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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1597 by gezelter, Tue Jul 26 15:49:24 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 46 | Line 46
46		* @time 13:51am
47		* @version 1.0
48		*/
49	+	#include <exception>
50	+	#include <iostream>
51	+	#include <sstream>
52	+	#include <string>
53
54		#include "brains/MoleculeCreator.hpp"
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
54	–	#include "io/parse_me.h"
58		#include "UseTheForce/ForceFieldFactory.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61		#include "math/SeqRandNumGen.hpp"
62	+	#include "mdParser/MDLexer.hpp"
63	+	#include "mdParser/MDParser.hpp"
64	+	#include "mdParser/MDTreeParser.hpp"
65	+	#include "mdParser/SimplePreprocessor.hpp"
66	+	#include "antlr/ANTLRException.hpp"
67	+	#include "antlr/TokenStreamRecognitionException.hpp"
68	+	#include "antlr/TokenStreamIOException.hpp"
69	+	#include "antlr/TokenStreamException.hpp"
70	+	#include "antlr/RecognitionException.hpp"
71	+	#include "antlr/CharStreamException.hpp"
72	+
73	+	#include "antlr/MismatchedCharException.hpp"
74	+	#include "antlr/MismatchedTokenException.hpp"
75	+	#include "antlr/NoViableAltForCharException.hpp"
76	+	#include "antlr/NoViableAltException.hpp"
77	+
78		#ifdef IS_MPI
60	–	#include "io/mpiBASS.h"
79		#include "math/ParallelRandNumGen.hpp"
80		#endif
81
82	<	namespace oopse {
82	>	namespace OpenMD {
83	>
84	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
85	>	Globals* simParams = NULL;
86	>	try {
87
88	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
88	>	// Create a preprocessor that preprocesses md file into an ostringstream
89	>	std::stringstream ppStream;
90	>	#ifdef IS_MPI
91	>	int streamSize;
92	>	const int masterNode = 0;
93	>	int commStatus;
94	>	if (worldRank == masterNode) {
95	>	#endif
96	>
97	>	SimplePreprocessor preprocessor;
98	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
99	>
100	>	#ifdef IS_MPI
101	>	//brocasting the stream size
102	>	streamSize = ppStream.str().size() +1;
103	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
104
105	<	#ifdef IS_MPI
105	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106	>
107	>
108	>	} else {
109	>	//get stream size
110	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
111
112	<	if (worldRank == 0) {
113	<	#endif // is_mpi
112	>	char* buf = new char[streamSize];
113	>	assert(buf);
114	>
115	>	//receive file content
116	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	>
118	>	ppStream.str(buf);
119	>	delete [] buf;
120
121	<	simParams->initalize();
122	<	set_interface_stamps(stamps, simParams);
121	>	}
122	>	#endif
123	>	// Create a scanner that reads from the input stream
124	>	MDLexer lexer(ppStream);
125	>	lexer.setFilename(filename);
126	>	lexer.initDeferredLineCount();
127	>
128	>	// Create a parser that reads from the scanner
129	>	MDParser parser(lexer);
130	>	parser.setFilename(filename);
131
132	<	#ifdef IS_MPI
132	>	// Create an observer that synchorizes file name change
133	>	FilenameObserver observer;
134	>	observer.setLexer(&lexer);
135	>	observer.setParser(&parser);
136	>	lexer.setObserver(&observer);
137	>
138	>	antlr::ASTFactory factory;
139	>	parser.initializeASTFactory(factory);
140	>	parser.setASTFactory(&factory);
141	>	parser.mdfile();
142
143	<	mpiEventInit();
143	>	// Create a tree parser that reads information into Globals
144	>	MDTreeParser treeParser;
145	>	treeParser.initializeASTFactory(factory);
146	>	treeParser.setASTFactory(&factory);
147	>	simParams = treeParser.walkTree(parser.getAST());
148	>	}
149
150	<	#endif
150	>
151	>	catch(antlr::MismatchedCharException& e) {
152	>	sprintf(painCave.errMsg,
153	>	"parser exception: %s %s:%d:%d\n",
154	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158	>	catch(antlr::MismatchedTokenException &e) {
159	>	sprintf(painCave.errMsg,
160	>	"parser exception: %s %s:%d:%d\n",
161	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
162	>	painCave.isFatal = 1;
163	>	simError();
164	>	}
165	>	catch(antlr::NoViableAltForCharException &e) {
166	>	sprintf(painCave.errMsg,
167	>	"parser exception: %s %s:%d:%d\n",
168	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
169	>	painCave.isFatal = 1;
170	>	simError();
171	>	}
172	>	catch(antlr::NoViableAltException &e) {
173	>	sprintf(painCave.errMsg,
174	>	"parser exception: %s %s:%d:%d\n",
175	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
176	>	painCave.isFatal = 1;
177	>	simError();
178	>	}
179	>
180	>	catch(antlr::TokenStreamRecognitionException& e) {
181	>	sprintf(painCave.errMsg,
182	>	"parser exception: %s %s:%d:%d\n",
183	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187	>
188	>	catch(antlr::TokenStreamIOException& e) {
189	>	sprintf(painCave.errMsg,
190	>	"parser exception: %s\n",
191	>	e.getMessage().c_str());
192	>	painCave.isFatal = 1;
193	>	simError();
194	>	}
195	>
196	>	catch(antlr::TokenStreamException& e) {
197	>	sprintf(painCave.errMsg,
198	>	"parser exception: %s\n",
199	>	e.getMessage().c_str());
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>	catch (antlr::RecognitionException& e) {
204	>	sprintf(painCave.errMsg,
205	>	"parser exception: %s %s:%d:%d\n",
206	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
207	>	painCave.isFatal = 1;
208	>	simError();
209	>	}
210	>	catch (antlr::CharStreamException& e) {
211	>	sprintf(painCave.errMsg,
212	>	"parser exception: %s\n",
213	>	e.getMessage().c_str());
214	>	painCave.isFatal = 1;
215	>	simError();
216	>	}
217	>	catch (OpenMDException& e) {
218	>	sprintf(painCave.errMsg,
219	>	"%s\n",
220	>	e.getMessage().c_str());
221	>	painCave.isFatal = 1;
222	>	simError();
223	>	}
224	>	catch (std::exception& e) {
225	>	sprintf(painCave.errMsg,
226	>	"parser exception: %s\n",
227	>	e.what());
228	>	painCave.isFatal = 1;
229	>	simError();
230	>	}
231
232	<	yacc_BASS(mdFileName.c_str());
232	>	return simParams;
233	>	}
234	>
235	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236	>	bool loadInitCoords) {
237	>
238	>	const int bufferSize = 65535;
239	>	char buffer[bufferSize];
240	>	int lineNo = 0;
241	>	std::string mdRawData;
242	>	int metaDataBlockStart = -1;
243	>	int metaDataBlockEnd = -1;
244	>	int i;
245	>	int mdOffset;
246
247	<	#ifdef IS_MPI
247	>	#ifdef IS_MPI
248	>	const int masterNode = 0;
249	>	if (worldRank == masterNode) {
250	>	#endif
251
252	<	throwMPIEvent(NULL);
253	<	} else {
254	<	set_interface_stamps(stamps, simParams);
255	<	mpiEventInit();
256	<	MPIcheckPoint();
257	<	mpiEventLoop();
258	<	}
252	>	std::ifstream mdFile_(mdFileName.c_str());
253	>
254	>	if (mdFile_.fail()) {
255	>	sprintf(painCave.errMsg,
256	>	"SimCreator: Cannot open file: %s\n",
257	>	mdFileName.c_str());
258	>	painCave.isFatal = 1;
259	>	simError();
260	>	}
261
262	<	#endif
262	>	mdFile_.getline(buffer, bufferSize);
263	>	++lineNo;
264	>	std::string line = trimLeftCopy(buffer);
265	>	i = CaseInsensitiveFind(line, "<OpenMD");
266	>	if (static_cast<size_t>(i) == string::npos) {
267	>	// try the older file strings to see if that works:
268	>	i = CaseInsensitiveFind(line, "<OOPSE");
269	>	}
270	>
271	>	if (static_cast<size_t>(i) == string::npos) {
272	>	// still no luck!
273	>	sprintf(painCave.errMsg,
274	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
275	>	mdFileName.c_str());
276	>	painCave.isFatal = 1;
277	>	simError();
278	>	}
279
280	<	}
280	>	//scan through the input stream and find MetaData tag
281	>	while(mdFile_.getline(buffer, bufferSize)) {
282	>	++lineNo;
283	>
284	>	std::string line = trimLeftCopy(buffer);
285	>	if (metaDataBlockStart == -1) {
286	>	i = CaseInsensitiveFind(line, "<MetaData>");
287	>	if (i != string::npos) {
288	>	metaDataBlockStart = lineNo;
289	>	mdOffset = mdFile_.tellg();
290	>	}
291	>	} else {
292	>	i = CaseInsensitiveFind(line, "</MetaData>");
293	>	if (i != string::npos) {
294	>	metaDataBlockEnd = lineNo;
295	>	}
296	>	}
297	>	}
298
299	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
300	<
301	<	MakeStamps * stamps = new MakeStamps();
299	>	if (metaDataBlockStart == -1) {
300	>	sprintf(painCave.errMsg,
301	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
302	>	mdFileName.c_str());
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	if (metaDataBlockEnd == -1) {
307	>	sprintf(painCave.errMsg,
308	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
309	>	mdFileName.c_str());
310	>	painCave.isFatal = 1;
311	>	simError();
312	>	}
313	>
314	>	mdFile_.clear();
315	>	mdFile_.seekg(0);
316	>	mdFile_.seekg(mdOffset);
317
318	<	Globals * simParams = new Globals();
318	>	mdRawData.clear();
319
320	<	//parse meta-data file
321	<	parseFile(mdFileName, stamps, simParams);
320	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
321	>	mdFile_.getline(buffer, bufferSize);
322	>	mdRawData += buffer;
323	>	mdRawData += "\n";
324	>	}
325
326	<	//create the force field
327	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
328	<	simParams->getForceField());
326	>	mdFile_.close();
327	>
328	>	#ifdef IS_MPI
329	>	}
330	>	#endif
331	>
332	>	std::stringstream rawMetaDataStream(mdRawData);
333	>
334	>	//parse meta-data file
335	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
336
337	+	//create the force field
338	+	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
339	+
340		if (ff == NULL) {
341	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
342	<	simParams->getForceField());
341	>	sprintf(painCave.errMsg,
342	>	"ForceField Factory can not create %s force field\n",
343	>	simParams->getForceField().c_str());
344		painCave.isFatal = 1;
345		simError();
346		}
347	<
347	>
348		if (simParams->haveForceFieldFileName()) {
349		ff->setForceFieldFileName(simParams->getForceFieldFileName());
350		}
351
352		std::string forcefieldFileName;
353		forcefieldFileName = ff->getForceFieldFileName();
354	<
354	>
355		if (simParams->haveForceFieldVariant()) {
356		//If the force field has variant, the variant force field name will be
357		//Base.variant.frc. For exampel EAM.u6.frc
358	<
358	>
359		std::string variant = simParams->getForceFieldVariant();
360	<
360	>
361		std::string::size_type pos = forcefieldFileName.rfind(".frc");
362		variant = "." + variant;
363		if (pos != std::string::npos) {
#	Line 139 | Line 369 | namespace oopse {
369		}
370
371		ff->parse(forcefieldFileName);
142	–
143	–	//extract the molecule stamps
144	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
145	–	compList(stamps, simParams, moleculeStampPairs);
146	–
372		//create SimInfo
373	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
373	>	SimInfo * info = new SimInfo(ff, simParams);
374
375	<	//gather parameters (SimCreator only retrieves part of the parameters)
375	>	info->setRawMetaData(mdRawData);
376	>
377	>	//gather parameters (SimCreator only retrieves part of the
378	>	//parameters)
379		gatherParameters(info, mdFileName);
380	<
380	>
381		//divide the molecules and determine the global index of molecules
382		#ifdef IS_MPI
383		divideMolecules(info);
384		#endif
385	<
385	>
386		//create the molecules
387		createMolecules(info);
388	<
389	<
390	<	//allocate memory for DataStorage(circular reference, need to break it)
388	>
389	>	//allocate memory for DataStorage(circular reference, need to
390	>	//break it)
391		info->setSnapshotManager(new SimSnapshotManager(info));
392
393	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
394	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
395	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
393	>	//set the global index of atoms, rigidbodies and cutoffgroups
394	>	//(only need to be set once, the global index will never change
395	>	//again). Local indices of atoms and rigidbodies are already set
396	>	//by MoleculeCreator class which actually delegates the
397	>	//responsibility to LocalIndexManager.
398		setGlobalIndex(info);
399	<
400	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
401	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
402	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
403	<	//we can determine the beginning global indices of atoms before they get created.
399	>
400	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
401	>	//method, at that point atoms don't have the global index yet
402	>	//(their global index are all initialized to -1).  Therefore we
403	>	//have to call addInteractionPairs explicitly here. A way to work
404	>	//around is that we can determine the beginning global indices of
405	>	//atoms before they get created.
406		SimInfo::MoleculeIterator mi;
407		Molecule* mol;
408		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
409	<	info->addExcludePairs(mol);
409	>	info->addInteractionPairs(mol);
410		}
411
180	–
181	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
182	–	//eta, chi for NPT integrator)
412		if (loadInitCoords)
413	<	loadCoordinates(info);
185	<
413	>	loadCoordinates(info, mdFileName);
414		return info;
415		}
416	<
416	>
417		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
418	<
419	<	//figure out the ouput file names
418	>
419	>	//figure out the output file names
420		std::string prefix;
421	<
421	>
422		#ifdef IS_MPI
423	<
423	>
424		if (worldRank == 0) {
425		#endif // is_mpi
426		Globals * simParams = info->getSimParams();
#	Line 201 | Line 429 | namespace oopse {
429		} else {
430		prefix = getPrefix(mdfile);
431		}
432	<
432	>
433		info->setFinalConfigFileName(prefix + ".eor");
434		info->setDumpFileName(prefix + ".dump");
435		info->setStatFileName(prefix + ".stat");
436	<
436	>	info->setRestFileName(prefix + ".zang");
437	>
438		#ifdef IS_MPI
439	<
439	>
440		}
441	<
441	>
442		#endif
443	<
443	>
444		}
445	<
445	>
446		#ifdef IS_MPI
447		void SimCreator::divideMolecules(SimInfo *info) {
448	<	double numerator;
449	<	double denominator;
450	<	double precast;
451	<	double x;
452	<	double y;
453	<	double a;
448	>	RealType numerator;
449	>	RealType denominator;
450	>	RealType precast;
451	>	RealType x;
452	>	RealType y;
453	>	RealType a;
454		int old_atoms;
455		int add_atoms;
456		int new_atoms;
#	Line 237 | Line 466 | namespace oopse {
466		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
467
468		MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
469	<
469	>
470		if (nProcessors > nGlobalMols) {
471		sprintf(painCave.errMsg,
472		"nProcessors (%d) > nMol (%d)\n"
#	Line 245 | Line 474 | namespace oopse {
474		"\tthe number of molecules.  This will not result in a \n"
475		"\tusable division of atoms for force decomposition.\n"
476		"\tEither try a smaller number of processors, or run the\n"
477	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
478	<
477	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
478	>
479		painCave.isFatal = 1;
480		simError();
481		}
482	<
482	>
483		int seedValue;
484		Globals * simParams = info->getSimParams();
485		SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
#	Line 260 | Line 489 | namespace oopse {
489		}else {
490		myRandom = new SeqRandNumGen();
491		}
492	<
493	<
492	>
493	>
494		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
495	<
495	>
496		//initialize atomsPerProc
497		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
498	<
498	>
499		if (worldRank == 0) {
500		numerator = info->getNGlobalAtoms();
501		denominator = nProcessors;
502		precast = numerator / denominator;
503		nTarget = (int)(precast + 0.5);
504	<
504	>
505		for(i = 0; i < nGlobalMols; i++) {
506		done = 0;
507		loops = 0;
508	<
508	>
509		while (!done) {
510		loops++;
511	<
511	>
512		// Pick a processor at random
513	<
513	>
514		which_proc = (int) (myRandom->rand() * nProcessors);
515	<
515	>
516		//get the molecule stamp first
517		int stampId = info->getMoleculeStampId(i);
518		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
519	<
519	>
520		// How many atoms does this processor have so far?
521		old_atoms = atomsPerProc[which_proc];
522		add_atoms = moleculeStamp->getNAtoms();
523		new_atoms = old_atoms + add_atoms;
524	<
524	>
525		// If we've been through this loop too many times, we need
526		// to just give up and assign the molecule to this processor
527		// and be done with it.
528	<
528	>
529		if (loops > 100) {
530		sprintf(painCave.errMsg,
531		"I've tried 100 times to assign molecule %d to a "
532		" processor, but can't find a good spot.\n"
533		"I'm assigning it at random to processor %d.\n",
534		i, which_proc);
535	<
535	>
536		painCave.isFatal = 0;
537		simError();
538	<
538	>
539		molToProcMap[i] = which_proc;
540		atomsPerProc[which_proc] += add_atoms;
541	<
541	>
542		done = 1;
543		continue;
544		}
545	<
545	>
546		// If we can add this molecule to this processor without sending
547		// it above nTarget, then go ahead and do it:
548	<
548	>
549		if (new_atoms <= nTarget) {
550		molToProcMap[i] = which_proc;
551		atomsPerProc[which_proc] += add_atoms;
552	<
552	>
553		done = 1;
554		continue;
555		}
556	<
556	>
557		// The only situation left is when new_atoms > nTarget.  We
558		// want to accept this with some probability that dies off the
559		// farther we are from nTarget
560	<
560	>
561		// roughly:  x = new_atoms - nTarget
562		//           Pacc(x) = exp(- a * x)
563		// where a = penalty / (average atoms per molecule)
564	<
565	<	x = (double)(new_atoms - nTarget);
564	>
565	>	x = (RealType)(new_atoms - nTarget);
566		y = myRandom->rand();
567	<
567	>
568		if (y < exp(- a * x)) {
569		molToProcMap[i] = which_proc;
570		atomsPerProc[which_proc] += add_atoms;
571	<
571	>
572		done = 1;
573		continue;
574		} else {
#	Line 347 | Line 576 | namespace oopse {
576		}
577		}
578		}
579	<
579	>
580		delete myRandom;
581	<
581	>
582		// Spray out this nonsense to all other processors:
583	<
583	>
584		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
585		} else {
586	<
586	>
587		// Listen to your marching orders from processor 0:
588	<
588	>
589		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
590		}
591	+
592	+	cerr << "molToProcMap:\n";
593	+	for (int i = 0; i < molToProcMap.size(); i++) {
594	+	cerr << "m = " << i << " mtpr[m] = " << molToProcMap[i] <<"\n";
595	+	}
596
597		info->setMolToProcMap(molToProcMap);
598		sprintf(checkPointMsg,
599		"Successfully divided the molecules among the processors.\n");
600	<	MPIcheckPoint();
600	>	errorCheckPoint();
601		}
602	<
602	>
603		#endif
604	<
604	>
605		void SimCreator::createMolecules(SimInfo *info) {
606		MoleculeCreator molCreator;
607		int stampId;
608	<
608	>
609		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
610	<
610	>
611		#ifdef IS_MPI
612	<
612	>
613		if (info->getMolToProc(i) == worldRank) {
614		#endif
615	<
615	>
616		stampId = info->getMoleculeStampId(i);
617		Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
618		stampId, i, info->getLocalIndexManager());
619	<
619	>
620		info->addMolecule(mol);
621	<
621	>
622		#ifdef IS_MPI
623	<
623	>
624		}
625	<
625	>
626		#endif
627	<
627	>
628		} //end for(int i=0)
629		}
630	<
397	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
398	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
399	<	int i;
400	<	char * id;
401	<	LinkedMolStamp* extractedStamp = NULL;
402	<	MoleculeStamp * currentStamp;
403	<	Component** the_components = simParams->getComponents();
404	<	int n_components = simParams->getNComponents();
405	<
406	<	if (!simParams->haveNMol()) {
407	<	// we don't have the total number of molecules, so we assume it is
408	<	// given in each component
409	<
410	<	for(i = 0; i < n_components; i++) {
411	<	if (!the_components[i]->haveNMol()) {
412	<	// we have a problem
413	<	sprintf(painCave.errMsg,
414	<	"SimCreator Error. No global NMol or component NMol given.\n"
415	<	"\tCannot calculate the number of atoms.\n");
416	<
417	<	painCave.isFatal = 1;
418	<	simError();
419	<	}
420	<
421	<	id = the_components[i]->getType();
422	<
423	<	extractedStamp = stamps->extractMolStamp(id);
424	<	if (extractedStamp == NULL) {
425	<	sprintf(painCave.errMsg,
426	<	"SimCreator error: Component \"%s\" was not found in the "
427	<	"list of declared molecules\n", id);
428	<
429	<	painCave.isFatal = 1;
430	<	simError();
431	<	}
432	<
433	<	currentStamp = extractedStamp->getStamp();
434	<
435	<
436	<	moleculeStampPairs.push_back(
437	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
438	<	} //end for (i = 0; i < n_components; i++)
439	<	} else {
440	<	sprintf(painCave.errMsg, "SimSetup error.\n"
441	<	"\tSorry, the ability to specify total"
442	<	" nMols and then give molfractions in the components\n"
443	<	"\tis not currently supported."
444	<	" Please give nMol in the components.\n");
445	<
446	<	painCave.isFatal = 1;
447	<	simError();
448	<	}
449	<
450	<	#ifdef IS_MPI
451	<
452	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
453	<	MPIcheckPoint();
454	<
455	<	#endif // is_mpi
456	<
457	<	}
458	<
630	>
631		void SimCreator::setGlobalIndex(SimInfo *info) {
632		SimInfo::MoleculeIterator mi;
633		Molecule::AtomIterator ai;
634		Molecule::RigidBodyIterator ri;
635		Molecule::CutoffGroupIterator ci;
636	+	Molecule::IntegrableObjectIterator  ioi;
637		Molecule * mol;
638		Atom * atom;
639		RigidBody * rb;
#	Line 469 | Line 642 | namespace oopse {
642		int beginRigidBodyIndex;
643		int beginCutoffGroupIndex;
644		int nGlobalAtoms = info->getNGlobalAtoms();
472	–
473	–	#ifndef IS_MPI
645
646	+	/**@todo fixme */
647	+	#ifndef IS_MPI
648	+
649		beginAtomIndex = 0;
650		beginRigidBodyIndex = 0;
651		beginCutoffGroupIndex = 0;
652	<
652	>
653		#else
654	<
654	>
655		int nproc;
656		int myNode;
657	<
657	>
658		myNode = worldRank;
659		MPI_Comm_size(MPI_COMM_WORLD, &nproc);
660	<
660	>
661		std::vector < int > tmpAtomsInProc(nproc, 0);
662		std::vector < int > tmpRigidBodiesInProc(nproc, 0);
663		std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
664		std::vector < int > NumAtomsInProc(nproc, 0);
665		std::vector < int > NumRigidBodiesInProc(nproc, 0);
666		std::vector < int > NumCutoffGroupsInProc(nproc, 0);
667	<
667	>
668		tmpAtomsInProc[myNode] = info->getNAtoms();
669		tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
670		tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
671	<
671	>
672		//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
673		MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
674		MPI_SUM, MPI_COMM_WORLD);
#	Line 502 | Line 676 | namespace oopse {
676		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
677		MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
678		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
679	<
679	>
680		beginAtomIndex = 0;
681		beginRigidBodyIndex = 0;
682		beginCutoffGroupIndex = 0;
683	<
683	>
684		for(int i = 0; i < myNode; i++) {
685		beginAtomIndex += NumAtomsInProc[i];
686		beginRigidBodyIndex += NumRigidBodiesInProc[i];
687		beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
688		}
689	<
689	>
690		#endif
691	<
691	>
692		//rigidbody's index begins right after atom's
693		beginRigidBodyIndex += info->getNGlobalAtoms();
694	<
694	>
695		for(mol = info->beginMolecule(mi); mol != NULL;
696		mol = info->nextMolecule(mi)) {
697	<
697	>
698		//local index(index in DataStorge) of atom is important
699		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
700		atom->setGlobalIndex(beginAtomIndex++);
701		}
702	<
702	>
703		for(rb = mol->beginRigidBody(ri); rb != NULL;
704		rb = mol->nextRigidBody(ri)) {
705		rb->setGlobalIndex(beginRigidBodyIndex++);
706		}
707	<
707	>
708		//local index of cutoff group is trivial, it only depends on the order of travesing
709		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
710		cg = mol->nextCutoffGroup(ci)) {
711		cg->setGlobalIndex(beginCutoffGroupIndex++);
712		}
713		}
714	<
714	>
715		//fill globalGroupMembership
716	<	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
716	>	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), -1);
717		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
718		for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
719	<
719	>
720		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
721		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
722		}
723	<
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);
735	>	MPI_INT, MPI_MAX, MPI_COMM_WORLD);
736		info->setGlobalGroupMembership(tmpGroupMembership);
737	+
738	+	cerr << "ggm:\n";
739	+	for (int i = 0; i < tmpGroupMembership.size(); i++)
740	+	cerr << "i = " << i << "\t ggm(i) = " << tmpGroupMembership[i] << "\n";
741	+
742		#else
743		info->setGlobalGroupMembership(globalGroupMembership);
744		#endif
745	<
745	>
746		//fill molMembership
747		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
748
749		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
571	–
750		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
751		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
752		}
753		}
754	<
754	>
755		#ifdef IS_MPI
756	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
757	<
756	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
757	>
758		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
759		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
760
#	Line 585 | Line 763 | namespace oopse {
763		info->setGlobalMolMembership(globalMolMembership);
764		#endif
765
766	<	}
766	>	// nIOPerMol holds the number of integrable objects per molecule
767	>	// here the molecules are listed by their global indices.
768
769	<	void SimCreator::loadCoordinates(SimInfo* info) {
769	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
770	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
771	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
772	>	}
773	>
774	>	#ifdef IS_MPI
775	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
776	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
777	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
778	>	#else
779	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
780	>	#endif
781	>
782	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
783	>
784	>	int startingIndex = 0;
785	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
786	>	startingIOIndexForMol[i] = startingIndex;
787	>	startingIndex += numIntegrableObjectsPerMol[i];
788	>	}
789	>
790	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
791	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
792	>	int myGlobalIndex = mol->getGlobalIndex();
793	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
794	>	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
795	>	integrableObject = mol->nextIntegrableObject(ioi)) {
796	>	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
797	>	IOIndexToIntegrableObject[globalIO] = integrableObject;
798	>	globalIO++;
799	>	}
800	>	}
801	>	cerr << "ioi2io:\n";
802	>	for (int i = 0; i < IOIndexToIntegrableObject.size(); i++) {
803	>	if (IOIndexToIntegrableObject[i] != NULL) {
804	>	cerr << "i = " << i << "globalIOindex = " << IOIndexToIntegrableObject[i]->getGlobalIntegrableObjectIndex() << "\n";
805	>	}
806	>	}
807	>
808	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
809	>
810	>	}
811	>
812	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
813		Globals* simParams;
814	+
815		simParams = info->getSimParams();
816
817	<	if (!simParams->haveInitialConfig()) {
595	<	sprintf(painCave.errMsg,
596	<	"Cannot intialize a simulation without an initial configuration file.\n");
597	<	painCave.isFatal = 1;;
598	<	simError();
599	<	}
600	<
601	<	DumpReader reader(info, simParams->getInitialConfig());
817	>	DumpReader reader(info, mdFileName);
818		int nframes = reader.getNFrames();
819
820		if (nframes > 0) {
821		reader.readFrame(nframes - 1);
822		} else {
823		//invalid initial coordinate file
824	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
825	<	simParams->getInitialConfig());
824	>	sprintf(painCave.errMsg,
825	>	"Initial configuration file %s should at least contain one frame\n",
826	>	mdFileName.c_str());
827		painCave.isFatal = 1;
828		simError();
829		}
613	–
830		//copy the current snapshot to previous snapshot
831		info->getSnapshotManager()->advance();
832		}
833	+
834	+	} //end namespace OpenMD
835
618	–	} //end namespace oopse
836
620	–

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 403 by gezelter, Tue Mar 8 21:06:49 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC

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