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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 823 by chuckv, Thu Dec 29 16:03:11 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1711 by gezelter, Sat May 19 02:58:35 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 46 | Line 47
47		* @time 13:51am
48		* @version 1.0
49		*/
50	<
50	>	#include <exception>
51		#include <iostream>
52		#include <sstream>
53		#include <string>
#	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(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	–	}
163
164	<	catch(antlr::MismatchedCharException& e) {
165	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
166	<	}
167	<	catch(antlr::MismatchedTokenException &e) {
168	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
169	<	}
170	<	catch(antlr::NoViableAltForCharException &e) {
171	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
172	<	}
173	<	catch(antlr::NoViableAltException &e) {
174	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
175	<	}
176	<	catch(antlr::TokenStreamRecognitionException& e) {
177	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
178	<	}
179	<	catch(antlr::TokenStreamIOException& e) {
180	<	cerr<< "parser exception: " << e.getMessage() << endl;
181	<	}
182	<	catch(antlr::TokenStreamException& e) {
183	<	cerr<< "parser exception: " << e.getMessage() << endl;
184	<	}
185	<	catch (antlr::RecognitionException& e) {
186	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
187	<	}
188	<	catch (antlr::CharStreamException& e) {
189	<	cerr << "parser exception: " << e.getMessage() << endl;
190	<	}
191	<	catch (exception& e) {
192	<	cerr << "parser exception: " << e.what() << endl;
193	<	}
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	>	}
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	>	}
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 (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	+	int mdOffset;
260	+	int mdFileVersion;
261
262	+	#ifdef IS_MPI
263	+	const int masterNode = 0;
264	+	if (worldRank == masterNode) {
265	+	#endif
266	+
267	+	std::ifstream mdFile_(mdFileName.c_str());
268	+
269	+	if (mdFile_.fail()) {
270	+	sprintf(painCave.errMsg,
271	+	"SimCreator: Cannot open file: %s\n",
272	+	mdFileName.c_str());
273	+	painCave.isFatal = 1;
274	+	simError();
275	+	}
276	+
277	+	mdFile_.getline(buffer, bufferSize);
278	+	++lineNo;
279	+	std::string line = trimLeftCopy(buffer);
280	+	i = CaseInsensitiveFind(line, "<OpenMD");
281	+	if (static_cast<size_t>(i) == string::npos) {
282	+	// try the older file strings to see if that works:
283	+	i = CaseInsensitiveFind(line, "<OOPSE");
284	+	}
285	+
286	+	if (static_cast<size_t>(i) == string::npos) {
287	+	// still no luck!
288	+	sprintf(painCave.errMsg,
289	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
290	+	mdFileName.c_str());
291	+	painCave.isFatal = 1;
292	+	simError();
293	+	}
294	+
295	+	// found the correct opening string, now try to get the file
296	+	// format version number.
297	+
298	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
299	+	std::string fileType = tokenizer.nextToken();
300	+	toUpper(fileType);
301	+
302	+	mdFileVersion = 0;
303	+
304	+	if (fileType == "OPENMD") {
305	+	while (tokenizer.hasMoreTokens()) {
306	+	std::string token(tokenizer.nextToken());
307	+	toUpper(token);
308	+	if (token == "VERSION") {
309	+	mdFileVersion = tokenizer.nextTokenAsInt();
310	+	break;
311	+	}
312	+	}
313	+	}
314	+
315	+	//scan through the input stream and find MetaData tag
316	+	while(mdFile_.getline(buffer, bufferSize)) {
317	+	++lineNo;
318	+
319	+	std::string line = trimLeftCopy(buffer);
320	+	if (metaDataBlockStart == -1) {
321	+	i = CaseInsensitiveFind(line, "<MetaData>");
322	+	if (i != string::npos) {
323	+	metaDataBlockStart = lineNo;
324	+	mdOffset = mdFile_.tellg();
325	+	}
326	+	} else {
327	+	i = CaseInsensitiveFind(line, "</MetaData>");
328	+	if (i != string::npos) {
329	+	metaDataBlockEnd = lineNo;
330	+	}
331	+	}
332	+	}
333	+
334	+	if (metaDataBlockStart == -1) {
335	+	sprintf(painCave.errMsg,
336	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
337	+	mdFileName.c_str());
338	+	painCave.isFatal = 1;
339	+	simError();
340	+	}
341	+	if (metaDataBlockEnd == -1) {
342	+	sprintf(painCave.errMsg,
343	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
344	+	mdFileName.c_str());
345	+	painCave.isFatal = 1;
346	+	simError();
347	+	}
348	+
349	+	mdFile_.clear();
350	+	mdFile_.seekg(0);
351	+	mdFile_.seekg(mdOffset);
352	+
353	+	mdRawData.clear();
354	+
355	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
356	+	mdFile_.getline(buffer, bufferSize);
357	+	mdRawData += buffer;
358	+	mdRawData += "\n";
359	+	}
360	+
361	+	mdFile_.close();
362	+
363	+	#ifdef IS_MPI
364	+	}
365	+	#endif
366	+
367	+	std::stringstream rawMetaDataStream(mdRawData);
368	+
369		//parse meta-data file
370	<	Globals* simParams = parseFile(mdFileName);
370	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
371	>	metaDataBlockStart + 1);
372
373		//create the force field
374	<	ForceField * ff = ForceFieldFactory::getInstance()
375	<	->createForceField(simParams->getForceField());
194	<
374	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
375	>
376		if (ff == NULL) {
377		sprintf(painCave.errMsg,
378		"ForceField Factory can not create %s force field\n",
#	Line 224 | Line 405 | Globals* SimCreator::parseFile(const std::string mdFil
405		}
406
407		ff->parse(forcefieldFileName);
227	–	ff->setFortranForceOptions();
408		//create SimInfo
409		SimInfo * info = new SimInfo(ff, simParams);
410	+
411	+	info->setRawMetaData(mdRawData);
412
413	<	//gather parameters (SimCreator only retrieves part of the parameters)
413	>	//gather parameters (SimCreator only retrieves part of the
414	>	//parameters)
415		gatherParameters(info, mdFileName);
416
417		//divide the molecules and determine the global index of molecules
#	Line 239 | Line 422 | Globals* SimCreator::parseFile(const std::string mdFil
422		//create the molecules
423		createMolecules(info);
424
425	+	//find the storage layout
426	+
427	+	int storageLayout = computeStorageLayout(info);
428	+
429	+	cerr << "computed Storage Layout = " << storageLayout << "\n";
430	+
431	+	//allocate memory for DataStorage(circular reference, need to
432	+	//break it)
433	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435	<	//allocate memory for DataStorage(circular reference, need to break it)
436	<	info->setSnapshotManager(new SimSnapshotManager(info));
437	<
438	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
439	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
248	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
435	>	//set the global index of atoms, rigidbodies and cutoffgroups
436	>	//(only need to be set once, the global index will never change
437	>	//again). Local indices of atoms and rigidbodies are already set
438	>	//by MoleculeCreator class which actually delegates the
439	>	//responsibility to LocalIndexManager.
440		setGlobalIndex(info);
441
442	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
443	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
444	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
445	<	//we can determine the beginning global indices of atoms before they get created.
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 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);
263	<
455	>	loadCoordinates(info, mdFileName);
456		return info;
457		}
458
#	Line 295 | 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 324 | 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 412 | Line 604 | Globals* SimCreator::parseFile(const std::string mdFil
604		//           Pacc(x) = exp(- a * x)
605		// where a = penalty / (average atoms per molecule)
606
607	<	x = (double)(new_atoms - nTarget);
607	>	x = (RealType)(new_atoms - nTarget);
608		y = myRandom->rand();
609
610		if (y < exp(- a * x)) {
#	Line 442 | Line 634 | Globals* SimCreator::parseFile(const std::string mdFil
634		info->setMolToProcMap(molToProcMap);
635		sprintf(checkPointMsg,
636		"Successfully divided the molecules among the processors.\n");
637	<	MPIcheckPoint();
637	>	errorCheckPoint();
638		}
639
640		#endif
#	Line 459 | Line 651 | Globals* SimCreator::parseFile(const std::string mdFil
651		#endif
652
653		stampId = info->getMoleculeStampId(i);
654	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
655	<	stampId, i, info->getLocalIndexManager());
654	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
655	>	info->getMoleculeStamp(stampId),
656	>	stampId, i,
657	>	info->getLocalIndexManager());
658
659		info->addMolecule(mol);
660
#	Line 473 | Line 667 | Globals* SimCreator::parseFile(const std::string mdFil
667		} //end for(int i=0)
668		}
669
670	+	int SimCreator::computeStorageLayout(SimInfo* info) {
671	+
672	+	Globals* simParams = info->getSimParams();
673	+	int nRigidBodies = info->getNGlobalRigidBodies();
674	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
675	+	set<AtomType*>::iterator i;
676	+	bool hasDirectionalAtoms = false;
677	+	bool hasFixedCharge = false;
678	+	bool hasMultipoles = false;
679	+	bool hasPolarizable = false;
680	+	bool hasFluctuatingCharge = false;
681	+	bool hasMetallic = false;
682	+	int storageLayout = 0;
683	+	storageLayout |= DataStorage::dslPosition;
684	+	storageLayout |= DataStorage::dslVelocity;
685	+	storageLayout |= DataStorage::dslForce;
686	+
687	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
688	+
689	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
690	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
691	+	EAMAdapter ea = EAMAdapter( (*i) );
692	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
693	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
694	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
695	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
696	+
697	+	if (da.isDirectional()){
698	+	hasDirectionalAtoms = true;
699	+	}
700	+	if (ma.isMultipole()){
701	+	hasMultipoles = true;
702	+	}
703	+	if (ea.isEAM() || sca.isSuttonChen()){
704	+	hasMetallic = true;
705	+	}
706	+	if ( fca.isFixedCharge() ){
707	+	hasFixedCharge = true;
708	+	}
709	+	if ( fqa.isFluctuatingCharge() ){
710	+	hasFluctuatingCharge = true;
711	+	}
712	+	if ( pa.isPolarizable() ){
713	+	hasPolarizable = true;
714	+	}
715	+	}
716	+
717	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
718	+	storageLayout |= DataStorage::dslAmat;
719	+	if(storageLayout & DataStorage::dslVelocity) {
720	+	storageLayout |= DataStorage::dslAngularMomentum;
721	+	}
722	+	if (storageLayout & DataStorage::dslForce) {
723	+	storageLayout |= DataStorage::dslTorque;
724	+	}
725	+	}
726	+	if (hasMultipoles) {
727	+	storageLayout |= DataStorage::dslElectroFrame;
728	+	}
729	+	if (hasFixedCharge || hasFluctuatingCharge) {
730	+	storageLayout |= DataStorage::dslSkippedCharge;
731	+	}
732	+	if (hasMetallic) {
733	+	storageLayout |= DataStorage::dslDensity;
734	+	storageLayout |= DataStorage::dslFunctional;
735	+	storageLayout |= DataStorage::dslFunctionalDerivative;
736	+	}
737	+	if (hasPolarizable) {
738	+	storageLayout |= DataStorage::dslElectricField;
739	+	}
740	+	if (hasFluctuatingCharge){
741	+	storageLayout |= DataStorage::dslFlucQPosition;
742	+	if(storageLayout & DataStorage::dslVelocity) {
743	+	storageLayout |= DataStorage::dslFlucQVelocity;
744	+	}
745	+	if (storageLayout & DataStorage::dslForce) {
746	+	storageLayout |= DataStorage::dslFlucQForce;
747	+	}
748	+	}
749	+
750	+	if (simParams->getOutputParticlePotential()) {
751	+	storageLayout |= DataStorage::dslParticlePot;
752	+	}
753	+
754	+	return storageLayout;
755	+	}
756	+
757		void SimCreator::setGlobalIndex(SimInfo *info) {
758		SimInfo::MoleculeIterator mi;
759		Molecule::AtomIterator ai;
760		Molecule::RigidBodyIterator ri;
761		Molecule::CutoffGroupIterator ci;
762	+	Molecule::IntegrableObjectIterator  ioi;
763		Molecule * mol;
764		Atom * atom;
765		RigidBody * rb;
#	Line 487 | Line 769 | Globals* SimCreator::parseFile(const std::string mdFil
769		int beginCutoffGroupIndex;
770		int nGlobalAtoms = info->getNGlobalAtoms();
771
490	–	#ifndef IS_MPI
491	–
772		beginAtomIndex = 0;
773		beginRigidBodyIndex = 0;
774		beginCutoffGroupIndex = 0;
775	<
776	<	#else
497	<
498	<	int nproc;
499	<	int myNode;
500	<
501	<	myNode = worldRank;
502	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
503	<
504	<	std::vector < int > tmpAtomsInProc(nproc, 0);
505	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
506	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
507	<	std::vector < int > NumAtomsInProc(nproc, 0);
508	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
509	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
510	<
511	<	tmpAtomsInProc[myNode] = info->getNAtoms();
512	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
513	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
514	<
515	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
516	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
517	<	MPI_SUM, MPI_COMM_WORLD);
518	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
519	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
520	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
521	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
522	<
523	<	beginAtomIndex = 0;
524	<	beginRigidBodyIndex = 0;
525	<	beginCutoffGroupIndex = 0;
526	<
527	<	for(int i = 0; i < myNode; i++) {
528	<	beginAtomIndex += NumAtomsInProc[i];
529	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
530	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
531	<	}
532	<
533	<	#endif
534	<
535	<	//rigidbody's index begins right after atom's
536	<	beginRigidBodyIndex += info->getNGlobalAtoms();
537	<
538	<	for(mol = info->beginMolecule(mi); mol != NULL;
539	<	mol = info->nextMolecule(mi)) {
775	>
776	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
777
778	<	//local index(index in DataStorge) of atom is important
779	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
780	<	atom->setGlobalIndex(beginAtomIndex++);
778	>	#ifdef IS_MPI
779	>	if (info->getMolToProc(i) == worldRank) {
780	>	#endif
781	>	// stuff to do if I own this molecule
782	>	mol = info->getMoleculeByGlobalIndex(i);
783	>
784	>	//local index(index in DataStorge) of atom is important
785	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
786	>	atom->setGlobalIndex(beginAtomIndex++);
787	>	}
788	>
789	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
790	>	rb = mol->nextRigidBody(ri)) {
791	>	rb->setGlobalIndex(beginRigidBodyIndex++);
792	>	}
793	>
794	>	//local index of cutoff group is trivial, it only depends on
795	>	//the order of travesing
796	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
797	>	cg = mol->nextCutoffGroup(ci)) {
798	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
799	>	}
800	>
801	>	#ifdef IS_MPI
802	>	}  else {
803	>
804	>	// stuff to do if I don't own this molecule
805	>
806	>	int stampId = info->getMoleculeStampId(i);
807	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
808	>
809	>	beginAtomIndex += stamp->getNAtoms();
810	>	beginRigidBodyIndex += stamp->getNRigidBodies();
811	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
812		}
813	<
814	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
815	<	rb = mol->nextRigidBody(ri)) {
816	<	rb->setGlobalIndex(beginRigidBodyIndex++);
549	<	}
550	<
551	<	//local index of cutoff group is trivial, it only depends on the order of travesing
552	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
553	<	cg = mol->nextCutoffGroup(ci)) {
554	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
555	<	}
556	<	}
557	<
813	>	#endif
814	>
815	>	} //end for(int i=0)
816	>
817		//fill globalGroupMembership
818		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
819		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 566 | Line 825 | Globals* SimCreator::parseFile(const std::string mdFil
825
826		}
827		}
828	<
828	>
829		#ifdef IS_MPI
830		// Since the globalGroupMembership has been zero filled and we've only
831		// poked values into the atoms we know, we can do an Allreduce
832		// to get the full globalGroupMembership array (We think).
833		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
834		// docs said we could.
835	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
835	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
836		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
837		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
838		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 585 | Line 844 | Globals* SimCreator::parseFile(const std::string mdFil
844		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
845
846		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
588	–
847		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
849		}
850		}
851
852		#ifdef IS_MPI
853	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
853	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
854
855		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
856		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 601 | Line 859 | Globals* SimCreator::parseFile(const std::string mdFil
859		#else
860		info->setGlobalMolMembership(globalMolMembership);
861		#endif
862	+
863	+	// nIOPerMol holds the number of integrable objects per molecule
864	+	// here the molecules are listed by their global indices.
865	+
866	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
867	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
868	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
869	+	}
870
871	+	#ifdef IS_MPI
872	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
873	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
874	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
875	+	#else
876	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
877	+	#endif
878	+
879	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
880	+
881	+	int startingIndex = 0;
882	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
883	+	startingIOIndexForMol[i] = startingIndex;
884	+	startingIndex += numIntegrableObjectsPerMol[i];
885	+	}
886	+
887	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
888	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
889	+	int myGlobalIndex = mol->getGlobalIndex();
890	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
891	+	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
892	+	integrableObject = mol->nextIntegrableObject(ioi)) {
893	+	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
894	+	IOIndexToIntegrableObject[globalIO] = integrableObject;
895	+	globalIO++;
896	+	}
897	+	}
898	+
899	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
900	+
901		}
902
903	<	void SimCreator::loadCoordinates(SimInfo* info) {
903	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
904		Globals* simParams;
905	+
906		simParams = info->getSimParams();
907
908	<	if (!simParams->haveInitialConfig()) {
612	<	sprintf(painCave.errMsg,
613	<	"Cannot intialize a simulation without an initial configuration file.\n");
614	<	painCave.isFatal = 1;;
615	<	simError();
616	<	}
617	<
618	<	DumpReader reader(info, simParams->getInitialConfig());
908	>	DumpReader reader(info, mdFileName);
909		int nframes = reader.getNFrames();
910	<
910	>
911		if (nframes > 0) {
912		reader.readFrame(nframes - 1);
913		} else {
914		//invalid initial coordinate file
915		sprintf(painCave.errMsg,
916		"Initial configuration file %s should at least contain one frame\n",
917	<	simParams->getInitialConfig().c_str());
917	>	mdFileName.c_str());
918		painCave.isFatal = 1;
919		simError();
920		}
631	–
921		//copy the current snapshot to previous snapshot
922		info->getSnapshotManager()->advance();
923		}
924
925	<	} //end namespace oopse
925	>	} //end namespace OpenMD
926
927

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 823 by chuckv, Thu Dec 29 16:03:11 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1711 by gezelter, Sat May 19 02:58:35 2012 UTC

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