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root/OpenMD/trunk/src/brains/SimCreator.cpp

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 823 by chuckv, Thu Dec 29 16:03:11 2005 UTC vs.
Revision 1802 by gezelter, Wed Oct 3 14:07:28 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 46 | Line 47
47		* @time 13:51am
48		* @version 1.0
49		*/
50	<
50	>	#include <exception>
51		#include <iostream>
52		#include <sstream>
53		#include <string>
#	Line 55 | Line 56
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
59	<	#include "UseTheForce/ForceFieldFactory.hpp"
59	>	#include "brains/ForceField.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 76
76		#include "antlr/NoViableAltForCharException.hpp"
77		#include "antlr/NoViableAltException.hpp"
78
79	+	#include "types/DirectionalAdapter.hpp"
80	+	#include "types/MultipoleAdapter.hpp"
81	+	#include "types/EAMAdapter.hpp"
82	+	#include "types/SuttonChenAdapter.hpp"
83	+	#include "types/PolarizableAdapter.hpp"
84	+	#include "types/FixedChargeAdapter.hpp"
85	+	#include "types/FluctuatingChargeAdapter.hpp"
86	+
87		#ifdef IS_MPI
88	+	#include "mpi.h"
89		#include "math/ParallelRandNumGen.hpp"
90		#endif
91
92	<	namespace oopse {
92	>	namespace OpenMD {
93
94	<	Globals* SimCreator::parseFile(const std::string mdFileName){
95	<	Globals* simParams = NULL;
96	<	try {
94	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95	>	Globals* simParams = NULL;
96	>	try {
97
98	<	// Create a preprocessor that preprocesses md file into an ostringstream
99	<	std::stringstream ppStream;
98	>	// Create a preprocessor that preprocesses md file into an ostringstream
99	>	std::stringstream ppStream;
100		#ifdef IS_MPI
101	<	int streamSize;
102	<	const int masterNode = 0;
103	<	int commStatus;
104	<	if (worldRank == masterNode) {
105	<	#endif
101	>	int streamSize;
102	>	const int masterNode = 0;
103	>
104	>	if (worldRank == masterNode) {
105	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
106	>	#endif
107	>	SimplePreprocessor preprocessor;
108	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock,
109	>	ppStream);
110
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
111		#ifdef IS_MPI
112	<	//brocasting the stream size
113	<	streamSize = ppStream.str().size() +1;
114	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
112	>	//brocasting the stream size
113	>	streamSize = ppStream.str().size() +1;
114	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
115	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
116	>	streamSize, MPI::CHAR, masterNode);
117	>
118	>	} else {
119
120	<	commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
121	<
120	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
121	>
122	>	//get stream size
123	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
124	>
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127
128	<	} else {
129	<	//get stream size
110	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
128	>	//receive file content
129	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
130
131	<	char* buf = new char[streamSize];
132	<	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;
131	>	ppStream.str(buf);
132	>	delete [] buf;
133
134	<	}
134	>	}
135		#endif
136	<	// Create a scanner that reads from the input stream
137	<	MDLexer lexer(ppStream);
138	<	lexer.setFilename(mdFileName);
139	<	lexer.initDeferredLineCount();
136	>	// Create a scanner that reads from the input stream
137	>	MDLexer lexer(ppStream);
138	>	lexer.setFilename(filename);
139	>	lexer.initDeferredLineCount();
140
141	<	// Create a parser that reads from the scanner
142	<	MDParser parser(lexer);
143	<	parser.setFilename(mdFileName);
141	>	// Create a parser that reads from the scanner
142	>	MDParser parser(lexer);
143	>	parser.setFilename(filename);
144
145	<	// Create an observer that synchorizes file name change
146	<	FilenameObserver observer;
147	<	observer.setLexer(&lexer);
148	<	observer.setParser(&parser);
149	<	lexer.setObserver(&observer);
145	>	// Create an observer that synchorizes file name change
146	>	FilenameObserver observer;
147	>	observer.setLexer(&lexer);
148	>	observer.setParser(&parser);
149	>	lexer.setObserver(&observer);
150
151	<	antlr::ASTFactory factory;
152	<	parser.initializeASTFactory(factory);
153	<	parser.setASTFactory(&factory);
154	<	parser.mdfile();
151	>	antlr::ASTFactory factory;
152	>	parser.initializeASTFactory(factory);
153	>	parser.setASTFactory(&factory);
154	>	parser.mdfile();
155
156	<	// Create a tree parser that reads information into Globals
157	<	MDTreeParser treeParser;
158	<	treeParser.initializeASTFactory(factory);
159	<	treeParser.setASTFactory(&factory);
160	<	simParams = treeParser.walkTree(parser.getAST());
156	>	// Create a tree parser that reads information into Globals
157	>	MDTreeParser treeParser;
158	>	treeParser.initializeASTFactory(factory);
159	>	treeParser.setASTFactory(&factory);
160	>	simParams = treeParser.walkTree(parser.getAST());
161	>	}
162
149	–	}
163
164	<	catch(antlr::MismatchedCharException& e) {
165	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
166	<	}
167	<	catch(antlr::MismatchedTokenException &e) {
168	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
169	<	}
170	<	catch(antlr::NoViableAltForCharException &e) {
171	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
172	<	}
173	<	catch(antlr::NoViableAltException &e) {
174	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
175	<	}
176	<	catch(antlr::TokenStreamRecognitionException& e) {
177	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
178	<	}
179	<	catch(antlr::TokenStreamIOException& e) {
180	<	cerr<< "parser exception: " << e.getMessage() << endl;
181	<	}
182	<	catch(antlr::TokenStreamException& e) {
183	<	cerr<< "parser exception: " << e.getMessage() << endl;
184	<	}
185	<	catch (antlr::RecognitionException& e) {
186	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
187	<	}
188	<	catch (antlr::CharStreamException& e) {
189	<	cerr << "parser exception: " << e.getMessage() << endl;
190	<	}
191	<	catch (exception& e) {
192	<	cerr << "parser exception: " << e.what() << endl;
193	<	}
164	>	catch(antlr::MismatchedCharException& e) {
165	>	sprintf(painCave.errMsg,
166	>	"parser exception: %s %s:%d:%d\n",
167	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
168	>	painCave.isFatal = 1;
169	>	simError();
170	>	}
171	>	catch(antlr::MismatchedTokenException &e) {
172	>	sprintf(painCave.errMsg,
173	>	"parser exception: %s %s:%d:%d\n",
174	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	catch(antlr::NoViableAltForCharException &e) {
179	>	sprintf(painCave.errMsg,
180	>	"parser exception: %s %s:%d:%d\n",
181	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
185	>	catch(antlr::NoViableAltException &e) {
186	>	sprintf(painCave.errMsg,
187	>	"parser exception: %s %s:%d:%d\n",
188	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
189	>	painCave.isFatal = 1;
190	>	simError();
191	>	}
192	>
193	>	catch(antlr::TokenStreamRecognitionException& e) {
194	>	sprintf(painCave.errMsg,
195	>	"parser exception: %s %s:%d:%d\n",
196	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
197	>	painCave.isFatal = 1;
198	>	simError();
199	>	}
200	>
201	>	catch(antlr::TokenStreamIOException& e) {
202	>	sprintf(painCave.errMsg,
203	>	"parser exception: %s\n",
204	>	e.getMessage().c_str());
205	>	painCave.isFatal = 1;
206	>	simError();
207	>	}
208	>
209	>	catch(antlr::TokenStreamException& e) {
210	>	sprintf(painCave.errMsg,
211	>	"parser exception: %s\n",
212	>	e.getMessage().c_str());
213	>	painCave.isFatal = 1;
214	>	simError();
215	>	}
216	>	catch (antlr::RecognitionException& e) {
217	>	sprintf(painCave.errMsg,
218	>	"parser exception: %s %s:%d:%d\n",
219	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
220	>	painCave.isFatal = 1;
221	>	simError();
222	>	}
223	>	catch (antlr::CharStreamException& e) {
224	>	sprintf(painCave.errMsg,
225	>	"parser exception: %s\n",
226	>	e.getMessage().c_str());
227	>	painCave.isFatal = 1;
228	>	simError();
229	>	}
230	>	catch (OpenMDException& e) {
231	>	sprintf(painCave.errMsg,
232	>	"%s\n",
233	>	e.getMessage().c_str());
234	>	painCave.isFatal = 1;
235	>	simError();
236	>	}
237	>	catch (std::exception& e) {
238	>	sprintf(painCave.errMsg,
239	>	"parser exception: %s\n",
240	>	e.what());
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244
245	<	return simParams;
245	>	simParams->setMDfileVersion(mdFileVersion);
246	>	return simParams;
247		}
248
249		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250		bool loadInitCoords) {
251	+
252	+	const int bufferSize = 65535;
253	+	char buffer[bufferSize];
254	+	int lineNo = 0;
255	+	std::string mdRawData;
256	+	int metaDataBlockStart = -1;
257	+	int metaDataBlockEnd = -1;
258	+	int i;
259	+	streamoff mdOffset(0);
260	+	int mdFileVersion;
261
262	+
263	+	#ifdef IS_MPI
264	+	const int masterNode = 0;
265	+	if (worldRank == masterNode) {
266	+	#endif
267	+
268	+	std::ifstream mdFile_;
269	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
270	+
271	+	if (mdFile_.fail()) {
272	+	sprintf(painCave.errMsg,
273	+	"SimCreator: Cannot open file: %s\n",
274	+	mdFileName.c_str());
275	+	painCave.isFatal = 1;
276	+	simError();
277	+	}
278	+
279	+	mdFile_.getline(buffer, bufferSize);
280	+	++lineNo;
281	+	std::string line = trimLeftCopy(buffer);
282	+	i = CaseInsensitiveFind(line, "<OpenMD");
283	+	if (static_cast<size_t>(i) == string::npos) {
284	+	// try the older file strings to see if that works:
285	+	i = CaseInsensitiveFind(line, "<OOPSE");
286	+	}
287	+
288	+	if (static_cast<size_t>(i) == string::npos) {
289	+	// still no luck!
290	+	sprintf(painCave.errMsg,
291	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
292	+	mdFileName.c_str());
293	+	painCave.isFatal = 1;
294	+	simError();
295	+	}
296	+
297	+	// found the correct opening string, now try to get the file
298	+	// format version number.
299	+
300	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
301	+	std::string fileType = tokenizer.nextToken();
302	+	toUpper(fileType);
303	+
304	+	mdFileVersion = 0;
305	+
306	+	if (fileType == "OPENMD") {
307	+	while (tokenizer.hasMoreTokens()) {
308	+	std::string token(tokenizer.nextToken());
309	+	toUpper(token);
310	+	if (token == "VERSION") {
311	+	mdFileVersion = tokenizer.nextTokenAsInt();
312	+	break;
313	+	}
314	+	}
315	+	}
316	+
317	+	//scan through the input stream and find MetaData tag
318	+	while(mdFile_.getline(buffer, bufferSize)) {
319	+	++lineNo;
320	+
321	+	std::string line = trimLeftCopy(buffer);
322	+	if (metaDataBlockStart == -1) {
323	+	i = CaseInsensitiveFind(line, "<MetaData>");
324	+	if (i != string::npos) {
325	+	metaDataBlockStart = lineNo;
326	+	mdOffset = mdFile_.tellg();
327	+	}
328	+	} else {
329	+	i = CaseInsensitiveFind(line, "</MetaData>");
330	+	if (i != string::npos) {
331	+	metaDataBlockEnd = lineNo;
332	+	}
333	+	}
334	+	}
335	+
336	+	if (metaDataBlockStart == -1) {
337	+	sprintf(painCave.errMsg,
338	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
339	+	mdFileName.c_str());
340	+	painCave.isFatal = 1;
341	+	simError();
342	+	}
343	+	if (metaDataBlockEnd == -1) {
344	+	sprintf(painCave.errMsg,
345	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
346	+	mdFileName.c_str());
347	+	painCave.isFatal = 1;
348	+	simError();
349	+	}
350	+
351	+	mdFile_.clear();
352	+	mdFile_.seekg(0);
353	+	mdFile_.seekg(mdOffset);
354	+
355	+	mdRawData.clear();
356	+
357	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
358	+	mdFile_.getline(buffer, bufferSize);
359	+	mdRawData += buffer;
360	+	mdRawData += "\n";
361	+	}
362	+
363	+	mdFile_.close();
364	+
365	+	#ifdef IS_MPI
366	+	}
367	+	#endif
368	+
369	+	std::stringstream rawMetaDataStream(mdRawData);
370	+
371		//parse meta-data file
372	<	Globals* simParams = parseFile(mdFileName);
372	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373	>	metaDataBlockStart + 1);
374
375		//create the force field
376	<	ForceField * ff = ForceFieldFactory::getInstance()
377	<	->createForceField(simParams->getForceField());
194	<
376	>	ForceField * ff = new ForceField(simParams->getForceField());
377	>
378		if (ff == NULL) {
379		sprintf(painCave.errMsg,
380		"ForceField Factory can not create %s force field\n",
#	Line 224 | Line 407 | Globals* SimCreator::parseFile(const std::string mdFil
407		}
408
409		ff->parse(forcefieldFileName);
227	–	ff->setFortranForceOptions();
410		//create SimInfo
411		SimInfo * info = new SimInfo(ff, simParams);
412	+
413	+	info->setRawMetaData(mdRawData);
414
415	<	//gather parameters (SimCreator only retrieves part of the parameters)
415	>	//gather parameters (SimCreator only retrieves part of the
416	>	//parameters)
417		gatherParameters(info, mdFileName);
418
419		//divide the molecules and determine the global index of molecules
#	Line 239 | Line 424 | Globals* SimCreator::parseFile(const std::string mdFil
424		//create the molecules
425		createMolecules(info);
426
427	<
428	<	//allocate memory for DataStorage(circular reference, need to break it)
429	<	info->setSnapshotManager(new SimSnapshotManager(info));
427	>	//find the storage layout
428	>
429	>	int storageLayout = computeStorageLayout(info);
430	>
431	>	//allocate memory for DataStorage(circular reference, need to
432	>	//break it)
433	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
436	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
437	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
435	>	//set the global index of atoms, rigidbodies and cutoffgroups
436	>	//(only need to be set once, the global index will never change
437	>	//again). Local indices of atoms and rigidbodies are already set
438	>	//by MoleculeCreator class which actually delegates the
439	>	//responsibility to LocalIndexManager.
440		setGlobalIndex(info);
441
442	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
443	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
444	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
445	<	//we can determine the beginning global indices of atoms before they get created.
442	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
443	>	//method, at that point atoms don't have the global index yet
444	>	//(their global index are all initialized to -1).  Therefore we
445	>	//have to call addInteractionPairs explicitly here. A way to work
446	>	//around is that we can determine the beginning global indices of
447	>	//atoms before they get created.
448		SimInfo::MoleculeIterator mi;
449		Molecule* mol;
450		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
451	<	info->addExcludePairs(mol);
451	>	info->addInteractionPairs(mol);
452		}
453
454		if (loadInitCoords)
455	<	loadCoordinates(info);
263	<
455	>	loadCoordinates(info, mdFileName);
456		return info;
457		}
458
#	Line 295 | Line 487 | Globals* SimCreator::parseFile(const std::string mdFil
487
488		#ifdef IS_MPI
489		void SimCreator::divideMolecules(SimInfo *info) {
490	<	double numerator;
491	<	double denominator;
492	<	double precast;
493	<	double x;
494	<	double y;
495	<	double a;
490	>	RealType numerator;
491	>	RealType denominator;
492	>	RealType precast;
493	>	RealType x;
494	>	RealType y;
495	>	RealType a;
496		int old_atoms;
497		int add_atoms;
498		int new_atoms;
499		int nTarget;
500		int done;
501		int i;
310	–	int j;
502		int loops;
503		int which_proc;
504		int nProcessors;
#	Line 315 | Line 506 | Globals* SimCreator::parseFile(const std::string mdFil
506		int nGlobalMols = info->getNGlobalMolecules();
507		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
508
509	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
509	>	nProcessors = MPI::COMM_WORLD.Get_size();
510
511		if (nProcessors > nGlobalMols) {
512		sprintf(painCave.errMsg,
#	Line 324 | Line 515 | Globals* SimCreator::parseFile(const std::string mdFil
515		"\tthe number of molecules.  This will not result in a \n"
516		"\tusable division of atoms for force decomposition.\n"
517		"\tEither try a smaller number of processors, or run the\n"
518	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
518	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
519
520		painCave.isFatal = 1;
521		simError();
#	Line 353 | Line 544 | Globals* SimCreator::parseFile(const std::string mdFil
544		nTarget = (int)(precast + 0.5);
545
546		for(i = 0; i < nGlobalMols; i++) {
547	+
548		done = 0;
549		loops = 0;
550
#	Line 377 | Line 569 | Globals* SimCreator::parseFile(const std::string mdFil
569		// and be done with it.
570
571		if (loops > 100) {
572	+
573		sprintf(painCave.errMsg,
574	<	"I've tried 100 times to assign molecule %d to a "
575	<	" processor, but can't find a good spot.\n"
576	<	"I'm assigning it at random to processor %d.\n",
574	>	"There have been 100 attempts to assign molecule %d to an\n"
575	>	"\tunderworked processor, but there's no good place to\n"
576	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
577		i, which_proc);
578	<
578	>
579		painCave.isFatal = 0;
580	+	painCave.severity = OPENMD_INFO;
581		simError();
582
583		molToProcMap[i] = which_proc;
#	Line 412 | Line 606 | Globals* SimCreator::parseFile(const std::string mdFil
606		//           Pacc(x) = exp(- a * x)
607		// where a = penalty / (average atoms per molecule)
608
609	<	x = (double)(new_atoms - nTarget);
609	>	x = (RealType)(new_atoms - nTarget);
610		y = myRandom->rand();
611
612		if (y < exp(- a * x)) {
#	Line 428 | Line 622 | Globals* SimCreator::parseFile(const std::string mdFil
622		}
623
624		delete myRandom;
625	<
625	>
626		// Spray out this nonsense to all other processors:
627	<
434	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
627	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
628		} else {
629
630		// Listen to your marching orders from processor 0:
631	<
632	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
631	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
632	>
633		}
634
635		info->setMolToProcMap(molToProcMap);
636		sprintf(checkPointMsg,
637		"Successfully divided the molecules among the processors.\n");
638	<	MPIcheckPoint();
638	>	errorCheckPoint();
639		}
640
641		#endif
#	Line 459 | Line 652 | Globals* SimCreator::parseFile(const std::string mdFil
652		#endif
653
654		stampId = info->getMoleculeStampId(i);
655	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
656	<	stampId, i, info->getLocalIndexManager());
655	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
656	>	info->getMoleculeStamp(stampId),
657	>	stampId, i,
658	>	info->getLocalIndexManager());
659
660		info->addMolecule(mol);
661
#	Line 472 | Line 667 | Globals* SimCreator::parseFile(const std::string mdFil
667
668		} //end for(int i=0)
669		}
670	+
671	+	int SimCreator::computeStorageLayout(SimInfo* info) {
672	+
673	+	Globals* simParams = info->getSimParams();
674	+	int nRigidBodies = info->getNGlobalRigidBodies();
675	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
676	+	set<AtomType*>::iterator i;
677	+	bool hasDirectionalAtoms = false;
678	+	bool hasFixedCharge = false;
679	+	bool hasMultipoles = false;
680	+	bool hasPolarizable = false;
681	+	bool hasFluctuatingCharge = false;
682	+	bool hasMetallic = false;
683	+	int storageLayout = 0;
684	+	storageLayout |= DataStorage::dslPosition;
685	+	storageLayout |= DataStorage::dslVelocity;
686	+	storageLayout |= DataStorage::dslForce;
687	+
688	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
689	+
690	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
691	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
692	+	EAMAdapter ea = EAMAdapter( (*i) );
693	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
694	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
695	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
696	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
697	+
698	+	if (da.isDirectional()){
699	+	hasDirectionalAtoms = true;
700	+	}
701	+	if (ma.isMultipole()){
702	+	hasMultipoles = true;
703	+	}
704	+	if (ea.isEAM() || sca.isSuttonChen()){
705	+	hasMetallic = true;
706	+	}
707	+	if ( fca.isFixedCharge() ){
708	+	hasFixedCharge = true;
709	+	}
710	+	if ( fqa.isFluctuatingCharge() ){
711	+	hasFluctuatingCharge = true;
712	+	}
713	+	if ( pa.isPolarizable() ){
714	+	hasPolarizable = true;
715	+	}
716	+	}
717
718	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
719	+	storageLayout |= DataStorage::dslAmat;
720	+	if(storageLayout & DataStorage::dslVelocity) {
721	+	storageLayout |= DataStorage::dslAngularMomentum;
722	+	}
723	+	if (storageLayout & DataStorage::dslForce) {
724	+	storageLayout |= DataStorage::dslTorque;
725	+	}
726	+	}
727	+	if (hasMultipoles) {
728	+	storageLayout |= DataStorage::dslElectroFrame;
729	+	}
730	+	if (hasFixedCharge || hasFluctuatingCharge) {
731	+	storageLayout |= DataStorage::dslSkippedCharge;
732	+	}
733	+	if (hasMetallic) {
734	+	storageLayout |= DataStorage::dslDensity;
735	+	storageLayout |= DataStorage::dslFunctional;
736	+	storageLayout |= DataStorage::dslFunctionalDerivative;
737	+	}
738	+	if (hasPolarizable) {
739	+	storageLayout |= DataStorage::dslElectricField;
740	+	}
741	+	if (hasFluctuatingCharge){
742	+	storageLayout |= DataStorage::dslFlucQPosition;
743	+	if(storageLayout & DataStorage::dslVelocity) {
744	+	storageLayout |= DataStorage::dslFlucQVelocity;
745	+	}
746	+	if (storageLayout & DataStorage::dslForce) {
747	+	storageLayout |= DataStorage::dslFlucQForce;
748	+	}
749	+	}
750	+
751	+	// if the user has asked for them, make sure we've got the memory for the
752	+	// objects defined.
753	+
754	+	if (simParams->getOutputParticlePotential()) {
755	+	storageLayout |= DataStorage::dslParticlePot;
756	+	}
757	+
758	+	if (simParams->havePrintHeatFlux()) {
759	+	if (simParams->getPrintHeatFlux()) {
760	+	storageLayout |= DataStorage::dslParticlePot;
761	+	}
762	+	}
763	+
764	+	if (simParams->getOutputElectricField()) {
765	+	storageLayout |= DataStorage::dslElectricField;
766	+	}
767	+	if (simParams->getOutputFluctuatingCharges()) {
768	+	storageLayout |= DataStorage::dslFlucQPosition;
769	+	storageLayout |= DataStorage::dslFlucQVelocity;
770	+	storageLayout |= DataStorage::dslFlucQForce;
771	+	}
772	+
773	+	return storageLayout;
774	+	}
775	+
776		void SimCreator::setGlobalIndex(SimInfo *info) {
777		SimInfo::MoleculeIterator mi;
778		Molecule::AtomIterator ai;
779		Molecule::RigidBodyIterator ri;
780		Molecule::CutoffGroupIterator ci;
781	+	Molecule::IntegrableObjectIterator  ioi;
782		Molecule * mol;
783		Atom * atom;
784		RigidBody * rb;
#	Line 486 | Line 787 | Globals* SimCreator::parseFile(const std::string mdFil
787		int beginRigidBodyIndex;
788		int beginCutoffGroupIndex;
789		int nGlobalAtoms = info->getNGlobalAtoms();
790	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
791
490	–	#ifndef IS_MPI
491	–
792		beginAtomIndex = 0;
793	<	beginRigidBodyIndex = 0;
793	>	//rigidbody's index begins right after atom's
794	>	beginRigidBodyIndex = info->getNGlobalAtoms();
795		beginCutoffGroupIndex = 0;
796	<
797	<	#else
497	<
498	<	int nproc;
499	<	int myNode;
500	<
501	<	myNode = worldRank;
502	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
503	<
504	<	std::vector < int > tmpAtomsInProc(nproc, 0);
505	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
506	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
507	<	std::vector < int > NumAtomsInProc(nproc, 0);
508	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
509	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
510	<
511	<	tmpAtomsInProc[myNode] = info->getNAtoms();
512	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
513	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
514	<
515	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
516	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
517	<	MPI_SUM, MPI_COMM_WORLD);
518	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
519	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
520	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
521	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
522	<
523	<	beginAtomIndex = 0;
524	<	beginRigidBodyIndex = 0;
525	<	beginCutoffGroupIndex = 0;
526	<
527	<	for(int i = 0; i < myNode; i++) {
528	<	beginAtomIndex += NumAtomsInProc[i];
529	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
530	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
531	<	}
532	<
533	<	#endif
534	<
535	<	//rigidbody's index begins right after atom's
536	<	beginRigidBodyIndex += info->getNGlobalAtoms();
537	<
538	<	for(mol = info->beginMolecule(mi); mol != NULL;
539	<	mol = info->nextMolecule(mi)) {
796	>
797	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
798
799	<	//local index(index in DataStorge) of atom is important
800	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
801	<	atom->setGlobalIndex(beginAtomIndex++);
799	>	#ifdef IS_MPI
800	>	if (info->getMolToProc(i) == worldRank) {
801	>	#endif
802	>	// stuff to do if I own this molecule
803	>	mol = info->getMoleculeByGlobalIndex(i);
804	>
805	>	//local index(index in DataStorge) of atom is important
806	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
807	>	atom->setGlobalIndex(beginAtomIndex++);
808	>	}
809	>
810	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
811	>	rb = mol->nextRigidBody(ri)) {
812	>	rb->setGlobalIndex(beginRigidBodyIndex++);
813	>	}
814	>
815	>	//local index of cutoff group is trivial, it only depends on
816	>	//the order of travesing
817	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
818	>	cg = mol->nextCutoffGroup(ci)) {
819	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
820	>	}
821	>
822	>	#ifdef IS_MPI
823	>	}  else {
824	>
825	>	// stuff to do if I don't own this molecule
826	>
827	>	int stampId = info->getMoleculeStampId(i);
828	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
829	>
830	>	beginAtomIndex += stamp->getNAtoms();
831	>	beginRigidBodyIndex += stamp->getNRigidBodies();
832	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
833		}
834	<
835	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
836	<	rb = mol->nextRigidBody(ri)) {
837	<	rb->setGlobalIndex(beginRigidBodyIndex++);
549	<	}
550	<
551	<	//local index of cutoff group is trivial, it only depends on the order of travesing
552	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
553	<	cg = mol->nextCutoffGroup(ci)) {
554	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
555	<	}
556	<	}
557	<
834	>	#endif
835	>
836	>	} //end for(int i=0)
837	>
838		//fill globalGroupMembership
839		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
840		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 566 | Line 846 | Globals* SimCreator::parseFile(const std::string mdFil
846
847		}
848		}
849	<
849	>
850		#ifdef IS_MPI
851		// Since the globalGroupMembership has been zero filled and we've only
852		// poked values into the atoms we know, we can do an Allreduce
853		// to get the full globalGroupMembership array (We think).
854		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
855		// docs said we could.
856	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
857	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
858	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
856	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
857	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
858	>	&tmpGroupMembership[0], nGlobalAtoms,
859	>	MPI::INT, MPI::SUM);
860		info->setGlobalGroupMembership(tmpGroupMembership);
861		#else
862		info->setGlobalGroupMembership(globalGroupMembership);
863		#endif
864
865		//fill molMembership
866	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
866	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
867	>	info->getNGlobalRigidBodies(), 0);
868
869	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
870	<
869	>	for(mol = info->beginMolecule(mi); mol != NULL;
870	>	mol = info->nextMolecule(mi)) {
871		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
872		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
873		}
874	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
875	+	rb = mol->nextRigidBody(ri)) {
876	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
877	+	}
878		}
879
880		#ifdef IS_MPI
881	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
881	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
882	>	info->getNGlobalRigidBodies(), 0);
883	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
884	>	nGlobalAtoms + nGlobalRigidBodies,
885	>	MPI::INT, MPI::SUM);
886
597	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
598	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
599	–
887		info->setGlobalMolMembership(tmpMolMembership);
888		#else
889		info->setGlobalMolMembership(globalMolMembership);
890		#endif
891	+
892	+	// nIOPerMol holds the number of integrable objects per molecule
893	+	// here the molecules are listed by their global indices.
894	+
895	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
896	+	for (mol = info->beginMolecule(mi); mol != NULL;
897	+	mol = info->nextMolecule(mi)) {
898	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
899	+	}
900
901	<	}
902	<
903	<	void SimCreator::loadCoordinates(SimInfo* info) {
904	<	Globals* simParams;
905	<	simParams = info->getSimParams();
901	>	#ifdef IS_MPI
902	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
903	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
904	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
905	>	#else
906	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
907	>	#endif
908	>
909	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
910
911	<	if (!simParams->haveInitialConfig()) {
912	<	sprintf(painCave.errMsg,
913	<	"Cannot intialize a simulation without an initial configuration file.\n");
914	<	painCave.isFatal = 1;;
615	<	simError();
911	>	int startingIndex = 0;
912	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
913	>	startingIOIndexForMol[i] = startingIndex;
914	>	startingIndex += numIntegrableObjectsPerMol[i];
915		}
916
917	<	DumpReader reader(info, simParams->getInitialConfig());
918	<	int nframes = reader.getNFrames();
917	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
918	>	for (mol = info->beginMolecule(mi); mol != NULL;
919	>	mol = info->nextMolecule(mi)) {
920	>	int myGlobalIndex = mol->getGlobalIndex();
921	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
922	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
923	>	sd = mol->nextIntegrableObject(ioi)) {
924	>	sd->setGlobalIntegrableObjectIndex(globalIO);
925	>	IOIndexToIntegrableObject[globalIO] = sd;
926	>	globalIO++;
927	>	}
928	>	}
929	>
930	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
931
932	+	}
933	+
934	+	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
935	+
936	+	DumpReader reader(info, mdFileName);
937	+	int nframes = reader.getNFrames();
938	+
939		if (nframes > 0) {
940		reader.readFrame(nframes - 1);
941		} else {
942		//invalid initial coordinate file
943		sprintf(painCave.errMsg,
944		"Initial configuration file %s should at least contain one frame\n",
945	<	simParams->getInitialConfig().c_str());
945	>	mdFileName.c_str());
946		painCave.isFatal = 1;
947		simError();
948		}
631	–
949		//copy the current snapshot to previous snapshot
950		info->getSnapshotManager()->advance();
951		}
952
953	<	} //end namespace oopse
953	>	} //end namespace OpenMD
954
955

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 823 by chuckv, Thu Dec 29 16:03:11 2005 UTC vs.
Revision 1802 by gezelter, Wed Oct 3 14:07:28 2012 UTC

#	Line 0 | Line 1
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