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root/OpenMD/trunk/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.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
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,
108	>	ppStream);
109	>
110	>	#ifdef IS_MPI
111	>	//brocasting the stream size
112	>	streamSize = ppStream.str().size() +1;
113	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
114	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
115	>
116	>	} else {
117	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
118	>
119	>	//get stream size
120	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121	>
122	>	char* buf = new char[streamSize];
123	>	assert(buf);
124	>
125	>	//receive file content
126	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
127	>
128	>	ppStream.str(buf);
129	>	delete [] buf;
130	>	}
131	>	#endif
132	>	// Create a scanner that reads from the input stream
133	>	MDLexer lexer(ppStream);
134	>	lexer.setFilename(filename);
135	>	lexer.initDeferredLineCount();
136
137	<	#ifdef IS_MPI
137	>	// Create a parser that reads from the scanner
138	>	MDParser parser(lexer);
139	>	parser.setFilename(filename);
140	>
141	>	// Create an observer that synchorizes file name change
142	>	FilenameObserver observer;
143	>	observer.setLexer(&lexer);
144	>	observer.setParser(&parser);
145	>	lexer.setObserver(&observer);
146
147	<	if (worldRank == 0) {
148	<	#endif // is_mpi
147	>	antlr::ASTFactory factory;
148	>	parser.initializeASTFactory(factory);
149	>	parser.setASTFactory(&factory);
150	>	parser.mdfile();
151	>
152	>	// Create a tree parser that reads information into Globals
153	>	MDTreeParser treeParser;
154	>	treeParser.initializeASTFactory(factory);
155	>	treeParser.setASTFactory(&factory);
156	>	simParams = treeParser.walkTree(parser.getAST());
157	>	}
158	>
159
160	<	simParams->initalize();
161	<	set_interface_stamps(stamps, simParams);
160	>	catch(antlr::MismatchedCharException& e) {
161	>	sprintf(painCave.errMsg,
162	>	"parser exception: %s %s:%d:%d\n",
163	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
164	>	painCave.isFatal = 1;
165	>	simError();
166	>	}
167	>	catch(antlr::MismatchedTokenException &e) {
168	>	sprintf(painCave.errMsg,
169	>	"parser exception: %s %s:%d:%d\n",
170	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
171	>	painCave.isFatal = 1;
172	>	simError();
173	>	}
174	>	catch(antlr::NoViableAltForCharException &e) {
175	>	sprintf(painCave.errMsg,
176	>	"parser exception: %s %s:%d:%d\n",
177	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
178	>	painCave.isFatal = 1;
179	>	simError();
180	>	}
181	>	catch(antlr::NoViableAltException &e) {
182	>	sprintf(painCave.errMsg,
183	>	"parser exception: %s %s:%d:%d\n",
184	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
185	>	painCave.isFatal = 1;
186	>	simError();
187	>	}
188
189	<	#ifdef IS_MPI
190	<
191	<	mpiEventInit();
192	<
193	<	#endif
194	<
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();
189	>	catch(antlr::TokenStreamRecognitionException& e) {
190	>	sprintf(painCave.errMsg,
191	>	"parser exception: %s %s:%d:%d\n",
192	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
193	>	painCave.isFatal = 1;
194	>	simError();
195		}
196	<
197	<	#endif
198	<
196	>
197	>	catch(antlr::TokenStreamIOException& e) {
198	>	sprintf(painCave.errMsg,
199	>	"parser exception: %s\n",
200	>	e.getMessage().c_str());
201	>	painCave.isFatal = 1;
202	>	simError();
203	>	}
204	>
205	>	catch(antlr::TokenStreamException& e) {
206	>	sprintf(painCave.errMsg,
207	>	"parser exception: %s\n",
208	>	e.getMessage().c_str());
209	>	painCave.isFatal = 1;
210	>	simError();
211	>	}
212	>	catch (antlr::RecognitionException& e) {
213	>	sprintf(painCave.errMsg,
214	>	"parser exception: %s %s:%d:%d\n",
215	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
216	>	painCave.isFatal = 1;
217	>	simError();
218	>	}
219	>	catch (antlr::CharStreamException& e) {
220	>	sprintf(painCave.errMsg,
221	>	"parser exception: %s\n",
222	>	e.getMessage().c_str());
223	>	painCave.isFatal = 1;
224	>	simError();
225	>	}
226	>	catch (OpenMDException& e) {
227	>	sprintf(painCave.errMsg,
228	>	"%s\n",
229	>	e.getMessage().c_str());
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	catch (std::exception& e) {
234	>	sprintf(painCave.errMsg,
235	>	"parser exception: %s\n",
236	>	e.what());
237	>	painCave.isFatal = 1;
238	>	simError();
239	>	}
240	>
241	>	simParams->setMDfileVersion(mdFileVersion);
242	>	return simParams;
243		}
244
245	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
246	<
101	<	MakeStamps * stamps = new MakeStamps();
245	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
246	>	bool loadInitCoords) {
247
248	<	Globals * simParams = new Globals();
249	<
248	>	const int bufferSize = 65535;
249	>	char buffer[bufferSize];
250	>	int lineNo = 0;
251	>	std::string mdRawData;
252	>	int metaDataBlockStart = -1;
253	>	int metaDataBlockEnd = -1;
254	>	int i, j;
255	>	streamoff mdOffset;
256	>	int mdFileVersion;
257	>
258	>	// Create a string for embedding the version information in the MetaData
259	>	std::string version;
260	>	version.assign("## Last run using OpenMD Version: ");
261	>	version.append(OPENMD_VERSION_MAJOR);
262	>	version.append(".");
263	>	version.append(OPENMD_VERSION_MINOR);
264	>
265	>	std::string svnrev;
266	>	//convert a macro from compiler to a string in c++
267	>	STR_DEFINE(svnrev, SVN_REV );
268	>	version.append(" Revision: ");
269	>	// If there's no SVN revision, just call this the RELEASE revision.
270	>	if (!svnrev.empty()) {
271	>	version.append(svnrev);
272	>	} else {
273	>	version.append("RELEASE");
274	>	}
275	>
276	>	#ifdef IS_MPI
277	>	const int masterNode = 0;
278	>	if (worldRank == masterNode) {
279	>	#endif
280	>
281	>	std::ifstream mdFile_;
282	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
283	>
284	>	if (mdFile_.fail()) {
285	>	sprintf(painCave.errMsg,
286	>	"SimCreator: Cannot open file: %s\n",
287	>	mdFileName.c_str());
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291	>
292	>	mdFile_.getline(buffer, bufferSize);
293	>	++lineNo;
294	>	std::string line = trimLeftCopy(buffer);
295	>	i = CaseInsensitiveFind(line, "<OpenMD");
296	>	if (static_cast<size_t>(i) == string::npos) {
297	>	// try the older file strings to see if that works:
298	>	i = CaseInsensitiveFind(line, "<OOPSE");
299	>	}
300	>
301	>	if (static_cast<size_t>(i) == string::npos) {
302	>	// still no luck!
303	>	sprintf(painCave.errMsg,
304	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
305	>	mdFileName.c_str());
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	// found the correct opening string, now try to get the file
311	>	// format version number.
312	>
313	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
314	>	std::string fileType = tokenizer.nextToken();
315	>	toUpper(fileType);
316	>
317	>	mdFileVersion = 0;
318	>
319	>	if (fileType == "OPENMD") {
320	>	while (tokenizer.hasMoreTokens()) {
321	>	std::string token(tokenizer.nextToken());
322	>	toUpper(token);
323	>	if (token == "VERSION") {
324	>	mdFileVersion = tokenizer.nextTokenAsInt();
325	>	break;
326	>	}
327	>	}
328	>	}
329	>
330	>	//scan through the input stream and find MetaData tag
331	>	while(mdFile_.getline(buffer, bufferSize)) {
332	>	++lineNo;
333	>
334	>	std::string line = trimLeftCopy(buffer);
335	>	if (metaDataBlockStart == -1) {
336	>	i = CaseInsensitiveFind(line, "<MetaData>");
337	>	if (i != string::npos) {
338	>	metaDataBlockStart = lineNo;
339	>	mdOffset = mdFile_.tellg();
340	>	}
341	>	} else {
342	>	i = CaseInsensitiveFind(line, "</MetaData>");
343	>	if (i != string::npos) {
344	>	metaDataBlockEnd = lineNo;
345	>	}
346	>	}
347	>	}
348	>
349	>	if (metaDataBlockStart == -1) {
350	>	sprintf(painCave.errMsg,
351	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
352	>	mdFileName.c_str());
353	>	painCave.isFatal = 1;
354	>	simError();
355	>	}
356	>	if (metaDataBlockEnd == -1) {
357	>	sprintf(painCave.errMsg,
358	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
359	>	mdFileName.c_str());
360	>	painCave.isFatal = 1;
361	>	simError();
362	>	}
363	>
364	>	mdFile_.clear();
365	>	mdFile_.seekg(0);
366	>	mdFile_.seekg(mdOffset);
367	>
368	>	mdRawData.clear();
369	>
370	>	bool foundVersion = false;
371	>
372	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
373	>	mdFile_.getline(buffer, bufferSize);
374	>	std::string line = trimLeftCopy(buffer);
375	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
376	>	if (static_cast<size_t>(j) != string::npos) {
377	>	foundVersion = true;
378	>	mdRawData += version;
379	>	} else {
380	>	mdRawData += buffer;
381	>	}
382	>	mdRawData += "\n";
383	>	}
384	>
385	>	if (!foundVersion) mdRawData += version + "\n";
386	>
387	>	mdFile_.close();
388	>
389	>	#ifdef IS_MPI
390	>	}
391	>	#endif
392	>
393	>	std::stringstream rawMetaDataStream(mdRawData);
394	>
395		//parse meta-data file
396	<	parseFile(mdFileName, stamps, simParams);
396	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
397	>	metaDataBlockStart + 1);
398
399		//create the force field
400	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
401	<	simParams->getForceField());
111	<
400	>	ForceField * ff = new ForceField(simParams->getForceField());
401	>
402		if (ff == NULL) {
403	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
404	<	simParams->getForceField());
403	>	sprintf(painCave.errMsg,
404	>	"ForceField Factory can not create %s force field\n",
405	>	simParams->getForceField().c_str());
406		painCave.isFatal = 1;
407		simError();
408		}
#	Line 140 | Line 431 | namespace oopse {
431		}
432
433		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
434		//create SimInfo
435	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
436	<
437	<	//gather parameters (SimCreator only retrieves part of the parameters)
435	>	SimInfo * info = new SimInfo(ff, simParams);
436	>
437	>	info->setRawMetaData(mdRawData);
438	>
439	>	//gather parameters (SimCreator only retrieves part of the
440	>	//parameters)
441		gatherParameters(info, mdFileName);
442
443		//divide the molecules and determine the global index of molecules
#	Line 159 | Line 448 | namespace oopse {
448		//create the molecules
449		createMolecules(info);
450
451	+	//find the storage layout
452	+
453	+	int storageLayout = computeStorageLayout(info);
454	+
455	+	//allocate memory for DataStorage(circular reference, need to
456	+	//break it)
457	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
458
459	<	//allocate memory for DataStorage(circular reference, need to break it)
460	<	info->setSnapshotManager(new SimSnapshotManager(info));
461	<
462	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
463	<	//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.
459	>	//set the global index of atoms, rigidbodies and cutoffgroups
460	>	//(only need to be set once, the global index will never change
461	>	//again). Local indices of atoms and rigidbodies are already set
462	>	//by MoleculeCreator class which actually delegates the
463	>	//responsibility to LocalIndexManager.
464		setGlobalIndex(info);
465
466	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
467	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
468	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
469	<	//we can determine the beginning global indices of atoms before they get created.
466	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
467	>	//method, at that point atoms don't have the global index yet
468	>	//(their global index are all initialized to -1).  Therefore we
469	>	//have to call addInteractionPairs explicitly here. A way to work
470	>	//around is that we can determine the beginning global indices of
471	>	//atoms before they get created.
472		SimInfo::MoleculeIterator mi;
473		Molecule* mol;
474		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
475	<	info->addExcludePairs(mol);
475	>	info->addInteractionPairs(mol);
476		}
477
478		if (loadInitCoords)
479	<	loadCoordinates(info);
183	<
479	>	loadCoordinates(info, mdFileName);
480		return info;
481		}
482
483		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
484
485	<	//figure out the ouput file names
485	>	//figure out the output file names
486		std::string prefix;
487
488		#ifdef IS_MPI
#	Line 215 | Line 511 | namespace oopse {
511
512		#ifdef IS_MPI
513		void SimCreator::divideMolecules(SimInfo *info) {
514	<	double numerator;
219	<	double denominator;
220	<	double precast;
221	<	double x;
222	<	double y;
223	<	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;
514	>	RealType a;
515		int nProcessors;
516		std::vector<int> atomsPerProc;
517		int nGlobalMols = info->getNGlobalMolecules();
518	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
518	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
519	>	// error
520	>	// condition:
521
522	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
522	>	nProcessors = MPI::COMM_WORLD.Get_size();
523
524		if (nProcessors > nGlobalMols) {
525		sprintf(painCave.errMsg,
#	Line 244 | Line 528 | namespace oopse {
528		"\tthe number of molecules.  This will not result in a \n"
529		"\tusable division of atoms for force decomposition.\n"
530		"\tEither try a smaller number of processors, or run the\n"
531	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
531	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
532	>	nGlobalMols);
533
534		painCave.isFatal = 1;
535		simError();
536		}
537
253	–	int seedValue;
538		Globals * simParams = info->getSimParams();
539	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
539	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
540	>	//random number generator
541		if (simParams->haveSeed()) {
542	<	seedValue = simParams->getSeed();
542	>	int seedValue = simParams->getSeed();
543		myRandom = new SeqRandNumGen(seedValue);
544		}else {
545		myRandom = new SeqRandNumGen();
#	Line 267 | Line 552 | namespace oopse {
552		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
553
554		if (worldRank == 0) {
555	<	numerator = info->getNGlobalAtoms();
556	<	denominator = nProcessors;
557	<	precast = numerator / denominator;
558	<	nTarget = (int)(precast + 0.5);
555	>	RealType numerator = info->getNGlobalAtoms();
556	>	RealType denominator = nProcessors;
557	>	RealType precast = numerator / denominator;
558	>	int nTarget = (int)(precast + 0.5);
559
560	<	for(i = 0; i < nGlobalMols; i++) {
561	<	done = 0;
562	<	loops = 0;
560	>	for(int i = 0; i < nGlobalMols; i++) {
561	>
562	>	int done = 0;
563	>	int loops = 0;
564
565		while (!done) {
566		loops++;
567
568		// Pick a processor at random
569
570	<	which_proc = (int) (myRandom->rand() * nProcessors);
570	>	int which_proc = (int) (myRandom->rand() * nProcessors);
571
572		//get the molecule stamp first
573		int stampId = info->getMoleculeStampId(i);
574		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
575
576		// How many atoms does this processor have so far?
577	<	old_atoms = atomsPerProc[which_proc];
578	<	add_atoms = moleculeStamp->getNAtoms();
579	<	new_atoms = old_atoms + add_atoms;
577	>	int old_atoms = atomsPerProc[which_proc];
578	>	int add_atoms = moleculeStamp->getNAtoms();
579	>	int new_atoms = old_atoms + add_atoms;
580
581		// If we've been through this loop too many times, we need
582		// to just give up and assign the molecule to this processor
583		// and be done with it.
584
585		if (loops > 100) {
586	+
587		sprintf(painCave.errMsg,
588	<	"I've tried 100 times to assign molecule %d to a "
589	<	" processor, but can't find a good spot.\n"
590	<	"I'm assigning it at random to processor %d.\n",
588	>	"There have been 100 attempts to assign molecule %d to an\n"
589	>	"\tunderworked processor, but there's no good place to\n"
590	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
591		i, which_proc);
592	<
592	>
593		painCave.isFatal = 0;
594	+	painCave.severity = OPENMD_INFO;
595		simError();
596
597		molToProcMap[i] = which_proc;
#	Line 332 | Line 620 | namespace oopse {
620		//           Pacc(x) = exp(- a * x)
621		// where a = penalty / (average atoms per molecule)
622
623	<	x = (double)(new_atoms - nTarget);
624	<	y = myRandom->rand();
623	>	RealType x = (RealType)(new_atoms - nTarget);
624	>	RealType y = myRandom->rand();
625
626		if (y < exp(- a * x)) {
627		molToProcMap[i] = which_proc;
#	Line 348 | Line 636 | namespace oopse {
636		}
637
638		delete myRandom;
639	<
639	>
640		// Spray out this nonsense to all other processors:
641	<
354	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
641	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
642		} else {
643
644		// Listen to your marching orders from processor 0:
645	<
646	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
645	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
646	>
647		}
648
649		info->setMolToProcMap(molToProcMap);
650		sprintf(checkPointMsg,
651		"Successfully divided the molecules among the processors.\n");
652	<	MPIcheckPoint();
652	>	errorCheckPoint();
653		}
654
655		#endif
#	Line 379 | Line 666 | namespace oopse {
666		#endif
667
668		stampId = info->getMoleculeStampId(i);
669	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
670	<	stampId, i, info->getLocalIndexManager());
669	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
670	>	info->getMoleculeStamp(stampId),
671	>	stampId, i,
672	>	info->getLocalIndexManager());
673
674		info->addMolecule(mol);
675
#	Line 392 | Line 681 | namespace oopse {
681
682		} //end for(int i=0)
683		}
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();
684
685	<	if (!simParams->haveNMol()) {
686	<	// we don't have the total number of molecules, so we assume it is
687	<	// given in each component
688	<
689	<	for(i = 0; i < n_components; i++) {
690	<	if (!the_components[i]->haveNMol()) {
691	<	// we have a problem
692	<	sprintf(painCave.errMsg,
693	<	"SimCreator Error. No global NMol or component NMol given.\n"
694	<	"\tCannot calculate the number of atoms.\n");
695	<
696	<	painCave.isFatal = 1;
697	<	simError();
698	<	}
699	<
700	<	id = the_components[i]->getType();
701	<
702	<	extractedStamp = stamps->extractMolStamp(id);
703	<	if (extractedStamp == NULL) {
704	<	sprintf(painCave.errMsg,
705	<	"SimCreator error: Component \"%s\" was not found in the "
706	<	"list of declared molecules\n", id);
707	<
708	<	painCave.isFatal = 1;
709	<	simError();
710	<	}
711	<
712	<	currentStamp = extractedStamp->getStamp();
713	<
714	<
715	<	moleculeStampPairs.push_back(
716	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
717	<	} //end for (i = 0; i < n_components; i++)
718	<	} else {
719	<	sprintf(painCave.errMsg, "SimSetup error.\n"
720	<	"\tSorry, the ability to specify total"
721	<	" nMols and then give molfractions in the components\n"
722	<	"\tis not currently supported."
723	<	" Please give nMol in the components.\n");
724	<
725	<	painCave.isFatal = 1;
726	<	simError();
685	>	int SimCreator::computeStorageLayout(SimInfo* info) {
686	>
687	>	Globals* simParams = info->getSimParams();
688	>	int nRigidBodies = info->getNGlobalRigidBodies();
689	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
690	>	set<AtomType*>::iterator i;
691	>	bool hasDirectionalAtoms = false;
692	>	bool hasFixedCharge = false;
693	>	bool hasDipoles = false;
694	>	bool hasQuadrupoles = false;
695	>	bool hasPolarizable = false;
696	>	bool hasFluctuatingCharge = false;
697	>	bool hasMetallic = false;
698	>	int storageLayout = 0;
699	>	storageLayout |= DataStorage::dslPosition;
700	>	storageLayout |= DataStorage::dslVelocity;
701	>	storageLayout |= DataStorage::dslForce;
702	>
703	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
704	>
705	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
706	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
707	>	EAMAdapter ea = EAMAdapter( (*i) );
708	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
709	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
710	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
711	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
712	>
713	>	if (da.isDirectional()){
714	>	hasDirectionalAtoms = true;
715	>	}
716	>	if (ma.isDipole()){
717	>	hasDipoles = true;
718	>	}
719	>	if (ma.isQuadrupole()){
720	>	hasQuadrupoles = true;
721	>	}
722	>	if (ea.isEAM() || sca.isSuttonChen()){
723	>	hasMetallic = true;
724	>	}
725	>	if ( fca.isFixedCharge() ){
726	>	hasFixedCharge = true;
727	>	}
728	>	if ( fqa.isFluctuatingCharge() ){
729	>	hasFluctuatingCharge = true;
730	>	}
731	>	if ( pa.isPolarizable() ){
732	>	hasPolarizable = true;
733	>	}
734		}
735
736	<	#ifdef IS_MPI
736	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
737	>	storageLayout |= DataStorage::dslAmat;
738	>	if(storageLayout & DataStorage::dslVelocity) {
739	>	storageLayout |= DataStorage::dslAngularMomentum;
740	>	}
741	>	if (storageLayout & DataStorage::dslForce) {
742	>	storageLayout |= DataStorage::dslTorque;
743	>	}
744	>	}
745	>	if (hasDipoles) {
746	>	storageLayout |= DataStorage::dslDipole;
747	>	}
748	>	if (hasQuadrupoles) {
749	>	storageLayout |= DataStorage::dslQuadrupole;
750	>	}
751	>	if (hasFixedCharge || hasFluctuatingCharge) {
752	>	storageLayout |= DataStorage::dslSkippedCharge;
753	>	}
754	>	if (hasMetallic) {
755	>	storageLayout |= DataStorage::dslDensity;
756	>	storageLayout |= DataStorage::dslFunctional;
757	>	storageLayout |= DataStorage::dslFunctionalDerivative;
758	>	}
759	>	if (hasPolarizable) {
760	>	storageLayout |= DataStorage::dslElectricField;
761	>	}
762	>	if (hasFluctuatingCharge){
763	>	storageLayout |= DataStorage::dslFlucQPosition;
764	>	if(storageLayout & DataStorage::dslVelocity) {
765	>	storageLayout |= DataStorage::dslFlucQVelocity;
766	>	}
767	>	if (storageLayout & DataStorage::dslForce) {
768	>	storageLayout |= DataStorage::dslFlucQForce;
769	>	}
770	>	}
771
772	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
773	<	MPIcheckPoint();
774	<
775	<	#endif // is_mpi
776	<
772	>	// if the user has asked for them, make sure we've got the memory for the
773	>	// objects defined.
774	>
775	>	if (simParams->getOutputParticlePotential()) {
776	>	storageLayout |= DataStorage::dslParticlePot;
777	>	}
778	>
779	>	if (simParams->havePrintHeatFlux()) {
780	>	if (simParams->getPrintHeatFlux()) {
781	>	storageLayout |= DataStorage::dslParticlePot;
782	>	}
783	>	}
784	>
785	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
786	>	storageLayout |= DataStorage::dslElectricField;
787	>	}
788	>
789	>	if (simParams->getOutputFluctuatingCharges()) {
790	>	storageLayout |= DataStorage::dslFlucQPosition;
791	>	storageLayout |= DataStorage::dslFlucQVelocity;
792	>	storageLayout |= DataStorage::dslFlucQForce;
793	>	}
794	>
795	>	info->setStorageLayout(storageLayout);
796	>
797	>	return storageLayout;
798		}
799	<
799	>
800		void SimCreator::setGlobalIndex(SimInfo *info) {
801		SimInfo::MoleculeIterator mi;
802		Molecule::AtomIterator ai;
803		Molecule::RigidBodyIterator ri;
804		Molecule::CutoffGroupIterator ci;
805	+	Molecule::IntegrableObjectIterator  ioi;
806		Molecule * mol;
807		Atom * atom;
808		RigidBody * rb;
#	Line 468 | Line 811 | namespace oopse {
811		int beginRigidBodyIndex;
812		int beginCutoffGroupIndex;
813		int nGlobalAtoms = info->getNGlobalAtoms();
814	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
815
472	–	#ifndef IS_MPI
473	–
816		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	–
817		//rigidbody's index begins right after atom's
818	<	beginRigidBodyIndex += info->getNGlobalAtoms();
819	<
820	<	for(mol = info->beginMolecule(mi); mol != NULL;
821	<	mol = info->nextMolecule(mi)) {
818	>	beginRigidBodyIndex = info->getNGlobalAtoms();
819	>	beginCutoffGroupIndex = 0;
820	>
821	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
822
823	<	//local index(index in DataStorge) of atom is important
824	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	<	atom->setGlobalIndex(beginAtomIndex++);
823	>	#ifdef IS_MPI
824	>	if (info->getMolToProc(i) == worldRank) {
825	>	#endif
826	>	// stuff to do if I own this molecule
827	>	mol = info->getMoleculeByGlobalIndex(i);
828	>
829	>	//local index(index in DataStorge) of atom is important
830	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
831	>	atom->setGlobalIndex(beginAtomIndex++);
832	>	}
833	>
834	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
835	>	rb = mol->nextRigidBody(ri)) {
836	>	rb->setGlobalIndex(beginRigidBodyIndex++);
837	>	}
838	>
839	>	//local index of cutoff group is trivial, it only depends on
840	>	//the order of travesing
841	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
842	>	cg = mol->nextCutoffGroup(ci)) {
843	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
844	>	}
845	>
846	>	#ifdef IS_MPI
847	>	}  else {
848	>
849	>	// stuff to do if I don't own this molecule
850	>
851	>	int stampId = info->getMoleculeStampId(i);
852	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
853	>
854	>	beginAtomIndex += stamp->getNAtoms();
855	>	beginRigidBodyIndex += stamp->getNRigidBodies();
856	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
857		}
858	<
859	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
860	<	rb = mol->nextRigidBody(ri)) {
861	<	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	<
858	>	#endif
859	>
860	>	} //end for(int i=0)
861	>
862		//fill globalGroupMembership
863		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
864		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 548 | Line 870 | namespace oopse {
870
871		}
872		}
873	<
873	>
874		#ifdef IS_MPI
875		// Since the globalGroupMembership has been zero filled and we've only
876		// poked values into the atoms we know, we can do an Allreduce
877		// to get the full globalGroupMembership array (We think).
878		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
879		// docs said we could.
880	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
881	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
882	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
880	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
881	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
882	>	&tmpGroupMembership[0], nGlobalAtoms,
883	>	MPI::INT, MPI::SUM);
884		info->setGlobalGroupMembership(tmpGroupMembership);
885		#else
886		info->setGlobalGroupMembership(globalGroupMembership);
887		#endif
888
889		//fill molMembership
890	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
890	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
891	>	info->getNGlobalRigidBodies(), 0);
892
893	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
894	<
893	>	for(mol = info->beginMolecule(mi); mol != NULL;
894	>	mol = info->nextMolecule(mi)) {
895		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
897		}
898	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
899	+	rb = mol->nextRigidBody(ri)) {
900	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
901	+	}
902		}
903
904		#ifdef IS_MPI
905	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
905	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
906	>	info->getNGlobalRigidBodies(), 0);
907	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
908	>	nGlobalAtoms + nGlobalRigidBodies,
909	>	MPI::INT, MPI::SUM);
910
579	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
580	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
581	–
911		info->setGlobalMolMembership(tmpMolMembership);
912		#else
913		info->setGlobalMolMembership(globalMolMembership);
914		#endif
915	+
916	+	// nIOPerMol holds the number of integrable objects per molecule
917	+	// here the molecules are listed by their global indices.
918	+
919	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
920	+	for (mol = info->beginMolecule(mi); mol != NULL;
921	+	mol = info->nextMolecule(mi)) {
922	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
923	+	}
924
925	<	}
926	<
927	<	void SimCreator::loadCoordinates(SimInfo* info) {
928	<	Globals* simParams;
929	<	simParams = info->getSimParams();
925	>	#ifdef IS_MPI
926	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
927	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
928	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
929	>	#else
930	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
931	>	#endif
932	>
933	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
934
935	<	if (!simParams->haveInitialConfig()) {
936	<	sprintf(painCave.errMsg,
937	<	"Cannot intialize a simulation without an initial configuration file.\n");
938	<	painCave.isFatal = 1;;
597	<	simError();
935	>	int startingIndex = 0;
936	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
937	>	startingIOIndexForMol[i] = startingIndex;
938	>	startingIndex += numIntegrableObjectsPerMol[i];
939		}
940
941	<	DumpReader reader(info, simParams->getInitialConfig());
941	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
942	>	for (mol = info->beginMolecule(mi); mol != NULL;
943	>	mol = info->nextMolecule(mi)) {
944	>	int myGlobalIndex = mol->getGlobalIndex();
945	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
946	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
947	>	sd = mol->nextIntegrableObject(ioi)) {
948	>	sd->setGlobalIntegrableObjectIndex(globalIO);
949	>	IOIndexToIntegrableObject[globalIO] = sd;
950	>	globalIO++;
951	>	}
952	>	}
953	>
954	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
955	>
956	>	}
957	>
958	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
959	>
960	>	DumpReader reader(info, mdFileName);
961		int nframes = reader.getNFrames();
962
963		if (nframes > 0) {
#	Line 606 | Line 966 | namespace oopse {
966		//invalid initial coordinate file
967		sprintf(painCave.errMsg,
968		"Initial configuration file %s should at least contain one frame\n",
969	<	simParams->getInitialConfig());
969	>	mdFileName.c_str());
970		painCave.isFatal = 1;
971		simError();
972		}
613	–
973		//copy the current snapshot to previous snapshot
974		info->getSnapshotManager()->advance();
975		}
976
977	<	} //end namespace oopse
977	>	} //end namespace OpenMD
978
979

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 436 by tim, Fri Mar 11 17:50:11 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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