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

Comparing:
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 1874 by gezelter, Wed May 15 15:09:35 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	<	simParams->initalize();
160	<	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	<
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();
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, bool loadInitCoords) {
245	<
101	<	MakeStamps * stamps = new MakeStamps();
102	<
103	<	Globals * simParams = new Globals();
244	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
245	>	bool loadInitCoords) {
246
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()->createForceField(
400	<	simParams->getForceField());
111	<
399	>	ForceField * ff = new ForceField(simParams->getForceField());
400	>
401		if (ff == NULL) {
402	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
403	<	simParams->getForceField());
402	>	sprintf(painCave.errMsg,
403	>	"ForceField Factory can not create %s force field\n",
404	>	simParams->getForceField().c_str());
405		painCave.isFatal = 1;
406		simError();
407		}
#	Line 140 | Line 430 | namespace oopse {
430		}
431
432		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
433		//create SimInfo
434	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
435	<
436	<	//gather parameters (SimCreator only retrieves part of the parameters)
434	>	SimInfo * info = new SimInfo(ff, simParams);
435	>
436	>	info->setRawMetaData(mdRawData);
437	>
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 159 | 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
168	<	//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);
183	<
478	>	loadCoordinates(info, mdFileName);
479		return info;
480		}
481
482		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
483
484	<	//figure out the ouput file names
484	>	//figure out the output file names
485		std::string prefix;
486
487		#ifdef IS_MPI
#	Line 215 | Line 510 | namespace oopse {
510
511		#ifdef IS_MPI
512		void SimCreator::divideMolecules(SimInfo *info) {
513	<	double numerator;
514	<	double denominator;
515	<	double precast;
516	<	double x;
517	<	double y;
518	<	double a;
224	<	int old_atoms;
225	<	int add_atoms;
226	<	int new_atoms;
227	<	int nTarget;
228	<	int done;
229	<	int i;
230	<	int j;
231	<	int loops;
232	<	int which_proc;
513	>	RealType numerator;
514	>	RealType denominator;
515	>	RealType precast;
516	>	RealType x;
517	>	RealType y;
518	>	RealType a;
519		int nProcessors;
520		std::vector<int> atomsPerProc;
521		int nGlobalMols = info->getNGlobalMolecules();
522	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
522	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
523	>	// error
524	>	// condition:
525
526	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
526	>	nProcessors = MPI::COMM_WORLD.Get_size();
527
528		if (nProcessors > nGlobalMols) {
529		sprintf(painCave.errMsg,
#	Line 244 | Line 532 | namespace oopse {
532		"\tthe number of molecules.  This will not result in a \n"
533		"\tusable division of atoms for force decomposition.\n"
534		"\tEither try a smaller number of processors, or run the\n"
535	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
535	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
536	>	nGlobalMols);
537
538		painCave.isFatal = 1;
539		simError();
540		}
541
253	–	int seedValue;
542		Globals * simParams = info->getSimParams();
543	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
543	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
544	>	//random number generator
545		if (simParams->haveSeed()) {
546	<	seedValue = simParams->getSeed();
546	>	int seedValue = simParams->getSeed();
547		myRandom = new SeqRandNumGen(seedValue);
548		}else {
549		myRandom = new SeqRandNumGen();
#	Line 270 | Line 559 | namespace oopse {
559		numerator = info->getNGlobalAtoms();
560		denominator = nProcessors;
561		precast = numerator / denominator;
562	<	nTarget = (int)(precast + 0.5);
562	>	int nTarget = (int)(precast + 0.5);
563
564	<	for(i = 0; i < nGlobalMols; i++) {
565	<	done = 0;
566	<	loops = 0;
564	>	for(int i = 0; i < nGlobalMols; i++) {
565	>
566	>	int done = 0;
567	>	int loops = 0;
568
569		while (!done) {
570		loops++;
571
572		// Pick a processor at random
573
574	<	which_proc = (int) (myRandom->rand() * nProcessors);
574	>	int which_proc = (int) (myRandom->rand() * nProcessors);
575
576		//get the molecule stamp first
577		int stampId = info->getMoleculeStampId(i);
578		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
579
580		// How many atoms does this processor have so far?
581	<	old_atoms = atomsPerProc[which_proc];
582	<	add_atoms = moleculeStamp->getNAtoms();
583	<	new_atoms = old_atoms + add_atoms;
581	>	int old_atoms = atomsPerProc[which_proc];
582	>	int add_atoms = moleculeStamp->getNAtoms();
583	>	int new_atoms = old_atoms + add_atoms;
584
585		// If we've been through this loop too many times, we need
586		// to just give up and assign the molecule to this processor
587		// and be done with it.
588
589		if (loops > 100) {
590	+
591		sprintf(painCave.errMsg,
592	<	"I've tried 100 times to assign molecule %d to a "
593	<	" processor, but can't find a good spot.\n"
594	<	"I'm assigning it at random to processor %d.\n",
592	>	"There have been 100 attempts to assign molecule %d to an\n"
593	>	"\tunderworked processor, but there's no good place to\n"
594	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
595		i, which_proc);
596	<
596	>
597		painCave.isFatal = 0;
598	+	painCave.severity = OPENMD_INFO;
599		simError();
600
601		molToProcMap[i] = which_proc;
#	Line 332 | Line 624 | namespace oopse {
624		//           Pacc(x) = exp(- a * x)
625		// where a = penalty / (average atoms per molecule)
626
627	<	x = (double)(new_atoms - nTarget);
627	>	x = (RealType)(new_atoms - nTarget);
628		y = myRandom->rand();
629
630		if (y < exp(- a * x)) {
#	Line 348 | Line 640 | namespace oopse {
640		}
641
642		delete myRandom;
643	<
643	>
644		// Spray out this nonsense to all other processors:
645	<
354	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
645	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
646		} else {
647
648		// Listen to your marching orders from processor 0:
649	<
650	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
649	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
650	>
651		}
652
653		info->setMolToProcMap(molToProcMap);
654		sprintf(checkPointMsg,
655		"Successfully divided the molecules among the processors.\n");
656	<	MPIcheckPoint();
656	>	errorCheckPoint();
657		}
658
659		#endif
#	Line 379 | Line 670 | namespace oopse {
670		#endif
671
672		stampId = info->getMoleculeStampId(i);
673	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
674	<	stampId, i, info->getLocalIndexManager());
673	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
674	>	info->getMoleculeStamp(stampId),
675	>	stampId, i,
676	>	info->getLocalIndexManager());
677
678		info->addMolecule(mol);
679
#	Line 392 | Line 685 | namespace oopse {
685
686		} //end for(int i=0)
687		}
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();
688
689	<	if (!simParams->haveNMol()) {
690	<	// we don't have the total number of molecules, so we assume it is
691	<	// given in each component
692	<
693	<	for(i = 0; i < n_components; i++) {
694	<	if (!the_components[i]->haveNMol()) {
695	<	// we have a problem
696	<	sprintf(painCave.errMsg,
697	<	"SimCreator Error. No global NMol or component NMol given.\n"
698	<	"\tCannot calculate the number of atoms.\n");
699	<
700	<	painCave.isFatal = 1;
701	<	simError();
702	<	}
703	<
704	<	id = the_components[i]->getType();
705	<
706	<	extractedStamp = stamps->extractMolStamp(id);
707	<	if (extractedStamp == NULL) {
708	<	sprintf(painCave.errMsg,
709	<	"SimCreator error: Component \"%s\" was not found in the "
710	<	"list of declared molecules\n", id);
711	<
712	<	painCave.isFatal = 1;
713	<	simError();
714	<	}
715	<
716	<	currentStamp = extractedStamp->getStamp();
717	<
718	<
719	<	moleculeStampPairs.push_back(
720	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
721	<	} //end for (i = 0; i < n_components; i++)
722	<	} else {
723	<	sprintf(painCave.errMsg, "SimSetup error.\n"
724	<	"\tSorry, the ability to specify total"
725	<	" nMols and then give molfractions in the components\n"
726	<	"\tis not currently supported."
727	<	" Please give nMol in the components.\n");
728	<
729	<	painCave.isFatal = 1;
730	<	simError();
689	>	int SimCreator::computeStorageLayout(SimInfo* info) {
690	>
691	>	Globals* simParams = info->getSimParams();
692	>	int nRigidBodies = info->getNGlobalRigidBodies();
693	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
694	>	set<AtomType*>::iterator i;
695	>	bool hasDirectionalAtoms = false;
696	>	bool hasFixedCharge = false;
697	>	bool hasDipoles = false;
698	>	bool hasQuadrupoles = false;
699	>	bool hasPolarizable = false;
700	>	bool hasFluctuatingCharge = false;
701	>	bool hasMetallic = false;
702	>	int storageLayout = 0;
703	>	storageLayout |= DataStorage::dslPosition;
704	>	storageLayout |= DataStorage::dslVelocity;
705	>	storageLayout |= DataStorage::dslForce;
706	>
707	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
708	>
709	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
710	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
711	>	EAMAdapter ea = EAMAdapter( (*i) );
712	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
713	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
714	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
715	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
716	>
717	>	if (da.isDirectional()){
718	>	hasDirectionalAtoms = true;
719	>	}
720	>	if (ma.isDipole()){
721	>	hasDipoles = true;
722	>	}
723	>	if (ma.isQuadrupole()){
724	>	hasQuadrupoles = true;
725	>	}
726	>	if (ea.isEAM() || sca.isSuttonChen()){
727	>	hasMetallic = true;
728	>	}
729	>	if ( fca.isFixedCharge() ){
730	>	hasFixedCharge = true;
731	>	}
732	>	if ( fqa.isFluctuatingCharge() ){
733	>	hasFluctuatingCharge = true;
734	>	}
735	>	if ( pa.isPolarizable() ){
736	>	hasPolarizable = true;
737	>	}
738		}
739
740	<	#ifdef IS_MPI
740	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
741	>	storageLayout |= DataStorage::dslAmat;
742	>	if(storageLayout & DataStorage::dslVelocity) {
743	>	storageLayout |= DataStorage::dslAngularMomentum;
744	>	}
745	>	if (storageLayout & DataStorage::dslForce) {
746	>	storageLayout |= DataStorage::dslTorque;
747	>	}
748	>	}
749	>	if (hasDipoles) {
750	>	storageLayout |= DataStorage::dslDipole;
751	>	}
752	>	if (hasQuadrupoles) {
753	>	storageLayout |= DataStorage::dslQuadrupole;
754	>	}
755	>	if (hasFixedCharge || hasFluctuatingCharge) {
756	>	storageLayout |= DataStorage::dslSkippedCharge;
757	>	}
758	>	if (hasMetallic) {
759	>	storageLayout |= DataStorage::dslDensity;
760	>	storageLayout |= DataStorage::dslFunctional;
761	>	storageLayout |= DataStorage::dslFunctionalDerivative;
762	>	}
763	>	if (hasPolarizable) {
764	>	storageLayout |= DataStorage::dslElectricField;
765	>	}
766	>	if (hasFluctuatingCharge){
767	>	storageLayout |= DataStorage::dslFlucQPosition;
768	>	if(storageLayout & DataStorage::dslVelocity) {
769	>	storageLayout |= DataStorage::dslFlucQVelocity;
770	>	}
771	>	if (storageLayout & DataStorage::dslForce) {
772	>	storageLayout |= DataStorage::dslFlucQForce;
773	>	}
774	>	}
775
776	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
777	<	MPIcheckPoint();
778	<
779	<	#endif // is_mpi
780	<
776	>	// if the user has asked for them, make sure we've got the memory for the
777	>	// objects defined.
778	>
779	>	if (simParams->getOutputParticlePotential()) {
780	>	storageLayout |= DataStorage::dslParticlePot;
781	>	}
782	>
783	>	if (simParams->havePrintHeatFlux()) {
784	>	if (simParams->getPrintHeatFlux()) {
785	>	storageLayout |= DataStorage::dslParticlePot;
786	>	}
787	>	}
788	>
789	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
790	>	storageLayout |= DataStorage::dslElectricField;
791	>	}
792	>
793	>	if (simParams->getOutputFluctuatingCharges()) {
794	>	storageLayout |= DataStorage::dslFlucQPosition;
795	>	storageLayout |= DataStorage::dslFlucQVelocity;
796	>	storageLayout |= DataStorage::dslFlucQForce;
797	>	}
798	>
799	>	info->setStorageLayout(storageLayout);
800	>
801	>	return storageLayout;
802		}
803	<
803	>
804		void SimCreator::setGlobalIndex(SimInfo *info) {
805		SimInfo::MoleculeIterator mi;
806		Molecule::AtomIterator ai;
807		Molecule::RigidBodyIterator ri;
808		Molecule::CutoffGroupIterator ci;
809	+	Molecule::IntegrableObjectIterator  ioi;
810		Molecule * mol;
811		Atom * atom;
812		RigidBody * rb;
#	Line 468 | Line 815 | namespace oopse {
815		int beginRigidBodyIndex;
816		int beginCutoffGroupIndex;
817		int nGlobalAtoms = info->getNGlobalAtoms();
818	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
819
472	–	#ifndef IS_MPI
473	–
820		beginAtomIndex = 0;
475	–	beginRigidBodyIndex = 0;
476	–	beginCutoffGroupIndex = 0;
477	–
478	–	#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	–
821		//rigidbody's index begins right after atom's
822	<	beginRigidBodyIndex += info->getNGlobalAtoms();
823	<
824	<	for(mol = info->beginMolecule(mi); mol != NULL;
825	<	mol = info->nextMolecule(mi)) {
822	>	beginRigidBodyIndex = info->getNGlobalAtoms();
823	>	beginCutoffGroupIndex = 0;
824	>
825	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
826
827	<	//local index(index in DataStorge) of atom is important
828	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
829	<	atom->setGlobalIndex(beginAtomIndex++);
827	>	#ifdef IS_MPI
828	>	if (info->getMolToProc(i) == worldRank) {
829	>	#endif
830	>	// stuff to do if I own this molecule
831	>	mol = info->getMoleculeByGlobalIndex(i);
832	>
833	>	//local index(index in DataStorge) of atom is important
834	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
835	>	atom->setGlobalIndex(beginAtomIndex++);
836	>	}
837	>
838	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
839	>	rb = mol->nextRigidBody(ri)) {
840	>	rb->setGlobalIndex(beginRigidBodyIndex++);
841	>	}
842	>
843	>	//local index of cutoff group is trivial, it only depends on
844	>	//the order of travesing
845	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
846	>	cg = mol->nextCutoffGroup(ci)) {
847	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
848	>	}
849	>
850	>	#ifdef IS_MPI
851	>	}  else {
852	>
853	>	// stuff to do if I don't own this molecule
854	>
855	>	int stampId = info->getMoleculeStampId(i);
856	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
857	>
858	>	beginAtomIndex += stamp->getNAtoms();
859	>	beginRigidBodyIndex += stamp->getNRigidBodies();
860	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
861		}
862	<
863	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
864	<	rb = mol->nextRigidBody(ri)) {
865	<	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	<
862	>	#endif
863	>
864	>	} //end for(int i=0)
865	>
866		//fill globalGroupMembership
867		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
868		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 548 | Line 874 | namespace oopse {
874
875		}
876		}
877	<
877	>
878		#ifdef IS_MPI
879		// Since the globalGroupMembership has been zero filled and we've only
880		// poked values into the atoms we know, we can do an Allreduce
881		// to get the full globalGroupMembership array (We think).
882		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
883		// docs said we could.
884	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
885	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
886	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
884	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
885	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
886	>	&tmpGroupMembership[0], nGlobalAtoms,
887	>	MPI::INT, MPI::SUM);
888		info->setGlobalGroupMembership(tmpGroupMembership);
889		#else
890		info->setGlobalGroupMembership(globalGroupMembership);
891		#endif
892
893		//fill molMembership
894	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
894	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
895	>	info->getNGlobalRigidBodies(), 0);
896
897	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
898	<
897	>	for(mol = info->beginMolecule(mi); mol != NULL;
898	>	mol = info->nextMolecule(mi)) {
899		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
900		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
901		}
902	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
903	+	rb = mol->nextRigidBody(ri)) {
904	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
905	+	}
906		}
907
908		#ifdef IS_MPI
909	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
909	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
910	>	info->getNGlobalRigidBodies(), 0);
911	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
912	>	nGlobalAtoms + nGlobalRigidBodies,
913	>	MPI::INT, MPI::SUM);
914
579	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
580	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
581	–
915		info->setGlobalMolMembership(tmpMolMembership);
916		#else
917		info->setGlobalMolMembership(globalMolMembership);
918		#endif
919	+
920	+	// nIOPerMol holds the number of integrable objects per molecule
921	+	// here the molecules are listed by their global indices.
922	+
923	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
924	+	for (mol = info->beginMolecule(mi); mol != NULL;
925	+	mol = info->nextMolecule(mi)) {
926	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
927	+	}
928
929	<	}
930	<
931	<	void SimCreator::loadCoordinates(SimInfo* info) {
932	<	Globals* simParams;
933	<	simParams = info->getSimParams();
929	>	#ifdef IS_MPI
930	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
931	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
932	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
933	>	#else
934	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
935	>	#endif
936	>
937	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
938
939	<	if (!simParams->haveInitialConfig()) {
940	<	sprintf(painCave.errMsg,
941	<	"Cannot intialize a simulation without an initial configuration file.\n");
942	<	painCave.isFatal = 1;;
597	<	simError();
939	>	int startingIndex = 0;
940	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
941	>	startingIOIndexForMol[i] = startingIndex;
942	>	startingIndex += numIntegrableObjectsPerMol[i];
943		}
944
945	<	DumpReader reader(info, simParams->getInitialConfig());
945	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
946	>	for (mol = info->beginMolecule(mi); mol != NULL;
947	>	mol = info->nextMolecule(mi)) {
948	>	int myGlobalIndex = mol->getGlobalIndex();
949	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
950	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
951	>	sd = mol->nextIntegrableObject(ioi)) {
952	>	sd->setGlobalIntegrableObjectIndex(globalIO);
953	>	IOIndexToIntegrableObject[globalIO] = sd;
954	>	globalIO++;
955	>	}
956	>	}
957	>
958	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
959	>
960	>	}
961	>
962	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
963	>
964	>	DumpReader reader(info, mdFileName);
965		int nframes = reader.getNFrames();
966
967		if (nframes > 0) {
#	Line 606 | Line 970 | namespace oopse {
970		//invalid initial coordinate file
971		sprintf(painCave.errMsg,
972		"Initial configuration file %s should at least contain one frame\n",
973	<	simParams->getInitialConfig());
973	>	mdFileName.c_str());
974		painCave.isFatal = 1;
975		simError();
976		}
613	–
977		//copy the current snapshot to previous snapshot
978		info->getSnapshotManager()->advance();
979		}
980
981	<	} //end namespace oopse
981	>	} //end namespace OpenMD
982
983

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 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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