ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/src/brains/SimCreator.cpp

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2069 by gezelter, Thu Mar 5 16:30:23 2015 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, 234107 (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		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49	+
50	+	#ifdef IS_MPI
51	+	#include "mpi.h"
52	+	#include "math/ParallelRandNumGen.hpp"
53	+	#endif
54	+
55		#include <exception>
56		#include <iostream>
57		#include <sstream>
#	Line 55 | Line 61
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67	+	#include "utils/Revision.hpp"
68		#include "math/SeqRandNumGen.hpp"
69		#include "mdParser/MDLexer.hpp"
70		#include "mdParser/MDParser.hpp"
#	Line 75 | Line 82
82		#include "antlr/NoViableAltForCharException.hpp"
83		#include "antlr/NoViableAltException.hpp"
84
85	<	#ifdef IS_MPI
86	<	#include "math/ParallelRandNumGen.hpp"
87	<	#endif
85	>	#include "types/DirectionalAdapter.hpp"
86	>	#include "types/MultipoleAdapter.hpp"
87	>	#include "types/EAMAdapter.hpp"
88	>	#include "types/SuttonChenAdapter.hpp"
89	>	#include "types/PolarizableAdapter.hpp"
90	>	#include "types/FixedChargeAdapter.hpp"
91	>	#include "types/FluctuatingChargeAdapter.hpp"
92
93	<	namespace oopse {
93	>
94	>	namespace OpenMD {
95
96	<	Globals* SimCreator::parseFile(const std::string mdFileName){
97	<	Globals* simParams = NULL;
98	<	try {
96	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
97	>	Globals* simParams = NULL;
98	>	try {
99
100	<	// Create a preprocessor that preprocesses md file into an ostringstream
101	<	std::stringstream ppStream;
100	>	// Create a preprocessor that preprocesses md file into an ostringstream
101	>	std::stringstream ppStream;
102		#ifdef IS_MPI
103	<	int streamSize;
104	<	const int masterNode = 0;
105	<	int commStatus;
106	<	if (worldRank == masterNode) {
107	<	#endif
103	>	int streamSize;
104	>	const int masterNode = 0;
105	>
106	>	if (worldRank == masterNode) {
107	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
108	>	#endif
109	>	SimplePreprocessor preprocessor;
110	>	preprocessor.preprocess(rawMetaDataStream, filename,
111	>	startOfMetaDataBlock, ppStream);
112
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
113		#ifdef IS_MPI
114	<	//brocasting the stream size
115	<	streamSize = ppStream.str().size() +1;
116	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
114	>	//broadcasting the stream size
115	>	streamSize = ppStream.str().size() +1;
116	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
117	>	MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
118	>	streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
119	>	} else {
120
121	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
122	<
121	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
122	>
123	>	//get stream size
124	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127
128	<	} else {
129	<	//get stream size
110	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
111	<
112	<	char* buf = new char[streamSize];
113	<	assert(buf);
114	<
115	<	//receive file content
116	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	<
118	<	ppStream.str(buf);
119	<	delete buf;
128	>	//receive file content
129	>	MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
130
131	<	}
131	>	ppStream.str(buf);
132	>	delete [] buf;
133	>	}
134		#endif
135	<	// Create a scanner that reads from the input stream
136	<	MDLexer lexer(ppStream);
137	<	lexer.setFilename(mdFileName);
138	<	lexer.initDeferredLineCount();
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139
140	<	// Create a parser that reads from the scanner
141	<	MDParser parser(lexer);
142	<	parser.setFilename(mdFileName);
140	>	// Create a parser that reads from the scanner
141	>	MDParser parser(lexer);
142	>	parser.setFilename(filename);
143
144	<	// Create an observer that synchorizes file name change
145	<	FilenameObserver observer;
146	<	observer.setLexer(&lexer);
147	<	observer.setParser(&parser);
148	<	lexer.setObserver(&observer);
144	>	// Create an observer that synchorizes file name change
145	>	FilenameObserver observer;
146	>	observer.setLexer(&lexer);
147	>	observer.setParser(&parser);
148	>	lexer.setObserver(&observer);
149
150	<	antlr::ASTFactory factory;
151	<	parser.initializeASTFactory(factory);
152	<	parser.setASTFactory(&factory);
153	<	parser.mdfile();
150	>	antlr::ASTFactory factory;
151	>	parser.initializeASTFactory(factory);
152	>	parser.setASTFactory(&factory);
153	>	parser.mdfile();
154	>	// Create a tree parser that reads information into Globals
155	>	MDTreeParser treeParser;
156	>	treeParser.initializeASTFactory(factory);
157	>	treeParser.setASTFactory(&factory);
158	>	simParams = treeParser.walkTree(parser.getAST());
159	>	}
160
143	–	// Create a tree parser that reads information into Globals
144	–	MDTreeParser treeParser;
145	–	treeParser.initializeASTFactory(factory);
146	–	treeParser.setASTFactory(&factory);
147	–	simParams = treeParser.walkTree(parser.getAST());
148	–
149	–	}
150	–
161
162	<	catch(antlr::MismatchedCharException& e) {
163	<	sprintf(painCave.errMsg,
164	<	"parser exception: %s %s:%d:%d\n",
165	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	<	painCave.isFatal = 1;
167	<	simError();
168	<	}
169	<	catch(antlr::MismatchedTokenException &e) {
170	<	sprintf(painCave.errMsg,
171	<	"parser exception: %s %s:%d:%d\n",
172	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	<	painCave.isFatal = 1;
174	<	simError();
175	<	}
176	<	catch(antlr::NoViableAltForCharException &e) {
177	<	sprintf(painCave.errMsg,
178	<	"parser exception: %s %s:%d:%d\n",
179	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	<	painCave.isFatal = 1;
181	<	simError();
182	<	}
183	<	catch(antlr::NoViableAltException &e) {
184	<	sprintf(painCave.errMsg,
185	<	"parser exception: %s %s:%d:%d\n",
186	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
187	<	painCave.isFatal = 1;
188	<	simError();
189	<	}
162	>	catch(antlr::MismatchedCharException& e) {
163	>	sprintf(painCave.errMsg,
164	>	"parser exception: %s %s:%d:%d\n",
165	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	>	painCave.isFatal = 1;
167	>	simError();
168	>	}
169	>	catch(antlr::MismatchedTokenException &e) {
170	>	sprintf(painCave.errMsg,
171	>	"parser exception: %s %s:%d:%d\n",
172	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	>	painCave.isFatal = 1;
174	>	simError();
175	>	}
176	>	catch(antlr::NoViableAltForCharException &e) {
177	>	sprintf(painCave.errMsg,
178	>	"parser exception: %s %s:%d:%d\n",
179	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	>	painCave.isFatal = 1;
181	>	simError();
182	>	}
183	>	catch(antlr::NoViableAltException &e) {
184	>	sprintf(painCave.errMsg,
185	>	"parser exception: %s %s:%d:%d\n",
186	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
187	>	painCave.isFatal = 1;
188	>	simError();
189	>	}
190
191	<	catch(antlr::TokenStreamRecognitionException& e) {
192	<	sprintf(painCave.errMsg,
193	<	"parser exception: %s %s:%d:%d\n",
194	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
191	>	catch(antlr::TokenStreamRecognitionException& e) {
192	>	sprintf(painCave.errMsg,
193	>	"parser exception: %s %s:%d:%d\n",
194	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
195	>	painCave.isFatal = 1;
196	>	simError();
197	>	}
198
199	<	catch(antlr::TokenStreamIOException& e) {
200	<	sprintf(painCave.errMsg,
201	<	"parser exception: %s\n",
202	<	e.getMessage().c_str());
203	<	painCave.isFatal = 1;
204	<	simError();
205	<	}
199	>	catch(antlr::TokenStreamIOException& e) {
200	>	sprintf(painCave.errMsg,
201	>	"parser exception: %s\n",
202	>	e.getMessage().c_str());
203	>	painCave.isFatal = 1;
204	>	simError();
205	>	}
206
207	<	catch(antlr::TokenStreamException& e) {
208	<	sprintf(painCave.errMsg,
209	<	"parser exception: %s\n",
210	<	e.getMessage().c_str());
211	<	painCave.isFatal = 1;
212	<	simError();
213	<	}
214	<	catch (antlr::RecognitionException& e) {
215	<	sprintf(painCave.errMsg,
216	<	"parser exception: %s %s:%d:%d\n",
217	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
218	<	painCave.isFatal = 1;
219	<	simError();
220	<	}
221	<	catch (antlr::CharStreamException& e) {
222	<	sprintf(painCave.errMsg,
223	<	"parser exception: %s\n",
224	<	e.getMessage().c_str());
225	<	painCave.isFatal = 1;
226	<	simError();
227	<	}
228	<	catch (OOPSEException& e) {
229	<	sprintf(painCave.errMsg,
230	<	"%s\n",
231	<	e.getMessage().c_str());
232	<	painCave.isFatal = 1;
233	<	simError();
234	<	}
235	<	catch (std::exception& e) {
236	<	sprintf(painCave.errMsg,
237	<	"parser exception: %s\n",
238	<	e.what());
239	<	painCave.isFatal = 1;
240	<	simError();
241	<	}
207	>	catch(antlr::TokenStreamException& e) {
208	>	sprintf(painCave.errMsg,
209	>	"parser exception: %s\n",
210	>	e.getMessage().c_str());
211	>	painCave.isFatal = 1;
212	>	simError();
213	>	}
214	>	catch (antlr::RecognitionException& e) {
215	>	sprintf(painCave.errMsg,
216	>	"parser exception: %s %s:%d:%d\n",
217	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
218	>	painCave.isFatal = 1;
219	>	simError();
220	>	}
221	>	catch (antlr::CharStreamException& e) {
222	>	sprintf(painCave.errMsg,
223	>	"parser exception: %s\n",
224	>	e.getMessage().c_str());
225	>	painCave.isFatal = 1;
226	>	simError();
227	>	}
228	>	catch (OpenMDException& e) {
229	>	sprintf(painCave.errMsg,
230	>	"%s\n",
231	>	e.what());
232	>	painCave.isFatal = 1;
233	>	simError();
234	>	}
235	>	catch (std::exception& e) {
236	>	sprintf(painCave.errMsg,
237	>	"parser exception: %s\n",
238	>	e.what());
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242
243	<	return simParams;
243	>	simParams->setMDfileVersion(mdFileVersion);
244	>	return simParams;
245		}
246
247		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
248		bool loadInitCoords) {
249	+
250	+	const int bufferSize = 65535;
251	+	char buffer[bufferSize];
252	+	int lineNo = 0;
253	+	std::string mdRawData;
254	+	int metaDataBlockStart = -1;
255	+	int metaDataBlockEnd = -1;
256	+	streamoff mdOffset;
257	+	int mdFileVersion;
258
259	+	// Create a string for embedding the version information in the MetaData
260	+	std::string version;
261	+	version.assign("## Last run using OpenMD Version: ");
262	+	version.append(OPENMD_VERSION_MAJOR);
263	+	version.append(".");
264	+	version.append(OPENMD_VERSION_MINOR);
265	+
266	+	std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
267	+	//convert a macro from compiler to a string in c++
268	+	// STR_DEFINE(svnrev, SVN_REV );
269	+	version.append(" Revision: ");
270	+	// If there's no SVN revision, just call this the RELEASE revision.
271	+	if (!svnrev.empty()) {
272	+	version.append(svnrev);
273	+	} else {
274	+	version.append("RELEASE");
275	+	}
276	+
277	+	#ifdef IS_MPI
278	+	const int masterNode = 0;
279	+	if (worldRank == masterNode) {
280	+	#endif
281	+
282	+	std::ifstream mdFile_;
283	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
284	+
285	+	if (mdFile_.fail()) {
286	+	sprintf(painCave.errMsg,
287	+	"SimCreator: Cannot open file: %s\n",
288	+	mdFileName.c_str());
289	+	painCave.isFatal = 1;
290	+	simError();
291	+	}
292	+
293	+	mdFile_.getline(buffer, bufferSize);
294	+	++lineNo;
295	+	std::string line = trimLeftCopy(buffer);
296	+	std::size_t i = CaseInsensitiveFind(line, "<OpenMD");
297	+	if (i == string::npos) {
298	+	// try the older file strings to see if that works:
299	+	i = CaseInsensitiveFind(line, "<OOPSE");
300	+	}
301	+
302	+	if (i == string::npos) {
303	+	// still no luck!
304	+	sprintf(painCave.errMsg,
305	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
306	+	mdFileName.c_str());
307	+	painCave.isFatal = 1;
308	+	simError();
309	+	}
310	+
311	+	// found the correct opening string, now try to get the file
312	+	// format version number.
313	+
314	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
315	+	std::string fileType = tokenizer.nextToken();
316	+	toUpper(fileType);
317	+
318	+	mdFileVersion = 0;
319	+
320	+	if (fileType == "OPENMD") {
321	+	while (tokenizer.hasMoreTokens()) {
322	+	std::string token(tokenizer.nextToken());
323	+	toUpper(token);
324	+	if (token == "VERSION") {
325	+	mdFileVersion = tokenizer.nextTokenAsInt();
326	+	break;
327	+	}
328	+	}
329	+	}
330	+
331	+	//scan through the input stream and find MetaData tag
332	+	while(mdFile_.getline(buffer, bufferSize)) {
333	+	++lineNo;
334	+
335	+	std::string line = trimLeftCopy(buffer);
336	+	if (metaDataBlockStart == -1) {
337	+	std::size_t i = CaseInsensitiveFind(line, "<MetaData>");
338	+	if (i != string::npos) {
339	+	metaDataBlockStart = lineNo;
340	+	mdOffset = mdFile_.tellg();
341	+	}
342	+	} else {
343	+	std::size_t i = CaseInsensitiveFind(line, "</MetaData>");
344	+	if (i != string::npos) {
345	+	metaDataBlockEnd = lineNo;
346	+	}
347	+	}
348	+	}
349	+
350	+	if (metaDataBlockStart == -1) {
351	+	sprintf(painCave.errMsg,
352	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
353	+	mdFileName.c_str());
354	+	painCave.isFatal = 1;
355	+	simError();
356	+	}
357	+	if (metaDataBlockEnd == -1) {
358	+	sprintf(painCave.errMsg,
359	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
360	+	mdFileName.c_str());
361	+	painCave.isFatal = 1;
362	+	simError();
363	+	}
364	+
365	+	mdFile_.clear();
366	+	mdFile_.seekg(0);
367	+	mdFile_.seekg(mdOffset);
368	+
369	+	mdRawData.clear();
370	+
371	+	bool foundVersion = false;
372	+
373	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
374	+	mdFile_.getline(buffer, bufferSize);
375	+	std::string line = trimLeftCopy(buffer);
376	+	std::size_t j = CaseInsensitiveFind(line,
377	+	"## Last run using OpenMD Version");
378	+	if (j != string::npos) {
379	+	foundVersion = true;
380	+	mdRawData += version;
381	+	} else {
382	+	mdRawData += buffer;
383	+	}
384	+	mdRawData += "\n";
385	+	}
386	+
387	+	if (!foundVersion) mdRawData += version + "\n";
388	+
389	+	mdFile_.close();
390	+
391	+	#ifdef IS_MPI
392	+	}
393	+	#endif
394	+
395	+	std::stringstream rawMetaDataStream(mdRawData);
396	+
397		//parse meta-data file
398	<	Globals* simParams = parseFile(mdFileName);
398	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
399	>	metaDataBlockStart + 1);
400
401		//create the force field
402	<	ForceField * ff = ForceFieldFactory::getInstance()
403	<	->createForceField(simParams->getForceField());
245	<
402	>	ForceField * ff = new ForceField(simParams->getForceField());
403	>
404		if (ff == NULL) {
405		sprintf(painCave.errMsg,
406		"ForceField Factory can not create %s force field\n",
#	Line 275 | Line 433 | Globals* SimCreator::parseFile(const std::string mdFil
433		}
434
435		ff->parse(forcefieldFileName);
278	–	ff->setFortranForceOptions();
436		//create SimInfo
437		SimInfo * info = new SimInfo(ff, simParams);
438	+
439	+	info->setRawMetaData(mdRawData);
440
441		//gather parameters (SimCreator only retrieves part of the
442		//parameters)
#	Line 291 | Line 450 | Globals* SimCreator::parseFile(const std::string mdFil
450		//create the molecules
451		createMolecules(info);
452
453	<
453	>	//find the storage layout
454	>
455	>	int storageLayout = computeStorageLayout(info);
456	>
457		//allocate memory for DataStorage(circular reference, need to
458		//break it)
459	<	info->setSnapshotManager(new SimSnapshotManager(info));
459	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
460
461		//set the global index of atoms, rigidbodies and cutoffgroups
462		//(only need to be set once, the global index will never change
#	Line 303 | Line 465 | Globals* SimCreator::parseFile(const std::string mdFil
465		//responsibility to LocalIndexManager.
466		setGlobalIndex(info);
467
468	<	//Although addExcludePairs is called inside SimInfo's addMolecule
468	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
469		//method, at that point atoms don't have the global index yet
470		//(their global index are all initialized to -1).  Therefore we
471	<	//have to call addExcludePairs explicitly here. A way to work
471	>	//have to call addInteractionPairs explicitly here. A way to work
472		//around is that we can determine the beginning global indices of
473		//atoms before they get created.
474		SimInfo::MoleculeIterator mi;
475		Molecule* mol;
476		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
477	<	info->addExcludePairs(mol);
477	>	info->addInteractionPairs(mol);
478		}
479
480		if (loadInitCoords)
481	<	loadCoordinates(info);
320	<
481	>	loadCoordinates(info, mdFileName);
482		return info;
483		}
484
#	Line 352 | Line 513 | Globals* SimCreator::parseFile(const std::string mdFil
513
514		#ifdef IS_MPI
515		void SimCreator::divideMolecules(SimInfo *info) {
355	–	RealType numerator;
356	–	RealType denominator;
357	–	RealType precast;
358	–	RealType x;
359	–	RealType y;
516		RealType a;
361	–	int old_atoms;
362	–	int add_atoms;
363	–	int new_atoms;
364	–	int nTarget;
365	–	int done;
366	–	int i;
367	–	int j;
368	–	int loops;
369	–	int which_proc;
517		int nProcessors;
518		std::vector<int> atomsPerProc;
519		int nGlobalMols = info->getNGlobalMolecules();
520	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
520	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
521	>	// error
522	>	// condition:
523
524	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
524	>	MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
525
526		if (nProcessors > nGlobalMols) {
527		sprintf(painCave.errMsg,
#	Line 381 | Line 530 | Globals* SimCreator::parseFile(const std::string mdFil
530		"\tthe number of molecules.  This will not result in a \n"
531		"\tusable division of atoms for force decomposition.\n"
532		"\tEither try a smaller number of processors, or run the\n"
533	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
533	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
534	>	nGlobalMols);
535
536		painCave.isFatal = 1;
537		simError();
538		}
539
390	–	int seedValue;
540		Globals * simParams = info->getSimParams();
541	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
541	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
542	>	//random number generator
543		if (simParams->haveSeed()) {
544	<	seedValue = simParams->getSeed();
544	>	int seedValue = simParams->getSeed();
545		myRandom = new SeqRandNumGen(seedValue);
546		}else {
547		myRandom = new SeqRandNumGen();
#	Line 404 | Line 554 | Globals* SimCreator::parseFile(const std::string mdFil
554		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
555
556		if (worldRank == 0) {
557	<	numerator = info->getNGlobalAtoms();
558	<	denominator = nProcessors;
559	<	precast = numerator / denominator;
560	<	nTarget = (int)(precast + 0.5);
557	>	RealType numerator = info->getNGlobalAtoms();
558	>	RealType denominator = nProcessors;
559	>	RealType precast = numerator / denominator;
560	>	int nTarget = (int)(precast + 0.5);
561
562	<	for(i = 0; i < nGlobalMols; i++) {
563	<	done = 0;
564	<	loops = 0;
562	>	for(int i = 0; i < nGlobalMols; i++) {
563	>
564	>	int done = 0;
565	>	int loops = 0;
566
567		while (!done) {
568		loops++;
569
570		// Pick a processor at random
571
572	<	which_proc = (int) (myRandom->rand() * nProcessors);
572	>	int which_proc = (int) (myRandom->rand() * nProcessors);
573
574		//get the molecule stamp first
575		int stampId = info->getMoleculeStampId(i);
576		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
577
578		// How many atoms does this processor have so far?
579	<	old_atoms = atomsPerProc[which_proc];
580	<	add_atoms = moleculeStamp->getNAtoms();
581	<	new_atoms = old_atoms + add_atoms;
579	>	int old_atoms = atomsPerProc[which_proc];
580	>	int add_atoms = moleculeStamp->getNAtoms();
581	>	int new_atoms = old_atoms + add_atoms;
582
583		// If we've been through this loop too many times, we need
584		// to just give up and assign the molecule to this processor
585		// and be done with it.
586
587		if (loops > 100) {
588	+
589		sprintf(painCave.errMsg,
590	<	"I've tried 100 times to assign molecule %d to a "
591	<	" processor, but can't find a good spot.\n"
592	<	"I'm assigning it at random to processor %d.\n",
590	>	"There have been 100 attempts to assign molecule %d to an\n"
591	>	"\tunderworked processor, but there's no good place to\n"
592	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
593		i, which_proc);
594	<
594	>
595		painCave.isFatal = 0;
596	+	painCave.severity = OPENMD_INFO;
597		simError();
598
599		molToProcMap[i] = which_proc;
#	Line 469 | Line 622 | Globals* SimCreator::parseFile(const std::string mdFil
622		//           Pacc(x) = exp(- a * x)
623		// where a = penalty / (average atoms per molecule)
624
625	<	x = (RealType)(new_atoms - nTarget);
626	<	y = myRandom->rand();
625	>	RealType x = (RealType)(new_atoms - nTarget);
626	>	RealType y = myRandom->rand();
627
628		if (y < exp(- a * x)) {
629		molToProcMap[i] = which_proc;
#	Line 485 | Line 638 | Globals* SimCreator::parseFile(const std::string mdFil
638		}
639
640		delete myRandom;
641	<
641	>
642		// Spray out this nonsense to all other processors:
490	–
643		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644	+
645		} else {
646
647		// Listen to your marching orders from processor 0:
495	–
648		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
649	+
650		}
651
652		info->setMolToProcMap(molToProcMap);
653		sprintf(checkPointMsg,
654		"Successfully divided the molecules among the processors.\n");
655	<	MPIcheckPoint();
655	>	errorCheckPoint();
656		}
657
658		#endif
#	Line 516 | Line 669 | Globals* SimCreator::parseFile(const std::string mdFil
669		#endif
670
671		stampId = info->getMoleculeStampId(i);
672	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
673	<	stampId, i, info->getLocalIndexManager());
672	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
673	>	info->getMoleculeStamp(stampId),
674	>	stampId, i,
675	>	info->getLocalIndexManager());
676
677		info->addMolecule(mol);
678
#	Line 529 | Line 684 | Globals* SimCreator::parseFile(const std::string mdFil
684
685		} //end for(int i=0)
686		}
687	+
688	+	int SimCreator::computeStorageLayout(SimInfo* info) {
689	+
690	+	Globals* simParams = info->getSimParams();
691	+	int nRigidBodies = info->getNGlobalRigidBodies();
692	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
693	+	set<AtomType*>::iterator i;
694	+	bool hasDirectionalAtoms = false;
695	+	bool hasFixedCharge = false;
696	+	bool hasDipoles = false;
697	+	bool hasQuadrupoles = false;
698	+	bool hasPolarizable = false;
699	+	bool hasFluctuatingCharge = false;
700	+	bool hasMetallic = false;
701	+	int storageLayout = 0;
702	+	storageLayout |= DataStorage::dslPosition;
703	+	storageLayout |= DataStorage::dslVelocity;
704	+	storageLayout |= DataStorage::dslForce;
705	+
706	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
707	+
708	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
709	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
710	+	EAMAdapter ea = EAMAdapter( (*i) );
711	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
712	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
713	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
714	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
715	+
716	+	if (da.isDirectional()){
717	+	hasDirectionalAtoms = true;
718	+	}
719	+	if (ma.isDipole()){
720	+	hasDipoles = true;
721	+	}
722	+	if (ma.isQuadrupole()){
723	+	hasQuadrupoles = true;
724	+	}
725	+	if (ea.isEAM() || sca.isSuttonChen()){
726	+	hasMetallic = true;
727	+	}
728	+	if ( fca.isFixedCharge() ){
729	+	hasFixedCharge = true;
730	+	}
731	+	if ( fqa.isFluctuatingCharge() ){
732	+	hasFluctuatingCharge = true;
733	+	}
734	+	if ( pa.isPolarizable() ){
735	+	hasPolarizable = true;
736	+	}
737	+	}
738
739	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
740	+	storageLayout |= DataStorage::dslAmat;
741	+	if(storageLayout & DataStorage::dslVelocity) {
742	+	storageLayout |= DataStorage::dslAngularMomentum;
743	+	}
744	+	if (storageLayout & DataStorage::dslForce) {
745	+	storageLayout |= DataStorage::dslTorque;
746	+	}
747	+	}
748	+	if (hasDipoles) {
749	+	storageLayout |= DataStorage::dslDipole;
750	+	}
751	+	if (hasQuadrupoles) {
752	+	storageLayout |= DataStorage::dslQuadrupole;
753	+	}
754	+	if (hasFixedCharge || hasFluctuatingCharge) {
755	+	storageLayout |= DataStorage::dslSkippedCharge;
756	+	}
757	+	if (hasMetallic) {
758	+	storageLayout |= DataStorage::dslDensity;
759	+	storageLayout |= DataStorage::dslFunctional;
760	+	storageLayout |= DataStorage::dslFunctionalDerivative;
761	+	}
762	+	if (hasPolarizable) {
763	+	storageLayout |= DataStorage::dslElectricField;
764	+	}
765	+	if (hasFluctuatingCharge){
766	+	storageLayout |= DataStorage::dslFlucQPosition;
767	+	if(storageLayout & DataStorage::dslVelocity) {
768	+	storageLayout |= DataStorage::dslFlucQVelocity;
769	+	}
770	+	if (storageLayout & DataStorage::dslForce) {
771	+	storageLayout |= DataStorage::dslFlucQForce;
772	+	}
773	+	}
774	+
775	+	// if the user has asked for them, make sure we've got the memory for the
776	+	// objects defined.
777	+
778	+	if (simParams->getOutputParticlePotential()) {
779	+	storageLayout |= DataStorage::dslParticlePot;
780	+	}
781	+
782	+	if (simParams->havePrintHeatFlux()) {
783	+	if (simParams->getPrintHeatFlux()) {
784	+	storageLayout |= DataStorage::dslParticlePot;
785	+	}
786	+	}
787	+
788	+	if (simParams->getOutputElectricField() |
789	+	simParams->haveElectricField() | simParams->haveUniformField() |
790	+	simParams->haveUniformGradientStrength() |
791	+	simParams->haveUniformGradientDirection1() |
792	+	simParams->haveUniformGradientDirection2() ) {
793	+	storageLayout |= DataStorage::dslElectricField;
794	+	}
795	+
796	+	if (simParams->getOutputSitePotential() ) {
797	+	storageLayout |= DataStorage::dslSitePotential;
798	+	}
799	+
800	+	if (simParams->getOutputFluctuatingCharges()) {
801	+	storageLayout |= DataStorage::dslFlucQPosition;
802	+	storageLayout |= DataStorage::dslFlucQVelocity;
803	+	storageLayout |= DataStorage::dslFlucQForce;
804	+	}
805	+
806	+	info->setStorageLayout(storageLayout);
807	+
808	+	return storageLayout;
809	+	}
810	+
811		void SimCreator::setGlobalIndex(SimInfo *info) {
812		SimInfo::MoleculeIterator mi;
813		Molecule::AtomIterator ai;
814		Molecule::RigidBodyIterator ri;
815		Molecule::CutoffGroupIterator ci;
816	<	Molecule * mol;
817	<	Atom * atom;
818	<	RigidBody * rb;
819	<	CutoffGroup * cg;
816	>	Molecule::BondIterator boi;
817	>	Molecule::BendIterator bei;
818	>	Molecule::TorsionIterator ti;
819	>	Molecule::InversionIterator ii;
820	>	Molecule::IntegrableObjectIterator  ioi;
821	>	Molecule* mol;
822	>	Atom* atom;
823	>	RigidBody* rb;
824	>	CutoffGroup* cg;
825	>	Bond* bond;
826	>	Bend* bend;
827	>	Torsion* torsion;
828	>	Inversion* inversion;
829		int beginAtomIndex;
830		int beginRigidBodyIndex;
831		int beginCutoffGroupIndex;
832	+	int beginBondIndex;
833	+	int beginBendIndex;
834	+	int beginTorsionIndex;
835	+	int beginInversionIndex;
836	+	#ifdef IS_MPI
837		int nGlobalAtoms = info->getNGlobalAtoms();
838	<
839	<	#ifndef IS_MPI
838	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
839	>	#endif
840
841		beginAtomIndex = 0;
842	<	beginRigidBodyIndex = 0;
842	>	// The rigid body indices begin immediately after the atom indices:
843	>	beginRigidBodyIndex = info->getNGlobalAtoms();
844		beginCutoffGroupIndex = 0;
845	<
846	<	#else
847	<
848	<	int nproc;
849	<	int myNode;
850	<
558	<	myNode = worldRank;
559	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
560	<
561	<	std::vector < int > tmpAtomsInProc(nproc, 0);
562	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
563	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
564	<	std::vector < int > NumAtomsInProc(nproc, 0);
565	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
566	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
567	<
568	<	tmpAtomsInProc[myNode] = info->getNAtoms();
569	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
570	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
571	<
572	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
573	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
574	<	MPI_SUM, MPI_COMM_WORLD);
575	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
576	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
577	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
578	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
579	<
580	<	beginAtomIndex = 0;
581	<	beginRigidBodyIndex = 0;
582	<	beginCutoffGroupIndex = 0;
583	<
584	<	for(int i = 0; i < myNode; i++) {
585	<	beginAtomIndex += NumAtomsInProc[i];
586	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
587	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
588	<	}
589	<
590	<	#endif
591	<
592	<	//rigidbody's index begins right after atom's
593	<	beginRigidBodyIndex += info->getNGlobalAtoms();
594	<
595	<	for(mol = info->beginMolecule(mi); mol != NULL;
596	<	mol = info->nextMolecule(mi)) {
845	>	beginBondIndex = 0;
846	>	beginBendIndex = 0;
847	>	beginTorsionIndex = 0;
848	>	beginInversionIndex = 0;
849	>
850	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
851
852	<	//local index(index in DataStorge) of atom is important
853	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
854	<	atom->setGlobalIndex(beginAtomIndex++);
852	>	#ifdef IS_MPI
853	>	if (info->getMolToProc(i) == worldRank) {
854	>	#endif
855	>	// stuff to do if I own this molecule
856	>	mol = info->getMoleculeByGlobalIndex(i);
857	>
858	>	// The local index(index in DataStorge) of the atom is important:
859	>	for(atom = mol->beginAtom(ai); atom != NULL;
860	>	atom = mol->nextAtom(ai)) {
861	>	atom->setGlobalIndex(beginAtomIndex++);
862	>	}
863	>
864	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
865	>	rb = mol->nextRigidBody(ri)) {
866	>	rb->setGlobalIndex(beginRigidBodyIndex++);
867	>	}
868	>
869	>	// The local index of other objects only depends on the order
870	>	// of traversal:
871	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
872	>	cg = mol->nextCutoffGroup(ci)) {
873	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
874	>	}
875	>	for(bond = mol->beginBond(boi); bond != NULL;
876	>	bond = mol->nextBond(boi)) {
877	>	bond->setGlobalIndex(beginBondIndex++);
878	>	}
879	>	for(bend = mol->beginBend(bei); bend != NULL;
880	>	bend = mol->nextBend(bei)) {
881	>	bend->setGlobalIndex(beginBendIndex++);
882	>	}
883	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
884	>	torsion = mol->nextTorsion(ti)) {
885	>	torsion->setGlobalIndex(beginTorsionIndex++);
886	>	}
887	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
888	>	inversion = mol->nextInversion(ii)) {
889	>	inversion->setGlobalIndex(beginInversionIndex++);
890	>	}
891	>
892	>	#ifdef IS_MPI
893	>	}  else {
894	>
895	>	// stuff to do if I don't own this molecule
896	>
897	>	int stampId = info->getMoleculeStampId(i);
898	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
899	>
900	>	beginAtomIndex += stamp->getNAtoms();
901	>	beginRigidBodyIndex += stamp->getNRigidBodies();
902	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
903	>	beginBondIndex += stamp->getNBonds();
904	>	beginBendIndex += stamp->getNBends();
905	>	beginTorsionIndex += stamp->getNTorsions();
906	>	beginInversionIndex += stamp->getNInversions();
907		}
908	<
909	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
910	<	rb = mol->nextRigidBody(ri)) {
911	<	rb->setGlobalIndex(beginRigidBodyIndex++);
606	<	}
607	<
608	<	//local index of cutoff group is trivial, it only depends on the order of travesing
609	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
610	<	cg = mol->nextCutoffGroup(ci)) {
611	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
612	<	}
613	<	}
614	<
908	>	#endif
909	>
910	>	} //end for(int i=0)
911	>
912		//fill globalGroupMembership
913		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
914	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
915	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	<
914	>	for(mol = info->beginMolecule(mi); mol != NULL;
915	>	mol = info->nextMolecule(mi)) {
916	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
917	>	cg = mol->nextCutoffGroup(ci)) {
918		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
919		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
920		}
921
922		}
923		}
924	<
924	>
925		#ifdef IS_MPI
926		// Since the globalGroupMembership has been zero filled and we've only
927		// poked values into the atoms we know, we can do an Allreduce
928		// to get the full globalGroupMembership array (We think).
929		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
930		// docs said we could.
931	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
932	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
931	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
932	>	MPI_Allreduce(&globalGroupMembership[0],
933	>	&tmpGroupMembership[0], nGlobalAtoms,
934		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
935	+
936		info->setGlobalGroupMembership(tmpGroupMembership);
937		#else
938		info->setGlobalGroupMembership(globalGroupMembership);
939		#endif
940
941		//fill molMembership
942	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
942	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
943	>	info->getNGlobalRigidBodies(), 0);
944
945	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
946	<
945	>	for(mol = info->beginMolecule(mi); mol != NULL;
946	>	mol = info->nextMolecule(mi)) {
947		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
948		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
949		}
950	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
951	+	rb = mol->nextRigidBody(ri)) {
952	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
953	+	}
954		}
955
956		#ifdef IS_MPI
957	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
958	<
959	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
957	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
958	>	info->getNGlobalRigidBodies(), 0);
959	>	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
960	>	nGlobalAtoms + nGlobalRigidBodies,
961		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
962
963		info->setGlobalMolMembership(tmpMolMembership);
964		#else
965		info->setGlobalMolMembership(globalMolMembership);
966		#endif
967	+
968	+	// nIOPerMol holds the number of integrable objects per molecule
969	+	// here the molecules are listed by their global indices.
970	+
971	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
972	+	for (mol = info->beginMolecule(mi); mol != NULL;
973	+	mol = info->nextMolecule(mi)) {
974	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
975	+	}
976
977	<	}
978	<
979	<	void SimCreator::loadCoordinates(SimInfo* info) {
980	<	Globals* simParams;
981	<	simParams = info->getSimParams();
977	>	#ifdef IS_MPI
978	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
979	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
980	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
981	>	#else
982	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
983	>	#endif
984	>
985	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
986
987	<	if (!simParams->haveInitialConfig()) {
988	<	sprintf(painCave.errMsg,
989	<	"Cannot intialize a simulation without an initial configuration file.\n");
990	<	painCave.isFatal = 1;;
672	<	simError();
987	>	int startingIndex = 0;
988	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
989	>	startingIOIndexForMol[i] = startingIndex;
990	>	startingIndex += numIntegrableObjectsPerMol[i];
991		}
992
993	<	DumpReader reader(info, simParams->getInitialConfig());
993	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
994	>	for (mol = info->beginMolecule(mi); mol != NULL;
995	>	mol = info->nextMolecule(mi)) {
996	>	int myGlobalIndex = mol->getGlobalIndex();
997	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
998	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
999	>	sd = mol->nextIntegrableObject(ioi)) {
1000	>	sd->setGlobalIntegrableObjectIndex(globalIO);
1001	>	IOIndexToIntegrableObject[globalIO] = sd;
1002	>	globalIO++;
1003	>	}
1004	>	}
1005	>
1006	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
1007	>
1008	>	}
1009	>
1010	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
1011	>
1012	>	DumpReader reader(info, mdFileName);
1013		int nframes = reader.getNFrames();
1014
1015		if (nframes > 0) {
#	Line 681 | Line 1018 | Globals* SimCreator::parseFile(const std::string mdFil
1018		//invalid initial coordinate file
1019		sprintf(painCave.errMsg,
1020		"Initial configuration file %s should at least contain one frame\n",
1021	<	simParams->getInitialConfig().c_str());
1021	>	mdFileName.c_str());
1022		painCave.isFatal = 1;
1023		simError();
1024		}
688	–
1025		//copy the current snapshot to previous snapshot
1026		info->getSnapshotManager()->advance();
1027		}
1028
1029	<	} //end namespace oopse
1029	>	} //end namespace OpenMD
1030
1031

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2069 by gezelter, Thu Mar 5 16:30:23 2015 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines