ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/development/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.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1825 by gezelter, Wed Jan 9 19:27:52 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, 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		/**
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 63 | Line 63
63		#include "mdParser/MDParser.hpp"
64		#include "mdParser/MDTreeParser.hpp"
65		#include "mdParser/SimplePreprocessor.hpp"
66	+	#include "antlr/ANTLRException.hpp"
67	+	#include "antlr/TokenStreamRecognitionException.hpp"
68	+	#include "antlr/TokenStreamIOException.hpp"
69	+	#include "antlr/TokenStreamException.hpp"
70	+	#include "antlr/RecognitionException.hpp"
71	+	#include "antlr/CharStreamException.hpp"
72
73	+	#include "antlr/MismatchedCharException.hpp"
74	+	#include "antlr/MismatchedTokenException.hpp"
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	>	int commStatus;
103	>	if (worldRank == masterNode) {
104	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108
87	–	SimplePreprocessor preprocessor;
88	–	preprocessor.preprocess(mdFileName, ppStream);
89	–
109		#ifdef IS_MPI
110	<	//brocasting the stream size
111	<	streamSize = ppStream.str().size() +1;
112	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
110	>	//brocasting the stream size
111	>	streamSize = ppStream.str().size() +1;
112	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
113
114	<	commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
114	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
115
116
117	<	} else {
118	<	//get stream size
119	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
117	>	} else {
118	>
119	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
120	>
121	>	//get stream size
122	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
123	>
124	>	char* buf = new char[streamSize];
125	>	assert(buf);
126
127	<	char* buf = new char[streamSize];
128	<	assert(buf);
127	>	//receive file content
128	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129
130	<	//receive file content
131	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
107	<
108	<	ppStream.str(buf);
109	<	delete buf;
130	>	ppStream.str(buf);
131	>	delete [] buf;
132
133	<	}
133	>	}
134		#endif
135	<	// Create a scanner that reads from the input stream
136	<	MDLexer lexer(ppStream);
137	<	lexer.setFilename(mdFileName);
138	<	lexer.initDeferredLineCount();
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139
140	<	// Create a parser that reads from the scanner
141	<	MDParser parser(lexer);
142	<	parser.setFilename(mdFileName);
140	>	// Create a parser that reads from the scanner
141	>	MDParser parser(lexer);
142	>	parser.setFilename(filename);
143
144	<	// Create an observer that synchorizes file name change
145	<	FilenameObserver observer;
146	<	observer.setLexer(&lexer);
147	<	observer.setParser(&parser);
148	<	lexer.setObserver(&observer);
144	>	// Create an observer that synchorizes file name change
145	>	FilenameObserver observer;
146	>	observer.setLexer(&lexer);
147	>	observer.setParser(&parser);
148	>	lexer.setObserver(&observer);
149
150	<	antlr::ASTFactory factory;
151	<	parser.initializeASTFactory(factory);
152	<	parser.setASTFactory(&factory);
153	<	parser.mdfile();
150	>	antlr::ASTFactory factory;
151	>	parser.initializeASTFactory(factory);
152	>	parser.setASTFactory(&factory);
153	>	parser.mdfile();
154
155	<	// Create a tree parser that reads information into Globals
156	<	MDTreeParser treeParser;
157	<	treeParser.initializeASTFactory(factory);
158	<	treeParser.setASTFactory(&factory);
159	<	simParams = treeParser.walkTree(parser.getAST());
155	>	// Create a tree parser that reads information into Globals
156	>	MDTreeParser treeParser;
157	>	treeParser.initializeASTFactory(factory);
158	>	treeParser.setASTFactory(&factory);
159	>	simParams = treeParser.walkTree(parser.getAST());
160	>	}
161
162	<	}
163	<	catch (exception& e) {
164	<	cerr << "parser exception: " << e.what() << endl;
165	<	}
162	>
163	>	catch(antlr::MismatchedCharException& e) {
164	>	sprintf(painCave.errMsg,
165	>	"parser exception: %s %s:%d:%d\n",
166	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>	catch(antlr::MismatchedTokenException &e) {
171	>	sprintf(painCave.errMsg,
172	>	"parser exception: %s %s:%d:%d\n",
173	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	catch(antlr::NoViableAltForCharException &e) {
178	>	sprintf(painCave.errMsg,
179	>	"parser exception: %s %s:%d:%d\n",
180	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184	>	catch(antlr::NoViableAltException &e) {
185	>	sprintf(painCave.errMsg,
186	>	"parser exception: %s %s:%d:%d\n",
187	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	>	painCave.isFatal = 1;
189	>	simError();
190	>	}
191	>
192	>	catch(antlr::TokenStreamRecognitionException& e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s %s:%d:%d\n",
195	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199	>
200	>	catch(antlr::TokenStreamIOException& e) {
201	>	sprintf(painCave.errMsg,
202	>	"parser exception: %s\n",
203	>	e.getMessage().c_str());
204	>	painCave.isFatal = 1;
205	>	simError();
206	>	}
207	>
208	>	catch(antlr::TokenStreamException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s\n",
211	>	e.getMessage().c_str());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>	catch (antlr::RecognitionException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s %s:%d:%d\n",
218	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (antlr::CharStreamException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"parser exception: %s\n",
225	>	e.getMessage().c_str());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (OpenMDException& e) {
230	>	sprintf(painCave.errMsg,
231	>	"%s\n",
232	>	e.getMessage().c_str());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>	catch (std::exception& e) {
237	>	sprintf(painCave.errMsg,
238	>	"parser exception: %s\n",
239	>	e.what());
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243
244	<	return simParams;
244	>	simParams->setMDfileVersion(mdFileVersion);
245	>	return simParams;
246		}
247
248		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
249		bool loadInitCoords) {
250	+
251	+	const int bufferSize = 65535;
252	+	char buffer[bufferSize];
253	+	int lineNo = 0;
254	+	std::string mdRawData;
255	+	int metaDataBlockStart = -1;
256	+	int metaDataBlockEnd = -1;
257	+	int i, j;
258	+	streamoff mdOffset;
259	+	int mdFileVersion;
260
261	+	// Create a string for embedding the version information in the MetaData
262	+	std::string version;
263	+	version.assign("## Last run using OpenMD Version: ");
264	+	version.append(OPENMD_VERSION_MAJOR);
265	+	version.append(".");
266	+	version.append(OPENMD_VERSION_MINOR);
267	+
268	+	std::string svnrev;
269	+	//convert a macro from compiler to a string in c++
270	+	STR_DEFINE(svnrev, SVN_REV );
271	+	version.append(" Revision: ");
272	+	// If there's no SVN revision, just call this the RELEASE revision.
273	+	if (!svnrev.empty()) {
274	+	version.append(svnrev);
275	+	} else {
276	+	version.append("RELEASE");
277	+	}
278	+
279	+	#ifdef IS_MPI
280	+	const int masterNode = 0;
281	+	if (worldRank == masterNode) {
282	+	#endif
283	+
284	+	std::ifstream mdFile_;
285	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
286	+
287	+	if (mdFile_.fail()) {
288	+	sprintf(painCave.errMsg,
289	+	"SimCreator: Cannot open file: %s\n",
290	+	mdFileName.c_str());
291	+	painCave.isFatal = 1;
292	+	simError();
293	+	}
294	+
295	+	mdFile_.getline(buffer, bufferSize);
296	+	++lineNo;
297	+	std::string line = trimLeftCopy(buffer);
298	+	i = CaseInsensitiveFind(line, "<OpenMD");
299	+	if (static_cast<size_t>(i) == string::npos) {
300	+	// try the older file strings to see if that works:
301	+	i = CaseInsensitiveFind(line, "<OOPSE");
302	+	}
303	+
304	+	if (static_cast<size_t>(i) == string::npos) {
305	+	// still no luck!
306	+	sprintf(painCave.errMsg,
307	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
308	+	mdFileName.c_str());
309	+	painCave.isFatal = 1;
310	+	simError();
311	+	}
312	+
313	+	// found the correct opening string, now try to get the file
314	+	// format version number.
315	+
316	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
317	+	std::string fileType = tokenizer.nextToken();
318	+	toUpper(fileType);
319	+
320	+	mdFileVersion = 0;
321	+
322	+	if (fileType == "OPENMD") {
323	+	while (tokenizer.hasMoreTokens()) {
324	+	std::string token(tokenizer.nextToken());
325	+	toUpper(token);
326	+	if (token == "VERSION") {
327	+	mdFileVersion = tokenizer.nextTokenAsInt();
328	+	break;
329	+	}
330	+	}
331	+	}
332	+
333	+	//scan through the input stream and find MetaData tag
334	+	while(mdFile_.getline(buffer, bufferSize)) {
335	+	++lineNo;
336	+
337	+	std::string line = trimLeftCopy(buffer);
338	+	if (metaDataBlockStart == -1) {
339	+	i = CaseInsensitiveFind(line, "<MetaData>");
340	+	if (i != string::npos) {
341	+	metaDataBlockStart = lineNo;
342	+	mdOffset = mdFile_.tellg();
343	+	}
344	+	} else {
345	+	i = CaseInsensitiveFind(line, "</MetaData>");
346	+	if (i != string::npos) {
347	+	metaDataBlockEnd = lineNo;
348	+	}
349	+	}
350	+	}
351	+
352	+	if (metaDataBlockStart == -1) {
353	+	sprintf(painCave.errMsg,
354	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
355	+	mdFileName.c_str());
356	+	painCave.isFatal = 1;
357	+	simError();
358	+	}
359	+	if (metaDataBlockEnd == -1) {
360	+	sprintf(painCave.errMsg,
361	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
362	+	mdFileName.c_str());
363	+	painCave.isFatal = 1;
364	+	simError();
365	+	}
366	+
367	+	mdFile_.clear();
368	+	mdFile_.seekg(0);
369	+	mdFile_.seekg(mdOffset);
370	+
371	+	mdRawData.clear();
372	+
373	+	bool foundVersion = false;
374	+
375	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
376	+	mdFile_.getline(buffer, bufferSize);
377	+	std::string line = trimLeftCopy(buffer);
378	+	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
379	+	if (static_cast<size_t>(j) != string::npos) {
380	+	foundVersion = true;
381	+	mdRawData += version;
382	+	} else {
383	+	mdRawData += buffer;
384	+	}
385	+	mdRawData += "\n";
386	+	}
387	+
388	+	if (!foundVersion) mdRawData += version + "\n";
389	+
390	+	mdFile_.close();
391	+
392	+	#ifdef IS_MPI
393	+	}
394	+	#endif
395	+
396	+	std::stringstream rawMetaDataStream(mdRawData);
397	+
398		//parse meta-data file
399	<	Globals* simParams = parseFile(mdFileName);
399	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
400	>	metaDataBlockStart + 1);
401
402		//create the force field
403	<	ForceField * ff = ForceFieldFactory::getInstance()
404	<	->createForceField(simParams->getForceField());
156	<
403	>	ForceField * ff = new ForceField(simParams->getForceField());
404	>
405		if (ff == NULL) {
406		sprintf(painCave.errMsg,
407		"ForceField Factory can not create %s force field\n",
#	Line 186 | Line 434 | Globals* SimCreator::parseFile(const std::string mdFil
434		}
435
436		ff->parse(forcefieldFileName);
189	–
437		//create SimInfo
438		SimInfo * info = new SimInfo(ff, simParams);
439	+
440	+	info->setRawMetaData(mdRawData);
441
442	<	//gather parameters (SimCreator only retrieves part of the parameters)
442	>	//gather parameters (SimCreator only retrieves part of the
443	>	//parameters)
444		gatherParameters(info, mdFileName);
445
446		//divide the molecules and determine the global index of molecules
#	Line 201 | Line 451 | Globals* SimCreator::parseFile(const std::string mdFil
451		//create the molecules
452		createMolecules(info);
453
454	+	//find the storage layout
455	+
456	+	int storageLayout = computeStorageLayout(info);
457	+
458	+	//allocate memory for DataStorage(circular reference, need to
459	+	//break it)
460	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
461
462	<	//allocate memory for DataStorage(circular reference, need to break it)
463	<	info->setSnapshotManager(new SimSnapshotManager(info));
464	<
465	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
466	<	//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.
462	>	//set the global index of atoms, rigidbodies and cutoffgroups
463	>	//(only need to be set once, the global index will never change
464	>	//again). Local indices of atoms and rigidbodies are already set
465	>	//by MoleculeCreator class which actually delegates the
466	>	//responsibility to LocalIndexManager.
467		setGlobalIndex(info);
468
469	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
470	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
471	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
472	<	//we can determine the beginning global indices of atoms before they get created.
469	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
470	>	//method, at that point atoms don't have the global index yet
471	>	//(their global index are all initialized to -1).  Therefore we
472	>	//have to call addInteractionPairs explicitly here. A way to work
473	>	//around is that we can determine the beginning global indices of
474	>	//atoms before they get created.
475		SimInfo::MoleculeIterator mi;
476		Molecule* mol;
477		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
478	<	info->addExcludePairs(mol);
478	>	info->addInteractionPairs(mol);
479		}
480
481		if (loadInitCoords)
482	<	loadCoordinates(info);
225	<
482	>	loadCoordinates(info, mdFileName);
483		return info;
484		}
485
#	Line 257 | Line 514 | Globals* SimCreator::parseFile(const std::string mdFil
514
515		#ifdef IS_MPI
516		void SimCreator::divideMolecules(SimInfo *info) {
517	<	double numerator;
518	<	double denominator;
519	<	double precast;
520	<	double x;
521	<	double y;
522	<	double a;
517	>	RealType numerator;
518	>	RealType denominator;
519	>	RealType precast;
520	>	RealType x;
521	>	RealType y;
522	>	RealType a;
523		int old_atoms;
524		int add_atoms;
525		int new_atoms;
#	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 hasDipoles = false;
708	+	bool hasQuadrupoles = false;
709	+	bool hasPolarizable = false;
710	+	bool hasFluctuatingCharge = false;
711	+	bool hasMetallic = false;
712	+	int storageLayout = 0;
713	+	storageLayout |= DataStorage::dslPosition;
714	+	storageLayout |= DataStorage::dslVelocity;
715	+	storageLayout |= DataStorage::dslForce;
716	+
717	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
718	+
719	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
720	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
721	+	EAMAdapter ea = EAMAdapter( (*i) );
722	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
723	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
724	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
725	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
726	+
727	+	if (da.isDirectional()){
728	+	hasDirectionalAtoms = true;
729	+	}
730	+	if (ma.isDipole()){
731	+	hasDipoles = true;
732	+	}
733	+	if (ma.isQuadrupole()){
734	+	hasQuadrupoles = true;
735	+	}
736	+	if (ea.isEAM() || sca.isSuttonChen()){
737	+	hasMetallic = true;
738	+	}
739	+	if ( fca.isFixedCharge() ){
740	+	hasFixedCharge = true;
741	+	}
742	+	if ( fqa.isFluctuatingCharge() ){
743	+	hasFluctuatingCharge = true;
744	+	}
745	+	if ( pa.isPolarizable() ){
746	+	hasPolarizable = true;
747	+	}
748	+	}
749	+
750	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
751	+	storageLayout |= DataStorage::dslAmat;
752	+	if(storageLayout & DataStorage::dslVelocity) {
753	+	storageLayout |= DataStorage::dslAngularMomentum;
754	+	}
755	+	if (storageLayout & DataStorage::dslForce) {
756	+	storageLayout |= DataStorage::dslTorque;
757	+	}
758	+	}
759	+	if (hasDipoles) {
760	+	storageLayout |= DataStorage::dslDipole;
761	+	}
762	+	if (hasQuadrupoles) {
763	+	storageLayout |= DataStorage::dslQuadrupole;
764	+	}
765	+	if (hasFixedCharge || hasFluctuatingCharge) {
766	+	storageLayout |= DataStorage::dslSkippedCharge;
767	+	}
768	+	if (hasMetallic) {
769	+	storageLayout |= DataStorage::dslDensity;
770	+	storageLayout |= DataStorage::dslFunctional;
771	+	storageLayout |= DataStorage::dslFunctionalDerivative;
772	+	}
773	+	if (hasPolarizable) {
774	+	storageLayout |= DataStorage::dslElectricField;
775	+	}
776	+	if (hasFluctuatingCharge){
777	+	storageLayout |= DataStorage::dslFlucQPosition;
778	+	if(storageLayout & DataStorage::dslVelocity) {
779	+	storageLayout |= DataStorage::dslFlucQVelocity;
780	+	}
781	+	if (storageLayout & DataStorage::dslForce) {
782	+	storageLayout |= DataStorage::dslFlucQForce;
783	+	}
784	+	}
785	+
786	+	// if the user has asked for them, make sure we've got the memory for the
787	+	// objects defined.
788	+
789	+	if (simParams->getOutputParticlePotential()) {
790	+	storageLayout |= DataStorage::dslParticlePot;
791	+	}
792	+
793	+	if (simParams->havePrintHeatFlux()) {
794	+	if (simParams->getPrintHeatFlux()) {
795	+	storageLayout |= DataStorage::dslParticlePot;
796	+	}
797	+	}
798	+
799	+	if (simParams->getOutputElectricField()) {
800	+	storageLayout |= DataStorage::dslElectricField;
801	+	}
802	+
803	+	if (simParams->getOutputFluctuatingCharges()) {
804	+	storageLayout |= DataStorage::dslFlucQPosition;
805	+	storageLayout |= DataStorage::dslFlucQVelocity;
806	+	storageLayout |= DataStorage::dslFlucQForce;
807	+	}
808	+
809	+	return storageLayout;
810	+	}
811	+
812		void SimCreator::setGlobalIndex(SimInfo *info) {
813		SimInfo::MoleculeIterator mi;
814		Molecule::AtomIterator ai;
815		Molecule::RigidBodyIterator ri;
816		Molecule::CutoffGroupIterator ci;
817	+	Molecule::IntegrableObjectIterator  ioi;
818		Molecule * mol;
819		Atom * atom;
820		RigidBody * rb;
#	Line 448 | Line 823 | Globals* SimCreator::parseFile(const std::string mdFil
823		int beginRigidBodyIndex;
824		int beginCutoffGroupIndex;
825		int nGlobalAtoms = info->getNGlobalAtoms();
826	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
827
452	–	#ifndef IS_MPI
453	–
828		beginAtomIndex = 0;
829	<	beginRigidBodyIndex = 0;
829	>	//rigidbody's index begins right after atom's
830	>	beginRigidBodyIndex = info->getNGlobalAtoms();
831		beginCutoffGroupIndex = 0;
832	<
833	<	#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)) {
832	>
833	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
834
835	<	//local index(index in DataStorge) of atom is important
836	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
837	<	atom->setGlobalIndex(beginAtomIndex++);
835	>	#ifdef IS_MPI
836	>	if (info->getMolToProc(i) == worldRank) {
837	>	#endif
838	>	// stuff to do if I own this molecule
839	>	mol = info->getMoleculeByGlobalIndex(i);
840	>
841	>	//local index(index in DataStorge) of atom is important
842	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
843	>	atom->setGlobalIndex(beginAtomIndex++);
844	>	}
845	>
846	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
847	>	rb = mol->nextRigidBody(ri)) {
848	>	rb->setGlobalIndex(beginRigidBodyIndex++);
849	>	}
850	>
851	>	//local index of cutoff group is trivial, it only depends on
852	>	//the order of travesing
853	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
854	>	cg = mol->nextCutoffGroup(ci)) {
855	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
856	>	}
857	>
858	>	#ifdef IS_MPI
859	>	}  else {
860	>
861	>	// stuff to do if I don't own this molecule
862	>
863	>	int stampId = info->getMoleculeStampId(i);
864	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
865	>
866	>	beginAtomIndex += stamp->getNAtoms();
867	>	beginRigidBodyIndex += stamp->getNRigidBodies();
868	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
869		}
870	<
871	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
872	<	rb = mol->nextRigidBody(ri)) {
873	<	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	<
870	>	#endif
871	>
872	>	} //end for(int i=0)
873	>
874		//fill globalGroupMembership
875		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
876		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 528 | Line 882 | Globals* SimCreator::parseFile(const std::string mdFil
882
883		}
884		}
885	<
885	>
886		#ifdef IS_MPI
887		// Since the globalGroupMembership has been zero filled and we've only
888		// poked values into the atoms we know, we can do an Allreduce
889		// to get the full globalGroupMembership array (We think).
890		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
891		// docs said we could.
892	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
893	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
894	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
892	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
893	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
894	>	&tmpGroupMembership[0], nGlobalAtoms,
895	>	MPI::INT, MPI::SUM);
896		info->setGlobalGroupMembership(tmpGroupMembership);
897		#else
898		info->setGlobalGroupMembership(globalGroupMembership);
899		#endif
900
901		//fill molMembership
902	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
902	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
903	>	info->getNGlobalRigidBodies(), 0);
904
905	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
906	<
905	>	for(mol = info->beginMolecule(mi); mol != NULL;
906	>	mol = info->nextMolecule(mi)) {
907		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
908		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
909		}
910	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
911	+	rb = mol->nextRigidBody(ri)) {
912	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
913	+	}
914		}
915
916		#ifdef IS_MPI
917	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
917	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
918	>	info->getNGlobalRigidBodies(), 0);
919	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
920	>	nGlobalAtoms + nGlobalRigidBodies,
921	>	MPI::INT, MPI::SUM);
922
559	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
560	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
561	–
923		info->setGlobalMolMembership(tmpMolMembership);
924		#else
925		info->setGlobalMolMembership(globalMolMembership);
926		#endif
927	+
928	+	// nIOPerMol holds the number of integrable objects per molecule
929	+	// here the molecules are listed by their global indices.
930	+
931	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
932	+	for (mol = info->beginMolecule(mi); mol != NULL;
933	+	mol = info->nextMolecule(mi)) {
934	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
935	+	}
936
937	<	}
938	<
939	<	void SimCreator::loadCoordinates(SimInfo* info) {
940	<	Globals* simParams;
941	<	simParams = info->getSimParams();
937	>	#ifdef IS_MPI
938	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
939	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
940	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
941	>	#else
942	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
943	>	#endif
944	>
945	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
946
947	<	if (!simParams->haveInitialConfig()) {
948	<	sprintf(painCave.errMsg,
949	<	"Cannot intialize a simulation without an initial configuration file.\n");
950	<	painCave.isFatal = 1;;
577	<	simError();
947	>	int startingIndex = 0;
948	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
949	>	startingIOIndexForMol[i] = startingIndex;
950	>	startingIndex += numIntegrableObjectsPerMol[i];
951		}
952
953	<	DumpReader reader(info, simParams->getInitialConfig());
953	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
954	>	for (mol = info->beginMolecule(mi); mol != NULL;
955	>	mol = info->nextMolecule(mi)) {
956	>	int myGlobalIndex = mol->getGlobalIndex();
957	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
958	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
959	>	sd = mol->nextIntegrableObject(ioi)) {
960	>	sd->setGlobalIntegrableObjectIndex(globalIO);
961	>	IOIndexToIntegrableObject[globalIO] = sd;
962	>	globalIO++;
963	>	}
964	>	}
965	>
966	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
967	>
968	>	}
969	>
970	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
971	>
972	>	DumpReader reader(info, mdFileName);
973		int nframes = reader.getNFrames();
974
975		if (nframes > 0) {
#	Line 586 | Line 978 | Globals* SimCreator::parseFile(const std::string mdFil
978		//invalid initial coordinate file
979		sprintf(painCave.errMsg,
980		"Initial configuration file %s should at least contain one frame\n",
981	<	simParams->getInitialConfig().c_str());
981	>	mdFileName.c_str());
982		painCave.isFatal = 1;
983		simError();
984		}
593	–
985		//copy the current snapshot to previous snapshot
986		info->getSnapshotManager()->advance();
987		}
988
989	<	} //end namespace oopse
989	>	} //end namespace OpenMD
990
991

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines