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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 514 by chrisfen, Thu Apr 21 14:12:19 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 46 | Line 46
46		* @time 13:51am
47		* @version 1.0
48		*/
49	+	#include <exception>
50	+	#include <iostream>
51	+	#include <sstream>
52	+	#include <string>
53
54		#include "brains/MoleculeCreator.hpp"
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
54	–	#include "io/parse_me.h"
58		#include "UseTheForce/ForceFieldFactory.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61		#include "math/SeqRandNumGen.hpp"
62	+	#include "mdParser/MDLexer.hpp"
63	+	#include "mdParser/MDParser.hpp"
64	+	#include "mdParser/MDTreeParser.hpp"
65	+	#include "mdParser/SimplePreprocessor.hpp"
66	+	#include "antlr/ANTLRException.hpp"
67	+	#include "antlr/TokenStreamRecognitionException.hpp"
68	+	#include "antlr/TokenStreamIOException.hpp"
69	+	#include "antlr/TokenStreamException.hpp"
70	+	#include "antlr/RecognitionException.hpp"
71	+	#include "antlr/CharStreamException.hpp"
72	+
73	+	#include "antlr/MismatchedCharException.hpp"
74	+	#include "antlr/MismatchedTokenException.hpp"
75	+	#include "antlr/NoViableAltForCharException.hpp"
76	+	#include "antlr/NoViableAltException.hpp"
77	+
78		#ifdef IS_MPI
79	<	#include "io/mpiBASS.h"
79	>	#include "mpi.h"
80		#include "math/ParallelRandNumGen.hpp"
81		#endif
82
83	<	namespace oopse {
83	>	namespace OpenMD {
84
85	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps,
86	<	Globals* simParams){
85	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
86	>	Globals* simParams = NULL;
87	>	try {
88	>
89	>	// Create a preprocessor that preprocesses md file into an ostringstream
90	>	std::stringstream ppStream;
91	>	#ifdef IS_MPI
92	>	int streamSize;
93	>	const int masterNode = 0;
94	>	int commStatus;
95	>	if (worldRank == masterNode) {
96	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
97	>	#endif
98	>	SimplePreprocessor preprocessor;
99	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
100	>
101	>	#ifdef IS_MPI
102	>	//brocasting the stream size
103	>	streamSize = ppStream.str().size() +1;
104	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
105	>
106	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107	>
108	>
109	>	} else {
110	>
111	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
112	>
113	>	//get stream size
114	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
115	>
116	>	char* buf = new char[streamSize];
117	>	assert(buf);
118	>
119	>	//receive file content
120	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
121	>
122	>	ppStream.str(buf);
123	>	delete [] buf;
124	>
125	>	}
126	>	#endif
127	>	// Create a scanner that reads from the input stream
128	>	MDLexer lexer(ppStream);
129	>	lexer.setFilename(filename);
130	>	lexer.initDeferredLineCount();
131
132	<	#ifdef IS_MPI
132	>	// Create a parser that reads from the scanner
133	>	MDParser parser(lexer);
134	>	parser.setFilename(filename);
135	>
136	>	// Create an observer that synchorizes file name change
137	>	FilenameObserver observer;
138	>	observer.setLexer(&lexer);
139	>	observer.setParser(&parser);
140	>	lexer.setObserver(&observer);
141
142	<	if (worldRank == 0) {
143	<	#endif // is_mpi
142	>	antlr::ASTFactory factory;
143	>	parser.initializeASTFactory(factory);
144	>	parser.setASTFactory(&factory);
145	>	parser.mdfile();
146	>
147	>	// Create a tree parser that reads information into Globals
148	>	MDTreeParser treeParser;
149	>	treeParser.initializeASTFactory(factory);
150	>	treeParser.setASTFactory(&factory);
151	>	simParams = treeParser.walkTree(parser.getAST());
152	>	}
153	>
154
155	<	simParams->initalize();
156	<	set_interface_stamps(stamps, simParams);
155	>	catch(antlr::MismatchedCharException& e) {
156	>	sprintf(painCave.errMsg,
157	>	"parser exception: %s %s:%d:%d\n",
158	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
159	>	painCave.isFatal = 1;
160	>	simError();
161	>	}
162	>	catch(antlr::MismatchedTokenException &e) {
163	>	sprintf(painCave.errMsg,
164	>	"parser exception: %s %s:%d:%d\n",
165	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	>	painCave.isFatal = 1;
167	>	simError();
168	>	}
169	>	catch(antlr::NoViableAltForCharException &e) {
170	>	sprintf(painCave.errMsg,
171	>	"parser exception: %s %s:%d:%d\n",
172	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	>	painCave.isFatal = 1;
174	>	simError();
175	>	}
176	>	catch(antlr::NoViableAltException &e) {
177	>	sprintf(painCave.errMsg,
178	>	"parser exception: %s %s:%d:%d\n",
179	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	>	painCave.isFatal = 1;
181	>	simError();
182	>	}
183
184	<	#ifdef IS_MPI
185	<
186	<	mpiEventInit();
187	<
188	<	#endif
189	<
83	<	yacc_BASS(mdFileName.c_str());
84	<
85	<	#ifdef IS_MPI
86	<
87	<	throwMPIEvent(NULL);
88	<	} else {
89	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
184	>	catch(antlr::TokenStreamRecognitionException& 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	<	#endif
193	<
191	>
192	>	catch(antlr::TokenStreamIOException& e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s\n",
195	>	e.getMessage().c_str());
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 (OpenMDException& 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	>	}
235	>
236	>	simParams->setMDfileVersion(mdFileVersion);
237	>	return simParams;
238		}
239
240		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
241		bool loadInitCoords) {
242
243	<	MakeStamps * stamps = new MakeStamps();
244	<
245	<	Globals * simParams = new Globals();
246	<
243	>	const int bufferSize = 65535;
244	>	char buffer[bufferSize];
245	>	int lineNo = 0;
246	>	std::string mdRawData;
247	>	int metaDataBlockStart = -1;
248	>	int metaDataBlockEnd = -1;
249	>	int i;
250	>	int mdOffset;
251	>	int mdFileVersion;
252	>
253	>	#ifdef IS_MPI
254	>	const int masterNode = 0;
255	>	if (worldRank == masterNode) {
256	>	#endif
257	>
258	>	std::ifstream mdFile_(mdFileName.c_str());
259	>
260	>	if (mdFile_.fail()) {
261	>	sprintf(painCave.errMsg,
262	>	"SimCreator: Cannot open file: %s\n",
263	>	mdFileName.c_str());
264	>	painCave.isFatal = 1;
265	>	simError();
266	>	}
267	>
268	>	mdFile_.getline(buffer, bufferSize);
269	>	++lineNo;
270	>	std::string line = trimLeftCopy(buffer);
271	>	i = CaseInsensitiveFind(line, "<OpenMD");
272	>	if (static_cast<size_t>(i) == string::npos) {
273	>	// try the older file strings to see if that works:
274	>	i = CaseInsensitiveFind(line, "<OOPSE");
275	>	}
276	>
277	>	if (static_cast<size_t>(i) == string::npos) {
278	>	// still no luck!
279	>	sprintf(painCave.errMsg,
280	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
281	>	mdFileName.c_str());
282	>	painCave.isFatal = 1;
283	>	simError();
284	>	}
285	>
286	>	// found the correct opening string, now try to get the file
287	>	// format version number.
288	>
289	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
290	>	std::string fileType = tokenizer.nextToken();
291	>	toUpper(fileType);
292	>
293	>	mdFileVersion = 0;
294	>
295	>	if (fileType == "OPENMD") {
296	>	while (tokenizer.hasMoreTokens()) {
297	>	std::string token(tokenizer.nextToken());
298	>	toUpper(token);
299	>	if (token == "VERSION") {
300	>	mdFileVersion = tokenizer.nextTokenAsInt();
301	>	break;
302	>	}
303	>	}
304	>	}
305	>
306	>	//scan through the input stream and find MetaData tag
307	>	while(mdFile_.getline(buffer, bufferSize)) {
308	>	++lineNo;
309	>
310	>	std::string line = trimLeftCopy(buffer);
311	>	if (metaDataBlockStart == -1) {
312	>	i = CaseInsensitiveFind(line, "<MetaData>");
313	>	if (i != string::npos) {
314	>	metaDataBlockStart = lineNo;
315	>	mdOffset = mdFile_.tellg();
316	>	}
317	>	} else {
318	>	i = CaseInsensitiveFind(line, "</MetaData>");
319	>	if (i != string::npos) {
320	>	metaDataBlockEnd = lineNo;
321	>	}
322	>	}
323	>	}
324	>
325	>	if (metaDataBlockStart == -1) {
326	>	sprintf(painCave.errMsg,
327	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
328	>	mdFileName.c_str());
329	>	painCave.isFatal = 1;
330	>	simError();
331	>	}
332	>	if (metaDataBlockEnd == -1) {
333	>	sprintf(painCave.errMsg,
334	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
335	>	mdFileName.c_str());
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>
340	>	mdFile_.clear();
341	>	mdFile_.seekg(0);
342	>	mdFile_.seekg(mdOffset);
343	>
344	>	mdRawData.clear();
345	>
346	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
347	>	mdFile_.getline(buffer, bufferSize);
348	>	mdRawData += buffer;
349	>	mdRawData += "\n";
350	>	}
351	>
352	>	mdFile_.close();
353	>
354	>	#ifdef IS_MPI
355	>	}
356	>	#endif
357	>
358	>	std::stringstream rawMetaDataStream(mdRawData);
359	>
360		//parse meta-data file
361	<	parseFile(mdFileName, stamps, simParams);
361	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
362	>	metaDataBlockStart + 1);
363
364		//create the force field
365	<	ForceField * ff = ForceFieldFactory::getInstance()
366	<	->createForceField(simParams->getForceField());
112	<
365	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
366	>
367		if (ff == NULL) {
368		sprintf(painCave.errMsg,
369		"ForceField Factory can not create %s force field\n",
370	<	simParams->getForceField());
370	>	simParams->getForceField().c_str());
371		painCave.isFatal = 1;
372		simError();
373		}
#	Line 142 | Line 396 | namespace oopse {
396		}
397
398		ff->parse(forcefieldFileName);
145	–
146	–	//extract the molecule stamps
147	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
148	–	compList(stamps, simParams, moleculeStampPairs);
149	–
399		//create SimInfo
400	<	SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
400	>	SimInfo * info = new SimInfo(ff, simParams);
401	>
402	>	info->setRawMetaData(mdRawData);
403
404	<	//gather parameters (SimCreator only retrieves part of the parameters)
404	>	//gather parameters (SimCreator only retrieves part of the
405	>	//parameters)
406		gatherParameters(info, mdFileName);
407
408		//divide the molecules and determine the global index of molecules
#	Line 161 | Line 413 | namespace oopse {
413		//create the molecules
414		createMolecules(info);
415
416	<
417	<	//allocate memory for DataStorage(circular reference, need to break it)
416	>	//allocate memory for DataStorage(circular reference, need to
417	>	//break it)
418		info->setSnapshotManager(new SimSnapshotManager(info));
419
420	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
421	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
422	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
420	>	//set the global index of atoms, rigidbodies and cutoffgroups
421	>	//(only need to be set once, the global index will never change
422	>	//again). Local indices of atoms and rigidbodies are already set
423	>	//by MoleculeCreator class which actually delegates the
424	>	//responsibility to LocalIndexManager.
425		setGlobalIndex(info);
426
427	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
428	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
429	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
430	<	//we can determine the beginning global indices of atoms before they get created.
427	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
428	>	//method, at that point atoms don't have the global index yet
429	>	//(their global index are all initialized to -1).  Therefore we
430	>	//have to call addInteractionPairs explicitly here. A way to work
431	>	//around is that we can determine the beginning global indices of
432	>	//atoms before they get created.
433		SimInfo::MoleculeIterator mi;
434		Molecule* mol;
435		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
436	<	info->addExcludePairs(mol);
436	>	info->addInteractionPairs(mol);
437		}
438
439		if (loadInitCoords)
440	<	loadCoordinates(info);
185	<
440	>	loadCoordinates(info, mdFileName);
441		return info;
442		}
443
444		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
445
446	<	//figure out the ouput file names
446	>	//figure out the output file names
447		std::string prefix;
448
449		#ifdef IS_MPI
#	Line 217 | Line 472 | namespace oopse {
472
473		#ifdef IS_MPI
474		void SimCreator::divideMolecules(SimInfo *info) {
475	<	double numerator;
476	<	double denominator;
477	<	double precast;
478	<	double x;
479	<	double y;
480	<	double a;
475	>	RealType numerator;
476	>	RealType denominator;
477	>	RealType precast;
478	>	RealType x;
479	>	RealType y;
480	>	RealType a;
481		int old_atoms;
482		int add_atoms;
483		int new_atoms;
#	Line 246 | Line 501 | namespace oopse {
501		"\tthe number of molecules.  This will not result in a \n"
502		"\tusable division of atoms for force decomposition.\n"
503		"\tEither try a smaller number of processors, or run the\n"
504	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
504	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
505
506		painCave.isFatal = 1;
507		simError();
#	Line 334 | Line 589 | namespace oopse {
589		//           Pacc(x) = exp(- a * x)
590		// where a = penalty / (average atoms per molecule)
591
592	<	x = (double)(new_atoms - nTarget);
592	>	x = (RealType)(new_atoms - nTarget);
593		y = myRandom->rand();
594
595		if (y < exp(- a * x)) {
#	Line 364 | Line 619 | namespace oopse {
619		info->setMolToProcMap(molToProcMap);
620		sprintf(checkPointMsg,
621		"Successfully divided the molecules among the processors.\n");
622	<	MPIcheckPoint();
622	>	errorCheckPoint();
623		}
624
625		#endif
#	Line 381 | Line 636 | namespace oopse {
636		#endif
637
638		stampId = info->getMoleculeStampId(i);
639	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
640	<	stampId, i, info->getLocalIndexManager());
639	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
640	>	info->getMoleculeStamp(stampId),
641	>	stampId, i,
642	>	info->getLocalIndexManager());
643
644		info->addMolecule(mol);
645
#	Line 394 | Line 651 | namespace oopse {
651
652		} //end for(int i=0)
653		}
397	–
398	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
399	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
400	–	int i;
401	–	char * id;
402	–	MoleculeStamp * currentStamp;
403	–	Component** the_components = simParams->getComponents();
404	–	int n_components = simParams->getNComponents();
654
406	–	if (!simParams->haveNMol()) {
407	–	// we don't have the total number of molecules, so we assume it is
408	–	// given in each component
409	–
410	–	for(i = 0; i < n_components; i++) {
411	–	if (!the_components[i]->haveNMol()) {
412	–	// we have a problem
413	–	sprintf(painCave.errMsg,
414	–	"SimCreator Error. No global NMol or component NMol given.\n"
415	–	"\tCannot calculate the number of atoms.\n");
416	–
417	–	painCave.isFatal = 1;
418	–	simError();
419	–	}
420	–
421	–	id = the_components[i]->getType();
422	–
423	–	currentStamp = stamps->getMolStamp(id);
424	–	if (currentStamp == NULL) {
425	–	sprintf(painCave.errMsg,
426	–	"SimCreator error: Component \"%s\" was not found in the "
427	–	"list of declared molecules\n", id);
428	–
429	–	painCave.isFatal = 1;
430	–	simError();
431	–	}
432	–
433	–	moleculeStampPairs.push_back(
434	–	std::make_pair(currentStamp, the_components[i]->getNMol()));
435	–	} //end for (i = 0; i < n_components; i++)
436	–	} else {
437	–	sprintf(painCave.errMsg, "SimSetup error.\n"
438	–	"\tSorry, the ability to specify total"
439	–	" nMols and then give molfractions in the components\n"
440	–	"\tis not currently supported."
441	–	" Please give nMol in the components.\n");
442	–
443	–	painCave.isFatal = 1;
444	–	simError();
445	–	}
446	–
447	–	#ifdef IS_MPI
448	–
449	–	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
450	–	MPIcheckPoint();
451	–
452	–	#endif // is_mpi
453	–
454	–	}
455	–
655		void SimCreator::setGlobalIndex(SimInfo *info) {
656		SimInfo::MoleculeIterator mi;
657		Molecule::AtomIterator ai;
658		Molecule::RigidBodyIterator ri;
659		Molecule::CutoffGroupIterator ci;
660	+	Molecule::IntegrableObjectIterator  ioi;
661		Molecule * mol;
662		Atom * atom;
663		RigidBody * rb;
#	Line 467 | Line 667 | namespace oopse {
667		int beginCutoffGroupIndex;
668		int nGlobalAtoms = info->getNGlobalAtoms();
669
470	–	#ifndef IS_MPI
471	–
670		beginAtomIndex = 0;
671		beginRigidBodyIndex = 0;
672		beginCutoffGroupIndex = 0;
673	<
674	<	#else
477	<
478	<	int nproc;
479	<	int myNode;
480	<
481	<	myNode = worldRank;
482	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
483	<
484	<	std::vector < int > tmpAtomsInProc(nproc, 0);
485	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
486	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
487	<	std::vector < int > NumAtomsInProc(nproc, 0);
488	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
489	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
490	<
491	<	tmpAtomsInProc[myNode] = info->getNAtoms();
492	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
493	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
494	<
495	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
496	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
497	<	MPI_SUM, MPI_COMM_WORLD);
498	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
499	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
500	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
501	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
502	<
503	<	beginAtomIndex = 0;
504	<	beginRigidBodyIndex = 0;
505	<	beginCutoffGroupIndex = 0;
506	<
507	<	for(int i = 0; i < myNode; i++) {
508	<	beginAtomIndex += NumAtomsInProc[i];
509	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
510	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
511	<	}
512	<
513	<	#endif
514	<
515	<	//rigidbody's index begins right after atom's
516	<	beginRigidBodyIndex += info->getNGlobalAtoms();
517	<
518	<	for(mol = info->beginMolecule(mi); mol != NULL;
519	<	mol = info->nextMolecule(mi)) {
673	>
674	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
675
676	<	//local index(index in DataStorge) of atom is important
677	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
678	<	atom->setGlobalIndex(beginAtomIndex++);
676	>	#ifdef IS_MPI
677	>	if (info->getMolToProc(i) == worldRank) {
678	>	#endif
679	>	// stuff to do if I own this molecule
680	>	mol = info->getMoleculeByGlobalIndex(i);
681	>
682	>	//local index(index in DataStorge) of atom is important
683	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
684	>	atom->setGlobalIndex(beginAtomIndex++);
685	>	}
686	>
687	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
688	>	rb = mol->nextRigidBody(ri)) {
689	>	rb->setGlobalIndex(beginRigidBodyIndex++);
690	>	}
691	>
692	>	//local index of cutoff group is trivial, it only depends on
693	>	//the order of travesing
694	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
695	>	cg = mol->nextCutoffGroup(ci)) {
696	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
697	>	}
698	>
699	>	#ifdef IS_MPI
700	>	}  else {
701	>
702	>	// stuff to do if I don't own this molecule
703	>
704	>	int stampId = info->getMoleculeStampId(i);
705	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
706	>
707	>	beginAtomIndex += stamp->getNAtoms();
708	>	beginRigidBodyIndex += stamp->getNRigidBodies();
709	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
710		}
711	<
712	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
713	<	rb = mol->nextRigidBody(ri)) {
714	<	rb->setGlobalIndex(beginRigidBodyIndex++);
529	<	}
530	<
531	<	//local index of cutoff group is trivial, it only depends on the order of travesing
532	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
533	<	cg = mol->nextCutoffGroup(ci)) {
534	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
535	<	}
536	<	}
537	<
711	>	#endif
712	>
713	>	} //end for(int i=0)
714	>
715		//fill globalGroupMembership
716		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
717		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 546 | Line 723 | namespace oopse {
723
724		}
725		}
726	<
726	>
727		#ifdef IS_MPI
728		// Since the globalGroupMembership has been zero filled and we've only
729		// poked values into the atoms we know, we can do an Allreduce
730		// to get the full globalGroupMembership array (We think).
731		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
732		// docs said we could.
733	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
733	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
734		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
735		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
736		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 565 | Line 742 | namespace oopse {
742		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
743
744		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
568	–
745		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
746		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
747		}
748		}
749
750		#ifdef IS_MPI
751	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
751	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
752
753		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
754		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 581 | Line 757 | namespace oopse {
757		#else
758		info->setGlobalMolMembership(globalMolMembership);
759		#endif
760	+
761	+	// nIOPerMol holds the number of integrable objects per molecule
762	+	// here the molecules are listed by their global indices.
763	+
764	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
765	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
766	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
767	+	}
768
769	+	#ifdef IS_MPI
770	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
771	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
772	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
773	+	#else
774	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
775	+	#endif
776	+
777	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
778	+
779	+	int startingIndex = 0;
780	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
781	+	startingIOIndexForMol[i] = startingIndex;
782	+	startingIndex += numIntegrableObjectsPerMol[i];
783	+	}
784	+
785	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
786	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
787	+	int myGlobalIndex = mol->getGlobalIndex();
788	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
789	+	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
790	+	integrableObject = mol->nextIntegrableObject(ioi)) {
791	+	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
792	+	IOIndexToIntegrableObject[globalIO] = integrableObject;
793	+	globalIO++;
794	+	}
795	+	}
796	+
797	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
798	+
799		}
800
801	<	void SimCreator::loadCoordinates(SimInfo* info) {
801	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
802		Globals* simParams;
803	+
804		simParams = info->getSimParams();
805
806	<	if (!simParams->haveInitialConfig()) {
592	<	sprintf(painCave.errMsg,
593	<	"Cannot intialize a simulation without an initial configuration file.\n");
594	<	painCave.isFatal = 1;;
595	<	simError();
596	<	}
597	<
598	<	DumpReader reader(info, simParams->getInitialConfig());
806	>	DumpReader reader(info, mdFileName);
807		int nframes = reader.getNFrames();
808	<
808	>
809		if (nframes > 0) {
810		reader.readFrame(nframes - 1);
811		} else {
812		//invalid initial coordinate file
813		sprintf(painCave.errMsg,
814		"Initial configuration file %s should at least contain one frame\n",
815	<	simParams->getInitialConfig());
815	>	mdFileName.c_str());
816		painCave.isFatal = 1;
817		simError();
818		}
611	–
819		//copy the current snapshot to previous snapshot
820		info->getSnapshotManager()->advance();
821		}
822
823	<	} //end namespace oopse
823	>	} //end namespace OpenMD
824
825

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 514 by chrisfen, Thu Apr 21 14:12:19 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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