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root/OpenMD/branches/development/src/brains/SimCreator.cpp

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trunk/src/brains/SimCreator.cpp (file contents), Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 76 | Line 76
76		#include "antlr/NoViableAltException.hpp"
77
78		#ifdef IS_MPI
79	+	#include "mpi.h"
80		#include "math/ParallelRandNumGen.hpp"
81		#endif
82
83	<	namespace oopse {
83	>	namespace OpenMD {
84
85	<	Globals* SimCreator::parseFile(const std::string mdFileName){
86	<	Globals* simParams = NULL;
87	<	try {
85	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
86	>	Globals* simParams = NULL;
87	>	try {
88
89	<	// Create a preprocessor that preprocesses md file into an ostringstream
90	<	std::stringstream ppStream;
89	>	// Create a preprocessor that preprocesses md file into an ostringstream
90	>	std::stringstream ppStream;
91		#ifdef IS_MPI
92	<	int streamSize;
93	<	const int masterNode = 0;
94	<	int commStatus;
95	<	if (worldRank == masterNode) {
96	<	#endif
92	>	int streamSize;
93	>	const int masterNode = 0;
94	>	int commStatus;
95	>	if (worldRank == masterNode) {
96	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
97	>	#endif
98	>	SimplePreprocessor preprocessor;
99	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
100
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
101		#ifdef IS_MPI
102	<	//brocasting the stream size
103	<	streamSize = ppStream.str().size() +1;
104	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
102	>	//brocasting the stream size
103	>	streamSize = ppStream.str().size() +1;
104	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
105
106	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107
108
109	<	} else {
110	<	//get stream size
111	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
109	>	} else {
110	>
111	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
112	>
113	>	//get stream size
114	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
115	>
116	>	char* buf = new char[streamSize];
117	>	assert(buf);
118
119	<	char* buf = new char[streamSize];
120	<	assert(buf);
119	>	//receive file content
120	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
121
122	<	//receive file content
123	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	<
118	<	ppStream.str(buf);
119	<	delete buf;
122	>	ppStream.str(buf);
123	>	delete [] buf;
124
125	<	}
125	>	}
126		#endif
127	<	// Create a scanner that reads from the input stream
128	<	MDLexer lexer(ppStream);
129	<	lexer.setFilename(mdFileName);
130	<	lexer.initDeferredLineCount();
127	>	// Create a scanner that reads from the input stream
128	>	MDLexer lexer(ppStream);
129	>	lexer.setFilename(filename);
130	>	lexer.initDeferredLineCount();
131
132	<	// Create a parser that reads from the scanner
133	<	MDParser parser(lexer);
134	<	parser.setFilename(mdFileName);
132	>	// Create a parser that reads from the scanner
133	>	MDParser parser(lexer);
134	>	parser.setFilename(filename);
135
136	<	// Create an observer that synchorizes file name change
137	<	FilenameObserver observer;
138	<	observer.setLexer(&lexer);
139	<	observer.setParser(&parser);
140	<	lexer.setObserver(&observer);
136	>	// Create an observer that synchorizes file name change
137	>	FilenameObserver observer;
138	>	observer.setLexer(&lexer);
139	>	observer.setParser(&parser);
140	>	lexer.setObserver(&observer);
141
142	<	antlr::ASTFactory factory;
143	<	parser.initializeASTFactory(factory);
144	<	parser.setASTFactory(&factory);
145	<	parser.mdfile();
142	>	antlr::ASTFactory factory;
143	>	parser.initializeASTFactory(factory);
144	>	parser.setASTFactory(&factory);
145	>	parser.mdfile();
146
147	<	// Create a tree parser that reads information into Globals
148	<	MDTreeParser treeParser;
149	<	treeParser.initializeASTFactory(factory);
150	<	treeParser.setASTFactory(&factory);
151	<	simParams = treeParser.walkTree(parser.getAST());
147	>	// Create a tree parser that reads information into Globals
148	>	MDTreeParser treeParser;
149	>	treeParser.initializeASTFactory(factory);
150	>	treeParser.setASTFactory(&factory);
151	>	simParams = treeParser.walkTree(parser.getAST());
152	>	}
153
149	–	}
150	–
154
155	<	catch(antlr::MismatchedCharException& e) {
156	<	sprintf(painCave.errMsg,
157	<	"parser exception: %s %s:%d:%d\n",
158	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
159	<	painCave.isFatal = 1;
160	<	simError();
161	<	}
162	<	catch(antlr::MismatchedTokenException &e) {
163	<	sprintf(painCave.errMsg,
164	<	"parser exception: %s %s:%d:%d\n",
165	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	<	painCave.isFatal = 1;
167	<	simError();
168	<	}
169	<	catch(antlr::NoViableAltForCharException &e) {
170	<	sprintf(painCave.errMsg,
171	<	"parser exception: %s %s:%d:%d\n",
172	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	<	painCave.isFatal = 1;
174	<	simError();
175	<	}
176	<	catch(antlr::NoViableAltException &e) {
177	<	sprintf(painCave.errMsg,
178	<	"parser exception: %s %s:%d:%d\n",
179	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	<	painCave.isFatal = 1;
181	<	simError();
182	<	}
155	>	catch(antlr::MismatchedCharException& e) {
156	>	sprintf(painCave.errMsg,
157	>	"parser exception: %s %s:%d:%d\n",
158	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
159	>	painCave.isFatal = 1;
160	>	simError();
161	>	}
162	>	catch(antlr::MismatchedTokenException &e) {
163	>	sprintf(painCave.errMsg,
164	>	"parser exception: %s %s:%d:%d\n",
165	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	>	painCave.isFatal = 1;
167	>	simError();
168	>	}
169	>	catch(antlr::NoViableAltForCharException &e) {
170	>	sprintf(painCave.errMsg,
171	>	"parser exception: %s %s:%d:%d\n",
172	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	>	painCave.isFatal = 1;
174	>	simError();
175	>	}
176	>	catch(antlr::NoViableAltException &e) {
177	>	sprintf(painCave.errMsg,
178	>	"parser exception: %s %s:%d:%d\n",
179	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	>	painCave.isFatal = 1;
181	>	simError();
182	>	}
183
184	<	catch(antlr::TokenStreamRecognitionException& e) {
185	<	sprintf(painCave.errMsg,
186	<	"parser exception: %s %s:%d:%d\n",
187	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	<	painCave.isFatal = 1;
189	<	simError();
190	<	}
184	>	catch(antlr::TokenStreamRecognitionException& e) {
185	>	sprintf(painCave.errMsg,
186	>	"parser exception: %s %s:%d:%d\n",
187	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	>	painCave.isFatal = 1;
189	>	simError();
190	>	}
191
192	<	catch(antlr::TokenStreamIOException& e) {
193	<	sprintf(painCave.errMsg,
194	<	"parser exception: %s\n",
195	<	e.getMessage().c_str());
196	<	painCave.isFatal = 1;
197	<	simError();
198	<	}
192	>	catch(antlr::TokenStreamIOException& e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s\n",
195	>	e.getMessage().c_str());
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199
200	<	catch(antlr::TokenStreamException& e) {
201	<	sprintf(painCave.errMsg,
202	<	"parser exception: %s\n",
203	<	e.getMessage().c_str());
204	<	painCave.isFatal = 1;
205	<	simError();
206	<	}
207	<	catch (antlr::RecognitionException& e) {
208	<	sprintf(painCave.errMsg,
209	<	"parser exception: %s %s:%d:%d\n",
210	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
211	<	painCave.isFatal = 1;
212	<	simError();
213	<	}
214	<	catch (antlr::CharStreamException& e) {
215	<	sprintf(painCave.errMsg,
216	<	"parser exception: %s\n",
217	<	e.getMessage().c_str());
218	<	painCave.isFatal = 1;
219	<	simError();
220	<	}
221	<	catch (OOPSEException& e) {
222	<	sprintf(painCave.errMsg,
223	<	"%s\n",
224	<	e.getMessage().c_str());
225	<	painCave.isFatal = 1;
226	<	simError();
227	<	}
228	<	catch (std::exception& e) {
229	<	sprintf(painCave.errMsg,
230	<	"parser exception: %s\n",
231	<	e.what());
232	<	painCave.isFatal = 1;
233	<	simError();
234	<	}
200	>	catch(antlr::TokenStreamException& e) {
201	>	sprintf(painCave.errMsg,
202	>	"parser exception: %s\n",
203	>	e.getMessage().c_str());
204	>	painCave.isFatal = 1;
205	>	simError();
206	>	}
207	>	catch (antlr::RecognitionException& e) {
208	>	sprintf(painCave.errMsg,
209	>	"parser exception: %s %s:%d:%d\n",
210	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
211	>	painCave.isFatal = 1;
212	>	simError();
213	>	}
214	>	catch (antlr::CharStreamException& e) {
215	>	sprintf(painCave.errMsg,
216	>	"parser exception: %s\n",
217	>	e.getMessage().c_str());
218	>	painCave.isFatal = 1;
219	>	simError();
220	>	}
221	>	catch (OpenMDException& e) {
222	>	sprintf(painCave.errMsg,
223	>	"%s\n",
224	>	e.getMessage().c_str());
225	>	painCave.isFatal = 1;
226	>	simError();
227	>	}
228	>	catch (std::exception& e) {
229	>	sprintf(painCave.errMsg,
230	>	"parser exception: %s\n",
231	>	e.what());
232	>	painCave.isFatal = 1;
233	>	simError();
234	>	}
235
236	<	return simParams;
236	>	simParams->setMDfileVersion(mdFileVersion);
237	>	return simParams;
238		}
239
240		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
241		bool loadInitCoords) {
242	+
243	+	const int bufferSize = 65535;
244	+	char buffer[bufferSize];
245	+	int lineNo = 0;
246	+	std::string mdRawData;
247	+	int metaDataBlockStart = -1;
248	+	int metaDataBlockEnd = -1;
249	+	int i;
250	+	int mdOffset;
251	+	int mdFileVersion;
252	+
253	+	#ifdef IS_MPI
254	+	const int masterNode = 0;
255	+	if (worldRank == masterNode) {
256	+	#endif
257	+
258	+	std::ifstream mdFile_(mdFileName.c_str());
259	+
260	+	if (mdFile_.fail()) {
261	+	sprintf(painCave.errMsg,
262	+	"SimCreator: Cannot open file: %s\n",
263	+	mdFileName.c_str());
264	+	painCave.isFatal = 1;
265	+	simError();
266	+	}
267	+
268	+	mdFile_.getline(buffer, bufferSize);
269	+	++lineNo;
270	+	std::string line = trimLeftCopy(buffer);
271	+	i = CaseInsensitiveFind(line, "<OpenMD");
272	+	if (static_cast<size_t>(i) == string::npos) {
273	+	// try the older file strings to see if that works:
274	+	i = CaseInsensitiveFind(line, "<OOPSE");
275	+	}
276	+
277	+	if (static_cast<size_t>(i) == string::npos) {
278	+	// still no luck!
279	+	sprintf(painCave.errMsg,
280	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
281	+	mdFileName.c_str());
282	+	painCave.isFatal = 1;
283	+	simError();
284	+	}
285	+
286	+	// found the correct opening string, now try to get the file
287	+	// format version number.
288
289	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
290	+	std::string fileType = tokenizer.nextToken();
291	+	toUpper(fileType);
292	+
293	+	mdFileVersion = 0;
294	+
295	+	if (fileType == "OPENMD") {
296	+	while (tokenizer.hasMoreTokens()) {
297	+	std::string token(tokenizer.nextToken());
298	+	toUpper(token);
299	+	if (token == "VERSION") {
300	+	mdFileVersion = tokenizer.nextTokenAsInt();
301	+	break;
302	+	}
303	+	}
304	+	}
305	+
306	+	//scan through the input stream and find MetaData tag
307	+	while(mdFile_.getline(buffer, bufferSize)) {
308	+	++lineNo;
309	+
310	+	std::string line = trimLeftCopy(buffer);
311	+	if (metaDataBlockStart == -1) {
312	+	i = CaseInsensitiveFind(line, "<MetaData>");
313	+	if (i != string::npos) {
314	+	metaDataBlockStart = lineNo;
315	+	mdOffset = mdFile_.tellg();
316	+	}
317	+	} else {
318	+	i = CaseInsensitiveFind(line, "</MetaData>");
319	+	if (i != string::npos) {
320	+	metaDataBlockEnd = lineNo;
321	+	}
322	+	}
323	+	}
324	+
325	+	if (metaDataBlockStart == -1) {
326	+	sprintf(painCave.errMsg,
327	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
328	+	mdFileName.c_str());
329	+	painCave.isFatal = 1;
330	+	simError();
331	+	}
332	+	if (metaDataBlockEnd == -1) {
333	+	sprintf(painCave.errMsg,
334	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
335	+	mdFileName.c_str());
336	+	painCave.isFatal = 1;
337	+	simError();
338	+	}
339	+
340	+	mdFile_.clear();
341	+	mdFile_.seekg(0);
342	+	mdFile_.seekg(mdOffset);
343	+
344	+	mdRawData.clear();
345	+
346	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
347	+	mdFile_.getline(buffer, bufferSize);
348	+	mdRawData += buffer;
349	+	mdRawData += "\n";
350	+	}
351	+
352	+	mdFile_.close();
353	+
354	+	#ifdef IS_MPI
355	+	}
356	+	#endif
357	+
358	+	std::stringstream rawMetaDataStream(mdRawData);
359	+
360		//parse meta-data file
361	<	Globals* simParams = parseFile(mdFileName);
361	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
362	>	metaDataBlockStart + 1);
363
364		//create the force field
365	<	ForceField * ff = ForceFieldFactory::getInstance()
366	<	->createForceField(simParams->getForceField());
245	<
365	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
366	>
367		if (ff == NULL) {
368		sprintf(painCave.errMsg,
369		"ForceField Factory can not create %s force field\n",
#	Line 275 | Line 396 | Globals* SimCreator::parseFile(const std::string mdFil
396		}
397
398		ff->parse(forcefieldFileName);
278	–	ff->setFortranForceOptions();
399		//create SimInfo
400		SimInfo * info = new SimInfo(ff, simParams);
401	+
402	+	info->setRawMetaData(mdRawData);
403
404		//gather parameters (SimCreator only retrieves part of the
405		//parameters)
#	Line 291 | Line 413 | Globals* SimCreator::parseFile(const std::string mdFil
413		//create the molecules
414		createMolecules(info);
415
294	–
416		//allocate memory for DataStorage(circular reference, need to
417		//break it)
418		info->setSnapshotManager(new SimSnapshotManager(info));
#	Line 303 | Line 424 | Globals* SimCreator::parseFile(const std::string mdFil
424		//responsibility to LocalIndexManager.
425		setGlobalIndex(info);
426
427	<	//Although addExcludePairs is called inside SimInfo's addMolecule
427	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
428		//method, at that point atoms don't have the global index yet
429		//(their global index are all initialized to -1).  Therefore we
430	<	//have to call addExcludePairs explicitly here. A way to work
430	>	//have to call addInteractionPairs explicitly here. A way to work
431		//around is that we can determine the beginning global indices of
432		//atoms before they get created.
433		SimInfo::MoleculeIterator mi;
434		Molecule* mol;
435		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
436	<	info->addExcludePairs(mol);
436	>	info->addInteractionPairs(mol);
437		}
438
439		if (loadInitCoords)
440	<	loadCoordinates(info);
320	<
440	>	loadCoordinates(info, mdFileName);
441		return info;
442		}
443
#	Line 352 | Line 472 | Globals* SimCreator::parseFile(const std::string mdFil
472
473		#ifdef IS_MPI
474		void SimCreator::divideMolecules(SimInfo *info) {
475	<	double numerator;
476	<	double denominator;
477	<	double precast;
478	<	double x;
479	<	double y;
480	<	double a;
475	>	RealType numerator;
476	>	RealType denominator;
477	>	RealType precast;
478	>	RealType x;
479	>	RealType y;
480	>	RealType a;
481		int old_atoms;
482		int add_atoms;
483		int new_atoms;
#	Line 381 | Line 501 | Globals* SimCreator::parseFile(const std::string mdFil
501		"\tthe number of molecules.  This will not result in a \n"
502		"\tusable division of atoms for force decomposition.\n"
503		"\tEither try a smaller number of processors, or run the\n"
504	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
504	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
505
506		painCave.isFatal = 1;
507		simError();
#	Line 469 | Line 589 | Globals* SimCreator::parseFile(const std::string mdFil
589		//           Pacc(x) = exp(- a * x)
590		// where a = penalty / (average atoms per molecule)
591
592	<	x = (double)(new_atoms - nTarget);
592	>	x = (RealType)(new_atoms - nTarget);
593		y = myRandom->rand();
594
595		if (y < exp(- a * x)) {
#	Line 499 | Line 619 | Globals* SimCreator::parseFile(const std::string mdFil
619		info->setMolToProcMap(molToProcMap);
620		sprintf(checkPointMsg,
621		"Successfully divided the molecules among the processors.\n");
622	<	MPIcheckPoint();
622	>	errorCheckPoint();
623		}
624
625		#endif
#	Line 516 | Line 636 | Globals* SimCreator::parseFile(const std::string mdFil
636		#endif
637
638		stampId = info->getMoleculeStampId(i);
639	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
640	<	stampId, i, info->getLocalIndexManager());
639	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
640	>	info->getMoleculeStamp(stampId),
641	>	stampId, i,
642	>	info->getLocalIndexManager());
643
644		info->addMolecule(mol);
645
#	Line 535 | Line 657 | Globals* SimCreator::parseFile(const std::string mdFil
657		Molecule::AtomIterator ai;
658		Molecule::RigidBodyIterator ri;
659		Molecule::CutoffGroupIterator ci;
660	+	Molecule::IntegrableObjectIterator  ioi;
661		Molecule * mol;
662		Atom * atom;
663		RigidBody * rb;
#	Line 544 | Line 667 | Globals* SimCreator::parseFile(const std::string mdFil
667		int beginCutoffGroupIndex;
668		int nGlobalAtoms = info->getNGlobalAtoms();
669
547	–	#ifndef IS_MPI
548	–
670		beginAtomIndex = 0;
671		beginRigidBodyIndex = 0;
672		beginCutoffGroupIndex = 0;
673	<
674	<	#else
554	<
555	<	int nproc;
556	<	int myNode;
557	<
558	<	myNode = worldRank;
559	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
560	<
561	<	std::vector < int > tmpAtomsInProc(nproc, 0);
562	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
563	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
564	<	std::vector < int > NumAtomsInProc(nproc, 0);
565	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
566	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
567	<
568	<	tmpAtomsInProc[myNode] = info->getNAtoms();
569	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
570	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
571	<
572	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
573	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
574	<	MPI_SUM, MPI_COMM_WORLD);
575	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
576	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
577	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
578	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
579	<
580	<	beginAtomIndex = 0;
581	<	beginRigidBodyIndex = 0;
582	<	beginCutoffGroupIndex = 0;
583	<
584	<	for(int i = 0; i < myNode; i++) {
585	<	beginAtomIndex += NumAtomsInProc[i];
586	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
587	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
588	<	}
589	<
590	<	#endif
591	<
592	<	//rigidbody's index begins right after atom's
593	<	beginRigidBodyIndex += info->getNGlobalAtoms();
594	<
595	<	for(mol = info->beginMolecule(mi); mol != NULL;
596	<	mol = info->nextMolecule(mi)) {
673	>
674	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
675
676	<	//local index(index in DataStorge) of atom is important
677	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
678	<	atom->setGlobalIndex(beginAtomIndex++);
676	>	#ifdef IS_MPI
677	>	if (info->getMolToProc(i) == worldRank) {
678	>	#endif
679	>	// stuff to do if I own this molecule
680	>	mol = info->getMoleculeByGlobalIndex(i);
681	>
682	>	//local index(index in DataStorge) of atom is important
683	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
684	>	atom->setGlobalIndex(beginAtomIndex++);
685	>	}
686	>
687	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
688	>	rb = mol->nextRigidBody(ri)) {
689	>	rb->setGlobalIndex(beginRigidBodyIndex++);
690	>	}
691	>
692	>	//local index of cutoff group is trivial, it only depends on
693	>	//the order of travesing
694	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
695	>	cg = mol->nextCutoffGroup(ci)) {
696	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
697	>	}
698	>
699	>	#ifdef IS_MPI
700	>	}  else {
701	>
702	>	// stuff to do if I don't own this molecule
703	>
704	>	int stampId = info->getMoleculeStampId(i);
705	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
706	>
707	>	beginAtomIndex += stamp->getNAtoms();
708	>	beginRigidBodyIndex += stamp->getNRigidBodies();
709	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
710		}
711	<
712	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
713	<	rb = mol->nextRigidBody(ri)) {
714	<	rb->setGlobalIndex(beginRigidBodyIndex++);
606	<	}
607	<
608	<	//local index of cutoff group is trivial, it only depends on the order of travesing
609	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
610	<	cg = mol->nextCutoffGroup(ci)) {
611	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
612	<	}
613	<	}
614	<
711	>	#endif
712	>
713	>	} //end for(int i=0)
714	>
715		//fill globalGroupMembership
716		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
717		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 623 | Line 723 | Globals* SimCreator::parseFile(const std::string mdFil
723
724		}
725		}
726	<
726	>
727		#ifdef IS_MPI
728		// Since the globalGroupMembership has been zero filled and we've only
729		// poked values into the atoms we know, we can do an Allreduce
730		// to get the full globalGroupMembership array (We think).
731		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
732		// docs said we could.
733	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
733	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
734		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
735		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
736		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 642 | Line 742 | Globals* SimCreator::parseFile(const std::string mdFil
742		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
743
744		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
645	–
745		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
746		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
747		}
748		}
749
750		#ifdef IS_MPI
751	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
751	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
752
753		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
754		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 658 | Line 757 | Globals* SimCreator::parseFile(const std::string mdFil
757		#else
758		info->setGlobalMolMembership(globalMolMembership);
759		#endif
760	+
761	+	// nIOPerMol holds the number of integrable objects per molecule
762	+	// here the molecules are listed by their global indices.
763	+
764	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
765	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
766	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
767	+	}
768
769	+	#ifdef IS_MPI
770	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
771	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
772	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
773	+	#else
774	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
775	+	#endif
776	+
777	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
778	+
779	+	int startingIndex = 0;
780	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
781	+	startingIOIndexForMol[i] = startingIndex;
782	+	startingIndex += numIntegrableObjectsPerMol[i];
783	+	}
784	+
785	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
786	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
787	+	int myGlobalIndex = mol->getGlobalIndex();
788	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
789	+	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
790	+	integrableObject = mol->nextIntegrableObject(ioi)) {
791	+	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
792	+	IOIndexToIntegrableObject[globalIO] = integrableObject;
793	+	globalIO++;
794	+	}
795	+	}
796	+
797	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
798	+
799		}
800
801	<	void SimCreator::loadCoordinates(SimInfo* info) {
801	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
802		Globals* simParams;
803	+
804		simParams = info->getSimParams();
805
806	<	if (!simParams->haveInitialConfig()) {
669	<	sprintf(painCave.errMsg,
670	<	"Cannot intialize a simulation without an initial configuration file.\n");
671	<	painCave.isFatal = 1;;
672	<	simError();
673	<	}
674	<
675	<	DumpReader reader(info, simParams->getInitialConfig());
806	>	DumpReader reader(info, mdFileName);
807		int nframes = reader.getNFrames();
808	<
808	>
809		if (nframes > 0) {
810		reader.readFrame(nframes - 1);
811		} else {
812		//invalid initial coordinate file
813		sprintf(painCave.errMsg,
814		"Initial configuration file %s should at least contain one frame\n",
815	<	simParams->getInitialConfig().c_str());
815	>	mdFileName.c_str());
816		painCave.isFatal = 1;
817		simError();
818		}
688	–
819		//copy the current snapshot to previous snapshot
820		info->getSnapshotManager()->advance();
821		}
822
823	<	} //end namespace oopse
823	>	} //end namespace OpenMD
824
825

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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