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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1810 by gezelter, Thu Nov 8 14:23:43 2012 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, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 46 | Line 47
47		* @time 13:51am
48		* @version 1.0
49		*/
50	+	#include <exception>
51	+	#include <iostream>
52	+	#include <sstream>
53	+	#include <string>
54
55		#include "brains/MoleculeCreator.hpp"
56		#include "brains/SimCreator.hpp"
57		#include "brains/SimSnapshotManager.hpp"
58		#include "io/DumpReader.hpp"
59	<	#include "io/parse_me.h"
55	<	#include "UseTheForce/ForceFieldFactory.hpp"
59	>	#include "brains/ForceField.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62		#include "math/SeqRandNumGen.hpp"
63	+	#include "mdParser/MDLexer.hpp"
64	+	#include "mdParser/MDParser.hpp"
65	+	#include "mdParser/MDTreeParser.hpp"
66	+	#include "mdParser/SimplePreprocessor.hpp"
67	+	#include "antlr/ANTLRException.hpp"
68	+	#include "antlr/TokenStreamRecognitionException.hpp"
69	+	#include "antlr/TokenStreamIOException.hpp"
70	+	#include "antlr/TokenStreamException.hpp"
71	+	#include "antlr/RecognitionException.hpp"
72	+	#include "antlr/CharStreamException.hpp"
73	+
74	+	#include "antlr/MismatchedCharException.hpp"
75	+	#include "antlr/MismatchedTokenException.hpp"
76	+	#include "antlr/NoViableAltForCharException.hpp"
77	+	#include "antlr/NoViableAltException.hpp"
78	+
79	+	#include "types/DirectionalAdapter.hpp"
80	+	#include "types/MultipoleAdapter.hpp"
81	+	#include "types/EAMAdapter.hpp"
82	+	#include "types/SuttonChenAdapter.hpp"
83	+	#include "types/PolarizableAdapter.hpp"
84	+	#include "types/FixedChargeAdapter.hpp"
85	+	#include "types/FluctuatingChargeAdapter.hpp"
86	+
87		#ifdef IS_MPI
88	<	#include "io/mpiBASS.h"
88	>	#include "mpi.h"
89		#include "math/ParallelRandNumGen.hpp"
90		#endif
91
92	<	namespace oopse {
92	>	namespace OpenMD {
93
94	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps,
95	<	Globals* simParams){
94	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95	>	Globals* simParams = NULL;
96	>	try {
97	>
98	>	// Create a preprocessor that preprocesses md file into an ostringstream
99	>	std::stringstream ppStream;
100	>	#ifdef IS_MPI
101	>	int streamSize;
102	>	const int masterNode = 0;
103	>
104	>	if (worldRank == masterNode) {
105	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
106	>	#endif
107	>	SimplePreprocessor preprocessor;
108	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock,
109	>	ppStream);
110	>
111	>	#ifdef IS_MPI
112	>	//brocasting the stream size
113	>	streamSize = ppStream.str().size() +1;
114	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
115	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
116	>	streamSize, MPI::CHAR, masterNode);
117	>
118	>	} else {
119	>
120	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
121	>
122	>	//get stream size
123	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
124	>
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127	>
128	>	//receive file content
129	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
130	>
131	>	ppStream.str(buf);
132	>	delete [] buf;
133	>
134	>	}
135	>	#endif
136	>	// Create a scanner that reads from the input stream
137	>	MDLexer lexer(ppStream);
138	>	lexer.setFilename(filename);
139	>	lexer.initDeferredLineCount();
140
141	<	#ifdef IS_MPI
141	>	// Create a parser that reads from the scanner
142	>	MDParser parser(lexer);
143	>	parser.setFilename(filename);
144	>
145	>	// Create an observer that synchorizes file name change
146	>	FilenameObserver observer;
147	>	observer.setLexer(&lexer);
148	>	observer.setParser(&parser);
149	>	lexer.setObserver(&observer);
150
151	<	if (worldRank == 0) {
152	<	#endif // is_mpi
151	>	antlr::ASTFactory factory;
152	>	parser.initializeASTFactory(factory);
153	>	parser.setASTFactory(&factory);
154	>	parser.mdfile();
155	>
156	>	// Create a tree parser that reads information into Globals
157	>	MDTreeParser treeParser;
158	>	treeParser.initializeASTFactory(factory);
159	>	treeParser.setASTFactory(&factory);
160	>	simParams = treeParser.walkTree(parser.getAST());
161	>	}
162	>
163
164	<	simParams->initalize();
165	<	set_interface_stamps(stamps, simParams);
164	>	catch(antlr::MismatchedCharException& e) {
165	>	sprintf(painCave.errMsg,
166	>	"parser exception: %s %s:%d:%d\n",
167	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
168	>	painCave.isFatal = 1;
169	>	simError();
170	>	}
171	>	catch(antlr::MismatchedTokenException &e) {
172	>	sprintf(painCave.errMsg,
173	>	"parser exception: %s %s:%d:%d\n",
174	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	catch(antlr::NoViableAltForCharException &e) {
179	>	sprintf(painCave.errMsg,
180	>	"parser exception: %s %s:%d:%d\n",
181	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
185	>	catch(antlr::NoViableAltException &e) {
186	>	sprintf(painCave.errMsg,
187	>	"parser exception: %s %s:%d:%d\n",
188	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
189	>	painCave.isFatal = 1;
190	>	simError();
191	>	}
192
193	<	#ifdef IS_MPI
194	<
195	<	mpiEventInit();
196	<
197	<	#endif
198	<
83	<	yacc_BASS(mdFileName.c_str());
84	<
85	<	#ifdef IS_MPI
86	<
87	<	throwMPIEvent(NULL);
88	<	} else {
89	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
193	>	catch(antlr::TokenStreamRecognitionException& e) {
194	>	sprintf(painCave.errMsg,
195	>	"parser exception: %s %s:%d:%d\n",
196	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
197	>	painCave.isFatal = 1;
198	>	simError();
199		}
200	<
201	<	#endif
202	<
200	>
201	>	catch(antlr::TokenStreamIOException& e) {
202	>	sprintf(painCave.errMsg,
203	>	"parser exception: %s\n",
204	>	e.getMessage().c_str());
205	>	painCave.isFatal = 1;
206	>	simError();
207	>	}
208	>
209	>	catch(antlr::TokenStreamException& e) {
210	>	sprintf(painCave.errMsg,
211	>	"parser exception: %s\n",
212	>	e.getMessage().c_str());
213	>	painCave.isFatal = 1;
214	>	simError();
215	>	}
216	>	catch (antlr::RecognitionException& e) {
217	>	sprintf(painCave.errMsg,
218	>	"parser exception: %s %s:%d:%d\n",
219	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
220	>	painCave.isFatal = 1;
221	>	simError();
222	>	}
223	>	catch (antlr::CharStreamException& e) {
224	>	sprintf(painCave.errMsg,
225	>	"parser exception: %s\n",
226	>	e.getMessage().c_str());
227	>	painCave.isFatal = 1;
228	>	simError();
229	>	}
230	>	catch (OpenMDException& e) {
231	>	sprintf(painCave.errMsg,
232	>	"%s\n",
233	>	e.getMessage().c_str());
234	>	painCave.isFatal = 1;
235	>	simError();
236	>	}
237	>	catch (std::exception& e) {
238	>	sprintf(painCave.errMsg,
239	>	"parser exception: %s\n",
240	>	e.what());
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>
245	>	simParams->setMDfileVersion(mdFileVersion);
246	>	return simParams;
247		}
248
249	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
249	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250	>	bool loadInitCoords) {
251
252	<	MakeStamps * stamps = new MakeStamps();
253	<
254	<	Globals * simParams = new Globals();
255	<
252	>	const int bufferSize = 65535;
253	>	char buffer[bufferSize];
254	>	int lineNo = 0;
255	>	std::string mdRawData;
256	>	int metaDataBlockStart = -1;
257	>	int metaDataBlockEnd = -1;
258	>	int i, j;
259	>	streamoff mdOffset(0);
260	>	int mdFileVersion;
261	>
262	>	// Create a string for embedding the version information in the MetaData
263	>	std::string version;
264	>	version.assign("## Last run using OpenMD Version: ");
265	>	version.append(OPENMD_VERSION_MAJOR);
266	>	version.append(".");
267	>	version.append(OPENMD_VERSION_MINOR);
268	>
269	>	std::string svnrev;
270	>	//convert a macro from compiler to a string in c++
271	>	STR_DEFINE(svnrev, SVN_REV );
272	>	version.append(" Revision: ");
273	>	// If there's no SVN revision, just call this the RELEASE revision.
274	>	if (!svnrev.empty()) {
275	>	version.append(svnrev);
276	>	} else {
277	>	version.append("RELEASE");
278	>	}
279	>
280	>	#ifdef IS_MPI
281	>	const int masterNode = 0;
282	>	if (worldRank == masterNode) {
283	>	#endif
284	>
285	>	std::ifstream mdFile_;
286	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
287	>
288	>	if (mdFile_.fail()) {
289	>	sprintf(painCave.errMsg,
290	>	"SimCreator: Cannot open file: %s\n",
291	>	mdFileName.c_str());
292	>	painCave.isFatal = 1;
293	>	simError();
294	>	}
295	>
296	>	mdFile_.getline(buffer, bufferSize);
297	>	++lineNo;
298	>	std::string line = trimLeftCopy(buffer);
299	>	i = CaseInsensitiveFind(line, "<OpenMD");
300	>	if (static_cast<size_t>(i) == string::npos) {
301	>	// try the older file strings to see if that works:
302	>	i = CaseInsensitiveFind(line, "<OOPSE");
303	>	}
304	>
305	>	if (static_cast<size_t>(i) == string::npos) {
306	>	// still no luck!
307	>	sprintf(painCave.errMsg,
308	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
309	>	mdFileName.c_str());
310	>	painCave.isFatal = 1;
311	>	simError();
312	>	}
313	>
314	>	// found the correct opening string, now try to get the file
315	>	// format version number.
316	>
317	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
318	>	std::string fileType = tokenizer.nextToken();
319	>	toUpper(fileType);
320	>
321	>	mdFileVersion = 0;
322	>
323	>	if (fileType == "OPENMD") {
324	>	while (tokenizer.hasMoreTokens()) {
325	>	std::string token(tokenizer.nextToken());
326	>	toUpper(token);
327	>	if (token == "VERSION") {
328	>	mdFileVersion = tokenizer.nextTokenAsInt();
329	>	break;
330	>	}
331	>	}
332	>	}
333	>
334	>	//scan through the input stream and find MetaData tag
335	>	while(mdFile_.getline(buffer, bufferSize)) {
336	>	++lineNo;
337	>
338	>	std::string line = trimLeftCopy(buffer);
339	>	if (metaDataBlockStart == -1) {
340	>	i = CaseInsensitiveFind(line, "<MetaData>");
341	>	if (i != string::npos) {
342	>	metaDataBlockStart = lineNo;
343	>	mdOffset = mdFile_.tellg();
344	>	}
345	>	} else {
346	>	i = CaseInsensitiveFind(line, "</MetaData>");
347	>	if (i != string::npos) {
348	>	metaDataBlockEnd = lineNo;
349	>	}
350	>	}
351	>	}
352	>
353	>	if (metaDataBlockStart == -1) {
354	>	sprintf(painCave.errMsg,
355	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
356	>	mdFileName.c_str());
357	>	painCave.isFatal = 1;
358	>	simError();
359	>	}
360	>	if (metaDataBlockEnd == -1) {
361	>	sprintf(painCave.errMsg,
362	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
363	>	mdFileName.c_str());
364	>	painCave.isFatal = 1;
365	>	simError();
366	>	}
367	>
368	>	mdFile_.clear();
369	>	mdFile_.seekg(0);
370	>	mdFile_.seekg(mdOffset);
371	>
372	>	mdRawData.clear();
373	>
374	>	bool foundVersion = false;
375	>
376	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
377	>	mdFile_.getline(buffer, bufferSize);
378	>	std::string line = trimLeftCopy(buffer);
379	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
380	>	if (static_cast<size_t>(j) != string::npos) {
381	>	foundVersion = true;
382	>	mdRawData += version;
383	>	} else {
384	>	mdRawData += buffer;
385	>	}
386	>	mdRawData += "\n";
387	>	}
388	>
389	>	if (!foundVersion) mdRawData += version + "\n";
390	>
391	>	mdFile_.close();
392	>
393	>	#ifdef IS_MPI
394	>	}
395	>	#endif
396	>
397	>	std::stringstream rawMetaDataStream(mdRawData);
398	>
399		//parse meta-data file
400	<	parseFile(mdFileName, stamps, simParams);
400	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
401	>	metaDataBlockStart + 1);
402
403		//create the force field
404	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
405	<	simParams->getForceField());
111	<
404	>	ForceField * ff = new ForceField(simParams->getForceField());
405	>
406		if (ff == NULL) {
407	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
408	<	simParams->getForceField());
407	>	sprintf(painCave.errMsg,
408	>	"ForceField Factory can not create %s force field\n",
409	>	simParams->getForceField().c_str());
410		painCave.isFatal = 1;
411		simError();
412		}
#	Line 140 | Line 435 | namespace oopse {
435		}
436
437		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
438		//create SimInfo
439	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
440	<
441	<	//gather parameters (SimCreator only retrieves part of the parameters)
439	>	SimInfo * info = new SimInfo(ff, simParams);
440	>
441	>	info->setRawMetaData(mdRawData);
442	>
443	>	//gather parameters (SimCreator only retrieves part of the
444	>	//parameters)
445		gatherParameters(info, mdFileName);
446
447		//divide the molecules and determine the global index of molecules
#	Line 159 | Line 452 | namespace oopse {
452		//create the molecules
453		createMolecules(info);
454
455	+	//find the storage layout
456	+
457	+	int storageLayout = computeStorageLayout(info);
458	+
459	+	//allocate memory for DataStorage(circular reference, need to
460	+	//break it)
461	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
462
463	<	//allocate memory for DataStorage(circular reference, need to break it)
464	<	info->setSnapshotManager(new SimSnapshotManager(info));
465	<
466	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
467	<	//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.
463	>	//set the global index of atoms, rigidbodies and cutoffgroups
464	>	//(only need to be set once, the global index will never change
465	>	//again). Local indices of atoms and rigidbodies are already set
466	>	//by MoleculeCreator class which actually delegates the
467	>	//responsibility to LocalIndexManager.
468		setGlobalIndex(info);
469
470	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
471	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
472	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
473	<	//we can determine the beginning global indices of atoms before they get created.
470	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
471	>	//method, at that point atoms don't have the global index yet
472	>	//(their global index are all initialized to -1).  Therefore we
473	>	//have to call addInteractionPairs explicitly here. A way to work
474	>	//around is that we can determine the beginning global indices of
475	>	//atoms before they get created.
476		SimInfo::MoleculeIterator mi;
477		Molecule* mol;
478		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
479	<	info->addExcludePairs(mol);
479	>	info->addInteractionPairs(mol);
480		}
481
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
482		if (loadInitCoords)
483	<	loadCoordinates(info);
186	<
483	>	loadCoordinates(info, mdFileName);
484		return info;
485		}
486
487		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
488
489	<	//figure out the ouput file names
489	>	//figure out the output file names
490		std::string prefix;
491
492		#ifdef IS_MPI
#	Line 218 | Line 515 | namespace oopse {
515
516		#ifdef IS_MPI
517		void SimCreator::divideMolecules(SimInfo *info) {
518	<	double numerator;
519	<	double denominator;
520	<	double precast;
521	<	double x;
522	<	double y;
523	<	double a;
518	>	RealType numerator;
519	>	RealType denominator;
520	>	RealType precast;
521	>	RealType x;
522	>	RealType y;
523	>	RealType a;
524		int old_atoms;
525		int add_atoms;
526		int new_atoms;
527		int nTarget;
528		int done;
529		int i;
233	–	int j;
530		int loops;
531		int which_proc;
532		int nProcessors;
#	Line 238 | Line 534 | namespace oopse {
534		int nGlobalMols = info->getNGlobalMolecules();
535		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
536
537	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
537	>	nProcessors = MPI::COMM_WORLD.Get_size();
538
539		if (nProcessors > nGlobalMols) {
540		sprintf(painCave.errMsg,
#	Line 247 | Line 543 | namespace oopse {
543		"\tthe number of molecules.  This will not result in a \n"
544		"\tusable division of atoms for force decomposition.\n"
545		"\tEither try a smaller number of processors, or run the\n"
546	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
546	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
547
548		painCave.isFatal = 1;
549		simError();
#	Line 276 | Line 572 | namespace oopse {
572		nTarget = (int)(precast + 0.5);
573
574		for(i = 0; i < nGlobalMols; i++) {
575	+
576		done = 0;
577		loops = 0;
578
#	Line 300 | Line 597 | namespace oopse {
597		// and be done with it.
598
599		if (loops > 100) {
600	+
601		sprintf(painCave.errMsg,
602	<	"I've tried 100 times to assign molecule %d to a "
603	<	" processor, but can't find a good spot.\n"
604	<	"I'm assigning it at random to processor %d.\n",
602	>	"There have been 100 attempts to assign molecule %d to an\n"
603	>	"\tunderworked processor, but there's no good place to\n"
604	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
605		i, which_proc);
606	<
606	>
607		painCave.isFatal = 0;
608	+	painCave.severity = OPENMD_INFO;
609		simError();
610
611		molToProcMap[i] = which_proc;
#	Line 335 | Line 634 | namespace oopse {
634		//           Pacc(x) = exp(- a * x)
635		// where a = penalty / (average atoms per molecule)
636
637	<	x = (double)(new_atoms - nTarget);
637	>	x = (RealType)(new_atoms - nTarget);
638		y = myRandom->rand();
639
640		if (y < exp(- a * x)) {
#	Line 351 | Line 650 | namespace oopse {
650		}
651
652		delete myRandom;
653	<
653	>
654		// Spray out this nonsense to all other processors:
655	<
357	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
655	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
656		} else {
657
658		// Listen to your marching orders from processor 0:
659	<
660	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
659	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
660	>
661		}
662
663		info->setMolToProcMap(molToProcMap);
664		sprintf(checkPointMsg,
665		"Successfully divided the molecules among the processors.\n");
666	<	MPIcheckPoint();
666	>	errorCheckPoint();
667		}
668
669		#endif
#	Line 382 | Line 680 | namespace oopse {
680		#endif
681
682		stampId = info->getMoleculeStampId(i);
683	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
684	<	stampId, i, info->getLocalIndexManager());
683	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
684	>	info->getMoleculeStamp(stampId),
685	>	stampId, i,
686	>	info->getLocalIndexManager());
687
688		info->addMolecule(mol);
689
#	Line 395 | Line 695 | namespace oopse {
695
696		} //end for(int i=0)
697		}
398	–
399	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
400	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
401	–	int i;
402	–	char * id;
403	–	LinkedMolStamp* extractedStamp = NULL;
404	–	MoleculeStamp * currentStamp;
405	–	Component** the_components = simParams->getComponents();
406	–	int n_components = simParams->getNComponents();
698
699	<	if (!simParams->haveNMol()) {
700	<	// we don't have the total number of molecules, so we assume it is
701	<	// given in each component
702	<
703	<	for(i = 0; i < n_components; i++) {
704	<	if (!the_components[i]->haveNMol()) {
705	<	// we have a problem
706	<	sprintf(painCave.errMsg,
707	<	"SimCreator Error. No global NMol or component NMol given.\n"
708	<	"\tCannot calculate the number of atoms.\n");
709	<
710	<	painCave.isFatal = 1;
711	<	simError();
712	<	}
713	<
714	<	id = the_components[i]->getType();
715	<
716	<	extractedStamp = stamps->extractMolStamp(id);
717	<	if (extractedStamp == NULL) {
718	<	sprintf(painCave.errMsg,
719	<	"SimCreator error: Component \"%s\" was not found in the "
720	<	"list of declared molecules\n", id);
721	<
722	<	painCave.isFatal = 1;
723	<	simError();
724	<	}
725	<
726	<	currentStamp = extractedStamp->getStamp();
727	<
728	<
729	<	moleculeStampPairs.push_back(
730	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
731	<	} //end for (i = 0; i < n_components; i++)
732	<	} else {
733	<	sprintf(painCave.errMsg, "SimSetup error.\n"
734	<	"\tSorry, the ability to specify total"
735	<	" nMols and then give molfractions in the components\n"
736	<	"\tis not currently supported."
737	<	" Please give nMol in the components.\n");
738	<
739	<	painCave.isFatal = 1;
740	<	simError();
699	>	int SimCreator::computeStorageLayout(SimInfo* info) {
700	>
701	>	Globals* simParams = info->getSimParams();
702	>	int nRigidBodies = info->getNGlobalRigidBodies();
703	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
704	>	set<AtomType*>::iterator i;
705	>	bool hasDirectionalAtoms = false;
706	>	bool hasFixedCharge = false;
707	>	bool hasMultipoles = false;
708	>	bool hasPolarizable = false;
709	>	bool hasFluctuatingCharge = false;
710	>	bool hasMetallic = false;
711	>	int storageLayout = 0;
712	>	storageLayout |= DataStorage::dslPosition;
713	>	storageLayout |= DataStorage::dslVelocity;
714	>	storageLayout |= DataStorage::dslForce;
715	>
716	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717	>
718	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
719	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
720	>	EAMAdapter ea = EAMAdapter( (*i) );
721	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
722	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
723	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
724	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
725	>
726	>	if (da.isDirectional()){
727	>	hasDirectionalAtoms = true;
728	>	}
729	>	if (ma.isMultipole()){
730	>	hasMultipoles = true;
731	>	}
732	>	if (ea.isEAM() || sca.isSuttonChen()){
733	>	hasMetallic = true;
734	>	}
735	>	if ( fca.isFixedCharge() ){
736	>	hasFixedCharge = true;
737	>	}
738	>	if ( fqa.isFluctuatingCharge() ){
739	>	hasFluctuatingCharge = true;
740	>	}
741	>	if ( pa.isPolarizable() ){
742	>	hasPolarizable = true;
743	>	}
744		}
745
746	<	#ifdef IS_MPI
746	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
747	>	storageLayout |= DataStorage::dslAmat;
748	>	if(storageLayout & DataStorage::dslVelocity) {
749	>	storageLayout |= DataStorage::dslAngularMomentum;
750	>	}
751	>	if (storageLayout & DataStorage::dslForce) {
752	>	storageLayout |= DataStorage::dslTorque;
753	>	}
754	>	}
755	>	if (hasMultipoles) {
756	>	storageLayout |= DataStorage::dslElectroFrame;
757	>	}
758	>	if (hasFixedCharge || hasFluctuatingCharge) {
759	>	storageLayout |= DataStorage::dslSkippedCharge;
760	>	}
761	>	if (hasMetallic) {
762	>	storageLayout |= DataStorage::dslDensity;
763	>	storageLayout |= DataStorage::dslFunctional;
764	>	storageLayout |= DataStorage::dslFunctionalDerivative;
765	>	}
766	>	if (hasPolarizable) {
767	>	storageLayout |= DataStorage::dslElectricField;
768	>	}
769	>	if (hasFluctuatingCharge){
770	>	storageLayout |= DataStorage::dslFlucQPosition;
771	>	if(storageLayout & DataStorage::dslVelocity) {
772	>	storageLayout |= DataStorage::dslFlucQVelocity;
773	>	}
774	>	if (storageLayout & DataStorage::dslForce) {
775	>	storageLayout |= DataStorage::dslFlucQForce;
776	>	}
777	>	}
778
779	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
780	<	MPIcheckPoint();
781	<
782	<	#endif // is_mpi
783	<
779	>	// if the user has asked for them, make sure we've got the memory for the
780	>	// objects defined.
781	>
782	>	if (simParams->getOutputParticlePotential()) {
783	>	storageLayout |= DataStorage::dslParticlePot;
784	>	}
785	>
786	>	if (simParams->havePrintHeatFlux()) {
787	>	if (simParams->getPrintHeatFlux()) {
788	>	storageLayout |= DataStorage::dslParticlePot;
789	>	}
790	>	}
791	>
792	>	if (simParams->getOutputElectricField()) {
793	>	storageLayout |= DataStorage::dslElectricField;
794	>	}
795	>	if (simParams->getOutputFluctuatingCharges()) {
796	>	storageLayout |= DataStorage::dslFlucQPosition;
797	>	storageLayout |= DataStorage::dslFlucQVelocity;
798	>	storageLayout |= DataStorage::dslFlucQForce;
799	>	}
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 471 | Line 815 | namespace oopse {
815		int beginRigidBodyIndex;
816		int beginCutoffGroupIndex;
817		int nGlobalAtoms = info->getNGlobalAtoms();
818	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
819
475	–	#ifndef IS_MPI
476	–
820		beginAtomIndex = 0;
478	–	beginRigidBodyIndex = 0;
479	–	beginCutoffGroupIndex = 0;
480	–
481	–	#else
482	–
483	–	int nproc;
484	–	int myNode;
485	–
486	–	myNode = worldRank;
487	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
488	–
489	–	std::vector < int > tmpAtomsInProc(nproc, 0);
490	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
491	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
492	–	std::vector < int > NumAtomsInProc(nproc, 0);
493	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
494	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
495	–
496	–	tmpAtomsInProc[myNode] = info->getNAtoms();
497	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
498	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
499	–
500	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
501	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
502	–	MPI_SUM, MPI_COMM_WORLD);
503	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
504	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
505	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
506	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
507	–
508	–	beginAtomIndex = 0;
509	–	beginRigidBodyIndex = 0;
510	–	beginCutoffGroupIndex = 0;
511	–
512	–	for(int i = 0; i < myNode; i++) {
513	–	beginAtomIndex += NumAtomsInProc[i];
514	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
515	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
516	–	}
517	–
518	–	#endif
519	–
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++);
534	<	}
535	<
536	<	//local index of cutoff group is trivial, it only depends on the order of travesing
537	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
538	<	cg = mol->nextCutoffGroup(ci)) {
539	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
540	<	}
541	<	}
542	<
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 551 | 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
582	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
583	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
584	–
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;;
600	<	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());
946	<	int nframes = reader.getNFrames();
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) {
968		reader.readFrame(nframes - 1);
969		} else {
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		}
616	–
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 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1810 by gezelter, Thu Nov 8 14:23:43 2012 UTC

#	Line 0 | Line 1
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