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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1826 by gezelter, Wed Jan 9 19:41:48 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, 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		/**
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	>	int commStatus;
103	>	if (worldRank == masterNode) {
104	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
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	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
113	>
114	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
115	>
116	>
117	>	} else {
118	>
119	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
120	>
121	>	//get stream size
122	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
123	>
124	>	char* buf = new char[streamSize];
125	>	assert(buf);
126	>
127	>	//receive file content
128	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129	>
130	>	ppStream.str(buf);
131	>	delete [] buf;
132	>
133	>	}
134	>	#endif
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139
140	<	#ifdef IS_MPI
140	>	// Create a parser that reads from the scanner
141	>	MDParser parser(lexer);
142	>	parser.setFilename(filename);
143	>
144	>	// Create an observer that synchorizes file name change
145	>	FilenameObserver observer;
146	>	observer.setLexer(&lexer);
147	>	observer.setParser(&parser);
148	>	lexer.setObserver(&observer);
149
150	<	if (worldRank == 0) {
151	<	#endif // is_mpi
150	>	antlr::ASTFactory factory;
151	>	parser.initializeASTFactory(factory);
152	>	parser.setASTFactory(&factory);
153	>	parser.mdfile();
154	>
155	>	// Create a tree parser that reads information into Globals
156	>	MDTreeParser treeParser;
157	>	treeParser.initializeASTFactory(factory);
158	>	treeParser.setASTFactory(&factory);
159	>	simParams = treeParser.walkTree(parser.getAST());
160	>	}
161	>
162
163	<	simParams->initalize();
164	<	set_interface_stamps(stamps, simParams);
163	>	catch(antlr::MismatchedCharException& e) {
164	>	sprintf(painCave.errMsg,
165	>	"parser exception: %s %s:%d:%d\n",
166	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>	catch(antlr::MismatchedTokenException &e) {
171	>	sprintf(painCave.errMsg,
172	>	"parser exception: %s %s:%d:%d\n",
173	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	catch(antlr::NoViableAltForCharException &e) {
178	>	sprintf(painCave.errMsg,
179	>	"parser exception: %s %s:%d:%d\n",
180	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184	>	catch(antlr::NoViableAltException &e) {
185	>	sprintf(painCave.errMsg,
186	>	"parser exception: %s %s:%d:%d\n",
187	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	>	painCave.isFatal = 1;
189	>	simError();
190	>	}
191
192	<	#ifdef IS_MPI
193	<
194	<	mpiEventInit();
195	<
196	<	#endif
197	<
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();
192	>	catch(antlr::TokenStreamRecognitionException& e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s %s:%d:%d\n",
195	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
196	>	painCave.isFatal = 1;
197	>	simError();
198		}
199	<
200	<	#endif
201	<
199	>
200	>	catch(antlr::TokenStreamIOException& e) {
201	>	sprintf(painCave.errMsg,
202	>	"parser exception: %s\n",
203	>	e.getMessage().c_str());
204	>	painCave.isFatal = 1;
205	>	simError();
206	>	}
207	>
208	>	catch(antlr::TokenStreamException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s\n",
211	>	e.getMessage().c_str());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>	catch (antlr::RecognitionException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s %s:%d:%d\n",
218	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (antlr::CharStreamException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"parser exception: %s\n",
225	>	e.getMessage().c_str());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (OpenMDException& e) {
230	>	sprintf(painCave.errMsg,
231	>	"%s\n",
232	>	e.getMessage().c_str());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>	catch (std::exception& e) {
237	>	sprintf(painCave.errMsg,
238	>	"parser exception: %s\n",
239	>	e.what());
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>
244	>	simParams->setMDfileVersion(mdFileVersion);
245	>	return simParams;
246		}
247
248	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
248	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
249	>	bool loadInitCoords) {
250
251	<	MakeStamps * stamps = new MakeStamps();
252	<
253	<	Globals * simParams = new Globals();
254	<
251	>	const int bufferSize = 65535;
252	>	char buffer[bufferSize];
253	>	int lineNo = 0;
254	>	std::string mdRawData;
255	>	int metaDataBlockStart = -1;
256	>	int metaDataBlockEnd = -1;
257	>	int i, j;
258	>	streamoff mdOffset;
259	>	int mdFileVersion;
260	>
261	>	// Create a string for embedding the version information in the MetaData
262	>	std::string version;
263	>	version.assign("## Last run using OpenMD Version: ");
264	>	version.append(OPENMD_VERSION_MAJOR);
265	>	version.append(".");
266	>	version.append(OPENMD_VERSION_MINOR);
267	>
268	>	std::string svnrev;
269	>	//convert a macro from compiler to a string in c++
270	>	STR_DEFINE(svnrev, SVN_REV );
271	>	version.append(" Revision: ");
272	>	// If there's no SVN revision, just call this the RELEASE revision.
273	>	if (!svnrev.empty()) {
274	>	version.append(svnrev);
275	>	} else {
276	>	version.append("RELEASE");
277	>	}
278	>
279	>	#ifdef IS_MPI
280	>	const int masterNode = 0;
281	>	if (worldRank == masterNode) {
282	>	#endif
283	>
284	>	std::ifstream mdFile_;
285	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
286	>
287	>	if (mdFile_.fail()) {
288	>	sprintf(painCave.errMsg,
289	>	"SimCreator: Cannot open file: %s\n",
290	>	mdFileName.c_str());
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294	>
295	>	mdFile_.getline(buffer, bufferSize);
296	>	++lineNo;
297	>	std::string line = trimLeftCopy(buffer);
298	>	i = CaseInsensitiveFind(line, "<OpenMD");
299	>	if (static_cast<size_t>(i) == string::npos) {
300	>	// try the older file strings to see if that works:
301	>	i = CaseInsensitiveFind(line, "<OOPSE");
302	>	}
303	>
304	>	if (static_cast<size_t>(i) == string::npos) {
305	>	// still no luck!
306	>	sprintf(painCave.errMsg,
307	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
308	>	mdFileName.c_str());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>
313	>	// found the correct opening string, now try to get the file
314	>	// format version number.
315	>
316	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
317	>	std::string fileType = tokenizer.nextToken();
318	>	toUpper(fileType);
319	>
320	>	mdFileVersion = 0;
321	>
322	>	if (fileType == "OPENMD") {
323	>	while (tokenizer.hasMoreTokens()) {
324	>	std::string token(tokenizer.nextToken());
325	>	toUpper(token);
326	>	if (token == "VERSION") {
327	>	mdFileVersion = tokenizer.nextTokenAsInt();
328	>	break;
329	>	}
330	>	}
331	>	}
332	>
333	>	//scan through the input stream and find MetaData tag
334	>	while(mdFile_.getline(buffer, bufferSize)) {
335	>	++lineNo;
336	>
337	>	std::string line = trimLeftCopy(buffer);
338	>	if (metaDataBlockStart == -1) {
339	>	i = CaseInsensitiveFind(line, "<MetaData>");
340	>	if (i != string::npos) {
341	>	metaDataBlockStart = lineNo;
342	>	mdOffset = mdFile_.tellg();
343	>	}
344	>	} else {
345	>	i = CaseInsensitiveFind(line, "</MetaData>");
346	>	if (i != string::npos) {
347	>	metaDataBlockEnd = lineNo;
348	>	}
349	>	}
350	>	}
351	>
352	>	if (metaDataBlockStart == -1) {
353	>	sprintf(painCave.errMsg,
354	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
355	>	mdFileName.c_str());
356	>	painCave.isFatal = 1;
357	>	simError();
358	>	}
359	>	if (metaDataBlockEnd == -1) {
360	>	sprintf(painCave.errMsg,
361	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
362	>	mdFileName.c_str());
363	>	painCave.isFatal = 1;
364	>	simError();
365	>	}
366	>
367	>	mdFile_.clear();
368	>	mdFile_.seekg(0);
369	>	mdFile_.seekg(mdOffset);
370	>
371	>	mdRawData.clear();
372	>
373	>	bool foundVersion = false;
374	>
375	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
376	>	mdFile_.getline(buffer, bufferSize);
377	>	std::string line = trimLeftCopy(buffer);
378	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
379	>	if (static_cast<size_t>(j) != string::npos) {
380	>	foundVersion = true;
381	>	mdRawData += version;
382	>	} else {
383	>	mdRawData += buffer;
384	>	}
385	>	mdRawData += "\n";
386	>	}
387	>
388	>	if (!foundVersion) mdRawData += version + "\n";
389	>
390	>	mdFile_.close();
391	>
392	>	#ifdef IS_MPI
393	>	}
394	>	#endif
395	>
396	>	std::stringstream rawMetaDataStream(mdRawData);
397	>
398		//parse meta-data file
399	<	parseFile(mdFileName, stamps, simParams);
399	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
400	>	metaDataBlockStart + 1);
401
402		//create the force field
403	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
404	<	simParams->getForceField());
111	<
403	>	ForceField * ff = new ForceField(simParams->getForceField());
404	>
405		if (ff == NULL) {
406	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
407	<	simParams->getForceField());
406	>	sprintf(painCave.errMsg,
407	>	"ForceField Factory can not create %s force field\n",
408	>	simParams->getForceField().c_str());
409		painCave.isFatal = 1;
410		simError();
411		}
#	Line 140 | Line 434 | namespace oopse {
434		}
435
436		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
437		//create SimInfo
438	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
439	<
440	<	//gather parameters (SimCreator only retrieves part of the parameters)
438	>	SimInfo * info = new SimInfo(ff, simParams);
439	>
440	>	info->setRawMetaData(mdRawData);
441	>
442	>	//gather parameters (SimCreator only retrieves part of the
443	>	//parameters)
444		gatherParameters(info, mdFileName);
445
446		//divide the molecules and determine the global index of molecules
#	Line 159 | Line 451 | namespace oopse {
451		//create the molecules
452		createMolecules(info);
453
454	+	//find the storage layout
455	+
456	+	int storageLayout = computeStorageLayout(info);
457	+
458	+	//allocate memory for DataStorage(circular reference, need to
459	+	//break it)
460	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
461
462	<	//allocate memory for DataStorage(circular reference, need to break it)
463	<	info->setSnapshotManager(new SimSnapshotManager(info));
464	<
465	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
466	<	//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.
462	>	//set the global index of atoms, rigidbodies and cutoffgroups
463	>	//(only need to be set once, the global index will never change
464	>	//again). Local indices of atoms and rigidbodies are already set
465	>	//by MoleculeCreator class which actually delegates the
466	>	//responsibility to LocalIndexManager.
467		setGlobalIndex(info);
468
469	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
470	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
471	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
472	<	//we can determine the beginning global indices of atoms before they get created.
469	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
470	>	//method, at that point atoms don't have the global index yet
471	>	//(their global index are all initialized to -1).  Therefore we
472	>	//have to call addInteractionPairs explicitly here. A way to work
473	>	//around is that we can determine the beginning global indices of
474	>	//atoms before they get created.
475		SimInfo::MoleculeIterator mi;
476		Molecule* mol;
477		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
478	<	info->addExcludePairs(mol);
478	>	info->addInteractionPairs(mol);
479		}
480
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
481		if (loadInitCoords)
482	<	loadCoordinates(info);
186	<
482	>	loadCoordinates(info, mdFileName);
483		return info;
484		}
485
486		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
487
488	<	//figure out the ouput file names
488	>	//figure out the output file names
489		std::string prefix;
490
491		#ifdef IS_MPI
#	Line 218 | Line 514 | namespace oopse {
514
515		#ifdef IS_MPI
516		void SimCreator::divideMolecules(SimInfo *info) {
517	<	double numerator;
518	<	double denominator;
519	<	double precast;
520	<	double x;
521	<	double y;
522	<	double a;
517	>	RealType numerator;
518	>	RealType denominator;
519	>	RealType precast;
520	>	RealType x;
521	>	RealType y;
522	>	RealType a;
523		int old_atoms;
524		int add_atoms;
525		int new_atoms;
526		int nTarget;
527		int done;
528		int i;
233	–	int j;
529		int loops;
530		int which_proc;
531		int nProcessors;
#	Line 238 | Line 533 | namespace oopse {
533		int nGlobalMols = info->getNGlobalMolecules();
534		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
535
536	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
536	>	nProcessors = MPI::COMM_WORLD.Get_size();
537
538		if (nProcessors > nGlobalMols) {
539		sprintf(painCave.errMsg,
#	Line 247 | Line 542 | namespace oopse {
542		"\tthe number of molecules.  This will not result in a \n"
543		"\tusable division of atoms for force decomposition.\n"
544		"\tEither try a smaller number of processors, or run the\n"
545	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
545	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
546
547		painCave.isFatal = 1;
548		simError();
#	Line 276 | Line 571 | namespace oopse {
571		nTarget = (int)(precast + 0.5);
572
573		for(i = 0; i < nGlobalMols; i++) {
574	+
575		done = 0;
576		loops = 0;
577
#	Line 300 | Line 596 | namespace oopse {
596		// and be done with it.
597
598		if (loops > 100) {
599	+
600		sprintf(painCave.errMsg,
601	<	"I've tried 100 times to assign molecule %d to a "
602	<	" processor, but can't find a good spot.\n"
603	<	"I'm assigning it at random to processor %d.\n",
601	>	"There have been 100 attempts to assign molecule %d to an\n"
602	>	"\tunderworked processor, but there's no good place to\n"
603	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
604		i, which_proc);
605	<
605	>
606		painCave.isFatal = 0;
607	+	painCave.severity = OPENMD_INFO;
608		simError();
609
610		molToProcMap[i] = which_proc;
#	Line 335 | Line 633 | namespace oopse {
633		//           Pacc(x) = exp(- a * x)
634		// where a = penalty / (average atoms per molecule)
635
636	<	x = (double)(new_atoms - nTarget);
636	>	x = (RealType)(new_atoms - nTarget);
637		y = myRandom->rand();
638
639		if (y < exp(- a * x)) {
#	Line 351 | Line 649 | namespace oopse {
649		}
650
651		delete myRandom;
652	<
652	>
653		// Spray out this nonsense to all other processors:
654	<
357	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
654	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655		} else {
656
657		// Listen to your marching orders from processor 0:
658	<
659	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
658	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
659	>
660		}
661
662		info->setMolToProcMap(molToProcMap);
663		sprintf(checkPointMsg,
664		"Successfully divided the molecules among the processors.\n");
665	<	MPIcheckPoint();
665	>	errorCheckPoint();
666		}
667
668		#endif
#	Line 382 | Line 679 | namespace oopse {
679		#endif
680
681		stampId = info->getMoleculeStampId(i);
682	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
683	<	stampId, i, info->getLocalIndexManager());
682	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
683	>	info->getMoleculeStamp(stampId),
684	>	stampId, i,
685	>	info->getLocalIndexManager());
686
687		info->addMolecule(mol);
688
#	Line 395 | Line 694 | namespace oopse {
694
695		} //end for(int i=0)
696		}
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();
697
698	<	if (!simParams->haveNMol()) {
699	<	// we don't have the total number of molecules, so we assume it is
700	<	// given in each component
701	<
702	<	for(i = 0; i < n_components; i++) {
703	<	if (!the_components[i]->haveNMol()) {
704	<	// we have a problem
705	<	sprintf(painCave.errMsg,
706	<	"SimCreator Error. No global NMol or component NMol given.\n"
707	<	"\tCannot calculate the number of atoms.\n");
708	<
709	<	painCave.isFatal = 1;
710	<	simError();
711	<	}
712	<
713	<	id = the_components[i]->getType();
714	<
715	<	extractedStamp = stamps->extractMolStamp(id);
716	<	if (extractedStamp == NULL) {
717	<	sprintf(painCave.errMsg,
718	<	"SimCreator error: Component \"%s\" was not found in the "
719	<	"list of declared molecules\n", id);
720	<
721	<	painCave.isFatal = 1;
722	<	simError();
723	<	}
724	<
725	<	currentStamp = extractedStamp->getStamp();
726	<
727	<
728	<	moleculeStampPairs.push_back(
729	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
730	<	} //end for (i = 0; i < n_components; i++)
731	<	} else {
732	<	sprintf(painCave.errMsg, "SimSetup error.\n"
733	<	"\tSorry, the ability to specify total"
734	<	" nMols and then give molfractions in the components\n"
735	<	"\tis not currently supported."
736	<	" Please give nMol in the components.\n");
737	<
738	<	painCave.isFatal = 1;
739	<	simError();
698	>	int SimCreator::computeStorageLayout(SimInfo* info) {
699	>
700	>	Globals* simParams = info->getSimParams();
701	>	int nRigidBodies = info->getNGlobalRigidBodies();
702	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
703	>	set<AtomType*>::iterator i;
704	>	bool hasDirectionalAtoms = false;
705	>	bool hasFixedCharge = false;
706	>	bool hasDipoles = false;
707	>	bool hasQuadrupoles = 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.isDipole()){
730	>	hasDipoles = true;
731	>	}
732	>	if (ma.isQuadrupole()){
733	>	hasQuadrupoles = true;
734	>	}
735	>	if (ea.isEAM() || sca.isSuttonChen()){
736	>	hasMetallic = true;
737	>	}
738	>	if ( fca.isFixedCharge() ){
739	>	hasFixedCharge = true;
740	>	}
741	>	if ( fqa.isFluctuatingCharge() ){
742	>	hasFluctuatingCharge = true;
743	>	}
744	>	if ( pa.isPolarizable() ){
745	>	hasPolarizable = true;
746	>	}
747		}
748
749	<	#ifdef IS_MPI
749	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
750	>	storageLayout |= DataStorage::dslAmat;
751	>	if(storageLayout & DataStorage::dslVelocity) {
752	>	storageLayout |= DataStorage::dslAngularMomentum;
753	>	}
754	>	if (storageLayout & DataStorage::dslForce) {
755	>	storageLayout |= DataStorage::dslTorque;
756	>	}
757	>	}
758	>	if (hasDipoles) {
759	>	storageLayout |= DataStorage::dslDipole;
760	>	}
761	>	if (hasQuadrupoles) {
762	>	storageLayout |= DataStorage::dslQuadrupole;
763	>	}
764	>	if (hasFixedCharge || hasFluctuatingCharge) {
765	>	storageLayout |= DataStorage::dslSkippedCharge;
766	>	}
767	>	if (hasMetallic) {
768	>	storageLayout |= DataStorage::dslDensity;
769	>	storageLayout |= DataStorage::dslFunctional;
770	>	storageLayout |= DataStorage::dslFunctionalDerivative;
771	>	}
772	>	if (hasPolarizable) {
773	>	storageLayout |= DataStorage::dslElectricField;
774	>	}
775	>	if (hasFluctuatingCharge){
776	>	storageLayout |= DataStorage::dslFlucQPosition;
777	>	if(storageLayout & DataStorage::dslVelocity) {
778	>	storageLayout |= DataStorage::dslFlucQVelocity;
779	>	}
780	>	if (storageLayout & DataStorage::dslForce) {
781	>	storageLayout |= DataStorage::dslFlucQForce;
782	>	}
783	>	}
784
785	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
786	<	MPIcheckPoint();
787	<
788	<	#endif // is_mpi
789	<
785	>	// if the user has asked for them, make sure we've got the memory for the
786	>	// objects defined.
787	>
788	>	if (simParams->getOutputParticlePotential()) {
789	>	storageLayout |= DataStorage::dslParticlePot;
790	>	}
791	>
792	>	if (simParams->havePrintHeatFlux()) {
793	>	if (simParams->getPrintHeatFlux()) {
794	>	storageLayout |= DataStorage::dslParticlePot;
795	>	}
796	>	}
797	>
798	>	if (simParams->getOutputElectricField()) {
799	>	storageLayout |= DataStorage::dslElectricField;
800	>	}
801	>
802	>	if (simParams->getOutputFluctuatingCharges()) {
803	>	storageLayout |= DataStorage::dslFlucQPosition;
804	>	storageLayout |= DataStorage::dslFlucQVelocity;
805	>	storageLayout |= DataStorage::dslFlucQForce;
806	>	}
807	>
808	>	return storageLayout;
809		}
810	<
810	>
811		void SimCreator::setGlobalIndex(SimInfo *info) {
812		SimInfo::MoleculeIterator mi;
813		Molecule::AtomIterator ai;
814		Molecule::RigidBodyIterator ri;
815		Molecule::CutoffGroupIterator ci;
816	+	Molecule::IntegrableObjectIterator  ioi;
817		Molecule * mol;
818		Atom * atom;
819		RigidBody * rb;
#	Line 471 | Line 822 | namespace oopse {
822		int beginRigidBodyIndex;
823		int beginCutoffGroupIndex;
824		int nGlobalAtoms = info->getNGlobalAtoms();
825	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
826
475	–	#ifndef IS_MPI
476	–
827		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	–
828		//rigidbody's index begins right after atom's
829	<	beginRigidBodyIndex += info->getNGlobalAtoms();
830	<
831	<	for(mol = info->beginMolecule(mi); mol != NULL;
832	<	mol = info->nextMolecule(mi)) {
829	>	beginRigidBodyIndex = info->getNGlobalAtoms();
830	>	beginCutoffGroupIndex = 0;
831	>
832	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
833
834	<	//local index(index in DataStorge) of atom is important
835	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
836	<	atom->setGlobalIndex(beginAtomIndex++);
834	>	#ifdef IS_MPI
835	>	if (info->getMolToProc(i) == worldRank) {
836	>	#endif
837	>	// stuff to do if I own this molecule
838	>	mol = info->getMoleculeByGlobalIndex(i);
839	>
840	>	//local index(index in DataStorge) of atom is important
841	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	>	atom->setGlobalIndex(beginAtomIndex++);
843	>	}
844	>
845	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
846	>	rb = mol->nextRigidBody(ri)) {
847	>	rb->setGlobalIndex(beginRigidBodyIndex++);
848	>	}
849	>
850	>	//local index of cutoff group is trivial, it only depends on
851	>	//the order of travesing
852	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
853	>	cg = mol->nextCutoffGroup(ci)) {
854	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
855	>	}
856	>
857	>	#ifdef IS_MPI
858	>	}  else {
859	>
860	>	// stuff to do if I don't own this molecule
861	>
862	>	int stampId = info->getMoleculeStampId(i);
863	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
864	>
865	>	beginAtomIndex += stamp->getNAtoms();
866	>	beginRigidBodyIndex += stamp->getNRigidBodies();
867	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
868		}
869	<
870	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
871	<	rb = mol->nextRigidBody(ri)) {
872	<	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	<
869	>	#endif
870	>
871	>	} //end for(int i=0)
872	>
873		//fill globalGroupMembership
874		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
875		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 551 | Line 881 | namespace oopse {
881
882		}
883		}
884	<
884	>
885		#ifdef IS_MPI
886		// Since the globalGroupMembership has been zero filled and we've only
887		// poked values into the atoms we know, we can do an Allreduce
888		// to get the full globalGroupMembership array (We think).
889		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
890		// docs said we could.
891	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
892	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
893	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
891	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
892	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
893	>	&tmpGroupMembership[0], nGlobalAtoms,
894	>	MPI::INT, MPI::SUM);
895		info->setGlobalGroupMembership(tmpGroupMembership);
896		#else
897		info->setGlobalGroupMembership(globalGroupMembership);
898		#endif
899
900		//fill molMembership
901	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
901	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
902	>	info->getNGlobalRigidBodies(), 0);
903
904	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
905	<
904	>	for(mol = info->beginMolecule(mi); mol != NULL;
905	>	mol = info->nextMolecule(mi)) {
906		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
908		}
909	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
910	+	rb = mol->nextRigidBody(ri)) {
911	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
912	+	}
913		}
914
915		#ifdef IS_MPI
916	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
916	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
917	>	info->getNGlobalRigidBodies(), 0);
918	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
919	>	nGlobalAtoms + nGlobalRigidBodies,
920	>	MPI::INT, MPI::SUM);
921
582	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
583	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
584	–
922		info->setGlobalMolMembership(tmpMolMembership);
923		#else
924		info->setGlobalMolMembership(globalMolMembership);
925		#endif
926	+
927	+	// nIOPerMol holds the number of integrable objects per molecule
928	+	// here the molecules are listed by their global indices.
929	+
930	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
931	+	for (mol = info->beginMolecule(mi); mol != NULL;
932	+	mol = info->nextMolecule(mi)) {
933	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
934	+	}
935
936	<	}
937	<
938	<	void SimCreator::loadCoordinates(SimInfo* info) {
939	<	Globals* simParams;
940	<	simParams = info->getSimParams();
936	>	#ifdef IS_MPI
937	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
938	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
939	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
940	>	#else
941	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
942	>	#endif
943	>
944	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
945
946	<	if (!simParams->haveInitialConfig()) {
947	<	sprintf(painCave.errMsg,
948	<	"Cannot intialize a simulation without an initial configuration file.\n");
949	<	painCave.isFatal = 1;;
600	<	simError();
946	>	int startingIndex = 0;
947	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
948	>	startingIOIndexForMol[i] = startingIndex;
949	>	startingIndex += numIntegrableObjectsPerMol[i];
950		}
951
952	<	DumpReader reader(info, simParams->getInitialConfig());
952	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
953	>	for (mol = info->beginMolecule(mi); mol != NULL;
954	>	mol = info->nextMolecule(mi)) {
955	>	int myGlobalIndex = mol->getGlobalIndex();
956	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
957	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
958	>	sd = mol->nextIntegrableObject(ioi)) {
959	>	sd->setGlobalIntegrableObjectIndex(globalIO);
960	>	IOIndexToIntegrableObject[globalIO] = sd;
961	>	globalIO++;
962	>	}
963	>	}
964	>
965	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
966	>
967	>	}
968	>
969	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
970	>
971	>	DumpReader reader(info, mdFileName);
972		int nframes = reader.getNFrames();
973
974		if (nframes > 0) {
#	Line 609 | Line 977 | namespace oopse {
977		//invalid initial coordinate file
978		sprintf(painCave.errMsg,
979		"Initial configuration file %s should at least contain one frame\n",
980	<	simParams->getInitialConfig());
980	>	mdFileName.c_str());
981		painCave.isFatal = 1;
982		simError();
983		}
616	–
984		//copy the current snapshot to previous snapshot
985		info->getSnapshotManager()->advance();
986		}
987
988	<	} //end namespace oopse
988	>	} //end namespace OpenMD
989
990

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1826 by gezelter, Wed Jan 9 19:41:48 2013 UTC

#	Line 0 | Line 1
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