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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 832 by tim, Fri Dec 30 15:32:55 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 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	<
49	>	#include <exception>
50		#include <iostream>
51		#include <sstream>
52		#include <string>
#	Line 55 | Line 55
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
58	<	#include "UseTheForce/ForceFieldFactory.hpp"
58	>	#include "brains/ForceField.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 75
75		#include "antlr/NoViableAltForCharException.hpp"
76		#include "antlr/NoViableAltException.hpp"
77
78	+	#include "types/DirectionalAdapter.hpp"
79	+	#include "types/MultipoleAdapter.hpp"
80	+	#include "types/EAMAdapter.hpp"
81	+	#include "types/SuttonChenAdapter.hpp"
82	+	#include "types/PolarizableAdapter.hpp"
83	+	#include "types/FixedChargeAdapter.hpp"
84	+	#include "types/FluctuatingChargeAdapter.hpp"
85	+
86		#ifdef IS_MPI
87	+	#include "mpi.h"
88		#include "math/ParallelRandNumGen.hpp"
89		#endif
90
91	<	namespace oopse {
91	>	namespace OpenMD {
92
93	<	Globals* SimCreator::parseFile(const std::string mdFileName){
94	<	Globals* simParams = NULL;
95	<	try {
93	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
94	>	Globals* simParams = NULL;
95	>	try {
96
97	<	// Create a preprocessor that preprocesses md file into an ostringstream
98	<	std::stringstream ppStream;
97	>	// Create a preprocessor that preprocesses md file into an ostringstream
98	>	std::stringstream ppStream;
99		#ifdef IS_MPI
100	<	int streamSize;
101	<	const int masterNode = 0;
102	<	int commStatus;
103	<	if (worldRank == masterNode) {
104	<	#endif
100	>	int streamSize;
101	>	const int masterNode = 0;
102	>
103	>	if (worldRank == masterNode) {
104	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock,
108	>	ppStream);
109
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
110		#ifdef IS_MPI
111	<	//brocasting the stream size
112	<	streamSize = ppStream.str().size() +1;
113	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
111	>	//brocasting the stream size
112	>	streamSize = ppStream.str().size() +1;
113	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
114	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
115	>
116	>	} else {
117	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
118
119	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
120	<
119	>	//get stream size
120	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121	>
122	>	char* buf = new char[streamSize];
123	>	assert(buf);
124
125	<	} else {
126	<	//get stream size
110	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
125	>	//receive file content
126	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
127
128	<	char* buf = new char[streamSize];
129	<	assert(buf);
130	<
115	<	//receive file content
116	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	<
118	<	ppStream.str(buf);
119	<	delete buf;
120	<
121	<	}
128	>	ppStream.str(buf);
129	>	delete [] buf;
130	>	}
131		#endif
132	<	// Create a scanner that reads from the input stream
133	<	MDLexer lexer(ppStream);
134	<	lexer.setFilename(mdFileName);
135	<	lexer.initDeferredLineCount();
132	>	// Create a scanner that reads from the input stream
133	>	MDLexer lexer(ppStream);
134	>	lexer.setFilename(filename);
135	>	lexer.initDeferredLineCount();
136
137	<	// Create a parser that reads from the scanner
138	<	MDParser parser(lexer);
139	<	parser.setFilename(mdFileName);
137	>	// Create a parser that reads from the scanner
138	>	MDParser parser(lexer);
139	>	parser.setFilename(filename);
140
141	<	// Create an observer that synchorizes file name change
142	<	FilenameObserver observer;
143	<	observer.setLexer(&lexer);
144	<	observer.setParser(&parser);
145	<	lexer.setObserver(&observer);
141	>	// Create an observer that synchorizes file name change
142	>	FilenameObserver observer;
143	>	observer.setLexer(&lexer);
144	>	observer.setParser(&parser);
145	>	lexer.setObserver(&observer);
146
147	<	antlr::ASTFactory factory;
148	<	parser.initializeASTFactory(factory);
149	<	parser.setASTFactory(&factory);
150	<	parser.mdfile();
147	>	antlr::ASTFactory factory;
148	>	parser.initializeASTFactory(factory);
149	>	parser.setASTFactory(&factory);
150	>	parser.mdfile();
151
152	<	// Create a tree parser that reads information into Globals
153	<	MDTreeParser treeParser;
154	<	treeParser.initializeASTFactory(factory);
155	<	treeParser.setASTFactory(&factory);
156	<	simParams = treeParser.walkTree(parser.getAST());
152	>	// Create a tree parser that reads information into Globals
153	>	MDTreeParser treeParser;
154	>	treeParser.initializeASTFactory(factory);
155	>	treeParser.setASTFactory(&factory);
156	>	simParams = treeParser.walkTree(parser.getAST());
157	>	}
158
149	–	}
159
160	<	catch(antlr::MismatchedCharException& e) {
161	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
162	<	}
163	<	catch(antlr::MismatchedTokenException &e) {
164	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
165	<	}
166	<	catch(antlr::NoViableAltForCharException &e) {
167	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
168	<	}
169	<	catch(antlr::NoViableAltException &e) {
170	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
171	<	}
172	<	catch(antlr::TokenStreamRecognitionException& e) {
173	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
174	<	}
175	<	catch(antlr::TokenStreamIOException& e) {
176	<	cerr<< "parser exception: " << e.getMessage() << endl;
177	<	}
178	<	catch(antlr::TokenStreamException& e) {
179	<	cerr<< "parser exception: " << e.getMessage() << endl;
180	<	}
181	<	catch (antlr::RecognitionException& e) {
182	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
183	<	}
184	<	catch (antlr::CharStreamException& e) {
185	<	cerr << "parser exception: " << e.getMessage() << endl;
186	<	}
187	<	catch (exception& e) {
188	<	cerr << "parser exception: " << e.what() << endl;
189	<	}
160	>	catch(antlr::MismatchedCharException& e) {
161	>	sprintf(painCave.errMsg,
162	>	"parser exception: %s %s:%d:%d\n",
163	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
164	>	painCave.isFatal = 1;
165	>	simError();
166	>	}
167	>	catch(antlr::MismatchedTokenException &e) {
168	>	sprintf(painCave.errMsg,
169	>	"parser exception: %s %s:%d:%d\n",
170	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
171	>	painCave.isFatal = 1;
172	>	simError();
173	>	}
174	>	catch(antlr::NoViableAltForCharException &e) {
175	>	sprintf(painCave.errMsg,
176	>	"parser exception: %s %s:%d:%d\n",
177	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
178	>	painCave.isFatal = 1;
179	>	simError();
180	>	}
181	>	catch(antlr::NoViableAltException &e) {
182	>	sprintf(painCave.errMsg,
183	>	"parser exception: %s %s:%d:%d\n",
184	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
185	>	painCave.isFatal = 1;
186	>	simError();
187	>	}
188	>
189	>	catch(antlr::TokenStreamRecognitionException& e) {
190	>	sprintf(painCave.errMsg,
191	>	"parser exception: %s %s:%d:%d\n",
192	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
193	>	painCave.isFatal = 1;
194	>	simError();
195	>	}
196	>
197	>	catch(antlr::TokenStreamIOException& e) {
198	>	sprintf(painCave.errMsg,
199	>	"parser exception: %s\n",
200	>	e.getMessage().c_str());
201	>	painCave.isFatal = 1;
202	>	simError();
203	>	}
204	>
205	>	catch(antlr::TokenStreamException& e) {
206	>	sprintf(painCave.errMsg,
207	>	"parser exception: %s\n",
208	>	e.getMessage().c_str());
209	>	painCave.isFatal = 1;
210	>	simError();
211	>	}
212	>	catch (antlr::RecognitionException& e) {
213	>	sprintf(painCave.errMsg,
214	>	"parser exception: %s %s:%d:%d\n",
215	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
216	>	painCave.isFatal = 1;
217	>	simError();
218	>	}
219	>	catch (antlr::CharStreamException& e) {
220	>	sprintf(painCave.errMsg,
221	>	"parser exception: %s\n",
222	>	e.getMessage().c_str());
223	>	painCave.isFatal = 1;
224	>	simError();
225	>	}
226	>	catch (OpenMDException& e) {
227	>	sprintf(painCave.errMsg,
228	>	"%s\n",
229	>	e.getMessage().c_str());
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	catch (std::exception& e) {
234	>	sprintf(painCave.errMsg,
235	>	"parser exception: %s\n",
236	>	e.what());
237	>	painCave.isFatal = 1;
238	>	simError();
239	>	}
240
241	<	return simParams;
241	>	simParams->setMDfileVersion(mdFileVersion);
242	>	return simParams;
243		}
244
245		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
246		bool loadInitCoords) {
247	+
248	+	const int bufferSize = 65535;
249	+	char buffer[bufferSize];
250	+	int lineNo = 0;
251	+	std::string mdRawData;
252	+	int metaDataBlockStart = -1;
253	+	int metaDataBlockEnd = -1;
254	+	int i, j;
255	+	streamoff mdOffset;
256	+	int mdFileVersion;
257
258	+	// Create a string for embedding the version information in the MetaData
259	+	std::string version;
260	+	version.assign("## Last run using OpenMD Version: ");
261	+	version.append(OPENMD_VERSION_MAJOR);
262	+	version.append(".");
263	+	version.append(OPENMD_VERSION_MINOR);
264	+
265	+	std::string svnrev;
266	+	//convert a macro from compiler to a string in c++
267	+	STR_DEFINE(svnrev, SVN_REV );
268	+	version.append(" Revision: ");
269	+	// If there's no SVN revision, just call this the RELEASE revision.
270	+	if (!svnrev.empty()) {
271	+	version.append(svnrev);
272	+	} else {
273	+	version.append("RELEASE");
274	+	}
275	+
276	+	#ifdef IS_MPI
277	+	const int masterNode = 0;
278	+	if (worldRank == masterNode) {
279	+	#endif
280	+
281	+	std::ifstream mdFile_;
282	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
283	+
284	+	if (mdFile_.fail()) {
285	+	sprintf(painCave.errMsg,
286	+	"SimCreator: Cannot open file: %s\n",
287	+	mdFileName.c_str());
288	+	painCave.isFatal = 1;
289	+	simError();
290	+	}
291	+
292	+	mdFile_.getline(buffer, bufferSize);
293	+	++lineNo;
294	+	std::string line = trimLeftCopy(buffer);
295	+	i = CaseInsensitiveFind(line, "<OpenMD");
296	+	if (static_cast<size_t>(i) == string::npos) {
297	+	// try the older file strings to see if that works:
298	+	i = CaseInsensitiveFind(line, "<OOPSE");
299	+	}
300	+
301	+	if (static_cast<size_t>(i) == string::npos) {
302	+	// still no luck!
303	+	sprintf(painCave.errMsg,
304	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
305	+	mdFileName.c_str());
306	+	painCave.isFatal = 1;
307	+	simError();
308	+	}
309	+
310	+	// found the correct opening string, now try to get the file
311	+	// format version number.
312	+
313	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
314	+	std::string fileType = tokenizer.nextToken();
315	+	toUpper(fileType);
316	+
317	+	mdFileVersion = 0;
318	+
319	+	if (fileType == "OPENMD") {
320	+	while (tokenizer.hasMoreTokens()) {
321	+	std::string token(tokenizer.nextToken());
322	+	toUpper(token);
323	+	if (token == "VERSION") {
324	+	mdFileVersion = tokenizer.nextTokenAsInt();
325	+	break;
326	+	}
327	+	}
328	+	}
329	+
330	+	//scan through the input stream and find MetaData tag
331	+	while(mdFile_.getline(buffer, bufferSize)) {
332	+	++lineNo;
333	+
334	+	std::string line = trimLeftCopy(buffer);
335	+	if (metaDataBlockStart == -1) {
336	+	i = CaseInsensitiveFind(line, "<MetaData>");
337	+	if (i != string::npos) {
338	+	metaDataBlockStart = lineNo;
339	+	mdOffset = mdFile_.tellg();
340	+	}
341	+	} else {
342	+	i = CaseInsensitiveFind(line, "</MetaData>");
343	+	if (i != string::npos) {
344	+	metaDataBlockEnd = lineNo;
345	+	}
346	+	}
347	+	}
348	+
349	+	if (metaDataBlockStart == -1) {
350	+	sprintf(painCave.errMsg,
351	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
352	+	mdFileName.c_str());
353	+	painCave.isFatal = 1;
354	+	simError();
355	+	}
356	+	if (metaDataBlockEnd == -1) {
357	+	sprintf(painCave.errMsg,
358	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
359	+	mdFileName.c_str());
360	+	painCave.isFatal = 1;
361	+	simError();
362	+	}
363	+
364	+	mdFile_.clear();
365	+	mdFile_.seekg(0);
366	+	mdFile_.seekg(mdOffset);
367	+
368	+	mdRawData.clear();
369	+
370	+	bool foundVersion = false;
371	+
372	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
373	+	mdFile_.getline(buffer, bufferSize);
374	+	std::string line = trimLeftCopy(buffer);
375	+	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
376	+	if (static_cast<size_t>(j) != string::npos) {
377	+	foundVersion = true;
378	+	mdRawData += version;
379	+	} else {
380	+	mdRawData += buffer;
381	+	}
382	+	mdRawData += "\n";
383	+	}
384	+
385	+	if (!foundVersion) mdRawData += version + "\n";
386	+
387	+	mdFile_.close();
388	+
389	+	#ifdef IS_MPI
390	+	}
391	+	#endif
392	+
393	+	std::stringstream rawMetaDataStream(mdRawData);
394	+
395		//parse meta-data file
396	<	Globals* simParams = parseFile(mdFileName);
396	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
397	>	metaDataBlockStart + 1);
398
399		//create the force field
400	<	ForceField * ff = ForceFieldFactory::getInstance()
401	<	->createForceField(simParams->getForceField());
194	<
400	>	ForceField * ff = new ForceField(simParams->getForceField());
401	>
402		if (ff == NULL) {
403		sprintf(painCave.errMsg,
404		"ForceField Factory can not create %s force field\n",
#	Line 224 | Line 431 | Globals* SimCreator::parseFile(const std::string mdFil
431		}
432
433		ff->parse(forcefieldFileName);
227	–	ff->setFortranForceOptions();
434		//create SimInfo
435		SimInfo * info = new SimInfo(ff, simParams);
436	+
437	+	info->setRawMetaData(mdRawData);
438
439	<	//gather parameters (SimCreator only retrieves part of the parameters)
439	>	//gather parameters (SimCreator only retrieves part of the
440	>	//parameters)
441		gatherParameters(info, mdFileName);
442
443		//divide the molecules and determine the global index of molecules
#	Line 239 | Line 448 | Globals* SimCreator::parseFile(const std::string mdFil
448		//create the molecules
449		createMolecules(info);
450
451	+	//find the storage layout
452	+
453	+	int storageLayout = computeStorageLayout(info);
454	+
455	+	//allocate memory for DataStorage(circular reference, need to
456	+	//break it)
457	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
458
459	<	//allocate memory for DataStorage(circular reference, need to break it)
460	<	info->setSnapshotManager(new SimSnapshotManager(info));
461	<
462	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
463	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
248	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
459	>	//set the global index of atoms, rigidbodies and cutoffgroups
460	>	//(only need to be set once, the global index will never change
461	>	//again). Local indices of atoms and rigidbodies are already set
462	>	//by MoleculeCreator class which actually delegates the
463	>	//responsibility to LocalIndexManager.
464		setGlobalIndex(info);
465
466	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
467	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
468	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
469	<	//we can determine the beginning global indices of atoms before they get created.
466	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
467	>	//method, at that point atoms don't have the global index yet
468	>	//(their global index are all initialized to -1).  Therefore we
469	>	//have to call addInteractionPairs explicitly here. A way to work
470	>	//around is that we can determine the beginning global indices of
471	>	//atoms before they get created.
472		SimInfo::MoleculeIterator mi;
473		Molecule* mol;
474		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
475	<	info->addExcludePairs(mol);
475	>	info->addInteractionPairs(mol);
476		}
477
478		if (loadInitCoords)
479	<	loadCoordinates(info);
263	<
479	>	loadCoordinates(info, mdFileName);
480		return info;
481		}
482
#	Line 295 | Line 511 | Globals* SimCreator::parseFile(const std::string mdFil
511
512		#ifdef IS_MPI
513		void SimCreator::divideMolecules(SimInfo *info) {
514	<	double numerator;
299	<	double denominator;
300	<	double precast;
301	<	double x;
302	<	double y;
303	<	double a;
304	<	int old_atoms;
305	<	int add_atoms;
306	<	int new_atoms;
307	<	int nTarget;
308	<	int done;
309	<	int i;
310	<	int j;
311	<	int loops;
312	<	int which_proc;
514	>	RealType a;
515		int nProcessors;
516		std::vector<int> atomsPerProc;
517		int nGlobalMols = info->getNGlobalMolecules();
518	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
518	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
519	>	// error
520	>	// condition:
521
522	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
522	>	nProcessors = MPI::COMM_WORLD.Get_size();
523
524		if (nProcessors > nGlobalMols) {
525		sprintf(painCave.errMsg,
#	Line 324 | Line 528 | Globals* SimCreator::parseFile(const std::string mdFil
528		"\tthe number of molecules.  This will not result in a \n"
529		"\tusable division of atoms for force decomposition.\n"
530		"\tEither try a smaller number of processors, or run the\n"
531	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
531	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
532	>	nGlobalMols);
533
534		painCave.isFatal = 1;
535		simError();
536		}
537
333	–	int seedValue;
538		Globals * simParams = info->getSimParams();
539	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
539	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
540	>	//random number generator
541		if (simParams->haveSeed()) {
542	<	seedValue = simParams->getSeed();
542	>	int seedValue = simParams->getSeed();
543		myRandom = new SeqRandNumGen(seedValue);
544		}else {
545		myRandom = new SeqRandNumGen();
#	Line 347 | Line 552 | Globals* SimCreator::parseFile(const std::string mdFil
552		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
553
554		if (worldRank == 0) {
555	<	numerator = info->getNGlobalAtoms();
556	<	denominator = nProcessors;
557	<	precast = numerator / denominator;
558	<	nTarget = (int)(precast + 0.5);
555	>	RealType numerator = info->getNGlobalAtoms();
556	>	RealType denominator = nProcessors;
557	>	RealType precast = numerator / denominator;
558	>	int nTarget = (int)(precast + 0.5);
559
560	<	for(i = 0; i < nGlobalMols; i++) {
561	<	done = 0;
562	<	loops = 0;
560	>	for(int i = 0; i < nGlobalMols; i++) {
561	>
562	>	int done = 0;
563	>	int loops = 0;
564
565		while (!done) {
566		loops++;
567
568		// Pick a processor at random
569
570	<	which_proc = (int) (myRandom->rand() * nProcessors);
570	>	int which_proc = (int) (myRandom->rand() * nProcessors);
571
572		//get the molecule stamp first
573		int stampId = info->getMoleculeStampId(i);
574		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
575
576		// How many atoms does this processor have so far?
577	<	old_atoms = atomsPerProc[which_proc];
578	<	add_atoms = moleculeStamp->getNAtoms();
579	<	new_atoms = old_atoms + add_atoms;
577	>	int old_atoms = atomsPerProc[which_proc];
578	>	int add_atoms = moleculeStamp->getNAtoms();
579	>	int new_atoms = old_atoms + add_atoms;
580
581		// If we've been through this loop too many times, we need
582		// to just give up and assign the molecule to this processor
583		// and be done with it.
584
585		if (loops > 100) {
586	+
587		sprintf(painCave.errMsg,
588	<	"I've tried 100 times to assign molecule %d to a "
589	<	" processor, but can't find a good spot.\n"
590	<	"I'm assigning it at random to processor %d.\n",
588	>	"There have been 100 attempts to assign molecule %d to an\n"
589	>	"\tunderworked processor, but there's no good place to\n"
590	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
591		i, which_proc);
592	<
592	>
593		painCave.isFatal = 0;
594	+	painCave.severity = OPENMD_INFO;
595		simError();
596
597		molToProcMap[i] = which_proc;
#	Line 412 | Line 620 | Globals* SimCreator::parseFile(const std::string mdFil
620		//           Pacc(x) = exp(- a * x)
621		// where a = penalty / (average atoms per molecule)
622
623	<	x = (double)(new_atoms - nTarget);
624	<	y = myRandom->rand();
623	>	RealType x = (RealType)(new_atoms - nTarget);
624	>	RealType y = myRandom->rand();
625
626		if (y < exp(- a * x)) {
627		molToProcMap[i] = which_proc;
#	Line 428 | Line 636 | Globals* SimCreator::parseFile(const std::string mdFil
636		}
637
638		delete myRandom;
639	<
639	>
640		// Spray out this nonsense to all other processors:
641	<
434	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
641	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
642		} else {
643
644		// Listen to your marching orders from processor 0:
645	<
646	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
645	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
646	>
647		}
648
649		info->setMolToProcMap(molToProcMap);
650		sprintf(checkPointMsg,
651		"Successfully divided the molecules among the processors.\n");
652	<	MPIcheckPoint();
652	>	errorCheckPoint();
653		}
654
655		#endif
#	Line 459 | Line 666 | Globals* SimCreator::parseFile(const std::string mdFil
666		#endif
667
668		stampId = info->getMoleculeStampId(i);
669	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
670	<	stampId, i, info->getLocalIndexManager());
669	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
670	>	info->getMoleculeStamp(stampId),
671	>	stampId, i,
672	>	info->getLocalIndexManager());
673
674		info->addMolecule(mol);
675
#	Line 472 | Line 681 | Globals* SimCreator::parseFile(const std::string mdFil
681
682		} //end for(int i=0)
683		}
684	+
685	+	int SimCreator::computeStorageLayout(SimInfo* info) {
686	+
687	+	Globals* simParams = info->getSimParams();
688	+	int nRigidBodies = info->getNGlobalRigidBodies();
689	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
690	+	set<AtomType*>::iterator i;
691	+	bool hasDirectionalAtoms = false;
692	+	bool hasFixedCharge = false;
693	+	bool hasDipoles = false;
694	+	bool hasQuadrupoles = false;
695	+	bool hasPolarizable = false;
696	+	bool hasFluctuatingCharge = false;
697	+	bool hasMetallic = false;
698	+	int storageLayout = 0;
699	+	storageLayout |= DataStorage::dslPosition;
700	+	storageLayout |= DataStorage::dslVelocity;
701	+	storageLayout |= DataStorage::dslForce;
702	+
703	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
704	+
705	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
706	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
707	+	EAMAdapter ea = EAMAdapter( (*i) );
708	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
709	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
710	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
711	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
712	+
713	+	if (da.isDirectional()){
714	+	hasDirectionalAtoms = true;
715	+	}
716	+	if (ma.isDipole()){
717	+	hasDipoles = true;
718	+	}
719	+	if (ma.isQuadrupole()){
720	+	hasQuadrupoles = true;
721	+	}
722	+	if (ea.isEAM() || sca.isSuttonChen()){
723	+	hasMetallic = true;
724	+	}
725	+	if ( fca.isFixedCharge() ){
726	+	hasFixedCharge = true;
727	+	}
728	+	if ( fqa.isFluctuatingCharge() ){
729	+	hasFluctuatingCharge = true;
730	+	}
731	+	if ( pa.isPolarizable() ){
732	+	hasPolarizable = true;
733	+	}
734	+	}
735
736	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
737	+	storageLayout |= DataStorage::dslAmat;
738	+	if(storageLayout & DataStorage::dslVelocity) {
739	+	storageLayout |= DataStorage::dslAngularMomentum;
740	+	}
741	+	if (storageLayout & DataStorage::dslForce) {
742	+	storageLayout |= DataStorage::dslTorque;
743	+	}
744	+	}
745	+	if (hasDipoles) {
746	+	storageLayout |= DataStorage::dslDipole;
747	+	}
748	+	if (hasQuadrupoles) {
749	+	storageLayout |= DataStorage::dslQuadrupole;
750	+	}
751	+	if (hasFixedCharge || hasFluctuatingCharge) {
752	+	storageLayout |= DataStorage::dslSkippedCharge;
753	+	}
754	+	if (hasMetallic) {
755	+	storageLayout |= DataStorage::dslDensity;
756	+	storageLayout |= DataStorage::dslFunctional;
757	+	storageLayout |= DataStorage::dslFunctionalDerivative;
758	+	}
759	+	if (hasPolarizable) {
760	+	storageLayout |= DataStorage::dslElectricField;
761	+	}
762	+	if (hasFluctuatingCharge){
763	+	storageLayout |= DataStorage::dslFlucQPosition;
764	+	if(storageLayout & DataStorage::dslVelocity) {
765	+	storageLayout |= DataStorage::dslFlucQVelocity;
766	+	}
767	+	if (storageLayout & DataStorage::dslForce) {
768	+	storageLayout |= DataStorage::dslFlucQForce;
769	+	}
770	+	}
771	+
772	+	// if the user has asked for them, make sure we've got the memory for the
773	+	// objects defined.
774	+
775	+	if (simParams->getOutputParticlePotential()) {
776	+	storageLayout |= DataStorage::dslParticlePot;
777	+	}
778	+
779	+	if (simParams->havePrintHeatFlux()) {
780	+	if (simParams->getPrintHeatFlux()) {
781	+	storageLayout |= DataStorage::dslParticlePot;
782	+	}
783	+	}
784	+
785	+	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
786	+	storageLayout |= DataStorage::dslElectricField;
787	+	}
788	+
789	+	if (simParams->getOutputFluctuatingCharges()) {
790	+	storageLayout |= DataStorage::dslFlucQPosition;
791	+	storageLayout |= DataStorage::dslFlucQVelocity;
792	+	storageLayout |= DataStorage::dslFlucQForce;
793	+	}
794	+
795	+	info->setStorageLayout(storageLayout);
796	+
797	+	return storageLayout;
798	+	}
799	+
800		void SimCreator::setGlobalIndex(SimInfo *info) {
801		SimInfo::MoleculeIterator mi;
802		Molecule::AtomIterator ai;
803		Molecule::RigidBodyIterator ri;
804		Molecule::CutoffGroupIterator ci;
805	+	Molecule::IntegrableObjectIterator  ioi;
806		Molecule * mol;
807		Atom * atom;
808		RigidBody * rb;
#	Line 486 | Line 811 | Globals* SimCreator::parseFile(const std::string mdFil
811		int beginRigidBodyIndex;
812		int beginCutoffGroupIndex;
813		int nGlobalAtoms = info->getNGlobalAtoms();
814	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
815
490	–	#ifndef IS_MPI
491	–
816		beginAtomIndex = 0;
493	–	beginRigidBodyIndex = 0;
494	–	beginCutoffGroupIndex = 0;
495	–
496	–	#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	–
817		//rigidbody's index begins right after atom's
818	<	beginRigidBodyIndex += info->getNGlobalAtoms();
819	<
820	<	for(mol = info->beginMolecule(mi); mol != NULL;
821	<	mol = info->nextMolecule(mi)) {
818	>	beginRigidBodyIndex = info->getNGlobalAtoms();
819	>	beginCutoffGroupIndex = 0;
820	>
821	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
822
823	<	//local index(index in DataStorge) of atom is important
824	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	<	atom->setGlobalIndex(beginAtomIndex++);
823	>	#ifdef IS_MPI
824	>	if (info->getMolToProc(i) == worldRank) {
825	>	#endif
826	>	// stuff to do if I own this molecule
827	>	mol = info->getMoleculeByGlobalIndex(i);
828	>
829	>	//local index(index in DataStorge) of atom is important
830	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
831	>	atom->setGlobalIndex(beginAtomIndex++);
832	>	}
833	>
834	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
835	>	rb = mol->nextRigidBody(ri)) {
836	>	rb->setGlobalIndex(beginRigidBodyIndex++);
837	>	}
838	>
839	>	//local index of cutoff group is trivial, it only depends on
840	>	//the order of travesing
841	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
842	>	cg = mol->nextCutoffGroup(ci)) {
843	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
844	>	}
845	>
846	>	#ifdef IS_MPI
847	>	}  else {
848	>
849	>	// stuff to do if I don't own this molecule
850	>
851	>	int stampId = info->getMoleculeStampId(i);
852	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
853	>
854	>	beginAtomIndex += stamp->getNAtoms();
855	>	beginRigidBodyIndex += stamp->getNRigidBodies();
856	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
857		}
858	<
859	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
860	<	rb = mol->nextRigidBody(ri)) {
861	<	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	<
858	>	#endif
859	>
860	>	} //end for(int i=0)
861	>
862		//fill globalGroupMembership
863		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
864		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 566 | Line 870 | Globals* SimCreator::parseFile(const std::string mdFil
870
871		}
872		}
873	<
873	>
874		#ifdef IS_MPI
875		// Since the globalGroupMembership has been zero filled and we've only
876		// poked values into the atoms we know, we can do an Allreduce
877		// to get the full globalGroupMembership array (We think).
878		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
879		// docs said we could.
880	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
881	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
882	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
880	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
881	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
882	>	&tmpGroupMembership[0], nGlobalAtoms,
883	>	MPI::INT, MPI::SUM);
884		info->setGlobalGroupMembership(tmpGroupMembership);
885		#else
886		info->setGlobalGroupMembership(globalGroupMembership);
887		#endif
888
889		//fill molMembership
890	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
890	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
891	>	info->getNGlobalRigidBodies(), 0);
892
893	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
894	<
893	>	for(mol = info->beginMolecule(mi); mol != NULL;
894	>	mol = info->nextMolecule(mi)) {
895		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
897		}
898	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
899	+	rb = mol->nextRigidBody(ri)) {
900	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
901	+	}
902		}
903
904		#ifdef IS_MPI
905	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
905	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
906	>	info->getNGlobalRigidBodies(), 0);
907	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
908	>	nGlobalAtoms + nGlobalRigidBodies,
909	>	MPI::INT, MPI::SUM);
910
597	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
598	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
599	–
911		info->setGlobalMolMembership(tmpMolMembership);
912		#else
913		info->setGlobalMolMembership(globalMolMembership);
914		#endif
915	+
916	+	// nIOPerMol holds the number of integrable objects per molecule
917	+	// here the molecules are listed by their global indices.
918	+
919	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
920	+	for (mol = info->beginMolecule(mi); mol != NULL;
921	+	mol = info->nextMolecule(mi)) {
922	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
923	+	}
924
925	<	}
926	<
927	<	void SimCreator::loadCoordinates(SimInfo* info) {
928	<	Globals* simParams;
929	<	simParams = info->getSimParams();
925	>	#ifdef IS_MPI
926	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
927	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
928	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
929	>	#else
930	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
931	>	#endif
932	>
933	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
934
935	<	if (!simParams->haveInitialConfig()) {
936	<	sprintf(painCave.errMsg,
937	<	"Cannot intialize a simulation without an initial configuration file.\n");
938	<	painCave.isFatal = 1;;
615	<	simError();
935	>	int startingIndex = 0;
936	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
937	>	startingIOIndexForMol[i] = startingIndex;
938	>	startingIndex += numIntegrableObjectsPerMol[i];
939		}
940
941	<	DumpReader reader(info, simParams->getInitialConfig());
941	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
942	>	for (mol = info->beginMolecule(mi); mol != NULL;
943	>	mol = info->nextMolecule(mi)) {
944	>	int myGlobalIndex = mol->getGlobalIndex();
945	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
946	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
947	>	sd = mol->nextIntegrableObject(ioi)) {
948	>	sd->setGlobalIntegrableObjectIndex(globalIO);
949	>	IOIndexToIntegrableObject[globalIO] = sd;
950	>	globalIO++;
951	>	}
952	>	}
953	>
954	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
955	>
956	>	}
957	>
958	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
959	>
960	>	DumpReader reader(info, mdFileName);
961		int nframes = reader.getNFrames();
962
963		if (nframes > 0) {
#	Line 624 | Line 966 | Globals* SimCreator::parseFile(const std::string mdFil
966		//invalid initial coordinate file
967		sprintf(painCave.errMsg,
968		"Initial configuration file %s should at least contain one frame\n",
969	<	simParams->getInitialConfig().c_str());
969	>	mdFileName.c_str());
970		painCave.isFatal = 1;
971		simError();
972		}
631	–
973		//copy the current snapshot to previous snapshot
974		info->getSnapshotManager()->advance();
975		}
976
977	<	} //end namespace oopse
977	>	} //end namespace OpenMD
978
979

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 832 by tim, Fri Dec 30 15:32:55 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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