ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 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	<	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	<
82	<	yacc_BASS(mdFileName.c_str());
83	<
84	<	#ifdef IS_MPI
85	<
86	<	throwMPIEvent(NULL);
87	<	} else {
88	<	set_interface_stamps(stamps, simParams);
89	<	mpiEventInit();
90	<	MPIcheckPoint();
91	<	mpiEventLoop();
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,
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;
259	>	streamoff mdOffset(0);
260	>	int mdFileVersion;
261	>
262	>
263	>	#ifdef IS_MPI
264	>	const int masterNode = 0;
265	>	if (worldRank == masterNode) {
266	>	#endif
267	>
268	>	std::ifstream mdFile_;
269	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
270	>
271	>	if (mdFile_.fail()) {
272	>	sprintf(painCave.errMsg,
273	>	"SimCreator: Cannot open file: %s\n",
274	>	mdFileName.c_str());
275	>	painCave.isFatal = 1;
276	>	simError();
277	>	}
278	>
279	>	mdFile_.getline(buffer, bufferSize);
280	>	++lineNo;
281	>	std::string line = trimLeftCopy(buffer);
282	>	i = CaseInsensitiveFind(line, "<OpenMD");
283	>	if (static_cast<size_t>(i) == string::npos) {
284	>	// try the older file strings to see if that works:
285	>	i = CaseInsensitiveFind(line, "<OOPSE");
286	>	}
287	>
288	>	if (static_cast<size_t>(i) == string::npos) {
289	>	// still no luck!
290	>	sprintf(painCave.errMsg,
291	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
292	>	mdFileName.c_str());
293	>	painCave.isFatal = 1;
294	>	simError();
295	>	}
296	>
297	>	// found the correct opening string, now try to get the file
298	>	// format version number.
299	>
300	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
301	>	std::string fileType = tokenizer.nextToken();
302	>	toUpper(fileType);
303	>
304	>	mdFileVersion = 0;
305	>
306	>	if (fileType == "OPENMD") {
307	>	while (tokenizer.hasMoreTokens()) {
308	>	std::string token(tokenizer.nextToken());
309	>	toUpper(token);
310	>	if (token == "VERSION") {
311	>	mdFileVersion = tokenizer.nextTokenAsInt();
312	>	break;
313	>	}
314	>	}
315	>	}
316	>
317	>	//scan through the input stream and find MetaData tag
318	>	while(mdFile_.getline(buffer, bufferSize)) {
319	>	++lineNo;
320	>
321	>	std::string line = trimLeftCopy(buffer);
322	>	if (metaDataBlockStart == -1) {
323	>	i = CaseInsensitiveFind(line, "<MetaData>");
324	>	if (i != string::npos) {
325	>	metaDataBlockStart = lineNo;
326	>	mdOffset = mdFile_.tellg();
327	>	}
328	>	} else {
329	>	i = CaseInsensitiveFind(line, "</MetaData>");
330	>	if (i != string::npos) {
331	>	metaDataBlockEnd = lineNo;
332	>	}
333	>	}
334	>	}
335	>
336	>	if (metaDataBlockStart == -1) {
337	>	sprintf(painCave.errMsg,
338	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
339	>	mdFileName.c_str());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343	>	if (metaDataBlockEnd == -1) {
344	>	sprintf(painCave.errMsg,
345	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
346	>	mdFileName.c_str());
347	>	painCave.isFatal = 1;
348	>	simError();
349	>	}
350	>
351	>	mdFile_.clear();
352	>	mdFile_.seekg(0);
353	>	mdFile_.seekg(mdOffset);
354	>
355	>	mdRawData.clear();
356	>
357	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
358	>	mdFile_.getline(buffer, bufferSize);
359	>	mdRawData += buffer;
360	>	mdRawData += "\n";
361	>	}
362	>
363	>	mdFile_.close();
364	>
365	>	#ifdef IS_MPI
366	>	}
367	>	#endif
368	>
369	>	std::stringstream rawMetaDataStream(mdRawData);
370	>
371		//parse meta-data file
372	<	parseFile(mdFileName, stamps, simParams);
372	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373	>	metaDataBlockStart + 1);
374
375		//create the force field
376	<	ForceField * ff = ForceFieldFactory::getInstance()
377	<	->createForceField(simParams->getForceField());
111	<
376	>	ForceField * ff = new ForceField(simParams->getForceField());
377	>
378		if (ff == NULL) {
379		sprintf(painCave.errMsg,
380		"ForceField Factory can not create %s force field\n",
#	Line 141 | Line 407 | namespace oopse {
407		}
408
409		ff->parse(forcefieldFileName);
144	–
145	–	//extract the molecule stamps
146	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
147	–	compList(stamps, simParams, moleculeStampPairs);
148	–
410		//create SimInfo
411	<	SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
411	>	SimInfo * info = new SimInfo(ff, simParams);
412	>
413	>	info->setRawMetaData(mdRawData);
414
415	<	//gather parameters (SimCreator only retrieves part of the parameters)
415	>	//gather parameters (SimCreator only retrieves part of the
416	>	//parameters)
417		gatherParameters(info, mdFileName);
418
419		//divide the molecules and determine the global index of molecules
#	Line 160 | Line 424 | namespace oopse {
424		//create the molecules
425		createMolecules(info);
426
427	+	//find the storage layout
428	+
429	+	int storageLayout = computeStorageLayout(info);
430	+
431	+	//allocate memory for DataStorage(circular reference, need to
432	+	//break it)
433	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435	<	//allocate memory for DataStorage(circular reference, need to break it)
436	<	info->setSnapshotManager(new SimSnapshotManager(info));
437	<
438	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
439	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
169	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
435	>	//set the global index of atoms, rigidbodies and cutoffgroups
436	>	//(only need to be set once, the global index will never change
437	>	//again). Local indices of atoms and rigidbodies are already set
438	>	//by MoleculeCreator class which actually delegates the
439	>	//responsibility to LocalIndexManager.
440		setGlobalIndex(info);
441
442	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
443	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
444	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
445	<	//we can determine the beginning global indices of atoms before they get created.
442	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
443	>	//method, at that point atoms don't have the global index yet
444	>	//(their global index are all initialized to -1).  Therefore we
445	>	//have to call addInteractionPairs explicitly here. A way to work
446	>	//around is that we can determine the beginning global indices of
447	>	//atoms before they get created.
448		SimInfo::MoleculeIterator mi;
449		Molecule* mol;
450		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
451	<	info->addExcludePairs(mol);
451	>	info->addInteractionPairs(mol);
452		}
453
454		if (loadInitCoords)
455	<	loadCoordinates(info);
184	<
455	>	loadCoordinates(info, mdFileName);
456		return info;
457		}
458
459		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
460
461	<	//figure out the ouput file names
461	>	//figure out the output file names
462		std::string prefix;
463
464		#ifdef IS_MPI
#	Line 216 | Line 487 | namespace oopse {
487
488		#ifdef IS_MPI
489		void SimCreator::divideMolecules(SimInfo *info) {
490	<	double numerator;
491	<	double denominator;
492	<	double precast;
493	<	double x;
494	<	double y;
495	<	double a;
490	>	RealType numerator;
491	>	RealType denominator;
492	>	RealType precast;
493	>	RealType x;
494	>	RealType y;
495	>	RealType a;
496		int old_atoms;
497		int add_atoms;
498		int new_atoms;
499		int nTarget;
500		int done;
501		int i;
231	–	int j;
502		int loops;
503		int which_proc;
504		int nProcessors;
#	Line 236 | Line 506 | namespace oopse {
506		int nGlobalMols = info->getNGlobalMolecules();
507		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
508
509	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
509	>	nProcessors = MPI::COMM_WORLD.Get_size();
510
511		if (nProcessors > nGlobalMols) {
512		sprintf(painCave.errMsg,
#	Line 245 | Line 515 | namespace oopse {
515		"\tthe number of molecules.  This will not result in a \n"
516		"\tusable division of atoms for force decomposition.\n"
517		"\tEither try a smaller number of processors, or run the\n"
518	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
518	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
519
520		painCave.isFatal = 1;
521		simError();
#	Line 274 | Line 544 | namespace oopse {
544		nTarget = (int)(precast + 0.5);
545
546		for(i = 0; i < nGlobalMols; i++) {
547	+
548		done = 0;
549		loops = 0;
550
#	Line 298 | Line 569 | namespace oopse {
569		// and be done with it.
570
571		if (loops > 100) {
572	+
573		sprintf(painCave.errMsg,
574	<	"I've tried 100 times to assign molecule %d to a "
575	<	" processor, but can't find a good spot.\n"
576	<	"I'm assigning it at random to processor %d.\n",
574	>	"There have been 100 attempts to assign molecule %d to an\n"
575	>	"\tunderworked processor, but there's no good place to\n"
576	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
577		i, which_proc);
578	<
578	>
579		painCave.isFatal = 0;
580	+	painCave.severity = OPENMD_INFO;
581		simError();
582
583		molToProcMap[i] = which_proc;
#	Line 333 | Line 606 | namespace oopse {
606		//           Pacc(x) = exp(- a * x)
607		// where a = penalty / (average atoms per molecule)
608
609	<	x = (double)(new_atoms - nTarget);
609	>	x = (RealType)(new_atoms - nTarget);
610		y = myRandom->rand();
611
612		if (y < exp(- a * x)) {
#	Line 349 | Line 622 | namespace oopse {
622		}
623
624		delete myRandom;
625	<
625	>
626		// Spray out this nonsense to all other processors:
627	<
355	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
627	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
628		} else {
629
630		// Listen to your marching orders from processor 0:
631	<
632	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
631	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
632	>
633		}
634
635		info->setMolToProcMap(molToProcMap);
636		sprintf(checkPointMsg,
637		"Successfully divided the molecules among the processors.\n");
638	<	MPIcheckPoint();
638	>	errorCheckPoint();
639		}
640
641		#endif
#	Line 380 | Line 652 | namespace oopse {
652		#endif
653
654		stampId = info->getMoleculeStampId(i);
655	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
656	<	stampId, i, info->getLocalIndexManager());
655	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
656	>	info->getMoleculeStamp(stampId),
657	>	stampId, i,
658	>	info->getLocalIndexManager());
659
660		info->addMolecule(mol);
661
#	Line 393 | Line 667 | namespace oopse {
667
668		} //end for(int i=0)
669		}
396	–
397	–	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
398	–	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
399	–	int i;
400	–	char * id;
401	–	MoleculeStamp * currentStamp;
402	–	Component** the_components = simParams->getComponents();
403	–	int n_components = simParams->getNComponents();
670
671	<	if (!simParams->haveNMol()) {
406	<	// we don't have the total number of molecules, so we assume it is
407	<	// given in each component
408	<
409	<	for(i = 0; i < n_components; i++) {
410	<	if (!the_components[i]->haveNMol()) {
411	<	// we have a problem
412	<	sprintf(painCave.errMsg,
413	<	"SimCreator Error. No global NMol or component NMol given.\n"
414	<	"\tCannot calculate the number of atoms.\n");
415	<
416	<	painCave.isFatal = 1;
417	<	simError();
418	<	}
419	<
420	<	id = the_components[i]->getType();
671	>	int SimCreator::computeStorageLayout(SimInfo* info) {
672
673	<	currentStamp = stamps->getMolStamp(id);
674	<	if (currentStamp == NULL) {
675	<	sprintf(painCave.errMsg,
676	<	"SimCreator error: Component \"%s\" was not found in the "
677	<	"list of declared molecules\n", id);
678	<
679	<	painCave.isFatal = 1;
680	<	simError();
681	<	}
682	<
683	<	moleculeStampPairs.push_back(
684	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
685	<	} //end for (i = 0; i < n_components; i++)
686	<	} else {
687	<	sprintf(painCave.errMsg, "SimSetup error.\n"
688	<	"\tSorry, the ability to specify total"
689	<	" nMols and then give molfractions in the components\n"
690	<	"\tis not currently supported."
691	<	" Please give nMol in the components.\n");
692	<
693	<	painCave.isFatal = 1;
694	<	simError();
673	>	Globals* simParams = info->getSimParams();
674	>	int nRigidBodies = info->getNGlobalRigidBodies();
675	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
676	>	set<AtomType*>::iterator i;
677	>	bool hasDirectionalAtoms = false;
678	>	bool hasFixedCharge = false;
679	>	bool hasMultipoles = false;
680	>	bool hasPolarizable = false;
681	>	bool hasFluctuatingCharge = false;
682	>	bool hasMetallic = false;
683	>	int storageLayout = 0;
684	>	storageLayout |= DataStorage::dslPosition;
685	>	storageLayout |= DataStorage::dslVelocity;
686	>	storageLayout |= DataStorage::dslForce;
687	>
688	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
689	>
690	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
691	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
692	>	EAMAdapter ea = EAMAdapter( (*i) );
693	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
694	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
695	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
696	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
697	>
698	>	if (da.isDirectional()){
699	>	hasDirectionalAtoms = true;
700	>	}
701	>	if (ma.isMultipole()){
702	>	hasMultipoles = true;
703	>	}
704	>	if (ea.isEAM() || sca.isSuttonChen()){
705	>	hasMetallic = true;
706	>	}
707	>	if ( fca.isFixedCharge() ){
708	>	hasFixedCharge = true;
709	>	}
710	>	if ( fqa.isFluctuatingCharge() ){
711	>	hasFluctuatingCharge = true;
712	>	}
713	>	if ( pa.isPolarizable() ){
714	>	hasPolarizable = true;
715	>	}
716		}
717
718	<	#ifdef IS_MPI
718	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
719	>	storageLayout |= DataStorage::dslAmat;
720	>	if(storageLayout & DataStorage::dslVelocity) {
721	>	storageLayout |= DataStorage::dslAngularMomentum;
722	>	}
723	>	if (storageLayout & DataStorage::dslForce) {
724	>	storageLayout |= DataStorage::dslTorque;
725	>	}
726	>	}
727	>	if (hasMultipoles) {
728	>	storageLayout |= DataStorage::dslElectroFrame;
729	>	}
730	>	if (hasFixedCharge || hasFluctuatingCharge) {
731	>	storageLayout |= DataStorage::dslSkippedCharge;
732	>	}
733	>	if (hasMetallic) {
734	>	storageLayout |= DataStorage::dslDensity;
735	>	storageLayout |= DataStorage::dslFunctional;
736	>	storageLayout |= DataStorage::dslFunctionalDerivative;
737	>	}
738	>	if (hasPolarizable) {
739	>	storageLayout |= DataStorage::dslElectricField;
740	>	}
741	>	if (hasFluctuatingCharge){
742	>	storageLayout |= DataStorage::dslFlucQPosition;
743	>	if(storageLayout & DataStorage::dslVelocity) {
744	>	storageLayout |= DataStorage::dslFlucQVelocity;
745	>	}
746	>	if (storageLayout & DataStorage::dslForce) {
747	>	storageLayout |= DataStorage::dslFlucQForce;
748	>	}
749	>	}
750
751	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
752	<	MPIcheckPoint();
753	<
754	<	#endif // is_mpi
755	<
751	>	// if the user has asked for them, make sure we've got the memory for the
752	>	// objects defined.
753	>
754	>	if (simParams->getOutputParticlePotential()) {
755	>	storageLayout |= DataStorage::dslParticlePot;
756	>	}
757	>
758	>	if (simParams->havePrintHeatFlux()) {
759	>	if (simParams->getPrintHeatFlux()) {
760	>	storageLayout |= DataStorage::dslParticlePot;
761	>	}
762	>	}
763	>
764	>	if (simParams->getOutputElectricField()) {
765	>	storageLayout |= DataStorage::dslElectricField;
766	>	}
767	>	if (simParams->getOutputFluctuatingCharges()) {
768	>	storageLayout |= DataStorage::dslFlucQPosition;
769	>	storageLayout |= DataStorage::dslFlucQVelocity;
770	>	storageLayout |= DataStorage::dslFlucQForce;
771	>	}
772	>
773	>	return storageLayout;
774		}
775	<
775	>
776		void SimCreator::setGlobalIndex(SimInfo *info) {
777		SimInfo::MoleculeIterator mi;
778		Molecule::AtomIterator ai;
779		Molecule::RigidBodyIterator ri;
780		Molecule::CutoffGroupIterator ci;
781	+	Molecule::IntegrableObjectIterator  ioi;
782		Molecule * mol;
783		Atom * atom;
784		RigidBody * rb;
#	Line 466 | Line 788 | namespace oopse {
788		int beginCutoffGroupIndex;
789		int nGlobalAtoms = info->getNGlobalAtoms();
790
469	–	#ifndef IS_MPI
470	–
791		beginAtomIndex = 0;
472	–	beginRigidBodyIndex = 0;
473	–	beginCutoffGroupIndex = 0;
474	–
475	–	#else
476	–
477	–	int nproc;
478	–	int myNode;
479	–
480	–	myNode = worldRank;
481	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
482	–
483	–	std::vector < int > tmpAtomsInProc(nproc, 0);
484	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
485	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
486	–	std::vector < int > NumAtomsInProc(nproc, 0);
487	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
488	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
489	–
490	–	tmpAtomsInProc[myNode] = info->getNAtoms();
491	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
492	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
493	–
494	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
495	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
496	–	MPI_SUM, MPI_COMM_WORLD);
497	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
498	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
499	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
500	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
501	–
502	–	beginAtomIndex = 0;
503	–	beginRigidBodyIndex = 0;
504	–	beginCutoffGroupIndex = 0;
505	–
506	–	for(int i = 0; i < myNode; i++) {
507	–	beginAtomIndex += NumAtomsInProc[i];
508	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
509	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
510	–	}
511	–
512	–	#endif
513	–
792		//rigidbody's index begins right after atom's
793	<	beginRigidBodyIndex += info->getNGlobalAtoms();
794	<
795	<	for(mol = info->beginMolecule(mi); mol != NULL;
796	<	mol = info->nextMolecule(mi)) {
793	>	beginRigidBodyIndex = info->getNGlobalAtoms();
794	>	beginCutoffGroupIndex = 0;
795	>
796	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
797
798	<	//local index(index in DataStorge) of atom is important
799	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
800	<	atom->setGlobalIndex(beginAtomIndex++);
798	>	#ifdef IS_MPI
799	>	if (info->getMolToProc(i) == worldRank) {
800	>	#endif
801	>	// stuff to do if I own this molecule
802	>	mol = info->getMoleculeByGlobalIndex(i);
803	>
804	>	//local index(index in DataStorge) of atom is important
805	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
806	>	atom->setGlobalIndex(beginAtomIndex++);
807	>	}
808	>
809	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
810	>	rb = mol->nextRigidBody(ri)) {
811	>	rb->setGlobalIndex(beginRigidBodyIndex++);
812	>	}
813	>
814	>	//local index of cutoff group is trivial, it only depends on
815	>	//the order of travesing
816	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
817	>	cg = mol->nextCutoffGroup(ci)) {
818	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
819	>	}
820	>
821	>	#ifdef IS_MPI
822	>	}  else {
823	>
824	>	// stuff to do if I don't own this molecule
825	>
826	>	int stampId = info->getMoleculeStampId(i);
827	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
828	>
829	>	beginAtomIndex += stamp->getNAtoms();
830	>	beginRigidBodyIndex += stamp->getNRigidBodies();
831	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
832		}
833	<
834	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
835	<	rb = mol->nextRigidBody(ri)) {
836	<	rb->setGlobalIndex(beginRigidBodyIndex++);
528	<	}
529	<
530	<	//local index of cutoff group is trivial, it only depends on the order of travesing
531	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
532	<	cg = mol->nextCutoffGroup(ci)) {
533	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
534	<	}
535	<	}
536	<
833	>	#endif
834	>
835	>	} //end for(int i=0)
836	>
837		//fill globalGroupMembership
838		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
839		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 545 | Line 845 | namespace oopse {
845
846		}
847		}
848	<
848	>
849		#ifdef IS_MPI
850		// Since the globalGroupMembership has been zero filled and we've only
851		// poked values into the atoms we know, we can do an Allreduce
852		// to get the full globalGroupMembership array (We think).
853		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
854		// docs said we could.
855	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
856	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
857	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
855	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
856	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
857	>	&tmpGroupMembership[0], nGlobalAtoms,
858	>	MPI::INT, MPI::SUM);
859		info->setGlobalGroupMembership(tmpGroupMembership);
860		#else
861		info->setGlobalGroupMembership(globalGroupMembership);
#	Line 564 | Line 865 | namespace oopse {
865		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
866
867		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
567	–
868		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
870		}
871		}
872
873		#ifdef IS_MPI
874	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
874	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
875	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
876	>	nGlobalAtoms,
877	>	MPI::INT, MPI::SUM);
878
576	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
577	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
578	–
879		info->setGlobalMolMembership(tmpMolMembership);
880		#else
881		info->setGlobalMolMembership(globalMolMembership);
882		#endif
883	+
884	+	// nIOPerMol holds the number of integrable objects per molecule
885	+	// here the molecules are listed by their global indices.
886	+
887	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
888	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
889	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
890	+	}
891
892	<	}
893	<
894	<	void SimCreator::loadCoordinates(SimInfo* info) {
895	<	Globals* simParams;
896	<	simParams = info->getSimParams();
892	>	#ifdef IS_MPI
893	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
894	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
895	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
896	>	#else
897	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
898	>	#endif
899	>
900	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
901
902	<	if (!simParams->haveInitialConfig()) {
903	<	sprintf(painCave.errMsg,
904	<	"Cannot intialize a simulation without an initial configuration file.\n");
905	<	painCave.isFatal = 1;;
594	<	simError();
902	>	int startingIndex = 0;
903	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
904	>	startingIOIndexForMol[i] = startingIndex;
905	>	startingIndex += numIntegrableObjectsPerMol[i];
906		}
907
908	<	DumpReader reader(info, simParams->getInitialConfig());
909	<	int nframes = reader.getNFrames();
908	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
909	>	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
910	>	int myGlobalIndex = mol->getGlobalIndex();
911	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
912	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
913	>	sd = mol->nextIntegrableObject(ioi)) {
914	>	sd->setGlobalIntegrableObjectIndex(globalIO);
915	>	IOIndexToIntegrableObject[globalIO] = sd;
916	>	globalIO++;
917	>	}
918	>	}
919	>
920	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
921
922	+	}
923	+
924	+	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
925	+
926	+	DumpReader reader(info, mdFileName);
927	+	int nframes = reader.getNFrames();
928	+
929		if (nframes > 0) {
930		reader.readFrame(nframes - 1);
931		} else {
932		//invalid initial coordinate file
933		sprintf(painCave.errMsg,
934		"Initial configuration file %s should at least contain one frame\n",
935	<	simParams->getInitialConfig().c_str());
935	>	mdFileName.c_str());
936		painCave.isFatal = 1;
937		simError();
938		}
610	–
939		//copy the current snapshot to previous snapshot
940		info->getSnapshotManager()->advance();
941		}
942
943	<	} //end namespace oopse
943	>	} //end namespace OpenMD
944
945

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines