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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 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 76 | Line 77
77		#include "antlr/NoViableAltException.hpp"
78
79		#ifdef IS_MPI
80	+	#include "mpi.h"
81		#include "math/ParallelRandNumGen.hpp"
82		#endif
83
84	<	namespace oopse {
84	>	namespace OpenMD {
85
86	<	Globals* SimCreator::parseFile(const std::string mdFileName){
87	<	Globals* simParams = NULL;
88	<	try {
86	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
87	>	Globals* simParams = NULL;
88	>	try {
89
90	<	// Create a preprocessor that preprocesses md file into an ostringstream
91	<	std::stringstream ppStream;
90	>	// Create a preprocessor that preprocesses md file into an ostringstream
91	>	std::stringstream ppStream;
92		#ifdef IS_MPI
93	<	int streamSize;
94	<	const int masterNode = 0;
95	<	int commStatus;
96	<	if (worldRank == masterNode) {
97	<	#endif
93	>	int streamSize;
94	>	const int masterNode = 0;
95	>	int commStatus;
96	>	if (worldRank == masterNode) {
97	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
98	>	#endif
99	>	SimplePreprocessor preprocessor;
100	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
101
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
102		#ifdef IS_MPI
103	<	//brocasting the stream size
104	<	streamSize = ppStream.str().size() +1;
105	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
103	>	//brocasting the stream size
104	>	streamSize = ppStream.str().size() +1;
105	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
106
107	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
108
109
110	<	} else {
111	<	//get stream size
112	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
110	>	} else {
111	>
112	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
113	>
114	>	//get stream size
115	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
116	>
117	>	char* buf = new char[streamSize];
118	>	assert(buf);
119
120	<	char* buf = new char[streamSize];
121	<	assert(buf);
120	>	//receive file content
121	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
122
123	<	//receive file content
124	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	<
118	<	ppStream.str(buf);
119	<	delete buf;
123	>	ppStream.str(buf);
124	>	delete [] buf;
125
126	<	}
126	>	}
127		#endif
128	<	// Create a scanner that reads from the input stream
129	<	MDLexer lexer(ppStream);
130	<	lexer.setFilename(mdFileName);
131	<	lexer.initDeferredLineCount();
128	>	// Create a scanner that reads from the input stream
129	>	MDLexer lexer(ppStream);
130	>	lexer.setFilename(filename);
131	>	lexer.initDeferredLineCount();
132
133	<	// Create a parser that reads from the scanner
134	<	MDParser parser(lexer);
135	<	parser.setFilename(mdFileName);
133	>	// Create a parser that reads from the scanner
134	>	MDParser parser(lexer);
135	>	parser.setFilename(filename);
136
137	<	// Create an observer that synchorizes file name change
138	<	FilenameObserver observer;
139	<	observer.setLexer(&lexer);
140	<	observer.setParser(&parser);
141	<	lexer.setObserver(&observer);
137	>	// Create an observer that synchorizes file name change
138	>	FilenameObserver observer;
139	>	observer.setLexer(&lexer);
140	>	observer.setParser(&parser);
141	>	lexer.setObserver(&observer);
142
143	<	antlr::ASTFactory factory;
144	<	parser.initializeASTFactory(factory);
145	<	parser.setASTFactory(&factory);
146	<	parser.mdfile();
143	>	antlr::ASTFactory factory;
144	>	parser.initializeASTFactory(factory);
145	>	parser.setASTFactory(&factory);
146	>	parser.mdfile();
147
148	<	// Create a tree parser that reads information into Globals
149	<	MDTreeParser treeParser;
150	<	treeParser.initializeASTFactory(factory);
151	<	treeParser.setASTFactory(&factory);
152	<	simParams = treeParser.walkTree(parser.getAST());
148	>	// Create a tree parser that reads information into Globals
149	>	MDTreeParser treeParser;
150	>	treeParser.initializeASTFactory(factory);
151	>	treeParser.setASTFactory(&factory);
152	>	simParams = treeParser.walkTree(parser.getAST());
153	>	}
154
149	–	}
150	–
155
156	<	catch(antlr::MismatchedCharException& e) {
157	<	sprintf(painCave.errMsg,
158	<	"parser exception: %s %s:%d:%d\n",
159	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
160	<	painCave.isFatal = 1;
161	<	simError();
162	<	}
163	<	catch(antlr::MismatchedTokenException &e) {
164	<	sprintf(painCave.errMsg,
165	<	"parser exception: %s %s:%d:%d\n",
166	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
170	<	catch(antlr::NoViableAltForCharException &e) {
171	<	sprintf(painCave.errMsg,
172	<	"parser exception: %s %s:%d:%d\n",
173	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	<	painCave.isFatal = 1;
175	<	simError();
176	<	}
177	<	catch(antlr::NoViableAltException &e) {
178	<	sprintf(painCave.errMsg,
179	<	"parser exception: %s %s:%d:%d\n",
180	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	<	painCave.isFatal = 1;
182	<	simError();
183	<	}
156	>	catch(antlr::MismatchedCharException& e) {
157	>	sprintf(painCave.errMsg,
158	>	"parser exception: %s %s:%d:%d\n",
159	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
160	>	painCave.isFatal = 1;
161	>	simError();
162	>	}
163	>	catch(antlr::MismatchedTokenException &e) {
164	>	sprintf(painCave.errMsg,
165	>	"parser exception: %s %s:%d:%d\n",
166	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>	catch(antlr::NoViableAltForCharException &e) {
171	>	sprintf(painCave.errMsg,
172	>	"parser exception: %s %s:%d:%d\n",
173	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	catch(antlr::NoViableAltException &e) {
178	>	sprintf(painCave.errMsg,
179	>	"parser exception: %s %s:%d:%d\n",
180	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184
185	<	catch(antlr::TokenStreamRecognitionException& e) {
186	<	sprintf(painCave.errMsg,
187	<	"parser exception: %s %s:%d:%d\n",
188	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
189	<	painCave.isFatal = 1;
190	<	simError();
191	<	}
185	>	catch(antlr::TokenStreamRecognitionException& e) {
186	>	sprintf(painCave.errMsg,
187	>	"parser exception: %s %s:%d:%d\n",
188	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
189	>	painCave.isFatal = 1;
190	>	simError();
191	>	}
192
193	<	catch(antlr::TokenStreamIOException& e) {
194	<	sprintf(painCave.errMsg,
195	<	"parser exception: %s\n",
196	<	e.getMessage().c_str());
197	<	painCave.isFatal = 1;
198	<	simError();
199	<	}
193	>	catch(antlr::TokenStreamIOException& e) {
194	>	sprintf(painCave.errMsg,
195	>	"parser exception: %s\n",
196	>	e.getMessage().c_str());
197	>	painCave.isFatal = 1;
198	>	simError();
199	>	}
200
201	<	catch(antlr::TokenStreamException& e) {
202	<	sprintf(painCave.errMsg,
203	<	"parser exception: %s\n",
204	<	e.getMessage().c_str());
205	<	painCave.isFatal = 1;
206	<	simError();
207	<	}
208	<	catch (antlr::RecognitionException& e) {
209	<	sprintf(painCave.errMsg,
210	<	"parser exception: %s %s:%d:%d\n",
211	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
215	<	catch (antlr::CharStreamException& e) {
216	<	sprintf(painCave.errMsg,
217	<	"parser exception: %s\n",
218	<	e.getMessage().c_str());
219	<	painCave.isFatal = 1;
220	<	simError();
221	<	}
222	<	catch (OOPSEException& e) {
223	<	sprintf(painCave.errMsg,
224	<	"%s\n",
225	<	e.getMessage().c_str());
226	<	painCave.isFatal = 1;
227	<	simError();
228	<	}
229	<	catch (std::exception& e) {
230	<	sprintf(painCave.errMsg,
231	<	"parser exception: %s\n",
232	<	e.what());
233	<	painCave.isFatal = 1;
234	<	simError();
235	<	}
201	>	catch(antlr::TokenStreamException& e) {
202	>	sprintf(painCave.errMsg,
203	>	"parser exception: %s\n",
204	>	e.getMessage().c_str());
205	>	painCave.isFatal = 1;
206	>	simError();
207	>	}
208	>	catch (antlr::RecognitionException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s %s:%d:%d\n",
211	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>	catch (antlr::CharStreamException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s\n",
218	>	e.getMessage().c_str());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (OpenMDException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"%s\n",
225	>	e.getMessage().c_str());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (std::exception& e) {
230	>	sprintf(painCave.errMsg,
231	>	"parser exception: %s\n",
232	>	e.what());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236
237	<	return simParams;
237	>	simParams->setMDfileVersion(mdFileVersion);
238	>	return simParams;
239		}
240
241		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
242		bool loadInitCoords) {
243	+
244	+	const int bufferSize = 65535;
245	+	char buffer[bufferSize];
246	+	int lineNo = 0;
247	+	std::string mdRawData;
248	+	int metaDataBlockStart = -1;
249	+	int metaDataBlockEnd = -1;
250	+	int i;
251	+	int mdOffset;
252	+	int mdFileVersion;
253
254	+	#ifdef IS_MPI
255	+	const int masterNode = 0;
256	+	if (worldRank == masterNode) {
257	+	#endif
258	+
259	+	std::ifstream mdFile_(mdFileName.c_str());
260	+
261	+	if (mdFile_.fail()) {
262	+	sprintf(painCave.errMsg,
263	+	"SimCreator: Cannot open file: %s\n",
264	+	mdFileName.c_str());
265	+	painCave.isFatal = 1;
266	+	simError();
267	+	}
268	+
269	+	mdFile_.getline(buffer, bufferSize);
270	+	++lineNo;
271	+	std::string line = trimLeftCopy(buffer);
272	+	i = CaseInsensitiveFind(line, "<OpenMD");
273	+	if (static_cast<size_t>(i) == string::npos) {
274	+	// try the older file strings to see if that works:
275	+	i = CaseInsensitiveFind(line, "<OOPSE");
276	+	}
277	+
278	+	if (static_cast<size_t>(i) == string::npos) {
279	+	// still no luck!
280	+	sprintf(painCave.errMsg,
281	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
282	+	mdFileName.c_str());
283	+	painCave.isFatal = 1;
284	+	simError();
285	+	}
286	+
287	+	// found the correct opening string, now try to get the file
288	+	// format version number.
289	+
290	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
291	+	std::string fileType = tokenizer.nextToken();
292	+	toUpper(fileType);
293	+
294	+	mdFileVersion = 0;
295	+
296	+	if (fileType == "OPENMD") {
297	+	while (tokenizer.hasMoreTokens()) {
298	+	std::string token(tokenizer.nextToken());
299	+	toUpper(token);
300	+	if (token == "VERSION") {
301	+	mdFileVersion = tokenizer.nextTokenAsInt();
302	+	break;
303	+	}
304	+	}
305	+	}
306	+
307	+	//scan through the input stream and find MetaData tag
308	+	while(mdFile_.getline(buffer, bufferSize)) {
309	+	++lineNo;
310	+
311	+	std::string line = trimLeftCopy(buffer);
312	+	if (metaDataBlockStart == -1) {
313	+	i = CaseInsensitiveFind(line, "<MetaData>");
314	+	if (i != string::npos) {
315	+	metaDataBlockStart = lineNo;
316	+	mdOffset = mdFile_.tellg();
317	+	}
318	+	} else {
319	+	i = CaseInsensitiveFind(line, "</MetaData>");
320	+	if (i != string::npos) {
321	+	metaDataBlockEnd = lineNo;
322	+	}
323	+	}
324	+	}
325	+
326	+	if (metaDataBlockStart == -1) {
327	+	sprintf(painCave.errMsg,
328	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
329	+	mdFileName.c_str());
330	+	painCave.isFatal = 1;
331	+	simError();
332	+	}
333	+	if (metaDataBlockEnd == -1) {
334	+	sprintf(painCave.errMsg,
335	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
336	+	mdFileName.c_str());
337	+	painCave.isFatal = 1;
338	+	simError();
339	+	}
340	+
341	+	mdFile_.clear();
342	+	mdFile_.seekg(0);
343	+	mdFile_.seekg(mdOffset);
344	+
345	+	mdRawData.clear();
346	+
347	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
348	+	mdFile_.getline(buffer, bufferSize);
349	+	mdRawData += buffer;
350	+	mdRawData += "\n";
351	+	}
352	+
353	+	mdFile_.close();
354	+
355	+	#ifdef IS_MPI
356	+	}
357	+	#endif
358	+
359	+	std::stringstream rawMetaDataStream(mdRawData);
360	+
361		//parse meta-data file
362	<	Globals* simParams = parseFile(mdFileName);
362	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
363	>	metaDataBlockStart + 1);
364
365		//create the force field
366	<	ForceField * ff = ForceFieldFactory::getInstance()
367	<	->createForceField(simParams->getForceField());
245	<
366	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
367	>
368		if (ff == NULL) {
369		sprintf(painCave.errMsg,
370		"ForceField Factory can not create %s force field\n",
#	Line 275 | Line 397 | Globals* SimCreator::parseFile(const std::string mdFil
397		}
398
399		ff->parse(forcefieldFileName);
278	–	ff->setFortranForceOptions();
400		//create SimInfo
401		SimInfo * info = new SimInfo(ff, simParams);
402	+
403	+	info->setRawMetaData(mdRawData);
404
405		//gather parameters (SimCreator only retrieves part of the
406		//parameters)
#	Line 291 | Line 414 | Globals* SimCreator::parseFile(const std::string mdFil
414		//create the molecules
415		createMolecules(info);
416
294	–
417		//allocate memory for DataStorage(circular reference, need to
418		//break it)
419		info->setSnapshotManager(new SimSnapshotManager(info));
#	Line 303 | Line 425 | Globals* SimCreator::parseFile(const std::string mdFil
425		//responsibility to LocalIndexManager.
426		setGlobalIndex(info);
427
428	<	//Although addExcludePairs is called inside SimInfo's addMolecule
428	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
429		//method, at that point atoms don't have the global index yet
430		//(their global index are all initialized to -1).  Therefore we
431	<	//have to call addExcludePairs explicitly here. A way to work
431	>	//have to call addInteractionPairs explicitly here. A way to work
432		//around is that we can determine the beginning global indices of
433		//atoms before they get created.
434		SimInfo::MoleculeIterator mi;
435		Molecule* mol;
436		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
437	<	info->addExcludePairs(mol);
437	>	info->addInteractionPairs(mol);
438		}
439
440		if (loadInitCoords)
441	<	loadCoordinates(info);
320	<
441	>	loadCoordinates(info, mdFileName);
442		return info;
443		}
444
#	Line 352 | Line 473 | Globals* SimCreator::parseFile(const std::string mdFil
473
474		#ifdef IS_MPI
475		void SimCreator::divideMolecules(SimInfo *info) {
476	<	double numerator;
477	<	double denominator;
478	<	double precast;
479	<	double x;
480	<	double y;
481	<	double a;
476	>	RealType numerator;
477	>	RealType denominator;
478	>	RealType precast;
479	>	RealType x;
480	>	RealType y;
481	>	RealType a;
482		int old_atoms;
483		int add_atoms;
484		int new_atoms;
#	Line 381 | Line 502 | Globals* SimCreator::parseFile(const std::string mdFil
502		"\tthe number of molecules.  This will not result in a \n"
503		"\tusable division of atoms for force decomposition.\n"
504		"\tEither try a smaller number of processors, or run the\n"
505	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
505	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
506
507		painCave.isFatal = 1;
508		simError();
#	Line 469 | Line 590 | Globals* SimCreator::parseFile(const std::string mdFil
590		//           Pacc(x) = exp(- a * x)
591		// where a = penalty / (average atoms per molecule)
592
593	<	x = (double)(new_atoms - nTarget);
593	>	x = (RealType)(new_atoms - nTarget);
594		y = myRandom->rand();
595
596		if (y < exp(- a * x)) {
#	Line 499 | Line 620 | Globals* SimCreator::parseFile(const std::string mdFil
620		info->setMolToProcMap(molToProcMap);
621		sprintf(checkPointMsg,
622		"Successfully divided the molecules among the processors.\n");
623	<	MPIcheckPoint();
623	>	errorCheckPoint();
624		}
625
626		#endif
#	Line 516 | Line 637 | Globals* SimCreator::parseFile(const std::string mdFil
637		#endif
638
639		stampId = info->getMoleculeStampId(i);
640	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
641	<	stampId, i, info->getLocalIndexManager());
640	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
641	>	info->getMoleculeStamp(stampId),
642	>	stampId, i,
643	>	info->getLocalIndexManager());
644
645		info->addMolecule(mol);
646
#	Line 535 | Line 658 | Globals* SimCreator::parseFile(const std::string mdFil
658		Molecule::AtomIterator ai;
659		Molecule::RigidBodyIterator ri;
660		Molecule::CutoffGroupIterator ci;
661	+	Molecule::IntegrableObjectIterator  ioi;
662		Molecule * mol;
663		Atom * atom;
664		RigidBody * rb;
#	Line 543 | Line 667 | Globals* SimCreator::parseFile(const std::string mdFil
667		int beginRigidBodyIndex;
668		int beginCutoffGroupIndex;
669		int nGlobalAtoms = info->getNGlobalAtoms();
546	–
547	–	#ifndef IS_MPI
548	–
549	–	beginAtomIndex = 0;
550	–	beginRigidBodyIndex = 0;
551	–	beginCutoffGroupIndex = 0;
552	–
553	–	#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);
670
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	–
671		beginAtomIndex = 0;
672		beginRigidBodyIndex = 0;
673		beginCutoffGroupIndex = 0;
674	<
675	<	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)) {
674	>
675	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
676
677	<	//local index(index in DataStorge) of atom is important
678	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
679	<	atom->setGlobalIndex(beginAtomIndex++);
677	>	#ifdef IS_MPI
678	>	if (info->getMolToProc(i) == worldRank) {
679	>	#endif
680	>	// stuff to do if I own this molecule
681	>	mol = info->getMoleculeByGlobalIndex(i);
682	>
683	>	//local index(index in DataStorge) of atom is important
684	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	>	atom->setGlobalIndex(beginAtomIndex++);
686	>	}
687	>
688	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
689	>	rb = mol->nextRigidBody(ri)) {
690	>	rb->setGlobalIndex(beginRigidBodyIndex++);
691	>	}
692	>
693	>	//local index of cutoff group is trivial, it only depends on
694	>	//the order of travesing
695	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
696	>	cg = mol->nextCutoffGroup(ci)) {
697	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
698	>	}
699	>
700	>	#ifdef IS_MPI
701	>	}  else {
702	>
703	>	// stuff to do if I don't own this molecule
704	>
705	>	int stampId = info->getMoleculeStampId(i);
706	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
707	>
708	>	beginAtomIndex += stamp->getNAtoms();
709	>	beginRigidBodyIndex += stamp->getNRigidBodies();
710	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
711		}
712	<
713	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
714	<	rb = mol->nextRigidBody(ri)) {
715	<	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	<
712	>	#endif
713	>
714	>	} //end for(int i=0)
715	>
716		//fill globalGroupMembership
717		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
718		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 623 | Line 724 | Globals* SimCreator::parseFile(const std::string mdFil
724
725		}
726		}
727	<
727	>
728		#ifdef IS_MPI
729		// Since the globalGroupMembership has been zero filled and we've only
730		// poked values into the atoms we know, we can do an Allreduce
731		// to get the full globalGroupMembership array (We think).
732		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
733		// docs said we could.
734	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
734	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
735		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
736		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
737		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 642 | Line 743 | Globals* SimCreator::parseFile(const std::string mdFil
743		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
744
745		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
645	–
746		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
747		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
748		}
749		}
750
751		#ifdef IS_MPI
752	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
752	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
753
754		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
755		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 658 | Line 758 | Globals* SimCreator::parseFile(const std::string mdFil
758		#else
759		info->setGlobalMolMembership(globalMolMembership);
760		#endif
761	+
762	+	// nIOPerMol holds the number of integrable objects per molecule
763	+	// here the molecules are listed by their global indices.
764	+
765	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
766	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
767	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
768	+	}
769
770	+	#ifdef IS_MPI
771	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
772	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
773	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
774	+	#else
775	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
776	+	#endif
777	+
778	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
779	+
780	+	int startingIndex = 0;
781	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
782	+	startingIOIndexForMol[i] = startingIndex;
783	+	startingIndex += numIntegrableObjectsPerMol[i];
784	+	}
785	+
786	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
787	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
788	+	int myGlobalIndex = mol->getGlobalIndex();
789	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
790	+	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
791	+	integrableObject = mol->nextIntegrableObject(ioi)) {
792	+	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
793	+	IOIndexToIntegrableObject[globalIO] = integrableObject;
794	+	globalIO++;
795	+	}
796	+	}
797	+
798	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
799	+
800		}
801
802	<	void SimCreator::loadCoordinates(SimInfo* info) {
802	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
803		Globals* simParams;
804	+
805		simParams = info->getSimParams();
806
807	<	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());
807	>	DumpReader reader(info, mdFileName);
808		int nframes = reader.getNFrames();
809	<
809	>
810		if (nframes > 0) {
811		reader.readFrame(nframes - 1);
812		} else {
813		//invalid initial coordinate file
814		sprintf(painCave.errMsg,
815		"Initial configuration file %s should at least contain one frame\n",
816	<	simParams->getInitialConfig().c_str());
816	>	mdFileName.c_str());
817		painCave.isFatal = 1;
818		simError();
819		}
688	–
820		//copy the current snapshot to previous snapshot
821		info->getSnapshotManager()->advance();
822		}
823
824	<	} //end namespace oopse
824	>	} //end namespace OpenMD
825
826

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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