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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 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, 234107 (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		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include "mpi.h"
52	+	#include "math/ParallelRandNumGen.hpp"
53	+	#endif
54	+
55	+	#include <exception>
56		#include <iostream>
57		#include <sstream>
58		#include <string>
#	Line 55 | Line 61
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67		#include "math/SeqRandNumGen.hpp"
#	Line 63 | Line 69
69		#include "mdParser/MDParser.hpp"
70		#include "mdParser/MDTreeParser.hpp"
71		#include "mdParser/SimplePreprocessor.hpp"
72	+	#include "antlr/ANTLRException.hpp"
73	+	#include "antlr/TokenStreamRecognitionException.hpp"
74	+	#include "antlr/TokenStreamIOException.hpp"
75	+	#include "antlr/TokenStreamException.hpp"
76	+	#include "antlr/RecognitionException.hpp"
77	+	#include "antlr/CharStreamException.hpp"
78
79	+	#include "antlr/MismatchedCharException.hpp"
80	+	#include "antlr/MismatchedTokenException.hpp"
81	+	#include "antlr/NoViableAltForCharException.hpp"
82	+	#include "antlr/NoViableAltException.hpp"
83
84	<	#ifdef IS_MPI
85	<	#include "math/ParallelRandNumGen.hpp"
86	<	#endif
84	>	#include "types/DirectionalAdapter.hpp"
85	>	#include "types/MultipoleAdapter.hpp"
86	>	#include "types/EAMAdapter.hpp"
87	>	#include "types/SuttonChenAdapter.hpp"
88	>	#include "types/PolarizableAdapter.hpp"
89	>	#include "types/FixedChargeAdapter.hpp"
90	>	#include "types/FluctuatingChargeAdapter.hpp"
91
92	<	namespace oopse {
92	>
93	>	namespace OpenMD {
94
95	<	Globals* SimCreator::parseFile(const std::string mdFileName){
96	<	Globals* simParams = NULL;
97	<	try {
95	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
96	>	Globals* simParams = NULL;
97	>	try {
98
99	<	// Create a preprocessor that preprocesses md file into an ostringstream
100	<	std::stringstream ppStream;
99	>	// Create a preprocessor that preprocesses md file into an ostringstream
100	>	std::stringstream ppStream;
101		#ifdef IS_MPI
102	<	int streamSize;
103	<	const int masterNode = 0;
104	<	int commStatus;
105	<	if (worldRank == masterNode) {
106	<	#endif
102	>	int streamSize;
103	>	const int masterNode = 0;
104	>
105	>	if (worldRank == masterNode) {
106	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
107	>	#endif
108	>	SimplePreprocessor preprocessor;
109	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
110
87	–	SimplePreprocessor preprocessor;
88	–	preprocessor.preprocess(mdFileName, ppStream);
89	–
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())), streamSize, MPI::CHAR, masterNode);
116	>
117	>	} else {
118	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
119
120	<	commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
121	<
120	>	//get stream size
121	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
122	>
123	>	char* buf = new char[streamSize];
124	>	assert(buf);
125
126	<	} else {
127	<	//get stream size
100	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
126	>	//receive file content
127	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
128
129	<	char* buf = new char[streamSize];
130	<	assert(buf);
131	<
105	<	//receive file content
106	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107	<
108	<	ppStream.str(buf);
109	<	delete buf;
110	<
111	<	}
129	>	ppStream.str(buf);
130	>	delete [] buf;
131	>	}
132		#endif
133	<	// Create a scanner that reads from the input stream
134	<	MDLexer lexer(ppStream);
135	<	lexer.setFilename(mdFileName);
136	<	lexer.initDeferredLineCount();
133	>	// Create a scanner that reads from the input stream
134	>	MDLexer lexer(ppStream);
135	>	lexer.setFilename(filename);
136	>	lexer.initDeferredLineCount();
137
138	<	// Create a parser that reads from the scanner
139	<	MDParser parser(lexer);
140	<	parser.setFilename(mdFileName);
138	>	// Create a parser that reads from the scanner
139	>	MDParser parser(lexer);
140	>	parser.setFilename(filename);
141
142	<	// Create an observer that synchorizes file name change
143	<	FilenameObserver observer;
144	<	observer.setLexer(&lexer);
145	<	observer.setParser(&parser);
146	<	lexer.setObserver(&observer);
142	>	// Create an observer that synchorizes file name change
143	>	FilenameObserver observer;
144	>	observer.setLexer(&lexer);
145	>	observer.setParser(&parser);
146	>	lexer.setObserver(&observer);
147
148	<	antlr::ASTFactory factory;
149	<	parser.initializeASTFactory(factory);
150	<	parser.setASTFactory(&factory);
151	<	parser.mdfile();
148	>	antlr::ASTFactory factory;
149	>	parser.initializeASTFactory(factory);
150	>	parser.setASTFactory(&factory);
151	>	parser.mdfile();
152
153	<	// Create a tree parser that reads information into Globals
154	<	MDTreeParser treeParser;
155	<	treeParser.initializeASTFactory(factory);
156	<	treeParser.setASTFactory(&factory);
157	<	simParams = treeParser.walkTree(parser.getAST());
153	>	// Create a tree parser that reads information into Globals
154	>	MDTreeParser treeParser;
155	>	treeParser.initializeASTFactory(factory);
156	>	treeParser.setASTFactory(&factory);
157	>	simParams = treeParser.walkTree(parser.getAST());
158	>	}
159
160	<	}
161	<	catch (exception& e) {
162	<	cerr << "parser exception: " << e.what() << endl;
163	<	}
160	>
161	>	catch(antlr::MismatchedCharException& e) {
162	>	sprintf(painCave.errMsg,
163	>	"parser exception: %s %s:%d:%d\n",
164	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
165	>	painCave.isFatal = 1;
166	>	simError();
167	>	}
168	>	catch(antlr::MismatchedTokenException &e) {
169	>	sprintf(painCave.errMsg,
170	>	"parser exception: %s %s:%d:%d\n",
171	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
172	>	painCave.isFatal = 1;
173	>	simError();
174	>	}
175	>	catch(antlr::NoViableAltForCharException &e) {
176	>	sprintf(painCave.errMsg,
177	>	"parser exception: %s %s:%d:%d\n",
178	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
179	>	painCave.isFatal = 1;
180	>	simError();
181	>	}
182	>	catch(antlr::NoViableAltException &e) {
183	>	sprintf(painCave.errMsg,
184	>	"parser exception: %s %s:%d:%d\n",
185	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
186	>	painCave.isFatal = 1;
187	>	simError();
188	>	}
189	>
190	>	catch(antlr::TokenStreamRecognitionException& e) {
191	>	sprintf(painCave.errMsg,
192	>	"parser exception: %s %s:%d:%d\n",
193	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
194	>	painCave.isFatal = 1;
195	>	simError();
196	>	}
197	>
198	>	catch(antlr::TokenStreamIOException& e) {
199	>	sprintf(painCave.errMsg,
200	>	"parser exception: %s\n",
201	>	e.getMessage().c_str());
202	>	painCave.isFatal = 1;
203	>	simError();
204	>	}
205	>
206	>	catch(antlr::TokenStreamException& e) {
207	>	sprintf(painCave.errMsg,
208	>	"parser exception: %s\n",
209	>	e.getMessage().c_str());
210	>	painCave.isFatal = 1;
211	>	simError();
212	>	}
213	>	catch (antlr::RecognitionException& e) {
214	>	sprintf(painCave.errMsg,
215	>	"parser exception: %s %s:%d:%d\n",
216	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
217	>	painCave.isFatal = 1;
218	>	simError();
219	>	}
220	>	catch (antlr::CharStreamException& e) {
221	>	sprintf(painCave.errMsg,
222	>	"parser exception: %s\n",
223	>	e.getMessage().c_str());
224	>	painCave.isFatal = 1;
225	>	simError();
226	>	}
227	>	catch (OpenMDException& e) {
228	>	sprintf(painCave.errMsg,
229	>	"%s\n",
230	>	e.getMessage().c_str());
231	>	painCave.isFatal = 1;
232	>	simError();
233	>	}
234	>	catch (std::exception& e) {
235	>	sprintf(painCave.errMsg,
236	>	"parser exception: %s\n",
237	>	e.what());
238	>	painCave.isFatal = 1;
239	>	simError();
240	>	}
241
242	<	return simParams;
242	>	simParams->setMDfileVersion(mdFileVersion);
243	>	return simParams;
244		}
245
246		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
247		bool loadInitCoords) {
248	+
249	+	const int bufferSize = 65535;
250	+	char buffer[bufferSize];
251	+	int lineNo = 0;
252	+	std::string mdRawData;
253	+	int metaDataBlockStart = -1;
254	+	int metaDataBlockEnd = -1;
255	+	int i, j;
256	+	streamoff mdOffset;
257	+	int mdFileVersion;
258
259	+	// Create a string for embedding the version information in the MetaData
260	+	std::string version;
261	+	version.assign("## Last run using OpenMD Version: ");
262	+	version.append(OPENMD_VERSION_MAJOR);
263	+	version.append(".");
264	+	version.append(OPENMD_VERSION_MINOR);
265	+
266	+	std::string svnrev;
267	+	//convert a macro from compiler to a string in c++
268	+	STR_DEFINE(svnrev, SVN_REV );
269	+	version.append(" Revision: ");
270	+	// If there's no SVN revision, just call this the RELEASE revision.
271	+	if (!svnrev.empty()) {
272	+	version.append(svnrev);
273	+	} else {
274	+	version.append("RELEASE");
275	+	}
276	+
277	+	#ifdef IS_MPI
278	+	const int masterNode = 0;
279	+	if (worldRank == masterNode) {
280	+	#endif
281	+
282	+	std::ifstream mdFile_;
283	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
284	+
285	+	if (mdFile_.fail()) {
286	+	sprintf(painCave.errMsg,
287	+	"SimCreator: Cannot open file: %s\n",
288	+	mdFileName.c_str());
289	+	painCave.isFatal = 1;
290	+	simError();
291	+	}
292	+
293	+	mdFile_.getline(buffer, bufferSize);
294	+	++lineNo;
295	+	std::string line = trimLeftCopy(buffer);
296	+	i = CaseInsensitiveFind(line, "<OpenMD");
297	+	if (static_cast<size_t>(i) == string::npos) {
298	+	// try the older file strings to see if that works:
299	+	i = CaseInsensitiveFind(line, "<OOPSE");
300	+	}
301	+
302	+	if (static_cast<size_t>(i) == string::npos) {
303	+	// still no luck!
304	+	sprintf(painCave.errMsg,
305	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
306	+	mdFileName.c_str());
307	+	painCave.isFatal = 1;
308	+	simError();
309	+	}
310	+
311	+	// found the correct opening string, now try to get the file
312	+	// format version number.
313	+
314	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
315	+	std::string fileType = tokenizer.nextToken();
316	+	toUpper(fileType);
317	+
318	+	mdFileVersion = 0;
319	+
320	+	if (fileType == "OPENMD") {
321	+	while (tokenizer.hasMoreTokens()) {
322	+	std::string token(tokenizer.nextToken());
323	+	toUpper(token);
324	+	if (token == "VERSION") {
325	+	mdFileVersion = tokenizer.nextTokenAsInt();
326	+	break;
327	+	}
328	+	}
329	+	}
330	+
331	+	//scan through the input stream and find MetaData tag
332	+	while(mdFile_.getline(buffer, bufferSize)) {
333	+	++lineNo;
334	+
335	+	std::string line = trimLeftCopy(buffer);
336	+	if (metaDataBlockStart == -1) {
337	+	i = CaseInsensitiveFind(line, "<MetaData>");
338	+	if (i != string::npos) {
339	+	metaDataBlockStart = lineNo;
340	+	mdOffset = mdFile_.tellg();
341	+	}
342	+	} else {
343	+	i = CaseInsensitiveFind(line, "</MetaData>");
344	+	if (i != string::npos) {
345	+	metaDataBlockEnd = lineNo;
346	+	}
347	+	}
348	+	}
349	+
350	+	if (metaDataBlockStart == -1) {
351	+	sprintf(painCave.errMsg,
352	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
353	+	mdFileName.c_str());
354	+	painCave.isFatal = 1;
355	+	simError();
356	+	}
357	+	if (metaDataBlockEnd == -1) {
358	+	sprintf(painCave.errMsg,
359	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
360	+	mdFileName.c_str());
361	+	painCave.isFatal = 1;
362	+	simError();
363	+	}
364	+
365	+	mdFile_.clear();
366	+	mdFile_.seekg(0);
367	+	mdFile_.seekg(mdOffset);
368	+
369	+	mdRawData.clear();
370	+
371	+	bool foundVersion = false;
372	+
373	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
374	+	mdFile_.getline(buffer, bufferSize);
375	+	std::string line = trimLeftCopy(buffer);
376	+	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
377	+	if (static_cast<size_t>(j) != string::npos) {
378	+	foundVersion = true;
379	+	mdRawData += version;
380	+	} else {
381	+	mdRawData += buffer;
382	+	}
383	+	mdRawData += "\n";
384	+	}
385	+
386	+	if (!foundVersion) mdRawData += version + "\n";
387	+
388	+	mdFile_.close();
389	+
390	+	#ifdef IS_MPI
391	+	}
392	+	#endif
393	+
394	+	std::stringstream rawMetaDataStream(mdRawData);
395	+
396		//parse meta-data file
397	<	Globals* simParams = parseFile(mdFileName);
397	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
398	>	metaDataBlockStart + 1);
399
400		//create the force field
401	<	ForceField * ff = ForceFieldFactory::getInstance()
402	<	->createForceField(simParams->getForceField());
156	<
401	>	ForceField * ff = new ForceField(simParams->getForceField());
402	>
403		if (ff == NULL) {
404		sprintf(painCave.errMsg,
405		"ForceField Factory can not create %s force field\n",
#	Line 186 | Line 432 | Globals* SimCreator::parseFile(const std::string mdFil
432		}
433
434		ff->parse(forcefieldFileName);
189	–
435		//create SimInfo
436		SimInfo * info = new SimInfo(ff, simParams);
437	+
438	+	info->setRawMetaData(mdRawData);
439
440	<	//gather parameters (SimCreator only retrieves part of the parameters)
440	>	//gather parameters (SimCreator only retrieves part of the
441	>	//parameters)
442		gatherParameters(info, mdFileName);
443
444		//divide the molecules and determine the global index of molecules
#	Line 201 | Line 449 | Globals* SimCreator::parseFile(const std::string mdFil
449		//create the molecules
450		createMolecules(info);
451
452	+	//find the storage layout
453	+
454	+	int storageLayout = computeStorageLayout(info);
455	+
456	+	//allocate memory for DataStorage(circular reference, need to
457	+	//break it)
458	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
459
460	<	//allocate memory for DataStorage(circular reference, need to break it)
461	<	info->setSnapshotManager(new SimSnapshotManager(info));
462	<
463	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
464	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
210	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
460	>	//set the global index of atoms, rigidbodies and cutoffgroups
461	>	//(only need to be set once, the global index will never change
462	>	//again). Local indices of atoms and rigidbodies are already set
463	>	//by MoleculeCreator class which actually delegates the
464	>	//responsibility to LocalIndexManager.
465		setGlobalIndex(info);
466
467	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
468	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
469	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
470	<	//we can determine the beginning global indices of atoms before they get created.
467	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
468	>	//method, at that point atoms don't have the global index yet
469	>	//(their global index are all initialized to -1).  Therefore we
470	>	//have to call addInteractionPairs explicitly here. A way to work
471	>	//around is that we can determine the beginning global indices of
472	>	//atoms before they get created.
473		SimInfo::MoleculeIterator mi;
474		Molecule* mol;
475		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
476	<	info->addExcludePairs(mol);
476	>	info->addInteractionPairs(mol);
477		}
478
479		if (loadInitCoords)
480	<	loadCoordinates(info);
225	<
480	>	loadCoordinates(info, mdFileName);
481		return info;
482		}
483
#	Line 257 | Line 512 | Globals* SimCreator::parseFile(const std::string mdFil
512
513		#ifdef IS_MPI
514		void SimCreator::divideMolecules(SimInfo *info) {
515	<	double numerator;
261	<	double denominator;
262	<	double precast;
263	<	double x;
264	<	double y;
265	<	double a;
266	<	int old_atoms;
267	<	int add_atoms;
268	<	int new_atoms;
269	<	int nTarget;
270	<	int done;
271	<	int i;
272	<	int j;
273	<	int loops;
274	<	int which_proc;
515	>	RealType a;
516		int nProcessors;
517		std::vector<int> atomsPerProc;
518		int nGlobalMols = info->getNGlobalMolecules();
519	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
519	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
520	>	// error
521	>	// condition:
522
523	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
523	>	nProcessors = MPI::COMM_WORLD.Get_size();
524
525		if (nProcessors > nGlobalMols) {
526		sprintf(painCave.errMsg,
#	Line 286 | Line 529 | Globals* SimCreator::parseFile(const std::string mdFil
529		"\tthe number of molecules.  This will not result in a \n"
530		"\tusable division of atoms for force decomposition.\n"
531		"\tEither try a smaller number of processors, or run the\n"
532	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
532	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
533	>	nGlobalMols);
534
535		painCave.isFatal = 1;
536		simError();
537		}
538
295	–	int seedValue;
539		Globals * simParams = info->getSimParams();
540	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
540	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
541	>	//random number generator
542		if (simParams->haveSeed()) {
543	<	seedValue = simParams->getSeed();
543	>	int seedValue = simParams->getSeed();
544		myRandom = new SeqRandNumGen(seedValue);
545		}else {
546		myRandom = new SeqRandNumGen();
#	Line 309 | Line 553 | Globals* SimCreator::parseFile(const std::string mdFil
553		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
554
555		if (worldRank == 0) {
556	<	numerator = info->getNGlobalAtoms();
557	<	denominator = nProcessors;
558	<	precast = numerator / denominator;
559	<	nTarget = (int)(precast + 0.5);
556	>	RealType numerator = info->getNGlobalAtoms();
557	>	RealType denominator = nProcessors;
558	>	RealType precast = numerator / denominator;
559	>	int nTarget = (int)(precast + 0.5);
560
561	<	for(i = 0; i < nGlobalMols; i++) {
562	<	done = 0;
563	<	loops = 0;
561	>	for(int i = 0; i < nGlobalMols; i++) {
562	>
563	>	int done = 0;
564	>	int loops = 0;
565
566		while (!done) {
567		loops++;
568
569		// Pick a processor at random
570
571	<	which_proc = (int) (myRandom->rand() * nProcessors);
571	>	int which_proc = (int) (myRandom->rand() * nProcessors);
572
573		//get the molecule stamp first
574		int stampId = info->getMoleculeStampId(i);
575		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
576
577		// How many atoms does this processor have so far?
578	<	old_atoms = atomsPerProc[which_proc];
579	<	add_atoms = moleculeStamp->getNAtoms();
580	<	new_atoms = old_atoms + add_atoms;
578	>	int old_atoms = atomsPerProc[which_proc];
579	>	int add_atoms = moleculeStamp->getNAtoms();
580	>	int new_atoms = old_atoms + add_atoms;
581
582		// If we've been through this loop too many times, we need
583		// to just give up and assign the molecule to this processor
584		// and be done with it.
585
586		if (loops > 100) {
587	+
588		sprintf(painCave.errMsg,
589	<	"I've tried 100 times to assign molecule %d to a "
590	<	" processor, but can't find a good spot.\n"
591	<	"I'm assigning it at random to processor %d.\n",
589	>	"There have been 100 attempts to assign molecule %d to an\n"
590	>	"\tunderworked processor, but there's no good place to\n"
591	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
592		i, which_proc);
593	<
593	>
594		painCave.isFatal = 0;
595	+	painCave.severity = OPENMD_INFO;
596		simError();
597
598		molToProcMap[i] = which_proc;
#	Line 374 | Line 621 | Globals* SimCreator::parseFile(const std::string mdFil
621		//           Pacc(x) = exp(- a * x)
622		// where a = penalty / (average atoms per molecule)
623
624	<	x = (double)(new_atoms - nTarget);
625	<	y = myRandom->rand();
624	>	RealType x = (RealType)(new_atoms - nTarget);
625	>	RealType y = myRandom->rand();
626
627		if (y < exp(- a * x)) {
628		molToProcMap[i] = which_proc;
#	Line 390 | Line 637 | Globals* SimCreator::parseFile(const std::string mdFil
637		}
638
639		delete myRandom;
640	<
640	>
641		// Spray out this nonsense to all other processors:
642	<
396	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
642	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
643		} else {
644
645		// Listen to your marching orders from processor 0:
646	<
647	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
646	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
647	>
648		}
649
650		info->setMolToProcMap(molToProcMap);
651		sprintf(checkPointMsg,
652		"Successfully divided the molecules among the processors.\n");
653	<	MPIcheckPoint();
653	>	errorCheckPoint();
654		}
655
656		#endif
#	Line 421 | Line 667 | Globals* SimCreator::parseFile(const std::string mdFil
667		#endif
668
669		stampId = info->getMoleculeStampId(i);
670	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
671	<	stampId, i, info->getLocalIndexManager());
670	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
671	>	info->getMoleculeStamp(stampId),
672	>	stampId, i,
673	>	info->getLocalIndexManager());
674
675		info->addMolecule(mol);
676
#	Line 435 | Line 683 | Globals* SimCreator::parseFile(const std::string mdFil
683		} //end for(int i=0)
684		}
685
686	+	int SimCreator::computeStorageLayout(SimInfo* info) {
687	+
688	+	Globals* simParams = info->getSimParams();
689	+	int nRigidBodies = info->getNGlobalRigidBodies();
690	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
691	+	set<AtomType*>::iterator i;
692	+	bool hasDirectionalAtoms = false;
693	+	bool hasFixedCharge = false;
694	+	bool hasDipoles = false;
695	+	bool hasQuadrupoles = false;
696	+	bool hasPolarizable = false;
697	+	bool hasFluctuatingCharge = false;
698	+	bool hasMetallic = false;
699	+	int storageLayout = 0;
700	+	storageLayout |= DataStorage::dslPosition;
701	+	storageLayout |= DataStorage::dslVelocity;
702	+	storageLayout |= DataStorage::dslForce;
703	+
704	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
705	+
706	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
707	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
708	+	EAMAdapter ea = EAMAdapter( (*i) );
709	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
710	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
711	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
712	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
713	+
714	+	if (da.isDirectional()){
715	+	hasDirectionalAtoms = true;
716	+	}
717	+	if (ma.isDipole()){
718	+	hasDipoles = true;
719	+	}
720	+	if (ma.isQuadrupole()){
721	+	hasQuadrupoles = true;
722	+	}
723	+	if (ea.isEAM() || sca.isSuttonChen()){
724	+	hasMetallic = true;
725	+	}
726	+	if ( fca.isFixedCharge() ){
727	+	hasFixedCharge = true;
728	+	}
729	+	if ( fqa.isFluctuatingCharge() ){
730	+	hasFluctuatingCharge = true;
731	+	}
732	+	if ( pa.isPolarizable() ){
733	+	hasPolarizable = true;
734	+	}
735	+	}
736	+
737	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
738	+	storageLayout |= DataStorage::dslAmat;
739	+	if(storageLayout & DataStorage::dslVelocity) {
740	+	storageLayout |= DataStorage::dslAngularMomentum;
741	+	}
742	+	if (storageLayout & DataStorage::dslForce) {
743	+	storageLayout |= DataStorage::dslTorque;
744	+	}
745	+	}
746	+	if (hasDipoles) {
747	+	storageLayout |= DataStorage::dslDipole;
748	+	}
749	+	if (hasQuadrupoles) {
750	+	storageLayout |= DataStorage::dslQuadrupole;
751	+	}
752	+	if (hasFixedCharge || hasFluctuatingCharge) {
753	+	storageLayout |= DataStorage::dslSkippedCharge;
754	+	}
755	+	if (hasMetallic) {
756	+	storageLayout |= DataStorage::dslDensity;
757	+	storageLayout |= DataStorage::dslFunctional;
758	+	storageLayout |= DataStorage::dslFunctionalDerivative;
759	+	}
760	+	if (hasPolarizable) {
761	+	storageLayout |= DataStorage::dslElectricField;
762	+	}
763	+	if (hasFluctuatingCharge){
764	+	storageLayout |= DataStorage::dslFlucQPosition;
765	+	if(storageLayout & DataStorage::dslVelocity) {
766	+	storageLayout |= DataStorage::dslFlucQVelocity;
767	+	}
768	+	if (storageLayout & DataStorage::dslForce) {
769	+	storageLayout |= DataStorage::dslFlucQForce;
770	+	}
771	+	}
772	+
773	+	// if the user has asked for them, make sure we've got the memory for the
774	+	// objects defined.
775	+
776	+	if (simParams->getOutputParticlePotential()) {
777	+	storageLayout |= DataStorage::dslParticlePot;
778	+	}
779	+
780	+	if (simParams->havePrintHeatFlux()) {
781	+	if (simParams->getPrintHeatFlux()) {
782	+	storageLayout |= DataStorage::dslParticlePot;
783	+	}
784	+	}
785	+
786	+	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
787	+	storageLayout |= DataStorage::dslElectricField;
788	+	}
789	+
790	+	if (simParams->getOutputFluctuatingCharges()) {
791	+	storageLayout |= DataStorage::dslFlucQPosition;
792	+	storageLayout |= DataStorage::dslFlucQVelocity;
793	+	storageLayout |= DataStorage::dslFlucQForce;
794	+	}
795	+
796	+	info->setStorageLayout(storageLayout);
797	+
798	+	return storageLayout;
799	+	}
800	+
801		void SimCreator::setGlobalIndex(SimInfo *info) {
802		SimInfo::MoleculeIterator mi;
803		Molecule::AtomIterator ai;
804		Molecule::RigidBodyIterator ri;
805		Molecule::CutoffGroupIterator ci;
806	<	Molecule * mol;
807	<	Atom * atom;
808	<	RigidBody * rb;
809	<	CutoffGroup * cg;
806	>	Molecule::BondIterator boi;
807	>	Molecule::BendIterator bei;
808	>	Molecule::TorsionIterator ti;
809	>	Molecule::InversionIterator ii;
810	>	Molecule::IntegrableObjectIterator  ioi;
811	>	Molecule* mol;
812	>	Atom* atom;
813	>	RigidBody* rb;
814	>	CutoffGroup* cg;
815	>	Bond* bond;
816	>	Bend* bend;
817	>	Torsion* torsion;
818	>	Inversion* inversion;
819		int beginAtomIndex;
820		int beginRigidBodyIndex;
821		int beginCutoffGroupIndex;
822	+	int beginBondIndex;
823	+	int beginBendIndex;
824	+	int beginTorsionIndex;
825	+	int beginInversionIndex;
826		int nGlobalAtoms = info->getNGlobalAtoms();
827	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
828
452	–	#ifndef IS_MPI
453	–
829		beginAtomIndex = 0;
830	<	beginRigidBodyIndex = 0;
830	>	// The rigid body indices begin immediately after the atom indices:
831	>	beginRigidBodyIndex = info->getNGlobalAtoms();
832		beginCutoffGroupIndex = 0;
833	<
834	<	#else
835	<
836	<	int nproc;
837	<	int myNode;
838	<
463	<	myNode = worldRank;
464	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
465	<
466	<	std::vector < int > tmpAtomsInProc(nproc, 0);
467	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
468	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
469	<	std::vector < int > NumAtomsInProc(nproc, 0);
470	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
471	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
472	<
473	<	tmpAtomsInProc[myNode] = info->getNAtoms();
474	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
475	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
476	<
477	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
478	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
479	<	MPI_SUM, MPI_COMM_WORLD);
480	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
481	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
482	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
483	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
484	<
485	<	beginAtomIndex = 0;
486	<	beginRigidBodyIndex = 0;
487	<	beginCutoffGroupIndex = 0;
488	<
489	<	for(int i = 0; i < myNode; i++) {
490	<	beginAtomIndex += NumAtomsInProc[i];
491	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
492	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
493	<	}
494	<
495	<	#endif
496	<
497	<	//rigidbody's index begins right after atom's
498	<	beginRigidBodyIndex += info->getNGlobalAtoms();
499	<
500	<	for(mol = info->beginMolecule(mi); mol != NULL;
501	<	mol = info->nextMolecule(mi)) {
833	>	beginBondIndex = 0;
834	>	beginBendIndex = 0;
835	>	beginTorsionIndex = 0;
836	>	beginInversionIndex = 0;
837	>
838	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
839
840	<	//local index(index in DataStorge) of atom is important
841	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	<	atom->setGlobalIndex(beginAtomIndex++);
840	>	#ifdef IS_MPI
841	>	if (info->getMolToProc(i) == worldRank) {
842	>	#endif
843	>	// stuff to do if I own this molecule
844	>	mol = info->getMoleculeByGlobalIndex(i);
845	>
846	>	// The local index(index in DataStorge) of the atom is important:
847	>	for(atom = mol->beginAtom(ai); atom != NULL;
848	>	atom = mol->nextAtom(ai)) {
849	>	atom->setGlobalIndex(beginAtomIndex++);
850	>	}
851	>
852	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
853	>	rb = mol->nextRigidBody(ri)) {
854	>	rb->setGlobalIndex(beginRigidBodyIndex++);
855	>	}
856	>
857	>	// The local index of other objects only depends on the order
858	>	// of traversal:
859	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
860	>	cg = mol->nextCutoffGroup(ci)) {
861	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
862	>	}
863	>	for(bond = mol->beginBond(boi); bond != NULL;
864	>	bond = mol->nextBond(boi)) {
865	>	bond->setGlobalIndex(beginBondIndex++);
866	>	}
867	>	for(bend = mol->beginBend(bei); bend != NULL;
868	>	bend = mol->nextBend(bei)) {
869	>	bend->setGlobalIndex(beginBendIndex++);
870	>	}
871	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
872	>	torsion = mol->nextTorsion(ti)) {
873	>	torsion->setGlobalIndex(beginTorsionIndex++);
874	>	}
875	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
876	>	inversion = mol->nextInversion(ii)) {
877	>	inversion->setGlobalIndex(beginInversionIndex++);
878	>	}
879	>
880	>	#ifdef IS_MPI
881	>	}  else {
882	>
883	>	// stuff to do if I don't own this molecule
884	>
885	>	int stampId = info->getMoleculeStampId(i);
886	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
887	>
888	>	beginAtomIndex += stamp->getNAtoms();
889	>	beginRigidBodyIndex += stamp->getNRigidBodies();
890	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
891	>	beginBondIndex += stamp->getNBonds();
892	>	beginBendIndex += stamp->getNBends();
893	>	beginTorsionIndex += stamp->getNTorsions();
894	>	beginInversionIndex += stamp->getNInversions();
895		}
896	<
897	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
898	<	rb = mol->nextRigidBody(ri)) {
899	<	rb->setGlobalIndex(beginRigidBodyIndex++);
511	<	}
512	<
513	<	//local index of cutoff group is trivial, it only depends on the order of travesing
514	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
515	<	cg = mol->nextCutoffGroup(ci)) {
516	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
517	<	}
518	<	}
519	<
896	>	#endif
897	>
898	>	} //end for(int i=0)
899	>
900		//fill globalGroupMembership
901		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
902	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
903	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
904	<
902	>	for(mol = info->beginMolecule(mi); mol != NULL;
903	>	mol = info->nextMolecule(mi)) {
904	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
905	>	cg = mol->nextCutoffGroup(ci)) {
906		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
907		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
908		}
909
910		}
911		}
912	<
912	>
913		#ifdef IS_MPI
914		// Since the globalGroupMembership has been zero filled and we've only
915		// poked values into the atoms we know, we can do an Allreduce
916		// to get the full globalGroupMembership array (We think).
917		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
918		// docs said we could.
919	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
920	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
921	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
919	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
920	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
921	>	&tmpGroupMembership[0], nGlobalAtoms,
922	>	MPI::INT, MPI::SUM);
923		info->setGlobalGroupMembership(tmpGroupMembership);
924		#else
925		info->setGlobalGroupMembership(globalGroupMembership);
926		#endif
927
928		//fill molMembership
929	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
929	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
930	>	info->getNGlobalRigidBodies(), 0);
931
932	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
933	<
932	>	for(mol = info->beginMolecule(mi); mol != NULL;
933	>	mol = info->nextMolecule(mi)) {
934		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
935		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
936		}
937	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
938	+	rb = mol->nextRigidBody(ri)) {
939	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
940	+	}
941		}
942
943		#ifdef IS_MPI
944	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
944	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
945	>	info->getNGlobalRigidBodies(), 0);
946	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
947	>	nGlobalAtoms + nGlobalRigidBodies,
948	>	MPI::INT, MPI::SUM);
949
559	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
560	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
561	–
950		info->setGlobalMolMembership(tmpMolMembership);
951		#else
952		info->setGlobalMolMembership(globalMolMembership);
953		#endif
954	+
955	+	// nIOPerMol holds the number of integrable objects per molecule
956	+	// here the molecules are listed by their global indices.
957	+
958	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
959	+	for (mol = info->beginMolecule(mi); mol != NULL;
960	+	mol = info->nextMolecule(mi)) {
961	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
962	+	}
963
964	<	}
965	<
966	<	void SimCreator::loadCoordinates(SimInfo* info) {
967	<	Globals* simParams;
968	<	simParams = info->getSimParams();
964	>	#ifdef IS_MPI
965	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
966	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
967	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
968	>	#else
969	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
970	>	#endif
971	>
972	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
973
974	<	if (!simParams->haveInitialConfig()) {
975	<	sprintf(painCave.errMsg,
976	<	"Cannot intialize a simulation without an initial configuration file.\n");
977	<	painCave.isFatal = 1;;
577	<	simError();
974	>	int startingIndex = 0;
975	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
976	>	startingIOIndexForMol[i] = startingIndex;
977	>	startingIndex += numIntegrableObjectsPerMol[i];
978		}
979
980	<	DumpReader reader(info, simParams->getInitialConfig());
980	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
981	>	for (mol = info->beginMolecule(mi); mol != NULL;
982	>	mol = info->nextMolecule(mi)) {
983	>	int myGlobalIndex = mol->getGlobalIndex();
984	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
985	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
986	>	sd = mol->nextIntegrableObject(ioi)) {
987	>	sd->setGlobalIntegrableObjectIndex(globalIO);
988	>	IOIndexToIntegrableObject[globalIO] = sd;
989	>	globalIO++;
990	>	}
991	>	}
992	>
993	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
994	>
995	>	}
996	>
997	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
998	>
999	>	DumpReader reader(info, mdFileName);
1000		int nframes = reader.getNFrames();
1001
1002		if (nframes > 0) {
#	Line 586 | Line 1005 | Globals* SimCreator::parseFile(const std::string mdFil
1005		//invalid initial coordinate file
1006		sprintf(painCave.errMsg,
1007		"Initial configuration file %s should at least contain one frame\n",
1008	<	simParams->getInitialConfig().c_str());
1008	>	mdFileName.c_str());
1009		painCave.isFatal = 1;
1010		simError();
1011		}
593	–
1012		//copy the current snapshot to previous snapshot
1013		info->getSnapshotManager()->advance();
1014		}
1015
1016	<	} //end namespace oopse
1016	>	} //end namespace OpenMD
1017
1018

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 0 | Line 1
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