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 1782 by gezelter, Wed Aug 22 02:28:28 2012 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		/**
#	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	>	int commStatus;
104	>	if (worldRank == masterNode) {
105	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
106	>	#endif
107	>	SimplePreprocessor preprocessor;
108	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
109	>
110	>	#ifdef IS_MPI
111	>	//brocasting the stream size
112	>	streamSize = ppStream.str().size() +1;
113	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
114	>
115	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
116	>
117	>
118	>	} else {
119	>
120	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121	>
122	>	//get stream size
123	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124	>
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127	>
128	>	//receive file content
129	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
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;
260	>	int mdFileVersion;
261	>
262	>	#ifdef IS_MPI
263	>	const int masterNode = 0;
264	>	if (worldRank == masterNode) {
265	>	#endif
266	>
267	>	std::ifstream mdFile_(mdFileName.c_str());
268	>
269	>	if (mdFile_.fail()) {
270	>	sprintf(painCave.errMsg,
271	>	"SimCreator: Cannot open file: %s\n",
272	>	mdFileName.c_str());
273	>	painCave.isFatal = 1;
274	>	simError();
275	>	}
276	>
277	>	mdFile_.getline(buffer, bufferSize);
278	>	++lineNo;
279	>	std::string line = trimLeftCopy(buffer);
280	>	i = CaseInsensitiveFind(line, "<OpenMD");
281	>	if (static_cast<size_t>(i) == string::npos) {
282	>	// try the older file strings to see if that works:
283	>	i = CaseInsensitiveFind(line, "<OOPSE");
284	>	}
285	>
286	>	if (static_cast<size_t>(i) == string::npos) {
287	>	// still no luck!
288	>	sprintf(painCave.errMsg,
289	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
290	>	mdFileName.c_str());
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294	>
295	>	// found the correct opening string, now try to get the file
296	>	// format version number.
297	>
298	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
299	>	std::string fileType = tokenizer.nextToken();
300	>	toUpper(fileType);
301	>
302	>	mdFileVersion = 0;
303	>
304	>	if (fileType == "OPENMD") {
305	>	while (tokenizer.hasMoreTokens()) {
306	>	std::string token(tokenizer.nextToken());
307	>	toUpper(token);
308	>	if (token == "VERSION") {
309	>	mdFileVersion = tokenizer.nextTokenAsInt();
310	>	break;
311	>	}
312	>	}
313	>	}
314	>
315	>	//scan through the input stream and find MetaData tag
316	>	while(mdFile_.getline(buffer, bufferSize)) {
317	>	++lineNo;
318	>
319	>	std::string line = trimLeftCopy(buffer);
320	>	if (metaDataBlockStart == -1) {
321	>	i = CaseInsensitiveFind(line, "<MetaData>");
322	>	if (i != string::npos) {
323	>	metaDataBlockStart = lineNo;
324	>	mdOffset = mdFile_.tellg();
325	>	}
326	>	} else {
327	>	i = CaseInsensitiveFind(line, "</MetaData>");
328	>	if (i != string::npos) {
329	>	metaDataBlockEnd = lineNo;
330	>	}
331	>	}
332	>	}
333	>
334	>	if (metaDataBlockStart == -1) {
335	>	sprintf(painCave.errMsg,
336	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
337	>	mdFileName.c_str());
338	>	painCave.isFatal = 1;
339	>	simError();
340	>	}
341	>	if (metaDataBlockEnd == -1) {
342	>	sprintf(painCave.errMsg,
343	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
344	>	mdFileName.c_str());
345	>	painCave.isFatal = 1;
346	>	simError();
347	>	}
348	>
349	>	mdFile_.clear();
350	>	mdFile_.seekg(0);
351	>	mdFile_.seekg(mdOffset);
352	>
353	>	mdRawData.clear();
354	>
355	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
356	>	mdFile_.getline(buffer, bufferSize);
357	>	mdRawData += buffer;
358	>	mdRawData += "\n";
359	>	}
360	>
361	>	mdFile_.close();
362	>
363	>	#ifdef IS_MPI
364	>	}
365	>	#endif
366	>
367	>	std::stringstream rawMetaDataStream(mdRawData);
368	>
369		//parse meta-data file
370	<	parseFile(mdFileName, stamps, simParams);
370	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
371	>	metaDataBlockStart + 1);
372
373		//create the force field
374	<	ForceField * ff = ForceFieldFactory::getInstance()
375	<	->createForceField(simParams->getForceField());
111	<
374	>	ForceField * ff = new ForceField(simParams->getForceField());
375	>
376		if (ff == NULL) {
377		sprintf(painCave.errMsg,
378		"ForceField Factory can not create %s force field\n",
#	Line 141 | Line 405 | namespace oopse {
405		}
406
407		ff->parse(forcefieldFileName);
144	–
145	–	//extract the molecule stamps
146	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
147	–	compList(stamps, simParams, moleculeStampPairs);
148	–
408		//create SimInfo
409	<	SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
409	>	SimInfo * info = new SimInfo(ff, simParams);
410	>
411	>	info->setRawMetaData(mdRawData);
412
413	<	//gather parameters (SimCreator only retrieves part of the parameters)
413	>	//gather parameters (SimCreator only retrieves part of the
414	>	//parameters)
415		gatherParameters(info, mdFileName);
416
417		//divide the molecules and determine the global index of molecules
#	Line 160 | Line 422 | namespace oopse {
422		//create the molecules
423		createMolecules(info);
424
425	+	//find the storage layout
426	+
427	+	int storageLayout = computeStorageLayout(info);
428	+
429	+	//allocate memory for DataStorage(circular reference, need to
430	+	//break it)
431	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
432
433	<	//allocate memory for DataStorage(circular reference, need to break it)
434	<	info->setSnapshotManager(new SimSnapshotManager(info));
435	<
436	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
437	<	//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.
433	>	//set the global index of atoms, rigidbodies and cutoffgroups
434	>	//(only need to be set once, the global index will never change
435	>	//again). Local indices of atoms and rigidbodies are already set
436	>	//by MoleculeCreator class which actually delegates the
437	>	//responsibility to LocalIndexManager.
438		setGlobalIndex(info);
439
440	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
441	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
442	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
443	<	//we can determine the beginning global indices of atoms before they get created.
440	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
441	>	//method, at that point atoms don't have the global index yet
442	>	//(their global index are all initialized to -1).  Therefore we
443	>	//have to call addInteractionPairs explicitly here. A way to work
444	>	//around is that we can determine the beginning global indices of
445	>	//atoms before they get created.
446		SimInfo::MoleculeIterator mi;
447		Molecule* mol;
448		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
449	<	info->addExcludePairs(mol);
449	>	info->addInteractionPairs(mol);
450		}
451
452		if (loadInitCoords)
453	<	loadCoordinates(info);
184	<
453	>	loadCoordinates(info, mdFileName);
454		return info;
455		}
456
457		void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
458
459	<	//figure out the ouput file names
459	>	//figure out the output file names
460		std::string prefix;
461
462		#ifdef IS_MPI
#	Line 216 | Line 485 | namespace oopse {
485
486		#ifdef IS_MPI
487		void SimCreator::divideMolecules(SimInfo *info) {
488	<	double numerator;
489	<	double denominator;
490	<	double precast;
491	<	double x;
492	<	double y;
493	<	double a;
488	>	RealType numerator;
489	>	RealType denominator;
490	>	RealType precast;
491	>	RealType x;
492	>	RealType y;
493	>	RealType a;
494		int old_atoms;
495		int add_atoms;
496		int new_atoms;
#	Line 245 | Line 514 | namespace oopse {
514		"\tthe number of molecules.  This will not result in a \n"
515		"\tusable division of atoms for force decomposition.\n"
516		"\tEither try a smaller number of processors, or run the\n"
517	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
517	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
518
519		painCave.isFatal = 1;
520		simError();
#	Line 333 | Line 602 | namespace oopse {
602		//           Pacc(x) = exp(- a * x)
603		// where a = penalty / (average atoms per molecule)
604
605	<	x = (double)(new_atoms - nTarget);
605	>	x = (RealType)(new_atoms - nTarget);
606		y = myRandom->rand();
607
608		if (y < exp(- a * x)) {
#	Line 363 | Line 632 | namespace oopse {
632		info->setMolToProcMap(molToProcMap);
633		sprintf(checkPointMsg,
634		"Successfully divided the molecules among the processors.\n");
635	<	MPIcheckPoint();
635	>	errorCheckPoint();
636		}
637
638		#endif
#	Line 380 | Line 649 | namespace oopse {
649		#endif
650
651		stampId = info->getMoleculeStampId(i);
652	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
653	<	stampId, i, info->getLocalIndexManager());
652	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
653	>	info->getMoleculeStamp(stampId),
654	>	stampId, i,
655	>	info->getLocalIndexManager());
656
657		info->addMolecule(mol);
658
#	Line 393 | Line 664 | namespace oopse {
664
665		} //end for(int i=0)
666		}
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();
667
668	<	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();
668	>	int SimCreator::computeStorageLayout(SimInfo* info) {
669
670	<	currentStamp = stamps->getMolStamp(id);
671	<	if (currentStamp == NULL) {
672	<	sprintf(painCave.errMsg,
673	<	"SimCreator error: Component \"%s\" was not found in the "
674	<	"list of declared molecules\n", id);
675	<
676	<	painCave.isFatal = 1;
677	<	simError();
678	<	}
679	<
680	<	moleculeStampPairs.push_back(
681	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
682	<	} //end for (i = 0; i < n_components; i++)
683	<	} else {
684	<	sprintf(painCave.errMsg, "SimSetup error.\n"
685	<	"\tSorry, the ability to specify total"
686	<	" nMols and then give molfractions in the components\n"
687	<	"\tis not currently supported."
688	<	" Please give nMol in the components.\n");
689	<
690	<	painCave.isFatal = 1;
691	<	simError();
670	>	Globals* simParams = info->getSimParams();
671	>	int nRigidBodies = info->getNGlobalRigidBodies();
672	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
673	>	set<AtomType*>::iterator i;
674	>	bool hasDirectionalAtoms = false;
675	>	bool hasFixedCharge = false;
676	>	bool hasMultipoles = false;
677	>	bool hasPolarizable = false;
678	>	bool hasFluctuatingCharge = false;
679	>	bool hasMetallic = false;
680	>	int storageLayout = 0;
681	>	storageLayout |= DataStorage::dslPosition;
682	>	storageLayout |= DataStorage::dslVelocity;
683	>	storageLayout |= DataStorage::dslForce;
684	>
685	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
686	>
687	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
688	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
689	>	EAMAdapter ea = EAMAdapter( (*i) );
690	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
691	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
692	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
693	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
694	>
695	>	if (da.isDirectional()){
696	>	hasDirectionalAtoms = true;
697	>	}
698	>	if (ma.isMultipole()){
699	>	hasMultipoles = true;
700	>	}
701	>	if (ea.isEAM() || sca.isSuttonChen()){
702	>	hasMetallic = true;
703	>	}
704	>	if ( fca.isFixedCharge() ){
705	>	hasFixedCharge = true;
706	>	}
707	>	if ( fqa.isFluctuatingCharge() ){
708	>	hasFluctuatingCharge = true;
709	>	}
710	>	if ( pa.isPolarizable() ){
711	>	hasPolarizable = true;
712	>	}
713		}
714
715	<	#ifdef IS_MPI
715	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
716	>	storageLayout |= DataStorage::dslAmat;
717	>	if(storageLayout & DataStorage::dslVelocity) {
718	>	storageLayout |= DataStorage::dslAngularMomentum;
719	>	}
720	>	if (storageLayout & DataStorage::dslForce) {
721	>	storageLayout |= DataStorage::dslTorque;
722	>	}
723	>	}
724	>	if (hasMultipoles) {
725	>	storageLayout |= DataStorage::dslElectroFrame;
726	>	}
727	>	if (hasFixedCharge || hasFluctuatingCharge) {
728	>	storageLayout |= DataStorage::dslSkippedCharge;
729	>	}
730	>	if (hasMetallic) {
731	>	storageLayout |= DataStorage::dslDensity;
732	>	storageLayout |= DataStorage::dslFunctional;
733	>	storageLayout |= DataStorage::dslFunctionalDerivative;
734	>	}
735	>	if (hasPolarizable) {
736	>	storageLayout |= DataStorage::dslElectricField;
737	>	}
738	>	if (hasFluctuatingCharge){
739	>	storageLayout |= DataStorage::dslFlucQPosition;
740	>	if(storageLayout & DataStorage::dslVelocity) {
741	>	storageLayout |= DataStorage::dslFlucQVelocity;
742	>	}
743	>	if (storageLayout & DataStorage::dslForce) {
744	>	storageLayout |= DataStorage::dslFlucQForce;
745	>	}
746	>	}
747
748	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
749	<	MPIcheckPoint();
750	<
751	<	#endif // is_mpi
752	<
748	>	// if the user has asked for them, make sure we've got the memory for the
749	>	// objects defined.
750	>
751	>	if (simParams->getOutputParticlePotential()) {
752	>	storageLayout |= DataStorage::dslParticlePot;
753	>	}
754	>
755	>	if (simParams->havePrintHeatFlux()) {
756	>	if (simParams->getPrintHeatFlux()) {
757	>	storageLayout |= DataStorage::dslParticlePot;
758	>	}
759	>	}
760	>
761	>	if (simParams->getOutputElectricField()) {
762	>	storageLayout |= DataStorage::dslElectricField;
763	>	}
764	>	if (simParams->getOutputFluctuatingCharges()) {
765	>	storageLayout |= DataStorage::dslFlucQPosition;
766	>	storageLayout |= DataStorage::dslFlucQVelocity;
767	>	storageLayout |= DataStorage::dslFlucQForce;
768	>	}
769	>
770	>	return storageLayout;
771		}
772	<
772	>
773		void SimCreator::setGlobalIndex(SimInfo *info) {
774		SimInfo::MoleculeIterator mi;
775		Molecule::AtomIterator ai;
776		Molecule::RigidBodyIterator ri;
777		Molecule::CutoffGroupIterator ci;
778	+	Molecule::IntegrableObjectIterator  ioi;
779		Molecule * mol;
780		Atom * atom;
781		RigidBody * rb;
#	Line 466 | Line 785 | namespace oopse {
785		int beginCutoffGroupIndex;
786		int nGlobalAtoms = info->getNGlobalAtoms();
787
469	–	#ifndef IS_MPI
470	–
788		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	–
789		//rigidbody's index begins right after atom's
790	<	beginRigidBodyIndex += info->getNGlobalAtoms();
791	<
792	<	for(mol = info->beginMolecule(mi); mol != NULL;
793	<	mol = info->nextMolecule(mi)) {
790	>	beginRigidBodyIndex = info->getNGlobalAtoms();
791	>	beginCutoffGroupIndex = 0;
792	>
793	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
794
795	<	//local index(index in DataStorge) of atom is important
796	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
797	<	atom->setGlobalIndex(beginAtomIndex++);
795	>	#ifdef IS_MPI
796	>	if (info->getMolToProc(i) == worldRank) {
797	>	#endif
798	>	// stuff to do if I own this molecule
799	>	mol = info->getMoleculeByGlobalIndex(i);
800	>
801	>	//local index(index in DataStorge) of atom is important
802	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
803	>	atom->setGlobalIndex(beginAtomIndex++);
804	>	}
805	>
806	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
807	>	rb = mol->nextRigidBody(ri)) {
808	>	rb->setGlobalIndex(beginRigidBodyIndex++);
809	>	}
810	>
811	>	//local index of cutoff group is trivial, it only depends on
812	>	//the order of travesing
813	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
814	>	cg = mol->nextCutoffGroup(ci)) {
815	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
816	>	}
817	>
818	>	#ifdef IS_MPI
819	>	}  else {
820	>
821	>	// stuff to do if I don't own this molecule
822	>
823	>	int stampId = info->getMoleculeStampId(i);
824	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
825	>
826	>	beginAtomIndex += stamp->getNAtoms();
827	>	beginRigidBodyIndex += stamp->getNRigidBodies();
828	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
829		}
830	<
831	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
832	<	rb = mol->nextRigidBody(ri)) {
833	<	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	<
830	>	#endif
831	>
832	>	} //end for(int i=0)
833	>
834		//fill globalGroupMembership
835		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
836		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 545 | Line 842 | namespace oopse {
842
843		}
844		}
845	<
845	>
846		#ifdef IS_MPI
847		// Since the globalGroupMembership has been zero filled and we've only
848		// poked values into the atoms we know, we can do an Allreduce
849		// to get the full globalGroupMembership array (We think).
850		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
851		// docs said we could.
852	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
852	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
853		MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
854		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
855		info->setGlobalGroupMembership(tmpGroupMembership);
#	Line 564 | Line 861 | namespace oopse {
861		std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
862
863		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
567	–
864		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
865		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
866		}
867		}
868
869		#ifdef IS_MPI
870	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
870	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
871
872		MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
873		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#	Line 580 | Line 876 | namespace oopse {
876		#else
877		info->setGlobalMolMembership(globalMolMembership);
878		#endif
879	+
880	+	// nIOPerMol holds the number of integrable objects per molecule
881	+	// here the molecules are listed by their global indices.
882	+
883	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
884	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
885	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
886	+	}
887
888	+	#ifdef IS_MPI
889	+	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
890	+	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
891	+	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
892	+	#else
893	+	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
894	+	#endif
895	+
896	+	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
897	+
898	+	int startingIndex = 0;
899	+	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
900	+	startingIOIndexForMol[i] = startingIndex;
901	+	startingIndex += numIntegrableObjectsPerMol[i];
902	+	}
903	+
904	+	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
905	+	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
906	+	int myGlobalIndex = mol->getGlobalIndex();
907	+	int globalIO = startingIOIndexForMol[myGlobalIndex];
908	+	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
909	+	sd = mol->nextIntegrableObject(ioi)) {
910	+	sd->setGlobalIntegrableObjectIndex(globalIO);
911	+	IOIndexToIntegrableObject[globalIO] = sd;
912	+	globalIO++;
913	+	}
914	+	}
915	+
916	+	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
917	+
918		}
919
920	<	void SimCreator::loadCoordinates(SimInfo* info) {
920	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
921		Globals* simParams;
922	+
923		simParams = info->getSimParams();
924
925	<	if (!simParams->haveInitialConfig()) {
591	<	sprintf(painCave.errMsg,
592	<	"Cannot intialize a simulation without an initial configuration file.\n");
593	<	painCave.isFatal = 1;;
594	<	simError();
595	<	}
596	<
597	<	DumpReader reader(info, simParams->getInitialConfig());
925	>	DumpReader reader(info, mdFileName);
926		int nframes = reader.getNFrames();
927	<
927	>
928		if (nframes > 0) {
929		reader.readFrame(nframes - 1);
930		} else {
931		//invalid initial coordinate file
932		sprintf(painCave.errMsg,
933		"Initial configuration file %s should at least contain one frame\n",
934	<	simParams->getInitialConfig().c_str());
934	>	mdFileName.c_str());
935		painCave.isFatal = 1;
936		simError();
937		}
610	–
938		//copy the current snapshot to previous snapshot
939		info->getSnapshotManager()->advance();
940		}
941
942	<	} //end namespace oopse
942	>	} //end namespace OpenMD
943
944

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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

Diff Legend

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