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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 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 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
79	<	#include "io/mpiBASS.h"
79	>	#include "mpi.h"
80		#include "math/ParallelRandNumGen.hpp"
81		#endif
82
83	<	namespace oopse {
83	>	namespace OpenMD {
84	>
85	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
86	>	Globals* simParams = NULL;
87	>	try {
88
89	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
89	>	// Create a preprocessor that preprocesses md file into an ostringstream
90	>	std::stringstream ppStream;
91	>	#ifdef IS_MPI
92	>	int streamSize;
93	>	const int masterNode = 0;
94	>	int commStatus;
95	>	if (worldRank == masterNode) {
96	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
97	>	#endif
98	>	SimplePreprocessor preprocessor;
99	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
100	>
101	>	#ifdef IS_MPI
102	>	//brocasting the stream size
103	>	streamSize = ppStream.str().size() +1;
104	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
105
106	<	#ifdef IS_MPI
106	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107	>
108	>
109	>	} else {
110
111	<	if (worldRank == 0) {
71	<	#endif // is_mpi
111	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
112
113	<	simParams->initalize();
114	<	set_interface_stamps(stamps, simParams);
113	>	//get stream size
114	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
115
116	<	#ifdef IS_MPI
116	>	char* buf = new char[streamSize];
117	>	assert(buf);
118	>
119	>	//receive file content
120	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
121	>
122	>	ppStream.str(buf);
123	>	delete [] buf;
124
125	<	mpiEventInit();
125	>	}
126	>	#endif
127	>	// Create a scanner that reads from the input stream
128	>	MDLexer lexer(ppStream);
129	>	lexer.setFilename(filename);
130	>	lexer.initDeferredLineCount();
131	>
132	>	// Create a parser that reads from the scanner
133	>	MDParser parser(lexer);
134	>	parser.setFilename(filename);
135
136	<	#endif
136	>	// Create an observer that synchorizes file name change
137	>	FilenameObserver observer;
138	>	observer.setLexer(&lexer);
139	>	observer.setParser(&parser);
140	>	lexer.setObserver(&observer);
141	>
142	>	antlr::ASTFactory factory;
143	>	parser.initializeASTFactory(factory);
144	>	parser.setASTFactory(&factory);
145	>	parser.mdfile();
146
147	<	yacc_BASS(mdFileName.c_str());
147	>	// Create a tree parser that reads information into Globals
148	>	MDTreeParser treeParser;
149	>	treeParser.initializeASTFactory(factory);
150	>	treeParser.setASTFactory(&factory);
151	>	simParams = treeParser.walkTree(parser.getAST());
152	>	}
153
154	<	#ifdef IS_MPI
155	<
156	<	throwMPIEvent(NULL);
157	<	} else {
158	<	set_interface_stamps(stamps, simParams);
159	<	mpiEventInit();
160	<	MPIcheckPoint();
91	<	mpiEventLoop();
154	>
155	>	catch(antlr::MismatchedCharException& e) {
156	>	sprintf(painCave.errMsg,
157	>	"parser exception: %s %s:%d:%d\n",
158	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
159	>	painCave.isFatal = 1;
160	>	simError();
161		}
162	+	catch(antlr::MismatchedTokenException &e) {
163	+	sprintf(painCave.errMsg,
164	+	"parser exception: %s %s:%d:%d\n",
165	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	+	painCave.isFatal = 1;
167	+	simError();
168	+	}
169	+	catch(antlr::NoViableAltForCharException &e) {
170	+	sprintf(painCave.errMsg,
171	+	"parser exception: %s %s:%d:%d\n",
172	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	+	painCave.isFatal = 1;
174	+	simError();
175	+	}
176	+	catch(antlr::NoViableAltException &e) {
177	+	sprintf(painCave.errMsg,
178	+	"parser exception: %s %s:%d:%d\n",
179	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	+	painCave.isFatal = 1;
181	+	simError();
182	+	}
183	+
184	+	catch(antlr::TokenStreamRecognitionException& e) {
185	+	sprintf(painCave.errMsg,
186	+	"parser exception: %s %s:%d:%d\n",
187	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	+	painCave.isFatal = 1;
189	+	simError();
190	+	}
191	+
192	+	catch(antlr::TokenStreamIOException& e) {
193	+	sprintf(painCave.errMsg,
194	+	"parser exception: %s\n",
195	+	e.getMessage().c_str());
196	+	painCave.isFatal = 1;
197	+	simError();
198	+	}
199	+
200	+	catch(antlr::TokenStreamException& e) {
201	+	sprintf(painCave.errMsg,
202	+	"parser exception: %s\n",
203	+	e.getMessage().c_str());
204	+	painCave.isFatal = 1;
205	+	simError();
206	+	}
207	+	catch (antlr::RecognitionException& e) {
208	+	sprintf(painCave.errMsg,
209	+	"parser exception: %s %s:%d:%d\n",
210	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
211	+	painCave.isFatal = 1;
212	+	simError();
213	+	}
214	+	catch (antlr::CharStreamException& e) {
215	+	sprintf(painCave.errMsg,
216	+	"parser exception: %s\n",
217	+	e.getMessage().c_str());
218	+	painCave.isFatal = 1;
219	+	simError();
220	+	}
221	+	catch (OpenMDException& e) {
222	+	sprintf(painCave.errMsg,
223	+	"%s\n",
224	+	e.getMessage().c_str());
225	+	painCave.isFatal = 1;
226	+	simError();
227	+	}
228	+	catch (std::exception& e) {
229	+	sprintf(painCave.errMsg,
230	+	"parser exception: %s\n",
231	+	e.what());
232	+	painCave.isFatal = 1;
233	+	simError();
234	+	}
235
236	<	#endif
237	<
236	>	simParams->setMDfileVersion(mdFileVersion);
237	>	return simParams;
238		}
239	<
240	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
241	<
242	<	MakeStamps * stamps = new MakeStamps();
243	<
244	<	Globals * simParams = new Globals();
245	<
246	<	//parse meta-data file
247	<	parseFile(mdFileName, stamps, simParams);
239	>
240	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
241	>	bool loadInitCoords) {
242	>
243	>	const int bufferSize = 65535;
244	>	char buffer[bufferSize];
245	>	int lineNo = 0;
246	>	std::string mdRawData;
247	>	int metaDataBlockStart = -1;
248	>	int metaDataBlockEnd = -1;
249	>	int i;
250	>	int mdOffset;
251	>	int mdFileVersion;
252
253	<	//create the force field
254	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
255	<	simParams->getForceField());
253	>	#ifdef IS_MPI
254	>	const int masterNode = 0;
255	>	if (worldRank == masterNode) {
256	>	#endif
257	>
258	>	std::ifstream mdFile_(mdFileName.c_str());
259	>
260	>	if (mdFile_.fail()) {
261	>	sprintf(painCave.errMsg,
262	>	"SimCreator: Cannot open file: %s\n",
263	>	mdFileName.c_str());
264	>	painCave.isFatal = 1;
265	>	simError();
266	>	}
267	>
268	>	mdFile_.getline(buffer, bufferSize);
269	>	++lineNo;
270	>	std::string line = trimLeftCopy(buffer);
271	>	i = CaseInsensitiveFind(line, "<OpenMD");
272	>	if (static_cast<size_t>(i) == string::npos) {
273	>	// try the older file strings to see if that works:
274	>	i = CaseInsensitiveFind(line, "<OOPSE");
275	>	}
276	>
277	>	if (static_cast<size_t>(i) == string::npos) {
278	>	// still no luck!
279	>	sprintf(painCave.errMsg,
280	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
281	>	mdFileName.c_str());
282	>	painCave.isFatal = 1;
283	>	simError();
284	>	}
285	>
286	>	// found the correct opening string, now try to get the file
287	>	// format version number.
288	>
289	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
290	>	std::string fileType = tokenizer.nextToken();
291	>	toUpper(fileType);
292	>
293	>	mdFileVersion = 0;
294	>
295	>	if (fileType == "OPENMD") {
296	>	while (tokenizer.hasMoreTokens()) {
297	>	std::string token(tokenizer.nextToken());
298	>	toUpper(token);
299	>	if (token == "VERSION") {
300	>	mdFileVersion = tokenizer.nextTokenAsInt();
301	>	break;
302	>	}
303	>	}
304	>	}
305	>
306	>	//scan through the input stream and find MetaData tag
307	>	while(mdFile_.getline(buffer, bufferSize)) {
308	>	++lineNo;
309	>
310	>	std::string line = trimLeftCopy(buffer);
311	>	if (metaDataBlockStart == -1) {
312	>	i = CaseInsensitiveFind(line, "<MetaData>");
313	>	if (i != string::npos) {
314	>	metaDataBlockStart = lineNo;
315	>	mdOffset = mdFile_.tellg();
316	>	}
317	>	} else {
318	>	i = CaseInsensitiveFind(line, "</MetaData>");
319	>	if (i != string::npos) {
320	>	metaDataBlockEnd = lineNo;
321	>	}
322	>	}
323	>	}
324	>
325	>	if (metaDataBlockStart == -1) {
326	>	sprintf(painCave.errMsg,
327	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
328	>	mdFileName.c_str());
329	>	painCave.isFatal = 1;
330	>	simError();
331	>	}
332	>	if (metaDataBlockEnd == -1) {
333	>	sprintf(painCave.errMsg,
334	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
335	>	mdFileName.c_str());
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>
340	>	mdFile_.clear();
341	>	mdFile_.seekg(0);
342	>	mdFile_.seekg(mdOffset);
343	>
344	>	mdRawData.clear();
345	>
346	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
347	>	mdFile_.getline(buffer, bufferSize);
348	>	mdRawData += buffer;
349	>	mdRawData += "\n";
350	>	}
351	>
352	>	mdFile_.close();
353	>
354	>	#ifdef IS_MPI
355	>	}
356	>	#endif
357	>
358	>	std::stringstream rawMetaDataStream(mdRawData);
359	>
360	>	//parse meta-data file
361	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
362	>	metaDataBlockStart + 1);
363
364	+	//create the force field
365	+	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
366	+
367		if (ff == NULL) {
368	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
369	<	simParams->getForceField());
368	>	sprintf(painCave.errMsg,
369	>	"ForceField Factory can not create %s force field\n",
370	>	simParams->getForceField().c_str());
371		painCave.isFatal = 1;
372		simError();
373		}
374	<
374	>
375		if (simParams->haveForceFieldFileName()) {
376		ff->setForceFieldFileName(simParams->getForceFieldFileName());
377		}
378
379		std::string forcefieldFileName;
380		forcefieldFileName = ff->getForceFieldFileName();
381	<
381	>
382		if (simParams->haveForceFieldVariant()) {
383		//If the force field has variant, the variant force field name will be
384		//Base.variant.frc. For exampel EAM.u6.frc
385	<
385	>
386		std::string variant = simParams->getForceFieldVariant();
387	<
387	>
388		std::string::size_type pos = forcefieldFileName.rfind(".frc");
389		variant = "." + variant;
390		if (pos != std::string::npos) {
#	Line 139 | Line 396 | namespace oopse {
396		}
397
398		ff->parse(forcefieldFileName);
142	–
143	–	//extract the molecule stamps
144	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
145	–	compList(stamps, simParams, moleculeStampPairs);
146	–
399		//create SimInfo
400	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
400	>	SimInfo * info = new SimInfo(ff, simParams);
401
402	<	//gather parameters (SimCreator only retrieves part of the parameters)
402	>	info->setRawMetaData(mdRawData);
403	>
404	>	//gather parameters (SimCreator only retrieves part of the
405	>	//parameters)
406		gatherParameters(info, mdFileName);
407	<
407	>
408		//divide the molecules and determine the global index of molecules
409		#ifdef IS_MPI
410		divideMolecules(info);
411		#endif
412	<
412	>
413		//create the molecules
414		createMolecules(info);
415	<
416	<
417	<	//allocate memory for DataStorage(circular reference, need to break it)
415	>
416	>	//allocate memory for DataStorage(circular reference, need to
417	>	//break it)
418		info->setSnapshotManager(new SimSnapshotManager(info));
419
420	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
421	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
422	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
420	>	//set the global index of atoms, rigidbodies and cutoffgroups
421	>	//(only need to be set once, the global index will never change
422	>	//again). Local indices of atoms and rigidbodies are already set
423	>	//by MoleculeCreator class which actually delegates the
424	>	//responsibility to LocalIndexManager.
425		setGlobalIndex(info);
426	<
427	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
428	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
429	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
430	<	//we can determine the beginning global indices of atoms before they get created.
426	>
427	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
428	>	//method, at that point atoms don't have the global index yet
429	>	//(their global index are all initialized to -1).  Therefore we
430	>	//have to call addInteractionPairs explicitly here. A way to work
431	>	//around is that we can determine the beginning global indices of
432	>	//atoms before they get created.
433		SimInfo::MoleculeIterator mi;
434		Molecule* mol;
435		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
436	<	info->addExcludePairs(mol);
436	>	info->addInteractionPairs(mol);
437		}
438
180	–
181	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
182	–	//eta, chi for NPT integrator)
439		if (loadInitCoords)
440	<	loadCoordinates(info);
185	<
440	>	loadCoordinates(info, mdFileName);
441		return info;
442		}
443	<
443	>
444		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
445	<
446	<	//figure out the ouput file names
445	>
446	>	//figure out the output file names
447		std::string prefix;
448	<
448	>
449		#ifdef IS_MPI
450	<
450	>
451		if (worldRank == 0) {
452		#endif // is_mpi
453		Globals * simParams = info->getSimParams();
#	Line 201 | Line 456 | namespace oopse {
456		} else {
457		prefix = getPrefix(mdfile);
458		}
459	<
459	>
460		info->setFinalConfigFileName(prefix + ".eor");
461		info->setDumpFileName(prefix + ".dump");
462		info->setStatFileName(prefix + ".stat");
463	<
463	>	info->setRestFileName(prefix + ".zang");
464	>
465		#ifdef IS_MPI
466	<
466	>
467		}
468	<
468	>
469		#endif
470	<
470	>
471		}
472	<
472	>
473		#ifdef IS_MPI
474		void SimCreator::divideMolecules(SimInfo *info) {
475	<	double numerator;
476	<	double denominator;
477	<	double precast;
478	<	double x;
479	<	double y;
480	<	double a;
475	>	RealType numerator;
476	>	RealType denominator;
477	>	RealType precast;
478	>	RealType x;
479	>	RealType y;
480	>	RealType a;
481		int old_atoms;
482		int add_atoms;
483		int new_atoms;
#	Line 237 | Line 493 | namespace oopse {
493		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
494
495		MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
496	<
496	>
497		if (nProcessors > nGlobalMols) {
498		sprintf(painCave.errMsg,
499		"nProcessors (%d) > nMol (%d)\n"
#	Line 245 | Line 501 | namespace oopse {
501		"\tthe number of molecules.  This will not result in a \n"
502		"\tusable division of atoms for force decomposition.\n"
503		"\tEither try a smaller number of processors, or run the\n"
504	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
505	<
504	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
505	>
506		painCave.isFatal = 1;
507		simError();
508		}
509	<
509	>
510		int seedValue;
511		Globals * simParams = info->getSimParams();
512		SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
#	Line 260 | Line 516 | namespace oopse {
516		}else {
517		myRandom = new SeqRandNumGen();
518		}
519	<
520	<
519	>
520	>
521		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
522	<
522	>
523		//initialize atomsPerProc
524		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
525	<
525	>
526		if (worldRank == 0) {
527		numerator = info->getNGlobalAtoms();
528		denominator = nProcessors;
529		precast = numerator / denominator;
530		nTarget = (int)(precast + 0.5);
531	<
531	>
532		for(i = 0; i < nGlobalMols; i++) {
533		done = 0;
534		loops = 0;
535	<
535	>
536		while (!done) {
537		loops++;
538	<
538	>
539		// Pick a processor at random
540	<
540	>
541		which_proc = (int) (myRandom->rand() * nProcessors);
542	<
542	>
543		//get the molecule stamp first
544		int stampId = info->getMoleculeStampId(i);
545		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
546	<
546	>
547		// How many atoms does this processor have so far?
548		old_atoms = atomsPerProc[which_proc];
549		add_atoms = moleculeStamp->getNAtoms();
550		new_atoms = old_atoms + add_atoms;
551	<
551	>
552		// If we've been through this loop too many times, we need
553		// to just give up and assign the molecule to this processor
554		// and be done with it.
555	<
555	>
556		if (loops > 100) {
557		sprintf(painCave.errMsg,
558		"I've tried 100 times to assign molecule %d to a "
559		" processor, but can't find a good spot.\n"
560		"I'm assigning it at random to processor %d.\n",
561		i, which_proc);
562	<
562	>
563		painCave.isFatal = 0;
564		simError();
565	<
565	>
566		molToProcMap[i] = which_proc;
567		atomsPerProc[which_proc] += add_atoms;
568	<
568	>
569		done = 1;
570		continue;
571		}
572	<
572	>
573		// If we can add this molecule to this processor without sending
574		// it above nTarget, then go ahead and do it:
575	<
575	>
576		if (new_atoms <= nTarget) {
577		molToProcMap[i] = which_proc;
578		atomsPerProc[which_proc] += add_atoms;
579	<
579	>
580		done = 1;
581		continue;
582		}
583	<
583	>
584		// The only situation left is when new_atoms > nTarget.  We
585		// want to accept this with some probability that dies off the
586		// farther we are from nTarget
587	<
587	>
588		// roughly:  x = new_atoms - nTarget
589		//           Pacc(x) = exp(- a * x)
590		// where a = penalty / (average atoms per molecule)
591	<
592	<	x = (double)(new_atoms - nTarget);
591	>
592	>	x = (RealType)(new_atoms - nTarget);
593		y = myRandom->rand();
594	<
594	>
595		if (y < exp(- a * x)) {
596		molToProcMap[i] = which_proc;
597		atomsPerProc[which_proc] += add_atoms;
598	<
598	>
599		done = 1;
600		continue;
601		} else {
#	Line 347 | Line 603 | namespace oopse {
603		}
604		}
605		}
606	<
606	>
607		delete myRandom;
608	<
608	>
609		// Spray out this nonsense to all other processors:
610	<
610	>
611		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
612		} else {
613	<
613	>
614		// Listen to your marching orders from processor 0:
615	<
615	>
616		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
617		}
618	<
618	>
619		info->setMolToProcMap(molToProcMap);
620		sprintf(checkPointMsg,
621		"Successfully divided the molecules among the processors.\n");
622	<	MPIcheckPoint();
622	>	errorCheckPoint();
623		}
624	<
624	>
625		#endif
626	<
626	>
627		void SimCreator::createMolecules(SimInfo *info) {
628		MoleculeCreator molCreator;
629		int stampId;
630	<
630	>
631		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
632	<
632	>
633		#ifdef IS_MPI
634	<
634	>
635		if (info->getMolToProc(i) == worldRank) {
636		#endif
637	<
637	>
638		stampId = info->getMoleculeStampId(i);
639	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
640	<	stampId, i, info->getLocalIndexManager());
641	<
639	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
640	>	info->getMoleculeStamp(stampId),
641	>	stampId, i,
642	>	info->getLocalIndexManager());
643	>
644		info->addMolecule(mol);
645	<
645	>
646		#ifdef IS_MPI
647	<
647	>
648		}
649	<
649	>
650		#endif
651	<
651	>
652		} //end for(int i=0)
653		}
654	<
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	<
654	>
655		void SimCreator::setGlobalIndex(SimInfo *info) {
656		SimInfo::MoleculeIterator mi;
657		Molecule::AtomIterator ai;
658		Molecule::RigidBodyIterator ri;
659		Molecule::CutoffGroupIterator ci;
660	+	Molecule::IntegrableObjectIterator  ioi;
661		Molecule * mol;
662		Atom * atom;
663		RigidBody * rb;
#	Line 470 | Line 667 | namespace oopse {
667		int beginCutoffGroupIndex;
668		int nGlobalAtoms = info->getNGlobalAtoms();
669
473	–	#ifndef IS_MPI
474	–
670		beginAtomIndex = 0;
671		beginRigidBodyIndex = 0;
672		beginCutoffGroupIndex = 0;
673
674	<	#else
674	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
675	>
676	>	#ifdef IS_MPI
677	>	if (info->getMolToProc(i) == worldRank) {
678	>	#endif
679	>	// stuff to do if I own this molecule
680	>	mol = info->getMoleculeByGlobalIndex(i);
681
682	<	int nproc;
683	<	int myNode;
682	>	//local index(index in DataStorge) of atom is important
683	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
684	>	atom->setGlobalIndex(beginAtomIndex++);
685	>	}
686	>
687	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
688	>	rb = mol->nextRigidBody(ri)) {
689	>	rb->setGlobalIndex(beginRigidBodyIndex++);
690	>	}
691	>
692	>	//local index of cutoff group is trivial, it only depends on
693	>	//the order of travesing
694	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
695	>	cg = mol->nextCutoffGroup(ci)) {
696	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
697	>	}
698	>
699	>	#ifdef IS_MPI
700	>	}  else {
701
702	<	myNode = worldRank;
703	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
702	>	// stuff to do if I don't own this molecule
703	>
704	>	int stampId = info->getMoleculeStampId(i);
705	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
706
707	<	std::vector < int > tmpAtomsInProc(nproc, 0);
708	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
709	<	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++);
707	>	beginAtomIndex += stamp->getNAtoms();
708	>	beginRigidBodyIndex += stamp->getNRigidBodies();
709	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
710		}
711	+	#endif
712
713	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
530	<	rb = mol->nextRigidBody(ri)) {
531	<	rb->setGlobalIndex(beginRigidBodyIndex++);
532	<	}
713	>	} //end for(int i=0)
714
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	–
715		//fill globalGroupMembership
716		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
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);
736		info->setGlobalGroupMembership(tmpGroupMembership);
737		#else
738		info->setGlobalGroupMembership(globalGroupMembership);
739		#endif
740	<
740	>
741		//fill molMembership
742		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
743
744		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
571	–
745		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
746		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
747		}
748		}
749	<
749	>
750		#ifdef IS_MPI
751	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
752	<
751	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
752	>
753		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
754		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
755
#	Line 585 | Line 758 | namespace oopse {
758		info->setGlobalMolMembership(globalMolMembership);
759		#endif
760
761	<	}
761	>	// nIOPerMol holds the number of integrable objects per molecule
762	>	// here the molecules are listed by their global indices.
763
764	<	void SimCreator::loadCoordinates(SimInfo* info) {
764	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
765	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
766	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
767	>	}
768	>
769	>	#ifdef IS_MPI
770	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
771	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
772	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
773	>	#else
774	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
775	>	#endif
776	>
777	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
778	>
779	>	int startingIndex = 0;
780	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
781	>	startingIOIndexForMol[i] = startingIndex;
782	>	startingIndex += numIntegrableObjectsPerMol[i];
783	>	}
784	>
785	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
786	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
787	>	int myGlobalIndex = mol->getGlobalIndex();
788	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
789	>	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
790	>	integrableObject = mol->nextIntegrableObject(ioi)) {
791	>	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
792	>	IOIndexToIntegrableObject[globalIO] = integrableObject;
793	>	globalIO++;
794	>	}
795	>	}
796	>
797	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
798	>
799	>	}
800	>
801	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
802		Globals* simParams;
803	+
804		simParams = info->getSimParams();
805
806	<	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());
806	>	DumpReader reader(info, mdFileName);
807		int nframes = reader.getNFrames();
808
809		if (nframes > 0) {
810		reader.readFrame(nframes - 1);
811		} else {
812		//invalid initial coordinate file
813	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
814	<	simParams->getInitialConfig());
813	>	sprintf(painCave.errMsg,
814	>	"Initial configuration file %s should at least contain one frame\n",
815	>	mdFileName.c_str());
816		painCave.isFatal = 1;
817		simError();
818		}
613	–
819		//copy the current snapshot to previous snapshot
820		info->getSnapshotManager()->advance();
821		}
822	+
823	+	} //end namespace OpenMD
824
618	–	} //end namespace oopse
825
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 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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