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

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 46 | Line 47
47		* @time 13:51am
48		* @version 1.0
49		*/
50	+	#include <exception>
51	+	#include <iostream>
52	+	#include <sstream>
53	+	#include <string>
54
55		#include "brains/MoleculeCreator.hpp"
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
54	–	#include "io/parse_me.h"
59		#include "UseTheForce/ForceFieldFactory.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62		#include "math/SeqRandNumGen.hpp"
63	+	#include "mdParser/MDLexer.hpp"
64	+	#include "mdParser/MDParser.hpp"
65	+	#include "mdParser/MDTreeParser.hpp"
66	+	#include "mdParser/SimplePreprocessor.hpp"
67	+	#include "antlr/ANTLRException.hpp"
68	+	#include "antlr/TokenStreamRecognitionException.hpp"
69	+	#include "antlr/TokenStreamIOException.hpp"
70	+	#include "antlr/TokenStreamException.hpp"
71	+	#include "antlr/RecognitionException.hpp"
72	+	#include "antlr/CharStreamException.hpp"
73	+
74	+	#include "antlr/MismatchedCharException.hpp"
75	+	#include "antlr/MismatchedTokenException.hpp"
76	+	#include "antlr/NoViableAltForCharException.hpp"
77	+	#include "antlr/NoViableAltException.hpp"
78	+
79		#ifdef IS_MPI
80	<	#include "io/mpiBASS.h"
80	>	#include "mpi.h"
81		#include "math/ParallelRandNumGen.hpp"
82		#endif
83
84	<	namespace oopse {
84	>	namespace OpenMD {
85	>
86	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
87	>	Globals* simParams = NULL;
88	>	try {
89
90	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
90	>	// Create a preprocessor that preprocesses md file into an ostringstream
91	>	std::stringstream ppStream;
92	>	#ifdef IS_MPI
93	>	int streamSize;
94	>	const int masterNode = 0;
95	>	int commStatus;
96	>	if (worldRank == masterNode) {
97	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
98	>	#endif
99	>	SimplePreprocessor preprocessor;
100	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
101	>
102	>	#ifdef IS_MPI
103	>	//brocasting the stream size
104	>	streamSize = ppStream.str().size() +1;
105	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
106
107	<	#ifdef IS_MPI
107	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
108	>
109	>
110	>	} else {
111
112	<	if (worldRank == 0) {
71	<	#endif // is_mpi
112	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
113
114	<	simParams->initalize();
115	<	set_interface_stamps(stamps, simParams);
114	>	//get stream size
115	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
116
117	<	#ifdef IS_MPI
117	>	char* buf = new char[streamSize];
118	>	assert(buf);
119	>
120	>	//receive file content
121	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
122	>
123	>	ppStream.str(buf);
124	>	delete [] buf;
125
126	<	mpiEventInit();
126	>	}
127	>	#endif
128	>	// Create a scanner that reads from the input stream
129	>	MDLexer lexer(ppStream);
130	>	lexer.setFilename(filename);
131	>	lexer.initDeferredLineCount();
132	>
133	>	// Create a parser that reads from the scanner
134	>	MDParser parser(lexer);
135	>	parser.setFilename(filename);
136
137	<	#endif
137	>	// Create an observer that synchorizes file name change
138	>	FilenameObserver observer;
139	>	observer.setLexer(&lexer);
140	>	observer.setParser(&parser);
141	>	lexer.setObserver(&observer);
142	>
143	>	antlr::ASTFactory factory;
144	>	parser.initializeASTFactory(factory);
145	>	parser.setASTFactory(&factory);
146	>	parser.mdfile();
147
148	<	yacc_BASS(mdFileName.c_str());
148	>	// Create a tree parser that reads information into Globals
149	>	MDTreeParser treeParser;
150	>	treeParser.initializeASTFactory(factory);
151	>	treeParser.setASTFactory(&factory);
152	>	simParams = treeParser.walkTree(parser.getAST());
153	>	}
154
155	<	#ifdef IS_MPI
156	<
157	<	throwMPIEvent(NULL);
158	<	} else {
159	<	set_interface_stamps(stamps, simParams);
160	<	mpiEventInit();
161	<	MPIcheckPoint();
91	<	mpiEventLoop();
155	>
156	>	catch(antlr::MismatchedCharException& e) {
157	>	sprintf(painCave.errMsg,
158	>	"parser exception: %s %s:%d:%d\n",
159	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
160	>	painCave.isFatal = 1;
161	>	simError();
162		}
163	+	catch(antlr::MismatchedTokenException &e) {
164	+	sprintf(painCave.errMsg,
165	+	"parser exception: %s %s:%d:%d\n",
166	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
167	+	painCave.isFatal = 1;
168	+	simError();
169	+	}
170	+	catch(antlr::NoViableAltForCharException &e) {
171	+	sprintf(painCave.errMsg,
172	+	"parser exception: %s %s:%d:%d\n",
173	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	+	painCave.isFatal = 1;
175	+	simError();
176	+	}
177	+	catch(antlr::NoViableAltException &e) {
178	+	sprintf(painCave.errMsg,
179	+	"parser exception: %s %s:%d:%d\n",
180	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	+	painCave.isFatal = 1;
182	+	simError();
183	+	}
184	+
185	+	catch(antlr::TokenStreamRecognitionException& e) {
186	+	sprintf(painCave.errMsg,
187	+	"parser exception: %s %s:%d:%d\n",
188	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
189	+	painCave.isFatal = 1;
190	+	simError();
191	+	}
192	+
193	+	catch(antlr::TokenStreamIOException& e) {
194	+	sprintf(painCave.errMsg,
195	+	"parser exception: %s\n",
196	+	e.getMessage().c_str());
197	+	painCave.isFatal = 1;
198	+	simError();
199	+	}
200	+
201	+	catch(antlr::TokenStreamException& e) {
202	+	sprintf(painCave.errMsg,
203	+	"parser exception: %s\n",
204	+	e.getMessage().c_str());
205	+	painCave.isFatal = 1;
206	+	simError();
207	+	}
208	+	catch (antlr::RecognitionException& e) {
209	+	sprintf(painCave.errMsg,
210	+	"parser exception: %s %s:%d:%d\n",
211	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
212	+	painCave.isFatal = 1;
213	+	simError();
214	+	}
215	+	catch (antlr::CharStreamException& e) {
216	+	sprintf(painCave.errMsg,
217	+	"parser exception: %s\n",
218	+	e.getMessage().c_str());
219	+	painCave.isFatal = 1;
220	+	simError();
221	+	}
222	+	catch (OpenMDException& e) {
223	+	sprintf(painCave.errMsg,
224	+	"%s\n",
225	+	e.getMessage().c_str());
226	+	painCave.isFatal = 1;
227	+	simError();
228	+	}
229	+	catch (std::exception& e) {
230	+	sprintf(painCave.errMsg,
231	+	"parser exception: %s\n",
232	+	e.what());
233	+	painCave.isFatal = 1;
234	+	simError();
235	+	}
236
237	<	#endif
238	<
237	>	simParams->setMDfileVersion(mdFileVersion);
238	>	return simParams;
239		}
240	<
241	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
242	<
243	<	MakeStamps * stamps = new MakeStamps();
244	<
245	<	Globals * simParams = new Globals();
246	<
247	<	//parse meta-data file
248	<	parseFile(mdFileName, stamps, simParams);
240	>
241	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
242	>	bool loadInitCoords) {
243	>
244	>	const int bufferSize = 65535;
245	>	char buffer[bufferSize];
246	>	int lineNo = 0;
247	>	std::string mdRawData;
248	>	int metaDataBlockStart = -1;
249	>	int metaDataBlockEnd = -1;
250	>	int i;
251	>	int mdOffset;
252	>	int mdFileVersion;
253
254	<	//create the force field
255	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
256	<	simParams->getForceField());
254	>	#ifdef IS_MPI
255	>	const int masterNode = 0;
256	>	if (worldRank == masterNode) {
257	>	#endif
258	>
259	>	std::ifstream mdFile_(mdFileName.c_str());
260	>
261	>	if (mdFile_.fail()) {
262	>	sprintf(painCave.errMsg,
263	>	"SimCreator: Cannot open file: %s\n",
264	>	mdFileName.c_str());
265	>	painCave.isFatal = 1;
266	>	simError();
267	>	}
268	>
269	>	mdFile_.getline(buffer, bufferSize);
270	>	++lineNo;
271	>	std::string line = trimLeftCopy(buffer);
272	>	i = CaseInsensitiveFind(line, "<OpenMD");
273	>	if (static_cast<size_t>(i) == string::npos) {
274	>	// try the older file strings to see if that works:
275	>	i = CaseInsensitiveFind(line, "<OOPSE");
276	>	}
277	>
278	>	if (static_cast<size_t>(i) == string::npos) {
279	>	// still no luck!
280	>	sprintf(painCave.errMsg,
281	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
282	>	mdFileName.c_str());
283	>	painCave.isFatal = 1;
284	>	simError();
285	>	}
286	>
287	>	// found the correct opening string, now try to get the file
288	>	// format version number.
289	>
290	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
291	>	std::string fileType = tokenizer.nextToken();
292	>	toUpper(fileType);
293	>
294	>	mdFileVersion = 0;
295	>
296	>	if (fileType == "OPENMD") {
297	>	while (tokenizer.hasMoreTokens()) {
298	>	std::string token(tokenizer.nextToken());
299	>	toUpper(token);
300	>	if (token == "VERSION") {
301	>	mdFileVersion = tokenizer.nextTokenAsInt();
302	>	break;
303	>	}
304	>	}
305	>	}
306	>
307	>	//scan through the input stream and find MetaData tag
308	>	while(mdFile_.getline(buffer, bufferSize)) {
309	>	++lineNo;
310	>
311	>	std::string line = trimLeftCopy(buffer);
312	>	if (metaDataBlockStart == -1) {
313	>	i = CaseInsensitiveFind(line, "<MetaData>");
314	>	if (i != string::npos) {
315	>	metaDataBlockStart = lineNo;
316	>	mdOffset = mdFile_.tellg();
317	>	}
318	>	} else {
319	>	i = CaseInsensitiveFind(line, "</MetaData>");
320	>	if (i != string::npos) {
321	>	metaDataBlockEnd = lineNo;
322	>	}
323	>	}
324	>	}
325	>
326	>	if (metaDataBlockStart == -1) {
327	>	sprintf(painCave.errMsg,
328	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
329	>	mdFileName.c_str());
330	>	painCave.isFatal = 1;
331	>	simError();
332	>	}
333	>	if (metaDataBlockEnd == -1) {
334	>	sprintf(painCave.errMsg,
335	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
336	>	mdFileName.c_str());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>
341	>	mdFile_.clear();
342	>	mdFile_.seekg(0);
343	>	mdFile_.seekg(mdOffset);
344	>
345	>	mdRawData.clear();
346	>
347	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
348	>	mdFile_.getline(buffer, bufferSize);
349	>	mdRawData += buffer;
350	>	mdRawData += "\n";
351	>	}
352	>
353	>	mdFile_.close();
354	>
355	>	#ifdef IS_MPI
356	>	}
357	>	#endif
358	>
359	>	std::stringstream rawMetaDataStream(mdRawData);
360	>
361	>	//parse meta-data file
362	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
363	>	metaDataBlockStart + 1);
364
365	+	//create the force field
366	+	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
367	+
368		if (ff == NULL) {
369	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
370	<	simParams->getForceField());
369	>	sprintf(painCave.errMsg,
370	>	"ForceField Factory can not create %s force field\n",
371	>	simParams->getForceField().c_str());
372		painCave.isFatal = 1;
373		simError();
374		}
375	<
375	>
376		if (simParams->haveForceFieldFileName()) {
377		ff->setForceFieldFileName(simParams->getForceFieldFileName());
378		}
379
380		std::string forcefieldFileName;
381		forcefieldFileName = ff->getForceFieldFileName();
382	<
382	>
383		if (simParams->haveForceFieldVariant()) {
384		//If the force field has variant, the variant force field name will be
385		//Base.variant.frc. For exampel EAM.u6.frc
386	<
386	>
387		std::string variant = simParams->getForceFieldVariant();
388	<
388	>
389		std::string::size_type pos = forcefieldFileName.rfind(".frc");
390		variant = "." + variant;
391		if (pos != std::string::npos) {
#	Line 139 | Line 397 | namespace oopse {
397		}
398
399		ff->parse(forcefieldFileName);
142	–
143	–	//extract the molecule stamps
144	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
145	–	compList(stamps, simParams, moleculeStampPairs);
146	–
400		//create SimInfo
401	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
401	>	SimInfo * info = new SimInfo(ff, simParams);
402
403	<	//gather parameters (SimCreator only retrieves part of the parameters)
403	>	info->setRawMetaData(mdRawData);
404	>
405	>	//gather parameters (SimCreator only retrieves part of the
406	>	//parameters)
407		gatherParameters(info, mdFileName);
408	<
408	>
409		//divide the molecules and determine the global index of molecules
410		#ifdef IS_MPI
411		divideMolecules(info);
412		#endif
413	<
413	>
414		//create the molecules
415		createMolecules(info);
416	<
417	<
418	<	//allocate memory for DataStorage(circular reference, need to break it)
416	>
417	>	//allocate memory for DataStorage(circular reference, need to
418	>	//break it)
419		info->setSnapshotManager(new SimSnapshotManager(info));
420
421	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
422	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
423	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
421	>	//set the global index of atoms, rigidbodies and cutoffgroups
422	>	//(only need to be set once, the global index will never change
423	>	//again). Local indices of atoms and rigidbodies are already set
424	>	//by MoleculeCreator class which actually delegates the
425	>	//responsibility to LocalIndexManager.
426		setGlobalIndex(info);
427	<
428	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
429	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
430	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
431	<	//we can determine the beginning global indices of atoms before they get created.
427	>
428	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
429	>	//method, at that point atoms don't have the global index yet
430	>	//(their global index are all initialized to -1).  Therefore we
431	>	//have to call addInteractionPairs explicitly here. A way to work
432	>	//around is that we can determine the beginning global indices of
433	>	//atoms before they get created.
434		SimInfo::MoleculeIterator mi;
435		Molecule* mol;
436		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
437	<	info->addExcludePairs(mol);
437	>	info->addInteractionPairs(mol);
438		}
439
180	–
181	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
182	–	//eta, chi for NPT integrator)
440		if (loadInitCoords)
441	<	loadCoordinates(info);
185	<
441	>	loadCoordinates(info, mdFileName);
442		return info;
443		}
444	<
444	>
445		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
446	<
447	<	//figure out the ouput file names
446	>
447	>	//figure out the output file names
448		std::string prefix;
449	<
449	>
450		#ifdef IS_MPI
451	<
451	>
452		if (worldRank == 0) {
453		#endif // is_mpi
454		Globals * simParams = info->getSimParams();
#	Line 201 | Line 457 | namespace oopse {
457		} else {
458		prefix = getPrefix(mdfile);
459		}
460	<
460	>
461		info->setFinalConfigFileName(prefix + ".eor");
462		info->setDumpFileName(prefix + ".dump");
463		info->setStatFileName(prefix + ".stat");
464	<
464	>	info->setRestFileName(prefix + ".zang");
465	>
466		#ifdef IS_MPI
467	<
467	>
468		}
469	<
469	>
470		#endif
471	<
471	>
472		}
473	<
473	>
474		#ifdef IS_MPI
475		void SimCreator::divideMolecules(SimInfo *info) {
476	<	double numerator;
477	<	double denominator;
478	<	double precast;
479	<	double x;
480	<	double y;
481	<	double a;
476	>	RealType numerator;
477	>	RealType denominator;
478	>	RealType precast;
479	>	RealType x;
480	>	RealType y;
481	>	RealType a;
482		int old_atoms;
483		int add_atoms;
484		int new_atoms;
#	Line 237 | Line 494 | namespace oopse {
494		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
495
496		MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
497	<
497	>
498		if (nProcessors > nGlobalMols) {
499		sprintf(painCave.errMsg,
500		"nProcessors (%d) > nMol (%d)\n"
#	Line 245 | Line 502 | namespace oopse {
502		"\tthe number of molecules.  This will not result in a \n"
503		"\tusable division of atoms for force decomposition.\n"
504		"\tEither try a smaller number of processors, or run the\n"
505	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
506	<
505	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
506	>
507		painCave.isFatal = 1;
508		simError();
509		}
510	<
510	>
511		int seedValue;
512		Globals * simParams = info->getSimParams();
513		SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
#	Line 260 | Line 517 | namespace oopse {
517		}else {
518		myRandom = new SeqRandNumGen();
519		}
520	<
521	<
520	>
521	>
522		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
523	<
523	>
524		//initialize atomsPerProc
525		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
526	<
526	>
527		if (worldRank == 0) {
528		numerator = info->getNGlobalAtoms();
529		denominator = nProcessors;
530		precast = numerator / denominator;
531		nTarget = (int)(precast + 0.5);
532	<
532	>
533		for(i = 0; i < nGlobalMols; i++) {
534		done = 0;
535		loops = 0;
536	<
536	>
537		while (!done) {
538		loops++;
539	<
539	>
540		// Pick a processor at random
541	<
541	>
542		which_proc = (int) (myRandom->rand() * nProcessors);
543	<
543	>
544		//get the molecule stamp first
545		int stampId = info->getMoleculeStampId(i);
546		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
547	<
547	>
548		// How many atoms does this processor have so far?
549		old_atoms = atomsPerProc[which_proc];
550		add_atoms = moleculeStamp->getNAtoms();
551		new_atoms = old_atoms + add_atoms;
552	<
552	>
553		// If we've been through this loop too many times, we need
554		// to just give up and assign the molecule to this processor
555		// and be done with it.
556	<
556	>
557		if (loops > 100) {
558		sprintf(painCave.errMsg,
559		"I've tried 100 times to assign molecule %d to a "
560		" processor, but can't find a good spot.\n"
561		"I'm assigning it at random to processor %d.\n",
562		i, which_proc);
563	<
563	>
564		painCave.isFatal = 0;
565		simError();
566	<
566	>
567		molToProcMap[i] = which_proc;
568		atomsPerProc[which_proc] += add_atoms;
569	<
569	>
570		done = 1;
571		continue;
572		}
573	<
573	>
574		// If we can add this molecule to this processor without sending
575		// it above nTarget, then go ahead and do it:
576	<
576	>
577		if (new_atoms <= nTarget) {
578		molToProcMap[i] = which_proc;
579		atomsPerProc[which_proc] += add_atoms;
580	<
580	>
581		done = 1;
582		continue;
583		}
584	<
584	>
585		// The only situation left is when new_atoms > nTarget.  We
586		// want to accept this with some probability that dies off the
587		// farther we are from nTarget
588	<
588	>
589		// roughly:  x = new_atoms - nTarget
590		//           Pacc(x) = exp(- a * x)
591		// where a = penalty / (average atoms per molecule)
592	<
593	<	x = (double)(new_atoms - nTarget);
592	>
593	>	x = (RealType)(new_atoms - nTarget);
594		y = myRandom->rand();
595	<
595	>
596		if (y < exp(- a * x)) {
597		molToProcMap[i] = which_proc;
598		atomsPerProc[which_proc] += add_atoms;
599	<
599	>
600		done = 1;
601		continue;
602		} else {
#	Line 347 | Line 604 | namespace oopse {
604		}
605		}
606		}
607	<
607	>
608		delete myRandom;
609	<
609	>
610		// Spray out this nonsense to all other processors:
611	<
611	>
612		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
613		} else {
614	<
614	>
615		// Listen to your marching orders from processor 0:
616	<
616	>
617		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
618		}
619	<
619	>
620		info->setMolToProcMap(molToProcMap);
621		sprintf(checkPointMsg,
622		"Successfully divided the molecules among the processors.\n");
623	<	MPIcheckPoint();
623	>	errorCheckPoint();
624		}
625	<
625	>
626		#endif
627	<
627	>
628		void SimCreator::createMolecules(SimInfo *info) {
629		MoleculeCreator molCreator;
630		int stampId;
631	<
631	>
632		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
633	<
633	>
634		#ifdef IS_MPI
635	<
635	>
636		if (info->getMolToProc(i) == worldRank) {
637		#endif
638	<
638	>
639		stampId = info->getMoleculeStampId(i);
640	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
641	<	stampId, i, info->getLocalIndexManager());
642	<
640	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
641	>	info->getMoleculeStamp(stampId),
642	>	stampId, i,
643	>	info->getLocalIndexManager());
644	>
645		info->addMolecule(mol);
646	<
646	>
647		#ifdef IS_MPI
648	<
648	>
649		}
650	<
650	>
651		#endif
652	<
652	>
653		} //end for(int i=0)
654		}
655	<
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	<
655	>
656		void SimCreator::setGlobalIndex(SimInfo *info) {
657		SimInfo::MoleculeIterator mi;
658		Molecule::AtomIterator ai;
659		Molecule::RigidBodyIterator ri;
660		Molecule::CutoffGroupIterator ci;
661	+	Molecule::IntegrableObjectIterator  ioi;
662		Molecule * mol;
663		Atom * atom;
664		RigidBody * rb;
#	Line 470 | Line 668 | namespace oopse {
668		int beginCutoffGroupIndex;
669		int nGlobalAtoms = info->getNGlobalAtoms();
670
473	–	#ifndef IS_MPI
474	–
671		beginAtomIndex = 0;
672		beginRigidBodyIndex = 0;
673		beginCutoffGroupIndex = 0;
674
675	<	#else
675	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
676	>
677	>	#ifdef IS_MPI
678	>	if (info->getMolToProc(i) == worldRank) {
679	>	#endif
680	>	// stuff to do if I own this molecule
681	>	mol = info->getMoleculeByGlobalIndex(i);
682
683	<	int nproc;
684	<	int myNode;
683	>	//local index(index in DataStorge) of atom is important
684	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	>	atom->setGlobalIndex(beginAtomIndex++);
686	>	}
687	>
688	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
689	>	rb = mol->nextRigidBody(ri)) {
690	>	rb->setGlobalIndex(beginRigidBodyIndex++);
691	>	}
692	>
693	>	//local index of cutoff group is trivial, it only depends on
694	>	//the order of travesing
695	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
696	>	cg = mol->nextCutoffGroup(ci)) {
697	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
698	>	}
699	>
700	>	#ifdef IS_MPI
701	>	}  else {
702
703	<	myNode = worldRank;
704	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
703	>	// stuff to do if I don't own this molecule
704	>
705	>	int stampId = info->getMoleculeStampId(i);
706	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
707
708	<	std::vector < int > tmpAtomsInProc(nproc, 0);
709	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
710	<	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++);
708	>	beginAtomIndex += stamp->getNAtoms();
709	>	beginRigidBodyIndex += stamp->getNRigidBodies();
710	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
711		}
712	+	#endif
713
714	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
530	<	rb = mol->nextRigidBody(ri)) {
531	<	rb->setGlobalIndex(beginRigidBodyIndex++);
532	<	}
714	>	} //end for(int i=0)
715
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	–
716		//fill globalGroupMembership
717		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
718		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
719		for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
720	<
720	>
721		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
722		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
723		}
724	<
724	>
725		}
726		}
727	<
727	>
728		#ifdef IS_MPI
729		// Since the globalGroupMembership has been zero filled and we've only
730		// poked values into the atoms we know, we can do an Allreduce
731		// to get the full globalGroupMembership array (We think).
732		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
733		// docs said we could.
734	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
734	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
735		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
736		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
737		info->setGlobalGroupMembership(tmpGroupMembership);
738		#else
739		info->setGlobalGroupMembership(globalGroupMembership);
740		#endif
741	<
741	>
742		//fill molMembership
743		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
744
745		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
571	–
746		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
747		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
748		}
749		}
750	<
750	>
751		#ifdef IS_MPI
752	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
753	<
752	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
753	>
754		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
755		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
756
#	Line 585 | Line 759 | namespace oopse {
759		info->setGlobalMolMembership(globalMolMembership);
760		#endif
761
762	<	}
762	>	// nIOPerMol holds the number of integrable objects per molecule
763	>	// here the molecules are listed by their global indices.
764
765	<	void SimCreator::loadCoordinates(SimInfo* info) {
765	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
766	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
767	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
768	>	}
769	>
770	>	#ifdef IS_MPI
771	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
772	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
773	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
774	>	#else
775	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
776	>	#endif
777	>
778	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
779	>
780	>	int startingIndex = 0;
781	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
782	>	startingIOIndexForMol[i] = startingIndex;
783	>	startingIndex += numIntegrableObjectsPerMol[i];
784	>	}
785	>
786	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
787	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
788	>	int myGlobalIndex = mol->getGlobalIndex();
789	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
790	>	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
791	>	integrableObject = mol->nextIntegrableObject(ioi)) {
792	>	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
793	>	IOIndexToIntegrableObject[globalIO] = integrableObject;
794	>	globalIO++;
795	>	}
796	>	}
797	>
798	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
799	>
800	>	}
801	>
802	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
803		Globals* simParams;
804	+
805		simParams = info->getSimParams();
806
807	<	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());
807	>	DumpReader reader(info, mdFileName);
808		int nframes = reader.getNFrames();
809
810		if (nframes > 0) {
811		reader.readFrame(nframes - 1);
812		} else {
813		//invalid initial coordinate file
814	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
815	<	simParams->getInitialConfig());
814	>	sprintf(painCave.errMsg,
815	>	"Initial configuration file %s should at least contain one frame\n",
816	>	mdFileName.c_str());
817		painCave.isFatal = 1;
818		simError();
819		}
613	–
820		//copy the current snapshot to previous snapshot
821		info->getSnapshotManager()->advance();
822		}
823	+
824	+	} //end namespace OpenMD
825
618	–	} //end namespace oopse
826
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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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