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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 297 by tim, Mon Feb 7 19:14:26 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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
50	–	#include <sprng.h>
51	–
55		#include "brains/MoleculeCreator.hpp"
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
56	–	#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"
81	<	#include "math/randomSPRNG.hpp"
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) {
72	<	#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();
92	<	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
237	>	simParams->setMDfileVersion(mdFileVersion);
238	>	return simParams;
239	>	}
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	<	}
254	>	#ifdef IS_MPI
255	>	const int masterNode = 0;
256	>	if (worldRank == masterNode) {
257	>	#endif
258
259	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
260	<
261	<	MakeStamps * stamps = new MakeStamps();
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	<	Globals * simParams = new Globals();
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	<	//parse meta-data file
291	<	parseFile(mdFileName, stamps, simParams);
290	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
291	>	std::string fileType = tokenizer.nextToken();
292	>	toUpper(fileType);
293
294	<	//create the force field
295	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
296	<	simParams->getForceField());
297	<
298	<	if (ff == NULL) {
299	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
300	<	simParams->getForceField());
301	<	painCave.isFatal = 1;
302	<	simError();
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,
370	+	"ForceField Factory can not create %s force field\n",
371	+	simParams->getForceField().c_str());
372	+	painCave.isFatal = 1;
373	+	simError();
374	+	}
375	+
376		if (simParams->haveForceFieldFileName()) {
377	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
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	<
387	<	std::string variant = simParams->getForceFieldVariant();
388	<
389	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
390	<	variant = "." + variant;
391	<	if (pos != std::string::npos) {
392	<	forcefieldFileName.insert(pos, variant);
393	<	} else {
394	<	//If the default force field file name does not containt .frc suffix, just append the .variant
395	<	forcefieldFileName.append(variant);
396	<	}
384	>	//If the force field has variant, the variant force field name will be
385	>	//Base.variant.frc. For exampel EAM.u6.frc
386	>
387	>	std::string variant = simParams->getForceFieldVariant();
388	>
389	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
390	>	variant = "." + variant;
391	>	if (pos != std::string::npos) {
392	>	forcefieldFileName.insert(pos, variant);
393	>	} else {
394	>	//If the default force field file name does not containt .frc suffix, just append the .variant
395	>	forcefieldFileName.append(variant);
396	>	}
397		}
398
399		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
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
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
440		if (loadInitCoords)
441	<	loadCoordinates(info);
186	<
441	>	loadCoordinates(info, mdFileName);
442		return info;
443	<	}
444	<
445	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
446	<
447	<	//setup seed for random number generator
193	<	int seedValue;
194	<	Globals * simParams = info->getSimParams();
195	<
196	<	if (simParams->haveSeed()) {
197	<	seedValue = simParams->getSeed();
198	<
199	<	if (seedValue < 100000000 ) {
200	<	sprintf(painCave.errMsg,
201	<	"Seed for sprng library should contain at least 9 digits\n"
202	<	"OOPSE will generate a seed for user\n");
203	<
204	<	painCave.isFatal = 0;
205	<	simError();
206	<
207	<	//using seed generated by system instead of invalid seed set by user
208	<
209	<	#ifndef IS_MPI
210	<
211	<	seedValue = make_sprng_seed();
212	<
213	<	#else
214	<
215	<	if (worldRank == 0) {
216	<	seedValue = make_sprng_seed();
217	<	}
218	<
219	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
220	<
221	<	#endif
222	<
223	<	} //end if (seedValue /1000000000 == 0)
224	<	} else {
225	<
226	<	#ifndef IS_MPI
227	<
228	<	seedValue = make_sprng_seed();
229	<
230	<	#else
231	<
232	<	if (worldRank == 0) {
233	<	seedValue = make_sprng_seed();
234	<	}
235	<
236	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
237	<
238	<	#endif
239	<
240	<	} //end of simParams->haveSeed()
241	<
242	<	info->setSeed(seedValue);
243	<
244	<
245	<	//figure out the ouput file names
443	>	}
444	>
445	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
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	<
455	<	if (simParams->haveFinalConfig()) {
456	<	prefix = getPrefix(simParams->getFinalConfig());
457	<	} else {
458	<	prefix = getPrefix(mdfile);
459	<	}
460	<
461	<	info->setFinalConfigFileName(prefix + ".eor");
462	<	info->setDumpFileName(prefix + ".dump");
463	<	info->setStatFileName(prefix + ".stat");
464	<
454	>	Globals * simParams = info->getSimParams();
455	>	if (simParams->haveFinalConfig()) {
456	>	prefix = getPrefix(simParams->getFinalConfig());
457	>	} else {
458	>	prefix = getPrefix(mdfile);
459	>	}
460	>
461	>	info->setFinalConfigFileName(prefix + ".eor");
462	>	info->setDumpFileName(prefix + ".dump");
463	>	info->setStatFileName(prefix + ".stat");
464	>	info->setRestFileName(prefix + ".zang");
465	>
466		#ifdef IS_MPI
467	<
467	>
468		}
469	<
469	>
470		#endif
471	<
472	<	}
473	<
471	>
472	>	}
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;
475	>	void SimCreator::divideMolecules(SimInfo *info) {
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 287 | Line 490 | void SimCreator::divideMolecules(SimInfo *info) {
490		int which_proc;
491		int nProcessors;
492		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
493		int nGlobalMols = info->getNGlobalMolecules();
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"
501	<	"\tThe number of processors is larger than\n"
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	<
507	<	painCave.isFatal = 1;
508	<	simError();
499	>	sprintf(painCave.errMsg,
500	>	"nProcessors (%d) > nMol (%d)\n"
501	>	"\tThe number of processors is larger than\n"
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 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
514	>	if (simParams->haveSeed()) {
515	>	seedValue = simParams->getSeed();
516	>	myRandom = new SeqRandNumGen(seedValue);
517	>	}else {
518	>	myRandom = new SeqRandNumGen();
519	>	}
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	<
533	<	for(i = 0; i < nGlobalMols; i++) {
534	<	done = 0;
535	<	loops = 0;
536	<
537	<	while (!done) {
538	<	loops++;
539	<
540	<	// Pick a processor at random
541	<
542	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
543	<
544	<	//get the molecule stamp first
545	<	int stampId = info->getMoleculeStampId(i);
546	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
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	<
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	<
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	<
564	<	painCave.isFatal = 0;
565	<	simError();
566	<
567	<	molToProcMap[i] = which_proc;
568	<	atomsPerProc[which_proc] += add_atoms;
569	<
570	<	done = 1;
571	<	continue;
572	<	}
573	<
574	<	// If we can add this molecule to this processor without sending
575	<	// it above nTarget, then go ahead and do it:
576	<
577	<	if (new_atoms <= nTarget) {
578	<	molToProcMap[i] = which_proc;
579	<	atomsPerProc[which_proc] += add_atoms;
580	<
581	<	done = 1;
582	<	continue;
583	<	}
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	<
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);
594	<	y = myRandom.getRandom();
595	<
596	<	if (y < exp(- a * x)) {
597	<	molToProcMap[i] = which_proc;
598	<	atomsPerProc[which_proc] += add_atoms;
599	<
600	<	done = 1;
601	<	continue;
602	<	} else {
603	<	continue;
604	<	}
392	<	}
528	>	numerator = info->getNGlobalAtoms();
529	>	denominator = nProcessors;
530	>	precast = numerator / denominator;
531	>	nTarget = (int)(precast + 0.5);
532	>
533	>	for(i = 0; i < nGlobalMols; i++) {
534	>	done = 0;
535	>	loops = 0;
536	>
537	>	while (!done) {
538	>	loops++;
539	>
540	>	// Pick a processor at random
541	>
542	>	which_proc = (int) (myRandom->rand() * nProcessors);
543	>
544	>	//get the molecule stamp first
545	>	int stampId = info->getMoleculeStampId(i);
546	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
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	>
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	>
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	>
564	>	painCave.isFatal = 0;
565	>	simError();
566	>
567	>	molToProcMap[i] = which_proc;
568	>	atomsPerProc[which_proc] += add_atoms;
569	>
570	>	done = 1;
571	>	continue;
572	>	}
573	>
574	>	// If we can add this molecule to this processor without sending
575	>	// it above nTarget, then go ahead and do it:
576	>
577	>	if (new_atoms <= nTarget) {
578	>	molToProcMap[i] = which_proc;
579	>	atomsPerProc[which_proc] += add_atoms;
580	>
581	>	done = 1;
582	>	continue;
583	>	}
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	>
589	>	// roughly:  x = new_atoms - nTarget
590	>	//           Pacc(x) = exp(- a * x)
591	>	// where a = penalty / (average atoms per molecule)
592	>
593	>	x = (RealType)(new_atoms - nTarget);
594	>	y = myRandom->rand();
595	>
596	>	if (y < exp(- a * x)) {
597	>	molToProcMap[i] = which_proc;
598	>	atomsPerProc[which_proc] += add_atoms;
599	>
600	>	done = 1;
601	>	continue;
602	>	} else {
603	>	continue;
604	>	}
605		}
606	<
607	<	// Spray out this nonsense to all other processors:
608	<
609	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
606	>	}
607	>
608	>	delete myRandom;
609	>
610	>	// Spray out this nonsense to all other processors:
611	>
612	>	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
613		} else {
614	<
615	<	// Listen to your marching orders from processor 0:
616	<
617	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
614	>
615	>	// Listen to your marching orders from processor 0:
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();
624	<	}
625	<
623	>	errorCheckPoint();
624	>	}
625	>
626		#endif
627	<
628	<	void SimCreator::createMolecules(SimInfo *info) {
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	<
636	<	if (info->getMolToProc(i) == worldRank) {
635	>
636	>	if (info->getMolToProc(i) == worldRank) {
637		#endif
638	<
639	<	stampId = info->getMoleculeStampId(i);
640	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
641	<	stampId, i, info->getLocalIndexManager());
642	<
643	<	info->addMolecule(mol);
644	<
638	>
639	>	stampId = info->getMoleculeStampId(i);
640	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
641	>	info->getMoleculeStamp(stampId),
642	>	stampId, i,
643	>	info->getLocalIndexManager());
644	>
645	>	info->addMolecule(mol);
646	>
647		#ifdef IS_MPI
648	<
649	<	}
650	<
648	>
649	>	}
650	>
651		#endif
652	<
652	>
653		} //end for(int i=0)
654	<	}
655	<
656	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
440	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
441	<	int i;
442	<	char * id;
443	<	MoleculeStamp * currentStamp;
444	<	Component** the_components = simParams->getComponents();
445	<	int n_components = simParams->getNComponents();
446	<
447	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
450	<
451	<	for(i = 0; i < n_components; i++) {
452	<	if (!the_components[i]->haveNMol()) {
453	<	// we have a problem
454	<	sprintf(painCave.errMsg,
455	<	"SimCreator Error. No global NMol or component NMol given.\n"
456	<	"\tCannot calculate the number of atoms.\n");
457	<
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<
462	<	id = the_components[i]->getType();
463	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
464	<
465	<	if (currentStamp == NULL) {
466	<	sprintf(painCave.errMsg,
467	<	"SimCreator error: Component \"%s\" was not found in the "
468	<	"list of declared molecules\n", id);
469	<
470	<	painCave.isFatal = 1;
471	<	simError();
472	<	}
473	<
474	<	moleculeStampPairs.push_back(
475	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
476	<	} //end for (i = 0; i < n_components; i++)
477	<	} else {
478	<	sprintf(painCave.errMsg, "SimSetup error.\n"
479	<	"\tSorry, the ability to specify total"
480	<	" nMols and then give molfractions in the components\n"
481	<	"\tis not currently supported."
482	<	" Please give nMol in the components.\n");
483	<
484	<	painCave.isFatal = 1;
485	<	simError();
486	<	}
487	<
488	<	#ifdef IS_MPI
489	<
490	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
491	<	MPIcheckPoint();
492	<
493	<	#endif // is_mpi
494	<
495	<	}
496	<
497	<	void SimCreator::setGlobalIndex(SimInfo *info) {
654	>	}
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 508 | Line 668 | void SimCreator::setGlobalIndex(SimInfo *info) {
668		int beginCutoffGroupIndex;
669		int nGlobalAtoms = info->getNGlobalAtoms();
670
511	–	#ifndef IS_MPI
512	–
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
519	–	int nproc;
520	–	int myNode;
521	–
522	–	myNode = worldRank;
523	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524	–
525	–	std::vector < int > tmpAtomsInProc(nproc, 0);
526	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528	–	std::vector < int > NumAtomsInProc(nproc, 0);
529	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
530	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531	–
532	–	tmpAtomsInProc[myNode] = info->getNAtoms();
533	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535	–
536	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538	–	MPI_SUM, MPI_COMM_WORLD);
539	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543	–
544	–	beginAtomIndex = 0;
545	–	beginRigidBodyIndex = 0;
546	–	beginCutoffGroupIndex = 0;
547	–
548	–	for(int i = 0; i < myNode; i++) {
549	–	beginAtomIndex += NumAtomsInProc[i];
550	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
551	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552	–	}
553	–
554	–	#endif
555	–
556	–	//rigidbody's index begins right after atom's
557	–	beginRigidBodyIndex += info->getNGlobalAtoms();
558	–
559	–	for(mol = info->beginMolecule(mi); mol != NULL;
560	–	mol = info->nextMolecule(mi)) {
561	–
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++);
685	>	atom->setGlobalIndex(beginAtomIndex++);
686		}
687	<
687	>
688		for(rb = mol->beginRigidBody(ri); rb != NULL;
689		rb = mol->nextRigidBody(ri)) {
690	<	rb->setGlobalIndex(beginRigidBodyIndex++);
690	>	rb->setGlobalIndex(beginRigidBodyIndex++);
691		}
692	<
693	<	//local index of cutoff group is trivial, it only depends on the order of travesing
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	<	}
697	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
698	>	}
699	>
700	>	#ifdef IS_MPI
701	>	}  else {
702
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	+	beginAtomIndex += stamp->getNAtoms();
709	+	beginRigidBodyIndex += stamp->getNRigidBodies();
710	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
711	+	}
712	+	#endif
713	+
714	+	} //end for(int i=0)
715	+
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	<
721	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
722	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
723	<	}
724	<
725	<	}
719	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
720	>
721	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
722	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
723	>	}
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);
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)) {
746	<
747	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
748	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
612	<	}
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 623 | Line 759 | void SimCreator::setGlobalIndex(SimInfo *info) {
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()) {
633	<	sprintf(painCave.errMsg,
634	<	"Cannot intialize a simulation without an initial configuration file.\n");
635	<	painCave.isFatal = 1;;
636	<	simError();
637	<	}
638	<
639	<	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);
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());
816	<	painCave.isFatal = 1;
817	<	simError();
813	>	//invalid initial coordinate file
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		}
651	–
820		//copy the current snapshot to previous snapshot
821		info->getSnapshotManager()->advance();
822	<	}
822	>	}
823	>
824	>	} //end namespace OpenMD
825
656	–	} //end namespace oopse
826
658	–

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 297 by tim, Mon Feb 7 19:14:26 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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