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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 1613 by gezelter, Thu Aug 18 20:18:19 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 mdFileVersion, 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	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
96	>	#endif
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
110	<	if (worldRank == 0) {
71	<	#endif // is_mpi
110	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
111
112	<	simParams->initalize();
113	<	set_interface_stamps(stamps, simParams);
112	>	//get stream size
113	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
114
115	<	#ifdef IS_MPI
115	>	char* buf = new char[streamSize];
116	>	assert(buf);
117	>
118	>	//receive file content
119	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
120	>
121	>	ppStream.str(buf);
122	>	delete [] buf;
123
124	<	mpiEventInit();
124	>	}
125	>	#endif
126	>	// Create a scanner that reads from the input stream
127	>	MDLexer lexer(ppStream);
128	>	lexer.setFilename(filename);
129	>	lexer.initDeferredLineCount();
130	>
131	>	// Create a parser that reads from the scanner
132	>	MDParser parser(lexer);
133	>	parser.setFilename(filename);
134
135	<	#endif
135	>	// Create an observer that synchorizes file name change
136	>	FilenameObserver observer;
137	>	observer.setLexer(&lexer);
138	>	observer.setParser(&parser);
139	>	lexer.setObserver(&observer);
140	>
141	>	antlr::ASTFactory factory;
142	>	parser.initializeASTFactory(factory);
143	>	parser.setASTFactory(&factory);
144	>	parser.mdfile();
145
146	<	yacc_BASS(mdFileName.c_str());
146	>	// Create a tree parser that reads information into Globals
147	>	MDTreeParser treeParser;
148	>	treeParser.initializeASTFactory(factory);
149	>	treeParser.setASTFactory(&factory);
150	>	simParams = treeParser.walkTree(parser.getAST());
151	>	}
152
153	<	#ifdef IS_MPI
154	<
155	<	throwMPIEvent(NULL);
156	<	} else {
157	<	set_interface_stamps(stamps, simParams);
158	<	mpiEventInit();
159	<	MPIcheckPoint();
91	<	mpiEventLoop();
153	>
154	>	catch(antlr::MismatchedCharException& e) {
155	>	sprintf(painCave.errMsg,
156	>	"parser exception: %s %s:%d:%d\n",
157	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
158	>	painCave.isFatal = 1;
159	>	simError();
160		}
161	+	catch(antlr::MismatchedTokenException &e) {
162	+	sprintf(painCave.errMsg,
163	+	"parser exception: %s %s:%d:%d\n",
164	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
165	+	painCave.isFatal = 1;
166	+	simError();
167	+	}
168	+	catch(antlr::NoViableAltForCharException &e) {
169	+	sprintf(painCave.errMsg,
170	+	"parser exception: %s %s:%d:%d\n",
171	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
172	+	painCave.isFatal = 1;
173	+	simError();
174	+	}
175	+	catch(antlr::NoViableAltException &e) {
176	+	sprintf(painCave.errMsg,
177	+	"parser exception: %s %s:%d:%d\n",
178	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
179	+	painCave.isFatal = 1;
180	+	simError();
181	+	}
182	+
183	+	catch(antlr::TokenStreamRecognitionException& e) {
184	+	sprintf(painCave.errMsg,
185	+	"parser exception: %s %s:%d:%d\n",
186	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
187	+	painCave.isFatal = 1;
188	+	simError();
189	+	}
190	+
191	+	catch(antlr::TokenStreamIOException& e) {
192	+	sprintf(painCave.errMsg,
193	+	"parser exception: %s\n",
194	+	e.getMessage().c_str());
195	+	painCave.isFatal = 1;
196	+	simError();
197	+	}
198	+
199	+	catch(antlr::TokenStreamException& e) {
200	+	sprintf(painCave.errMsg,
201	+	"parser exception: %s\n",
202	+	e.getMessage().c_str());
203	+	painCave.isFatal = 1;
204	+	simError();
205	+	}
206	+	catch (antlr::RecognitionException& e) {
207	+	sprintf(painCave.errMsg,
208	+	"parser exception: %s %s:%d:%d\n",
209	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
210	+	painCave.isFatal = 1;
211	+	simError();
212	+	}
213	+	catch (antlr::CharStreamException& e) {
214	+	sprintf(painCave.errMsg,
215	+	"parser exception: %s\n",
216	+	e.getMessage().c_str());
217	+	painCave.isFatal = 1;
218	+	simError();
219	+	}
220	+	catch (OpenMDException& e) {
221	+	sprintf(painCave.errMsg,
222	+	"%s\n",
223	+	e.getMessage().c_str());
224	+	painCave.isFatal = 1;
225	+	simError();
226	+	}
227	+	catch (std::exception& e) {
228	+	sprintf(painCave.errMsg,
229	+	"parser exception: %s\n",
230	+	e.what());
231	+	painCave.isFatal = 1;
232	+	simError();
233	+	}
234
235	<	#endif
236	<
235	>	simParams->setMDfileVersion(mdFileVersion);
236	>	return simParams;
237		}
238	<
239	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
240	<
241	<	MakeStamps * stamps = new MakeStamps();
242	<
243	<	Globals * simParams = new Globals();
244	<
245	<	//parse meta-data file
246	<	parseFile(mdFileName, stamps, simParams);
238	>
239	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
240	>	bool loadInitCoords) {
241	>
242	>	const int bufferSize = 65535;
243	>	char buffer[bufferSize];
244	>	int lineNo = 0;
245	>	std::string mdRawData;
246	>	int metaDataBlockStart = -1;
247	>	int metaDataBlockEnd = -1;
248	>	int i;
249	>	int mdOffset;
250	>	int mdFileVersion;
251
252	<	//create the force field
253	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
254	<	simParams->getForceField());
252	>	#ifdef IS_MPI
253	>	const int masterNode = 0;
254	>	if (worldRank == masterNode) {
255	>	#endif
256	>
257	>	std::ifstream mdFile_(mdFileName.c_str());
258	>
259	>	if (mdFile_.fail()) {
260	>	sprintf(painCave.errMsg,
261	>	"SimCreator: Cannot open file: %s\n",
262	>	mdFileName.c_str());
263	>	painCave.isFatal = 1;
264	>	simError();
265	>	}
266	>
267	>	mdFile_.getline(buffer, bufferSize);
268	>	++lineNo;
269	>	std::string line = trimLeftCopy(buffer);
270	>	i = CaseInsensitiveFind(line, "<OpenMD");
271	>	if (static_cast<size_t>(i) == string::npos) {
272	>	// try the older file strings to see if that works:
273	>	i = CaseInsensitiveFind(line, "<OOPSE");
274	>	}
275	>
276	>	if (static_cast<size_t>(i) == string::npos) {
277	>	// still no luck!
278	>	sprintf(painCave.errMsg,
279	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
280	>	mdFileName.c_str());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>
285	>	// found the correct opening string, now try to get the file
286	>	// format version number.
287	>
288	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
289	>	std::string fileType = tokenizer.nextToken();
290	>	toUpper(fileType);
291	>
292	>	mdFileVersion = 0;
293	>
294	>	if (fileType == "OPENMD") {
295	>	while (tokenizer.hasMoreTokens()) {
296	>	std::string token(tokenizer.nextToken());
297	>	toUpper(token);
298	>	if (token == "VERSION") {
299	>	mdFileVersion = tokenizer.nextTokenAsInt();
300	>	break;
301	>	}
302	>	}
303	>	}
304	>
305	>	//scan through the input stream and find MetaData tag
306	>	while(mdFile_.getline(buffer, bufferSize)) {
307	>	++lineNo;
308	>
309	>	std::string line = trimLeftCopy(buffer);
310	>	if (metaDataBlockStart == -1) {
311	>	i = CaseInsensitiveFind(line, "<MetaData>");
312	>	if (i != string::npos) {
313	>	metaDataBlockStart = lineNo;
314	>	mdOffset = mdFile_.tellg();
315	>	}
316	>	} else {
317	>	i = CaseInsensitiveFind(line, "</MetaData>");
318	>	if (i != string::npos) {
319	>	metaDataBlockEnd = lineNo;
320	>	}
321	>	}
322	>	}
323	>
324	>	if (metaDataBlockStart == -1) {
325	>	sprintf(painCave.errMsg,
326	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
327	>	mdFileName.c_str());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	if (metaDataBlockEnd == -1) {
332	>	sprintf(painCave.errMsg,
333	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
334	>	mdFileName.c_str());
335	>	painCave.isFatal = 1;
336	>	simError();
337	>	}
338	>
339	>	mdFile_.clear();
340	>	mdFile_.seekg(0);
341	>	mdFile_.seekg(mdOffset);
342	>
343	>	mdRawData.clear();
344	>
345	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
346	>	mdFile_.getline(buffer, bufferSize);
347	>	mdRawData += buffer;
348	>	mdRawData += "\n";
349	>	}
350	>
351	>	mdFile_.close();
352	>
353	>	#ifdef IS_MPI
354	>	}
355	>	#endif
356	>
357	>	std::stringstream rawMetaDataStream(mdRawData);
358	>
359	>	//parse meta-data file
360	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
361	>	metaDataBlockStart + 1);
362
363	+	//create the force field
364	+	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
365	+
366		if (ff == NULL) {
367	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
368	<	simParams->getForceField());
367	>	sprintf(painCave.errMsg,
368	>	"ForceField Factory can not create %s force field\n",
369	>	simParams->getForceField().c_str());
370		painCave.isFatal = 1;
371		simError();
372		}
373	<
373	>
374		if (simParams->haveForceFieldFileName()) {
375		ff->setForceFieldFileName(simParams->getForceFieldFileName());
376		}
377
378		std::string forcefieldFileName;
379		forcefieldFileName = ff->getForceFieldFileName();
380	<
380	>
381		if (simParams->haveForceFieldVariant()) {
382		//If the force field has variant, the variant force field name will be
383		//Base.variant.frc. For exampel EAM.u6.frc
384	<
384	>
385		std::string variant = simParams->getForceFieldVariant();
386	<
386	>
387		std::string::size_type pos = forcefieldFileName.rfind(".frc");
388		variant = "." + variant;
389		if (pos != std::string::npos) {
#	Line 139 | Line 395 | namespace oopse {
395		}
396
397		ff->parse(forcefieldFileName);
142	–
143	–	//extract the molecule stamps
144	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
145	–	compList(stamps, simParams, moleculeStampPairs);
146	–
398		//create SimInfo
399	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
399	>	SimInfo * info = new SimInfo(ff, simParams);
400
401	<	//gather parameters (SimCreator only retrieves part of the parameters)
401	>	info->setRawMetaData(mdRawData);
402	>
403	>	//gather parameters (SimCreator only retrieves part of the
404	>	//parameters)
405		gatherParameters(info, mdFileName);
406	<
406	>
407		//divide the molecules and determine the global index of molecules
408		#ifdef IS_MPI
409		divideMolecules(info);
410		#endif
411	<
411	>
412		//create the molecules
413		createMolecules(info);
414	<
415	<
416	<	//allocate memory for DataStorage(circular reference, need to break it)
414	>
415	>	//allocate memory for DataStorage(circular reference, need to
416	>	//break it)
417		info->setSnapshotManager(new SimSnapshotManager(info));
418
419	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
420	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
421	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
419	>	//set the global index of atoms, rigidbodies and cutoffgroups
420	>	//(only need to be set once, the global index will never change
421	>	//again). Local indices of atoms and rigidbodies are already set
422	>	//by MoleculeCreator class which actually delegates the
423	>	//responsibility to LocalIndexManager.
424		setGlobalIndex(info);
425	<
426	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
427	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
428	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
429	<	//we can determine the beginning global indices of atoms before they get created.
425	>
426	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
427	>	//method, at that point atoms don't have the global index yet
428	>	//(their global index are all initialized to -1).  Therefore we
429	>	//have to call addInteractionPairs explicitly here. A way to work
430	>	//around is that we can determine the beginning global indices of
431	>	//atoms before they get created.
432		SimInfo::MoleculeIterator mi;
433		Molecule* mol;
434		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
435	<	info->addExcludePairs(mol);
435	>	info->addInteractionPairs(mol);
436		}
437
180	–
181	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
182	–	//eta, chi for NPT integrator)
438		if (loadInitCoords)
439	<	loadCoordinates(info);
185	<
439	>	loadCoordinates(info, mdFileName);
440		return info;
441		}
442	<
442	>
443		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
444	<
445	<	//figure out the ouput file names
444	>
445	>	//figure out the output file names
446		std::string prefix;
447	<
447	>
448		#ifdef IS_MPI
449	<
449	>
450		if (worldRank == 0) {
451		#endif // is_mpi
452		Globals * simParams = info->getSimParams();
#	Line 201 | Line 455 | namespace oopse {
455		} else {
456		prefix = getPrefix(mdfile);
457		}
458	<
458	>
459		info->setFinalConfigFileName(prefix + ".eor");
460		info->setDumpFileName(prefix + ".dump");
461		info->setStatFileName(prefix + ".stat");
462	<
462	>	info->setRestFileName(prefix + ".zang");
463	>
464		#ifdef IS_MPI
465	<
465	>
466		}
467	<
467	>
468		#endif
469	<
469	>
470		}
471	<
471	>
472		#ifdef IS_MPI
473		void SimCreator::divideMolecules(SimInfo *info) {
474	<	double numerator;
475	<	double denominator;
476	<	double precast;
477	<	double x;
478	<	double y;
479	<	double a;
474	>	RealType numerator;
475	>	RealType denominator;
476	>	RealType precast;
477	>	RealType x;
478	>	RealType y;
479	>	RealType a;
480		int old_atoms;
481		int add_atoms;
482		int new_atoms;
#	Line 237 | Line 492 | namespace oopse {
492		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
493
494		MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
495	<
495	>
496		if (nProcessors > nGlobalMols) {
497		sprintf(painCave.errMsg,
498		"nProcessors (%d) > nMol (%d)\n"
#	Line 245 | Line 500 | namespace oopse {
500		"\tthe number of molecules.  This will not result in a \n"
501		"\tusable division of atoms for force decomposition.\n"
502		"\tEither try a smaller number of processors, or run the\n"
503	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
504	<
503	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
504	>
505		painCave.isFatal = 1;
506		simError();
507		}
508	<
508	>
509		int seedValue;
510		Globals * simParams = info->getSimParams();
511		SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
#	Line 260 | Line 515 | namespace oopse {
515		}else {
516		myRandom = new SeqRandNumGen();
517		}
518	<
519	<
518	>
519	>
520		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
521	<
521	>
522		//initialize atomsPerProc
523		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
524	<
524	>
525		if (worldRank == 0) {
526		numerator = info->getNGlobalAtoms();
527		denominator = nProcessors;
528		precast = numerator / denominator;
529		nTarget = (int)(precast + 0.5);
530	<
530	>
531		for(i = 0; i < nGlobalMols; i++) {
532		done = 0;
533		loops = 0;
534	<
534	>
535		while (!done) {
536		loops++;
537	<
537	>
538		// Pick a processor at random
539	<
539	>
540		which_proc = (int) (myRandom->rand() * nProcessors);
541	<
541	>
542		//get the molecule stamp first
543		int stampId = info->getMoleculeStampId(i);
544		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
545	<
545	>
546		// How many atoms does this processor have so far?
547		old_atoms = atomsPerProc[which_proc];
548		add_atoms = moleculeStamp->getNAtoms();
549		new_atoms = old_atoms + add_atoms;
550	<
550	>
551		// If we've been through this loop too many times, we need
552		// to just give up and assign the molecule to this processor
553		// and be done with it.
554	<
554	>
555		if (loops > 100) {
556		sprintf(painCave.errMsg,
557		"I've tried 100 times to assign molecule %d to a "
558		" processor, but can't find a good spot.\n"
559		"I'm assigning it at random to processor %d.\n",
560		i, which_proc);
561	<
561	>
562		painCave.isFatal = 0;
563		simError();
564	<
564	>
565		molToProcMap[i] = which_proc;
566		atomsPerProc[which_proc] += add_atoms;
567	<
567	>
568		done = 1;
569		continue;
570		}
571	<
571	>
572		// If we can add this molecule to this processor without sending
573		// it above nTarget, then go ahead and do it:
574	<
574	>
575		if (new_atoms <= nTarget) {
576		molToProcMap[i] = which_proc;
577		atomsPerProc[which_proc] += add_atoms;
578	<
578	>
579		done = 1;
580		continue;
581		}
582	<
582	>
583		// The only situation left is when new_atoms > nTarget.  We
584		// want to accept this with some probability that dies off the
585		// farther we are from nTarget
586	<
586	>
587		// roughly:  x = new_atoms - nTarget
588		//           Pacc(x) = exp(- a * x)
589		// where a = penalty / (average atoms per molecule)
590	<
591	<	x = (double)(new_atoms - nTarget);
590	>
591	>	x = (RealType)(new_atoms - nTarget);
592		y = myRandom->rand();
593	<
593	>
594		if (y < exp(- a * x)) {
595		molToProcMap[i] = which_proc;
596		atomsPerProc[which_proc] += add_atoms;
597	<
597	>
598		done = 1;
599		continue;
600		} else {
#	Line 347 | Line 602 | namespace oopse {
602		}
603		}
604		}
605	<
605	>
606		delete myRandom;
607	<
607	>
608		// Spray out this nonsense to all other processors:
609	<
609	>
610		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
611		} else {
612	<
612	>
613		// Listen to your marching orders from processor 0:
614	<
614	>
615		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
616		}
617	<
617	>
618		info->setMolToProcMap(molToProcMap);
619		sprintf(checkPointMsg,
620		"Successfully divided the molecules among the processors.\n");
621	<	MPIcheckPoint();
621	>	errorCheckPoint();
622		}
623	<
623	>
624		#endif
625	<
625	>
626		void SimCreator::createMolecules(SimInfo *info) {
627		MoleculeCreator molCreator;
628		int stampId;
629	<
629	>
630		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
631	<
631	>
632		#ifdef IS_MPI
633	<
633	>
634		if (info->getMolToProc(i) == worldRank) {
635		#endif
636	<
636	>
637		stampId = info->getMoleculeStampId(i);
638	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
639	<	stampId, i, info->getLocalIndexManager());
640	<
638	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
639	>	info->getMoleculeStamp(stampId),
640	>	stampId, i,
641	>	info->getLocalIndexManager());
642	>
643		info->addMolecule(mol);
644	<
644	>
645		#ifdef IS_MPI
646	<
646	>
647		}
648	<
648	>
649		#endif
650	<
650	>
651		} //end for(int i=0)
652		}
653	<
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	<
653	>
654		void SimCreator::setGlobalIndex(SimInfo *info) {
655		SimInfo::MoleculeIterator mi;
656		Molecule::AtomIterator ai;
657		Molecule::RigidBodyIterator ri;
658		Molecule::CutoffGroupIterator ci;
659	+	Molecule::IntegrableObjectIterator  ioi;
660		Molecule * mol;
661		Atom * atom;
662		RigidBody * rb;
#	Line 470 | Line 666 | namespace oopse {
666		int beginCutoffGroupIndex;
667		int nGlobalAtoms = info->getNGlobalAtoms();
668
473	–	#ifndef IS_MPI
474	–
669		beginAtomIndex = 0;
670		beginRigidBodyIndex = 0;
671		beginCutoffGroupIndex = 0;
672
673	<	#else
673	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
674	>
675	>	#ifdef IS_MPI
676	>	if (info->getMolToProc(i) == worldRank) {
677	>	#endif
678	>	// stuff to do if I own this molecule
679	>	mol = info->getMoleculeByGlobalIndex(i);
680
681	<	int nproc;
682	<	int myNode;
681	>	//local index(index in DataStorge) of atom is important
682	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
683	>	atom->setGlobalIndex(beginAtomIndex++);
684	>	}
685	>
686	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
687	>	rb = mol->nextRigidBody(ri)) {
688	>	rb->setGlobalIndex(beginRigidBodyIndex++);
689	>	}
690	>
691	>	//local index of cutoff group is trivial, it only depends on
692	>	//the order of travesing
693	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
694	>	cg = mol->nextCutoffGroup(ci)) {
695	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
696	>	}
697	>
698	>	#ifdef IS_MPI
699	>	}  else {
700
701	<	myNode = worldRank;
702	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
701	>	// stuff to do if I don't own this molecule
702	>
703	>	int stampId = info->getMoleculeStampId(i);
704	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
705
706	<	std::vector < int > tmpAtomsInProc(nproc, 0);
707	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
708	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
490	<	std::vector < int > NumAtomsInProc(nproc, 0);
491	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
492	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
493	<
494	<	tmpAtomsInProc[myNode] = info->getNAtoms();
495	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
496	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
497	<
498	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
499	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
500	<	MPI_SUM, MPI_COMM_WORLD);
501	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
502	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
503	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
504	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
505	<
506	<	beginAtomIndex = 0;
507	<	beginRigidBodyIndex = 0;
508	<	beginCutoffGroupIndex = 0;
509	<
510	<	for(int i = 0; i < myNode; i++) {
511	<	beginAtomIndex += NumAtomsInProc[i];
512	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
513	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
514	<	}
515	<
516	<	#endif
517	<
518	<	//rigidbody's index begins right after atom's
519	<	beginRigidBodyIndex += info->getNGlobalAtoms();
520	<
521	<	for(mol = info->beginMolecule(mi); mol != NULL;
522	<	mol = info->nextMolecule(mi)) {
523	<
524	<	//local index(index in DataStorge) of atom is important
525	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
526	<	atom->setGlobalIndex(beginAtomIndex++);
706	>	beginAtomIndex += stamp->getNAtoms();
707	>	beginRigidBodyIndex += stamp->getNRigidBodies();
708	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
709		}
710	+	#endif
711
712	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
530	<	rb = mol->nextRigidBody(ri)) {
531	<	rb->setGlobalIndex(beginRigidBodyIndex++);
532	<	}
712	>	} //end for(int i=0)
713
534	–	//local index of cutoff group is trivial, it only depends on the order of travesing
535	–	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
536	–	cg = mol->nextCutoffGroup(ci)) {
537	–	cg->setGlobalIndex(beginCutoffGroupIndex++);
538	–	}
539	–	}
540	–
714		//fill globalGroupMembership
715		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
716		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
717		for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
718	<
718	>
719		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
720		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
721		}
722	<
722	>
723		}
724		}
725	<
725	>
726		#ifdef IS_MPI
727		// Since the globalGroupMembership has been zero filled and we've only
728		// poked values into the atoms we know, we can do an Allreduce
729		// to get the full globalGroupMembership array (We think).
730		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
731		// docs said we could.
732	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
732	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
733		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
734		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
735		info->setGlobalGroupMembership(tmpGroupMembership);
736		#else
737		info->setGlobalGroupMembership(globalGroupMembership);
738		#endif
739	<
739	>
740		//fill molMembership
741		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
742
743		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
571	–
744		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
745		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
746		}
747		}
748	<
748	>
749		#ifdef IS_MPI
750	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
751	<
750	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
751	>
752		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
753		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
754
#	Line 585 | Line 757 | namespace oopse {
757		info->setGlobalMolMembership(globalMolMembership);
758		#endif
759
760	<	}
760	>	// nIOPerMol holds the number of integrable objects per molecule
761	>	// here the molecules are listed by their global indices.
762
763	<	void SimCreator::loadCoordinates(SimInfo* info) {
763	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
764	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
765	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
766	>	}
767	>
768	>	#ifdef IS_MPI
769	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
770	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
771	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
772	>	#else
773	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
774	>	#endif
775	>
776	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
777	>
778	>	int startingIndex = 0;
779	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
780	>	startingIOIndexForMol[i] = startingIndex;
781	>	startingIndex += numIntegrableObjectsPerMol[i];
782	>	}
783	>
784	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
785	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
786	>	int myGlobalIndex = mol->getGlobalIndex();
787	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
788	>	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
789	>	integrableObject = mol->nextIntegrableObject(ioi)) {
790	>	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
791	>	IOIndexToIntegrableObject[globalIO] = integrableObject;
792	>	globalIO++;
793	>	}
794	>	}
795	>
796	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
797	>
798	>	}
799	>
800	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
801		Globals* simParams;
802	+
803		simParams = info->getSimParams();
804
805	<	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());
805	>	DumpReader reader(info, mdFileName);
806		int nframes = reader.getNFrames();
807
808		if (nframes > 0) {
809		reader.readFrame(nframes - 1);
810		} else {
811		//invalid initial coordinate file
812	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
813	<	simParams->getInitialConfig());
812	>	sprintf(painCave.errMsg,
813	>	"Initial configuration file %s should at least contain one frame\n",
814	>	mdFileName.c_str());
815		painCave.isFatal = 1;
816		simError();
817		}
613	–
818		//copy the current snapshot to previous snapshot
819		info->getSnapshotManager()->advance();
820		}
821	+
822	+	} //end namespace OpenMD
823
618	–	} //end namespace oopse
824
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 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

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