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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1810 by gezelter, Thu Nov 8 14:23:43 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 63 | Line 64
64		#include "mdParser/MDParser.hpp"
65		#include "mdParser/MDTreeParser.hpp"
66		#include "mdParser/SimplePreprocessor.hpp"
67	+	#include "antlr/ANTLRException.hpp"
68	+	#include "antlr/TokenStreamRecognitionException.hpp"
69	+	#include "antlr/TokenStreamIOException.hpp"
70	+	#include "antlr/TokenStreamException.hpp"
71	+	#include "antlr/RecognitionException.hpp"
72	+	#include "antlr/CharStreamException.hpp"
73
74	+	#include "antlr/MismatchedCharException.hpp"
75	+	#include "antlr/MismatchedTokenException.hpp"
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
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())),
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
100	<	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);
104	<
105	<	//receive file content
106	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107	<
108	<	ppStream.str(buf);
109	<	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
163	<	}
164	<	catch (exception& e) {
165	<	cerr << "parser exception: " << e.what() << endl;
166	<	}
163	>
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, j;
259	+	streamoff mdOffset(0);
260	+	int mdFileVersion;
261
262	+	// Create a string for embedding the version information in the MetaData
263	+	std::string version;
264	+	version.assign("## Last run using OpenMD Version: ");
265	+	version.append(OPENMD_VERSION_MAJOR);
266	+	version.append(".");
267	+	version.append(OPENMD_VERSION_MINOR);
268	+
269	+	std::string svnrev;
270	+	//convert a macro from compiler to a string in c++
271	+	STR_DEFINE(svnrev, SVN_REV );
272	+	version.append(" Revision: ");
273	+	// If there's no SVN revision, just call this the RELEASE revision.
274	+	if (!svnrev.empty()) {
275	+	version.append(svnrev);
276	+	} else {
277	+	version.append("RELEASE");
278	+	}
279	+
280	+	#ifdef IS_MPI
281	+	const int masterNode = 0;
282	+	if (worldRank == masterNode) {
283	+	#endif
284	+
285	+	std::ifstream mdFile_;
286	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
287	+
288	+	if (mdFile_.fail()) {
289	+	sprintf(painCave.errMsg,
290	+	"SimCreator: Cannot open file: %s\n",
291	+	mdFileName.c_str());
292	+	painCave.isFatal = 1;
293	+	simError();
294	+	}
295	+
296	+	mdFile_.getline(buffer, bufferSize);
297	+	++lineNo;
298	+	std::string line = trimLeftCopy(buffer);
299	+	i = CaseInsensitiveFind(line, "<OpenMD");
300	+	if (static_cast<size_t>(i) == string::npos) {
301	+	// try the older file strings to see if that works:
302	+	i = CaseInsensitiveFind(line, "<OOPSE");
303	+	}
304	+
305	+	if (static_cast<size_t>(i) == string::npos) {
306	+	// still no luck!
307	+	sprintf(painCave.errMsg,
308	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
309	+	mdFileName.c_str());
310	+	painCave.isFatal = 1;
311	+	simError();
312	+	}
313	+
314	+	// found the correct opening string, now try to get the file
315	+	// format version number.
316	+
317	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
318	+	std::string fileType = tokenizer.nextToken();
319	+	toUpper(fileType);
320	+
321	+	mdFileVersion = 0;
322	+
323	+	if (fileType == "OPENMD") {
324	+	while (tokenizer.hasMoreTokens()) {
325	+	std::string token(tokenizer.nextToken());
326	+	toUpper(token);
327	+	if (token == "VERSION") {
328	+	mdFileVersion = tokenizer.nextTokenAsInt();
329	+	break;
330	+	}
331	+	}
332	+	}
333	+
334	+	//scan through the input stream and find MetaData tag
335	+	while(mdFile_.getline(buffer, bufferSize)) {
336	+	++lineNo;
337	+
338	+	std::string line = trimLeftCopy(buffer);
339	+	if (metaDataBlockStart == -1) {
340	+	i = CaseInsensitiveFind(line, "<MetaData>");
341	+	if (i != string::npos) {
342	+	metaDataBlockStart = lineNo;
343	+	mdOffset = mdFile_.tellg();
344	+	}
345	+	} else {
346	+	i = CaseInsensitiveFind(line, "</MetaData>");
347	+	if (i != string::npos) {
348	+	metaDataBlockEnd = lineNo;
349	+	}
350	+	}
351	+	}
352	+
353	+	if (metaDataBlockStart == -1) {
354	+	sprintf(painCave.errMsg,
355	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
356	+	mdFileName.c_str());
357	+	painCave.isFatal = 1;
358	+	simError();
359	+	}
360	+	if (metaDataBlockEnd == -1) {
361	+	sprintf(painCave.errMsg,
362	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
363	+	mdFileName.c_str());
364	+	painCave.isFatal = 1;
365	+	simError();
366	+	}
367	+
368	+	mdFile_.clear();
369	+	mdFile_.seekg(0);
370	+	mdFile_.seekg(mdOffset);
371	+
372	+	mdRawData.clear();
373	+
374	+	bool foundVersion = false;
375	+
376	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
377	+	mdFile_.getline(buffer, bufferSize);
378	+	std::string line = trimLeftCopy(buffer);
379	+	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
380	+	if (static_cast<size_t>(j) != string::npos) {
381	+	foundVersion = true;
382	+	mdRawData += version;
383	+	} else {
384	+	mdRawData += buffer;
385	+	}
386	+	mdRawData += "\n";
387	+	}
388	+
389	+	if (!foundVersion) mdRawData += version + "\n";
390	+
391	+	mdFile_.close();
392	+
393	+	#ifdef IS_MPI
394	+	}
395	+	#endif
396	+
397	+	std::stringstream rawMetaDataStream(mdRawData);
398	+
399		//parse meta-data file
400	<	Globals* simParams = parseFile(mdFileName);
400	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
401	>	metaDataBlockStart + 1);
402
403		//create the force field
404	<	ForceField * ff = ForceFieldFactory::getInstance()
405	<	->createForceField(simParams->getForceField());
156	<
404	>	ForceField * ff = new ForceField(simParams->getForceField());
405	>
406		if (ff == NULL) {
407		sprintf(painCave.errMsg,
408		"ForceField Factory can not create %s force field\n",
#	Line 186 | Line 435 | Globals* SimCreator::parseFile(const std::string mdFil
435		}
436
437		ff->parse(forcefieldFileName);
189	–
438		//create SimInfo
439		SimInfo * info = new SimInfo(ff, simParams);
440	+
441	+	info->setRawMetaData(mdRawData);
442
443	<	//gather parameters (SimCreator only retrieves part of the parameters)
443	>	//gather parameters (SimCreator only retrieves part of the
444	>	//parameters)
445		gatherParameters(info, mdFileName);
446
447		//divide the molecules and determine the global index of molecules
#	Line 201 | Line 452 | Globals* SimCreator::parseFile(const std::string mdFil
452		//create the molecules
453		createMolecules(info);
454
455	+	//find the storage layout
456	+
457	+	int storageLayout = computeStorageLayout(info);
458	+
459	+	//allocate memory for DataStorage(circular reference, need to
460	+	//break it)
461	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
462
463	<	//allocate memory for DataStorage(circular reference, need to break it)
464	<	info->setSnapshotManager(new SimSnapshotManager(info));
465	<
466	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
467	<	//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.
463	>	//set the global index of atoms, rigidbodies and cutoffgroups
464	>	//(only need to be set once, the global index will never change
465	>	//again). Local indices of atoms and rigidbodies are already set
466	>	//by MoleculeCreator class which actually delegates the
467	>	//responsibility to LocalIndexManager.
468		setGlobalIndex(info);
469
470	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
471	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
472	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
473	<	//we can determine the beginning global indices of atoms before they get created.
470	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
471	>	//method, at that point atoms don't have the global index yet
472	>	//(their global index are all initialized to -1).  Therefore we
473	>	//have to call addInteractionPairs explicitly here. A way to work
474	>	//around is that we can determine the beginning global indices of
475	>	//atoms before they get created.
476		SimInfo::MoleculeIterator mi;
477		Molecule* mol;
478		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
479	<	info->addExcludePairs(mol);
479	>	info->addInteractionPairs(mol);
480		}
481
482		if (loadInitCoords)
483	<	loadCoordinates(info);
225	<
483	>	loadCoordinates(info, mdFileName);
484		return info;
485		}
486
#	Line 257 | Line 515 | Globals* SimCreator::parseFile(const std::string mdFil
515
516		#ifdef IS_MPI
517		void SimCreator::divideMolecules(SimInfo *info) {
518	<	double numerator;
519	<	double denominator;
520	<	double precast;
521	<	double x;
522	<	double y;
523	<	double a;
518	>	RealType numerator;
519	>	RealType denominator;
520	>	RealType precast;
521	>	RealType x;
522	>	RealType y;
523	>	RealType a;
524		int old_atoms;
525		int add_atoms;
526		int new_atoms;
527		int nTarget;
528		int done;
529		int i;
272	–	int j;
530		int loops;
531		int which_proc;
532		int nProcessors;
#	Line 277 | Line 534 | Globals* SimCreator::parseFile(const std::string mdFil
534		int nGlobalMols = info->getNGlobalMolecules();
535		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
536
537	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
537	>	nProcessors = MPI::COMM_WORLD.Get_size();
538
539		if (nProcessors > nGlobalMols) {
540		sprintf(painCave.errMsg,
#	Line 286 | Line 543 | Globals* SimCreator::parseFile(const std::string mdFil
543		"\tthe number of molecules.  This will not result in a \n"
544		"\tusable division of atoms for force decomposition.\n"
545		"\tEither try a smaller number of processors, or run the\n"
546	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
546	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
547
548		painCave.isFatal = 1;
549		simError();
#	Line 315 | Line 572 | Globals* SimCreator::parseFile(const std::string mdFil
572		nTarget = (int)(precast + 0.5);
573
574		for(i = 0; i < nGlobalMols; i++) {
575	+
576		done = 0;
577		loops = 0;
578
#	Line 339 | Line 597 | Globals* SimCreator::parseFile(const std::string mdFil
597		// and be done with it.
598
599		if (loops > 100) {
600	+
601		sprintf(painCave.errMsg,
602	<	"I've tried 100 times to assign molecule %d to a "
603	<	" processor, but can't find a good spot.\n"
604	<	"I'm assigning it at random to processor %d.\n",
602	>	"There have been 100 attempts to assign molecule %d to an\n"
603	>	"\tunderworked processor, but there's no good place to\n"
604	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
605		i, which_proc);
606	<
606	>
607		painCave.isFatal = 0;
608	+	painCave.severity = OPENMD_INFO;
609		simError();
610
611		molToProcMap[i] = which_proc;
#	Line 374 | Line 634 | Globals* SimCreator::parseFile(const std::string mdFil
634		//           Pacc(x) = exp(- a * x)
635		// where a = penalty / (average atoms per molecule)
636
637	<	x = (double)(new_atoms - nTarget);
637	>	x = (RealType)(new_atoms - nTarget);
638		y = myRandom->rand();
639
640		if (y < exp(- a * x)) {
#	Line 390 | Line 650 | Globals* SimCreator::parseFile(const std::string mdFil
650		}
651
652		delete myRandom;
653	<
653	>
654		// Spray out this nonsense to all other processors:
655	<
396	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
655	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
656		} else {
657
658		// Listen to your marching orders from processor 0:
659	<
660	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
659	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
660	>
661		}
662
663		info->setMolToProcMap(molToProcMap);
664		sprintf(checkPointMsg,
665		"Successfully divided the molecules among the processors.\n");
666	<	MPIcheckPoint();
666	>	errorCheckPoint();
667		}
668
669		#endif
#	Line 421 | Line 680 | Globals* SimCreator::parseFile(const std::string mdFil
680		#endif
681
682		stampId = info->getMoleculeStampId(i);
683	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
684	<	stampId, i, info->getLocalIndexManager());
683	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
684	>	info->getMoleculeStamp(stampId),
685	>	stampId, i,
686	>	info->getLocalIndexManager());
687
688		info->addMolecule(mol);
689
#	Line 435 | Line 696 | Globals* SimCreator::parseFile(const std::string mdFil
696		} //end for(int i=0)
697		}
698
699	+	int SimCreator::computeStorageLayout(SimInfo* info) {
700	+
701	+	Globals* simParams = info->getSimParams();
702	+	int nRigidBodies = info->getNGlobalRigidBodies();
703	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
704	+	set<AtomType*>::iterator i;
705	+	bool hasDirectionalAtoms = false;
706	+	bool hasFixedCharge = false;
707	+	bool hasMultipoles = false;
708	+	bool hasPolarizable = false;
709	+	bool hasFluctuatingCharge = false;
710	+	bool hasMetallic = false;
711	+	int storageLayout = 0;
712	+	storageLayout |= DataStorage::dslPosition;
713	+	storageLayout |= DataStorage::dslVelocity;
714	+	storageLayout |= DataStorage::dslForce;
715	+
716	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717	+
718	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
719	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
720	+	EAMAdapter ea = EAMAdapter( (*i) );
721	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
722	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
723	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
724	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
725	+
726	+	if (da.isDirectional()){
727	+	hasDirectionalAtoms = true;
728	+	}
729	+	if (ma.isMultipole()){
730	+	hasMultipoles = true;
731	+	}
732	+	if (ea.isEAM() || sca.isSuttonChen()){
733	+	hasMetallic = true;
734	+	}
735	+	if ( fca.isFixedCharge() ){
736	+	hasFixedCharge = true;
737	+	}
738	+	if ( fqa.isFluctuatingCharge() ){
739	+	hasFluctuatingCharge = true;
740	+	}
741	+	if ( pa.isPolarizable() ){
742	+	hasPolarizable = true;
743	+	}
744	+	}
745	+
746	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
747	+	storageLayout |= DataStorage::dslAmat;
748	+	if(storageLayout & DataStorage::dslVelocity) {
749	+	storageLayout |= DataStorage::dslAngularMomentum;
750	+	}
751	+	if (storageLayout & DataStorage::dslForce) {
752	+	storageLayout |= DataStorage::dslTorque;
753	+	}
754	+	}
755	+	if (hasMultipoles) {
756	+	storageLayout |= DataStorage::dslElectroFrame;
757	+	}
758	+	if (hasFixedCharge || hasFluctuatingCharge) {
759	+	storageLayout |= DataStorage::dslSkippedCharge;
760	+	}
761	+	if (hasMetallic) {
762	+	storageLayout |= DataStorage::dslDensity;
763	+	storageLayout |= DataStorage::dslFunctional;
764	+	storageLayout |= DataStorage::dslFunctionalDerivative;
765	+	}
766	+	if (hasPolarizable) {
767	+	storageLayout |= DataStorage::dslElectricField;
768	+	}
769	+	if (hasFluctuatingCharge){
770	+	storageLayout |= DataStorage::dslFlucQPosition;
771	+	if(storageLayout & DataStorage::dslVelocity) {
772	+	storageLayout |= DataStorage::dslFlucQVelocity;
773	+	}
774	+	if (storageLayout & DataStorage::dslForce) {
775	+	storageLayout |= DataStorage::dslFlucQForce;
776	+	}
777	+	}
778	+
779	+	// if the user has asked for them, make sure we've got the memory for the
780	+	// objects defined.
781	+
782	+	if (simParams->getOutputParticlePotential()) {
783	+	storageLayout |= DataStorage::dslParticlePot;
784	+	}
785	+
786	+	if (simParams->havePrintHeatFlux()) {
787	+	if (simParams->getPrintHeatFlux()) {
788	+	storageLayout |= DataStorage::dslParticlePot;
789	+	}
790	+	}
791	+
792	+	if (simParams->getOutputElectricField()) {
793	+	storageLayout |= DataStorage::dslElectricField;
794	+	}
795	+	if (simParams->getOutputFluctuatingCharges()) {
796	+	storageLayout |= DataStorage::dslFlucQPosition;
797	+	storageLayout |= DataStorage::dslFlucQVelocity;
798	+	storageLayout |= DataStorage::dslFlucQForce;
799	+	}
800	+
801	+	return storageLayout;
802	+	}
803	+
804		void SimCreator::setGlobalIndex(SimInfo *info) {
805		SimInfo::MoleculeIterator mi;
806		Molecule::AtomIterator ai;
807		Molecule::RigidBodyIterator ri;
808		Molecule::CutoffGroupIterator ci;
809	+	Molecule::IntegrableObjectIterator  ioi;
810		Molecule * mol;
811		Atom * atom;
812		RigidBody * rb;
#	Line 448 | Line 815 | Globals* SimCreator::parseFile(const std::string mdFil
815		int beginRigidBodyIndex;
816		int beginCutoffGroupIndex;
817		int nGlobalAtoms = info->getNGlobalAtoms();
818	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
819
452	–	#ifndef IS_MPI
453	–
820		beginAtomIndex = 0;
821	<	beginRigidBodyIndex = 0;
821	>	//rigidbody's index begins right after atom's
822	>	beginRigidBodyIndex = info->getNGlobalAtoms();
823		beginCutoffGroupIndex = 0;
824	<
825	<	#else
459	<
460	<	int nproc;
461	<	int myNode;
462	<
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)) {
824	>
825	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
826
827	<	//local index(index in DataStorge) of atom is important
828	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
829	<	atom->setGlobalIndex(beginAtomIndex++);
827	>	#ifdef IS_MPI
828	>	if (info->getMolToProc(i) == worldRank) {
829	>	#endif
830	>	// stuff to do if I own this molecule
831	>	mol = info->getMoleculeByGlobalIndex(i);
832	>
833	>	//local index(index in DataStorge) of atom is important
834	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
835	>	atom->setGlobalIndex(beginAtomIndex++);
836	>	}
837	>
838	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
839	>	rb = mol->nextRigidBody(ri)) {
840	>	rb->setGlobalIndex(beginRigidBodyIndex++);
841	>	}
842	>
843	>	//local index of cutoff group is trivial, it only depends on
844	>	//the order of travesing
845	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
846	>	cg = mol->nextCutoffGroup(ci)) {
847	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
848	>	}
849	>
850	>	#ifdef IS_MPI
851	>	}  else {
852	>
853	>	// stuff to do if I don't own this molecule
854	>
855	>	int stampId = info->getMoleculeStampId(i);
856	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
857	>
858	>	beginAtomIndex += stamp->getNAtoms();
859	>	beginRigidBodyIndex += stamp->getNRigidBodies();
860	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
861		}
862	<
863	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
864	<	rb = mol->nextRigidBody(ri)) {
865	<	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	<
862	>	#endif
863	>
864	>	} //end for(int i=0)
865	>
866		//fill globalGroupMembership
867		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
868		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 528 | Line 874 | Globals* SimCreator::parseFile(const std::string mdFil
874
875		}
876		}
877	<
877	>
878		#ifdef IS_MPI
879		// Since the globalGroupMembership has been zero filled and we've only
880		// poked values into the atoms we know, we can do an Allreduce
881		// to get the full globalGroupMembership array (We think).
882		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
883		// docs said we could.
884	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
885	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
886	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
884	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
885	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
886	>	&tmpGroupMembership[0], nGlobalAtoms,
887	>	MPI::INT, MPI::SUM);
888		info->setGlobalGroupMembership(tmpGroupMembership);
889		#else
890		info->setGlobalGroupMembership(globalGroupMembership);
891		#endif
892
893		//fill molMembership
894	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
894	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
895	>	info->getNGlobalRigidBodies(), 0);
896
897	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
898	<
897	>	for(mol = info->beginMolecule(mi); mol != NULL;
898	>	mol = info->nextMolecule(mi)) {
899		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
900		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
901		}
902	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
903	+	rb = mol->nextRigidBody(ri)) {
904	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
905	+	}
906		}
907
908		#ifdef IS_MPI
909	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
909	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
910	>	info->getNGlobalRigidBodies(), 0);
911	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
912	>	nGlobalAtoms + nGlobalRigidBodies,
913	>	MPI::INT, MPI::SUM);
914
559	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
560	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
561	–
915		info->setGlobalMolMembership(tmpMolMembership);
916		#else
917		info->setGlobalMolMembership(globalMolMembership);
918		#endif
919	+
920	+	// nIOPerMol holds the number of integrable objects per molecule
921	+	// here the molecules are listed by their global indices.
922	+
923	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
924	+	for (mol = info->beginMolecule(mi); mol != NULL;
925	+	mol = info->nextMolecule(mi)) {
926	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
927	+	}
928
929	<	}
930	<
931	<	void SimCreator::loadCoordinates(SimInfo* info) {
932	<	Globals* simParams;
933	<	simParams = info->getSimParams();
929	>	#ifdef IS_MPI
930	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
931	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
932	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
933	>	#else
934	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
935	>	#endif
936	>
937	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
938
939	<	if (!simParams->haveInitialConfig()) {
940	<	sprintf(painCave.errMsg,
941	<	"Cannot intialize a simulation without an initial configuration file.\n");
942	<	painCave.isFatal = 1;;
577	<	simError();
939	>	int startingIndex = 0;
940	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
941	>	startingIOIndexForMol[i] = startingIndex;
942	>	startingIndex += numIntegrableObjectsPerMol[i];
943		}
944
945	<	DumpReader reader(info, simParams->getInitialConfig());
946	<	int nframes = reader.getNFrames();
945	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
946	>	for (mol = info->beginMolecule(mi); mol != NULL;
947	>	mol = info->nextMolecule(mi)) {
948	>	int myGlobalIndex = mol->getGlobalIndex();
949	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
950	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
951	>	sd = mol->nextIntegrableObject(ioi)) {
952	>	sd->setGlobalIntegrableObjectIndex(globalIO);
953	>	IOIndexToIntegrableObject[globalIO] = sd;
954	>	globalIO++;
955	>	}
956	>	}
957	>
958	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
959
960	+	}
961	+
962	+	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
963	+
964	+	DumpReader reader(info, mdFileName);
965	+	int nframes = reader.getNFrames();
966	+
967		if (nframes > 0) {
968		reader.readFrame(nframes - 1);
969		} else {
970		//invalid initial coordinate file
971		sprintf(painCave.errMsg,
972		"Initial configuration file %s should at least contain one frame\n",
973	<	simParams->getInitialConfig().c_str());
973	>	mdFileName.c_str());
974		painCave.isFatal = 1;
975		simError();
976		}
593	–
977		//copy the current snapshot to previous snapshot
978		info->getSnapshotManager()->advance();
979		}
980
981	<	} //end namespace oopse
981	>	} //end namespace OpenMD
982
983

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1810 by gezelter, Thu Nov 8 14:23:43 2012 UTC

#	Line 0 | Line 1
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