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trunk/src/brains/SimCreator.cpp (file contents), Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 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 55 | Line 56
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
59	<	#include "UseTheForce/ForceFieldFactory.hpp"
59	>	#include "brains/ForceField.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 76
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 "mpi.h"
89		#include "math/ParallelRandNumGen.hpp"
90		#endif
91
92	<	namespace oopse {
92	>	namespace OpenMD {
93
94	<	Globals* SimCreator::parseFile(const std::string mdFileName){
95	<	Globals* simParams = NULL;
96	<	try {
94	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95	>	Globals* simParams = NULL;
96	>	try {
97
98	<	// Create a preprocessor that preprocesses md file into an ostringstream
99	<	std::stringstream ppStream;
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	<	#endif
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
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
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);
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	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
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	<	//get stream size
120	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
118	>	} else {
119	>
120	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121	>
122	>	//get stream size
123	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124	>
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127
128	<	char* buf = new char[streamSize];
129	<	assert(buf);
128	>	//receive file content
129	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
130
131	<	//receive file content
132	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	<
118	<	ppStream.str(buf);
119	<	delete buf;
131	>	ppStream.str(buf);
132	>	delete [] buf;
133
134	<	}
134	>	}
135		#endif
136	<	// Create a scanner that reads from the input stream
137	<	MDLexer lexer(ppStream);
138	<	lexer.setFilename(mdFileName);
139	<	lexer.initDeferredLineCount();
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(mdFileName);
141	>	// Create a parser that reads from the scanner
142	>	MDParser parser(lexer);
143	>	parser.setFilename(filename);
144
145	<	// Create an observer that synchorizes file name change
146	<	FilenameObserver observer;
147	<	observer.setLexer(&lexer);
148	<	observer.setParser(&parser);
149	<	lexer.setObserver(&observer);
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();
151	>	antlr::ASTFactory factory;
152	>	parser.initializeASTFactory(factory);
153	>	parser.setASTFactory(&factory);
154	>	parser.mdfile();
155
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());
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
149	–	}
150	–
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	<	}
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	<	}
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	<	}
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 (OOPSEException& 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	<	}
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	<	return simParams;
245	>	simParams->setMDfileVersion(mdFileVersion);
246	>	return simParams;
247		}
248
249		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250		bool loadInitCoords) {
251	+
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	+
262	+
263	+	#ifdef IS_MPI
264	+	const int masterNode = 0;
265	+	if (worldRank == masterNode) {
266	+	#endif
267	+
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(mdFileName);
372	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373	>	metaDataBlockStart + 1);
374
375		//create the force field
376	<	ForceField * ff = ForceFieldFactory::getInstance()
377	<	->createForceField(simParams->getForceField());
245	<
376	>	ForceField * ff = new ForceField(simParams->getForceField());
377	>
378		if (ff == NULL) {
379		sprintf(painCave.errMsg,
380		"ForceField Factory can not create %s force field\n",
#	Line 275 | Line 407 | Globals* SimCreator::parseFile(const std::string mdFil
407		}
408
409		ff->parse(forcefieldFileName);
278	–	ff->setFortranForceOptions();
410		//create SimInfo
411		SimInfo * info = new SimInfo(ff, simParams);
412	+
413	+	info->setRawMetaData(mdRawData);
414
415		//gather parameters (SimCreator only retrieves part of the
416		//parameters)
#	Line 291 | Line 424 | Globals* SimCreator::parseFile(const std::string mdFil
424		//create the molecules
425		createMolecules(info);
426
427	<
427	>	//find the storage layout
428	>
429	>	int storageLayout = computeStorageLayout(info);
430	>
431		//allocate memory for DataStorage(circular reference, need to
432		//break it)
433	<	info->setSnapshotManager(new SimSnapshotManager(info));
433	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435		//set the global index of atoms, rigidbodies and cutoffgroups
436		//(only need to be set once, the global index will never change
#	Line 303 | Line 439 | Globals* SimCreator::parseFile(const std::string mdFil
439		//responsibility to LocalIndexManager.
440		setGlobalIndex(info);
441
442	<	//Although addExcludePairs is called inside SimInfo's addMolecule
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 addExcludePairs explicitly here. A way to work
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
454		if (loadInitCoords)
455	<	loadCoordinates(info);
320	<
455	>	loadCoordinates(info, mdFileName);
456		return info;
457		}
458
#	Line 352 | Line 487 | Globals* SimCreator::parseFile(const std::string mdFil
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 372 | Line 507 | Globals* SimCreator::parseFile(const std::string mdFil
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);
510	>	nProcessors = MPI::COMM_WORLD.Get_size();
511
512		if (nProcessors > nGlobalMols) {
513		sprintf(painCave.errMsg,
#	Line 381 | Line 516 | Globals* SimCreator::parseFile(const std::string mdFil
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);
519	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
520
521		painCave.isFatal = 1;
522		simError();
#	Line 410 | Line 545 | Globals* SimCreator::parseFile(const std::string mdFil
545		nTarget = (int)(precast + 0.5);
546
547		for(i = 0; i < nGlobalMols; i++) {
548	+
549		done = 0;
550		loops = 0;
551
#	Line 434 | Line 570 | Globals* SimCreator::parseFile(const std::string mdFil
570		// and be done with it.
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
584		molToProcMap[i] = which_proc;
#	Line 469 | Line 607 | Globals* SimCreator::parseFile(const std::string mdFil
607		//           Pacc(x) = exp(- a * x)
608		// where a = penalty / (average atoms per molecule)
609
610	<	x = (double)(new_atoms - nTarget);
610	>	x = (RealType)(new_atoms - nTarget);
611		y = myRandom->rand();
612
613		if (y < exp(- a * x)) {
#	Line 485 | Line 623 | Globals* SimCreator::parseFile(const std::string mdFil
623		}
624
625		delete myRandom;
626	<
626	>
627		// Spray out this nonsense to all other processors:
628	<
491	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
628	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
629		} else {
630
631		// Listen to your marching orders from processor 0:
632	<
633	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
632	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
633	>
634		}
635
636		info->setMolToProcMap(molToProcMap);
637		sprintf(checkPointMsg,
638		"Successfully divided the molecules among the processors.\n");
639	<	MPIcheckPoint();
639	>	errorCheckPoint();
640		}
641
642		#endif
#	Line 516 | Line 653 | Globals* SimCreator::parseFile(const std::string mdFil
653		#endif
654
655		stampId = info->getMoleculeStampId(i);
656	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
657	<	stampId, i, info->getLocalIndexManager());
656	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
657	>	info->getMoleculeStamp(stampId),
658	>	stampId, i,
659	>	info->getLocalIndexManager());
660
661		info->addMolecule(mol);
662
#	Line 529 | Line 668 | Globals* SimCreator::parseFile(const std::string mdFil
668
669		} //end for(int i=0)
670		}
671	+
672	+	int SimCreator::computeStorageLayout(SimInfo* info) {
673	+
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	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
691	+
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	+	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	+	if (simParams->getOutputParticlePotential()) {
763	+	storageLayout |= DataStorage::dslParticlePot;
764	+	}
765	+
766	+	if (simParams->havePrintHeatFlux()) {
767	+	if (simParams->getPrintHeatFlux()) {
768	+	storageLayout |= DataStorage::dslParticlePot;
769	+	}
770	+	}
771	+
772	+	if (simParams->getOutputElectricField()) {
773	+	storageLayout |= DataStorage::dslElectricField;
774	+	}
775	+
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) {
786		SimInfo::MoleculeIterator mi;
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 543 | Line 796 | Globals* SimCreator::parseFile(const std::string mdFil
796		int beginRigidBodyIndex;
797		int beginCutoffGroupIndex;
798		int nGlobalAtoms = info->getNGlobalAtoms();
799	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
800
547	–	#ifndef IS_MPI
548	–
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
554	<
555	<	int nproc;
556	<	int myNode;
557	<
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)) {
805	>
806	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
807
808	<	//local index(index in DataStorge) of atom is important
809	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
810	<	atom->setGlobalIndex(beginAtomIndex++);
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	>	//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	>	// 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	>	beginAtomIndex += stamp->getNAtoms();
840	>	beginRigidBodyIndex += stamp->getNRigidBodies();
841	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
842		}
843	<
844	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
845	<	rb = mol->nextRigidBody(ri)) {
846	<	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	<
843	>	#endif
844	>
845	>	} //end for(int i=0)
846	>
847		//fill globalGroupMembership
848		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
849		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 623 | Line 855 | Globals* SimCreator::parseFile(const std::string mdFil
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
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
889		#ifdef IS_MPI
890	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
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
654	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
655	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
656	–
896		info->setGlobalMolMembership(tmpMolMembership);
897		#else
898		info->setGlobalMolMembership(globalMolMembership);
899		#endif
900	+
901	+	// nIOPerMol holds the number of integrable objects per molecule
902	+	// here the molecules are listed by their global indices.
903	+
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) {
943	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
944		Globals* simParams;
945	+
946		simParams = info->getSimParams();
947
948	<	if (!simParams->haveInitialConfig()) {
669	<	sprintf(painCave.errMsg,
670	<	"Cannot intialize a simulation without an initial configuration file.\n");
671	<	painCave.isFatal = 1;;
672	<	simError();
673	<	}
674	<
675	<	DumpReader reader(info, simParams->getInitialConfig());
948	>	DumpReader reader(info, mdFileName);
949		int nframes = reader.getNFrames();
950	<
950	>
951		if (nframes > 0) {
952		reader.readFrame(nframes - 1);
953		} else {
954		//invalid initial coordinate file
955		sprintf(painCave.errMsg,
956		"Initial configuration file %s should at least contain one frame\n",
957	<	simParams->getInitialConfig().c_str());
957	>	mdFileName.c_str());
958		painCave.isFatal = 1;
959		simError();
960		}
688	–
961		//copy the current snapshot to previous snapshot
962		info->getSnapshotManager()->advance();
963		}
964
965	<	} //end namespace oopse
965	>	} //end namespace OpenMD
966
967

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 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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