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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 1826 by gezelter, Wed Jan 9 19:41:48 2013 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	<	}
188	<
189	<	catch(antlr::TokenStreamIOException& e) {
190	<	sprintf(painCave.errMsg,
191	<	"parser exception: %s\n",
192	<	e.getMessage().c_str());
193	<	painCave.isFatal = 1;
194	<	simError();
195	<	}
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::TokenStreamException& e) {
201	<	sprintf(painCave.errMsg,
202	<	"parser exception: %s\n",
203	<	e.getMessage().c_str());
204	<	painCave.isFatal = 1;
205	<	simError();
206	<	}
207	<	catch (antlr::RecognitionException& e) {
208	<	sprintf(painCave.errMsg,
209	<	"parser exception: %s %s:%d:%d\n",
210	<	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
211	<	painCave.isFatal = 1;
212	<	simError();
213	<	}
214	<	catch (antlr::CharStreamException& e) {
215	<	sprintf(painCave.errMsg,
216	<	"parser exception: %s\n",
217	<	e.getMessage().c_str());
218	<	painCave.isFatal = 1;
219	<	simError();
220	<	}
221	<	catch (OOPSEException& e) {
222	<	sprintf(painCave.errMsg,
223	<	"%s\n",
224	<	e.getMessage().c_str());
225	<	painCave.isFatal = 1;
226	<	simError();
227	<	}
228	<	catch (std::exception& e) {
229	<	sprintf(painCave.errMsg,
230	<	"parser exception: %s\n",
231	<	e.what());
232	<	painCave.isFatal = 1;
233	<	simError();
234	<	}
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::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, j;
258	+	streamoff mdOffset;
259	+	int mdFileVersion;
260
261	+	// Create a string for embedding the version information in the MetaData
262	+	std::string version;
263	+	version.assign("## Last run using OpenMD Version: ");
264	+	version.append(OPENMD_VERSION_MAJOR);
265	+	version.append(".");
266	+	version.append(OPENMD_VERSION_MINOR);
267	+
268	+	std::string svnrev;
269	+	//convert a macro from compiler to a string in c++
270	+	STR_DEFINE(svnrev, SVN_REV );
271	+	version.append(" Revision: ");
272	+	// If there's no SVN revision, just call this the RELEASE revision.
273	+	if (!svnrev.empty()) {
274	+	version.append(svnrev);
275	+	} else {
276	+	version.append("RELEASE");
277	+	}
278	+
279	+	#ifdef IS_MPI
280	+	const int masterNode = 0;
281	+	if (worldRank == masterNode) {
282	+	#endif
283	+
284	+	std::ifstream mdFile_;
285	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
286	+
287	+	if (mdFile_.fail()) {
288	+	sprintf(painCave.errMsg,
289	+	"SimCreator: Cannot open file: %s\n",
290	+	mdFileName.c_str());
291	+	painCave.isFatal = 1;
292	+	simError();
293	+	}
294	+
295	+	mdFile_.getline(buffer, bufferSize);
296	+	++lineNo;
297	+	std::string line = trimLeftCopy(buffer);
298	+	i = CaseInsensitiveFind(line, "<OpenMD");
299	+	if (static_cast<size_t>(i) == string::npos) {
300	+	// try the older file strings to see if that works:
301	+	i = CaseInsensitiveFind(line, "<OOPSE");
302	+	}
303	+
304	+	if (static_cast<size_t>(i) == string::npos) {
305	+	// still no luck!
306	+	sprintf(painCave.errMsg,
307	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
308	+	mdFileName.c_str());
309	+	painCave.isFatal = 1;
310	+	simError();
311	+	}
312	+
313	+	// found the correct opening string, now try to get the file
314	+	// format version number.
315	+
316	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
317	+	std::string fileType = tokenizer.nextToken();
318	+	toUpper(fileType);
319	+
320	+	mdFileVersion = 0;
321	+
322	+	if (fileType == "OPENMD") {
323	+	while (tokenizer.hasMoreTokens()) {
324	+	std::string token(tokenizer.nextToken());
325	+	toUpper(token);
326	+	if (token == "VERSION") {
327	+	mdFileVersion = tokenizer.nextTokenAsInt();
328	+	break;
329	+	}
330	+	}
331	+	}
332	+
333	+	//scan through the input stream and find MetaData tag
334	+	while(mdFile_.getline(buffer, bufferSize)) {
335	+	++lineNo;
336	+
337	+	std::string line = trimLeftCopy(buffer);
338	+	if (metaDataBlockStart == -1) {
339	+	i = CaseInsensitiveFind(line, "<MetaData>");
340	+	if (i != string::npos) {
341	+	metaDataBlockStart = lineNo;
342	+	mdOffset = mdFile_.tellg();
343	+	}
344	+	} else {
345	+	i = CaseInsensitiveFind(line, "</MetaData>");
346	+	if (i != string::npos) {
347	+	metaDataBlockEnd = lineNo;
348	+	}
349	+	}
350	+	}
351	+
352	+	if (metaDataBlockStart == -1) {
353	+	sprintf(painCave.errMsg,
354	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
355	+	mdFileName.c_str());
356	+	painCave.isFatal = 1;
357	+	simError();
358	+	}
359	+	if (metaDataBlockEnd == -1) {
360	+	sprintf(painCave.errMsg,
361	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
362	+	mdFileName.c_str());
363	+	painCave.isFatal = 1;
364	+	simError();
365	+	}
366	+
367	+	mdFile_.clear();
368	+	mdFile_.seekg(0);
369	+	mdFile_.seekg(mdOffset);
370	+
371	+	mdRawData.clear();
372	+
373	+	bool foundVersion = false;
374	+
375	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
376	+	mdFile_.getline(buffer, bufferSize);
377	+	std::string line = trimLeftCopy(buffer);
378	+	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
379	+	if (static_cast<size_t>(j) != string::npos) {
380	+	foundVersion = true;
381	+	mdRawData += version;
382	+	} else {
383	+	mdRawData += buffer;
384	+	}
385	+	mdRawData += "\n";
386	+	}
387	+
388	+	if (!foundVersion) mdRawData += version + "\n";
389	+
390	+	mdFile_.close();
391	+
392	+	#ifdef IS_MPI
393	+	}
394	+	#endif
395	+
396	+	std::stringstream rawMetaDataStream(mdRawData);
397	+
398		//parse meta-data file
399	<	Globals* simParams = parseFile(mdFileName);
399	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
400	>	metaDataBlockStart + 1);
401
402		//create the force field
403	<	ForceField * ff = ForceFieldFactory::getInstance()
404	<	->createForceField(simParams->getForceField());
245	<
403	>	ForceField * ff = new ForceField(simParams->getForceField());
404	>
405		if (ff == NULL) {
406		sprintf(painCave.errMsg,
407		"ForceField Factory can not create %s force field\n",
#	Line 275 | Line 434 | Globals* SimCreator::parseFile(const std::string mdFil
434		}
435
436		ff->parse(forcefieldFileName);
278	–	ff->setFortranForceOptions();
437		//create SimInfo
438		SimInfo * info = new SimInfo(ff, simParams);
439	+
440	+	info->setRawMetaData(mdRawData);
441
442		//gather parameters (SimCreator only retrieves part of the
443		//parameters)
#	Line 291 | Line 451 | Globals* SimCreator::parseFile(const std::string mdFil
451		//create the molecules
452		createMolecules(info);
453
454	<
454	>	//find the storage layout
455	>
456	>	int storageLayout = computeStorageLayout(info);
457	>
458		//allocate memory for DataStorage(circular reference, need to
459		//break it)
460	<	info->setSnapshotManager(new SimSnapshotManager(info));
460	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
461
462		//set the global index of atoms, rigidbodies and cutoffgroups
463		//(only need to be set once, the global index will never change
#	Line 303 | Line 466 | Globals* SimCreator::parseFile(const std::string mdFil
466		//responsibility to LocalIndexManager.
467		setGlobalIndex(info);
468
469	<	//Although addExcludePairs is called inside SimInfo's addMolecule
469	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
470		//method, at that point atoms don't have the global index yet
471		//(their global index are all initialized to -1).  Therefore we
472	<	//have to call addExcludePairs explicitly here. A way to work
472	>	//have to call addInteractionPairs explicitly here. A way to work
473		//around is that we can determine the beginning global indices of
474		//atoms before they get created.
475		SimInfo::MoleculeIterator mi;
476		Molecule* mol;
477		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
478	<	info->addExcludePairs(mol);
478	>	info->addInteractionPairs(mol);
479		}
480
481		if (loadInitCoords)
482	<	loadCoordinates(info);
320	<
482	>	loadCoordinates(info, mdFileName);
483		return info;
484		}
485
#	Line 352 | Line 514 | Globals* SimCreator::parseFile(const std::string mdFil
514
515		#ifdef IS_MPI
516		void SimCreator::divideMolecules(SimInfo *info) {
517	<	double numerator;
518	<	double denominator;
519	<	double precast;
520	<	double x;
521	<	double y;
522	<	double a;
517	>	RealType numerator;
518	>	RealType denominator;
519	>	RealType precast;
520	>	RealType x;
521	>	RealType y;
522	>	RealType a;
523		int old_atoms;
524		int add_atoms;
525		int new_atoms;
526		int nTarget;
527		int done;
528		int i;
367	–	int j;
529		int loops;
530		int which_proc;
531		int nProcessors;
#	Line 372 | Line 533 | Globals* SimCreator::parseFile(const std::string mdFil
533		int nGlobalMols = info->getNGlobalMolecules();
534		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
535
536	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
536	>	nProcessors = MPI::COMM_WORLD.Get_size();
537
538		if (nProcessors > nGlobalMols) {
539		sprintf(painCave.errMsg,
#	Line 381 | Line 542 | Globals* SimCreator::parseFile(const std::string mdFil
542		"\tthe number of molecules.  This will not result in a \n"
543		"\tusable division of atoms for force decomposition.\n"
544		"\tEither try a smaller number of processors, or run the\n"
545	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
545	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
546
547		painCave.isFatal = 1;
548		simError();
#	Line 410 | Line 571 | Globals* SimCreator::parseFile(const std::string mdFil
571		nTarget = (int)(precast + 0.5);
572
573		for(i = 0; i < nGlobalMols; i++) {
574	+
575		done = 0;
576		loops = 0;
577
#	Line 434 | Line 596 | Globals* SimCreator::parseFile(const std::string mdFil
596		// and be done with it.
597
598		if (loops > 100) {
599	+
600		sprintf(painCave.errMsg,
601	<	"I've tried 100 times to assign molecule %d to a "
602	<	" processor, but can't find a good spot.\n"
603	<	"I'm assigning it at random to processor %d.\n",
601	>	"There have been 100 attempts to assign molecule %d to an\n"
602	>	"\tunderworked processor, but there's no good place to\n"
603	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
604		i, which_proc);
605	<
605	>
606		painCave.isFatal = 0;
607	+	painCave.severity = OPENMD_INFO;
608		simError();
609
610		molToProcMap[i] = which_proc;
#	Line 469 | Line 633 | Globals* SimCreator::parseFile(const std::string mdFil
633		//           Pacc(x) = exp(- a * x)
634		// where a = penalty / (average atoms per molecule)
635
636	<	x = (double)(new_atoms - nTarget);
636	>	x = (RealType)(new_atoms - nTarget);
637		y = myRandom->rand();
638
639		if (y < exp(- a * x)) {
#	Line 485 | Line 649 | Globals* SimCreator::parseFile(const std::string mdFil
649		}
650
651		delete myRandom;
652	<
652	>
653		// Spray out this nonsense to all other processors:
654	<
491	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
654	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655		} else {
656
657		// Listen to your marching orders from processor 0:
658	<
659	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
658	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
659	>
660		}
661
662		info->setMolToProcMap(molToProcMap);
663		sprintf(checkPointMsg,
664		"Successfully divided the molecules among the processors.\n");
665	<	MPIcheckPoint();
665	>	errorCheckPoint();
666		}
667
668		#endif
#	Line 516 | Line 679 | Globals* SimCreator::parseFile(const std::string mdFil
679		#endif
680
681		stampId = info->getMoleculeStampId(i);
682	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
683	<	stampId, i, info->getLocalIndexManager());
682	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
683	>	info->getMoleculeStamp(stampId),
684	>	stampId, i,
685	>	info->getLocalIndexManager());
686
687		info->addMolecule(mol);
688
#	Line 530 | Line 695 | Globals* SimCreator::parseFile(const std::string mdFil
695		} //end for(int i=0)
696		}
697
698	+	int SimCreator::computeStorageLayout(SimInfo* info) {
699	+
700	+	Globals* simParams = info->getSimParams();
701	+	int nRigidBodies = info->getNGlobalRigidBodies();
702	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
703	+	set<AtomType*>::iterator i;
704	+	bool hasDirectionalAtoms = false;
705	+	bool hasFixedCharge = false;
706	+	bool hasDipoles = false;
707	+	bool hasQuadrupoles = false;
708	+	bool hasPolarizable = false;
709	+	bool hasFluctuatingCharge = false;
710	+	bool hasMetallic = false;
711	+	int storageLayout = 0;
712	+	storageLayout |= DataStorage::dslPosition;
713	+	storageLayout |= DataStorage::dslVelocity;
714	+	storageLayout |= DataStorage::dslForce;
715	+
716	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717	+
718	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
719	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
720	+	EAMAdapter ea = EAMAdapter( (*i) );
721	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
722	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
723	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
724	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
725	+
726	+	if (da.isDirectional()){
727	+	hasDirectionalAtoms = true;
728	+	}
729	+	if (ma.isDipole()){
730	+	hasDipoles = true;
731	+	}
732	+	if (ma.isQuadrupole()){
733	+	hasQuadrupoles = true;
734	+	}
735	+	if (ea.isEAM() || sca.isSuttonChen()){
736	+	hasMetallic = true;
737	+	}
738	+	if ( fca.isFixedCharge() ){
739	+	hasFixedCharge = true;
740	+	}
741	+	if ( fqa.isFluctuatingCharge() ){
742	+	hasFluctuatingCharge = true;
743	+	}
744	+	if ( pa.isPolarizable() ){
745	+	hasPolarizable = true;
746	+	}
747	+	}
748	+
749	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
750	+	storageLayout |= DataStorage::dslAmat;
751	+	if(storageLayout & DataStorage::dslVelocity) {
752	+	storageLayout |= DataStorage::dslAngularMomentum;
753	+	}
754	+	if (storageLayout & DataStorage::dslForce) {
755	+	storageLayout |= DataStorage::dslTorque;
756	+	}
757	+	}
758	+	if (hasDipoles) {
759	+	storageLayout |= DataStorage::dslDipole;
760	+	}
761	+	if (hasQuadrupoles) {
762	+	storageLayout |= DataStorage::dslQuadrupole;
763	+	}
764	+	if (hasFixedCharge || hasFluctuatingCharge) {
765	+	storageLayout |= DataStorage::dslSkippedCharge;
766	+	}
767	+	if (hasMetallic) {
768	+	storageLayout |= DataStorage::dslDensity;
769	+	storageLayout |= DataStorage::dslFunctional;
770	+	storageLayout |= DataStorage::dslFunctionalDerivative;
771	+	}
772	+	if (hasPolarizable) {
773	+	storageLayout |= DataStorage::dslElectricField;
774	+	}
775	+	if (hasFluctuatingCharge){
776	+	storageLayout |= DataStorage::dslFlucQPosition;
777	+	if(storageLayout & DataStorage::dslVelocity) {
778	+	storageLayout |= DataStorage::dslFlucQVelocity;
779	+	}
780	+	if (storageLayout & DataStorage::dslForce) {
781	+	storageLayout |= DataStorage::dslFlucQForce;
782	+	}
783	+	}
784	+
785	+	// if the user has asked for them, make sure we've got the memory for the
786	+	// objects defined.
787	+
788	+	if (simParams->getOutputParticlePotential()) {
789	+	storageLayout |= DataStorage::dslParticlePot;
790	+	}
791	+
792	+	if (simParams->havePrintHeatFlux()) {
793	+	if (simParams->getPrintHeatFlux()) {
794	+	storageLayout |= DataStorage::dslParticlePot;
795	+	}
796	+	}
797	+
798	+	if (simParams->getOutputElectricField()) {
799	+	storageLayout |= DataStorage::dslElectricField;
800	+	}
801	+
802	+	if (simParams->getOutputFluctuatingCharges()) {
803	+	storageLayout |= DataStorage::dslFlucQPosition;
804	+	storageLayout |= DataStorage::dslFlucQVelocity;
805	+	storageLayout |= DataStorage::dslFlucQForce;
806	+	}
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::IntegrableObjectIterator  ioi;
817		Molecule * mol;
818		Atom * atom;
819		RigidBody * rb;
#	Line 543 | Line 822 | Globals* SimCreator::parseFile(const std::string mdFil
822		int beginRigidBodyIndex;
823		int beginCutoffGroupIndex;
824		int nGlobalAtoms = info->getNGlobalAtoms();
825	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
826
547	–	#ifndef IS_MPI
548	–
827		beginAtomIndex = 0;
550	–	beginRigidBodyIndex = 0;
551	–	beginCutoffGroupIndex = 0;
552	–
553	–	#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	–
828		//rigidbody's index begins right after atom's
829	<	beginRigidBodyIndex += info->getNGlobalAtoms();
830	<
831	<	for(mol = info->beginMolecule(mi); mol != NULL;
832	<	mol = info->nextMolecule(mi)) {
829	>	beginRigidBodyIndex = info->getNGlobalAtoms();
830	>	beginCutoffGroupIndex = 0;
831	>
832	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
833
834	<	//local index(index in DataStorge) of atom is important
835	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
836	<	atom->setGlobalIndex(beginAtomIndex++);
834	>	#ifdef IS_MPI
835	>	if (info->getMolToProc(i) == worldRank) {
836	>	#endif
837	>	// stuff to do if I own this molecule
838	>	mol = info->getMoleculeByGlobalIndex(i);
839	>
840	>	//local index(index in DataStorge) of atom is important
841	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	>	atom->setGlobalIndex(beginAtomIndex++);
843	>	}
844	>
845	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
846	>	rb = mol->nextRigidBody(ri)) {
847	>	rb->setGlobalIndex(beginRigidBodyIndex++);
848	>	}
849	>
850	>	//local index of cutoff group is trivial, it only depends on
851	>	//the order of travesing
852	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
853	>	cg = mol->nextCutoffGroup(ci)) {
854	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
855	>	}
856	>
857	>	#ifdef IS_MPI
858	>	}  else {
859	>
860	>	// stuff to do if I don't own this molecule
861	>
862	>	int stampId = info->getMoleculeStampId(i);
863	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
864	>
865	>	beginAtomIndex += stamp->getNAtoms();
866	>	beginRigidBodyIndex += stamp->getNRigidBodies();
867	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
868		}
869	<
870	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
871	<	rb = mol->nextRigidBody(ri)) {
872	<	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	<
869	>	#endif
870	>
871	>	} //end for(int i=0)
872	>
873		//fill globalGroupMembership
874		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
875		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 623 | Line 881 | Globals* SimCreator::parseFile(const std::string mdFil
881
882		}
883		}
884	<
884	>
885		#ifdef IS_MPI
886		// Since the globalGroupMembership has been zero filled and we've only
887		// poked values into the atoms we know, we can do an Allreduce
888		// to get the full globalGroupMembership array (We think).
889		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
890		// docs said we could.
891	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
892	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
893	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
891	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
892	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
893	>	&tmpGroupMembership[0], nGlobalAtoms,
894	>	MPI::INT, MPI::SUM);
895		info->setGlobalGroupMembership(tmpGroupMembership);
896		#else
897		info->setGlobalGroupMembership(globalGroupMembership);
898		#endif
899
900		//fill molMembership
901	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
901	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
902	>	info->getNGlobalRigidBodies(), 0);
903
904	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
905	<
904	>	for(mol = info->beginMolecule(mi); mol != NULL;
905	>	mol = info->nextMolecule(mi)) {
906		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
908		}
909	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
910	+	rb = mol->nextRigidBody(ri)) {
911	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
912	+	}
913		}
914
915		#ifdef IS_MPI
916	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
916	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
917	>	info->getNGlobalRigidBodies(), 0);
918	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
919	>	nGlobalAtoms + nGlobalRigidBodies,
920	>	MPI::INT, MPI::SUM);
921
654	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
655	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
656	–
922		info->setGlobalMolMembership(tmpMolMembership);
923		#else
924		info->setGlobalMolMembership(globalMolMembership);
925		#endif
926	+
927	+	// nIOPerMol holds the number of integrable objects per molecule
928	+	// here the molecules are listed by their global indices.
929	+
930	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
931	+	for (mol = info->beginMolecule(mi); mol != NULL;
932	+	mol = info->nextMolecule(mi)) {
933	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
934	+	}
935
936	<	}
937	<
938	<	void SimCreator::loadCoordinates(SimInfo* info) {
939	<	Globals* simParams;
940	<	simParams = info->getSimParams();
936	>	#ifdef IS_MPI
937	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
938	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
939	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
940	>	#else
941	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
942	>	#endif
943	>
944	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
945
946	<	if (!simParams->haveInitialConfig()) {
947	<	sprintf(painCave.errMsg,
948	<	"Cannot intialize a simulation without an initial configuration file.\n");
949	<	painCave.isFatal = 1;;
672	<	simError();
946	>	int startingIndex = 0;
947	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
948	>	startingIOIndexForMol[i] = startingIndex;
949	>	startingIndex += numIntegrableObjectsPerMol[i];
950		}
951
952	<	DumpReader reader(info, simParams->getInitialConfig());
952	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
953	>	for (mol = info->beginMolecule(mi); mol != NULL;
954	>	mol = info->nextMolecule(mi)) {
955	>	int myGlobalIndex = mol->getGlobalIndex();
956	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
957	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
958	>	sd = mol->nextIntegrableObject(ioi)) {
959	>	sd->setGlobalIntegrableObjectIndex(globalIO);
960	>	IOIndexToIntegrableObject[globalIO] = sd;
961	>	globalIO++;
962	>	}
963	>	}
964	>
965	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
966	>
967	>	}
968	>
969	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
970	>
971	>	DumpReader reader(info, mdFileName);
972		int nframes = reader.getNFrames();
973
974		if (nframes > 0) {
#	Line 681 | Line 977 | Globals* SimCreator::parseFile(const std::string mdFil
977		//invalid initial coordinate file
978		sprintf(painCave.errMsg,
979		"Initial configuration file %s should at least contain one frame\n",
980	<	simParams->getInitialConfig().c_str());
980	>	mdFileName.c_str());
981		painCave.isFatal = 1;
982		simError();
983		}
688	–
984		//copy the current snapshot to previous snapshot
985		info->getSnapshotManager()->advance();
986		}
987
988	<	} //end namespace oopse
988	>	} //end namespace OpenMD
989
990

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 1826 by gezelter, Wed Jan 9 19:41:48 2013 UTC

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