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root/OpenMD/branches/development/src/brains/SimCreator.cpp

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trunk/src/brains/SimCreator.cpp (file contents), Revision 490 by tim, Wed Apr 13 18:41:17 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 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	+	#include <exception>
50	+	#include <iostream>
51	+	#include <sstream>
52	+	#include <string>
53
54		#include "brains/MoleculeCreator.hpp"
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
58	<	#include "io/parse_me.h"
55	<	#include "UseTheForce/ForceFieldFactory.hpp"
58	>	#include "brains/ForceField.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61		#include "math/SeqRandNumGen.hpp"
62	+	#include "mdParser/MDLexer.hpp"
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 "io/mpiBASS.h"
87	>	#include "mpi.h"
88		#include "math/ParallelRandNumGen.hpp"
89		#endif
90
91	<	namespace oopse {
91	>	namespace OpenMD {
92
93	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps,
94	<	Globals* simParams){
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;
99	>	#ifdef IS_MPI
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	>
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);
113	>
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	>
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	>	//receive file content
128	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129	>
130	>	ppStream.str(buf);
131	>	delete [] buf;
132	>
133	>	}
134	>	#endif
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139
140	<	#ifdef IS_MPI
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);
149
150	<	if (worldRank == 0) {
151	<	#endif // is_mpi
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());
160	>	}
161	>
162
163	<	simParams->initalize();
164	<	set_interface_stamps(stamps, simParams);
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	<	#ifdef IS_MPI
193	<
194	<	mpiEventInit();
195	<
196	<	#endif
197	<
83	<	yacc_BASS(mdFileName.c_str());
84	<
85	<	#ifdef IS_MPI
86	<
87	<	throwMPIEvent(NULL);
88	<	} else {
89	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
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	<	#endif
201	<
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	>	simParams->setMDfileVersion(mdFileVersion);
245	>	return simParams;
246		}
247
248	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
248	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
249	>	bool loadInitCoords) {
250
251	<	MakeStamps * stamps = new MakeStamps();
252	<
253	<	Globals * simParams = new Globals();
254	<
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;
258	>	streamoff mdOffset;
259	>	int mdFileVersion;
260	>
261	>
262	>	#ifdef IS_MPI
263	>	const int masterNode = 0;
264	>	if (worldRank == masterNode) {
265	>	#endif
266	>
267	>	std::ifstream mdFile_;
268	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
269	>
270	>	if (mdFile_.fail()) {
271	>	sprintf(painCave.errMsg,
272	>	"SimCreator: Cannot open file: %s\n",
273	>	mdFileName.c_str());
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>
278	>	mdFile_.getline(buffer, bufferSize);
279	>	++lineNo;
280	>	std::string line = trimLeftCopy(buffer);
281	>	i = CaseInsensitiveFind(line, "<OpenMD");
282	>	if (static_cast<size_t>(i) == string::npos) {
283	>	// try the older file strings to see if that works:
284	>	i = CaseInsensitiveFind(line, "<OOPSE");
285	>	}
286	>
287	>	if (static_cast<size_t>(i) == string::npos) {
288	>	// still no luck!
289	>	sprintf(painCave.errMsg,
290	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
291	>	mdFileName.c_str());
292	>	painCave.isFatal = 1;
293	>	simError();
294	>	}
295	>
296	>	// found the correct opening string, now try to get the file
297	>	// format version number.
298	>
299	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
300	>	std::string fileType = tokenizer.nextToken();
301	>	toUpper(fileType);
302	>
303	>	mdFileVersion = 0;
304	>
305	>	if (fileType == "OPENMD") {
306	>	while (tokenizer.hasMoreTokens()) {
307	>	std::string token(tokenizer.nextToken());
308	>	toUpper(token);
309	>	if (token == "VERSION") {
310	>	mdFileVersion = tokenizer.nextTokenAsInt();
311	>	break;
312	>	}
313	>	}
314	>	}
315	>
316	>	//scan through the input stream and find MetaData tag
317	>	while(mdFile_.getline(buffer, bufferSize)) {
318	>	++lineNo;
319	>
320	>	std::string line = trimLeftCopy(buffer);
321	>	if (metaDataBlockStart == -1) {
322	>	i = CaseInsensitiveFind(line, "<MetaData>");
323	>	if (i != string::npos) {
324	>	metaDataBlockStart = lineNo;
325	>	mdOffset = mdFile_.tellg();
326	>	}
327	>	} else {
328	>	i = CaseInsensitiveFind(line, "</MetaData>");
329	>	if (i != string::npos) {
330	>	metaDataBlockEnd = lineNo;
331	>	}
332	>	}
333	>	}
334	>
335	>	if (metaDataBlockStart == -1) {
336	>	sprintf(painCave.errMsg,
337	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
338	>	mdFileName.c_str());
339	>	painCave.isFatal = 1;
340	>	simError();
341	>	}
342	>	if (metaDataBlockEnd == -1) {
343	>	sprintf(painCave.errMsg,
344	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
345	>	mdFileName.c_str());
346	>	painCave.isFatal = 1;
347	>	simError();
348	>	}
349	>
350	>	mdFile_.clear();
351	>	mdFile_.seekg(0);
352	>	mdFile_.seekg(mdOffset);
353	>
354	>	mdRawData.clear();
355	>
356	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
357	>	mdFile_.getline(buffer, bufferSize);
358	>	mdRawData += buffer;
359	>	mdRawData += "\n";
360	>	}
361	>
362	>	mdFile_.close();
363	>
364	>	#ifdef IS_MPI
365	>	}
366	>	#endif
367	>
368	>	std::stringstream rawMetaDataStream(mdRawData);
369	>
370		//parse meta-data file
371	<	parseFile(mdFileName, stamps, simParams);
371	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
372	>	metaDataBlockStart + 1);
373
374		//create the force field
375	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
376	<	simParams->getForceField());
111	<
375	>	ForceField * ff = new ForceField(simParams->getForceField());
376	>
377		if (ff == NULL) {
378	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
379	<	simParams->getForceField());
378	>	sprintf(painCave.errMsg,
379	>	"ForceField Factory can not create %s force field\n",
380	>	simParams->getForceField().c_str());
381		painCave.isFatal = 1;
382		simError();
383		}
#	Line 140 | Line 406 | namespace oopse {
406		}
407
408		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
409		//create SimInfo
410	<	SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
410	>	SimInfo * info = new SimInfo(ff, simParams);
411	>
412	>	info->setRawMetaData(mdRawData);
413
414	<	//gather parameters (SimCreator only retrieves part of the parameters)
414	>	//gather parameters (SimCreator only retrieves part of the
415	>	//parameters)
416		gatherParameters(info, mdFileName);
417
418		//divide the molecules and determine the global index of molecules
#	Line 159 | Line 423 | namespace oopse {
423		//create the molecules
424		createMolecules(info);
425
426	+	//find the storage layout
427	+
428	+	int storageLayout = computeStorageLayout(info);
429	+
430	+	//allocate memory for DataStorage(circular reference, need to
431	+	//break it)
432	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
433
434	<	//allocate memory for DataStorage(circular reference, need to break it)
435	<	info->setSnapshotManager(new SimSnapshotManager(info));
436	<
437	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
438	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
168	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
434	>	//set the global index of atoms, rigidbodies and cutoffgroups
435	>	//(only need to be set once, the global index will never change
436	>	//again). Local indices of atoms and rigidbodies are already set
437	>	//by MoleculeCreator class which actually delegates the
438	>	//responsibility to LocalIndexManager.
439		setGlobalIndex(info);
440
441	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
442	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
443	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
444	<	//we can determine the beginning global indices of atoms before they get created.
441	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
442	>	//method, at that point atoms don't have the global index yet
443	>	//(their global index are all initialized to -1).  Therefore we
444	>	//have to call addInteractionPairs explicitly here. A way to work
445	>	//around is that we can determine the beginning global indices of
446	>	//atoms before they get created.
447		SimInfo::MoleculeIterator mi;
448		Molecule* mol;
449		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
450	<	info->addExcludePairs(mol);
450	>	info->addInteractionPairs(mol);
451		}
452
453		if (loadInitCoords)
454	<	loadCoordinates(info);
183	<
454	>	loadCoordinates(info, mdFileName);
455		return info;
456		}
457
458		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
459
460	<	//figure out the ouput file names
460	>	//figure out the output file names
461		std::string prefix;
462
463		#ifdef IS_MPI
#	Line 215 | Line 486 | namespace oopse {
486
487		#ifdef IS_MPI
488		void SimCreator::divideMolecules(SimInfo *info) {
489	<	double numerator;
490	<	double denominator;
491	<	double precast;
492	<	double x;
493	<	double y;
494	<	double a;
489	>	RealType numerator;
490	>	RealType denominator;
491	>	RealType precast;
492	>	RealType x;
493	>	RealType y;
494	>	RealType a;
495		int old_atoms;
496		int add_atoms;
497		int new_atoms;
#	Line 235 | Line 506 | namespace oopse {
506		int nGlobalMols = info->getNGlobalMolecules();
507		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
508
509	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
509	>	nProcessors = MPI::COMM_WORLD.Get_size();
510
511		if (nProcessors > nGlobalMols) {
512		sprintf(painCave.errMsg,
#	Line 244 | Line 515 | namespace oopse {
515		"\tthe number of molecules.  This will not result in a \n"
516		"\tusable division of atoms for force decomposition.\n"
517		"\tEither try a smaller number of processors, or run the\n"
518	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
518	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
519
520		painCave.isFatal = 1;
521		simError();
#	Line 273 | Line 544 | namespace oopse {
544		nTarget = (int)(precast + 0.5);
545
546		for(i = 0; i < nGlobalMols; i++) {
547	+
548		done = 0;
549		loops = 0;
550
#	Line 297 | Line 569 | namespace oopse {
569		// and be done with it.
570
571		if (loops > 100) {
572	+
573		sprintf(painCave.errMsg,
574	<	"I've tried 100 times to assign molecule %d to a "
575	<	" processor, but can't find a good spot.\n"
576	<	"I'm assigning it at random to processor %d.\n",
574	>	"There have been 100 attempts to assign molecule %d to an\n"
575	>	"\tunderworked processor, but there's no good place to\n"
576	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
577		i, which_proc);
578	<
578	>
579		painCave.isFatal = 0;
580	+	painCave.severity = OPENMD_INFO;
581		simError();
582
583		molToProcMap[i] = which_proc;
#	Line 332 | Line 606 | namespace oopse {
606		//           Pacc(x) = exp(- a * x)
607		// where a = penalty / (average atoms per molecule)
608
609	<	x = (double)(new_atoms - nTarget);
609	>	x = (RealType)(new_atoms - nTarget);
610		y = myRandom->rand();
611
612		if (y < exp(- a * x)) {
#	Line 348 | Line 622 | namespace oopse {
622		}
623
624		delete myRandom;
625	<
625	>
626		// Spray out this nonsense to all other processors:
627	<
354	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
627	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
628		} else {
629
630		// Listen to your marching orders from processor 0:
631	<
632	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
631	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
632	>
633		}
634
635		info->setMolToProcMap(molToProcMap);
636		sprintf(checkPointMsg,
637		"Successfully divided the molecules among the processors.\n");
638	<	MPIcheckPoint();
638	>	errorCheckPoint();
639		}
640
641		#endif
#	Line 379 | Line 652 | namespace oopse {
652		#endif
653
654		stampId = info->getMoleculeStampId(i);
655	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
656	<	stampId, i, info->getLocalIndexManager());
655	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
656	>	info->getMoleculeStamp(stampId),
657	>	stampId, i,
658	>	info->getLocalIndexManager());
659
660		info->addMolecule(mol);
661
#	Line 392 | Line 667 | namespace oopse {
667
668		} //end for(int i=0)
669		}
395	–
396	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
397	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
398	–	int i;
399	–	char * id;
400	–	MoleculeStamp * currentStamp;
401	–	Component** the_components = simParams->getComponents();
402	–	int n_components = simParams->getNComponents();
670
671	<	if (!simParams->haveNMol()) {
405	<	// we don't have the total number of molecules, so we assume it is
406	<	// given in each component
407	<
408	<	for(i = 0; i < n_components; i++) {
409	<	if (!the_components[i]->haveNMol()) {
410	<	// we have a problem
411	<	sprintf(painCave.errMsg,
412	<	"SimCreator Error. No global NMol or component NMol given.\n"
413	<	"\tCannot calculate the number of atoms.\n");
414	<
415	<	painCave.isFatal = 1;
416	<	simError();
417	<	}
418	<
419	<	id = the_components[i]->getType();
671	>	int SimCreator::computeStorageLayout(SimInfo* info) {
672
673	<	currentStamp = stamps->getMolStamp(id);
674	<	if (currentStamp == NULL) {
675	<	sprintf(painCave.errMsg,
676	<	"SimCreator error: Component \"%s\" was not found in the "
677	<	"list of declared molecules\n", id);
678	<
679	<	painCave.isFatal = 1;
680	<	simError();
681	<	}
682	<
683	<	moleculeStampPairs.push_back(
684	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
685	<	} //end for (i = 0; i < n_components; i++)
686	<	} else {
687	<	sprintf(painCave.errMsg, "SimSetup error.\n"
688	<	"\tSorry, the ability to specify total"
689	<	" nMols and then give molfractions in the components\n"
690	<	"\tis not currently supported."
691	<	" Please give nMol in the components.\n");
692	<
693	<	painCave.isFatal = 1;
694	<	simError();
673	>	Globals* simParams = info->getSimParams();
674	>	int nRigidBodies = info->getNGlobalRigidBodies();
675	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
676	>	set<AtomType*>::iterator i;
677	>	bool hasDirectionalAtoms = false;
678	>	bool hasFixedCharge = false;
679	>	bool hasDipoles = false;
680	>	bool hasQuadrupoles = false;
681	>	bool hasPolarizable = false;
682	>	bool hasFluctuatingCharge = false;
683	>	bool hasMetallic = false;
684	>	int storageLayout = 0;
685	>	storageLayout |= DataStorage::dslPosition;
686	>	storageLayout |= DataStorage::dslVelocity;
687	>	storageLayout |= DataStorage::dslForce;
688	>
689	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
690	>
691	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
692	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
693	>	EAMAdapter ea = EAMAdapter( (*i) );
694	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
695	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
696	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
697	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
698	>
699	>	if (da.isDirectional()){
700	>	hasDirectionalAtoms = true;
701	>	}
702	>	if (ma.isDipole()){
703	>	hasDipoles = true;
704	>	}
705	>	if (ma.isQuadrupole()){
706	>	hasQuadrupoles = true;
707	>	}
708	>	if (ea.isEAM() || sca.isSuttonChen()){
709	>	hasMetallic = true;
710	>	}
711	>	if ( fca.isFixedCharge() ){
712	>	hasFixedCharge = true;
713	>	}
714	>	if ( fqa.isFluctuatingCharge() ){
715	>	hasFluctuatingCharge = true;
716	>	}
717	>	if ( pa.isPolarizable() ){
718	>	hasPolarizable = true;
719	>	}
720		}
721
722	<	#ifdef IS_MPI
722	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
723	>	storageLayout |= DataStorage::dslAmat;
724	>	if(storageLayout & DataStorage::dslVelocity) {
725	>	storageLayout |= DataStorage::dslAngularMomentum;
726	>	}
727	>	if (storageLayout & DataStorage::dslForce) {
728	>	storageLayout |= DataStorage::dslTorque;
729	>	}
730	>	}
731	>	if (hasDipoles) {
732	>	storageLayout |= DataStorage::dslDipole;
733	>	}
734	>	if (hasQuadrupoles) {
735	>	storageLayout |= DataStorage::dslQuadrupole;
736	>	}
737	>	if (hasFixedCharge || hasFluctuatingCharge) {
738	>	storageLayout |= DataStorage::dslSkippedCharge;
739	>	}
740	>	if (hasMetallic) {
741	>	storageLayout |= DataStorage::dslDensity;
742	>	storageLayout |= DataStorage::dslFunctional;
743	>	storageLayout |= DataStorage::dslFunctionalDerivative;
744	>	}
745	>	if (hasPolarizable) {
746	>	storageLayout |= DataStorage::dslElectricField;
747	>	}
748	>	if (hasFluctuatingCharge){
749	>	storageLayout |= DataStorage::dslFlucQPosition;
750	>	if(storageLayout & DataStorage::dslVelocity) {
751	>	storageLayout |= DataStorage::dslFlucQVelocity;
752	>	}
753	>	if (storageLayout & DataStorage::dslForce) {
754	>	storageLayout |= DataStorage::dslFlucQForce;
755	>	}
756	>	}
757
758	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
759	<	MPIcheckPoint();
760	<
761	<	#endif // is_mpi
762	<
758	>	// if the user has asked for them, make sure we've got the memory for the
759	>	// objects defined.
760	>
761	>	if (simParams->getOutputParticlePotential()) {
762	>	storageLayout |= DataStorage::dslParticlePot;
763	>	}
764	>
765	>	if (simParams->havePrintHeatFlux()) {
766	>	if (simParams->getPrintHeatFlux()) {
767	>	storageLayout |= DataStorage::dslParticlePot;
768	>	}
769	>	}
770	>
771	>	if (simParams->getOutputElectricField()) {
772	>	storageLayout |= DataStorage::dslElectricField;
773	>	}
774	>
775	>	if (simParams->getOutputFluctuatingCharges()) {
776	>	storageLayout |= DataStorage::dslFlucQPosition;
777	>	storageLayout |= DataStorage::dslFlucQVelocity;
778	>	storageLayout |= DataStorage::dslFlucQForce;
779	>	}
780	>
781	>	return storageLayout;
782		}
783	<
783	>
784		void SimCreator::setGlobalIndex(SimInfo *info) {
785		SimInfo::MoleculeIterator mi;
786		Molecule::AtomIterator ai;
787		Molecule::RigidBodyIterator ri;
788		Molecule::CutoffGroupIterator ci;
789	+	Molecule::IntegrableObjectIterator  ioi;
790		Molecule * mol;
791		Atom * atom;
792		RigidBody * rb;
#	Line 464 | Line 795 | namespace oopse {
795		int beginRigidBodyIndex;
796		int beginCutoffGroupIndex;
797		int nGlobalAtoms = info->getNGlobalAtoms();
798	<
468	<	#ifndef IS_MPI
798	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
799
800		beginAtomIndex = 0;
471	–	beginRigidBodyIndex = 0;
472	–	beginCutoffGroupIndex = 0;
473	–
474	–	#else
475	–
476	–	int nproc;
477	–	int myNode;
478	–
479	–	myNode = worldRank;
480	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
481	–
482	–	std::vector < int > tmpAtomsInProc(nproc, 0);
483	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
484	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
485	–	std::vector < int > NumAtomsInProc(nproc, 0);
486	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
487	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
488	–
489	–	tmpAtomsInProc[myNode] = info->getNAtoms();
490	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
491	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
492	–
493	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
494	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
495	–	MPI_SUM, MPI_COMM_WORLD);
496	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
497	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
498	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
499	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
500	–
501	–	beginAtomIndex = 0;
502	–	beginRigidBodyIndex = 0;
503	–	beginCutoffGroupIndex = 0;
504	–
505	–	for(int i = 0; i < myNode; i++) {
506	–	beginAtomIndex += NumAtomsInProc[i];
507	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
508	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
509	–	}
510	–
511	–	#endif
512	–
801		//rigidbody's index begins right after atom's
802	<	beginRigidBodyIndex += info->getNGlobalAtoms();
803	<
804	<	for(mol = info->beginMolecule(mi); mol != NULL;
805	<	mol = info->nextMolecule(mi)) {
802	>	beginRigidBodyIndex = info->getNGlobalAtoms();
803	>	beginCutoffGroupIndex = 0;
804	>
805	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
806
807	<	//local index(index in DataStorge) of atom is important
808	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
809	<	atom->setGlobalIndex(beginAtomIndex++);
807	>	#ifdef IS_MPI
808	>	if (info->getMolToProc(i) == worldRank) {
809	>	#endif
810	>	// stuff to do if I own this molecule
811	>	mol = info->getMoleculeByGlobalIndex(i);
812	>
813	>	//local index(index in DataStorge) of atom is important
814	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
815	>	atom->setGlobalIndex(beginAtomIndex++);
816	>	}
817	>
818	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
819	>	rb = mol->nextRigidBody(ri)) {
820	>	rb->setGlobalIndex(beginRigidBodyIndex++);
821	>	}
822	>
823	>	//local index of cutoff group is trivial, it only depends on
824	>	//the order of travesing
825	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
826	>	cg = mol->nextCutoffGroup(ci)) {
827	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
828	>	}
829	>
830	>	#ifdef IS_MPI
831	>	}  else {
832	>
833	>	// stuff to do if I don't own this molecule
834	>
835	>	int stampId = info->getMoleculeStampId(i);
836	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
837	>
838	>	beginAtomIndex += stamp->getNAtoms();
839	>	beginRigidBodyIndex += stamp->getNRigidBodies();
840	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
841		}
842	<
843	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
844	<	rb = mol->nextRigidBody(ri)) {
845	<	rb->setGlobalIndex(beginRigidBodyIndex++);
527	<	}
528	<
529	<	//local index of cutoff group is trivial, it only depends on the order of travesing
530	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
531	<	cg = mol->nextCutoffGroup(ci)) {
532	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
533	<	}
534	<	}
535	<
842	>	#endif
843	>
844	>	} //end for(int i=0)
845	>
846		//fill globalGroupMembership
847		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
848		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 544 | Line 854 | namespace oopse {
854
855		}
856		}
857	<
857	>
858		#ifdef IS_MPI
859		// Since the globalGroupMembership has been zero filled and we've only
860		// poked values into the atoms we know, we can do an Allreduce
861		// to get the full globalGroupMembership array (We think).
862		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
863		// docs said we could.
864	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
865	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
866	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
864	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
865	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
866	>	&tmpGroupMembership[0], nGlobalAtoms,
867	>	MPI::INT, MPI::SUM);
868		info->setGlobalGroupMembership(tmpGroupMembership);
869		#else
870		info->setGlobalGroupMembership(globalGroupMembership);
871		#endif
872
873		//fill molMembership
874	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
874	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
875	>	info->getNGlobalRigidBodies(), 0);
876
877	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
878	<
877	>	for(mol = info->beginMolecule(mi); mol != NULL;
878	>	mol = info->nextMolecule(mi)) {
879		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
880		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
881		}
882	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
883	+	rb = mol->nextRigidBody(ri)) {
884	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
885	+	}
886		}
887
888		#ifdef IS_MPI
889	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
889	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
890	>	info->getNGlobalRigidBodies(), 0);
891	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
892	>	nGlobalAtoms + nGlobalRigidBodies,
893	>	MPI::INT, MPI::SUM);
894
575	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
576	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
577	–
895		info->setGlobalMolMembership(tmpMolMembership);
896		#else
897		info->setGlobalMolMembership(globalMolMembership);
898		#endif
899	+
900	+	// nIOPerMol holds the number of integrable objects per molecule
901	+	// here the molecules are listed by their global indices.
902	+
903	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
904	+	for (mol = info->beginMolecule(mi); mol != NULL;
905	+	mol = info->nextMolecule(mi)) {
906	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
907	+	}
908
909	+	#ifdef IS_MPI
910	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
911	+	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
912	+	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
913	+	#else
914	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
915	+	#endif
916	+
917	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
918	+
919	+	int startingIndex = 0;
920	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
921	+	startingIOIndexForMol[i] = startingIndex;
922	+	startingIndex += numIntegrableObjectsPerMol[i];
923	+	}
924	+
925	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
926	+	for (mol = info->beginMolecule(mi); mol != NULL;
927	+	mol = info->nextMolecule(mi)) {
928	+	int myGlobalIndex = mol->getGlobalIndex();
929	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
930	+	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
931	+	sd = mol->nextIntegrableObject(ioi)) {
932	+	sd->setGlobalIntegrableObjectIndex(globalIO);
933	+	IOIndexToIntegrableObject[globalIO] = sd;
934	+	globalIO++;
935	+	}
936	+	}
937	+
938	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
939	+
940		}
941
942	<	void SimCreator::loadCoordinates(SimInfo* info) {
942	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
943		Globals* simParams;
944	+
945		simParams = info->getSimParams();
946
947	<	if (!simParams->haveInitialConfig()) {
590	<	sprintf(painCave.errMsg,
591	<	"Cannot intialize a simulation without an initial configuration file.\n");
592	<	painCave.isFatal = 1;;
593	<	simError();
594	<	}
595	<
596	<	DumpReader reader(info, simParams->getInitialConfig());
947	>	DumpReader reader(info, mdFileName);
948		int nframes = reader.getNFrames();
949	<
949	>
950		if (nframes > 0) {
951		reader.readFrame(nframes - 1);
952		} else {
953		//invalid initial coordinate file
954		sprintf(painCave.errMsg,
955		"Initial configuration file %s should at least contain one frame\n",
956	<	simParams->getInitialConfig());
956	>	mdFileName.c_str());
957		painCave.isFatal = 1;
958		simError();
959		}
609	–
960		//copy the current snapshot to previous snapshot
961		info->getSnapshotManager()->advance();
962		}
963
964	<	} //end namespace oopse
964	>	} //end namespace OpenMD
965
966

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 490 by tim, Wed Apr 13 18:41:17 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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