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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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	+	#include <exception>
51	+	#include <iostream>
52	+	#include <sstream>
53	+	#include <string>
54
55		#include "brains/MoleculeCreator.hpp"
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
54	–	#include "io/parse_me.h"
59		#include "UseTheForce/ForceFieldFactory.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62		#include "math/SeqRandNumGen.hpp"
63	+	#include "mdParser/MDLexer.hpp"
64	+	#include "mdParser/MDParser.hpp"
65	+	#include "mdParser/MDTreeParser.hpp"
66	+	#include "mdParser/SimplePreprocessor.hpp"
67	+	#include "antlr/ANTLRException.hpp"
68	+	#include "antlr/TokenStreamRecognitionException.hpp"
69	+	#include "antlr/TokenStreamIOException.hpp"
70	+	#include "antlr/TokenStreamException.hpp"
71	+	#include "antlr/RecognitionException.hpp"
72	+	#include "antlr/CharStreamException.hpp"
73	+
74	+	#include "antlr/MismatchedCharException.hpp"
75	+	#include "antlr/MismatchedTokenException.hpp"
76	+	#include "antlr/NoViableAltForCharException.hpp"
77	+	#include "antlr/NoViableAltException.hpp"
78	+
79		#ifdef IS_MPI
80	<	#include "io/mpiBASS.h"
80	>	#include "mpi.h"
81		#include "math/ParallelRandNumGen.hpp"
82		#endif
83
84	<	namespace oopse {
84	>	namespace OpenMD {
85
86	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps,
87	<	Globals* simParams){
86	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
87	>	Globals* simParams = NULL;
88	>	try {
89	>
90	>	// Create a preprocessor that preprocesses md file into an ostringstream
91	>	std::stringstream ppStream;
92	>	#ifdef IS_MPI
93	>	int streamSize;
94	>	const int masterNode = 0;
95	>	int commStatus;
96	>	if (worldRank == masterNode) {
97	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
98	>	#endif
99	>	SimplePreprocessor preprocessor;
100	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
101	>
102	>	#ifdef IS_MPI
103	>	//brocasting the stream size
104	>	streamSize = ppStream.str().size() +1;
105	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
106	>
107	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
108	>
109	>
110	>	} else {
111	>
112	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
113	>
114	>	//get stream size
115	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
116	>
117	>	char* buf = new char[streamSize];
118	>	assert(buf);
119	>
120	>	//receive file content
121	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
122	>
123	>	ppStream.str(buf);
124	>	delete [] buf;
125	>
126	>	}
127	>	#endif
128	>	// Create a scanner that reads from the input stream
129	>	MDLexer lexer(ppStream);
130	>	lexer.setFilename(filename);
131	>	lexer.initDeferredLineCount();
132
133	<	#ifdef IS_MPI
133	>	// Create a parser that reads from the scanner
134	>	MDParser parser(lexer);
135	>	parser.setFilename(filename);
136	>
137	>	// Create an observer that synchorizes file name change
138	>	FilenameObserver observer;
139	>	observer.setLexer(&lexer);
140	>	observer.setParser(&parser);
141	>	lexer.setObserver(&observer);
142
143	<	if (worldRank == 0) {
144	<	#endif // is_mpi
143	>	antlr::ASTFactory factory;
144	>	parser.initializeASTFactory(factory);
145	>	parser.setASTFactory(&factory);
146	>	parser.mdfile();
147	>
148	>	// Create a tree parser that reads information into Globals
149	>	MDTreeParser treeParser;
150	>	treeParser.initializeASTFactory(factory);
151	>	treeParser.setASTFactory(&factory);
152	>	simParams = treeParser.walkTree(parser.getAST());
153	>	}
154	>
155
156	<	set_interface_stamps(stamps, simParams);
156	>	catch(antlr::MismatchedCharException& e) {
157	>	sprintf(painCave.errMsg,
158	>	"parser exception: %s %s:%d:%d\n",
159	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
160	>	painCave.isFatal = 1;
161	>	simError();
162	>	}
163	>	catch(antlr::MismatchedTokenException &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::NoViableAltForCharException &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::NoViableAltException &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
185	<	#ifdef IS_MPI
186	<
187	<	mpiEventInit();
188	<
189	<	#endif
190	<
82	<	yacc_BASS(mdFileName.c_str());
83	<
84	<	#ifdef IS_MPI
85	<
86	<	throwMPIEvent(NULL);
87	<	} else {
88	<	set_interface_stamps(stamps, simParams);
89	<	mpiEventInit();
90	<	MPIcheckPoint();
91	<	mpiEventLoop();
185	>	catch(antlr::TokenStreamRecognitionException& 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	<	#endif
194	<
192	>
193	>	catch(antlr::TokenStreamIOException& e) {
194	>	sprintf(painCave.errMsg,
195	>	"parser exception: %s\n",
196	>	e.getMessage().c_str());
197	>	painCave.isFatal = 1;
198	>	simError();
199	>	}
200	>
201	>	catch(antlr::TokenStreamException& e) {
202	>	sprintf(painCave.errMsg,
203	>	"parser exception: %s\n",
204	>	e.getMessage().c_str());
205	>	painCave.isFatal = 1;
206	>	simError();
207	>	}
208	>	catch (antlr::RecognitionException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s %s:%d:%d\n",
211	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>	catch (antlr::CharStreamException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s\n",
218	>	e.getMessage().c_str());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (OpenMDException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"%s\n",
225	>	e.getMessage().c_str());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (std::exception& e) {
230	>	sprintf(painCave.errMsg,
231	>	"parser exception: %s\n",
232	>	e.what());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>
237	>	simParams->setMDfileVersion(mdFileVersion);
238	>	return simParams;
239		}
240
241		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
242		bool loadInitCoords) {
243
244	<	MakeStamps * stamps = new MakeStamps();
245	<
246	<	Globals * simParams = new Globals();
247	<
244	>	const int bufferSize = 65535;
245	>	char buffer[bufferSize];
246	>	int lineNo = 0;
247	>	std::string mdRawData;
248	>	int metaDataBlockStart = -1;
249	>	int metaDataBlockEnd = -1;
250	>	int i;
251	>	int mdOffset;
252	>	int mdFileVersion;
253	>
254	>	#ifdef IS_MPI
255	>	const int masterNode = 0;
256	>	if (worldRank == masterNode) {
257	>	#endif
258	>
259	>	std::ifstream mdFile_(mdFileName.c_str());
260	>
261	>	if (mdFile_.fail()) {
262	>	sprintf(painCave.errMsg,
263	>	"SimCreator: Cannot open file: %s\n",
264	>	mdFileName.c_str());
265	>	painCave.isFatal = 1;
266	>	simError();
267	>	}
268	>
269	>	mdFile_.getline(buffer, bufferSize);
270	>	++lineNo;
271	>	std::string line = trimLeftCopy(buffer);
272	>	i = CaseInsensitiveFind(line, "<OpenMD");
273	>	if (static_cast<size_t>(i) == string::npos) {
274	>	// try the older file strings to see if that works:
275	>	i = CaseInsensitiveFind(line, "<OOPSE");
276	>	}
277	>
278	>	if (static_cast<size_t>(i) == string::npos) {
279	>	// still no luck!
280	>	sprintf(painCave.errMsg,
281	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
282	>	mdFileName.c_str());
283	>	painCave.isFatal = 1;
284	>	simError();
285	>	}
286	>
287	>	// found the correct opening string, now try to get the file
288	>	// format version number.
289	>
290	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
291	>	std::string fileType = tokenizer.nextToken();
292	>	toUpper(fileType);
293	>
294	>	mdFileVersion = 0;
295	>
296	>	if (fileType == "OPENMD") {
297	>	while (tokenizer.hasMoreTokens()) {
298	>	std::string token(tokenizer.nextToken());
299	>	toUpper(token);
300	>	if (token == "VERSION") {
301	>	mdFileVersion = tokenizer.nextTokenAsInt();
302	>	break;
303	>	}
304	>	}
305	>	}
306	>
307	>	//scan through the input stream and find MetaData tag
308	>	while(mdFile_.getline(buffer, bufferSize)) {
309	>	++lineNo;
310	>
311	>	std::string line = trimLeftCopy(buffer);
312	>	if (metaDataBlockStart == -1) {
313	>	i = CaseInsensitiveFind(line, "<MetaData>");
314	>	if (i != string::npos) {
315	>	metaDataBlockStart = lineNo;
316	>	mdOffset = mdFile_.tellg();
317	>	}
318	>	} else {
319	>	i = CaseInsensitiveFind(line, "</MetaData>");
320	>	if (i != string::npos) {
321	>	metaDataBlockEnd = lineNo;
322	>	}
323	>	}
324	>	}
325	>
326	>	if (metaDataBlockStart == -1) {
327	>	sprintf(painCave.errMsg,
328	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
329	>	mdFileName.c_str());
330	>	painCave.isFatal = 1;
331	>	simError();
332	>	}
333	>	if (metaDataBlockEnd == -1) {
334	>	sprintf(painCave.errMsg,
335	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
336	>	mdFileName.c_str());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>
341	>	mdFile_.clear();
342	>	mdFile_.seekg(0);
343	>	mdFile_.seekg(mdOffset);
344	>
345	>	mdRawData.clear();
346	>
347	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
348	>	mdFile_.getline(buffer, bufferSize);
349	>	mdRawData += buffer;
350	>	mdRawData += "\n";
351	>	}
352	>
353	>	mdFile_.close();
354	>
355	>	#ifdef IS_MPI
356	>	}
357	>	#endif
358	>
359	>	std::stringstream rawMetaDataStream(mdRawData);
360	>
361		//parse meta-data file
362	<	parseFile(mdFileName, stamps, simParams);
362	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
363	>	metaDataBlockStart + 1);
364
365		//create the force field
366	<	ForceField * ff = ForceFieldFactory::getInstance()
367	<	->createForceField(simParams->getForceField());
111	<
366	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
367	>
368		if (ff == NULL) {
369		sprintf(painCave.errMsg,
370		"ForceField Factory can not create %s force field\n",
#	Line 141 | Line 397 | namespace oopse {
397		}
398
399		ff->parse(forcefieldFileName);
144	–
145	–	//extract the molecule stamps
146	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
147	–	compList(stamps, simParams, moleculeStampPairs);
148	–
400		//create SimInfo
401	<	SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
401	>	SimInfo * info = new SimInfo(ff, simParams);
402	>
403	>	info->setRawMetaData(mdRawData);
404
405	<	//gather parameters (SimCreator only retrieves part of the parameters)
405	>	//gather parameters (SimCreator only retrieves part of the
406	>	//parameters)
407		gatherParameters(info, mdFileName);
408
409		//divide the molecules and determine the global index of molecules
#	Line 160 | Line 414 | namespace oopse {
414		//create the molecules
415		createMolecules(info);
416
417	<
418	<	//allocate memory for DataStorage(circular reference, need to break it)
417	>	//allocate memory for DataStorage(circular reference, need to
418	>	//break it)
419		info->setSnapshotManager(new SimSnapshotManager(info));
420
421	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
422	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
423	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
421	>	//set the global index of atoms, rigidbodies and cutoffgroups
422	>	//(only need to be set once, the global index will never change
423	>	//again). Local indices of atoms and rigidbodies are already set
424	>	//by MoleculeCreator class which actually delegates the
425	>	//responsibility to LocalIndexManager.
426		setGlobalIndex(info);
427
428	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
429	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
430	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
431	<	//we can determine the beginning global indices of atoms before they get created.
428	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
429	>	//method, at that point atoms don't have the global index yet
430	>	//(their global index are all initialized to -1).  Therefore we
431	>	//have to call addInteractionPairs explicitly here. A way to work
432	>	//around is that we can determine the beginning global indices of
433	>	//atoms before they get created.
434		SimInfo::MoleculeIterator mi;
435		Molecule* mol;
436		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
437	<	info->addExcludePairs(mol);
437	>	info->addInteractionPairs(mol);
438		}
439
440		if (loadInitCoords)
441	<	loadCoordinates(info);
184	<
441	>	loadCoordinates(info, mdFileName);
442		return info;
443		}
444
445		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
446
447	<	//figure out the ouput file names
447	>	//figure out the output file names
448		std::string prefix;
449
450		#ifdef IS_MPI
#	Line 216 | Line 473 | namespace oopse {
473
474		#ifdef IS_MPI
475		void SimCreator::divideMolecules(SimInfo *info) {
476	<	double numerator;
477	<	double denominator;
478	<	double precast;
479	<	double x;
480	<	double y;
481	<	double a;
476	>	RealType numerator;
477	>	RealType denominator;
478	>	RealType precast;
479	>	RealType x;
480	>	RealType y;
481	>	RealType a;
482		int old_atoms;
483		int add_atoms;
484		int new_atoms;
#	Line 245 | Line 502 | namespace oopse {
502		"\tthe number of molecules.  This will not result in a \n"
503		"\tusable division of atoms for force decomposition.\n"
504		"\tEither try a smaller number of processors, or run the\n"
505	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
505	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
506
507		painCave.isFatal = 1;
508		simError();
#	Line 333 | Line 590 | namespace oopse {
590		//           Pacc(x) = exp(- a * x)
591		// where a = penalty / (average atoms per molecule)
592
593	<	x = (double)(new_atoms - nTarget);
593	>	x = (RealType)(new_atoms - nTarget);
594		y = myRandom->rand();
595
596		if (y < exp(- a * x)) {
#	Line 363 | Line 620 | namespace oopse {
620		info->setMolToProcMap(molToProcMap);
621		sprintf(checkPointMsg,
622		"Successfully divided the molecules among the processors.\n");
623	<	MPIcheckPoint();
623	>	errorCheckPoint();
624		}
625
626		#endif
#	Line 380 | Line 637 | namespace oopse {
637		#endif
638
639		stampId = info->getMoleculeStampId(i);
640	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
641	<	stampId, i, info->getLocalIndexManager());
640	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
641	>	info->getMoleculeStamp(stampId),
642	>	stampId, i,
643	>	info->getLocalIndexManager());
644
645		info->addMolecule(mol);
646
#	Line 393 | Line 652 | namespace oopse {
652
653		} //end for(int i=0)
654		}
396	–
397	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
398	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
399	–	int i;
400	–	char * id;
401	–	MoleculeStamp * currentStamp;
402	–	Component** the_components = simParams->getComponents();
403	–	int n_components = simParams->getNComponents();
655
405	–	if (!simParams->haveNMol()) {
406	–	// we don't have the total number of molecules, so we assume it is
407	–	// given in each component
408	–
409	–	for(i = 0; i < n_components; i++) {
410	–	if (!the_components[i]->haveNMol()) {
411	–	// we have a problem
412	–	sprintf(painCave.errMsg,
413	–	"SimCreator Error. No global NMol or component NMol given.\n"
414	–	"\tCannot calculate the number of atoms.\n");
415	–
416	–	painCave.isFatal = 1;
417	–	simError();
418	–	}
419	–
420	–	id = the_components[i]->getType();
421	–
422	–	currentStamp = stamps->getMolStamp(id);
423	–	if (currentStamp == NULL) {
424	–	sprintf(painCave.errMsg,
425	–	"SimCreator error: Component \"%s\" was not found in the "
426	–	"list of declared molecules\n", id);
427	–
428	–	painCave.isFatal = 1;
429	–	simError();
430	–	}
431	–
432	–	moleculeStampPairs.push_back(
433	–	std::make_pair(currentStamp, the_components[i]->getNMol()));
434	–	} //end for (i = 0; i < n_components; i++)
435	–	} else {
436	–	sprintf(painCave.errMsg, "SimSetup error.\n"
437	–	"\tSorry, the ability to specify total"
438	–	" nMols and then give molfractions in the components\n"
439	–	"\tis not currently supported."
440	–	" Please give nMol in the components.\n");
441	–
442	–	painCave.isFatal = 1;
443	–	simError();
444	–	}
445	–
446	–	#ifdef IS_MPI
447	–
448	–	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
449	–	MPIcheckPoint();
450	–
451	–	#endif // is_mpi
452	–
453	–	}
454	–
656		void SimCreator::setGlobalIndex(SimInfo *info) {
657		SimInfo::MoleculeIterator mi;
658		Molecule::AtomIterator ai;
659		Molecule::RigidBodyIterator ri;
660		Molecule::CutoffGroupIterator ci;
661	+	Molecule::IntegrableObjectIterator  ioi;
662		Molecule * mol;
663		Atom * atom;
664		RigidBody * rb;
#	Line 465 | Line 667 | namespace oopse {
667		int beginRigidBodyIndex;
668		int beginCutoffGroupIndex;
669		int nGlobalAtoms = info->getNGlobalAtoms();
468	–
469	–	#ifndef IS_MPI
470	–
471	–	beginAtomIndex = 0;
472	–	beginRigidBodyIndex = 0;
473	–	beginCutoffGroupIndex = 0;
474	–
475	–	#else
476	–
477	–	int nproc;
478	–	int myNode;
479	–
480	–	myNode = worldRank;
481	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
482	–
483	–	std::vector < int > tmpAtomsInProc(nproc, 0);
484	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
485	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
486	–	std::vector < int > NumAtomsInProc(nproc, 0);
487	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
488	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
670
490	–	tmpAtomsInProc[myNode] = info->getNAtoms();
491	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
492	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
493	–
494	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
495	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
496	–	MPI_SUM, MPI_COMM_WORLD);
497	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
498	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
499	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
500	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
501	–
671		beginAtomIndex = 0;
672		beginRigidBodyIndex = 0;
673		beginCutoffGroupIndex = 0;
674	<
675	<	for(int i = 0; i < myNode; i++) {
507	<	beginAtomIndex += NumAtomsInProc[i];
508	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
509	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
510	<	}
511	<
512	<	#endif
513	<
514	<	//rigidbody's index begins right after atom's
515	<	beginRigidBodyIndex += info->getNGlobalAtoms();
516	<
517	<	for(mol = info->beginMolecule(mi); mol != NULL;
518	<	mol = info->nextMolecule(mi)) {
674	>
675	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
676
677	<	//local index(index in DataStorge) of atom is important
678	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
679	<	atom->setGlobalIndex(beginAtomIndex++);
677	>	#ifdef IS_MPI
678	>	if (info->getMolToProc(i) == worldRank) {
679	>	#endif
680	>	// stuff to do if I own this molecule
681	>	mol = info->getMoleculeByGlobalIndex(i);
682	>
683	>	//local index(index in DataStorge) of atom is important
684	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	>	atom->setGlobalIndex(beginAtomIndex++);
686	>	}
687	>
688	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
689	>	rb = mol->nextRigidBody(ri)) {
690	>	rb->setGlobalIndex(beginRigidBodyIndex++);
691	>	}
692	>
693	>	//local index of cutoff group is trivial, it only depends on
694	>	//the order of travesing
695	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
696	>	cg = mol->nextCutoffGroup(ci)) {
697	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
698	>	}
699	>
700	>	#ifdef IS_MPI
701	>	}  else {
702	>
703	>	// stuff to do if I don't own this molecule
704	>
705	>	int stampId = info->getMoleculeStampId(i);
706	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
707	>
708	>	beginAtomIndex += stamp->getNAtoms();
709	>	beginRigidBodyIndex += stamp->getNRigidBodies();
710	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
711		}
712	<
713	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
714	<	rb = mol->nextRigidBody(ri)) {
715	<	rb->setGlobalIndex(beginRigidBodyIndex++);
528	<	}
529	<
530	<	//local index of cutoff group is trivial, it only depends on the order of travesing
531	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
532	<	cg = mol->nextCutoffGroup(ci)) {
533	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
534	<	}
535	<	}
536	<
712	>	#endif
713	>
714	>	} //end for(int i=0)
715	>
716		//fill globalGroupMembership
717		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
718		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 545 | Line 724 | namespace oopse {
724
725		}
726		}
727	<
727	>
728		#ifdef IS_MPI
729		// Since the globalGroupMembership has been zero filled and we've only
730		// poked values into the atoms we know, we can do an Allreduce
731		// to get the full globalGroupMembership array (We think).
732		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
733		// docs said we could.
734	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
734	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
735		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
736		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
737		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 564 | Line 743 | namespace oopse {
743		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
744
745		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
567	–
746		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
747		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
748		}
749		}
750
751		#ifdef IS_MPI
752	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
752	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
753
754		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
755		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 580 | Line 758 | namespace oopse {
758		#else
759		info->setGlobalMolMembership(globalMolMembership);
760		#endif
761	+
762	+	// nIOPerMol holds the number of integrable objects per molecule
763	+	// here the molecules are listed by their global indices.
764	+
765	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
766	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
767	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
768	+	}
769
770	+	#ifdef IS_MPI
771	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
772	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
773	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
774	+	#else
775	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
776	+	#endif
777	+
778	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
779	+
780	+	int startingIndex = 0;
781	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
782	+	startingIOIndexForMol[i] = startingIndex;
783	+	startingIndex += numIntegrableObjectsPerMol[i];
784	+	}
785	+
786	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
787	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
788	+	int myGlobalIndex = mol->getGlobalIndex();
789	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
790	+	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
791	+	integrableObject = mol->nextIntegrableObject(ioi)) {
792	+	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
793	+	IOIndexToIntegrableObject[globalIO] = integrableObject;
794	+	globalIO++;
795	+	}
796	+	}
797	+
798	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
799	+
800		}
801
802	<	void SimCreator::loadCoordinates(SimInfo* info) {
802	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
803		Globals* simParams;
804	+
805		simParams = info->getSimParams();
806
807	<	if (!simParams->haveInitialConfig()) {
591	<	sprintf(painCave.errMsg,
592	<	"Cannot intialize a simulation without an initial configuration file.\n");
593	<	painCave.isFatal = 1;;
594	<	simError();
595	<	}
596	<
597	<	DumpReader reader(info, simParams->getInitialConfig());
807	>	DumpReader reader(info, mdFileName);
808		int nframes = reader.getNFrames();
809	<
809	>
810		if (nframes > 0) {
811		reader.readFrame(nframes - 1);
812		} else {
813		//invalid initial coordinate file
814		sprintf(painCave.errMsg,
815		"Initial configuration file %s should at least contain one frame\n",
816	<	simParams->getInitialConfig().c_str());
816	>	mdFileName.c_str());
817		painCave.isFatal = 1;
818		simError();
819		}
610	–
820		//copy the current snapshot to previous snapshot
821		info->getSnapshotManager()->advance();
822		}
823
824	<	} //end namespace oopse
824	>	} //end namespace OpenMD
825
826

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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