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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1976 by gezelter, Wed Mar 12 20:01:15 2014 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	+
50	+	#ifdef IS_MPI
51	+	#include "mpi.h"
52	+	#include "math/ParallelRandNumGen.hpp"
53	+	#endif
54	+
55		#include <exception>
56		#include <iostream>
57		#include <sstream>
#	Line 55 | Line 61
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67	+	#include "utils/Revision.hpp"
68		#include "math/SeqRandNumGen.hpp"
69		#include "mdParser/MDLexer.hpp"
70		#include "mdParser/MDParser.hpp"
#	Line 75 | Line 82
82		#include "antlr/NoViableAltForCharException.hpp"
83		#include "antlr/NoViableAltException.hpp"
84
85	<	#ifdef IS_MPI
86	<	#include "math/ParallelRandNumGen.hpp"
87	<	#endif
85	>	#include "types/DirectionalAdapter.hpp"
86	>	#include "types/MultipoleAdapter.hpp"
87	>	#include "types/EAMAdapter.hpp"
88	>	#include "types/SuttonChenAdapter.hpp"
89	>	#include "types/PolarizableAdapter.hpp"
90	>	#include "types/FixedChargeAdapter.hpp"
91	>	#include "types/FluctuatingChargeAdapter.hpp"
92
93	<	namespace oopse {
93	>
94	>	namespace OpenMD {
95
96	<	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
96	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
97		Globals* simParams = NULL;
98		try {
99
#	Line 90 | Line 102 | namespace oopse {
102		#ifdef IS_MPI
103		int streamSize;
104		const int masterNode = 0;
105	<	int commStatus;
105	>
106		if (worldRank == masterNode) {
107	<	#endif
108	<
107	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
108	>	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
109	>	#endif
110		SimplePreprocessor preprocessor;
111	<	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
111	>	preprocessor.preprocess(rawMetaDataStream, filename,
112	>	startOfMetaDataBlock, ppStream);
113
114		#ifdef IS_MPI
115	<	//brocasting the stream size
115	>	//broadcasting the stream size
116		streamSize = ppStream.str().size() +1;
117	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
117	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
118	>	MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
119	>	streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
120
121	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
122	<
123	<
121	>	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
122	>	// MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
123	>	//                       streamSize, MPI::CHAR, masterNode);
124	>
125		} else {
126	+
127	+	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
128	+	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
129	+
130		//get stream size
131	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
132	<
131	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
132	>	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
133		char* buf = new char[streamSize];
134		assert(buf);
135
136		//receive file content
137	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
138	<
118	<	ppStream.str(buf);
119	<	delete buf;
137	>	MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
138	>	// MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
139
140	+	ppStream.str(buf);
141	+	delete [] buf;
142		}
143		#endif
144		// Create a scanner that reads from the input stream
#	Line 139 | Line 160 | namespace oopse {
160		parser.initializeASTFactory(factory);
161		parser.setASTFactory(&factory);
162		parser.mdfile();
142	–
163		// Create a tree parser that reads information into Globals
164		MDTreeParser treeParser;
165		treeParser.initializeASTFactory(factory);
166		treeParser.setASTFactory(&factory);
167		simParams = treeParser.walkTree(parser.getAST());
148	–
168		}
169
170
#	Line 215 | Line 234 | namespace oopse {
234		painCave.isFatal = 1;
235		simError();
236		}
237	<	catch (OOPSEException& e) {
237	>	catch (OpenMDException& e) {
238		sprintf(painCave.errMsg,
239		"%s\n",
240		e.getMessage().c_str());
#	Line 230 | Line 249 | namespace oopse {
249		simError();
250		}
251
252	+	simParams->setMDfileVersion(mdFileVersion);
253		return simParams;
254		}
255
256		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
257		bool loadInitCoords) {
258	<
258	>
259		const int bufferSize = 65535;
260		char buffer[bufferSize];
261		int lineNo = 0;
262		std::string mdRawData;
263		int metaDataBlockStart = -1;
264		int metaDataBlockEnd = -1;
265	<	int i;
266	<	int mdOffset;
265	>	int i, j;
266	>	streamoff mdOffset;
267	>	int mdFileVersion;
268
269	+	// Create a string for embedding the version information in the MetaData
270	+	std::string version;
271	+	version.assign("## Last run using OpenMD Version: ");
272	+	version.append(OPENMD_VERSION_MAJOR);
273	+	version.append(".");
274	+	version.append(OPENMD_VERSION_MINOR);
275	+
276	+	std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
277	+	//convert a macro from compiler to a string in c++
278	+	// STR_DEFINE(svnrev, SVN_REV );
279	+	version.append(" Revision: ");
280	+	// If there's no SVN revision, just call this the RELEASE revision.
281	+	if (!svnrev.empty()) {
282	+	version.append(svnrev);
283	+	} else {
284	+	version.append("RELEASE");
285	+	}
286	+
287		#ifdef IS_MPI
288		const int masterNode = 0;
289		if (worldRank == masterNode) {
290		#endif
291
292	<	std::ifstream mdFile_(mdFileName.c_str());
292	>	std::ifstream mdFile_;
293	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
294
295		if (mdFile_.fail()) {
296		sprintf(painCave.errMsg,
#	Line 263 | Line 303 | namespace oopse {
303		mdFile_.getline(buffer, bufferSize);
304		++lineNo;
305		std::string line = trimLeftCopy(buffer);
306	<	i = CaseInsensitiveFind(line, "<OOPSE");
307	<	if (i == string::npos) {
306	>	i = CaseInsensitiveFind(line, "<OpenMD");
307	>	if (static_cast<size_t>(i) == string::npos) {
308	>	// try the older file strings to see if that works:
309	>	i = CaseInsensitiveFind(line, "<OOPSE");
310	>	}
311	>
312	>	if (static_cast<size_t>(i) == string::npos) {
313	>	// still no luck!
314		sprintf(painCave.errMsg,
315	<	"SimCreator: File: %s is not an OOPSE file!\n",
315	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
316		mdFileName.c_str());
317		painCave.isFatal = 1;
318		simError();
319		}
320	+
321	+	// found the correct opening string, now try to get the file
322	+	// format version number.
323
324	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
325	+	std::string fileType = tokenizer.nextToken();
326	+	toUpper(fileType);
327	+
328	+	mdFileVersion = 0;
329	+
330	+	if (fileType == "OPENMD") {
331	+	while (tokenizer.hasMoreTokens()) {
332	+	std::string token(tokenizer.nextToken());
333	+	toUpper(token);
334	+	if (token == "VERSION") {
335	+	mdFileVersion = tokenizer.nextTokenAsInt();
336	+	break;
337	+	}
338	+	}
339	+	}
340	+
341		//scan through the input stream and find MetaData tag
342		while(mdFile_.getline(buffer, bufferSize)) {
343		++lineNo;
#	Line 312 | Line 378 | namespace oopse {
378
379		mdRawData.clear();
380
381	+	bool foundVersion = false;
382	+
383		for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
384		mdFile_.getline(buffer, bufferSize);
385	<	mdRawData += buffer;
385	>	std::string line = trimLeftCopy(buffer);
386	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
387	>	if (static_cast<size_t>(j) != string::npos) {
388	>	foundVersion = true;
389	>	mdRawData += version;
390	>	} else {
391	>	mdRawData += buffer;
392	>	}
393		mdRawData += "\n";
394		}
395	<
395	>
396	>	if (!foundVersion) mdRawData += version + "\n";
397	>
398		mdFile_.close();
399
400		#ifdef IS_MPI
#	Line 327 | Line 404 | namespace oopse {
404		std::stringstream rawMetaDataStream(mdRawData);
405
406		//parse meta-data file
407	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
407	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
408	>	metaDataBlockStart + 1);
409
410		//create the force field
411	<	ForceField * ff = ForceFieldFactory::getInstance()
412	<	->createForceField(simParams->getForceField());
335	<
411	>	ForceField * ff = new ForceField(simParams->getForceField());
412	>
413		if (ff == NULL) {
414		sprintf(painCave.errMsg,
415		"ForceField Factory can not create %s force field\n",
#	Line 365 | Line 442 | namespace oopse {
442		}
443
444		ff->parse(forcefieldFileName);
368	–	ff->setFortranForceOptions();
445		//create SimInfo
446		SimInfo * info = new SimInfo(ff, simParams);
447
#	Line 383 | Line 459 | namespace oopse {
459		//create the molecules
460		createMolecules(info);
461
462	<
462	>	//find the storage layout
463	>
464	>	int storageLayout = computeStorageLayout(info);
465	>
466		//allocate memory for DataStorage(circular reference, need to
467		//break it)
468	<	info->setSnapshotManager(new SimSnapshotManager(info));
468	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
469
470		//set the global index of atoms, rigidbodies and cutoffgroups
471		//(only need to be set once, the global index will never change
#	Line 395 | Line 474 | namespace oopse {
474		//responsibility to LocalIndexManager.
475		setGlobalIndex(info);
476
477	<	//Although addExcludePairs is called inside SimInfo's addMolecule
477	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
478		//method, at that point atoms don't have the global index yet
479		//(their global index are all initialized to -1).  Therefore we
480	<	//have to call addExcludePairs explicitly here. A way to work
480	>	//have to call addInteractionPairs explicitly here. A way to work
481		//around is that we can determine the beginning global indices of
482		//atoms before they get created.
483		SimInfo::MoleculeIterator mi;
484		Molecule* mol;
485		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
486	<	info->addExcludePairs(mol);
486	>	info->addInteractionPairs(mol);
487		}
488
489		if (loadInitCoords)
490		loadCoordinates(info, mdFileName);
412	–
491		return info;
492		}
493
#	Line 444 | Line 522 | namespace oopse {
522
523		#ifdef IS_MPI
524		void SimCreator::divideMolecules(SimInfo *info) {
447	–	RealType numerator;
448	–	RealType denominator;
449	–	RealType precast;
450	–	RealType x;
451	–	RealType y;
525		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;
526		int nProcessors;
527		std::vector<int> atomsPerProc;
528		int nGlobalMols = info->getNGlobalMolecules();
529	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
529	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
530	>	// error
531	>	// condition:
532
533	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
533	>	MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
534	>	//nProcessors = MPI::COMM_WORLD.Get_size();
535
536		if (nProcessors > nGlobalMols) {
537		sprintf(painCave.errMsg,
#	Line 473 | Line 540 | namespace oopse {
540		"\tthe number of molecules.  This will not result in a \n"
541		"\tusable division of atoms for force decomposition.\n"
542		"\tEither try a smaller number of processors, or run the\n"
543	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
543	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
544	>	nGlobalMols);
545
546		painCave.isFatal = 1;
547		simError();
548		}
549
482	–	int seedValue;
550		Globals * simParams = info->getSimParams();
551	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
551	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
552	>	//random number generator
553		if (simParams->haveSeed()) {
554	<	seedValue = simParams->getSeed();
554	>	int seedValue = simParams->getSeed();
555		myRandom = new SeqRandNumGen(seedValue);
556		}else {
557		myRandom = new SeqRandNumGen();
#	Line 496 | Line 564 | namespace oopse {
564		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
565
566		if (worldRank == 0) {
567	<	numerator = info->getNGlobalAtoms();
568	<	denominator = nProcessors;
569	<	precast = numerator / denominator;
570	<	nTarget = (int)(precast + 0.5);
567	>	RealType numerator = info->getNGlobalAtoms();
568	>	RealType denominator = nProcessors;
569	>	RealType precast = numerator / denominator;
570	>	int nTarget = (int)(precast + 0.5);
571
572	<	for(i = 0; i < nGlobalMols; i++) {
573	<	done = 0;
574	<	loops = 0;
572	>	for(int i = 0; i < nGlobalMols; i++) {
573	>
574	>	int done = 0;
575	>	int loops = 0;
576
577		while (!done) {
578		loops++;
579
580		// Pick a processor at random
581
582	<	which_proc = (int) (myRandom->rand() * nProcessors);
582	>	int which_proc = (int) (myRandom->rand() * nProcessors);
583
584		//get the molecule stamp first
585		int stampId = info->getMoleculeStampId(i);
586		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
587
588		// How many atoms does this processor have so far?
589	<	old_atoms = atomsPerProc[which_proc];
590	<	add_atoms = moleculeStamp->getNAtoms();
591	<	new_atoms = old_atoms + add_atoms;
589	>	int old_atoms = atomsPerProc[which_proc];
590	>	int add_atoms = moleculeStamp->getNAtoms();
591	>	int new_atoms = old_atoms + add_atoms;
592
593		// If we've been through this loop too many times, we need
594		// to just give up and assign the molecule to this processor
595		// and be done with it.
596
597		if (loops > 100) {
598	+
599		sprintf(painCave.errMsg,
600	<	"I've tried 100 times to assign molecule %d to a "
601	<	" processor, but can't find a good spot.\n"
602	<	"I'm assigning it at random to processor %d.\n",
600	>	"There have been 100 attempts to assign molecule %d to an\n"
601	>	"\tunderworked processor, but there's no good place to\n"
602	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
603		i, which_proc);
604	<
604	>
605		painCave.isFatal = 0;
606	+	painCave.severity = OPENMD_INFO;
607		simError();
608
609		molToProcMap[i] = which_proc;
#	Line 561 | Line 632 | namespace oopse {
632		//           Pacc(x) = exp(- a * x)
633		// where a = penalty / (average atoms per molecule)
634
635	<	x = (RealType)(new_atoms - nTarget);
636	<	y = myRandom->rand();
635	>	RealType x = (RealType)(new_atoms - nTarget);
636	>	RealType y = myRandom->rand();
637
638		if (y < exp(- a * x)) {
639		molToProcMap[i] = which_proc;
#	Line 577 | Line 648 | namespace oopse {
648		}
649
650		delete myRandom;
651	<
651	>
652		// Spray out this nonsense to all other processors:
582	–
653		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
654	+	// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655		} else {
656
657		// Listen to your marching orders from processor 0:
587	–
658		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() | simParams->haveElectricField()) {
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	+	info->setStorageLayout(storageLayout);
810	+
811	+	return storageLayout;
812	+	}
813	+
814		void SimCreator::setGlobalIndex(SimInfo *info) {
815		SimInfo::MoleculeIterator mi;
816		Molecule::AtomIterator ai;
817		Molecule::RigidBodyIterator ri;
818		Molecule::CutoffGroupIterator ci;
819	+	Molecule::BondIterator boi;
820	+	Molecule::BendIterator bei;
821	+	Molecule::TorsionIterator ti;
822	+	Molecule::InversionIterator ii;
823		Molecule::IntegrableObjectIterator  ioi;
824	<	Molecule * mol;
825	<	Atom * atom;
826	<	RigidBody * rb;
827	<	CutoffGroup * cg;
824	>	Molecule* mol;
825	>	Atom* atom;
826	>	RigidBody* rb;
827	>	CutoffGroup* cg;
828	>	Bond* bond;
829	>	Bend* bend;
830	>	Torsion* torsion;
831	>	Inversion* inversion;
832		int beginAtomIndex;
833		int beginRigidBodyIndex;
834		int beginCutoffGroupIndex;
835	+	int beginBondIndex;
836	+	int beginBendIndex;
837	+	int beginTorsionIndex;
838	+	int beginInversionIndex;
839		int nGlobalAtoms = info->getNGlobalAtoms();
840	<
640	<	/**@todo fixme */
641	<	#ifndef IS_MPI
840	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
841
842		beginAtomIndex = 0;
843	<	beginRigidBodyIndex = 0;
843	>	// The rigid body indices begin immediately after the atom indices:
844	>	beginRigidBodyIndex = info->getNGlobalAtoms();
845		beginCutoffGroupIndex = 0;
846	<
847	<	#else
848	<
849	<	int nproc;
850	<	int myNode;
851	<
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	<
686	<	//rigidbody's index begins right after atom's
687	<	beginRigidBodyIndex += info->getNGlobalAtoms();
688	<
689	<	for(mol = info->beginMolecule(mi); mol != NULL;
690	<	mol = info->nextMolecule(mi)) {
846	>	beginBondIndex = 0;
847	>	beginBendIndex = 0;
848	>	beginTorsionIndex = 0;
849	>	beginInversionIndex = 0;
850	>
851	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
852
853	<	//local index(index in DataStorge) of atom is important
854	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
855	<	atom->setGlobalIndex(beginAtomIndex++);
853	>	#ifdef IS_MPI
854	>	if (info->getMolToProc(i) == worldRank) {
855	>	#endif
856	>	// stuff to do if I own this molecule
857	>	mol = info->getMoleculeByGlobalIndex(i);
858	>
859	>	// The local index(index in DataStorge) of the atom is important:
860	>	for(atom = mol->beginAtom(ai); atom != NULL;
861	>	atom = mol->nextAtom(ai)) {
862	>	atom->setGlobalIndex(beginAtomIndex++);
863	>	}
864	>
865	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
866	>	rb = mol->nextRigidBody(ri)) {
867	>	rb->setGlobalIndex(beginRigidBodyIndex++);
868	>	}
869	>
870	>	// The local index of other objects only depends on the order
871	>	// of traversal:
872	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
873	>	cg = mol->nextCutoffGroup(ci)) {
874	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
875	>	}
876	>	for(bond = mol->beginBond(boi); bond != NULL;
877	>	bond = mol->nextBond(boi)) {
878	>	bond->setGlobalIndex(beginBondIndex++);
879	>	}
880	>	for(bend = mol->beginBend(bei); bend != NULL;
881	>	bend = mol->nextBend(bei)) {
882	>	bend->setGlobalIndex(beginBendIndex++);
883	>	}
884	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
885	>	torsion = mol->nextTorsion(ti)) {
886	>	torsion->setGlobalIndex(beginTorsionIndex++);
887	>	}
888	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
889	>	inversion = mol->nextInversion(ii)) {
890	>	inversion->setGlobalIndex(beginInversionIndex++);
891	>	}
892	>
893	>	#ifdef IS_MPI
894	>	}  else {
895	>
896	>	// stuff to do if I don't own this molecule
897	>
898	>	int stampId = info->getMoleculeStampId(i);
899	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
900	>
901	>	beginAtomIndex += stamp->getNAtoms();
902	>	beginRigidBodyIndex += stamp->getNRigidBodies();
903	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
904	>	beginBondIndex += stamp->getNBonds();
905	>	beginBendIndex += stamp->getNBends();
906	>	beginTorsionIndex += stamp->getNTorsions();
907	>	beginInversionIndex += stamp->getNInversions();
908		}
909	<
910	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
911	<	rb = mol->nextRigidBody(ri)) {
912	<	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	<
909	>	#endif
910	>
911	>	} //end for(int i=0)
912	>
913		//fill globalGroupMembership
914		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
915	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
916	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
917	<
915	>	for(mol = info->beginMolecule(mi); mol != NULL;
916	>	mol = info->nextMolecule(mi)) {
917	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
918	>	cg = mol->nextCutoffGroup(ci)) {
919		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
920		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
921		}
922
923		}
924		}
925	<
925	>
926		#ifdef IS_MPI
927		// Since the globalGroupMembership has been zero filled and we've only
928		// poked values into the atoms we know, we can do an Allreduce
929		// to get the full globalGroupMembership array (We think).
930		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
931		// docs said we could.
932	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
933	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
932	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
933	>	MPI_Allreduce(&globalGroupMembership[0],
934	>	&tmpGroupMembership[0], nGlobalAtoms,
935		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
936	+	// MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
937	+	//                           &tmpGroupMembership[0], nGlobalAtoms,
938	+	//                           MPI::INT, MPI::SUM);
939		info->setGlobalGroupMembership(tmpGroupMembership);
940		#else
941		info->setGlobalGroupMembership(globalGroupMembership);
942		#endif
943
944		//fill molMembership
945	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
945	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
946	>	info->getNGlobalRigidBodies(), 0);
947
948	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
949	<
948	>	for(mol = info->beginMolecule(mi); mol != NULL;
949	>	mol = info->nextMolecule(mi)) {
950		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
951		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
952		}
953	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
954	+	rb = mol->nextRigidBody(ri)) {
955	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
956	+	}
957		}
958
959		#ifdef IS_MPI
960	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
961	<
962	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
960	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
961	>	info->getNGlobalRigidBodies(), 0);
962	>	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
963	>	nGlobalAtoms + nGlobalRigidBodies,
964		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
965	+	// MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
966	+	//                           nGlobalAtoms + nGlobalRigidBodies,
967	+	//                           MPI::INT, MPI::SUM);
968
969		info->setGlobalMolMembership(tmpMolMembership);
970		#else
#	Line 757 | Line 975 | namespace oopse {
975		// here the molecules are listed by their global indices.
976
977		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
978	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
978	>	for (mol = info->beginMolecule(mi); mol != NULL;
979	>	mol = info->nextMolecule(mi)) {
980		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
981		}
982
983		#ifdef IS_MPI
984		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
985		MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
986	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
986	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
987	>	// MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
988	>	//                           info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
989		#else
990		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
991		#endif
992
993	<	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
994	<
995	<	int startingIndex = 0;
996	<	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
997	<	startingIOIndexForMol[i] = startingIndex;
998	<	startingIndex += numIntegrableObjectsPerMol[i];
999	<	}
1000	<
1001	<	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
1002	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
993	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
994	>
995	>	int startingIndex = 0;
996	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
997	>	startingIOIndexForMol[i] = startingIndex;
998	>	startingIndex += numIntegrableObjectsPerMol[i];
999	>	}
1000	>
1001	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
1002	>	for (mol = info->beginMolecule(mi); mol != NULL;
1003	>	mol = info->nextMolecule(mi)) {
1004		int myGlobalIndex = mol->getGlobalIndex();
1005		int globalIO = startingIOIndexForMol[myGlobalIndex];
1006	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
1007	<	integrableObject = mol->nextIntegrableObject(ioi)) {
1008	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
1009	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
1010	<	globalIO++;
1006	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
1007	>	sd = mol->nextIntegrableObject(ioi)) {
1008	>	sd->setGlobalIntegrableObjectIndex(globalIO);
1009	>	IOIndexToIntegrableObject[globalIO] = sd;
1010	>	globalIO++;
1011		}
1012		}
1013	<
1014	<	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
1015	<
1013	>
1014	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
1015	>
1016		}
1017
1018		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
797	–	Globals* simParams;
798	–	simParams = info->getSimParams();
1019
800	–
1020		DumpReader reader(info, mdFileName);
1021		int nframes = reader.getNFrames();
1022
#	Line 811 | Line 1030 | int startingIndex = 0;
1030		painCave.isFatal = 1;
1031		simError();
1032		}
814	–
1033		//copy the current snapshot to previous snapshot
1034		info->getSnapshotManager()->advance();
1035		}
1036
1037	<	} //end namespace oopse
1037	>	} //end namespace OpenMD
1038
1039

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1976 by gezelter, Wed Mar 12 20:01:15 2014 UTC

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