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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 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include "mpi.h"
52	+	#include "math/ParallelRandNumGen.hpp"
53	+	#endif
54	+
55	+	#include <exception>
56	+	#include <iostream>
57	+	#include <sstream>
58	+	#include <string>
59	+
60		#include "brains/MoleculeCreator.hpp"
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "io/parse_me.h"
55	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67		#include "math/SeqRandNumGen.hpp"
68	<	#ifdef IS_MPI
69	<	#include "io/mpiBASS.h"
70	<	#include "math/ParallelRandNumGen.hpp"
71	<	#endif
68	>	#include "mdParser/MDLexer.hpp"
69	>	#include "mdParser/MDParser.hpp"
70	>	#include "mdParser/MDTreeParser.hpp"
71	>	#include "mdParser/SimplePreprocessor.hpp"
72	>	#include "antlr/ANTLRException.hpp"
73	>	#include "antlr/TokenStreamRecognitionException.hpp"
74	>	#include "antlr/TokenStreamIOException.hpp"
75	>	#include "antlr/TokenStreamException.hpp"
76	>	#include "antlr/RecognitionException.hpp"
77	>	#include "antlr/CharStreamException.hpp"
78
79	<	namespace oopse {
79	>	#include "antlr/MismatchedCharException.hpp"
80	>	#include "antlr/MismatchedTokenException.hpp"
81	>	#include "antlr/NoViableAltForCharException.hpp"
82	>	#include "antlr/NoViableAltException.hpp"
83	>
84	>	#include "types/DirectionalAdapter.hpp"
85	>	#include "types/MultipoleAdapter.hpp"
86	>	#include "types/EAMAdapter.hpp"
87	>	#include "types/SuttonChenAdapter.hpp"
88	>	#include "types/PolarizableAdapter.hpp"
89	>	#include "types/FixedChargeAdapter.hpp"
90	>	#include "types/FluctuatingChargeAdapter.hpp"
91	>
92	>
93	>	namespace OpenMD {
94
95	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps,
96	<	Globals* simParams){
95	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
96	>	Globals* simParams = NULL;
97	>	try {
98	>
99	>	// Create a preprocessor that preprocesses md file into an ostringstream
100	>	std::stringstream ppStream;
101	>	#ifdef IS_MPI
102	>	int streamSize;
103	>	const int masterNode = 0;
104	>
105	>	if (worldRank == masterNode) {
106	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
107	>	#endif
108	>	SimplePreprocessor preprocessor;
109	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, 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())), streamSize, MPI::CHAR, masterNode);
116	>
117	>	} else {
118	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
119	>
120	>	//get stream size
121	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
122	>
123	>	char* buf = new char[streamSize];
124	>	assert(buf);
125	>
126	>	//receive file content
127	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
128	>
129	>	ppStream.str(buf);
130	>	delete [] buf;
131	>	}
132	>	#endif
133	>	// Create a scanner that reads from the input stream
134	>	MDLexer lexer(ppStream);
135	>	lexer.setFilename(filename);
136	>	lexer.initDeferredLineCount();
137
138	<	#ifdef IS_MPI
138	>	// Create a parser that reads from the scanner
139	>	MDParser parser(lexer);
140	>	parser.setFilename(filename);
141	>
142	>	// Create an observer that synchorizes file name change
143	>	FilenameObserver observer;
144	>	observer.setLexer(&lexer);
145	>	observer.setParser(&parser);
146	>	lexer.setObserver(&observer);
147
148	<	if (worldRank == 0) {
149	<	#endif // is_mpi
148	>	antlr::ASTFactory factory;
149	>	parser.initializeASTFactory(factory);
150	>	parser.setASTFactory(&factory);
151	>	parser.mdfile();
152	>
153	>	// Create a tree parser that reads information into Globals
154	>	MDTreeParser treeParser;
155	>	treeParser.initializeASTFactory(factory);
156	>	treeParser.setASTFactory(&factory);
157	>	simParams = treeParser.walkTree(parser.getAST());
158	>	}
159	>
160
161	<	simParams->initalize();
162	<	set_interface_stamps(stamps, simParams);
161	>	catch(antlr::MismatchedCharException& e) {
162	>	sprintf(painCave.errMsg,
163	>	"parser exception: %s %s:%d:%d\n",
164	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
165	>	painCave.isFatal = 1;
166	>	simError();
167	>	}
168	>	catch(antlr::MismatchedTokenException &e) {
169	>	sprintf(painCave.errMsg,
170	>	"parser exception: %s %s:%d:%d\n",
171	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
172	>	painCave.isFatal = 1;
173	>	simError();
174	>	}
175	>	catch(antlr::NoViableAltForCharException &e) {
176	>	sprintf(painCave.errMsg,
177	>	"parser exception: %s %s:%d:%d\n",
178	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
179	>	painCave.isFatal = 1;
180	>	simError();
181	>	}
182	>	catch(antlr::NoViableAltException &e) {
183	>	sprintf(painCave.errMsg,
184	>	"parser exception: %s %s:%d:%d\n",
185	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
186	>	painCave.isFatal = 1;
187	>	simError();
188	>	}
189
190	<	#ifdef IS_MPI
191	<
192	<	mpiEventInit();
193	<
194	<	#endif
195	<
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();
190	>	catch(antlr::TokenStreamRecognitionException& e) {
191	>	sprintf(painCave.errMsg,
192	>	"parser exception: %s %s:%d:%d\n",
193	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
194	>	painCave.isFatal = 1;
195	>	simError();
196		}
197	<
198	<	#endif
199	<
197	>
198	>	catch(antlr::TokenStreamIOException& e) {
199	>	sprintf(painCave.errMsg,
200	>	"parser exception: %s\n",
201	>	e.getMessage().c_str());
202	>	painCave.isFatal = 1;
203	>	simError();
204	>	}
205	>
206	>	catch(antlr::TokenStreamException& e) {
207	>	sprintf(painCave.errMsg,
208	>	"parser exception: %s\n",
209	>	e.getMessage().c_str());
210	>	painCave.isFatal = 1;
211	>	simError();
212	>	}
213	>	catch (antlr::RecognitionException& e) {
214	>	sprintf(painCave.errMsg,
215	>	"parser exception: %s %s:%d:%d\n",
216	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
217	>	painCave.isFatal = 1;
218	>	simError();
219	>	}
220	>	catch (antlr::CharStreamException& e) {
221	>	sprintf(painCave.errMsg,
222	>	"parser exception: %s\n",
223	>	e.getMessage().c_str());
224	>	painCave.isFatal = 1;
225	>	simError();
226	>	}
227	>	catch (OpenMDException& e) {
228	>	sprintf(painCave.errMsg,
229	>	"%s\n",
230	>	e.getMessage().c_str());
231	>	painCave.isFatal = 1;
232	>	simError();
233	>	}
234	>	catch (std::exception& e) {
235	>	sprintf(painCave.errMsg,
236	>	"parser exception: %s\n",
237	>	e.what());
238	>	painCave.isFatal = 1;
239	>	simError();
240	>	}
241	>
242	>	simParams->setMDfileVersion(mdFileVersion);
243	>	return simParams;
244		}
245
246	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
246	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
247	>	bool loadInitCoords) {
248
249	<	MakeStamps * stamps = new MakeStamps();
250	<
251	<	Globals * simParams = new Globals();
252	<
249	>	const int bufferSize = 65535;
250	>	char buffer[bufferSize];
251	>	int lineNo = 0;
252	>	std::string mdRawData;
253	>	int metaDataBlockStart = -1;
254	>	int metaDataBlockEnd = -1;
255	>	int i, j;
256	>	streamoff mdOffset;
257	>	int mdFileVersion;
258	>
259	>	// Create a string for embedding the version information in the MetaData
260	>	std::string version;
261	>	version.assign("## Last run using OpenMD Version: ");
262	>	version.append(OPENMD_VERSION_MAJOR);
263	>	version.append(".");
264	>	version.append(OPENMD_VERSION_MINOR);
265	>
266	>	std::string svnrev;
267	>	//convert a macro from compiler to a string in c++
268	>	STR_DEFINE(svnrev, SVN_REV );
269	>	version.append(" Revision: ");
270	>	// If there's no SVN revision, just call this the RELEASE revision.
271	>	if (!svnrev.empty()) {
272	>	version.append(svnrev);
273	>	} else {
274	>	version.append("RELEASE");
275	>	}
276	>
277	>	#ifdef IS_MPI
278	>	const int masterNode = 0;
279	>	if (worldRank == masterNode) {
280	>	#endif
281	>
282	>	std::ifstream mdFile_;
283	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
284	>
285	>	if (mdFile_.fail()) {
286	>	sprintf(painCave.errMsg,
287	>	"SimCreator: Cannot open file: %s\n",
288	>	mdFileName.c_str());
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292	>
293	>	mdFile_.getline(buffer, bufferSize);
294	>	++lineNo;
295	>	std::string line = trimLeftCopy(buffer);
296	>	i = CaseInsensitiveFind(line, "<OpenMD");
297	>	if (static_cast<size_t>(i) == string::npos) {
298	>	// try the older file strings to see if that works:
299	>	i = CaseInsensitiveFind(line, "<OOPSE");
300	>	}
301	>
302	>	if (static_cast<size_t>(i) == string::npos) {
303	>	// still no luck!
304	>	sprintf(painCave.errMsg,
305	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
306	>	mdFileName.c_str());
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	// found the correct opening string, now try to get the file
312	>	// format version number.
313	>
314	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
315	>	std::string fileType = tokenizer.nextToken();
316	>	toUpper(fileType);
317	>
318	>	mdFileVersion = 0;
319	>
320	>	if (fileType == "OPENMD") {
321	>	while (tokenizer.hasMoreTokens()) {
322	>	std::string token(tokenizer.nextToken());
323	>	toUpper(token);
324	>	if (token == "VERSION") {
325	>	mdFileVersion = tokenizer.nextTokenAsInt();
326	>	break;
327	>	}
328	>	}
329	>	}
330	>
331	>	//scan through the input stream and find MetaData tag
332	>	while(mdFile_.getline(buffer, bufferSize)) {
333	>	++lineNo;
334	>
335	>	std::string line = trimLeftCopy(buffer);
336	>	if (metaDataBlockStart == -1) {
337	>	i = CaseInsensitiveFind(line, "<MetaData>");
338	>	if (i != string::npos) {
339	>	metaDataBlockStart = lineNo;
340	>	mdOffset = mdFile_.tellg();
341	>	}
342	>	} else {
343	>	i = CaseInsensitiveFind(line, "</MetaData>");
344	>	if (i != string::npos) {
345	>	metaDataBlockEnd = lineNo;
346	>	}
347	>	}
348	>	}
349	>
350	>	if (metaDataBlockStart == -1) {
351	>	sprintf(painCave.errMsg,
352	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
353	>	mdFileName.c_str());
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
357	>	if (metaDataBlockEnd == -1) {
358	>	sprintf(painCave.errMsg,
359	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
360	>	mdFileName.c_str());
361	>	painCave.isFatal = 1;
362	>	simError();
363	>	}
364	>
365	>	mdFile_.clear();
366	>	mdFile_.seekg(0);
367	>	mdFile_.seekg(mdOffset);
368	>
369	>	mdRawData.clear();
370	>
371	>	bool foundVersion = false;
372	>
373	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
374	>	mdFile_.getline(buffer, bufferSize);
375	>	std::string line = trimLeftCopy(buffer);
376	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
377	>	if (static_cast<size_t>(j) != string::npos) {
378	>	foundVersion = true;
379	>	mdRawData += version;
380	>	} else {
381	>	mdRawData += buffer;
382	>	}
383	>	mdRawData += "\n";
384	>	}
385	>
386	>	if (!foundVersion) mdRawData += version + "\n";
387	>
388	>	mdFile_.close();
389	>
390	>	#ifdef IS_MPI
391	>	}
392	>	#endif
393	>
394	>	std::stringstream rawMetaDataStream(mdRawData);
395	>
396		//parse meta-data file
397	<	parseFile(mdFileName, stamps, simParams);
397	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
398	>	metaDataBlockStart + 1);
399
400		//create the force field
401	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
402	<	simParams->getForceField());
111	<
401	>	ForceField * ff = new ForceField(simParams->getForceField());
402	>
403		if (ff == NULL) {
404	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
405	<	simParams->getForceField());
404	>	sprintf(painCave.errMsg,
405	>	"ForceField Factory can not create %s force field\n",
406	>	simParams->getForceField().c_str());
407		painCave.isFatal = 1;
408		simError();
409		}
#	Line 140 | Line 432 | namespace oopse {
432		}
433
434		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
435		//create SimInfo
436	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
437	<
438	<	//gather parameters (SimCreator only retrieves part of the parameters)
436	>	SimInfo * info = new SimInfo(ff, simParams);
437	>
438	>	info->setRawMetaData(mdRawData);
439	>
440	>	//gather parameters (SimCreator only retrieves part of the
441	>	//parameters)
442		gatherParameters(info, mdFileName);
443
444		//divide the molecules and determine the global index of molecules
#	Line 159 | Line 449 | namespace oopse {
449		//create the molecules
450		createMolecules(info);
451
452	+	//find the storage layout
453	+
454	+	int storageLayout = computeStorageLayout(info);
455	+
456	+	//allocate memory for DataStorage(circular reference, need to
457	+	//break it)
458	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
459
460	<	//allocate memory for DataStorage(circular reference, need to break it)
461	<	info->setSnapshotManager(new SimSnapshotManager(info));
462	<
463	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
464	<	//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.
460	>	//set the global index of atoms, rigidbodies and cutoffgroups
461	>	//(only need to be set once, the global index will never change
462	>	//again). Local indices of atoms and rigidbodies are already set
463	>	//by MoleculeCreator class which actually delegates the
464	>	//responsibility to LocalIndexManager.
465		setGlobalIndex(info);
466
467	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
468	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
469	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
470	<	//we can determine the beginning global indices of atoms before they get created.
467	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
468	>	//method, at that point atoms don't have the global index yet
469	>	//(their global index are all initialized to -1).  Therefore we
470	>	//have to call addInteractionPairs explicitly here. A way to work
471	>	//around is that we can determine the beginning global indices of
472	>	//atoms before they get created.
473		SimInfo::MoleculeIterator mi;
474		Molecule* mol;
475		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
476	<	info->addExcludePairs(mol);
476	>	info->addInteractionPairs(mol);
477		}
478
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
479		if (loadInitCoords)
480	<	loadCoordinates(info);
186	<
480	>	loadCoordinates(info, mdFileName);
481		return info;
482		}
483
484		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
485
486	<	//figure out the ouput file names
486	>	//figure out the output file names
487		std::string prefix;
488
489		#ifdef IS_MPI
#	Line 218 | Line 512 | namespace oopse {
512
513		#ifdef IS_MPI
514		void SimCreator::divideMolecules(SimInfo *info) {
515	<	double numerator;
222	<	double denominator;
223	<	double precast;
224	<	double x;
225	<	double y;
226	<	double a;
227	<	int old_atoms;
228	<	int add_atoms;
229	<	int new_atoms;
230	<	int nTarget;
231	<	int done;
232	<	int i;
233	<	int j;
234	<	int loops;
235	<	int which_proc;
515	>	RealType a;
516		int nProcessors;
517		std::vector<int> atomsPerProc;
518		int nGlobalMols = info->getNGlobalMolecules();
519	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
519	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
520	>	// error
521	>	// condition:
522
523	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
523	>	nProcessors = MPI::COMM_WORLD.Get_size();
524
525		if (nProcessors > nGlobalMols) {
526		sprintf(painCave.errMsg,
#	Line 247 | Line 529 | namespace oopse {
529		"\tthe number of molecules.  This will not result in a \n"
530		"\tusable division of atoms for force decomposition.\n"
531		"\tEither try a smaller number of processors, or run the\n"
532	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
532	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
533	>	nGlobalMols);
534
535		painCave.isFatal = 1;
536		simError();
537		}
538
256	–	int seedValue;
539		Globals * simParams = info->getSimParams();
540	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
540	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
541	>	//random number generator
542		if (simParams->haveSeed()) {
543	<	seedValue = simParams->getSeed();
543	>	int seedValue = simParams->getSeed();
544		myRandom = new SeqRandNumGen(seedValue);
545		}else {
546		myRandom = new SeqRandNumGen();
#	Line 270 | Line 553 | namespace oopse {
553		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
554
555		if (worldRank == 0) {
556	<	numerator = info->getNGlobalAtoms();
557	<	denominator = nProcessors;
558	<	precast = numerator / denominator;
559	<	nTarget = (int)(precast + 0.5);
556	>	RealType numerator = info->getNGlobalAtoms();
557	>	RealType denominator = nProcessors;
558	>	RealType precast = numerator / denominator;
559	>	int nTarget = (int)(precast + 0.5);
560
561	<	for(i = 0; i < nGlobalMols; i++) {
562	<	done = 0;
563	<	loops = 0;
561	>	for(int i = 0; i < nGlobalMols; i++) {
562	>
563	>	int done = 0;
564	>	int loops = 0;
565
566		while (!done) {
567		loops++;
568
569		// Pick a processor at random
570
571	<	which_proc = (int) (myRandom->rand() * nProcessors);
571	>	int which_proc = (int) (myRandom->rand() * nProcessors);
572
573		//get the molecule stamp first
574		int stampId = info->getMoleculeStampId(i);
575		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
576
577		// How many atoms does this processor have so far?
578	<	old_atoms = atomsPerProc[which_proc];
579	<	add_atoms = moleculeStamp->getNAtoms();
580	<	new_atoms = old_atoms + add_atoms;
578	>	int old_atoms = atomsPerProc[which_proc];
579	>	int add_atoms = moleculeStamp->getNAtoms();
580	>	int new_atoms = old_atoms + add_atoms;
581
582		// If we've been through this loop too many times, we need
583		// to just give up and assign the molecule to this processor
584		// and be done with it.
585
586		if (loops > 100) {
587	+
588		sprintf(painCave.errMsg,
589	<	"I've tried 100 times to assign molecule %d to a "
590	<	" processor, but can't find a good spot.\n"
591	<	"I'm assigning it at random to processor %d.\n",
589	>	"There have been 100 attempts to assign molecule %d to an\n"
590	>	"\tunderworked processor, but there's no good place to\n"
591	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
592		i, which_proc);
593	<
593	>
594		painCave.isFatal = 0;
595	+	painCave.severity = OPENMD_INFO;
596		simError();
597
598		molToProcMap[i] = which_proc;
#	Line 335 | Line 621 | namespace oopse {
621		//           Pacc(x) = exp(- a * x)
622		// where a = penalty / (average atoms per molecule)
623
624	<	x = (double)(new_atoms - nTarget);
625	<	y = myRandom->rand();
624	>	RealType x = (RealType)(new_atoms - nTarget);
625	>	RealType y = myRandom->rand();
626
627		if (y < exp(- a * x)) {
628		molToProcMap[i] = which_proc;
#	Line 351 | Line 637 | namespace oopse {
637		}
638
639		delete myRandom;
640	<
640	>
641		// Spray out this nonsense to all other processors:
642	<
357	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
642	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
643		} else {
644
645		// Listen to your marching orders from processor 0:
646	<
647	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
646	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
647	>
648		}
649
650		info->setMolToProcMap(molToProcMap);
651		sprintf(checkPointMsg,
652		"Successfully divided the molecules among the processors.\n");
653	<	MPIcheckPoint();
653	>	errorCheckPoint();
654		}
655
656		#endif
#	Line 382 | Line 667 | namespace oopse {
667		#endif
668
669		stampId = info->getMoleculeStampId(i);
670	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
671	<	stampId, i, info->getLocalIndexManager());
670	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
671	>	info->getMoleculeStamp(stampId),
672	>	stampId, i,
673	>	info->getLocalIndexManager());
674
675		info->addMolecule(mol);
676
#	Line 395 | Line 682 | namespace oopse {
682
683		} //end for(int i=0)
684		}
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();
685
686	<	if (!simParams->haveNMol()) {
687	<	// we don't have the total number of molecules, so we assume it is
688	<	// given in each component
689	<
690	<	for(i = 0; i < n_components; i++) {
691	<	if (!the_components[i]->haveNMol()) {
692	<	// we have a problem
693	<	sprintf(painCave.errMsg,
694	<	"SimCreator Error. No global NMol or component NMol given.\n"
695	<	"\tCannot calculate the number of atoms.\n");
696	<
697	<	painCave.isFatal = 1;
698	<	simError();
699	<	}
700	<
701	<	id = the_components[i]->getType();
702	<
703	<	extractedStamp = stamps->extractMolStamp(id);
704	<	if (extractedStamp == NULL) {
705	<	sprintf(painCave.errMsg,
706	<	"SimCreator error: Component \"%s\" was not found in the "
707	<	"list of declared molecules\n", id);
708	<
709	<	painCave.isFatal = 1;
710	<	simError();
711	<	}
712	<
713	<	currentStamp = extractedStamp->getStamp();
714	<
715	<
716	<	moleculeStampPairs.push_back(
717	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
718	<	} //end for (i = 0; i < n_components; i++)
719	<	} else {
720	<	sprintf(painCave.errMsg, "SimSetup error.\n"
721	<	"\tSorry, the ability to specify total"
722	<	" nMols and then give molfractions in the components\n"
723	<	"\tis not currently supported."
724	<	" Please give nMol in the components.\n");
725	<
726	<	painCave.isFatal = 1;
727	<	simError();
686	>	int SimCreator::computeStorageLayout(SimInfo* info) {
687	>
688	>	Globals* simParams = info->getSimParams();
689	>	int nRigidBodies = info->getNGlobalRigidBodies();
690	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
691	>	set<AtomType*>::iterator i;
692	>	bool hasDirectionalAtoms = false;
693	>	bool hasFixedCharge = false;
694	>	bool hasDipoles = false;
695	>	bool hasQuadrupoles = false;
696	>	bool hasPolarizable = false;
697	>	bool hasFluctuatingCharge = false;
698	>	bool hasMetallic = false;
699	>	int storageLayout = 0;
700	>	storageLayout |= DataStorage::dslPosition;
701	>	storageLayout |= DataStorage::dslVelocity;
702	>	storageLayout |= DataStorage::dslForce;
703	>
704	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
705	>
706	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
707	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
708	>	EAMAdapter ea = EAMAdapter( (*i) );
709	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
710	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
711	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
712	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
713	>
714	>	if (da.isDirectional()){
715	>	hasDirectionalAtoms = true;
716	>	}
717	>	if (ma.isDipole()){
718	>	hasDipoles = true;
719	>	}
720	>	if (ma.isQuadrupole()){
721	>	hasQuadrupoles = true;
722	>	}
723	>	if (ea.isEAM() || sca.isSuttonChen()){
724	>	hasMetallic = true;
725	>	}
726	>	if ( fca.isFixedCharge() ){
727	>	hasFixedCharge = true;
728	>	}
729	>	if ( fqa.isFluctuatingCharge() ){
730	>	hasFluctuatingCharge = true;
731	>	}
732	>	if ( pa.isPolarizable() ){
733	>	hasPolarizable = true;
734	>	}
735		}
736
737	<	#ifdef IS_MPI
737	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
738	>	storageLayout |= DataStorage::dslAmat;
739	>	if(storageLayout & DataStorage::dslVelocity) {
740	>	storageLayout |= DataStorage::dslAngularMomentum;
741	>	}
742	>	if (storageLayout & DataStorage::dslForce) {
743	>	storageLayout |= DataStorage::dslTorque;
744	>	}
745	>	}
746	>	if (hasDipoles) {
747	>	storageLayout |= DataStorage::dslDipole;
748	>	}
749	>	if (hasQuadrupoles) {
750	>	storageLayout |= DataStorage::dslQuadrupole;
751	>	}
752	>	if (hasFixedCharge || hasFluctuatingCharge) {
753	>	storageLayout |= DataStorage::dslSkippedCharge;
754	>	}
755	>	if (hasMetallic) {
756	>	storageLayout |= DataStorage::dslDensity;
757	>	storageLayout |= DataStorage::dslFunctional;
758	>	storageLayout |= DataStorage::dslFunctionalDerivative;
759	>	}
760	>	if (hasPolarizable) {
761	>	storageLayout |= DataStorage::dslElectricField;
762	>	}
763	>	if (hasFluctuatingCharge){
764	>	storageLayout |= DataStorage::dslFlucQPosition;
765	>	if(storageLayout & DataStorage::dslVelocity) {
766	>	storageLayout |= DataStorage::dslFlucQVelocity;
767	>	}
768	>	if (storageLayout & DataStorage::dslForce) {
769	>	storageLayout |= DataStorage::dslFlucQForce;
770	>	}
771	>	}
772
773	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
774	<	MPIcheckPoint();
775	<
776	<	#endif // is_mpi
777	<
773	>	// if the user has asked for them, make sure we've got the memory for the
774	>	// objects defined.
775	>
776	>	if (simParams->getOutputParticlePotential()) {
777	>	storageLayout |= DataStorage::dslParticlePot;
778	>	}
779	>
780	>	if (simParams->havePrintHeatFlux()) {
781	>	if (simParams->getPrintHeatFlux()) {
782	>	storageLayout |= DataStorage::dslParticlePot;
783	>	}
784	>	}
785	>
786	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
787	>	storageLayout |= DataStorage::dslElectricField;
788	>	}
789	>
790	>	if (simParams->getOutputFluctuatingCharges()) {
791	>	storageLayout |= DataStorage::dslFlucQPosition;
792	>	storageLayout |= DataStorage::dslFlucQVelocity;
793	>	storageLayout |= DataStorage::dslFlucQForce;
794	>	}
795	>
796	>	info->setStorageLayout(storageLayout);
797	>
798	>	return storageLayout;
799		}
800	<
800	>
801		void SimCreator::setGlobalIndex(SimInfo *info) {
802		SimInfo::MoleculeIterator mi;
803		Molecule::AtomIterator ai;
804		Molecule::RigidBodyIterator ri;
805		Molecule::CutoffGroupIterator ci;
806	+	Molecule::IntegrableObjectIterator  ioi;
807		Molecule * mol;
808		Atom * atom;
809		RigidBody * rb;
#	Line 471 | Line 812 | namespace oopse {
812		int beginRigidBodyIndex;
813		int beginCutoffGroupIndex;
814		int nGlobalAtoms = info->getNGlobalAtoms();
815	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
816
475	–	#ifndef IS_MPI
476	–
817		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	–
818		//rigidbody's index begins right after atom's
819	<	beginRigidBodyIndex += info->getNGlobalAtoms();
820	<
821	<	for(mol = info->beginMolecule(mi); mol != NULL;
822	<	mol = info->nextMolecule(mi)) {
819	>	beginRigidBodyIndex = info->getNGlobalAtoms();
820	>	beginCutoffGroupIndex = 0;
821	>
822	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
823
824	<	//local index(index in DataStorge) of atom is important
825	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
826	<	atom->setGlobalIndex(beginAtomIndex++);
824	>	#ifdef IS_MPI
825	>	if (info->getMolToProc(i) == worldRank) {
826	>	#endif
827	>	// stuff to do if I own this molecule
828	>	mol = info->getMoleculeByGlobalIndex(i);
829	>
830	>	//local index(index in DataStorge) of atom is important
831	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
832	>	atom->setGlobalIndex(beginAtomIndex++);
833	>	}
834	>
835	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
836	>	rb = mol->nextRigidBody(ri)) {
837	>	rb->setGlobalIndex(beginRigidBodyIndex++);
838	>	}
839	>
840	>	//local index of cutoff group is trivial, it only depends on
841	>	//the order of travesing
842	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
843	>	cg = mol->nextCutoffGroup(ci)) {
844	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
845	>	}
846	>
847	>	#ifdef IS_MPI
848	>	}  else {
849	>
850	>	// stuff to do if I don't own this molecule
851	>
852	>	int stampId = info->getMoleculeStampId(i);
853	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
854	>
855	>	beginAtomIndex += stamp->getNAtoms();
856	>	beginRigidBodyIndex += stamp->getNRigidBodies();
857	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
858		}
859	<
860	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
861	<	rb = mol->nextRigidBody(ri)) {
862	<	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	<
859	>	#endif
860	>
861	>	} //end for(int i=0)
862	>
863		//fill globalGroupMembership
864		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
865		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 551 | Line 871 | namespace oopse {
871
872		}
873		}
874	<
874	>
875		#ifdef IS_MPI
876		// Since the globalGroupMembership has been zero filled and we've only
877		// poked values into the atoms we know, we can do an Allreduce
878		// to get the full globalGroupMembership array (We think).
879		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
880		// docs said we could.
881	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
882	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
883	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
881	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
882	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
883	>	&tmpGroupMembership[0], nGlobalAtoms,
884	>	MPI::INT, MPI::SUM);
885		info->setGlobalGroupMembership(tmpGroupMembership);
886		#else
887		info->setGlobalGroupMembership(globalGroupMembership);
888		#endif
889
890		//fill molMembership
891	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
891	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
892	>	info->getNGlobalRigidBodies(), 0);
893
894	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
895	<
894	>	for(mol = info->beginMolecule(mi); mol != NULL;
895	>	mol = info->nextMolecule(mi)) {
896		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
898		}
899	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
900	+	rb = mol->nextRigidBody(ri)) {
901	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
902	+	}
903		}
904
905		#ifdef IS_MPI
906	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
906	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
907	>	info->getNGlobalRigidBodies(), 0);
908	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
909	>	nGlobalAtoms + nGlobalRigidBodies,
910	>	MPI::INT, MPI::SUM);
911
582	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
583	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
584	–
912		info->setGlobalMolMembership(tmpMolMembership);
913		#else
914		info->setGlobalMolMembership(globalMolMembership);
915		#endif
916	+
917	+	// nIOPerMol holds the number of integrable objects per molecule
918	+	// here the molecules are listed by their global indices.
919	+
920	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
921	+	for (mol = info->beginMolecule(mi); mol != NULL;
922	+	mol = info->nextMolecule(mi)) {
923	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
924	+	}
925
926	<	}
927	<
928	<	void SimCreator::loadCoordinates(SimInfo* info) {
929	<	Globals* simParams;
930	<	simParams = info->getSimParams();
926	>	#ifdef IS_MPI
927	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
928	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
929	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
930	>	#else
931	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
932	>	#endif
933	>
934	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
935
936	<	if (!simParams->haveInitialConfig()) {
937	<	sprintf(painCave.errMsg,
938	<	"Cannot intialize a simulation without an initial configuration file.\n");
939	<	painCave.isFatal = 1;;
600	<	simError();
936	>	int startingIndex = 0;
937	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
938	>	startingIOIndexForMol[i] = startingIndex;
939	>	startingIndex += numIntegrableObjectsPerMol[i];
940		}
941
942	<	DumpReader reader(info, simParams->getInitialConfig());
942	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
943	>	for (mol = info->beginMolecule(mi); mol != NULL;
944	>	mol = info->nextMolecule(mi)) {
945	>	int myGlobalIndex = mol->getGlobalIndex();
946	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
947	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
948	>	sd = mol->nextIntegrableObject(ioi)) {
949	>	sd->setGlobalIntegrableObjectIndex(globalIO);
950	>	IOIndexToIntegrableObject[globalIO] = sd;
951	>	globalIO++;
952	>	}
953	>	}
954	>
955	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
956	>
957	>	}
958	>
959	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
960	>
961	>	DumpReader reader(info, mdFileName);
962		int nframes = reader.getNFrames();
963
964		if (nframes > 0) {
#	Line 609 | Line 967 | namespace oopse {
967		//invalid initial coordinate file
968		sprintf(painCave.errMsg,
969		"Initial configuration file %s should at least contain one frame\n",
970	<	simParams->getInitialConfig());
970	>	mdFileName.c_str());
971		painCave.isFatal = 1;
972		simError();
973		}
616	–
974		//copy the current snapshot to previous snapshot
975		info->getSnapshotManager()->advance();
976		}
977
978	<	} //end namespace oopse
978	>	} //end namespace OpenMD
979
980

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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