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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1880 by gezelter, Mon Jun 17 18:28:30 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49	+	#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	>
103	>	if (worldRank == masterNode) {
104	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108	>
109	>	#ifdef IS_MPI
110	>	//brocasting the stream size
111	>	streamSize = ppStream.str().size() +1;
112	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
113	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
114	>
115	>	} else {
116	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
117	>
118	>	//get stream size
119	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
120	>
121	>	char* buf = new char[streamSize];
122	>	assert(buf);
123	>
124	>	//receive file content
125	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
126	>
127	>	ppStream.str(buf);
128	>	delete [] buf;
129	>	}
130	>	#endif
131	>	// Create a scanner that reads from the input stream
132	>	MDLexer lexer(ppStream);
133	>	lexer.setFilename(filename);
134	>	lexer.initDeferredLineCount();
135
136	<	#ifdef IS_MPI
136	>	// Create a parser that reads from the scanner
137	>	MDParser parser(lexer);
138	>	parser.setFilename(filename);
139	>
140	>	// Create an observer that synchorizes file name change
141	>	FilenameObserver observer;
142	>	observer.setLexer(&lexer);
143	>	observer.setParser(&parser);
144	>	lexer.setObserver(&observer);
145
146	<	if (worldRank == 0) {
147	<	#endif // is_mpi
146	>	antlr::ASTFactory factory;
147	>	parser.initializeASTFactory(factory);
148	>	parser.setASTFactory(&factory);
149	>	parser.mdfile();
150	>
151	>	// Create a tree parser that reads information into Globals
152	>	MDTreeParser treeParser;
153	>	treeParser.initializeASTFactory(factory);
154	>	treeParser.setASTFactory(&factory);
155	>	simParams = treeParser.walkTree(parser.getAST());
156	>	}
157	>
158
159	<	set_interface_stamps(stamps, simParams);
159	>	catch(antlr::MismatchedCharException& e) {
160	>	sprintf(painCave.errMsg,
161	>	"parser exception: %s %s:%d:%d\n",
162	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
163	>	painCave.isFatal = 1;
164	>	simError();
165	>	}
166	>	catch(antlr::MismatchedTokenException &e) {
167	>	sprintf(painCave.errMsg,
168	>	"parser exception: %s %s:%d:%d\n",
169	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
170	>	painCave.isFatal = 1;
171	>	simError();
172	>	}
173	>	catch(antlr::NoViableAltForCharException &e) {
174	>	sprintf(painCave.errMsg,
175	>	"parser exception: %s %s:%d:%d\n",
176	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
177	>	painCave.isFatal = 1;
178	>	simError();
179	>	}
180	>	catch(antlr::NoViableAltException &e) {
181	>	sprintf(painCave.errMsg,
182	>	"parser exception: %s %s:%d:%d\n",
183	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187
188	<	#ifdef IS_MPI
189	<
190	<	mpiEventInit();
191	<
192	<	#endif
193	<
82	<	yacc_BASS(mdFileName.c_str());
83	<
84	<	#ifdef IS_MPI
85	<
86	<	throwMPIEvent(NULL);
87	<	} else {
88	<	set_interface_stamps(stamps, simParams);
89	<	mpiEventInit();
90	<	MPIcheckPoint();
91	<	mpiEventLoop();
188	>	catch(antlr::TokenStreamRecognitionException& e) {
189	>	sprintf(painCave.errMsg,
190	>	"parser exception: %s %s:%d:%d\n",
191	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
192	>	painCave.isFatal = 1;
193	>	simError();
194		}
195	<
196	<	#endif
197	<
195	>
196	>	catch(antlr::TokenStreamIOException& e) {
197	>	sprintf(painCave.errMsg,
198	>	"parser exception: %s\n",
199	>	e.getMessage().c_str());
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>
204	>	catch(antlr::TokenStreamException& e) {
205	>	sprintf(painCave.errMsg,
206	>	"parser exception: %s\n",
207	>	e.getMessage().c_str());
208	>	painCave.isFatal = 1;
209	>	simError();
210	>	}
211	>	catch (antlr::RecognitionException& e) {
212	>	sprintf(painCave.errMsg,
213	>	"parser exception: %s %s:%d:%d\n",
214	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218	>	catch (antlr::CharStreamException& e) {
219	>	sprintf(painCave.errMsg,
220	>	"parser exception: %s\n",
221	>	e.getMessage().c_str());
222	>	painCave.isFatal = 1;
223	>	simError();
224	>	}
225	>	catch (OpenMDException& e) {
226	>	sprintf(painCave.errMsg,
227	>	"%s\n",
228	>	e.getMessage().c_str());
229	>	painCave.isFatal = 1;
230	>	simError();
231	>	}
232	>	catch (std::exception& e) {
233	>	sprintf(painCave.errMsg,
234	>	"parser exception: %s\n",
235	>	e.what());
236	>	painCave.isFatal = 1;
237	>	simError();
238	>	}
239	>
240	>	simParams->setMDfileVersion(mdFileVersion);
241	>	return simParams;
242		}
243
244		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
245		bool loadInitCoords) {
246
247	<	MakeStamps * stamps = new MakeStamps();
248	<
249	<	Globals * simParams = new Globals();
250	<
247	>	const int bufferSize = 65535;
248	>	char buffer[bufferSize];
249	>	int lineNo = 0;
250	>	std::string mdRawData;
251	>	int metaDataBlockStart = -1;
252	>	int metaDataBlockEnd = -1;
253	>	int i, j;
254	>	streamoff mdOffset;
255	>	int mdFileVersion;
256	>
257	>	// Create a string for embedding the version information in the MetaData
258	>	std::string version;
259	>	version.assign("## Last run using OpenMD Version: ");
260	>	version.append(OPENMD_VERSION_MAJOR);
261	>	version.append(".");
262	>	version.append(OPENMD_VERSION_MINOR);
263	>
264	>	std::string svnrev;
265	>	//convert a macro from compiler to a string in c++
266	>	STR_DEFINE(svnrev, SVN_REV );
267	>	version.append(" Revision: ");
268	>	// If there's no SVN revision, just call this the RELEASE revision.
269	>	if (!svnrev.empty()) {
270	>	version.append(svnrev);
271	>	} else {
272	>	version.append("RELEASE");
273	>	}
274	>
275	>	#ifdef IS_MPI
276	>	const int masterNode = 0;
277	>	if (worldRank == masterNode) {
278	>	#endif
279	>
280	>	std::ifstream mdFile_;
281	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
282	>
283	>	if (mdFile_.fail()) {
284	>	sprintf(painCave.errMsg,
285	>	"SimCreator: Cannot open file: %s\n",
286	>	mdFileName.c_str());
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>
291	>	mdFile_.getline(buffer, bufferSize);
292	>	++lineNo;
293	>	std::string line = trimLeftCopy(buffer);
294	>	i = CaseInsensitiveFind(line, "<OpenMD");
295	>	if (static_cast<size_t>(i) == string::npos) {
296	>	// try the older file strings to see if that works:
297	>	i = CaseInsensitiveFind(line, "<OOPSE");
298	>	}
299	>
300	>	if (static_cast<size_t>(i) == string::npos) {
301	>	// still no luck!
302	>	sprintf(painCave.errMsg,
303	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
304	>	mdFileName.c_str());
305	>	painCave.isFatal = 1;
306	>	simError();
307	>	}
308	>
309	>	// found the correct opening string, now try to get the file
310	>	// format version number.
311	>
312	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
313	>	std::string fileType = tokenizer.nextToken();
314	>	toUpper(fileType);
315	>
316	>	mdFileVersion = 0;
317	>
318	>	if (fileType == "OPENMD") {
319	>	while (tokenizer.hasMoreTokens()) {
320	>	std::string token(tokenizer.nextToken());
321	>	toUpper(token);
322	>	if (token == "VERSION") {
323	>	mdFileVersion = tokenizer.nextTokenAsInt();
324	>	break;
325	>	}
326	>	}
327	>	}
328	>
329	>	//scan through the input stream and find MetaData tag
330	>	while(mdFile_.getline(buffer, bufferSize)) {
331	>	++lineNo;
332	>
333	>	std::string line = trimLeftCopy(buffer);
334	>	if (metaDataBlockStart == -1) {
335	>	i = CaseInsensitiveFind(line, "<MetaData>");
336	>	if (i != string::npos) {
337	>	metaDataBlockStart = lineNo;
338	>	mdOffset = mdFile_.tellg();
339	>	}
340	>	} else {
341	>	i = CaseInsensitiveFind(line, "</MetaData>");
342	>	if (i != string::npos) {
343	>	metaDataBlockEnd = lineNo;
344	>	}
345	>	}
346	>	}
347	>
348	>	if (metaDataBlockStart == -1) {
349	>	sprintf(painCave.errMsg,
350	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
351	>	mdFileName.c_str());
352	>	painCave.isFatal = 1;
353	>	simError();
354	>	}
355	>	if (metaDataBlockEnd == -1) {
356	>	sprintf(painCave.errMsg,
357	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
358	>	mdFileName.c_str());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	}
362	>
363	>	mdFile_.clear();
364	>	mdFile_.seekg(0);
365	>	mdFile_.seekg(mdOffset);
366	>
367	>	mdRawData.clear();
368	>
369	>	bool foundVersion = false;
370	>
371	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
372	>	mdFile_.getline(buffer, bufferSize);
373	>	std::string line = trimLeftCopy(buffer);
374	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
375	>	if (static_cast<size_t>(j) != string::npos) {
376	>	foundVersion = true;
377	>	mdRawData += version;
378	>	} else {
379	>	mdRawData += buffer;
380	>	}
381	>	mdRawData += "\n";
382	>	}
383	>
384	>	if (!foundVersion) mdRawData += version + "\n";
385	>
386	>	mdFile_.close();
387	>
388	>	#ifdef IS_MPI
389	>	}
390	>	#endif
391	>
392	>	std::stringstream rawMetaDataStream(mdRawData);
393	>
394		//parse meta-data file
395	<	parseFile(mdFileName, stamps, simParams);
395	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
396	>	metaDataBlockStart + 1);
397
398		//create the force field
399	<	ForceField * ff = ForceFieldFactory::getInstance()
400	<	->createForceField(simParams->getForceField());
111	<
399	>	ForceField * ff = new ForceField(simParams->getForceField());
400	>
401		if (ff == NULL) {
402		sprintf(painCave.errMsg,
403		"ForceField Factory can not create %s force field\n",
#	Line 141 | Line 430 | namespace oopse {
430		}
431
432		ff->parse(forcefieldFileName);
144	–
145	–	//extract the molecule stamps
146	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
147	–	compList(stamps, simParams, moleculeStampPairs);
148	–
433		//create SimInfo
434	<	SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
434	>	SimInfo * info = new SimInfo(ff, simParams);
435	>
436	>	info->setRawMetaData(mdRawData);
437
438	<	//gather parameters (SimCreator only retrieves part of the parameters)
438	>	//gather parameters (SimCreator only retrieves part of the
439	>	//parameters)
440		gatherParameters(info, mdFileName);
441
442		//divide the molecules and determine the global index of molecules
#	Line 160 | Line 447 | namespace oopse {
447		//create the molecules
448		createMolecules(info);
449
450	+	//find the storage layout
451	+
452	+	int storageLayout = computeStorageLayout(info);
453	+
454	+	//allocate memory for DataStorage(circular reference, need to
455	+	//break it)
456	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
457
458	<	//allocate memory for DataStorage(circular reference, need to break it)
459	<	info->setSnapshotManager(new SimSnapshotManager(info));
460	<
461	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
462	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
169	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
458	>	//set the global index of atoms, rigidbodies and cutoffgroups
459	>	//(only need to be set once, the global index will never change
460	>	//again). Local indices of atoms and rigidbodies are already set
461	>	//by MoleculeCreator class which actually delegates the
462	>	//responsibility to LocalIndexManager.
463		setGlobalIndex(info);
464
465	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
466	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
467	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
468	<	//we can determine the beginning global indices of atoms before they get created.
465	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
466	>	//method, at that point atoms don't have the global index yet
467	>	//(their global index are all initialized to -1).  Therefore we
468	>	//have to call addInteractionPairs explicitly here. A way to work
469	>	//around is that we can determine the beginning global indices of
470	>	//atoms before they get created.
471		SimInfo::MoleculeIterator mi;
472		Molecule* mol;
473		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
474	<	info->addExcludePairs(mol);
474	>	info->addInteractionPairs(mol);
475		}
476
477		if (loadInitCoords)
478	<	loadCoordinates(info);
184	<
478	>	loadCoordinates(info, mdFileName);
479		return info;
480		}
481
#	Line 216 | Line 510 | namespace oopse {
510
511		#ifdef IS_MPI
512		void SimCreator::divideMolecules(SimInfo *info) {
513	<	double numerator;
220	<	double denominator;
221	<	double precast;
222	<	double x;
223	<	double y;
224	<	double a;
225	<	int old_atoms;
226	<	int add_atoms;
227	<	int new_atoms;
228	<	int nTarget;
229	<	int done;
230	<	int i;
231	<	int j;
232	<	int loops;
233	<	int which_proc;
513	>	RealType a;
514		int nProcessors;
515		std::vector<int> atomsPerProc;
516		int nGlobalMols = info->getNGlobalMolecules();
517	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
517	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
518	>	// error
519	>	// condition:
520
521	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
521	>	nProcessors = MPI::COMM_WORLD.Get_size();
522
523		if (nProcessors > nGlobalMols) {
524		sprintf(painCave.errMsg,
#	Line 245 | Line 527 | namespace oopse {
527		"\tthe number of molecules.  This will not result in a \n"
528		"\tusable division of atoms for force decomposition.\n"
529		"\tEither try a smaller number of processors, or run the\n"
530	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
530	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
531	>	nGlobalMols);
532
533		painCave.isFatal = 1;
534		simError();
535		}
536
254	–	int seedValue;
537		Globals * simParams = info->getSimParams();
538	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
538	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
539	>	//random number generator
540		if (simParams->haveSeed()) {
541	<	seedValue = simParams->getSeed();
541	>	int seedValue = simParams->getSeed();
542		myRandom = new SeqRandNumGen(seedValue);
543		}else {
544		myRandom = new SeqRandNumGen();
#	Line 268 | Line 551 | namespace oopse {
551		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
552
553		if (worldRank == 0) {
554	<	numerator = info->getNGlobalAtoms();
555	<	denominator = nProcessors;
556	<	precast = numerator / denominator;
557	<	nTarget = (int)(precast + 0.5);
554	>	RealType numerator = info->getNGlobalAtoms();
555	>	RealType denominator = nProcessors;
556	>	RealType precast = numerator / denominator;
557	>	int nTarget = (int)(precast + 0.5);
558
559	<	for(i = 0; i < nGlobalMols; i++) {
560	<	done = 0;
561	<	loops = 0;
559	>	for(int i = 0; i < nGlobalMols; i++) {
560	>
561	>	int done = 0;
562	>	int loops = 0;
563
564		while (!done) {
565		loops++;
566
567		// Pick a processor at random
568
569	<	which_proc = (int) (myRandom->rand() * nProcessors);
569	>	int which_proc = (int) (myRandom->rand() * nProcessors);
570
571		//get the molecule stamp first
572		int stampId = info->getMoleculeStampId(i);
573		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
574
575		// How many atoms does this processor have so far?
576	<	old_atoms = atomsPerProc[which_proc];
577	<	add_atoms = moleculeStamp->getNAtoms();
578	<	new_atoms = old_atoms + add_atoms;
576	>	int old_atoms = atomsPerProc[which_proc];
577	>	int add_atoms = moleculeStamp->getNAtoms();
578	>	int new_atoms = old_atoms + add_atoms;
579
580		// If we've been through this loop too many times, we need
581		// to just give up and assign the molecule to this processor
582		// and be done with it.
583
584		if (loops > 100) {
585	+
586		sprintf(painCave.errMsg,
587	<	"I've tried 100 times to assign molecule %d to a "
588	<	" processor, but can't find a good spot.\n"
589	<	"I'm assigning it at random to processor %d.\n",
587	>	"There have been 100 attempts to assign molecule %d to an\n"
588	>	"\tunderworked processor, but there's no good place to\n"
589	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
590		i, which_proc);
591	<
591	>
592		painCave.isFatal = 0;
593	+	painCave.severity = OPENMD_INFO;
594		simError();
595
596		molToProcMap[i] = which_proc;
#	Line 333 | Line 619 | namespace oopse {
619		//           Pacc(x) = exp(- a * x)
620		// where a = penalty / (average atoms per molecule)
621
622	<	x = (double)(new_atoms - nTarget);
623	<	y = myRandom->rand();
622	>	RealType x = (RealType)(new_atoms - nTarget);
623	>	RealType y = myRandom->rand();
624
625		if (y < exp(- a * x)) {
626		molToProcMap[i] = which_proc;
#	Line 349 | Line 635 | namespace oopse {
635		}
636
637		delete myRandom;
638	<
638	>
639		// Spray out this nonsense to all other processors:
640	<
355	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
640	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
641		} else {
642
643		// Listen to your marching orders from processor 0:
644	<
645	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
645	>
646		}
647
648		info->setMolToProcMap(molToProcMap);
649		sprintf(checkPointMsg,
650		"Successfully divided the molecules among the processors.\n");
651	<	MPIcheckPoint();
651	>	errorCheckPoint();
652		}
653
654		#endif
#	Line 380 | Line 665 | namespace oopse {
665		#endif
666
667		stampId = info->getMoleculeStampId(i);
668	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
669	<	stampId, i, info->getLocalIndexManager());
668	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
669	>	info->getMoleculeStamp(stampId),
670	>	stampId, i,
671	>	info->getLocalIndexManager());
672
673		info->addMolecule(mol);
674
#	Line 393 | Line 680 | namespace oopse {
680
681		} //end for(int i=0)
682		}
396	–
397	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
398	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
399	–	int i;
400	–	char * id;
401	–	MoleculeStamp * currentStamp;
402	–	Component** the_components = simParams->getComponents();
403	–	int n_components = simParams->getNComponents();
683
684	<	if (!simParams->haveNMol()) {
406	<	// we don't have the total number of molecules, so we assume it is
407	<	// given in each component
408	<
409	<	for(i = 0; i < n_components; i++) {
410	<	if (!the_components[i]->haveNMol()) {
411	<	// we have a problem
412	<	sprintf(painCave.errMsg,
413	<	"SimCreator Error. No global NMol or component NMol given.\n"
414	<	"\tCannot calculate the number of atoms.\n");
415	<
416	<	painCave.isFatal = 1;
417	<	simError();
418	<	}
419	<
420	<	id = the_components[i]->getType();
684	>	int SimCreator::computeStorageLayout(SimInfo* info) {
685
686	<	currentStamp = stamps->getMolStamp(id);
687	<	if (currentStamp == NULL) {
688	<	sprintf(painCave.errMsg,
689	<	"SimCreator error: Component \"%s\" was not found in the "
690	<	"list of declared molecules\n", id);
691	<
692	<	painCave.isFatal = 1;
693	<	simError();
694	<	}
695	<
696	<	moleculeStampPairs.push_back(
697	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
698	<	} //end for (i = 0; i < n_components; i++)
699	<	} else {
700	<	sprintf(painCave.errMsg, "SimSetup error.\n"
701	<	"\tSorry, the ability to specify total"
702	<	" nMols and then give molfractions in the components\n"
703	<	"\tis not currently supported."
704	<	" Please give nMol in the components.\n");
705	<
706	<	painCave.isFatal = 1;
707	<	simError();
686	>	Globals* simParams = info->getSimParams();
687	>	int nRigidBodies = info->getNGlobalRigidBodies();
688	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
689	>	set<AtomType*>::iterator i;
690	>	bool hasDirectionalAtoms = false;
691	>	bool hasFixedCharge = false;
692	>	bool hasDipoles = false;
693	>	bool hasQuadrupoles = false;
694	>	bool hasPolarizable = false;
695	>	bool hasFluctuatingCharge = false;
696	>	bool hasMetallic = false;
697	>	int storageLayout = 0;
698	>	storageLayout |= DataStorage::dslPosition;
699	>	storageLayout |= DataStorage::dslVelocity;
700	>	storageLayout |= DataStorage::dslForce;
701	>
702	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
703	>
704	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
705	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
706	>	EAMAdapter ea = EAMAdapter( (*i) );
707	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
708	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
709	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
710	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
711	>
712	>	if (da.isDirectional()){
713	>	hasDirectionalAtoms = true;
714	>	}
715	>	if (ma.isDipole()){
716	>	hasDipoles = true;
717	>	}
718	>	if (ma.isQuadrupole()){
719	>	hasQuadrupoles = true;
720	>	}
721	>	if (ea.isEAM() || sca.isSuttonChen()){
722	>	hasMetallic = true;
723	>	}
724	>	if ( fca.isFixedCharge() ){
725	>	hasFixedCharge = true;
726	>	}
727	>	if ( fqa.isFluctuatingCharge() ){
728	>	hasFluctuatingCharge = true;
729	>	}
730	>	if ( pa.isPolarizable() ){
731	>	hasPolarizable = true;
732	>	}
733		}
734
735	<	#ifdef IS_MPI
735	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
736	>	storageLayout |= DataStorage::dslAmat;
737	>	if(storageLayout & DataStorage::dslVelocity) {
738	>	storageLayout |= DataStorage::dslAngularMomentum;
739	>	}
740	>	if (storageLayout & DataStorage::dslForce) {
741	>	storageLayout |= DataStorage::dslTorque;
742	>	}
743	>	}
744	>	if (hasDipoles) {
745	>	storageLayout |= DataStorage::dslDipole;
746	>	}
747	>	if (hasQuadrupoles) {
748	>	storageLayout |= DataStorage::dslQuadrupole;
749	>	}
750	>	if (hasFixedCharge || hasFluctuatingCharge) {
751	>	storageLayout |= DataStorage::dslSkippedCharge;
752	>	}
753	>	if (hasMetallic) {
754	>	storageLayout |= DataStorage::dslDensity;
755	>	storageLayout |= DataStorage::dslFunctional;
756	>	storageLayout |= DataStorage::dslFunctionalDerivative;
757	>	}
758	>	if (hasPolarizable) {
759	>	storageLayout |= DataStorage::dslElectricField;
760	>	}
761	>	if (hasFluctuatingCharge){
762	>	storageLayout |= DataStorage::dslFlucQPosition;
763	>	if(storageLayout & DataStorage::dslVelocity) {
764	>	storageLayout |= DataStorage::dslFlucQVelocity;
765	>	}
766	>	if (storageLayout & DataStorage::dslForce) {
767	>	storageLayout |= DataStorage::dslFlucQForce;
768	>	}
769	>	}
770
771	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
772	<	MPIcheckPoint();
773	<
774	<	#endif // is_mpi
775	<
771	>	// if the user has asked for them, make sure we've got the memory for the
772	>	// objects defined.
773	>
774	>	if (simParams->getOutputParticlePotential()) {
775	>	storageLayout |= DataStorage::dslParticlePot;
776	>	}
777	>
778	>	if (simParams->havePrintHeatFlux()) {
779	>	if (simParams->getPrintHeatFlux()) {
780	>	storageLayout |= DataStorage::dslParticlePot;
781	>	}
782	>	}
783	>
784	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
785	>	storageLayout |= DataStorage::dslElectricField;
786	>	}
787	>
788	>	if (simParams->getOutputFluctuatingCharges()) {
789	>	storageLayout |= DataStorage::dslFlucQPosition;
790	>	storageLayout |= DataStorage::dslFlucQVelocity;
791	>	storageLayout |= DataStorage::dslFlucQForce;
792	>	}
793	>
794	>	info->setStorageLayout(storageLayout);
795	>
796	>	return storageLayout;
797		}
798	<
798	>
799		void SimCreator::setGlobalIndex(SimInfo *info) {
800		SimInfo::MoleculeIterator mi;
801		Molecule::AtomIterator ai;
802		Molecule::RigidBodyIterator ri;
803		Molecule::CutoffGroupIterator ci;
804	+	Molecule::IntegrableObjectIterator  ioi;
805		Molecule * mol;
806		Atom * atom;
807		RigidBody * rb;
#	Line 465 | Line 810 | namespace oopse {
810		int beginRigidBodyIndex;
811		int beginCutoffGroupIndex;
812		int nGlobalAtoms = info->getNGlobalAtoms();
813	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
814
469	–	#ifndef IS_MPI
470	–
815		beginAtomIndex = 0;
472	–	beginRigidBodyIndex = 0;
473	–	beginCutoffGroupIndex = 0;
474	–
475	–	#else
476	–
477	–	int nproc;
478	–	int myNode;
479	–
480	–	myNode = worldRank;
481	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
482	–
483	–	std::vector < int > tmpAtomsInProc(nproc, 0);
484	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
485	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
486	–	std::vector < int > NumAtomsInProc(nproc, 0);
487	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
488	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
489	–
490	–	tmpAtomsInProc[myNode] = info->getNAtoms();
491	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
492	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
493	–
494	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
495	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
496	–	MPI_SUM, MPI_COMM_WORLD);
497	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
498	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
499	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
500	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
501	–
502	–	beginAtomIndex = 0;
503	–	beginRigidBodyIndex = 0;
504	–	beginCutoffGroupIndex = 0;
505	–
506	–	for(int i = 0; i < myNode; i++) {
507	–	beginAtomIndex += NumAtomsInProc[i];
508	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
509	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
510	–	}
511	–
512	–	#endif
513	–
816		//rigidbody's index begins right after atom's
817	<	beginRigidBodyIndex += info->getNGlobalAtoms();
818	<
819	<	for(mol = info->beginMolecule(mi); mol != NULL;
820	<	mol = info->nextMolecule(mi)) {
817	>	beginRigidBodyIndex = info->getNGlobalAtoms();
818	>	beginCutoffGroupIndex = 0;
819	>
820	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
821
822	<	//local index(index in DataStorge) of atom is important
823	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824	<	atom->setGlobalIndex(beginAtomIndex++);
822	>	#ifdef IS_MPI
823	>	if (info->getMolToProc(i) == worldRank) {
824	>	#endif
825	>	// stuff to do if I own this molecule
826	>	mol = info->getMoleculeByGlobalIndex(i);
827	>
828	>	//local index(index in DataStorge) of atom is important
829	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	>	atom->setGlobalIndex(beginAtomIndex++);
831	>	}
832	>
833	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
834	>	rb = mol->nextRigidBody(ri)) {
835	>	rb->setGlobalIndex(beginRigidBodyIndex++);
836	>	}
837	>
838	>	//local index of cutoff group is trivial, it only depends on
839	>	//the order of travesing
840	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
841	>	cg = mol->nextCutoffGroup(ci)) {
842	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
843	>	}
844	>
845	>	#ifdef IS_MPI
846	>	}  else {
847	>
848	>	// stuff to do if I don't own this molecule
849	>
850	>	int stampId = info->getMoleculeStampId(i);
851	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
852	>
853	>	beginAtomIndex += stamp->getNAtoms();
854	>	beginRigidBodyIndex += stamp->getNRigidBodies();
855	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
856		}
857	<
858	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
859	<	rb = mol->nextRigidBody(ri)) {
860	<	rb->setGlobalIndex(beginRigidBodyIndex++);
528	<	}
529	<
530	<	//local index of cutoff group is trivial, it only depends on the order of travesing
531	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
532	<	cg = mol->nextCutoffGroup(ci)) {
533	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
534	<	}
535	<	}
536	<
857	>	#endif
858	>
859	>	} //end for(int i=0)
860	>
861		//fill globalGroupMembership
862		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
863		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 545 | Line 869 | namespace oopse {
869
870		}
871		}
872	<
872	>
873		#ifdef IS_MPI
874		// Since the globalGroupMembership has been zero filled and we've only
875		// poked values into the atoms we know, we can do an Allreduce
876		// to get the full globalGroupMembership array (We think).
877		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
878		// docs said we could.
879	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
880	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
881	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
879	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
880	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
881	>	&tmpGroupMembership[0], nGlobalAtoms,
882	>	MPI::INT, MPI::SUM);
883		info->setGlobalGroupMembership(tmpGroupMembership);
884		#else
885		info->setGlobalGroupMembership(globalGroupMembership);
886		#endif
887
888		//fill molMembership
889	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
889	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
890	>	info->getNGlobalRigidBodies(), 0);
891
892	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
893	<
892	>	for(mol = info->beginMolecule(mi); mol != NULL;
893	>	mol = info->nextMolecule(mi)) {
894		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
896		}
897	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
898	+	rb = mol->nextRigidBody(ri)) {
899	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
900	+	}
901		}
902
903		#ifdef IS_MPI
904	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
904	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
905	>	info->getNGlobalRigidBodies(), 0);
906	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
907	>	nGlobalAtoms + nGlobalRigidBodies,
908	>	MPI::INT, MPI::SUM);
909
576	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
577	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
578	–
910		info->setGlobalMolMembership(tmpMolMembership);
911		#else
912		info->setGlobalMolMembership(globalMolMembership);
913		#endif
914	+
915	+	// nIOPerMol holds the number of integrable objects per molecule
916	+	// here the molecules are listed by their global indices.
917	+
918	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
919	+	for (mol = info->beginMolecule(mi); mol != NULL;
920	+	mol = info->nextMolecule(mi)) {
921	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
922	+	}
923
924	<	}
925	<
926	<	void SimCreator::loadCoordinates(SimInfo* info) {
927	<	Globals* simParams;
928	<	simParams = info->getSimParams();
924	>	#ifdef IS_MPI
925	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
926	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
927	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
928	>	#else
929	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
930	>	#endif
931	>
932	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
933
934	<	if (!simParams->haveInitialConfig()) {
935	<	sprintf(painCave.errMsg,
936	<	"Cannot intialize a simulation without an initial configuration file.\n");
937	<	painCave.isFatal = 1;;
594	<	simError();
934	>	int startingIndex = 0;
935	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
936	>	startingIOIndexForMol[i] = startingIndex;
937	>	startingIndex += numIntegrableObjectsPerMol[i];
938		}
939
940	<	DumpReader reader(info, simParams->getInitialConfig());
940	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
941	>	for (mol = info->beginMolecule(mi); mol != NULL;
942	>	mol = info->nextMolecule(mi)) {
943	>	int myGlobalIndex = mol->getGlobalIndex();
944	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
945	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
946	>	sd = mol->nextIntegrableObject(ioi)) {
947	>	sd->setGlobalIntegrableObjectIndex(globalIO);
948	>	IOIndexToIntegrableObject[globalIO] = sd;
949	>	globalIO++;
950	>	}
951	>	}
952	>
953	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
954	>
955	>	}
956	>
957	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
958	>
959	>	DumpReader reader(info, mdFileName);
960		int nframes = reader.getNFrames();
961
962		if (nframes > 0) {
#	Line 603 | Line 965 | namespace oopse {
965		//invalid initial coordinate file
966		sprintf(painCave.errMsg,
967		"Initial configuration file %s should at least contain one frame\n",
968	<	simParams->getInitialConfig().c_str());
968	>	mdFileName.c_str());
969		painCave.isFatal = 1;
970		simError();
971		}
610	–
972		//copy the current snapshot to previous snapshot
973		info->getSnapshotManager()->advance();
974		}
975
976	<	} //end namespace oopse
976	>	} //end namespace OpenMD
977
978

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1880 by gezelter, Mon Jun 17 18:28:30 2013 UTC

#	Line 0 | Line 1
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