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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1600 by gezelter, Wed Aug 3 20:20:37 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
60	–	#include "io/mpiBASS.h"
79		#include "math/ParallelRandNumGen.hpp"
80		#endif
81
82	<	namespace oopse {
82	>	namespace OpenMD {
83
84	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps,
85	<	Globals* simParams){
84	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
85	>	Globals* simParams = NULL;
86	>	try {
87	>
88	>	// Create a preprocessor that preprocesses md file into an ostringstream
89	>	std::stringstream ppStream;
90	>	#ifdef IS_MPI
91	>	int streamSize;
92	>	const int masterNode = 0;
93	>	int commStatus;
94	>	if (worldRank == masterNode) {
95	>	#endif
96	>
97	>	SimplePreprocessor preprocessor;
98	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
99	>
100	>	#ifdef IS_MPI
101	>	//brocasting the stream size
102	>	streamSize = ppStream.str().size() +1;
103	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
104	>
105	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106	>
107	>
108	>	} else {
109	>	//get stream size
110	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
111	>
112	>	char* buf = new char[streamSize];
113	>	assert(buf);
114	>
115	>	//receive file content
116	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	>
118	>	ppStream.str(buf);
119	>	delete [] buf;
120	>
121	>	}
122	>	#endif
123	>	// Create a scanner that reads from the input stream
124	>	MDLexer lexer(ppStream);
125	>	lexer.setFilename(filename);
126	>	lexer.initDeferredLineCount();
127
128	<	#ifdef IS_MPI
128	>	// Create a parser that reads from the scanner
129	>	MDParser parser(lexer);
130	>	parser.setFilename(filename);
131	>
132	>	// Create an observer that synchorizes file name change
133	>	FilenameObserver observer;
134	>	observer.setLexer(&lexer);
135	>	observer.setParser(&parser);
136	>	lexer.setObserver(&observer);
137
138	<	if (worldRank == 0) {
139	<	#endif // is_mpi
138	>	antlr::ASTFactory factory;
139	>	parser.initializeASTFactory(factory);
140	>	parser.setASTFactory(&factory);
141	>	parser.mdfile();
142	>
143	>	// Create a tree parser that reads information into Globals
144	>	MDTreeParser treeParser;
145	>	treeParser.initializeASTFactory(factory);
146	>	treeParser.setASTFactory(&factory);
147	>	simParams = treeParser.walkTree(parser.getAST());
148	>	}
149	>
150
151	<	simParams->initalize();
152	<	set_interface_stamps(stamps, simParams);
151	>	catch(antlr::MismatchedCharException& e) {
152	>	sprintf(painCave.errMsg,
153	>	"parser exception: %s %s:%d:%d\n",
154	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158	>	catch(antlr::MismatchedTokenException &e) {
159	>	sprintf(painCave.errMsg,
160	>	"parser exception: %s %s:%d:%d\n",
161	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
162	>	painCave.isFatal = 1;
163	>	simError();
164	>	}
165	>	catch(antlr::NoViableAltForCharException &e) {
166	>	sprintf(painCave.errMsg,
167	>	"parser exception: %s %s:%d:%d\n",
168	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
169	>	painCave.isFatal = 1;
170	>	simError();
171	>	}
172	>	catch(antlr::NoViableAltException &e) {
173	>	sprintf(painCave.errMsg,
174	>	"parser exception: %s %s:%d:%d\n",
175	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
176	>	painCave.isFatal = 1;
177	>	simError();
178	>	}
179
180	<	#ifdef IS_MPI
180	>	catch(antlr::TokenStreamRecognitionException& e) {
181	>	sprintf(painCave.errMsg,
182	>	"parser exception: %s %s:%d:%d\n",
183	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187	>
188	>	catch(antlr::TokenStreamIOException& e) {
189	>	sprintf(painCave.errMsg,
190	>	"parser exception: %s\n",
191	>	e.getMessage().c_str());
192	>	painCave.isFatal = 1;
193	>	simError();
194	>	}
195	>
196	>	catch(antlr::TokenStreamException& e) {
197	>	sprintf(painCave.errMsg,
198	>	"parser exception: %s\n",
199	>	e.getMessage().c_str());
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>	catch (antlr::RecognitionException& e) {
204	>	sprintf(painCave.errMsg,
205	>	"parser exception: %s %s:%d:%d\n",
206	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
207	>	painCave.isFatal = 1;
208	>	simError();
209	>	}
210	>	catch (antlr::CharStreamException& e) {
211	>	sprintf(painCave.errMsg,
212	>	"parser exception: %s\n",
213	>	e.getMessage().c_str());
214	>	painCave.isFatal = 1;
215	>	simError();
216	>	}
217	>	catch (OpenMDException& e) {
218	>	sprintf(painCave.errMsg,
219	>	"%s\n",
220	>	e.getMessage().c_str());
221	>	painCave.isFatal = 1;
222	>	simError();
223	>	}
224	>	catch (std::exception& e) {
225	>	sprintf(painCave.errMsg,
226	>	"parser exception: %s\n",
227	>	e.what());
228	>	painCave.isFatal = 1;
229	>	simError();
230	>	}
231	>
232	>	return simParams;
233	>	}
234	>
235	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236	>	bool loadInitCoords) {
237	>
238	>	const int bufferSize = 65535;
239	>	char buffer[bufferSize];
240	>	int lineNo = 0;
241	>	std::string mdRawData;
242	>	int metaDataBlockStart = -1;
243	>	int metaDataBlockEnd = -1;
244	>	int i;
245	>	int mdOffset;
246	>
247	>	#ifdef IS_MPI
248	>	const int masterNode = 0;
249	>	if (worldRank == masterNode) {
250	>	#endif
251	>
252	>	std::ifstream mdFile_(mdFileName.c_str());
253
254	<	mpiEventInit();
254	>	if (mdFile_.fail()) {
255	>	sprintf(painCave.errMsg,
256	>	"SimCreator: Cannot open file: %s\n",
257	>	mdFileName.c_str());
258	>	painCave.isFatal = 1;
259	>	simError();
260	>	}
261	>
262	>	mdFile_.getline(buffer, bufferSize);
263	>	++lineNo;
264	>	std::string line = trimLeftCopy(buffer);
265	>	i = CaseInsensitiveFind(line, "<OpenMD");
266	>	if (static_cast<size_t>(i) == string::npos) {
267	>	// try the older file strings to see if that works:
268	>	i = CaseInsensitiveFind(line, "<OOPSE");
269	>	}
270
271	<	#endif
272	<
273	<	yacc_BASS(mdFileName.c_str());
274	<
271	>	if (static_cast<size_t>(i) == string::npos) {
272	>	// still no luck!
273	>	sprintf(painCave.errMsg,
274	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
275	>	mdFileName.c_str());
276	>	painCave.isFatal = 1;
277	>	simError();
278	>	}
279	>
280	>	//scan through the input stream and find MetaData tag
281	>	while(mdFile_.getline(buffer, bufferSize)) {
282	>	++lineNo;
283	>
284	>	std::string line = trimLeftCopy(buffer);
285	>	if (metaDataBlockStart == -1) {
286	>	i = CaseInsensitiveFind(line, "<MetaData>");
287	>	if (i != string::npos) {
288	>	metaDataBlockStart = lineNo;
289	>	mdOffset = mdFile_.tellg();
290	>	}
291	>	} else {
292	>	i = CaseInsensitiveFind(line, "</MetaData>");
293	>	if (i != string::npos) {
294	>	metaDataBlockEnd = lineNo;
295	>	}
296	>	}
297	>	}
298	>
299	>	if (metaDataBlockStart == -1) {
300	>	sprintf(painCave.errMsg,
301	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
302	>	mdFileName.c_str());
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	if (metaDataBlockEnd == -1) {
307	>	sprintf(painCave.errMsg,
308	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
309	>	mdFileName.c_str());
310	>	painCave.isFatal = 1;
311	>	simError();
312	>	}
313	>
314	>	mdFile_.clear();
315	>	mdFile_.seekg(0);
316	>	mdFile_.seekg(mdOffset);
317	>
318	>	mdRawData.clear();
319	>
320	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
321	>	mdFile_.getline(buffer, bufferSize);
322	>	mdRawData += buffer;
323	>	mdRawData += "\n";
324	>	}
325	>
326	>	mdFile_.close();
327	>
328		#ifdef IS_MPI
86	–
87	–	throwMPIEvent(NULL);
88	–	} else {
89	–	set_interface_stamps(stamps, simParams);
90	–	mpiEventInit();
91	–	MPIcheckPoint();
92	–	mpiEventLoop();
329		}
94	–
330		#endif
331	<
332	<	}
333	<
99	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
100	<
101	<	MakeStamps * stamps = new MakeStamps();
102	<
103	<	Globals * simParams = new Globals();
104	<
331	>
332	>	std::stringstream rawMetaDataStream(mdRawData);
333	>
334		//parse meta-data file
335	<	parseFile(mdFileName, stamps, simParams);
335	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
336
337		//create the force field
338	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
339	<	simParams->getForceField());
111	<
338	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
339	>
340		if (ff == NULL) {
341	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
342	<	simParams->getForceField());
341	>	sprintf(painCave.errMsg,
342	>	"ForceField Factory can not create %s force field\n",
343	>	simParams->getForceField().c_str());
344		painCave.isFatal = 1;
345		simError();
346		}
#	Line 140 | Line 369 | namespace oopse {
369		}
370
371		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
372		//create SimInfo
373	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
374	<
375	<	//gather parameters (SimCreator only retrieves part of the parameters)
373	>	SimInfo * info = new SimInfo(ff, simParams);
374	>
375	>	info->setRawMetaData(mdRawData);
376	>
377	>	//gather parameters (SimCreator only retrieves part of the
378	>	//parameters)
379		gatherParameters(info, mdFileName);
380
381		//divide the molecules and determine the global index of molecules
#	Line 159 | Line 386 | namespace oopse {
386		//create the molecules
387		createMolecules(info);
388
389	<
390	<	//allocate memory for DataStorage(circular reference, need to break it)
389	>	//allocate memory for DataStorage(circular reference, need to
390	>	//break it)
391		info->setSnapshotManager(new SimSnapshotManager(info));
392
393	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
394	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
395	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
393	>	//set the global index of atoms, rigidbodies and cutoffgroups
394	>	//(only need to be set once, the global index will never change
395	>	//again). Local indices of atoms and rigidbodies are already set
396	>	//by MoleculeCreator class which actually delegates the
397	>	//responsibility to LocalIndexManager.
398		setGlobalIndex(info);
399
400	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
401	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
402	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
403	<	//we can determine the beginning global indices of atoms before they get created.
400	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
401	>	//method, at that point atoms don't have the global index yet
402	>	//(their global index are all initialized to -1).  Therefore we
403	>	//have to call addInteractionPairs explicitly here. A way to work
404	>	//around is that we can determine the beginning global indices of
405	>	//atoms before they get created.
406		SimInfo::MoleculeIterator mi;
407		Molecule* mol;
408		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
409	<	info->addExcludePairs(mol);
409	>	info->addInteractionPairs(mol);
410		}
411
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
412		if (loadInitCoords)
413	<	loadCoordinates(info);
186	<
413	>	loadCoordinates(info, mdFileName);
414		return info;
415		}
416
417		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
418
419	<	//figure out the ouput file names
419	>	//figure out the output file names
420		std::string prefix;
421
422		#ifdef IS_MPI
#	Line 218 | Line 445 | namespace oopse {
445
446		#ifdef IS_MPI
447		void SimCreator::divideMolecules(SimInfo *info) {
448	<	double numerator;
449	<	double denominator;
450	<	double precast;
451	<	double x;
452	<	double y;
453	<	double a;
448	>	RealType numerator;
449	>	RealType denominator;
450	>	RealType precast;
451	>	RealType x;
452	>	RealType y;
453	>	RealType a;
454		int old_atoms;
455		int add_atoms;
456		int new_atoms;
#	Line 247 | Line 474 | namespace oopse {
474		"\tthe number of molecules.  This will not result in a \n"
475		"\tusable division of atoms for force decomposition.\n"
476		"\tEither try a smaller number of processors, or run the\n"
477	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
477	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
478
479		painCave.isFatal = 1;
480		simError();
#	Line 335 | Line 562 | namespace oopse {
562		//           Pacc(x) = exp(- a * x)
563		// where a = penalty / (average atoms per molecule)
564
565	<	x = (double)(new_atoms - nTarget);
565	>	x = (RealType)(new_atoms - nTarget);
566		y = myRandom->rand();
567
568		if (y < exp(- a * x)) {
#	Line 362 | Line 589 | namespace oopse {
589		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
590		}
591
592	+	cerr << "molToProcMap:\n";
593	+	for (int i = 0; i < molToProcMap.size(); i++) {
594	+	cerr << "m = " << i << " mtpr[m] = " << molToProcMap[i] <<"\n";
595	+	}
596	+
597		info->setMolToProcMap(molToProcMap);
598		sprintf(checkPointMsg,
599		"Successfully divided the molecules among the processors.\n");
600	<	MPIcheckPoint();
600	>	errorCheckPoint();
601		}
602
603		#endif
#	Line 382 | Line 614 | namespace oopse {
614		#endif
615
616		stampId = info->getMoleculeStampId(i);
617	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
618	<	stampId, i, info->getLocalIndexManager());
617	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
618	>	info->getMoleculeStamp(stampId),
619	>	stampId, i,
620	>	info->getLocalIndexManager());
621
622		info->addMolecule(mol);
623
#	Line 395 | Line 629 | namespace oopse {
629
630		} //end for(int i=0)
631		}
398	–
399	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
400	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
401	–	int i;
402	–	char * id;
403	–	LinkedMolStamp* extractedStamp = NULL;
404	–	MoleculeStamp * currentStamp;
405	–	Component** the_components = simParams->getComponents();
406	–	int n_components = simParams->getNComponents();
632
408	–	if (!simParams->haveNMol()) {
409	–	// we don't have the total number of molecules, so we assume it is
410	–	// given in each component
411	–
412	–	for(i = 0; i < n_components; i++) {
413	–	if (!the_components[i]->haveNMol()) {
414	–	// we have a problem
415	–	sprintf(painCave.errMsg,
416	–	"SimCreator Error. No global NMol or component NMol given.\n"
417	–	"\tCannot calculate the number of atoms.\n");
418	–
419	–	painCave.isFatal = 1;
420	–	simError();
421	–	}
422	–
423	–	id = the_components[i]->getType();
424	–
425	–	extractedStamp = stamps->extractMolStamp(id);
426	–	if (extractedStamp == NULL) {
427	–	sprintf(painCave.errMsg,
428	–	"SimCreator error: Component \"%s\" was not found in the "
429	–	"list of declared molecules\n", id);
430	–
431	–	painCave.isFatal = 1;
432	–	simError();
433	–	}
434	–
435	–	currentStamp = extractedStamp->getStamp();
436	–
437	–
438	–	moleculeStampPairs.push_back(
439	–	std::make_pair(currentStamp, the_components[i]->getNMol()));
440	–	} //end for (i = 0; i < n_components; i++)
441	–	} else {
442	–	sprintf(painCave.errMsg, "SimSetup error.\n"
443	–	"\tSorry, the ability to specify total"
444	–	" nMols and then give molfractions in the components\n"
445	–	"\tis not currently supported."
446	–	" Please give nMol in the components.\n");
447	–
448	–	painCave.isFatal = 1;
449	–	simError();
450	–	}
451	–
452	–	#ifdef IS_MPI
453	–
454	–	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
455	–	MPIcheckPoint();
456	–
457	–	#endif // is_mpi
458	–
459	–	}
460	–
633		void SimCreator::setGlobalIndex(SimInfo *info) {
634		SimInfo::MoleculeIterator mi;
635		Molecule::AtomIterator ai;
636		Molecule::RigidBodyIterator ri;
637		Molecule::CutoffGroupIterator ci;
638	+	Molecule::IntegrableObjectIterator  ioi;
639		Molecule * mol;
640		Atom * atom;
641		RigidBody * rb;
#	Line 471 | Line 644 | namespace oopse {
644		int beginRigidBodyIndex;
645		int beginCutoffGroupIndex;
646		int nGlobalAtoms = info->getNGlobalAtoms();
474	–
475	–	#ifndef IS_MPI
476	–
477	–	beginAtomIndex = 0;
478	–	beginRigidBodyIndex = 0;
479	–	beginCutoffGroupIndex = 0;
480	–
481	–	#else
482	–
483	–	int nproc;
484	–	int myNode;
485	–
486	–	myNode = worldRank;
487	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
488	–
489	–	std::vector < int > tmpAtomsInProc(nproc, 0);
490	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
491	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
492	–	std::vector < int > NumAtomsInProc(nproc, 0);
493	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
494	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
495	–
496	–	tmpAtomsInProc[myNode] = info->getNAtoms();
497	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
498	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
647
500	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
501	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
502	–	MPI_SUM, MPI_COMM_WORLD);
503	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
504	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
505	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
506	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
507	–
648		beginAtomIndex = 0;
649		beginRigidBodyIndex = 0;
650		beginCutoffGroupIndex = 0;
651	<
652	<	for(int i = 0; i < myNode; i++) {
513	<	beginAtomIndex += NumAtomsInProc[i];
514	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
515	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
516	<	}
517	<
518	<	#endif
519	<
520	<	//rigidbody's index begins right after atom's
521	<	beginRigidBodyIndex += info->getNGlobalAtoms();
522	<
523	<	for(mol = info->beginMolecule(mi); mol != NULL;
524	<	mol = info->nextMolecule(mi)) {
651	>
652	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
653
654	<	//local index(index in DataStorge) of atom is important
655	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
656	<	atom->setGlobalIndex(beginAtomIndex++);
654	>	#ifdef IS_MPI
655	>	if (info->getMolToProc(i) == worldRank) {
656	>	#endif
657	>	// stuff to do if I own this molecule
658	>	mol = info->getMoleculeByGlobalIndex(i);
659	>
660	>	//local index(index in DataStorge) of atom is important
661	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
662	>	atom->setGlobalIndex(beginAtomIndex++);
663	>	}
664	>
665	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
666	>	rb = mol->nextRigidBody(ri)) {
667	>	rb->setGlobalIndex(beginRigidBodyIndex++);
668	>	}
669	>
670	>	//local index of cutoff group is trivial, it only depends on
671	>	//the order of travesing
672	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
673	>	cg = mol->nextCutoffGroup(ci)) {
674	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
675	>	}
676	>
677	>	#ifdef IS_MPI
678	>	}  else {
679	>
680	>	// stuff to do if I don't own this molecule
681	>
682	>	int stampId = info->getMoleculeStampId(i);
683	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
684	>
685	>	beginAtomIndex += stamp->getNAtoms();
686	>	beginRigidBodyIndex += stamp->getNRigidBodies();
687	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
688		}
689	<
690	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
691	<	rb = mol->nextRigidBody(ri)) {
692	<	rb->setGlobalIndex(beginRigidBodyIndex++);
534	<	}
535	<
536	<	//local index of cutoff group is trivial, it only depends on the order of travesing
537	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
538	<	cg = mol->nextCutoffGroup(ci)) {
539	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
540	<	}
541	<	}
542	<
689	>	#endif
690	>
691	>	} //end for(int i=0)
692	>
693		//fill globalGroupMembership
694		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
695		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 551 | Line 701 | namespace oopse {
701
702		}
703		}
704	<
704	>
705		#ifdef IS_MPI
706		// Since the globalGroupMembership has been zero filled and we've only
707		// poked values into the atoms we know, we can do an Allreduce
708		// to get the full globalGroupMembership array (We think).
709		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
710		// docs said we could.
711	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
711	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
712		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
713		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
714		info->setGlobalGroupMembership(tmpGroupMembership);
715	+
716	+	cerr << "ggm:\n";
717	+	for (int i = 0; i < tmpGroupMembership.size(); i++)
718	+	cerr << "i = " << i << "\t ggm(i) = " << tmpGroupMembership[i] << "\n";
719	+
720		#else
721		info->setGlobalGroupMembership(globalGroupMembership);
722		#endif
#	Line 570 | Line 725 | namespace oopse {
725		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
726
727		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
573	–
728		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
729		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
730		}
731		}
732
733		#ifdef IS_MPI
734	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
734	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
735
736		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
737		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 586 | Line 740 | namespace oopse {
740		#else
741		info->setGlobalMolMembership(globalMolMembership);
742		#endif
743	+
744	+	// nIOPerMol holds the number of integrable objects per molecule
745	+	// here the molecules are listed by their global indices.
746	+
747	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
748	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
749	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
750	+	}
751
752	+	#ifdef IS_MPI
753	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
754	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
755	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
756	+	#else
757	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
758	+	#endif
759	+
760	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
761	+
762	+	int startingIndex = 0;
763	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
764	+	startingIOIndexForMol[i] = startingIndex;
765	+	startingIndex += numIntegrableObjectsPerMol[i];
766	+	}
767	+
768	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
769	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
770	+	int myGlobalIndex = mol->getGlobalIndex();
771	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
772	+	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
773	+	integrableObject = mol->nextIntegrableObject(ioi)) {
774	+	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
775	+	IOIndexToIntegrableObject[globalIO] = integrableObject;
776	+	globalIO++;
777	+	}
778	+	}
779	+	cerr << "ioi2io:\n";
780	+	for (int i = 0; i < IOIndexToIntegrableObject.size(); i++) {
781	+	if (IOIndexToIntegrableObject[i] != NULL) {
782	+	cerr << "i = " << i << "globalIOindex = " << IOIndexToIntegrableObject[i]->getGlobalIntegrableObjectIndex() << "\n";
783	+	}
784	+	}
785	+
786	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
787	+
788		}
789
790	<	void SimCreator::loadCoordinates(SimInfo* info) {
790	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
791		Globals* simParams;
792	+
793		simParams = info->getSimParams();
794
795	<	if (!simParams->haveInitialConfig()) {
597	<	sprintf(painCave.errMsg,
598	<	"Cannot intialize a simulation without an initial configuration file.\n");
599	<	painCave.isFatal = 1;;
600	<	simError();
601	<	}
602	<
603	<	DumpReader reader(info, simParams->getInitialConfig());
795	>	DumpReader reader(info, mdFileName);
796		int nframes = reader.getNFrames();
797	<
797	>
798		if (nframes > 0) {
799		reader.readFrame(nframes - 1);
800		} else {
801		//invalid initial coordinate file
802		sprintf(painCave.errMsg,
803		"Initial configuration file %s should at least contain one frame\n",
804	<	simParams->getInitialConfig());
804	>	mdFileName.c_str());
805		painCave.isFatal = 1;
806		simError();
807		}
616	–
808		//copy the current snapshot to previous snapshot
809		info->getSnapshotManager()->advance();
810		}
811
812	<	} //end namespace oopse
812	>	} //end namespace OpenMD
813
814

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1600 by gezelter, Wed Aug 3 20:20:37 2011 UTC

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