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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 436 by tim, Fri Mar 11 17:50:11 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1714 by gezelter, Sat May 19 18:12:46 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		/**
#	Line 46 | Line 47
47		* @time 13:51am
48		* @version 1.0
49		*/
50	+	#include <exception>
51	+	#include <iostream>
52	+	#include <sstream>
53	+	#include <string>
54
55		#include "brains/MoleculeCreator.hpp"
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
54	–	#include "io/parse_me.h"
59		#include "UseTheForce/ForceFieldFactory.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62		#include "math/SeqRandNumGen.hpp"
63	+	#include "mdParser/MDLexer.hpp"
64	+	#include "mdParser/MDParser.hpp"
65	+	#include "mdParser/MDTreeParser.hpp"
66	+	#include "mdParser/SimplePreprocessor.hpp"
67	+	#include "antlr/ANTLRException.hpp"
68	+	#include "antlr/TokenStreamRecognitionException.hpp"
69	+	#include "antlr/TokenStreamIOException.hpp"
70	+	#include "antlr/TokenStreamException.hpp"
71	+	#include "antlr/RecognitionException.hpp"
72	+	#include "antlr/CharStreamException.hpp"
73	+
74	+	#include "antlr/MismatchedCharException.hpp"
75	+	#include "antlr/MismatchedTokenException.hpp"
76	+	#include "antlr/NoViableAltForCharException.hpp"
77	+	#include "antlr/NoViableAltException.hpp"
78	+
79	+	#include "types/DirectionalAdapter.hpp"
80	+	#include "types/MultipoleAdapter.hpp"
81	+	#include "types/EAMAdapter.hpp"
82	+	#include "types/SuttonChenAdapter.hpp"
83	+	#include "types/PolarizableAdapter.hpp"
84	+	#include "types/FixedChargeAdapter.hpp"
85	+	#include "types/FluctuatingChargeAdapter.hpp"
86	+
87		#ifdef IS_MPI
88	<	#include "io/mpiBASS.h"
88	>	#include "mpi.h"
89		#include "math/ParallelRandNumGen.hpp"
90		#endif
91
92	<	namespace oopse {
92	>	namespace OpenMD {
93
94	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps,
95	<	Globals* simParams){
94	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95	>	Globals* simParams = NULL;
96	>	try {
97	>
98	>	// Create a preprocessor that preprocesses md file into an ostringstream
99	>	std::stringstream ppStream;
100	>	#ifdef IS_MPI
101	>	int streamSize;
102	>	const int masterNode = 0;
103	>	int commStatus;
104	>	if (worldRank == masterNode) {
105	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
106	>	#endif
107	>	SimplePreprocessor preprocessor;
108	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
109	>
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);
114	>
115	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
116	>
117	>
118	>	} else {
119	>
120	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121	>
122	>	//get stream size
123	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124	>
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127	>
128	>	//receive file content
129	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
130	>
131	>	ppStream.str(buf);
132	>	delete [] buf;
133	>
134	>	}
135	>	#endif
136	>	// Create a scanner that reads from the input stream
137	>	MDLexer lexer(ppStream);
138	>	lexer.setFilename(filename);
139	>	lexer.initDeferredLineCount();
140
141	<	#ifdef IS_MPI
141	>	// Create a parser that reads from the scanner
142	>	MDParser parser(lexer);
143	>	parser.setFilename(filename);
144	>
145	>	// Create an observer that synchorizes file name change
146	>	FilenameObserver observer;
147	>	observer.setLexer(&lexer);
148	>	observer.setParser(&parser);
149	>	lexer.setObserver(&observer);
150
151	<	if (worldRank == 0) {
152	<	#endif // is_mpi
151	>	antlr::ASTFactory factory;
152	>	parser.initializeASTFactory(factory);
153	>	parser.setASTFactory(&factory);
154	>	parser.mdfile();
155	>
156	>	// Create a tree parser that reads information into Globals
157	>	MDTreeParser treeParser;
158	>	treeParser.initializeASTFactory(factory);
159	>	treeParser.setASTFactory(&factory);
160	>	simParams = treeParser.walkTree(parser.getAST());
161	>	}
162	>
163
164	<	simParams->initalize();
165	<	set_interface_stamps(stamps, simParams);
164	>	catch(antlr::MismatchedCharException& e) {
165	>	sprintf(painCave.errMsg,
166	>	"parser exception: %s %s:%d:%d\n",
167	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
168	>	painCave.isFatal = 1;
169	>	simError();
170	>	}
171	>	catch(antlr::MismatchedTokenException &e) {
172	>	sprintf(painCave.errMsg,
173	>	"parser exception: %s %s:%d:%d\n",
174	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	catch(antlr::NoViableAltForCharException &e) {
179	>	sprintf(painCave.errMsg,
180	>	"parser exception: %s %s:%d:%d\n",
181	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
185	>	catch(antlr::NoViableAltException &e) {
186	>	sprintf(painCave.errMsg,
187	>	"parser exception: %s %s:%d:%d\n",
188	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
189	>	painCave.isFatal = 1;
190	>	simError();
191	>	}
192
193	<	#ifdef IS_MPI
194	<
195	<	mpiEventInit();
196	<
197	<	#endif
198	<
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();
193	>	catch(antlr::TokenStreamRecognitionException& e) {
194	>	sprintf(painCave.errMsg,
195	>	"parser exception: %s %s:%d:%d\n",
196	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
197	>	painCave.isFatal = 1;
198	>	simError();
199		}
200	<
201	<	#endif
202	<
200	>
201	>	catch(antlr::TokenStreamIOException& e) {
202	>	sprintf(painCave.errMsg,
203	>	"parser exception: %s\n",
204	>	e.getMessage().c_str());
205	>	painCave.isFatal = 1;
206	>	simError();
207	>	}
208	>
209	>	catch(antlr::TokenStreamException& e) {
210	>	sprintf(painCave.errMsg,
211	>	"parser exception: %s\n",
212	>	e.getMessage().c_str());
213	>	painCave.isFatal = 1;
214	>	simError();
215	>	}
216	>	catch (antlr::RecognitionException& e) {
217	>	sprintf(painCave.errMsg,
218	>	"parser exception: %s %s:%d:%d\n",
219	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
220	>	painCave.isFatal = 1;
221	>	simError();
222	>	}
223	>	catch (antlr::CharStreamException& e) {
224	>	sprintf(painCave.errMsg,
225	>	"parser exception: %s\n",
226	>	e.getMessage().c_str());
227	>	painCave.isFatal = 1;
228	>	simError();
229	>	}
230	>	catch (OpenMDException& e) {
231	>	sprintf(painCave.errMsg,
232	>	"%s\n",
233	>	e.getMessage().c_str());
234	>	painCave.isFatal = 1;
235	>	simError();
236	>	}
237	>	catch (std::exception& e) {
238	>	sprintf(painCave.errMsg,
239	>	"parser exception: %s\n",
240	>	e.what());
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>
245	>	simParams->setMDfileVersion(mdFileVersion);
246	>	return simParams;
247		}
248
249	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
249	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250	>	bool loadInitCoords) {
251
252	<	MakeStamps * stamps = new MakeStamps();
253	<
254	<	Globals * simParams = new Globals();
255	<
252	>	const int bufferSize = 65535;
253	>	char buffer[bufferSize];
254	>	int lineNo = 0;
255	>	std::string mdRawData;
256	>	int metaDataBlockStart = -1;
257	>	int metaDataBlockEnd = -1;
258	>	int i;
259	>	int mdOffset;
260	>	int mdFileVersion;
261	>
262	>	#ifdef IS_MPI
263	>	const int masterNode = 0;
264	>	if (worldRank == masterNode) {
265	>	#endif
266	>
267	>	std::ifstream mdFile_(mdFileName.c_str());
268	>
269	>	if (mdFile_.fail()) {
270	>	sprintf(painCave.errMsg,
271	>	"SimCreator: Cannot open file: %s\n",
272	>	mdFileName.c_str());
273	>	painCave.isFatal = 1;
274	>	simError();
275	>	}
276	>
277	>	mdFile_.getline(buffer, bufferSize);
278	>	++lineNo;
279	>	std::string line = trimLeftCopy(buffer);
280	>	i = CaseInsensitiveFind(line, "<OpenMD");
281	>	if (static_cast<size_t>(i) == string::npos) {
282	>	// try the older file strings to see if that works:
283	>	i = CaseInsensitiveFind(line, "<OOPSE");
284	>	}
285	>
286	>	if (static_cast<size_t>(i) == string::npos) {
287	>	// still no luck!
288	>	sprintf(painCave.errMsg,
289	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
290	>	mdFileName.c_str());
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294	>
295	>	// found the correct opening string, now try to get the file
296	>	// format version number.
297	>
298	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
299	>	std::string fileType = tokenizer.nextToken();
300	>	toUpper(fileType);
301	>
302	>	mdFileVersion = 0;
303	>
304	>	if (fileType == "OPENMD") {
305	>	while (tokenizer.hasMoreTokens()) {
306	>	std::string token(tokenizer.nextToken());
307	>	toUpper(token);
308	>	if (token == "VERSION") {
309	>	mdFileVersion = tokenizer.nextTokenAsInt();
310	>	break;
311	>	}
312	>	}
313	>	}
314	>
315	>	//scan through the input stream and find MetaData tag
316	>	while(mdFile_.getline(buffer, bufferSize)) {
317	>	++lineNo;
318	>
319	>	std::string line = trimLeftCopy(buffer);
320	>	if (metaDataBlockStart == -1) {
321	>	i = CaseInsensitiveFind(line, "<MetaData>");
322	>	if (i != string::npos) {
323	>	metaDataBlockStart = lineNo;
324	>	mdOffset = mdFile_.tellg();
325	>	}
326	>	} else {
327	>	i = CaseInsensitiveFind(line, "</MetaData>");
328	>	if (i != string::npos) {
329	>	metaDataBlockEnd = lineNo;
330	>	}
331	>	}
332	>	}
333	>
334	>	if (metaDataBlockStart == -1) {
335	>	sprintf(painCave.errMsg,
336	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
337	>	mdFileName.c_str());
338	>	painCave.isFatal = 1;
339	>	simError();
340	>	}
341	>	if (metaDataBlockEnd == -1) {
342	>	sprintf(painCave.errMsg,
343	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
344	>	mdFileName.c_str());
345	>	painCave.isFatal = 1;
346	>	simError();
347	>	}
348	>
349	>	mdFile_.clear();
350	>	mdFile_.seekg(0);
351	>	mdFile_.seekg(mdOffset);
352	>
353	>	mdRawData.clear();
354	>
355	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
356	>	mdFile_.getline(buffer, bufferSize);
357	>	mdRawData += buffer;
358	>	mdRawData += "\n";
359	>	}
360	>
361	>	mdFile_.close();
362	>
363	>	#ifdef IS_MPI
364	>	}
365	>	#endif
366	>
367	>	std::stringstream rawMetaDataStream(mdRawData);
368	>
369		//parse meta-data file
370	<	parseFile(mdFileName, stamps, simParams);
370	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
371	>	metaDataBlockStart + 1);
372
373		//create the force field
374	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
375	<	simParams->getForceField());
111	<
374	>	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
375	>
376		if (ff == NULL) {
377	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
378	<	simParams->getForceField());
377	>	sprintf(painCave.errMsg,
378	>	"ForceField Factory can not create %s force field\n",
379	>	simParams->getForceField().c_str());
380		painCave.isFatal = 1;
381		simError();
382		}
#	Line 140 | Line 405 | namespace oopse {
405		}
406
407		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
408		//create SimInfo
409	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
410	<
411	<	//gather parameters (SimCreator only retrieves part of the parameters)
409	>	SimInfo * info = new SimInfo(ff, simParams);
410	>
411	>	info->setRawMetaData(mdRawData);
412	>
413	>	//gather parameters (SimCreator only retrieves part of the
414	>	//parameters)
415		gatherParameters(info, mdFileName);
416
417		//divide the molecules and determine the global index of molecules
#	Line 159 | Line 422 | namespace oopse {
422		//create the molecules
423		createMolecules(info);
424
425	<
426	<	//allocate memory for DataStorage(circular reference, need to break it)
427	<	info->setSnapshotManager(new SimSnapshotManager(info));
425	>	//find the storage layout
426	>
427	>	int storageLayout = computeStorageLayout(info);
428	>
429	>	cerr << "computed Storage Layout = " << storageLayout << "\n";
430	>
431	>	//allocate memory for DataStorage(circular reference, need to
432	>	//break it)
433	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
436	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
437	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
435	>	//set the global index of atoms, rigidbodies and cutoffgroups
436	>	//(only need to be set once, the global index will never change
437	>	//again). Local indices of atoms and rigidbodies are already set
438	>	//by MoleculeCreator class which actually delegates the
439	>	//responsibility to LocalIndexManager.
440		setGlobalIndex(info);
441
442	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
443	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
444	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
445	<	//we can determine the beginning global indices of atoms before they get created.
442	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
443	>	//method, at that point atoms don't have the global index yet
444	>	//(their global index are all initialized to -1).  Therefore we
445	>	//have to call addInteractionPairs explicitly here. A way to work
446	>	//around is that we can determine the beginning global indices of
447	>	//atoms before they get created.
448		SimInfo::MoleculeIterator mi;
449		Molecule* mol;
450		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
451	<	info->addExcludePairs(mol);
451	>	info->addInteractionPairs(mol);
452		}
453
454		if (loadInitCoords)
455	<	loadCoordinates(info);
183	<
455	>	loadCoordinates(info, mdFileName);
456		return info;
457		}
458
459		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
460
461	<	//figure out the ouput file names
461	>	//figure out the output file names
462		std::string prefix;
463
464		#ifdef IS_MPI
#	Line 215 | Line 487 | namespace oopse {
487
488		#ifdef IS_MPI
489		void SimCreator::divideMolecules(SimInfo *info) {
490	<	double numerator;
491	<	double denominator;
492	<	double precast;
493	<	double x;
494	<	double y;
495	<	double a;
490	>	RealType numerator;
491	>	RealType denominator;
492	>	RealType precast;
493	>	RealType x;
494	>	RealType y;
495	>	RealType a;
496		int old_atoms;
497		int add_atoms;
498		int new_atoms;
#	Line 244 | Line 516 | namespace oopse {
516		"\tthe number of molecules.  This will not result in a \n"
517		"\tusable division of atoms for force decomposition.\n"
518		"\tEither try a smaller number of processors, or run the\n"
519	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
519	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
520
521		painCave.isFatal = 1;
522		simError();
#	Line 332 | Line 604 | namespace oopse {
604		//           Pacc(x) = exp(- a * x)
605		// where a = penalty / (average atoms per molecule)
606
607	<	x = (double)(new_atoms - nTarget);
607	>	x = (RealType)(new_atoms - nTarget);
608		y = myRandom->rand();
609
610		if (y < exp(- a * x)) {
#	Line 362 | Line 634 | namespace oopse {
634		info->setMolToProcMap(molToProcMap);
635		sprintf(checkPointMsg,
636		"Successfully divided the molecules among the processors.\n");
637	<	MPIcheckPoint();
637	>	errorCheckPoint();
638		}
639
640		#endif
#	Line 379 | Line 651 | namespace oopse {
651		#endif
652
653		stampId = info->getMoleculeStampId(i);
654	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
655	<	stampId, i, info->getLocalIndexManager());
654	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
655	>	info->getMoleculeStamp(stampId),
656	>	stampId, i,
657	>	info->getLocalIndexManager());
658
659		info->addMolecule(mol);
660
#	Line 392 | Line 666 | namespace oopse {
666
667		} //end for(int i=0)
668		}
395	–
396	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
397	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
398	–	int i;
399	–	char * id;
400	–	LinkedMolStamp* extractedStamp = NULL;
401	–	MoleculeStamp * currentStamp;
402	–	Component** the_components = simParams->getComponents();
403	–	int n_components = simParams->getNComponents();
669
670	<	if (!simParams->haveNMol()) {
671	<	// we don't have the total number of molecules, so we assume it is
672	<	// given in each component
673	<
674	<	for(i = 0; i < n_components; i++) {
675	<	if (!the_components[i]->haveNMol()) {
676	<	// we have a problem
677	<	sprintf(painCave.errMsg,
678	<	"SimCreator Error. No global NMol or component NMol given.\n"
679	<	"\tCannot calculate the number of atoms.\n");
680	<
681	<	painCave.isFatal = 1;
682	<	simError();
683	<	}
684	<
685	<	id = the_components[i]->getType();
686	<
687	<	extractedStamp = stamps->extractMolStamp(id);
688	<	if (extractedStamp == NULL) {
689	<	sprintf(painCave.errMsg,
690	<	"SimCreator error: Component \"%s\" was not found in the "
691	<	"list of declared molecules\n", id);
692	<
693	<	painCave.isFatal = 1;
694	<	simError();
695	<	}
696	<
697	<	currentStamp = extractedStamp->getStamp();
698	<
699	<
700	<	moleculeStampPairs.push_back(
701	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
702	<	} //end for (i = 0; i < n_components; i++)
703	<	} else {
704	<	sprintf(painCave.errMsg, "SimSetup error.\n"
705	<	"\tSorry, the ability to specify total"
706	<	" nMols and then give molfractions in the components\n"
707	<	"\tis not currently supported."
708	<	" Please give nMol in the components.\n");
709	<
710	<	painCave.isFatal = 1;
711	<	simError();
670	>	int SimCreator::computeStorageLayout(SimInfo* info) {
671	>
672	>	Globals* simParams = info->getSimParams();
673	>	int nRigidBodies = info->getNGlobalRigidBodies();
674	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
675	>	set<AtomType*>::iterator i;
676	>	bool hasDirectionalAtoms = false;
677	>	bool hasFixedCharge = false;
678	>	bool hasMultipoles = false;
679	>	bool hasPolarizable = false;
680	>	bool hasFluctuatingCharge = false;
681	>	bool hasMetallic = false;
682	>	int storageLayout = 0;
683	>	storageLayout |= DataStorage::dslPosition;
684	>	storageLayout |= DataStorage::dslVelocity;
685	>	storageLayout |= DataStorage::dslForce;
686	>
687	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
688	>
689	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
690	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
691	>	EAMAdapter ea = EAMAdapter( (*i) );
692	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
693	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
694	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
695	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
696	>
697	>	if (da.isDirectional()){
698	>	hasDirectionalAtoms = true;
699	>	}
700	>	if (ma.isMultipole()){
701	>	hasMultipoles = true;
702	>	}
703	>	if (ea.isEAM() || sca.isSuttonChen()){
704	>	hasMetallic = true;
705	>	}
706	>	if ( fca.isFixedCharge() ){
707	>	hasFixedCharge = true;
708	>	}
709	>	if ( fqa.isFluctuatingCharge() ){
710	>	hasFluctuatingCharge = true;
711	>	}
712	>	if ( pa.isPolarizable() ){
713	>	hasPolarizable = true;
714	>	}
715		}
716
717	<	#ifdef IS_MPI
717	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
718	>	storageLayout |= DataStorage::dslAmat;
719	>	if(storageLayout & DataStorage::dslVelocity) {
720	>	storageLayout |= DataStorage::dslAngularMomentum;
721	>	}
722	>	if (storageLayout & DataStorage::dslForce) {
723	>	storageLayout |= DataStorage::dslTorque;
724	>	}
725	>	}
726	>	if (hasMultipoles) {
727	>	storageLayout |= DataStorage::dslElectroFrame;
728	>	}
729	>	if (hasFixedCharge || hasFluctuatingCharge) {
730	>	storageLayout |= DataStorage::dslSkippedCharge;
731	>	}
732	>	if (hasMetallic) {
733	>	storageLayout |= DataStorage::dslDensity;
734	>	storageLayout |= DataStorage::dslFunctional;
735	>	storageLayout |= DataStorage::dslFunctionalDerivative;
736	>	}
737	>	if (hasPolarizable) {
738	>	storageLayout |= DataStorage::dslElectricField;
739	>	}
740	>	if (hasFluctuatingCharge){
741	>	storageLayout |= DataStorage::dslFlucQPosition;
742	>	if(storageLayout & DataStorage::dslVelocity) {
743	>	storageLayout |= DataStorage::dslFlucQVelocity;
744	>	}
745	>	if (storageLayout & DataStorage::dslForce) {
746	>	storageLayout |= DataStorage::dslFlucQForce;
747	>	}
748	>	}
749
750	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
751	<	MPIcheckPoint();
752	<
753	<	#endif // is_mpi
754	<
750	>	// if the user has asked for them, make sure we've got the memory for the
751	>	// objects defined.
752	>
753	>	if (simParams->getOutputParticlePotential()) {
754	>	storageLayout |= DataStorage::dslParticlePot;
755	>	}
756	>	if (simParams->getOutputElectricField()) {
757	>	storageLayout |= DataStorage::dslElectricField;
758	>	}
759	>	if (simParams->getOutputFluctuatingCharges()) {
760	>	storageLayout |= DataStorage::dslFlucQPosition;
761	>	storageLayout |= DataStorage::dslFlucQVelocity;
762	>	storageLayout |= DataStorage::dslFlucQForce;
763	>	}
764	>
765	>	return storageLayout;
766		}
767	<
767	>
768		void SimCreator::setGlobalIndex(SimInfo *info) {
769		SimInfo::MoleculeIterator mi;
770		Molecule::AtomIterator ai;
771		Molecule::RigidBodyIterator ri;
772		Molecule::CutoffGroupIterator ci;
773	+	Molecule::IntegrableObjectIterator  ioi;
774		Molecule * mol;
775		Atom * atom;
776		RigidBody * rb;
#	Line 469 | Line 780 | namespace oopse {
780		int beginCutoffGroupIndex;
781		int nGlobalAtoms = info->getNGlobalAtoms();
782
472	–	#ifndef IS_MPI
473	–
783		beginAtomIndex = 0;
784		beginRigidBodyIndex = 0;
785		beginCutoffGroupIndex = 0;
786	<
787	<	#else
479	<
480	<	int nproc;
481	<	int myNode;
482	<
483	<	myNode = worldRank;
484	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
485	<
486	<	std::vector < int > tmpAtomsInProc(nproc, 0);
487	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
488	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
489	<	std::vector < int > NumAtomsInProc(nproc, 0);
490	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
491	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
492	<
493	<	tmpAtomsInProc[myNode] = info->getNAtoms();
494	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
495	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
496	<
497	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
498	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
499	<	MPI_SUM, MPI_COMM_WORLD);
500	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
501	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
502	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
503	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
504	<
505	<	beginAtomIndex = 0;
506	<	beginRigidBodyIndex = 0;
507	<	beginCutoffGroupIndex = 0;
508	<
509	<	for(int i = 0; i < myNode; i++) {
510	<	beginAtomIndex += NumAtomsInProc[i];
511	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
512	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
513	<	}
514	<
515	<	#endif
516	<
517	<	//rigidbody's index begins right after atom's
518	<	beginRigidBodyIndex += info->getNGlobalAtoms();
519	<
520	<	for(mol = info->beginMolecule(mi); mol != NULL;
521	<	mol = info->nextMolecule(mi)) {
786	>
787	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
788
789	<	//local index(index in DataStorge) of atom is important
790	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
791	<	atom->setGlobalIndex(beginAtomIndex++);
789	>	#ifdef IS_MPI
790	>	if (info->getMolToProc(i) == worldRank) {
791	>	#endif
792	>	// stuff to do if I own this molecule
793	>	mol = info->getMoleculeByGlobalIndex(i);
794	>
795	>	//local index(index in DataStorge) of atom is important
796	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
797	>	atom->setGlobalIndex(beginAtomIndex++);
798	>	}
799	>
800	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
801	>	rb = mol->nextRigidBody(ri)) {
802	>	rb->setGlobalIndex(beginRigidBodyIndex++);
803	>	}
804	>
805	>	//local index of cutoff group is trivial, it only depends on
806	>	//the order of travesing
807	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
808	>	cg = mol->nextCutoffGroup(ci)) {
809	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
810	>	}
811	>
812	>	#ifdef IS_MPI
813	>	}  else {
814	>
815	>	// stuff to do if I don't own this molecule
816	>
817	>	int stampId = info->getMoleculeStampId(i);
818	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
819	>
820	>	beginAtomIndex += stamp->getNAtoms();
821	>	beginRigidBodyIndex += stamp->getNRigidBodies();
822	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
823		}
824	<
825	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
826	<	rb = mol->nextRigidBody(ri)) {
827	<	rb->setGlobalIndex(beginRigidBodyIndex++);
531	<	}
532	<
533	<	//local index of cutoff group is trivial, it only depends on the order of travesing
534	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
535	<	cg = mol->nextCutoffGroup(ci)) {
536	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
537	<	}
538	<	}
539	<
824	>	#endif
825	>
826	>	} //end for(int i=0)
827	>
828		//fill globalGroupMembership
829		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
830		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 548 | Line 836 | namespace oopse {
836
837		}
838		}
839	<
839	>
840		#ifdef IS_MPI
841		// Since the globalGroupMembership has been zero filled and we've only
842		// poked values into the atoms we know, we can do an Allreduce
843		// to get the full globalGroupMembership array (We think).
844		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
845		// docs said we could.
846	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
846	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
847		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
848		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
849		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 567 | Line 855 | namespace oopse {
855		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
856
857		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
570	–
858		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
859		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
860		}
861		}
862
863		#ifdef IS_MPI
864	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
864	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
865
866		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
867		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 583 | Line 870 | namespace oopse {
870		#else
871		info->setGlobalMolMembership(globalMolMembership);
872		#endif
873	+
874	+	// nIOPerMol holds the number of integrable objects per molecule
875	+	// here the molecules are listed by their global indices.
876	+
877	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
878	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
879	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
880	+	}
881
882	+	#ifdef IS_MPI
883	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
884	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
885	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
886	+	#else
887	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
888	+	#endif
889	+
890	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
891	+
892	+	int startingIndex = 0;
893	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
894	+	startingIOIndexForMol[i] = startingIndex;
895	+	startingIndex += numIntegrableObjectsPerMol[i];
896	+	}
897	+
898	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
899	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
900	+	int myGlobalIndex = mol->getGlobalIndex();
901	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
902	+	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
903	+	integrableObject = mol->nextIntegrableObject(ioi)) {
904	+	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
905	+	IOIndexToIntegrableObject[globalIO] = integrableObject;
906	+	globalIO++;
907	+	}
908	+	}
909	+
910	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
911	+
912		}
913
914	<	void SimCreator::loadCoordinates(SimInfo* info) {
914	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
915		Globals* simParams;
916	+
917		simParams = info->getSimParams();
918
919	<	if (!simParams->haveInitialConfig()) {
594	<	sprintf(painCave.errMsg,
595	<	"Cannot intialize a simulation without an initial configuration file.\n");
596	<	painCave.isFatal = 1;;
597	<	simError();
598	<	}
599	<
600	<	DumpReader reader(info, simParams->getInitialConfig());
919	>	DumpReader reader(info, mdFileName);
920		int nframes = reader.getNFrames();
921	<
921	>
922		if (nframes > 0) {
923		reader.readFrame(nframes - 1);
924		} else {
925		//invalid initial coordinate file
926		sprintf(painCave.errMsg,
927		"Initial configuration file %s should at least contain one frame\n",
928	<	simParams->getInitialConfig());
928	>	mdFileName.c_str());
929		painCave.isFatal = 1;
930		simError();
931		}
613	–
932		//copy the current snapshot to previous snapshot
933		info->getSnapshotManager()->advance();
934		}
935
936	<	} //end namespace oopse
936	>	} //end namespace OpenMD
937
938

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 436 by tim, Fri Mar 11 17:50:11 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

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