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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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
50	–	#include <sprng.h>
51	–
54		#include "brains/MoleculeCreator.hpp"
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
56	–	#include "io/parse_me.h"
58		#include "UseTheForce/ForceFieldFactory.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61	<	#ifdef IS_MPI
62	<	#include "io/mpiBASS.h"
63	<	#include "math/randomSPRNG.hpp"
64	<	#endif
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	<	namespace oopse {
73	>	#include "antlr/MismatchedCharException.hpp"
74	>	#include "antlr/MismatchedTokenException.hpp"
75	>	#include "antlr/NoViableAltForCharException.hpp"
76	>	#include "antlr/NoViableAltException.hpp"
77
67	–	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
68	–
78		#ifdef IS_MPI
79	+	#include "math/ParallelRandNumGen.hpp"
80	+	#endif
81
82	<	if (worldRank == 0) {
83	<	#endif // is_mpi
82	>	namespace OpenMD {
83	>
84	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
85	>	Globals* simParams = NULL;
86	>	try {
87
88	<	simParams->initalize();
89	<	set_interface_stamps(stamps, simParams);
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	<	#ifdef IS_MPI
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	<	mpiEventInit();
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	<	#endif
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	>	// Create a parser that reads from the scanner
129	>	MDParser parser(lexer);
130	>	parser.setFilename(filename);
131
132	<	yacc_BASS(mdFileName.c_str());
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	>	antlr::ASTFactory factory;
139	>	parser.initializeASTFactory(factory);
140	>	parser.setASTFactory(&factory);
141	>	parser.mdfile();
142
143	<	#ifdef IS_MPI
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	<	throwMPIEvent(NULL);
151	<	} else {
152	<	set_interface_stamps(stamps, simParams);
153	<	mpiEventInit();
154	<	MPIcheckPoint();
155	<	mpiEventLoop();
150	>
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	+	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	<	#endif
233	<
234	<	}
235	<
236	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
232	>	return simParams;
233	>	}
234	>
235	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
236	>	bool loadInitCoords) {
237
238	<	MakeStamps * stamps = new MakeStamps();
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	<	Globals * simParams = new Globals();
247	>	#ifdef IS_MPI
248	>	const int masterNode = 0;
249	>	if (worldRank == masterNode) {
250	>	#endif
251
252	<	//parse meta-data file
253	<	parseFile(mdFileName, stamps, simParams);
252	>	std::ifstream mdFile_(mdFileName.c_str());
253	>
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	<	//create the force field
263	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
264	<	simParams->getForceField());
265	<
266	<	if (ff == NULL) {
267	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
268	<	simParams->getForceField());
269	<	painCave.isFatal = 1;
270	<	simError();
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	>	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
329		}
330	+	#endif
331
332	+	std::stringstream rawMetaDataStream(mdRawData);
333	+
334	+	//parse meta-data file
335	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
336	+
337	+	//create the force field
338	+	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
339	+
340	+	if (ff == NULL) {
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	+	}
347	+
348		if (simParams->haveForceFieldFileName()) {
349	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
349	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
350		}
351
352		std::string forcefieldFileName;
353		forcefieldFileName = ff->getForceFieldFileName();
354	<
354	>
355		if (simParams->haveForceFieldVariant()) {
356	<	//If the force field has variant, the variant force field name will be
357	<	//Base.variant.frc. For exampel EAM.u6.frc
358	<
359	<	std::string variant = simParams->getForceFieldVariant();
360	<
361	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
362	<	variant = "." + variant;
363	<	if (pos != std::string::npos) {
364	<	forcefieldFileName.insert(pos, variant);
365	<	} else {
366	<	//If the default force field file name does not containt .frc suffix, just append the .variant
367	<	forcefieldFileName.append(variant);
368	<	}
356	>	//If the force field has variant, the variant force field name will be
357	>	//Base.variant.frc. For exampel EAM.u6.frc
358	>
359	>	std::string variant = simParams->getForceFieldVariant();
360	>
361	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
362	>	variant = "." + variant;
363	>	if (pos != std::string::npos) {
364	>	forcefieldFileName.insert(pos, variant);
365	>	} else {
366	>	//If the default force field file name does not containt .frc suffix, just append the .variant
367	>	forcefieldFileName.append(variant);
368	>	}
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);
373	>	SimInfo * info = new SimInfo(ff, simParams);
374
375	<	//gather parameters (SimCreator only retrieves part of the parameters)
375	>	info->setRawMetaData(mdRawData);
376	>
377	>	//gather parameters (SimCreator only retrieves part of the
378	>	//parameters)
379		gatherParameters(info, mdFileName);
380	<
380	>
381		//divide the molecules and determine the global index of molecules
382		#ifdef IS_MPI
383		divideMolecules(info);
384		#endif
385	<
385	>
386		//create the molecules
387		createMolecules(info);
388	<
389	<
390	<	//allocate memory for DataStorage(circular reference, need to break it)
388	>
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.
399	>
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	<	//setup seed for random number generator
193	<	int seedValue;
194	<	Globals * simParams = info->getSimParams();
195	<
196	<	if (simParams->haveSeed()) {
197	<	seedValue = simParams->getSeed();
198	<
199	<	if (seedValue < 100000000 ) {
200	<	sprintf(painCave.errMsg,
201	<	"Seed for sprng library should contain at least 9 digits\n"
202	<	"OOPSE will generate a seed for user\n");
203	<
204	<	painCave.isFatal = 0;
205	<	simError();
206	<
207	<	//using seed generated by system instead of invalid seed set by user
208	<
209	<	#ifndef IS_MPI
210	<
211	<	seedValue = make_sprng_seed();
212	<
213	<	#else
214	<
215	<	if (worldRank == 0) {
216	<	seedValue = make_sprng_seed();
217	<	}
218	<
219	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
220	<
221	<	#endif
222	<
223	<	} //end if (seedValue /1000000000 == 0)
224	<	} else {
225	<
226	<	#ifndef IS_MPI
227	<
228	<	seedValue = make_sprng_seed();
229	<
230	<	#else
231	<
232	<	if (worldRank == 0) {
233	<	seedValue = make_sprng_seed();
234	<	}
235	<
236	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
237	<
238	<	#endif
239	<
240	<	} //end of simParams->haveSeed()
241	<
242	<	info->setSeed(seedValue);
243	<
244	<
245	<	//figure out the ouput file names
415	>	}
416	>
417	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
418	>
419	>	//figure out the output file names
420		std::string prefix;
421	<
421	>
422		#ifdef IS_MPI
423	<
423	>
424		if (worldRank == 0) {
425		#endif // is_mpi
426	<
427	<	if (simParams->haveFinalConfig()) {
428	<	prefix = getPrefix(simParams->getFinalConfig());
429	<	} else {
430	<	prefix = getPrefix(mdfile);
431	<	}
432	<
433	<	info->setFinalConfigFileName(prefix + ".eor");
434	<	info->setDumpFileName(prefix + ".dump");
435	<	info->setStatFileName(prefix + ".stat");
436	<
426	>	Globals * simParams = info->getSimParams();
427	>	if (simParams->haveFinalConfig()) {
428	>	prefix = getPrefix(simParams->getFinalConfig());
429	>	} else {
430	>	prefix = getPrefix(mdfile);
431	>	}
432	>
433	>	info->setFinalConfigFileName(prefix + ".eor");
434	>	info->setDumpFileName(prefix + ".dump");
435	>	info->setStatFileName(prefix + ".stat");
436	>	info->setRestFileName(prefix + ".zang");
437	>
438		#ifdef IS_MPI
439	<
439	>
440		}
441	<
441	>
442		#endif
443	<
444	<	}
445	<
443	>
444	>	}
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;
447	>	void SimCreator::divideMolecules(SimInfo *info) {
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 287 | Line 462 | void SimCreator::divideMolecules(SimInfo *info) {
462		int which_proc;
463		int nProcessors;
464		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
465		int nGlobalMols = info->getNGlobalMolecules();
466		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
467
468		MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
469	<
469	>
470		if (nProcessors > nGlobalMols) {
471	<	sprintf(painCave.errMsg,
472	<	"nProcessors (%d) > nMol (%d)\n"
473	<	"\tThe number of processors is larger than\n"
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);
478	<
479	<	painCave.isFatal = 1;
480	<	simError();
471	>	sprintf(painCave.errMsg,
472	>	"nProcessors (%d) > nMol (%d)\n"
473	>	"\tThe number of processors is larger than\n"
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 OpenMD.\n", nProcessors, nGlobalMols);
478	>
479	>	painCave.isFatal = 1;
480	>	simError();
481		}
482	<
482	>
483	>	int seedValue;
484	>	Globals * simParams = info->getSimParams();
485	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
486	>	if (simParams->haveSeed()) {
487	>	seedValue = simParams->getSeed();
488	>	myRandom = new SeqRandNumGen(seedValue);
489	>	}else {
490	>	myRandom = new SeqRandNumGen();
491	>	}
492	>
493	>
494		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
495	<
495	>
496		//initialize atomsPerProc
497		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
498	<
498	>
499		if (worldRank == 0) {
500	<	numerator = info->getNGlobalAtoms();
501	<	denominator = nProcessors;
502	<	precast = numerator / denominator;
503	<	nTarget = (int)(precast + 0.5);
504	<
505	<	for(i = 0; i < nGlobalMols; i++) {
506	<	done = 0;
507	<	loops = 0;
508	<
509	<	while (!done) {
510	<	loops++;
511	<
512	<	// Pick a processor at random
513	<
514	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
515	<
516	<	//get the molecule stamp first
517	<	int stampId = info->getMoleculeStampId(i);
518	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
519	<
520	<	// How many atoms does this processor have so far?
521	<	old_atoms = atomsPerProc[which_proc];
522	<	add_atoms = moleculeStamp->getNAtoms();
523	<	new_atoms = old_atoms + add_atoms;
524	<
525	<	// If we've been through this loop too many times, we need
526	<	// to just give up and assign the molecule to this processor
527	<	// and be done with it.
528	<
529	<	if (loops > 100) {
530	<	sprintf(painCave.errMsg,
531	<	"I've tried 100 times to assign molecule %d to a "
532	<	" processor, but can't find a good spot.\n"
533	<	"I'm assigning it at random to processor %d.\n",
534	<	i, which_proc);
535	<
536	<	painCave.isFatal = 0;
537	<	simError();
538	<
539	<	molToProcMap[i] = which_proc;
540	<	atomsPerProc[which_proc] += add_atoms;
541	<
542	<	done = 1;
543	<	continue;
544	<	}
545	<
546	<	// If we can add this molecule to this processor without sending
547	<	// it above nTarget, then go ahead and do it:
548	<
549	<	if (new_atoms <= nTarget) {
550	<	molToProcMap[i] = which_proc;
551	<	atomsPerProc[which_proc] += add_atoms;
552	<
553	<	done = 1;
554	<	continue;
555	<	}
556	<
557	<	// The only situation left is when new_atoms > nTarget.  We
558	<	// want to accept this with some probability that dies off the
559	<	// farther we are from nTarget
560	<
561	<	// roughly:  x = new_atoms - nTarget
562	<	//           Pacc(x) = exp(- a * x)
563	<	// where a = penalty / (average atoms per molecule)
564	<
565	<	x = (double)(new_atoms - nTarget);
566	<	y = myRandom.getRandom();
567	<
568	<	if (y < exp(- a * x)) {
569	<	molToProcMap[i] = which_proc;
570	<	atomsPerProc[which_proc] += add_atoms;
571	<
572	<	done = 1;
573	<	continue;
574	<	} else {
575	<	continue;
576	<	}
392	<	}
500	>	numerator = info->getNGlobalAtoms();
501	>	denominator = nProcessors;
502	>	precast = numerator / denominator;
503	>	nTarget = (int)(precast + 0.5);
504	>
505	>	for(i = 0; i < nGlobalMols; i++) {
506	>	done = 0;
507	>	loops = 0;
508	>
509	>	while (!done) {
510	>	loops++;
511	>
512	>	// Pick a processor at random
513	>
514	>	which_proc = (int) (myRandom->rand() * nProcessors);
515	>
516	>	//get the molecule stamp first
517	>	int stampId = info->getMoleculeStampId(i);
518	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
519	>
520	>	// How many atoms does this processor have so far?
521	>	old_atoms = atomsPerProc[which_proc];
522	>	add_atoms = moleculeStamp->getNAtoms();
523	>	new_atoms = old_atoms + add_atoms;
524	>
525	>	// If we've been through this loop too many times, we need
526	>	// to just give up and assign the molecule to this processor
527	>	// and be done with it.
528	>
529	>	if (loops > 100) {
530	>	sprintf(painCave.errMsg,
531	>	"I've tried 100 times to assign molecule %d to a "
532	>	" processor, but can't find a good spot.\n"
533	>	"I'm assigning it at random to processor %d.\n",
534	>	i, which_proc);
535	>
536	>	painCave.isFatal = 0;
537	>	simError();
538	>
539	>	molToProcMap[i] = which_proc;
540	>	atomsPerProc[which_proc] += add_atoms;
541	>
542	>	done = 1;
543	>	continue;
544	>	}
545	>
546	>	// If we can add this molecule to this processor without sending
547	>	// it above nTarget, then go ahead and do it:
548	>
549	>	if (new_atoms <= nTarget) {
550	>	molToProcMap[i] = which_proc;
551	>	atomsPerProc[which_proc] += add_atoms;
552	>
553	>	done = 1;
554	>	continue;
555	>	}
556	>
557	>	// The only situation left is when new_atoms > nTarget.  We
558	>	// want to accept this with some probability that dies off the
559	>	// farther we are from nTarget
560	>
561	>	// roughly:  x = new_atoms - nTarget
562	>	//           Pacc(x) = exp(- a * x)
563	>	// where a = penalty / (average atoms per molecule)
564	>
565	>	x = (RealType)(new_atoms - nTarget);
566	>	y = myRandom->rand();
567	>
568	>	if (y < exp(- a * x)) {
569	>	molToProcMap[i] = which_proc;
570	>	atomsPerProc[which_proc] += add_atoms;
571	>
572	>	done = 1;
573	>	continue;
574	>	} else {
575	>	continue;
576	>	}
577		}
578	<
579	<	// Spray out this nonsense to all other processors:
580	<
581	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
578	>	}
579	>
580	>	delete myRandom;
581	>
582	>	// Spray out this nonsense to all other processors:
583	>
584	>	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
585		} else {
586	<
587	<	// Listen to your marching orders from processor 0:
588	<
589	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
586	>
587	>	// Listen to your marching orders from processor 0:
588	>
589	>	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
590		}
591	<
591	>
592		info->setMolToProcMap(molToProcMap);
593		sprintf(checkPointMsg,
594		"Successfully divided the molecules among the processors.\n");
595	<	MPIcheckPoint();
596	<	}
597	<
595	>	errorCheckPoint();
596	>	}
597	>
598		#endif
599	<
600	<	void SimCreator::createMolecules(SimInfo *info) {
599	>
600	>	void SimCreator::createMolecules(SimInfo *info) {
601		MoleculeCreator molCreator;
602		int stampId;
603	<
603	>
604		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
605	<
605	>
606		#ifdef IS_MPI
607	<
608	<	if (info->getMolToProc(i) == worldRank) {
607	>
608	>	if (info->getMolToProc(i) == worldRank) {
609		#endif
610	<
611	<	stampId = info->getMoleculeStampId(i);
612	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
613	<	stampId, i, info->getLocalIndexManager());
614	<
615	<	info->addMolecule(mol);
616	<
610	>
611	>	stampId = info->getMoleculeStampId(i);
612	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
613	>	info->getMoleculeStamp(stampId),
614	>	stampId, i,
615	>	info->getLocalIndexManager());
616	>
617	>	info->addMolecule(mol);
618	>
619		#ifdef IS_MPI
620	<
621	<	}
622	<
620	>
621	>	}
622	>
623		#endif
624	<
624	>
625		} //end for(int i=0)
626	<	}
627	<
628	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
440	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
441	<	int i;
442	<	char * id;
443	<	MoleculeStamp * currentStamp;
444	<	Component** the_components = simParams->getComponents();
445	<	int n_components = simParams->getNComponents();
446	<
447	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
450	<
451	<	for(i = 0; i < n_components; i++) {
452	<	if (!the_components[i]->haveNMol()) {
453	<	// we have a problem
454	<	sprintf(painCave.errMsg,
455	<	"SimCreator Error. No global NMol or component NMol given.\n"
456	<	"\tCannot calculate the number of atoms.\n");
457	<
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<
462	<	id = the_components[i]->getType();
463	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
464	<
465	<	if (currentStamp == NULL) {
466	<	sprintf(painCave.errMsg,
467	<	"SimCreator error: Component \"%s\" was not found in the "
468	<	"list of declared molecules\n", id);
469	<
470	<	painCave.isFatal = 1;
471	<	simError();
472	<	}
473	<
474	<	moleculeStampPairs.push_back(
475	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
476	<	} //end for (i = 0; i < n_components; i++)
477	<	} else {
478	<	sprintf(painCave.errMsg, "SimSetup error.\n"
479	<	"\tSorry, the ability to specify total"
480	<	" nMols and then give molfractions in the components\n"
481	<	"\tis not currently supported."
482	<	" Please give nMol in the components.\n");
483	<
484	<	painCave.isFatal = 1;
485	<	simError();
486	<	}
487	<
488	<	#ifdef IS_MPI
489	<
490	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
491	<	MPIcheckPoint();
492	<
493	<	#endif // is_mpi
494	<
495	<	}
496	<
497	<	void SimCreator::setGlobalIndex(SimInfo *info) {
626	>	}
627	>
628	>	void SimCreator::setGlobalIndex(SimInfo *info) {
629		SimInfo::MoleculeIterator mi;
630		Molecule::AtomIterator ai;
631		Molecule::RigidBodyIterator ri;
632		Molecule::CutoffGroupIterator ci;
633	+	Molecule::IntegrableObjectIterator  ioi;
634		Molecule * mol;
635		Atom * atom;
636		RigidBody * rb;
#	Line 508 | Line 640 | void SimCreator::setGlobalIndex(SimInfo *info) {
640		int beginCutoffGroupIndex;
641		int nGlobalAtoms = info->getNGlobalAtoms();
642
511	–	#ifndef IS_MPI
512	–
643		beginAtomIndex = 0;
644		beginRigidBodyIndex = 0;
645		beginCutoffGroupIndex = 0;
646
647	<	#else
647	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
648	>
649	>	#ifdef IS_MPI
650	>	if (info->getMolToProc(i) == worldRank) {
651	>	#endif
652	>	// stuff to do if I own this molecule
653	>	mol = info->getMoleculeByGlobalIndex(i);
654
519	–	int nproc;
520	–	int myNode;
521	–
522	–	myNode = worldRank;
523	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524	–
525	–	std::vector < int > tmpAtomsInProc(nproc, 0);
526	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528	–	std::vector < int > NumAtomsInProc(nproc, 0);
529	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
530	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531	–
532	–	tmpAtomsInProc[myNode] = info->getNAtoms();
533	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535	–
536	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538	–	MPI_SUM, MPI_COMM_WORLD);
539	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543	–
544	–	beginAtomIndex = 0;
545	–	beginRigidBodyIndex = 0;
546	–	beginCutoffGroupIndex = 0;
547	–
548	–	for(int i = 0; i < myNode; i++) {
549	–	beginAtomIndex += NumAtomsInProc[i];
550	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
551	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552	–	}
553	–
554	–	#endif
555	–
556	–	for(mol = info->beginMolecule(mi); mol != NULL;
557	–	mol = info->nextMolecule(mi)) {
558	–
655		//local index(index in DataStorge) of atom is important
656		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
657	<	atom->setGlobalIndex(beginAtomIndex++);
657	>	atom->setGlobalIndex(beginAtomIndex++);
658		}
659	<
659	>
660		for(rb = mol->beginRigidBody(ri); rb != NULL;
661		rb = mol->nextRigidBody(ri)) {
662	<	rb->setGlobalIndex(beginRigidBodyIndex++);
662	>	rb->setGlobalIndex(beginRigidBodyIndex++);
663		}
664	<
665	<	//local index of cutoff group is trivial, it only depends on the order of travesing
664	>
665	>	//local index of cutoff group is trivial, it only depends on
666	>	//the order of travesing
667		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
668		cg = mol->nextCutoffGroup(ci)) {
669	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
670	<	}
671	<	}
669	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
670	>	}
671	>
672	>	#ifdef IS_MPI
673	>	}  else {
674
675	+	// stuff to do if I don't own this molecule
676	+
677	+	int stampId = info->getMoleculeStampId(i);
678	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
679	+
680	+	beginAtomIndex += stamp->getNAtoms();
681	+	beginRigidBodyIndex += stamp->getNRigidBodies();
682	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
683	+	}
684	+	#endif
685	+
686	+	} //end for(int i=0)
687	+
688		//fill globalGroupMembership
689		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
690		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
691	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
692	<
693	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
694	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
695	<	}
696	<
697	<	}
691	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
692	>
693	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
694	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
695	>	}
696	>
697	>	}
698		}
699	<
699	>
700		#ifdef IS_MPI
701		// Since the globalGroupMembership has been zero filled and we've only
702		// poked values into the atoms we know, we can do an Allreduce
703		// to get the full globalGroupMembership array (We think).
704		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
705		// docs said we could.
706	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
706	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
707		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
708		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
709	<	info->setGlobalGroupMembership(tmpGroupMembership);
709	>	info->setGlobalGroupMembership(tmpGroupMembership);
710		#else
711		info->setGlobalGroupMembership(globalGroupMembership);
712		#endif
713	<
713	>
714		//fill molMembership
715		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
716
717		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
718	<
719	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
720	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
609	<	}
718	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
720	>	}
721		}
722	<
722	>
723		#ifdef IS_MPI
724	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
725	<
724	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
725	>
726		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
727		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
728
#	Line 620 | Line 731 | void SimCreator::setGlobalIndex(SimInfo *info) {
731		info->setGlobalMolMembership(globalMolMembership);
732		#endif
733
734	<	}
734	>	// nIOPerMol holds the number of integrable objects per molecule
735	>	// here the molecules are listed by their global indices.
736
737	<	void SimCreator::loadCoordinates(SimInfo* info) {
737	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
738	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
739	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
740	>	}
741	>
742	>	#ifdef IS_MPI
743	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
744	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
745	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
746	>	#else
747	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
748	>	#endif
749	>
750	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
751	>
752	>	int startingIndex = 0;
753	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
754	>	startingIOIndexForMol[i] = startingIndex;
755	>	startingIndex += numIntegrableObjectsPerMol[i];
756	>	}
757	>
758	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
759	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
760	>	int myGlobalIndex = mol->getGlobalIndex();
761	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
762	>	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
763	>	integrableObject = mol->nextIntegrableObject(ioi)) {
764	>	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
765	>	IOIndexToIntegrableObject[globalIO] = integrableObject;
766	>	globalIO++;
767	>	}
768	>	}
769	>
770	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
771	>
772	>	}
773	>
774	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
775		Globals* simParams;
776	+
777		simParams = info->getSimParams();
778
779	<	if (!simParams->haveInitialConfig()) {
630	<	sprintf(painCave.errMsg,
631	<	"Cannot intialize a simulation without an initial configuration file.\n");
632	<	painCave.isFatal = 1;;
633	<	simError();
634	<	}
635	<
636	<	DumpReader reader(info, simParams->getInitialConfig());
779	>	DumpReader reader(info, mdFileName);
780		int nframes = reader.getNFrames();
781
782		if (nframes > 0) {
783	<	reader.readFrame(nframes - 1);
783	>	reader.readFrame(nframes - 1);
784		} else {
785	<	//invalid initial coordinate file
786	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
787	<	simParams->getInitialConfig());
788	<	painCave.isFatal = 1;
789	<	simError();
785	>	//invalid initial coordinate file
786	>	sprintf(painCave.errMsg,
787	>	"Initial configuration file %s should at least contain one frame\n",
788	>	mdFileName.c_str());
789	>	painCave.isFatal = 1;
790	>	simError();
791		}
648	–
792		//copy the current snapshot to previous snapshot
793		info->getSnapshotManager()->advance();
794	<	}
794	>	}
795	>
796	>	} //end namespace OpenMD
797
653	–	} //end namespace oopse
798
655	–

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

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