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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 845 by tim, Wed Jan 11 19:01:20 2006 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 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		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49		#include <exception>
#	Line 55 | Line 55
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
58	<	#include "UseTheForce/ForceFieldFactory.hpp"
58	>	#include "brains/ForceField.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 75
75		#include "antlr/NoViableAltForCharException.hpp"
76		#include "antlr/NoViableAltException.hpp"
77
78	+	#include "types/DirectionalAdapter.hpp"
79	+	#include "types/MultipoleAdapter.hpp"
80	+	#include "types/EAMAdapter.hpp"
81	+	#include "types/SuttonChenAdapter.hpp"
82	+	#include "types/PolarizableAdapter.hpp"
83	+	#include "types/FixedChargeAdapter.hpp"
84	+	#include "types/FluctuatingChargeAdapter.hpp"
85	+
86		#ifdef IS_MPI
87	+	#include "mpi.h"
88		#include "math/ParallelRandNumGen.hpp"
89		#endif
90
91	<	namespace oopse {
91	>	namespace OpenMD {
92
93	<	Globals* SimCreator::parseFile(const std::string mdFileName){
94	<	Globals* simParams = NULL;
95	<	try {
93	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
94	>	Globals* simParams = NULL;
95	>	try {
96
97	<	// Create a preprocessor that preprocesses md file into an ostringstream
98	<	std::stringstream ppStream;
97	>	// Create a preprocessor that preprocesses md file into an ostringstream
98	>	std::stringstream ppStream;
99		#ifdef IS_MPI
100	<	int streamSize;
101	<	const int masterNode = 0;
102	<	int commStatus;
103	<	if (worldRank == masterNode) {
104	<	#endif
100	>	int streamSize;
101	>	const int masterNode = 0;
102	>	int commStatus;
103	>	if (worldRank == masterNode) {
104	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
109		#ifdef IS_MPI
110	<	//brocasting the stream size
111	<	streamSize = ppStream.str().size() +1;
112	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
110	>	//brocasting the stream size
111	>	streamSize = ppStream.str().size() +1;
112	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
113
114	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
114	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
115
116
117	<	} else {
118	<	//get stream size
119	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
117	>	} else {
118	>
119	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
120	>
121	>	//get stream size
122	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
123	>
124	>	char* buf = new char[streamSize];
125	>	assert(buf);
126
127	<	char* buf = new char[streamSize];
128	<	assert(buf);
127	>	//receive file content
128	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129
130	<	//receive file content
131	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	<
118	<	ppStream.str(buf);
119	<	delete buf;
130	>	ppStream.str(buf);
131	>	delete [] buf;
132
133	<	}
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
155	<	// Create a tree parser that reads information into Globals
156	<	MDTreeParser treeParser;
157	<	treeParser.initializeASTFactory(factory);
158	<	treeParser.setASTFactory(&factory);
159	<	simParams = treeParser.walkTree(parser.getAST());
155	>	// Create a tree parser that reads information into Globals
156	>	MDTreeParser treeParser;
157	>	treeParser.initializeASTFactory(factory);
158	>	treeParser.setASTFactory(&factory);
159	>	simParams = treeParser.walkTree(parser.getAST());
160	>	}
161
149	–	}
150	–
162
163	<	catch(antlr::MismatchedCharException& 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::MismatchedTokenException &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::NoViableAltForCharException &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	<	catch(antlr::NoViableAltException &e) {
185	<	sprintf(painCave.errMsg,
186	<	"parser exception: %s %s:%d:%d\n",
187	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	<	painCave.isFatal = 1;
189	<	simError();
190	<	}
163	>	catch(antlr::MismatchedCharException& 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::MismatchedTokenException &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::NoViableAltForCharException &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	>	catch(antlr::NoViableAltException &e) {
185	>	sprintf(painCave.errMsg,
186	>	"parser exception: %s %s:%d:%d\n",
187	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	>	painCave.isFatal = 1;
189	>	simError();
190	>	}
191
192	<	catch(antlr::TokenStreamRecognitionException& e) {
193	<	sprintf(painCave.errMsg,
194	<	"parser exception: %s %s:%d:%d\n",
195	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
196	<	painCave.isFatal = 1;
197	<	simError();
198	<	}
192	>	catch(antlr::TokenStreamRecognitionException& e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s %s:%d:%d\n",
195	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199	>
200	>	catch(antlr::TokenStreamIOException& e) {
201	>	sprintf(painCave.errMsg,
202	>	"parser exception: %s\n",
203	>	e.getMessage().c_str());
204	>	painCave.isFatal = 1;
205	>	simError();
206	>	}
207
208	<	catch(antlr::TokenStreamIOException& e) {
209	<	sprintf(painCave.errMsg,
210	<	"parser exception: %s\n",
211	<	e.getMessage().c_str());
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
215	<
216	<	catch(antlr::TokenStreamException& e) {
217	<	sprintf(painCave.errMsg,
218	<	"parser exception: %s\n",
219	<	e.getMessage().c_str());
220	<	painCave.isFatal = 1;
221	<	simError();
222	<	}
223	<	catch (antlr::RecognitionException& e) {
224	<	sprintf(painCave.errMsg,
225	<	"parser exception: %s %s:%d:%d\n",
226	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
227	<	painCave.isFatal = 1;
228	<	simError();
229	<	}
230	<	catch (antlr::CharStreamException& e) {
231	<	sprintf(painCave.errMsg,
232	<	"parser exception: %s\n",
233	<	e.getMessage().c_str());
234	<	painCave.isFatal = 1;
235	<	simError();
236	<	}
237	<	catch (OOPSEException& e) {
238	<	sprintf(painCave.errMsg,
239	<	"%s\n",
240	<	e.getMessage().c_str());
241	<	painCave.isFatal = 1;
242	<	simError();
224	<	}
225	<	catch (std::exception& e) {
226	<	sprintf(painCave.errMsg,
227	<	"parser exception: %s\n",
228	<	e.what());
229	<	painCave.isFatal = 1;
230	<	simError();
231	<	}
208	>	catch(antlr::TokenStreamException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s\n",
211	>	e.getMessage().c_str());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>	catch (antlr::RecognitionException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s %s:%d:%d\n",
218	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (antlr::CharStreamException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"parser exception: %s\n",
225	>	e.getMessage().c_str());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (OpenMDException& e) {
230	>	sprintf(painCave.errMsg,
231	>	"%s\n",
232	>	e.getMessage().c_str());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>	catch (std::exception& e) {
237	>	sprintf(painCave.errMsg,
238	>	"parser exception: %s\n",
239	>	e.what());
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243
244	<	return simParams;
244	>	simParams->setMDfileVersion(mdFileVersion);
245	>	return simParams;
246		}
247
248		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
249		bool loadInitCoords) {
250	+
251	+	const int bufferSize = 65535;
252	+	char buffer[bufferSize];
253	+	int lineNo = 0;
254	+	std::string mdRawData;
255	+	int metaDataBlockStart = -1;
256	+	int metaDataBlockEnd = -1;
257	+	int i;
258	+	streamoff mdOffset;
259	+	int mdFileVersion;
260
261	+
262	+	#ifdef IS_MPI
263	+	const int masterNode = 0;
264	+	if (worldRank == masterNode) {
265	+	#endif
266	+
267	+	std::ifstream mdFile_;
268	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
269	+
270	+	if (mdFile_.fail()) {
271	+	sprintf(painCave.errMsg,
272	+	"SimCreator: Cannot open file: %s\n",
273	+	mdFileName.c_str());
274	+	painCave.isFatal = 1;
275	+	simError();
276	+	}
277	+
278	+	mdFile_.getline(buffer, bufferSize);
279	+	++lineNo;
280	+	std::string line = trimLeftCopy(buffer);
281	+	i = CaseInsensitiveFind(line, "<OpenMD");
282	+	if (static_cast<size_t>(i) == string::npos) {
283	+	// try the older file strings to see if that works:
284	+	i = CaseInsensitiveFind(line, "<OOPSE");
285	+	}
286	+
287	+	if (static_cast<size_t>(i) == string::npos) {
288	+	// still no luck!
289	+	sprintf(painCave.errMsg,
290	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
291	+	mdFileName.c_str());
292	+	painCave.isFatal = 1;
293	+	simError();
294	+	}
295	+
296	+	// found the correct opening string, now try to get the file
297	+	// format version number.
298	+
299	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
300	+	std::string fileType = tokenizer.nextToken();
301	+	toUpper(fileType);
302	+
303	+	mdFileVersion = 0;
304	+
305	+	if (fileType == "OPENMD") {
306	+	while (tokenizer.hasMoreTokens()) {
307	+	std::string token(tokenizer.nextToken());
308	+	toUpper(token);
309	+	if (token == "VERSION") {
310	+	mdFileVersion = tokenizer.nextTokenAsInt();
311	+	break;
312	+	}
313	+	}
314	+	}
315	+
316	+	//scan through the input stream and find MetaData tag
317	+	while(mdFile_.getline(buffer, bufferSize)) {
318	+	++lineNo;
319	+
320	+	std::string line = trimLeftCopy(buffer);
321	+	if (metaDataBlockStart == -1) {
322	+	i = CaseInsensitiveFind(line, "<MetaData>");
323	+	if (i != string::npos) {
324	+	metaDataBlockStart = lineNo;
325	+	mdOffset = mdFile_.tellg();
326	+	}
327	+	} else {
328	+	i = CaseInsensitiveFind(line, "</MetaData>");
329	+	if (i != string::npos) {
330	+	metaDataBlockEnd = lineNo;
331	+	}
332	+	}
333	+	}
334	+
335	+	if (metaDataBlockStart == -1) {
336	+	sprintf(painCave.errMsg,
337	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
338	+	mdFileName.c_str());
339	+	painCave.isFatal = 1;
340	+	simError();
341	+	}
342	+	if (metaDataBlockEnd == -1) {
343	+	sprintf(painCave.errMsg,
344	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
345	+	mdFileName.c_str());
346	+	painCave.isFatal = 1;
347	+	simError();
348	+	}
349	+
350	+	mdFile_.clear();
351	+	mdFile_.seekg(0);
352	+	mdFile_.seekg(mdOffset);
353	+
354	+	mdRawData.clear();
355	+
356	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
357	+	mdFile_.getline(buffer, bufferSize);
358	+	mdRawData += buffer;
359	+	mdRawData += "\n";
360	+	}
361	+
362	+	mdFile_.close();
363	+
364	+	#ifdef IS_MPI
365	+	}
366	+	#endif
367	+
368	+	std::stringstream rawMetaDataStream(mdRawData);
369	+
370		//parse meta-data file
371	<	Globals* simParams = parseFile(mdFileName);
371	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
372	>	metaDataBlockStart + 1);
373
374		//create the force field
375	<	ForceField * ff = ForceFieldFactory::getInstance()
376	<	->createForceField(simParams->getForceField());
245	<
375	>	ForceField * ff = new ForceField(simParams->getForceField());
376	>
377		if (ff == NULL) {
378		sprintf(painCave.errMsg,
379		"ForceField Factory can not create %s force field\n",
#	Line 275 | Line 406 | Globals* SimCreator::parseFile(const std::string mdFil
406		}
407
408		ff->parse(forcefieldFileName);
278	–	ff->setFortranForceOptions();
409		//create SimInfo
410		SimInfo * info = new SimInfo(ff, simParams);
411	+
412	+	info->setRawMetaData(mdRawData);
413
414	<	//gather parameters (SimCreator only retrieves part of the parameters)
414	>	//gather parameters (SimCreator only retrieves part of the
415	>	//parameters)
416		gatherParameters(info, mdFileName);
417
418		//divide the molecules and determine the global index of molecules
#	Line 290 | Line 423 | Globals* SimCreator::parseFile(const std::string mdFil
423		//create the molecules
424		createMolecules(info);
425
426	+	//find the storage layout
427	+
428	+	int storageLayout = computeStorageLayout(info);
429	+
430	+	//allocate memory for DataStorage(circular reference, need to
431	+	//break it)
432	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
433
434	<	//allocate memory for DataStorage(circular reference, need to break it)
435	<	info->setSnapshotManager(new SimSnapshotManager(info));
436	<
437	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
438	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
299	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
434	>	//set the global index of atoms, rigidbodies and cutoffgroups
435	>	//(only need to be set once, the global index will never change
436	>	//again). Local indices of atoms and rigidbodies are already set
437	>	//by MoleculeCreator class which actually delegates the
438	>	//responsibility to LocalIndexManager.
439		setGlobalIndex(info);
440
441	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
442	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
443	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
444	<	//we can determine the beginning global indices of atoms before they get created.
441	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
442	>	//method, at that point atoms don't have the global index yet
443	>	//(their global index are all initialized to -1).  Therefore we
444	>	//have to call addInteractionPairs explicitly here. A way to work
445	>	//around is that we can determine the beginning global indices of
446	>	//atoms before they get created.
447		SimInfo::MoleculeIterator mi;
448		Molecule* mol;
449		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
450	<	info->addExcludePairs(mol);
450	>	info->addInteractionPairs(mol);
451		}
452
453		if (loadInitCoords)
454	<	loadCoordinates(info);
314	<
454	>	loadCoordinates(info, mdFileName);
455		return info;
456		}
457
#	Line 346 | Line 486 | Globals* SimCreator::parseFile(const std::string mdFil
486
487		#ifdef IS_MPI
488		void SimCreator::divideMolecules(SimInfo *info) {
489	<	double numerator;
490	<	double denominator;
491	<	double precast;
492	<	double x;
493	<	double y;
494	<	double a;
489	>	RealType numerator;
490	>	RealType denominator;
491	>	RealType precast;
492	>	RealType x;
493	>	RealType y;
494	>	RealType a;
495		int old_atoms;
496		int add_atoms;
497		int new_atoms;
#	Line 366 | Line 506 | Globals* SimCreator::parseFile(const std::string mdFil
506		int nGlobalMols = info->getNGlobalMolecules();
507		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
508
509	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
509	>	nProcessors = MPI::COMM_WORLD.Get_size();
510
511		if (nProcessors > nGlobalMols) {
512		sprintf(painCave.errMsg,
#	Line 375 | Line 515 | Globals* SimCreator::parseFile(const std::string mdFil
515		"\tthe number of molecules.  This will not result in a \n"
516		"\tusable division of atoms for force decomposition.\n"
517		"\tEither try a smaller number of processors, or run the\n"
518	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
518	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
519
520		painCave.isFatal = 1;
521		simError();
#	Line 404 | Line 544 | Globals* SimCreator::parseFile(const std::string mdFil
544		nTarget = (int)(precast + 0.5);
545
546		for(i = 0; i < nGlobalMols; i++) {
547	+
548		done = 0;
549		loops = 0;
550
#	Line 428 | Line 569 | Globals* SimCreator::parseFile(const std::string mdFil
569		// and be done with it.
570
571		if (loops > 100) {
572	+
573		sprintf(painCave.errMsg,
574	<	"I've tried 100 times to assign molecule %d to a "
575	<	" processor, but can't find a good spot.\n"
576	<	"I'm assigning it at random to processor %d.\n",
574	>	"There have been 100 attempts to assign molecule %d to an\n"
575	>	"\tunderworked processor, but there's no good place to\n"
576	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
577		i, which_proc);
578	<
578	>
579		painCave.isFatal = 0;
580	+	painCave.severity = OPENMD_INFO;
581		simError();
582
583		molToProcMap[i] = which_proc;
#	Line 463 | Line 606 | Globals* SimCreator::parseFile(const std::string mdFil
606		//           Pacc(x) = exp(- a * x)
607		// where a = penalty / (average atoms per molecule)
608
609	<	x = (double)(new_atoms - nTarget);
609	>	x = (RealType)(new_atoms - nTarget);
610		y = myRandom->rand();
611
612		if (y < exp(- a * x)) {
#	Line 479 | Line 622 | Globals* SimCreator::parseFile(const std::string mdFil
622		}
623
624		delete myRandom;
625	<
625	>
626		// Spray out this nonsense to all other processors:
627	<
485	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
627	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
628		} else {
629
630		// Listen to your marching orders from processor 0:
631	<
632	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
631	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
632	>
633		}
634
635		info->setMolToProcMap(molToProcMap);
636		sprintf(checkPointMsg,
637		"Successfully divided the molecules among the processors.\n");
638	<	MPIcheckPoint();
638	>	errorCheckPoint();
639		}
640
641		#endif
#	Line 510 | Line 652 | Globals* SimCreator::parseFile(const std::string mdFil
652		#endif
653
654		stampId = info->getMoleculeStampId(i);
655	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
656	<	stampId, i, info->getLocalIndexManager());
655	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
656	>	info->getMoleculeStamp(stampId),
657	>	stampId, i,
658	>	info->getLocalIndexManager());
659
660		info->addMolecule(mol);
661
#	Line 523 | Line 667 | Globals* SimCreator::parseFile(const std::string mdFil
667
668		} //end for(int i=0)
669		}
670	+
671	+	int SimCreator::computeStorageLayout(SimInfo* info) {
672	+
673	+	Globals* simParams = info->getSimParams();
674	+	int nRigidBodies = info->getNGlobalRigidBodies();
675	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
676	+	set<AtomType*>::iterator i;
677	+	bool hasDirectionalAtoms = false;
678	+	bool hasFixedCharge = false;
679	+	bool hasDipoles = false;
680	+	bool hasQuadrupoles = false;
681	+	bool hasPolarizable = false;
682	+	bool hasFluctuatingCharge = false;
683	+	bool hasMetallic = false;
684	+	int storageLayout = 0;
685	+	storageLayout |= DataStorage::dslPosition;
686	+	storageLayout |= DataStorage::dslVelocity;
687	+	storageLayout |= DataStorage::dslForce;
688	+
689	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
690	+
691	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
692	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
693	+	EAMAdapter ea = EAMAdapter( (*i) );
694	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
695	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
696	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
697	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
698	+
699	+	if (da.isDirectional()){
700	+	hasDirectionalAtoms = true;
701	+	}
702	+	if (ma.isDipole()){
703	+	hasDipoles = true;
704	+	}
705	+	if (ma.isQuadrupole()){
706	+	hasQuadrupoles = true;
707	+	}
708	+	if (ea.isEAM() || sca.isSuttonChen()){
709	+	hasMetallic = true;
710	+	}
711	+	if ( fca.isFixedCharge() ){
712	+	hasFixedCharge = true;
713	+	}
714	+	if ( fqa.isFluctuatingCharge() ){
715	+	hasFluctuatingCharge = true;
716	+	}
717	+	if ( pa.isPolarizable() ){
718	+	hasPolarizable = true;
719	+	}
720	+	}
721
722	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
723	+	storageLayout |= DataStorage::dslAmat;
724	+	if(storageLayout & DataStorage::dslVelocity) {
725	+	storageLayout |= DataStorage::dslAngularMomentum;
726	+	}
727	+	if (storageLayout & DataStorage::dslForce) {
728	+	storageLayout |= DataStorage::dslTorque;
729	+	}
730	+	}
731	+	if (hasDipoles) {
732	+	storageLayout |= DataStorage::dslDipole;
733	+	}
734	+	if (hasQuadrupoles) {
735	+	storageLayout |= DataStorage::dslQuadrupole;
736	+	}
737	+	if (hasFixedCharge || hasFluctuatingCharge) {
738	+	storageLayout |= DataStorage::dslSkippedCharge;
739	+	}
740	+	if (hasMetallic) {
741	+	storageLayout |= DataStorage::dslDensity;
742	+	storageLayout |= DataStorage::dslFunctional;
743	+	storageLayout |= DataStorage::dslFunctionalDerivative;
744	+	}
745	+	if (hasPolarizable) {
746	+	storageLayout |= DataStorage::dslElectricField;
747	+	}
748	+	if (hasFluctuatingCharge){
749	+	storageLayout |= DataStorage::dslFlucQPosition;
750	+	if(storageLayout & DataStorage::dslVelocity) {
751	+	storageLayout |= DataStorage::dslFlucQVelocity;
752	+	}
753	+	if (storageLayout & DataStorage::dslForce) {
754	+	storageLayout |= DataStorage::dslFlucQForce;
755	+	}
756	+	}
757	+
758	+	// if the user has asked for them, make sure we've got the memory for the
759	+	// objects defined.
760	+
761	+	if (simParams->getOutputParticlePotential()) {
762	+	storageLayout |= DataStorage::dslParticlePot;
763	+	}
764	+
765	+	if (simParams->havePrintHeatFlux()) {
766	+	if (simParams->getPrintHeatFlux()) {
767	+	storageLayout |= DataStorage::dslParticlePot;
768	+	}
769	+	}
770	+
771	+	if (simParams->getOutputElectricField()) {
772	+	storageLayout |= DataStorage::dslElectricField;
773	+	}
774	+
775	+	if (simParams->getOutputFluctuatingCharges()) {
776	+	storageLayout |= DataStorage::dslFlucQPosition;
777	+	storageLayout |= DataStorage::dslFlucQVelocity;
778	+	storageLayout |= DataStorage::dslFlucQForce;
779	+	}
780	+
781	+	return storageLayout;
782	+	}
783	+
784		void SimCreator::setGlobalIndex(SimInfo *info) {
785		SimInfo::MoleculeIterator mi;
786		Molecule::AtomIterator ai;
787		Molecule::RigidBodyIterator ri;
788		Molecule::CutoffGroupIterator ci;
789	+	Molecule::IntegrableObjectIterator  ioi;
790		Molecule * mol;
791		Atom * atom;
792		RigidBody * rb;
#	Line 537 | Line 795 | Globals* SimCreator::parseFile(const std::string mdFil
795		int beginRigidBodyIndex;
796		int beginCutoffGroupIndex;
797		int nGlobalAtoms = info->getNGlobalAtoms();
798	<
541	<	#ifndef IS_MPI
798	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
799
800		beginAtomIndex = 0;
544	–	beginRigidBodyIndex = 0;
545	–	beginCutoffGroupIndex = 0;
546	–
547	–	#else
548	–
549	–	int nproc;
550	–	int myNode;
551	–
552	–	myNode = worldRank;
553	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
554	–
555	–	std::vector < int > tmpAtomsInProc(nproc, 0);
556	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
557	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
558	–	std::vector < int > NumAtomsInProc(nproc, 0);
559	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
560	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
561	–
562	–	tmpAtomsInProc[myNode] = info->getNAtoms();
563	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
564	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
565	–
566	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
567	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
568	–	MPI_SUM, MPI_COMM_WORLD);
569	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
570	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
571	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
572	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
573	–
574	–	beginAtomIndex = 0;
575	–	beginRigidBodyIndex = 0;
576	–	beginCutoffGroupIndex = 0;
577	–
578	–	for(int i = 0; i < myNode; i++) {
579	–	beginAtomIndex += NumAtomsInProc[i];
580	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
581	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
582	–	}
583	–
584	–	#endif
585	–
801		//rigidbody's index begins right after atom's
802	<	beginRigidBodyIndex += info->getNGlobalAtoms();
803	<
804	<	for(mol = info->beginMolecule(mi); mol != NULL;
805	<	mol = info->nextMolecule(mi)) {
802	>	beginRigidBodyIndex = info->getNGlobalAtoms();
803	>	beginCutoffGroupIndex = 0;
804	>
805	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
806
807	<	//local index(index in DataStorge) of atom is important
808	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
809	<	atom->setGlobalIndex(beginAtomIndex++);
807	>	#ifdef IS_MPI
808	>	if (info->getMolToProc(i) == worldRank) {
809	>	#endif
810	>	// stuff to do if I own this molecule
811	>	mol = info->getMoleculeByGlobalIndex(i);
812	>
813	>	//local index(index in DataStorge) of atom is important
814	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
815	>	atom->setGlobalIndex(beginAtomIndex++);
816	>	}
817	>
818	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
819	>	rb = mol->nextRigidBody(ri)) {
820	>	rb->setGlobalIndex(beginRigidBodyIndex++);
821	>	}
822	>
823	>	//local index of cutoff group is trivial, it only depends on
824	>	//the order of travesing
825	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
826	>	cg = mol->nextCutoffGroup(ci)) {
827	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
828	>	}
829	>
830	>	#ifdef IS_MPI
831	>	}  else {
832	>
833	>	// stuff to do if I don't own this molecule
834	>
835	>	int stampId = info->getMoleculeStampId(i);
836	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
837	>
838	>	beginAtomIndex += stamp->getNAtoms();
839	>	beginRigidBodyIndex += stamp->getNRigidBodies();
840	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
841		}
842	<
843	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
844	<	rb = mol->nextRigidBody(ri)) {
845	<	rb->setGlobalIndex(beginRigidBodyIndex++);
600	<	}
601	<
602	<	//local index of cutoff group is trivial, it only depends on the order of travesing
603	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
604	<	cg = mol->nextCutoffGroup(ci)) {
605	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
606	<	}
607	<	}
608	<
842	>	#endif
843	>
844	>	} //end for(int i=0)
845	>
846		//fill globalGroupMembership
847		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
848		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 617 | Line 854 | Globals* SimCreator::parseFile(const std::string mdFil
854
855		}
856		}
857	<
857	>
858		#ifdef IS_MPI
859		// Since the globalGroupMembership has been zero filled and we've only
860		// poked values into the atoms we know, we can do an Allreduce
861		// to get the full globalGroupMembership array (We think).
862		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
863		// docs said we could.
864	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
865	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
866	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
864	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
865	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
866	>	&tmpGroupMembership[0], nGlobalAtoms,
867	>	MPI::INT, MPI::SUM);
868		info->setGlobalGroupMembership(tmpGroupMembership);
869		#else
870		info->setGlobalGroupMembership(globalGroupMembership);
871		#endif
872
873		//fill molMembership
874	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
874	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
875	>	info->getNGlobalRigidBodies(), 0);
876
877	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
878	<
877	>	for(mol = info->beginMolecule(mi); mol != NULL;
878	>	mol = info->nextMolecule(mi)) {
879		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
880		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
881		}
882	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
883	+	rb = mol->nextRigidBody(ri)) {
884	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
885	+	}
886		}
887
888		#ifdef IS_MPI
889	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
889	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
890	>	info->getNGlobalRigidBodies(), 0);
891	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
892	>	nGlobalAtoms + nGlobalRigidBodies,
893	>	MPI::INT, MPI::SUM);
894
648	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
649	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
650	–
895		info->setGlobalMolMembership(tmpMolMembership);
896		#else
897		info->setGlobalMolMembership(globalMolMembership);
898		#endif
899	+
900	+	// nIOPerMol holds the number of integrable objects per molecule
901	+	// here the molecules are listed by their global indices.
902	+
903	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
904	+	for (mol = info->beginMolecule(mi); mol != NULL;
905	+	mol = info->nextMolecule(mi)) {
906	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
907	+	}
908
909	+	#ifdef IS_MPI
910	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
911	+	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
912	+	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
913	+	#else
914	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
915	+	#endif
916	+
917	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
918	+
919	+	int startingIndex = 0;
920	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
921	+	startingIOIndexForMol[i] = startingIndex;
922	+	startingIndex += numIntegrableObjectsPerMol[i];
923	+	}
924	+
925	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
926	+	for (mol = info->beginMolecule(mi); mol != NULL;
927	+	mol = info->nextMolecule(mi)) {
928	+	int myGlobalIndex = mol->getGlobalIndex();
929	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
930	+	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
931	+	sd = mol->nextIntegrableObject(ioi)) {
932	+	sd->setGlobalIntegrableObjectIndex(globalIO);
933	+	IOIndexToIntegrableObject[globalIO] = sd;
934	+	globalIO++;
935	+	}
936	+	}
937	+
938	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
939	+
940		}
941
942	<	void SimCreator::loadCoordinates(SimInfo* info) {
942	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
943		Globals* simParams;
944	+
945		simParams = info->getSimParams();
946
947	<	if (!simParams->haveInitialConfig()) {
663	<	sprintf(painCave.errMsg,
664	<	"Cannot intialize a simulation without an initial configuration file.\n");
665	<	painCave.isFatal = 1;;
666	<	simError();
667	<	}
668	<
669	<	DumpReader reader(info, simParams->getInitialConfig());
947	>	DumpReader reader(info, mdFileName);
948		int nframes = reader.getNFrames();
949	<
949	>
950		if (nframes > 0) {
951		reader.readFrame(nframes - 1);
952		} else {
953		//invalid initial coordinate file
954		sprintf(painCave.errMsg,
955		"Initial configuration file %s should at least contain one frame\n",
956	<	simParams->getInitialConfig().c_str());
956	>	mdFileName.c_str());
957		painCave.isFatal = 1;
958		simError();
959		}
682	–
960		//copy the current snapshot to previous snapshot
961		info->getSnapshotManager()->advance();
962		}
963
964	<	} //end namespace oopse
964	>	} //end namespace OpenMD
965
966

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 845 by tim, Wed Jan 11 19:01:20 2006 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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