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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 1880 by gezelter, Mon Jun 17 18:28:30 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, 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);
108
109		#ifdef IS_MPI
110		//brocasting the stream size
111		streamSize = ppStream.str().size() +1;
112	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
113	<
114	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106	<
107	<
112	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
113	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
114	>
115		} else {
116	+	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
117	+
118		//get stream size
119	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
120	<
119	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
120	>
121		char* buf = new char[streamSize];
122		assert(buf);
123
124		//receive file content
125	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
125	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
126
127		ppStream.str(buf);
128	<	delete buf;
120	<
128	>	delete [] buf;
129		}
130		#endif
131		// Create a scanner that reads from the input stream
#	Line 145 | Line 153 | namespace oopse {
153		treeParser.initializeASTFactory(factory);
154		treeParser.setASTFactory(&factory);
155		simParams = treeParser.walkTree(parser.getAST());
148	–
156		}
157
158
#	Line 215 | Line 222 | namespace oopse {
222		painCave.isFatal = 1;
223		simError();
224		}
225	<	catch (OOPSEException& e) {
225	>	catch (OpenMDException& e) {
226		sprintf(painCave.errMsg,
227		"%s\n",
228		e.getMessage().c_str());
#	Line 230 | Line 237 | namespace oopse {
237		simError();
238		}
239
240	+	simParams->setMDfileVersion(mdFileVersion);
241		return simParams;
242		}
243
244		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
245		bool loadInitCoords) {
246	<
246	>
247		const int bufferSize = 65535;
248		char buffer[bufferSize];
249		int lineNo = 0;
250		std::string mdRawData;
251		int metaDataBlockStart = -1;
252		int metaDataBlockEnd = -1;
253	<	int i;
254	<	int mdOffset;
253	>	int i, j;
254	>	streamoff mdOffset;
255	>	int mdFileVersion;
256
257	+	// Create a string for embedding the version information in the MetaData
258	+	std::string version;
259	+	version.assign("## Last run using OpenMD Version: ");
260	+	version.append(OPENMD_VERSION_MAJOR);
261	+	version.append(".");
262	+	version.append(OPENMD_VERSION_MINOR);
263	+
264	+	std::string svnrev;
265	+	//convert a macro from compiler to a string in c++
266	+	STR_DEFINE(svnrev, SVN_REV );
267	+	version.append(" Revision: ");
268	+	// If there's no SVN revision, just call this the RELEASE revision.
269	+	if (!svnrev.empty()) {
270	+	version.append(svnrev);
271	+	} else {
272	+	version.append("RELEASE");
273	+	}
274	+
275		#ifdef IS_MPI
276		const int masterNode = 0;
277		if (worldRank == masterNode) {
278		#endif
279
280	<	std::ifstream mdFile_(mdFileName.c_str());
280	>	std::ifstream mdFile_;
281	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
282
283		if (mdFile_.fail()) {
284		sprintf(painCave.errMsg,
#	Line 263 | Line 291 | namespace oopse {
291		mdFile_.getline(buffer, bufferSize);
292		++lineNo;
293		std::string line = trimLeftCopy(buffer);
294	<	i = CaseInsensitiveFind(line, "<OOPSE");
295	<	if (i == string::npos) {
294	>	i = CaseInsensitiveFind(line, "<OpenMD");
295	>	if (static_cast<size_t>(i) == string::npos) {
296	>	// try the older file strings to see if that works:
297	>	i = CaseInsensitiveFind(line, "<OOPSE");
298	>	}
299	>
300	>	if (static_cast<size_t>(i) == string::npos) {
301	>	// still no luck!
302		sprintf(painCave.errMsg,
303	<	"SimCreator: File: %s is not an OOPSE file!\n",
303	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
304		mdFileName.c_str());
305		painCave.isFatal = 1;
306		simError();
307		}
308	+
309	+	// found the correct opening string, now try to get the file
310	+	// format version number.
311
312	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
313	+	std::string fileType = tokenizer.nextToken();
314	+	toUpper(fileType);
315	+
316	+	mdFileVersion = 0;
317	+
318	+	if (fileType == "OPENMD") {
319	+	while (tokenizer.hasMoreTokens()) {
320	+	std::string token(tokenizer.nextToken());
321	+	toUpper(token);
322	+	if (token == "VERSION") {
323	+	mdFileVersion = tokenizer.nextTokenAsInt();
324	+	break;
325	+	}
326	+	}
327	+	}
328	+
329		//scan through the input stream and find MetaData tag
330		while(mdFile_.getline(buffer, bufferSize)) {
331		++lineNo;
#	Line 312 | Line 366 | namespace oopse {
366
367		mdRawData.clear();
368
369	+	bool foundVersion = false;
370	+
371		for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
372		mdFile_.getline(buffer, bufferSize);
373	<	mdRawData += buffer;
373	>	std::string line = trimLeftCopy(buffer);
374	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
375	>	if (static_cast<size_t>(j) != string::npos) {
376	>	foundVersion = true;
377	>	mdRawData += version;
378	>	} else {
379	>	mdRawData += buffer;
380	>	}
381		mdRawData += "\n";
382		}
383	<
383	>
384	>	if (!foundVersion) mdRawData += version + "\n";
385	>
386		mdFile_.close();
387
388		#ifdef IS_MPI
#	Line 327 | Line 392 | namespace oopse {
392		std::stringstream rawMetaDataStream(mdRawData);
393
394		//parse meta-data file
395	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
395	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
396	>	metaDataBlockStart + 1);
397
398		//create the force field
399	<	ForceField * ff = ForceFieldFactory::getInstance()
400	<	->createForceField(simParams->getForceField());
335	<
399	>	ForceField * ff = new ForceField(simParams->getForceField());
400	>
401		if (ff == NULL) {
402		sprintf(painCave.errMsg,
403		"ForceField Factory can not create %s force field\n",
#	Line 365 | Line 430 | namespace oopse {
430		}
431
432		ff->parse(forcefieldFileName);
368	–	ff->setFortranForceOptions();
433		//create SimInfo
434		SimInfo * info = new SimInfo(ff, simParams);
435
#	Line 383 | Line 447 | namespace oopse {
447		//create the molecules
448		createMolecules(info);
449
450	<
450	>	//find the storage layout
451	>
452	>	int storageLayout = computeStorageLayout(info);
453	>
454		//allocate memory for DataStorage(circular reference, need to
455		//break it)
456	<	info->setSnapshotManager(new SimSnapshotManager(info));
456	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
457
458		//set the global index of atoms, rigidbodies and cutoffgroups
459		//(only need to be set once, the global index will never change
#	Line 395 | Line 462 | namespace oopse {
462		//responsibility to LocalIndexManager.
463		setGlobalIndex(info);
464
465	<	//Although addExcludePairs is called inside SimInfo's addMolecule
465	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
466		//method, at that point atoms don't have the global index yet
467		//(their global index are all initialized to -1).  Therefore we
468	<	//have to call addExcludePairs explicitly here. A way to work
468	>	//have to call addInteractionPairs explicitly here. A way to work
469		//around is that we can determine the beginning global indices of
470		//atoms before they get created.
471		SimInfo::MoleculeIterator mi;
472		Molecule* mol;
473		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
474	<	info->addExcludePairs(mol);
474	>	info->addInteractionPairs(mol);
475		}
476
477		if (loadInitCoords)
478		loadCoordinates(info, mdFileName);
412	–
479		return info;
480		}
481
#	Line 444 | Line 510 | namespace oopse {
510
511		#ifdef IS_MPI
512		void SimCreator::divideMolecules(SimInfo *info) {
447	–	RealType numerator;
448	–	RealType denominator;
449	–	RealType precast;
450	–	RealType x;
451	–	RealType y;
513		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;
514		int nProcessors;
515		std::vector<int> atomsPerProc;
516		int nGlobalMols = info->getNGlobalMolecules();
517	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
517	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
518	>	// error
519	>	// condition:
520
521	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
521	>	nProcessors = MPI::COMM_WORLD.Get_size();
522
523		if (nProcessors > nGlobalMols) {
524		sprintf(painCave.errMsg,
#	Line 473 | Line 527 | namespace oopse {
527		"\tthe number of molecules.  This will not result in a \n"
528		"\tusable division of atoms for force decomposition.\n"
529		"\tEither try a smaller number of processors, or run the\n"
530	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
530	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
531	>	nGlobalMols);
532
533		painCave.isFatal = 1;
534		simError();
535		}
536
482	–	int seedValue;
537		Globals * simParams = info->getSimParams();
538	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
538	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
539	>	//random number generator
540		if (simParams->haveSeed()) {
541	<	seedValue = simParams->getSeed();
541	>	int seedValue = simParams->getSeed();
542		myRandom = new SeqRandNumGen(seedValue);
543		}else {
544		myRandom = new SeqRandNumGen();
#	Line 496 | Line 551 | namespace oopse {
551		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
552
553		if (worldRank == 0) {
554	<	numerator = info->getNGlobalAtoms();
555	<	denominator = nProcessors;
556	<	precast = numerator / denominator;
557	<	nTarget = (int)(precast + 0.5);
554	>	RealType numerator = info->getNGlobalAtoms();
555	>	RealType denominator = nProcessors;
556	>	RealType precast = numerator / denominator;
557	>	int nTarget = (int)(precast + 0.5);
558
559	<	for(i = 0; i < nGlobalMols; i++) {
560	<	done = 0;
561	<	loops = 0;
559	>	for(int i = 0; i < nGlobalMols; i++) {
560	>
561	>	int done = 0;
562	>	int loops = 0;
563
564		while (!done) {
565		loops++;
566
567		// Pick a processor at random
568
569	<	which_proc = (int) (myRandom->rand() * nProcessors);
569	>	int which_proc = (int) (myRandom->rand() * nProcessors);
570
571		//get the molecule stamp first
572		int stampId = info->getMoleculeStampId(i);
573		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
574
575		// How many atoms does this processor have so far?
576	<	old_atoms = atomsPerProc[which_proc];
577	<	add_atoms = moleculeStamp->getNAtoms();
578	<	new_atoms = old_atoms + add_atoms;
576	>	int old_atoms = atomsPerProc[which_proc];
577	>	int add_atoms = moleculeStamp->getNAtoms();
578	>	int new_atoms = old_atoms + add_atoms;
579
580		// If we've been through this loop too many times, we need
581		// to just give up and assign the molecule to this processor
582		// and be done with it.
583
584		if (loops > 100) {
585	+
586		sprintf(painCave.errMsg,
587	<	"I've tried 100 times to assign molecule %d to a "
588	<	" processor, but can't find a good spot.\n"
589	<	"I'm assigning it at random to processor %d.\n",
587	>	"There have been 100 attempts to assign molecule %d to an\n"
588	>	"\tunderworked processor, but there's no good place to\n"
589	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
590		i, which_proc);
591	<
591	>
592		painCave.isFatal = 0;
593	+	painCave.severity = OPENMD_INFO;
594		simError();
595
596		molToProcMap[i] = which_proc;
#	Line 561 | Line 619 | namespace oopse {
619		//           Pacc(x) = exp(- a * x)
620		// where a = penalty / (average atoms per molecule)
621
622	<	x = (RealType)(new_atoms - nTarget);
623	<	y = myRandom->rand();
622	>	RealType x = (RealType)(new_atoms - nTarget);
623	>	RealType y = myRandom->rand();
624
625		if (y < exp(- a * x)) {
626		molToProcMap[i] = which_proc;
#	Line 577 | Line 635 | namespace oopse {
635		}
636
637		delete myRandom;
638	<
638	>
639		// Spray out this nonsense to all other processors:
640	<
583	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
640	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
641		} else {
642
643		// Listen to your marching orders from processor 0:
644	<
645	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
645	>
646		}
647
648		info->setMolToProcMap(molToProcMap);
649		sprintf(checkPointMsg,
650		"Successfully divided the molecules among the processors.\n");
651	<	MPIcheckPoint();
651	>	errorCheckPoint();
652		}
653
654		#endif
#	Line 608 | Line 665 | namespace oopse {
665		#endif
666
667		stampId = info->getMoleculeStampId(i);
668	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
669	<	stampId, i, info->getLocalIndexManager());
668	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
669	>	info->getMoleculeStamp(stampId),
670	>	stampId, i,
671	>	info->getLocalIndexManager());
672
673		info->addMolecule(mol);
674
#	Line 622 | Line 681 | namespace oopse {
681		} //end for(int i=0)
682		}
683
684	+	int SimCreator::computeStorageLayout(SimInfo* info) {
685	+
686	+	Globals* simParams = info->getSimParams();
687	+	int nRigidBodies = info->getNGlobalRigidBodies();
688	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
689	+	set<AtomType*>::iterator i;
690	+	bool hasDirectionalAtoms = false;
691	+	bool hasFixedCharge = false;
692	+	bool hasDipoles = false;
693	+	bool hasQuadrupoles = false;
694	+	bool hasPolarizable = false;
695	+	bool hasFluctuatingCharge = false;
696	+	bool hasMetallic = false;
697	+	int storageLayout = 0;
698	+	storageLayout |= DataStorage::dslPosition;
699	+	storageLayout |= DataStorage::dslVelocity;
700	+	storageLayout |= DataStorage::dslForce;
701	+
702	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
703	+
704	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
705	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
706	+	EAMAdapter ea = EAMAdapter( (*i) );
707	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
708	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
709	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
710	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
711	+
712	+	if (da.isDirectional()){
713	+	hasDirectionalAtoms = true;
714	+	}
715	+	if (ma.isDipole()){
716	+	hasDipoles = true;
717	+	}
718	+	if (ma.isQuadrupole()){
719	+	hasQuadrupoles = true;
720	+	}
721	+	if (ea.isEAM() || sca.isSuttonChen()){
722	+	hasMetallic = true;
723	+	}
724	+	if ( fca.isFixedCharge() ){
725	+	hasFixedCharge = true;
726	+	}
727	+	if ( fqa.isFluctuatingCharge() ){
728	+	hasFluctuatingCharge = true;
729	+	}
730	+	if ( pa.isPolarizable() ){
731	+	hasPolarizable = true;
732	+	}
733	+	}
734	+
735	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
736	+	storageLayout |= DataStorage::dslAmat;
737	+	if(storageLayout & DataStorage::dslVelocity) {
738	+	storageLayout |= DataStorage::dslAngularMomentum;
739	+	}
740	+	if (storageLayout & DataStorage::dslForce) {
741	+	storageLayout |= DataStorage::dslTorque;
742	+	}
743	+	}
744	+	if (hasDipoles) {
745	+	storageLayout |= DataStorage::dslDipole;
746	+	}
747	+	if (hasQuadrupoles) {
748	+	storageLayout |= DataStorage::dslQuadrupole;
749	+	}
750	+	if (hasFixedCharge || hasFluctuatingCharge) {
751	+	storageLayout |= DataStorage::dslSkippedCharge;
752	+	}
753	+	if (hasMetallic) {
754	+	storageLayout |= DataStorage::dslDensity;
755	+	storageLayout |= DataStorage::dslFunctional;
756	+	storageLayout |= DataStorage::dslFunctionalDerivative;
757	+	}
758	+	if (hasPolarizable) {
759	+	storageLayout |= DataStorage::dslElectricField;
760	+	}
761	+	if (hasFluctuatingCharge){
762	+	storageLayout |= DataStorage::dslFlucQPosition;
763	+	if(storageLayout & DataStorage::dslVelocity) {
764	+	storageLayout |= DataStorage::dslFlucQVelocity;
765	+	}
766	+	if (storageLayout & DataStorage::dslForce) {
767	+	storageLayout |= DataStorage::dslFlucQForce;
768	+	}
769	+	}
770	+
771	+	// if the user has asked for them, make sure we've got the memory for the
772	+	// objects defined.
773	+
774	+	if (simParams->getOutputParticlePotential()) {
775	+	storageLayout |= DataStorage::dslParticlePot;
776	+	}
777	+
778	+	if (simParams->havePrintHeatFlux()) {
779	+	if (simParams->getPrintHeatFlux()) {
780	+	storageLayout |= DataStorage::dslParticlePot;
781	+	}
782	+	}
783	+
784	+	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
785	+	storageLayout |= DataStorage::dslElectricField;
786	+	}
787	+
788	+	if (simParams->getOutputFluctuatingCharges()) {
789	+	storageLayout |= DataStorage::dslFlucQPosition;
790	+	storageLayout |= DataStorage::dslFlucQVelocity;
791	+	storageLayout |= DataStorage::dslFlucQForce;
792	+	}
793	+
794	+	info->setStorageLayout(storageLayout);
795	+
796	+	return storageLayout;
797	+	}
798	+
799		void SimCreator::setGlobalIndex(SimInfo *info) {
800		SimInfo::MoleculeIterator mi;
801		Molecule::AtomIterator ai;
#	Line 636 | Line 810 | namespace oopse {
810		int beginRigidBodyIndex;
811		int beginCutoffGroupIndex;
812		int nGlobalAtoms = info->getNGlobalAtoms();
813	<
640	<	/**@todo fixme */
641	<	#ifndef IS_MPI
813	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
814
815		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	–
816		//rigidbody's index begins right after atom's
817	<	beginRigidBodyIndex += info->getNGlobalAtoms();
818	<
819	<	for(mol = info->beginMolecule(mi); mol != NULL;
820	<	mol = info->nextMolecule(mi)) {
817	>	beginRigidBodyIndex = info->getNGlobalAtoms();
818	>	beginCutoffGroupIndex = 0;
819	>
820	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
821
822	<	//local index(index in DataStorge) of atom is important
823	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824	<	atom->setGlobalIndex(beginAtomIndex++);
822	>	#ifdef IS_MPI
823	>	if (info->getMolToProc(i) == worldRank) {
824	>	#endif
825	>	// stuff to do if I own this molecule
826	>	mol = info->getMoleculeByGlobalIndex(i);
827	>
828	>	//local index(index in DataStorge) of atom is important
829	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	>	atom->setGlobalIndex(beginAtomIndex++);
831	>	}
832	>
833	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
834	>	rb = mol->nextRigidBody(ri)) {
835	>	rb->setGlobalIndex(beginRigidBodyIndex++);
836	>	}
837	>
838	>	//local index of cutoff group is trivial, it only depends on
839	>	//the order of travesing
840	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
841	>	cg = mol->nextCutoffGroup(ci)) {
842	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
843	>	}
844	>
845	>	#ifdef IS_MPI
846	>	}  else {
847	>
848	>	// stuff to do if I don't own this molecule
849	>
850	>	int stampId = info->getMoleculeStampId(i);
851	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
852	>
853	>	beginAtomIndex += stamp->getNAtoms();
854	>	beginRigidBodyIndex += stamp->getNRigidBodies();
855	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
856		}
857	<
858	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
859	<	rb = mol->nextRigidBody(ri)) {
860	<	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	<
857	>	#endif
858	>
859	>	} //end for(int i=0)
860	>
861		//fill globalGroupMembership
862		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
863		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 717 | Line 869 | namespace oopse {
869
870		}
871		}
872	<
872	>
873		#ifdef IS_MPI
874		// Since the globalGroupMembership has been zero filled and we've only
875		// poked values into the atoms we know, we can do an Allreduce
876		// to get the full globalGroupMembership array (We think).
877		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
878		// docs said we could.
879	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
880	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
881	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
879	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
880	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
881	>	&tmpGroupMembership[0], nGlobalAtoms,
882	>	MPI::INT, MPI::SUM);
883		info->setGlobalGroupMembership(tmpGroupMembership);
884		#else
885		info->setGlobalGroupMembership(globalGroupMembership);
886		#endif
887
888		//fill molMembership
889	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
889	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
890	>	info->getNGlobalRigidBodies(), 0);
891
892	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
893	<
892	>	for(mol = info->beginMolecule(mi); mol != NULL;
893	>	mol = info->nextMolecule(mi)) {
894		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
896		}
897	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
898	+	rb = mol->nextRigidBody(ri)) {
899	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
900	+	}
901		}
902
903		#ifdef IS_MPI
904	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
904	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
905	>	info->getNGlobalRigidBodies(), 0);
906	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
907	>	nGlobalAtoms + nGlobalRigidBodies,
908	>	MPI::INT, MPI::SUM);
909
748	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
749	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
750	–
910		info->setGlobalMolMembership(tmpMolMembership);
911		#else
912		info->setGlobalMolMembership(globalMolMembership);
#	Line 757 | Line 916 | namespace oopse {
916		// here the molecules are listed by their global indices.
917
918		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
919	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
919	>	for (mol = info->beginMolecule(mi); mol != NULL;
920	>	mol = info->nextMolecule(mi)) {
921		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
922		}
923
924		#ifdef IS_MPI
925		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
926	<	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
927	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
926	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
927	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
928		#else
929		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
930		#endif
931
932	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
933	<
934	<	int startingIndex = 0;
935	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
936	<	startingIOIndexForMol[i] = startingIndex;
937	<	startingIndex += numIntegrableObjectsPerMol[i];
938	<	}
939	<
940	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
941	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
932	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
933	>
934	>	int startingIndex = 0;
935	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
936	>	startingIOIndexForMol[i] = startingIndex;
937	>	startingIndex += numIntegrableObjectsPerMol[i];
938	>	}
939	>
940	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
941	>	for (mol = info->beginMolecule(mi); mol != NULL;
942	>	mol = info->nextMolecule(mi)) {
943		int myGlobalIndex = mol->getGlobalIndex();
944		int globalIO = startingIOIndexForMol[myGlobalIndex];
945	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
946	<	integrableObject = mol->nextIntegrableObject(ioi)) {
947	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
948	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
949	<	globalIO++;
945	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
946	>	sd = mol->nextIntegrableObject(ioi)) {
947	>	sd->setGlobalIntegrableObjectIndex(globalIO);
948	>	IOIndexToIntegrableObject[globalIO] = sd;
949	>	globalIO++;
950		}
951		}
952	<
953	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
954	<
952	>
953	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
954	>
955		}
956
957		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
797	–	Globals* simParams;
798	–	simParams = info->getSimParams();
958
800	–
959		DumpReader reader(info, mdFileName);
960		int nframes = reader.getNFrames();
961
#	Line 811 | Line 969 | int startingIndex = 0;
969		painCave.isFatal = 1;
970		simError();
971		}
814	–
972		//copy the current snapshot to previous snapshot
973		info->getSnapshotManager()->advance();
974		}
975
976	<	} //end namespace oopse
976	>	} //end namespace OpenMD
977
978

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
Revision 1880 by gezelter, Mon Jun 17 18:28:30 2013 UTC

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