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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 1803 by gezelter, Wed Oct 3 14:20:07 2012 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"
59	<	#include "io/parse_me.h"
55	<	#include "UseTheForce/ForceFieldFactory.hpp"
59	>	#include "brains/ForceField.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	+	#include "types/DirectionalAdapter.hpp"
80	+	#include "types/MultipoleAdapter.hpp"
81	+	#include "types/EAMAdapter.hpp"
82	+	#include "types/SuttonChenAdapter.hpp"
83	+	#include "types/PolarizableAdapter.hpp"
84	+	#include "types/FixedChargeAdapter.hpp"
85	+	#include "types/FluctuatingChargeAdapter.hpp"
86	+
87		#ifdef IS_MPI
88	<	#include "io/mpiBASS.h"
88	>	#include "mpi.h"
89		#include "math/ParallelRandNumGen.hpp"
90		#endif
91
92	<	namespace oopse {
92	>	namespace OpenMD {
93	>
94	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95	>	Globals* simParams = NULL;
96	>	try {
97
98	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
98	>	// Create a preprocessor that preprocesses md file into an ostringstream
99	>	std::stringstream ppStream;
100	>	#ifdef IS_MPI
101	>	int streamSize;
102	>	const int masterNode = 0;
103	>	int commStatus;
104	>	if (worldRank == masterNode) {
105	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
106	>	#endif
107	>	SimplePreprocessor preprocessor;
108	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
109	>
110	>	#ifdef IS_MPI
111	>	//brocasting the stream size
112	>	streamSize = ppStream.str().size() +1;
113	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
114
115	<	#ifdef IS_MPI
115	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
116	>
117	>
118	>	} else {
119
120	<	if (worldRank == 0) {
71	<	#endif // is_mpi
120	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121
122	<	simParams->initalize();
123	<	set_interface_stamps(stamps, simParams);
122	>	//get stream size
123	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124
125	<	#ifdef IS_MPI
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127	>
128	>	//receive file content
129	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
130	>
131	>	ppStream.str(buf);
132	>	delete [] buf;
133
134	<	mpiEventInit();
134	>	}
135	>	#endif
136	>	// Create a scanner that reads from the input stream
137	>	MDLexer lexer(ppStream);
138	>	lexer.setFilename(filename);
139	>	lexer.initDeferredLineCount();
140	>
141	>	// Create a parser that reads from the scanner
142	>	MDParser parser(lexer);
143	>	parser.setFilename(filename);
144
145	<	#endif
145	>	// Create an observer that synchorizes file name change
146	>	FilenameObserver observer;
147	>	observer.setLexer(&lexer);
148	>	observer.setParser(&parser);
149	>	lexer.setObserver(&observer);
150	>
151	>	antlr::ASTFactory factory;
152	>	parser.initializeASTFactory(factory);
153	>	parser.setASTFactory(&factory);
154	>	parser.mdfile();
155
156	<	yacc_BASS(mdFileName.c_str());
156	>	// Create a tree parser that reads information into Globals
157	>	MDTreeParser treeParser;
158	>	treeParser.initializeASTFactory(factory);
159	>	treeParser.setASTFactory(&factory);
160	>	simParams = treeParser.walkTree(parser.getAST());
161	>	}
162
163	<	#ifdef IS_MPI
164	<
165	<	throwMPIEvent(NULL);
166	<	} else {
167	<	set_interface_stamps(stamps, simParams);
168	<	mpiEventInit();
169	<	MPIcheckPoint();
91	<	mpiEventLoop();
163	>
164	>	catch(antlr::MismatchedCharException& e) {
165	>	sprintf(painCave.errMsg,
166	>	"parser exception: %s %s:%d:%d\n",
167	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
168	>	painCave.isFatal = 1;
169	>	simError();
170		}
171	+	catch(antlr::MismatchedTokenException &e) {
172	+	sprintf(painCave.errMsg,
173	+	"parser exception: %s %s:%d:%d\n",
174	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
175	+	painCave.isFatal = 1;
176	+	simError();
177	+	}
178	+	catch(antlr::NoViableAltForCharException &e) {
179	+	sprintf(painCave.errMsg,
180	+	"parser exception: %s %s:%d:%d\n",
181	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
182	+	painCave.isFatal = 1;
183	+	simError();
184	+	}
185	+	catch(antlr::NoViableAltException &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::TokenStreamRecognitionException& e) {
194	+	sprintf(painCave.errMsg,
195	+	"parser exception: %s %s:%d:%d\n",
196	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
197	+	painCave.isFatal = 1;
198	+	simError();
199	+	}
200	+
201	+	catch(antlr::TokenStreamIOException& e) {
202	+	sprintf(painCave.errMsg,
203	+	"parser exception: %s\n",
204	+	e.getMessage().c_str());
205	+	painCave.isFatal = 1;
206	+	simError();
207	+	}
208	+
209	+	catch(antlr::TokenStreamException& e) {
210	+	sprintf(painCave.errMsg,
211	+	"parser exception: %s\n",
212	+	e.getMessage().c_str());
213	+	painCave.isFatal = 1;
214	+	simError();
215	+	}
216	+	catch (antlr::RecognitionException& e) {
217	+	sprintf(painCave.errMsg,
218	+	"parser exception: %s %s:%d:%d\n",
219	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
220	+	painCave.isFatal = 1;
221	+	simError();
222	+	}
223	+	catch (antlr::CharStreamException& e) {
224	+	sprintf(painCave.errMsg,
225	+	"parser exception: %s\n",
226	+	e.getMessage().c_str());
227	+	painCave.isFatal = 1;
228	+	simError();
229	+	}
230	+	catch (OpenMDException& e) {
231	+	sprintf(painCave.errMsg,
232	+	"%s\n",
233	+	e.getMessage().c_str());
234	+	painCave.isFatal = 1;
235	+	simError();
236	+	}
237	+	catch (std::exception& e) {
238	+	sprintf(painCave.errMsg,
239	+	"parser exception: %s\n",
240	+	e.what());
241	+	painCave.isFatal = 1;
242	+	simError();
243	+	}
244
245	<	#endif
246	<
245	>	simParams->setMDfileVersion(mdFileVersion);
246	>	return simParams;
247		}
248	<
249	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
248	>
249	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250	>	bool loadInitCoords) {
251
252	<	MakeStamps * stamps = new MakeStamps();
252	>	const int bufferSize = 65535;
253	>	char buffer[bufferSize];
254	>	int lineNo = 0;
255	>	std::string mdRawData;
256	>	int metaDataBlockStart = -1;
257	>	int metaDataBlockEnd = -1;
258	>	int i;
259	>	streamoff mdOffset;
260	>	int mdFileVersion;
261
102	–	Globals * simParams = new Globals();
262
263	<	//parse meta-data file
264	<	parseFile(mdFileName, stamps, simParams);
263	>	#ifdef IS_MPI
264	>	const int masterNode = 0;
265	>	if (worldRank == masterNode) {
266	>	#endif
267
268	<	//create the force field
269	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
270	<	simParams->getForceField());
268	>	std::ifstream mdFile_;
269	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
270	>
271	>	if (mdFile_.fail()) {
272	>	sprintf(painCave.errMsg,
273	>	"SimCreator: Cannot open file: %s\n",
274	>	mdFileName.c_str());
275	>	painCave.isFatal = 1;
276	>	simError();
277	>	}
278	>
279	>	mdFile_.getline(buffer, bufferSize);
280	>	++lineNo;
281	>	std::string line = trimLeftCopy(buffer);
282	>	i = CaseInsensitiveFind(line, "<OpenMD");
283	>	if (static_cast<size_t>(i) == string::npos) {
284	>	// try the older file strings to see if that works:
285	>	i = CaseInsensitiveFind(line, "<OOPSE");
286	>	}
287	>
288	>	if (static_cast<size_t>(i) == string::npos) {
289	>	// still no luck!
290	>	sprintf(painCave.errMsg,
291	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
292	>	mdFileName.c_str());
293	>	painCave.isFatal = 1;
294	>	simError();
295	>	}
296	>
297	>	// found the correct opening string, now try to get the file
298	>	// format version number.
299	>
300	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
301	>	std::string fileType = tokenizer.nextToken();
302	>	toUpper(fileType);
303	>
304	>	mdFileVersion = 0;
305	>
306	>	if (fileType == "OPENMD") {
307	>	while (tokenizer.hasMoreTokens()) {
308	>	std::string token(tokenizer.nextToken());
309	>	toUpper(token);
310	>	if (token == "VERSION") {
311	>	mdFileVersion = tokenizer.nextTokenAsInt();
312	>	break;
313	>	}
314	>	}
315	>	}
316	>
317	>	//scan through the input stream and find MetaData tag
318	>	while(mdFile_.getline(buffer, bufferSize)) {
319	>	++lineNo;
320	>
321	>	std::string line = trimLeftCopy(buffer);
322	>	if (metaDataBlockStart == -1) {
323	>	i = CaseInsensitiveFind(line, "<MetaData>");
324	>	if (i != string::npos) {
325	>	metaDataBlockStart = lineNo;
326	>	mdOffset = mdFile_.tellg();
327	>	}
328	>	} else {
329	>	i = CaseInsensitiveFind(line, "</MetaData>");
330	>	if (i != string::npos) {
331	>	metaDataBlockEnd = lineNo;
332	>	}
333	>	}
334	>	}
335	>
336	>	if (metaDataBlockStart == -1) {
337	>	sprintf(painCave.errMsg,
338	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
339	>	mdFileName.c_str());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343	>	if (metaDataBlockEnd == -1) {
344	>	sprintf(painCave.errMsg,
345	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
346	>	mdFileName.c_str());
347	>	painCave.isFatal = 1;
348	>	simError();
349	>	}
350	>
351	>	mdFile_.clear();
352	>	mdFile_.seekg(0);
353	>	mdFile_.seekg(mdOffset);
354	>
355	>	mdRawData.clear();
356	>
357	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
358	>	mdFile_.getline(buffer, bufferSize);
359	>	mdRawData += buffer;
360	>	mdRawData += "\n";
361	>	}
362	>
363	>	mdFile_.close();
364	>
365	>	#ifdef IS_MPI
366	>	}
367	>	#endif
368	>
369	>	std::stringstream rawMetaDataStream(mdRawData);
370	>
371	>	//parse meta-data file
372	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373	>	metaDataBlockStart + 1);
374
375	+	//create the force field
376	+	ForceField * ff = new ForceField(simParams->getForceField());
377	+
378		if (ff == NULL) {
379	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
380	<	simParams->getForceField());
379	>	sprintf(painCave.errMsg,
380	>	"ForceField Factory can not create %s force field\n",
381	>	simParams->getForceField().c_str());
382		painCave.isFatal = 1;
383		simError();
384		}
385	<
385	>
386		if (simParams->haveForceFieldFileName()) {
387		ff->setForceFieldFileName(simParams->getForceFieldFileName());
388		}
389
390		std::string forcefieldFileName;
391		forcefieldFileName = ff->getForceFieldFileName();
392	<
392	>
393		if (simParams->haveForceFieldVariant()) {
394		//If the force field has variant, the variant force field name will be
395		//Base.variant.frc. For exampel EAM.u6.frc
396	<
396	>
397		std::string variant = simParams->getForceFieldVariant();
398	<
398	>
399		std::string::size_type pos = forcefieldFileName.rfind(".frc");
400		variant = "." + variant;
401		if (pos != std::string::npos) {
#	Line 139 | Line 407 | namespace oopse {
407		}
408
409		ff->parse(forcefieldFileName);
142	–
143	–	//extract the molecule stamps
144	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
145	–	compList(stamps, simParams, moleculeStampPairs);
146	–
410		//create SimInfo
411	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
411	>	SimInfo * info = new SimInfo(ff, simParams);
412
413	<	//gather parameters (SimCreator only retrieves part of the parameters)
413	>	info->setRawMetaData(mdRawData);
414	>
415	>	//gather parameters (SimCreator only retrieves part of the
416	>	//parameters)
417		gatherParameters(info, mdFileName);
418	<
418	>
419		//divide the molecules and determine the global index of molecules
420		#ifdef IS_MPI
421		divideMolecules(info);
422		#endif
423	<
423	>
424		//create the molecules
425		createMolecules(info);
426	+
427	+	//find the storage layout
428
429	+	int storageLayout = computeStorageLayout(info);
430
431	<	//allocate memory for DataStorage(circular reference, need to break it)
432	<	info->setSnapshotManager(new SimSnapshotManager(info));
431	>	//allocate memory for DataStorage(circular reference, need to
432	>	//break it)
433	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
436	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
437	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
435	>	//set the global index of atoms, rigidbodies and cutoffgroups
436	>	//(only need to be set once, the global index will never change
437	>	//again). Local indices of atoms and rigidbodies are already set
438	>	//by MoleculeCreator class which actually delegates the
439	>	//responsibility to LocalIndexManager.
440		setGlobalIndex(info);
441	<
442	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
443	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
444	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
445	<	//we can determine the beginning global indices of atoms before they get created.
441	>
442	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
443	>	//method, at that point atoms don't have the global index yet
444	>	//(their global index are all initialized to -1).  Therefore we
445	>	//have to call addInteractionPairs explicitly here. A way to work
446	>	//around is that we can determine the beginning global indices of
447	>	//atoms before they get created.
448		SimInfo::MoleculeIterator mi;
449		Molecule* mol;
450		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
451	<	info->addExcludePairs(mol);
451	>	info->addInteractionPairs(mol);
452		}
453
180	–
181	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
182	–	//eta, chi for NPT integrator)
454		if (loadInitCoords)
455	<	loadCoordinates(info);
185	<
455	>	loadCoordinates(info, mdFileName);
456		return info;
457		}
458	<
458	>
459		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
460	<
461	<	//figure out the ouput file names
460	>
461	>	//figure out the output file names
462		std::string prefix;
463	<
463	>
464		#ifdef IS_MPI
465	<
465	>
466		if (worldRank == 0) {
467		#endif // is_mpi
468		Globals * simParams = info->getSimParams();
#	Line 201 | Line 471 | namespace oopse {
471		} else {
472		prefix = getPrefix(mdfile);
473		}
474	<
474	>
475		info->setFinalConfigFileName(prefix + ".eor");
476		info->setDumpFileName(prefix + ".dump");
477		info->setStatFileName(prefix + ".stat");
478	<
478	>	info->setRestFileName(prefix + ".zang");
479	>
480		#ifdef IS_MPI
481	<
481	>
482		}
483	<
483	>
484		#endif
485	<
485	>
486		}
487	<
487	>
488		#ifdef IS_MPI
489		void SimCreator::divideMolecules(SimInfo *info) {
490	<	double numerator;
491	<	double denominator;
492	<	double precast;
493	<	double x;
494	<	double y;
495	<	double a;
490	>	RealType numerator;
491	>	RealType denominator;
492	>	RealType precast;
493	>	RealType x;
494	>	RealType y;
495	>	RealType a;
496		int old_atoms;
497		int add_atoms;
498		int new_atoms;
#	Line 236 | Line 507 | namespace oopse {
507		int nGlobalMols = info->getNGlobalMolecules();
508		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
509
510	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
511	<
510	>	nProcessors = MPI::COMM_WORLD.Get_size();
511	>
512		if (nProcessors > nGlobalMols) {
513		sprintf(painCave.errMsg,
514		"nProcessors (%d) > nMol (%d)\n"
#	Line 245 | Line 516 | namespace oopse {
516		"\tthe number of molecules.  This will not result in a \n"
517		"\tusable division of atoms for force decomposition.\n"
518		"\tEither try a smaller number of processors, or run the\n"
519	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
520	<
519	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
520	>
521		painCave.isFatal = 1;
522		simError();
523		}
524	<
524	>
525		int seedValue;
526		Globals * simParams = info->getSimParams();
527		SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
#	Line 260 | Line 531 | namespace oopse {
531		}else {
532		myRandom = new SeqRandNumGen();
533		}
534	<
535	<
534	>
535	>
536		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
537	<
537	>
538		//initialize atomsPerProc
539		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
540	<
540	>
541		if (worldRank == 0) {
542		numerator = info->getNGlobalAtoms();
543		denominator = nProcessors;
544		precast = numerator / denominator;
545		nTarget = (int)(precast + 0.5);
546	<
546	>
547		for(i = 0; i < nGlobalMols; i++) {
548	+
549		done = 0;
550		loops = 0;
551	<
551	>
552		while (!done) {
553		loops++;
554	<
554	>
555		// Pick a processor at random
556	<
556	>
557		which_proc = (int) (myRandom->rand() * nProcessors);
558	<
558	>
559		//get the molecule stamp first
560		int stampId = info->getMoleculeStampId(i);
561		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
562	<
562	>
563		// How many atoms does this processor have so far?
564		old_atoms = atomsPerProc[which_proc];
565		add_atoms = moleculeStamp->getNAtoms();
566		new_atoms = old_atoms + add_atoms;
567	<
567	>
568		// If we've been through this loop too many times, we need
569		// to just give up and assign the molecule to this processor
570		// and be done with it.
571	<
571	>
572		if (loops > 100) {
573	+
574		sprintf(painCave.errMsg,
575	<	"I've tried 100 times to assign molecule %d to a "
576	<	" processor, but can't find a good spot.\n"
577	<	"I'm assigning it at random to processor %d.\n",
575	>	"There have been 100 attempts to assign molecule %d to an\n"
576	>	"\tunderworked processor, but there's no good place to\n"
577	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
578		i, which_proc);
579	<
579	>
580		painCave.isFatal = 0;
581	+	painCave.severity = OPENMD_INFO;
582		simError();
583	<
583	>
584		molToProcMap[i] = which_proc;
585		atomsPerProc[which_proc] += add_atoms;
586	<
586	>
587		done = 1;
588		continue;
589		}
590	<
590	>
591		// If we can add this molecule to this processor without sending
592		// it above nTarget, then go ahead and do it:
593	<
593	>
594		if (new_atoms <= nTarget) {
595		molToProcMap[i] = which_proc;
596		atomsPerProc[which_proc] += add_atoms;
597	<
597	>
598		done = 1;
599		continue;
600		}
601	<
601	>
602		// The only situation left is when new_atoms > nTarget.  We
603		// want to accept this with some probability that dies off the
604		// farther we are from nTarget
605	<
605	>
606		// roughly:  x = new_atoms - nTarget
607		//           Pacc(x) = exp(- a * x)
608		// where a = penalty / (average atoms per molecule)
609	<
610	<	x = (double)(new_atoms - nTarget);
609	>
610	>	x = (RealType)(new_atoms - nTarget);
611		y = myRandom->rand();
612	<
612	>
613		if (y < exp(- a * x)) {
614		molToProcMap[i] = which_proc;
615		atomsPerProc[which_proc] += add_atoms;
616	<
616	>
617		done = 1;
618		continue;
619		} else {
#	Line 347 | Line 621 | namespace oopse {
621		}
622		}
623		}
624	<
624	>
625		delete myRandom;
352	–
353	–	// Spray out this nonsense to all other processors:
626
627	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
627	>	// Spray out this nonsense to all other processors:
628	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
629		} else {
630	<
630	>
631		// Listen to your marching orders from processor 0:
632	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
633
360	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
634		}
635	<
635	>
636		info->setMolToProcMap(molToProcMap);
637		sprintf(checkPointMsg,
638		"Successfully divided the molecules among the processors.\n");
639	<	MPIcheckPoint();
639	>	errorCheckPoint();
640		}
641	<
641	>
642		#endif
643	<
643	>
644		void SimCreator::createMolecules(SimInfo *info) {
645		MoleculeCreator molCreator;
646		int stampId;
647	<
647	>
648		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
649	<
649	>
650		#ifdef IS_MPI
651	<
651	>
652		if (info->getMolToProc(i) == worldRank) {
653		#endif
654	<
654	>
655		stampId = info->getMoleculeStampId(i);
656	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
657	<	stampId, i, info->getLocalIndexManager());
658	<
656	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
657	>	info->getMoleculeStamp(stampId),
658	>	stampId, i,
659	>	info->getLocalIndexManager());
660	>
661		info->addMolecule(mol);
662	<
662	>
663		#ifdef IS_MPI
664	<
664	>
665		}
666	<
666	>
667		#endif
668	<
668	>
669		} //end for(int i=0)
670		}
671	+
672	+	int SimCreator::computeStorageLayout(SimInfo* info) {
673
674	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
675	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
676	<	int i;
677	<	char * id;
678	<	LinkedMolStamp* extractedStamp = NULL;
679	<	MoleculeStamp * currentStamp;
680	<	Component** the_components = simParams->getComponents();
681	<	int n_components = simParams->getNComponents();
674	>	Globals* simParams = info->getSimParams();
675	>	int nRigidBodies = info->getNGlobalRigidBodies();
676	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
677	>	set<AtomType*>::iterator i;
678	>	bool hasDirectionalAtoms = false;
679	>	bool hasFixedCharge = false;
680	>	bool hasDipoles = false;
681	>	bool hasQuadrupoles = false;
682	>	bool hasPolarizable = false;
683	>	bool hasFluctuatingCharge = false;
684	>	bool hasMetallic = false;
685	>	int storageLayout = 0;
686	>	storageLayout |= DataStorage::dslPosition;
687	>	storageLayout |= DataStorage::dslVelocity;
688	>	storageLayout |= DataStorage::dslForce;
689
690	<	if (!simParams->haveNMol()) {
407	<	// we don't have the total number of molecules, so we assume it is
408	<	// given in each component
690	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
691
692	<	for(i = 0; i < n_components; i++) {
693	<	if (!the_components[i]->haveNMol()) {
694	<	// we have a problem
695	<	sprintf(painCave.errMsg,
696	<	"SimCreator Error. No global NMol or component NMol given.\n"
697	<	"\tCannot calculate the number of atoms.\n");
692	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
693	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
694	>	EAMAdapter ea = EAMAdapter( (*i) );
695	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
696	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
697	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
698	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
699
700	<	painCave.isFatal = 1;
701	<	simError();
702	<	}
703	<
704	<	id = the_components[i]->getType();
700	>	if (da.isDirectional()){
701	>	hasDirectionalAtoms = true;
702	>	}
703	>	if (ma.isDipole()){
704	>	hasDipoles = true;
705	>	}
706	>	if (ma.isQuadrupole()){
707	>	hasQuadrupoles = true;
708	>	}
709	>	if (ea.isEAM() || sca.isSuttonChen()){
710	>	hasMetallic = true;
711	>	}
712	>	if ( fca.isFixedCharge() ){
713	>	hasFixedCharge = true;
714	>	}
715	>	if ( fqa.isFluctuatingCharge() ){
716	>	hasFluctuatingCharge = true;
717	>	}
718	>	if ( pa.isPolarizable() ){
719	>	hasPolarizable = true;
720	>	}
721	>	}
722	>
723	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
724	>	storageLayout |= DataStorage::dslAmat;
725	>	if(storageLayout & DataStorage::dslVelocity) {
726	>	storageLayout |= DataStorage::dslAngularMomentum;
727	>	}
728	>	if (storageLayout & DataStorage::dslForce) {
729	>	storageLayout |= DataStorage::dslTorque;
730	>	}
731	>	}
732	>	if (hasDipoles) {
733	>	storageLayout |= DataStorage::dslDipole;
734	>	}
735	>	if (hasQuadrupoles) {
736	>	storageLayout |= DataStorage::dslQuadrupole;
737	>	}
738	>	if (hasFixedCharge || hasFluctuatingCharge) {
739	>	storageLayout |= DataStorage::dslSkippedCharge;
740	>	}
741	>	if (hasMetallic) {
742	>	storageLayout |= DataStorage::dslDensity;
743	>	storageLayout |= DataStorage::dslFunctional;
744	>	storageLayout |= DataStorage::dslFunctionalDerivative;
745	>	}
746	>	if (hasPolarizable) {
747	>	storageLayout |= DataStorage::dslElectricField;
748	>	}
749	>	if (hasFluctuatingCharge){
750	>	storageLayout |= DataStorage::dslFlucQPosition;
751	>	if(storageLayout & DataStorage::dslVelocity) {
752	>	storageLayout |= DataStorage::dslFlucQVelocity;
753	>	}
754	>	if (storageLayout & DataStorage::dslForce) {
755	>	storageLayout |= DataStorage::dslFlucQForce;
756	>	}
757	>	}
758	>
759	>	// if the user has asked for them, make sure we've got the memory for the
760	>	// objects defined.
761
762	<	extractedStamp = stamps->extractMolStamp(id);
763	<	if (extractedStamp == NULL) {
764	<	sprintf(painCave.errMsg,
426	<	"SimCreator error: Component \"%s\" was not found in the "
427	<	"list of declared molecules\n", id);
762	>	if (simParams->getOutputParticlePotential()) {
763	>	storageLayout |= DataStorage::dslParticlePot;
764	>	}
765
766	<	painCave.isFatal = 1;
767	<	simError();
768	<	}
766	>	if (simParams->havePrintHeatFlux()) {
767	>	if (simParams->getPrintHeatFlux()) {
768	>	storageLayout |= DataStorage::dslParticlePot;
769	>	}
770	>	}
771
772	<	currentStamp = extractedStamp->getStamp();
773	<
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();
772	>	if (simParams->getOutputElectricField()) {
773	>	storageLayout |= DataStorage::dslElectricField;
774		}
775
776	<	#ifdef IS_MPI
777	<
778	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
779	<	MPIcheckPoint();
780	<
455	<	#endif // is_mpi
776	>	if (simParams->getOutputFluctuatingCharges()) {
777	>	storageLayout |= DataStorage::dslFlucQPosition;
778	>	storageLayout |= DataStorage::dslFlucQVelocity;
779	>	storageLayout |= DataStorage::dslFlucQForce;
780	>	}
781
782	+	return storageLayout;
783		}
784
785		void SimCreator::setGlobalIndex(SimInfo *info) {
#	Line 461 | Line 787 | namespace oopse {
787		Molecule::AtomIterator ai;
788		Molecule::RigidBodyIterator ri;
789		Molecule::CutoffGroupIterator ci;
790	+	Molecule::IntegrableObjectIterator  ioi;
791		Molecule * mol;
792		Atom * atom;
793		RigidBody * rb;
#	Line 469 | Line 796 | namespace oopse {
796		int beginRigidBodyIndex;
797		int beginCutoffGroupIndex;
798		int nGlobalAtoms = info->getNGlobalAtoms();
799	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
800
473	–	#ifndef IS_MPI
474	–
801		beginAtomIndex = 0;
802	<	beginRigidBodyIndex = 0;
802	>	//rigidbody's index begins right after atom's
803	>	beginRigidBodyIndex = info->getNGlobalAtoms();
804		beginCutoffGroupIndex = 0;
805
806	<	#else
806	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
807	>
808	>	#ifdef IS_MPI
809	>	if (info->getMolToProc(i) == worldRank) {
810	>	#endif
811	>	// stuff to do if I own this molecule
812	>	mol = info->getMoleculeByGlobalIndex(i);
813
814	<	int nproc;
815	<	int myNode;
814	>	//local index(index in DataStorge) of atom is important
815	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
816	>	atom->setGlobalIndex(beginAtomIndex++);
817	>	}
818	>
819	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
820	>	rb = mol->nextRigidBody(ri)) {
821	>	rb->setGlobalIndex(beginRigidBodyIndex++);
822	>	}
823	>
824	>	//local index of cutoff group is trivial, it only depends on
825	>	//the order of travesing
826	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
827	>	cg = mol->nextCutoffGroup(ci)) {
828	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
829	>	}
830	>
831	>	#ifdef IS_MPI
832	>	}  else {
833
834	<	myNode = worldRank;
835	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
834	>	// stuff to do if I don't own this molecule
835	>
836	>	int stampId = info->getMoleculeStampId(i);
837	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
838
839	<	std::vector < int > tmpAtomsInProc(nproc, 0);
840	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
841	<	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++);
839	>	beginAtomIndex += stamp->getNAtoms();
840	>	beginRigidBodyIndex += stamp->getNRigidBodies();
841	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
842		}
843	+	#endif
844
845	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
530	<	rb = mol->nextRigidBody(ri)) {
531	<	rb->setGlobalIndex(beginRigidBodyIndex++);
532	<	}
845	>	} //end for(int i=0)
846
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	–
847		//fill globalGroupMembership
848		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
849		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
850		for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
851	<
851	>
852		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
853		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
854		}
855	<
855	>
856		}
857		}
858	<
858	>
859		#ifdef IS_MPI
860		// Since the globalGroupMembership has been zero filled and we've only
861		// poked values into the atoms we know, we can do an Allreduce
862		// to get the full globalGroupMembership array (We think).
863		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
864		// docs said we could.
865	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
866	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
867	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
865	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
866	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
867	>	&tmpGroupMembership[0], nGlobalAtoms,
868	>	MPI::INT, MPI::SUM);
869		info->setGlobalGroupMembership(tmpGroupMembership);
870		#else
871		info->setGlobalGroupMembership(globalGroupMembership);
872		#endif
873	<
873	>
874		//fill molMembership
875	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
875	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
876	>	info->getNGlobalRigidBodies(), 0);
877
878	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
879	<
878	>	for(mol = info->beginMolecule(mi); mol != NULL;
879	>	mol = info->nextMolecule(mi)) {
880		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
882		}
883	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
884	+	rb = mol->nextRigidBody(ri)) {
885	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
886	+	}
887		}
888	<
888	>
889		#ifdef IS_MPI
890	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
891	<
892	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
893	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
890	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
891	>	info->getNGlobalRigidBodies(), 0);
892	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
893	>	nGlobalAtoms + nGlobalRigidBodies,
894	>	MPI::INT, MPI::SUM);
895
896		info->setGlobalMolMembership(tmpMolMembership);
897		#else
898		info->setGlobalMolMembership(globalMolMembership);
899		#endif
900
901	<	}
901	>	// nIOPerMol holds the number of integrable objects per molecule
902	>	// here the molecules are listed by their global indices.
903
904	<	void SimCreator::loadCoordinates(SimInfo* info) {
904	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
905	>	for (mol = info->beginMolecule(mi); mol != NULL;
906	>	mol = info->nextMolecule(mi)) {
907	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
908	>	}
909	>
910	>	#ifdef IS_MPI
911	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
912	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
913	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
914	>	#else
915	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
916	>	#endif
917	>
918	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
919	>
920	>	int startingIndex = 0;
921	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
922	>	startingIOIndexForMol[i] = startingIndex;
923	>	startingIndex += numIntegrableObjectsPerMol[i];
924	>	}
925	>
926	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
927	>	for (mol = info->beginMolecule(mi); mol != NULL;
928	>	mol = info->nextMolecule(mi)) {
929	>	int myGlobalIndex = mol->getGlobalIndex();
930	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
931	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
932	>	sd = mol->nextIntegrableObject(ioi)) {
933	>	sd->setGlobalIntegrableObjectIndex(globalIO);
934	>	IOIndexToIntegrableObject[globalIO] = sd;
935	>	globalIO++;
936	>	}
937	>	}
938	>
939	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
940	>
941	>	}
942	>
943	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
944		Globals* simParams;
945	+
946		simParams = info->getSimParams();
947
948	<	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());
948	>	DumpReader reader(info, mdFileName);
949		int nframes = reader.getNFrames();
950
951		if (nframes > 0) {
952		reader.readFrame(nframes - 1);
953		} else {
954		//invalid initial coordinate file
955	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
956	<	simParams->getInitialConfig());
955	>	sprintf(painCave.errMsg,
956	>	"Initial configuration file %s should at least contain one frame\n",
957	>	mdFileName.c_str());
958		painCave.isFatal = 1;
959		simError();
960		}
613	–
961		//copy the current snapshot to previous snapshot
962		info->getSnapshotManager()->advance();
963		}
964	+
965	+	} //end namespace OpenMD
966
618	–	} //end namespace oopse
967
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 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

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