdRawData.clear();
369
370	+	bool foundVersion = false;
371	+
372		for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
373		mdFile_.getline(buffer, bufferSize);
374	<	mdRawData += buffer;
374	>	std::string line = trimLeftCopy(buffer);
375	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
376	>	if (static_cast<size_t>(j) != string::npos) {
377	>	foundVersion = true;
378	>	mdRawData += version;
379	>	} else {
380	>	mdRawData += buffer;
381	>	}
382		mdRawData += "\n";
383		}
384	<
384	>
385	>	if (!foundVersion) mdRawData += version + "\n";
386	>
387		mdFile_.close();
388
389		#ifdef IS_MPI
#	Line 327 | Line 393 | namespace oopse {
393		std::stringstream rawMetaDataStream(mdRawData);
394
395		//parse meta-data file
396	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
396	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
397	>	metaDataBlockStart + 1);
398
399		//create the force field
400	<	ForceField * ff = ForceFieldFactory::getInstance()
401	<	->createForceField(simParams->getForceField());
335	<
400	>	ForceField * ff = new ForceField(simParams->getForceField());
401	>
402		if (ff == NULL) {
403		sprintf(painCave.errMsg,
404		"ForceField Factory can not create %s force field\n",
#	Line 365 | Line 431 | namespace oopse {
431		}
432
433		ff->parse(forcefieldFileName);
368	–	ff->setFortranForceOptions();
434		//create SimInfo
435		SimInfo * info = new SimInfo(ff, simParams);
436
#	Line 383 | Line 448 | namespace oopse {
448		//create the molecules
449		createMolecules(info);
450
451	<
451	>	//find the storage layout
452	>
453	>	int storageLayout = computeStorageLayout(info);
454	>
455		//allocate memory for DataStorage(circular reference, need to
456		//break it)
457	<	info->setSnapshotManager(new SimSnapshotManager(info));
457	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
458
459		//set the global index of atoms, rigidbodies and cutoffgroups
460		//(only need to be set once, the global index will never change
#	Line 395 | Line 463 | namespace oopse {
463		//responsibility to LocalIndexManager.
464		setGlobalIndex(info);
465
466	<	//Although addExcludePairs is called inside SimInfo's addMolecule
466	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
467		//method, at that point atoms don't have the global index yet
468		//(their global index are all initialized to -1).  Therefore we
469	<	//have to call addExcludePairs explicitly here. A way to work
469	>	//have to call addInteractionPairs explicitly here. A way to work
470		//around is that we can determine the beginning global indices of
471		//atoms before they get created.
472		SimInfo::MoleculeIterator mi;
473		Molecule* mol;
474		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
475	<	info->addExcludePairs(mol);
475	>	info->addInteractionPairs(mol);
476		}
477
478		if (loadInitCoords)
479		loadCoordinates(info, mdFileName);
412	–
480		return info;
481		}
482
#	Line 444 | Line 511 | namespace oopse {
511
512		#ifdef IS_MPI
513		void SimCreator::divideMolecules(SimInfo *info) {
447	–	RealType numerator;
448	–	RealType denominator;
449	–	RealType precast;
450	–	RealType x;
451	–	RealType y;
514		RealType a;
453	–	int old_atoms;
454	–	int add_atoms;
455	–	int new_atoms;
456	–	int nTarget;
457	–	int done;
458	–	int i;
459	–	int j;
460	–	int loops;
461	–	int which_proc;
515		int nProcessors;
516		std::vector<int> atomsPerProc;
517		int nGlobalMols = info->getNGlobalMolecules();
518	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
518	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
519	>	// error
520	>	// condition:
521
522	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
522	>	nProcessors = MPI::COMM_WORLD.Get_size();
523
524		if (nProcessors > nGlobalMols) {
525		sprintf(painCave.errMsg,
#	Line 473 | Line 528 | namespace oopse {
528		"\tthe number of molecules.  This will not result in a \n"
529		"\tusable division of atoms for force decomposition.\n"
530		"\tEither try a smaller number of processors, or run the\n"
531	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
531	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
532	>	nGlobalMols);
533
534		painCave.isFatal = 1;
535		simError();
536		}
537
482	–	int seedValue;
538		Globals * simParams = info->getSimParams();
539	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
539	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
540	>	//random number generator
541		if (simParams->haveSeed()) {
542	<	seedValue = simParams->getSeed();
542	>	int seedValue = simParams->getSeed();
543		myRandom = new SeqRandNumGen(seedValue);
544		}else {
545		myRandom = new SeqRandNumGen();
#	Line 496 | Line 552 | namespace oopse {
552		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
553
554		if (worldRank == 0) {
555	<	numerator = info->getNGlobalAtoms();
556	<	denominator = nProcessors;
557	<	precast = numerator / denominator;
558	<	nTarget = (int)(precast + 0.5);
555	>	RealType numerator = info->getNGlobalAtoms();
556	>	RealType denominator = nProcessors;
557	>	RealType precast = numerator / denominator;
558	>	int nTarget = (int)(precast + 0.5);
559
560	<	for(i = 0; i < nGlobalMols; i++) {
561	<	done = 0;
562	<	loops = 0;
560	>	for(int i = 0; i < nGlobalMols; i++) {
561	>
562	>	int done = 0;
563	>	int loops = 0;
564
565		while (!done) {
566		loops++;
567
568		// Pick a processor at random
569
570	<	which_proc = (int) (myRandom->rand() * nProcessors);
570	>	int which_proc = (int) (myRandom->rand() * nProcessors);
571
572		//get the molecule stamp first
573		int stampId = info->getMoleculeStampId(i);
574		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
575
576		// How many atoms does this processor have so far?
577	<	old_atoms = atomsPerProc[which_proc];
578	<	add_atoms = moleculeStamp->getNAtoms();
579	<	new_atoms = old_atoms + add_atoms;
577	>	int old_atoms = atomsPerProc[which_proc];
578	>	int add_atoms = moleculeStamp->getNAtoms();
579	>	int new_atoms = old_atoms + add_atoms;
580
581		// If we've been through this loop too many times, we need
582		// to just give up and assign the molecule to this processor
583		// and be done with it.
584
585		if (loops > 100) {
586	+
587		sprintf(painCave.errMsg,
588	<	"I've tried 100 times to assign molecule %d to a "
589	<	" processor, but can't find a good spot.\n"
590	<	"I'm assigning it at random to processor %d.\n",
588	>	"There have been 100 attempts to assign molecule %d to an\n"
589	>	"\tunderworked processor, but there's no good place to\n"
590	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
591		i, which_proc);
592	<
592	>
593		painCave.isFatal = 0;
594	+	painCave.severity = OPENMD_INFO;
595		simError();
596
597		molToProcMap[i] = which_proc;
#	Line 561 | Line 620 | namespace oopse {
620		//           Pacc(x) = exp(- a * x)
621		// where a = penalty / (average atoms per molecule)
622
623	<	x = (RealType)(new_atoms - nTarget);
624	<	y = myRandom->rand();
623	>	RealType x = (RealType)(new_atoms - nTarget);
624	>	RealType y = myRandom->rand();
625
626		if (y < exp(- a * x)) {
627		molToProcMap[i] = which_proc;
#	Line 577 | Line 636 | namespace oopse {
636		}
637
638		delete myRandom;
639	<
639	>
640		// Spray out this nonsense to all other processors:
641	<
583	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
641	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
642		} else {
643
644		// Listen to your marching orders from processor 0:
645	<
646	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
645	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
646	>
647		}
648
649		info->setMolToProcMap(molToProcMap);
650		sprintf(checkPointMsg,
651		"Successfully divided the molecules among the processors.\n");
652	<	MPIcheckPoint();
652	>	errorCheckPoint();
653		}
654
655		#endif
#	Line 608 | Line 666 | namespace oopse {
666		#endif
667
668		stampId = info->getMoleculeStampId(i);
669	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
670	<	stampId, i, info->getLocalIndexManager());
669	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
670	>	info->getMoleculeStamp(stampId),
671	>	stampId, i,
672	>	info->getLocalIndexManager());
673
674		info->addMolecule(mol);
675
#	Line 621 | Line 681 | namespace oopse {
681
682		} //end for(int i=0)
683		}
684	+
685	+	int SimCreator::computeStorageLayout(SimInfo* info) {
686	+
687	+	Globals* simParams = info->getSimParams();
688	+	int nRigidBodies = info->getNGlobalRigidBodies();
689	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
690	+	set<AtomType*>::iterator i;
691	+	bool hasDirectionalAtoms = false;
692	+	bool hasFixedCharge = false;
693	+	bool hasDipoles = false;
694	+	bool hasQuadrupoles = false;
695	+	bool hasPolarizable = false;
696	+	bool hasFluctuatingCharge = false;
697	+	bool hasMetallic = false;
698	+	int storageLayout = 0;
699	+	storageLayout |= DataStorage::dslPosition;
700	+	storageLayout |= DataStorage::dslVelocity;
701	+	storageLayout |= DataStorage::dslForce;
702	+
703	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
704	+
705	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
706	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
707	+	EAMAdapter ea = EAMAdapter( (*i) );
708	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
709	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
710	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
711	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
712	+
713	+	if (da.isDirectional()){
714	+	hasDirectionalAtoms = true;
715	+	}
716	+	if (ma.isDipole()){
717	+	hasDipoles = true;
718	+	}
719	+	if (ma.isQuadrupole()){
720	+	hasQuadrupoles = true;
721	+	}
722	+	if (ea.isEAM() || sca.isSuttonChen()){
723	+	hasMetallic = true;
724	+	}
725	+	if ( fca.isFixedCharge() ){
726	+	hasFixedCharge = true;
727	+	}
728	+	if ( fqa.isFluctuatingCharge() ){
729	+	hasFluctuatingCharge = true;
730	+	}
731	+	if ( pa.isPolarizable() ){
732	+	hasPolarizable = true;
733	+	}
734	+	}
735
736	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
737	+	storageLayout |= DataStorage::dslAmat;
738	+	if(storageLayout & DataStorage::dslVelocity) {
739	+	storageLayout |= DataStorage::dslAngularMomentum;
740	+	}
741	+	if (storageLayout & DataStorage::dslForce) {
742	+	storageLayout |= DataStorage::dslTorque;
743	+	}
744	+	}
745	+	if (hasDipoles) {
746	+	storageLayout |= DataStorage::dslDipole;
747	+	}
748	+	if (hasQuadrupoles) {
749	+	storageLayout |= DataStorage::dslQuadrupole;
750	+	}
751	+	if (hasFixedCharge || hasFluctuatingCharge) {
752	+	storageLayout |= DataStorage::dslSkippedCharge;
753	+	}
754	+	if (hasMetallic) {
755	+	storageLayout |= DataStorage::dslDensity;
756	+	storageLayout |= DataStorage::dslFunctional;
757	+	storageLayout |= DataStorage::dslFunctionalDerivative;
758	+	}
759	+	if (hasPolarizable) {
760	+	storageLayout |= DataStorage::dslElectricField;
761	+	}
762	+	if (hasFluctuatingCharge){
763	+	storageLayout |= DataStorage::dslFlucQPosition;
764	+	if(storageLayout & DataStorage::dslVelocity) {
765	+	storageLayout |= DataStorage::dslFlucQVelocity;
766	+	}
767	+	if (storageLayout & DataStorage::dslForce) {
768	+	storageLayout |= DataStorage::dslFlucQForce;
769	+	}
770	+	}
771	+
772	+	// if the user has asked for them, make sure we've got the memory for the
773	+	// objects defined.
774	+
775	+	if (simParams->getOutputParticlePotential()) {
776	+	storageLayout |= DataStorage::dslParticlePot;
777	+	}
778	+
779	+	if (simParams->havePrintHeatFlux()) {
780	+	if (simParams->getPrintHeatFlux()) {
781	+	storageLayout |= DataStorage::dslParticlePot;
782	+	}
783	+	}
784	+
785	+	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
786	+	storageLayout |= DataStorage::dslElectricField;
787	+	}
788	+
789	+	if (simParams->getOutputFluctuatingCharges()) {
790	+	storageLayout |= DataStorage::dslFlucQPosition;
791	+	storageLayout |= DataStorage::dslFlucQVelocity;
792	+	storageLayout |= DataStorage::dslFlucQForce;
793	+	}
794	+
795	+	info->setStorageLayout(storageLayout);
796	+
797	+	return storageLayout;
798	+	}
799	+
800		void SimCreator::setGlobalIndex(SimInfo *info) {
801		SimInfo::MoleculeIterator mi;
802		Molecule::AtomIterator ai;
#	Line 636 | Line 811 | namespace oopse {
811		int beginRigidBodyIndex;
812		int beginCutoffGroupIndex;
813		int nGlobalAtoms = info->getNGlobalAtoms();
814	<
640	<	/**@todo fixme */
641	<	#ifndef IS_MPI
814	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
815
816		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	–
817		//rigidbody's index begins right after atom's
818	<	beginRigidBodyIndex += info->getNGlobalAtoms();
819	<
820	<	for(mol = info->beginMolecule(mi); mol != NULL;
821	<	mol = info->nextMolecule(mi)) {
818	>	beginRigidBodyIndex = info->getNGlobalAtoms();
819	>	beginCutoffGroupIndex = 0;
820	>
821	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
822
823	<	//local index(index in DataStorge) of atom is important
824	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	<	atom->setGlobalIndex(beginAtomIndex++);
823	>	#ifdef IS_MPI
824	>	if (info->getMolToProc(i) == worldRank) {
825	>	#endif
826	>	// stuff to do if I own this molecule
827	>	mol = info->getMoleculeByGlobalIndex(i);
828	>
829	>	//local index(index in DataStorge) of atom is important
830	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
831	>	atom->setGlobalIndex(beginAtomIndex++);
832	>	}
833	>
834	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
835	>	rb = mol->nextRigidBody(ri)) {
836	>	rb->setGlobalIndex(beginRigidBodyIndex++);
837	>	}
838	>
839	>	//local index of cutoff group is trivial, it only depends on
840	>	//the order of travesing
841	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
842	>	cg = mol->nextCutoffGroup(ci)) {
843	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
844	>	}
845	>
846	>	#ifdef IS_MPI
847	>	}  else {
848	>
849	>	// stuff to do if I don't own this molecule
850	>
851	>	int stampId = info->getMoleculeStampId(i);
852	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
853	>
854	>	beginAtomIndex += stamp->getNAtoms();
855	>	beginRigidBodyIndex += stamp->getNRigidBodies();
856	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
857		}
858	<
859	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
860	<	rb = mol->nextRigidBody(ri)) {
861	<	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	<
858	>	#endif
859	>
860	>	} //end for(int i=0)
861	>
862		//fill globalGroupMembership
863		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
864		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 717 | Line 870 | namespace oopse {
870
871		}
872		}
873	<
873	>
874		#ifdef IS_MPI
875		// Since the globalGroupMembership has been zero filled and we've only
876		// poked values into the atoms we know, we can do an Allreduce
877		// to get the full globalGroupMembership array (We think).
878		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
879		// docs said we could.
880	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
881	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
882	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
880	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
881	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
882	>	&tmpGroupMembership[0], nGlobalAtoms,
883	>	MPI::INT, MPI::SUM);
884		info->setGlobalGroupMembership(tmpGroupMembership);
885		#else
886		info->setGlobalGroupMembership(globalGroupMembership);
887		#endif
888
889		//fill molMembership
890	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
890	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
891	>	info->getNGlobalRigidBodies(), 0);
892
893	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
894	<
893	>	for(mol = info->beginMolecule(mi); mol != NULL;
894	>	mol = info->nextMolecule(mi)) {
895		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
897		}
898	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
899	+	rb = mol->nextRigidBody(ri)) {
900	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
901	+	}
902		}
903
904		#ifdef IS_MPI
905	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
905	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
906	>	info->getNGlobalRigidBodies(), 0);
907	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
908	>	nGlobalAtoms + nGlobalRigidBodies,
909	>	MPI::INT, MPI::SUM);
910
748	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
749	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
750	–
911		info->setGlobalMolMembership(tmpMolMembership);
912		#else
913		info->setGlobalMolMembership(globalMolMembership);
#	Line 757 | Line 917 | namespace oopse {
917		// here the molecules are listed by their global indices.
918
919		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
920	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
920	>	for (mol = info->beginMolecule(mi); mol != NULL;
921	>	mol = info->nextMolecule(mi)) {
922		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
923		}
924
925		#ifdef IS_MPI
926		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
927	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
928	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
927	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
928	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
929		#else
930		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
931		#endif
932
933	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
934	<
935	<	int startingIndex = 0;
936	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
937	<	startingIOIndexForMol[i] = startingIndex;
938	<	startingIndex += numIntegrableObjectsPerMol[i];
939	<	}
940	<
941	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
942	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
933	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
934	>
935	>	int startingIndex = 0;
936	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
937	>	startingIOIndexForMol[i] = startingIndex;
938	>	startingIndex += numIntegrableObjectsPerMol[i];
939	>	}
940	>
941	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
942	>	for (mol = info->beginMolecule(mi); mol != NULL;
943	>	mol = info->nextMolecule(mi)) {
944		int myGlobalIndex = mol->getGlobalIndex();
945		int globalIO = startingIOIndexForMol[myGlobalIndex];
946	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
947	<	integrableObject = mol->nextIntegrableObject(ioi)) {
948	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
949	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
950	<	globalIO++;
946	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
947	>	sd = mol->nextIntegrableObject(ioi)) {
948	>	sd->setGlobalIntegrableObjectIndex(globalIO);
949	>	IOIndexToIntegrableObject[globalIO] = sd;
950	>	globalIO++;
951		}
952		}
953	<
954	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
955	<
953	>
954	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
955	>
956		}
957
958		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
797	–	Globals* simParams;
798	–	simParams = info->getSimParams();
959
800	–
960		DumpReader reader(info, mdFileName);
961		int nframes = reader.getNFrames();
962
#	Line 811 | Line 970 | int startingIndex = 0;
970		painCave.isFatal = 1;
971		simError();
972		}
814	–
973		//copy the current snapshot to previous snapshot
974		info->getSnapshotManager()->advance();
975		}
976
977	<	} //end namespace oopse
977	>	} //end namespace OpenMD
978
979

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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