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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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
50	–	#include <sprng.h>
51	–
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"
57	<	#include "UseTheForce/ForceFieldFactory.hpp"
59	>	#include "brains/ForceField.hpp"
60		#include "utils/simError.h"
61		#include "utils/StringUtils.hpp"
62	<	#ifdef IS_MPI
63	<	#include "io/mpiBASS.h"
64	<	#include "math/randomSPRNG.hpp"
65	<	#endif
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	<	namespace oopse {
74	>	#include "antlr/MismatchedCharException.hpp"
75	>	#include "antlr/MismatchedTokenException.hpp"
76	>	#include "antlr/NoViableAltForCharException.hpp"
77	>	#include "antlr/NoViableAltException.hpp"
78
79	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
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 "mpi.h"
89	+	#include "math/ParallelRandNumGen.hpp"
90	+	#endif
91
92	<	if (worldRank == 0) {
93	<	#endif // is_mpi
92	>	namespace OpenMD {
93	>
94	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95	>	Globals* simParams = NULL;
96	>	try {
97
98	<	simParams->initalize();
99	<	set_interface_stamps(stamps, simParams);
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	<	#ifdef IS_MPI
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	<	mpiEventInit();
120	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121
122	<	#endif
122	>	//get stream size
123	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124
125	<	yacc_BASS(mdFileName.c_str());
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	<	#ifdef IS_MPI
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	>	// Create a parser that reads from the scanner
142	>	MDParser parser(lexer);
143	>	parser.setFilename(filename);
144
145	<	throwMPIEvent(NULL);
146	<	} else {
147	<	set_interface_stamps(stamps, simParams);
148	<	mpiEventInit();
149	<	MPIcheckPoint();
150	<	mpiEventLoop();
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	>	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	<	#endif
163	>
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	>	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	>	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	<	}
246	<
247	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
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();
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
103	–	Globals * simParams = new Globals();
262
263	<	//parse meta-data file
264	<	parseFile(mdFileName, stamps, simParams);
263	>	#ifdef IS_MPI
264	>	const int masterNode = 0;
265	>	if (worldRank == masterNode) {
266	>	#endif
267
268	<	//create the force field
269	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
270	<	simParams->getForceField());
271	<
272	<	if (ff == NULL) {
273	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
274	<	simParams->getForceField());
275	<	painCave.isFatal = 1;
276	<	simError();
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	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373	+	metaDataBlockStart + 1);
374	+
375	+	//create the force field
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",
381	+	simParams->getForceField().c_str());
382	+	painCave.isFatal = 1;
383	+	simError();
384	+	}
385	+
386		if (simParams->haveForceFieldFileName()) {
387	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
387	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
388		}
389
390		std::string forcefieldFileName;
391		forcefieldFileName = ff->getForceFieldFileName();
392	<
392	>
393		if (simParams->haveForceFieldVariant()) {
394	<	//If the force field has variant, the variant force field name will be
395	<	//Base.variant.frc. For exampel EAM.u6.frc
396	<
397	<	std::string variant = simParams->getForceFieldVariant();
398	<
399	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
400	<	variant = "." + variant;
401	<	if (pos != std::string::npos) {
402	<	forcefieldFileName.insert(pos, variant);
403	<	} else {
404	<	//If the default force field file name does not containt .frc suffix, just append the .variant
405	<	forcefieldFileName.append(variant);
406	<	}
394	>	//If the force field has variant, the variant force field name will be
395	>	//Base.variant.frc. For exampel EAM.u6.frc
396	>
397	>	std::string variant = simParams->getForceFieldVariant();
398	>
399	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
400	>	variant = "." + variant;
401	>	if (pos != std::string::npos) {
402	>	forcefieldFileName.insert(pos, variant);
403	>	} else {
404	>	//If the default force field file name does not containt .frc suffix, just append the .variant
405	>	forcefieldFileName.append(variant);
406	>	}
407		}
408
409		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
410		//create SimInfo
411	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
411	>	SimInfo * info = new SimInfo(ff, simParams);
412
413	<	//gather parameters (SimCreator only retrieves part of the parameters)
413	>	info->setRawMetaData(mdRawData);
414	>
415	>	//gather parameters (SimCreator only retrieves part of the
416	>	//parameters)
417		gatherParameters(info, mdFileName);
418	<
418	>
419		//divide the molecules and determine the global index of molecules
420		#ifdef IS_MPI
421		divideMolecules(info);
422		#endif
423	<
423	>
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 break it)
432	<	info->setSnapshotManager(new SimSnapshotManager(info));
431	>	//allocate memory for DataStorage(circular reference, need to
432	>	//break it)
433	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434
435	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
436	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
437	<	//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.
441	>
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
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
454		if (loadInitCoords)
455	<	loadCoordinates(info);
186	<
455	>	loadCoordinates(info, mdFileName);
456		return info;
457	<	}
458	<
459	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
460	<
461	<	//setup seed for random number generator
193	<	int seedValue;
194	<	Globals * simParams = info->getSimParams();
195	<
196	<	if (simParams->haveSeed()) {
197	<	seedValue = simParams->getSeed();
198	<
199	<	if (seedValue < 100000000 ) {
200	<	sprintf(painCave.errMsg,
201	<	"Seed for sprng library should contain at least 9 digits\n"
202	<	"OOPSE will generate a seed for user\n");
203	<
204	<	painCave.isFatal = 0;
205	<	simError();
206	<
207	<	//using seed generated by system instead of invalid seed set by user
208	<
209	<	#ifndef IS_MPI
210	<
211	<	seedValue = make_sprng_seed();
212	<
213	<	#else
214	<
215	<	if (worldRank == 0) {
216	<	seedValue = make_sprng_seed();
217	<	}
218	<
219	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
220	<
221	<	#endif
222	<
223	<	} //end if (seedValue /1000000000 == 0)
224	<	} else {
225	<
226	<	#ifndef IS_MPI
227	<
228	<	seedValue = make_sprng_seed();
229	<
230	<	#else
231	<
232	<	if (worldRank == 0) {
233	<	seedValue = make_sprng_seed();
234	<	}
235	<
236	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
237	<
238	<	#endif
239	<
240	<	} //end of simParams->haveSeed()
241	<
242	<	info->setSeed(seedValue);
243	<
244	<
245	<	//figure out the ouput file names
457	>	}
458	>
459	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
460	>
461	>	//figure out the output file names
462		std::string prefix;
463	<
463	>
464		#ifdef IS_MPI
465	<
465	>
466		if (worldRank == 0) {
467		#endif // is_mpi
468	<
469	<	if (simParams->haveFinalConfig()) {
470	<	prefix = getPrefix(simParams->getFinalConfig());
471	<	} else {
472	<	prefix = getPrefix(mdfile);
473	<	}
474	<
475	<	info->setFinalConfigFileName(prefix + ".eor");
476	<	info->setDumpFileName(prefix + ".dump");
477	<	info->setStatFileName(prefix + ".stat");
478	<
468	>	Globals * simParams = info->getSimParams();
469	>	if (simParams->haveFinalConfig()) {
470	>	prefix = getPrefix(simParams->getFinalConfig());
471	>	} else {
472	>	prefix = getPrefix(mdfile);
473	>	}
474	>
475	>	info->setFinalConfigFileName(prefix + ".eor");
476	>	info->setDumpFileName(prefix + ".dump");
477	>	info->setStatFileName(prefix + ".stat");
478	>	info->setRestFileName(prefix + ".zang");
479	>
480		#ifdef IS_MPI
481	<
481	>
482		}
483	<
483	>
484		#endif
485	<
486	<	}
487	<
485	>
486	>	}
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;
489	>	void SimCreator::divideMolecules(SimInfo *info) {
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;
#	Line 287 | Line 504 | void SimCreator::divideMolecules(SimInfo *info) {
504		int which_proc;
505		int nProcessors;
506		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
507		int nGlobalMols = info->getNGlobalMolecules();
508		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
509
510	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
511	<
510	>	nProcessors = MPI::COMM_WORLD.Get_size();
511	>
512		if (nProcessors > nGlobalMols) {
513	<	sprintf(painCave.errMsg,
514	<	"nProcessors (%d) > nMol (%d)\n"
515	<	"\tThe number of processors is larger than\n"
516	<	"\tthe number of molecules.  This will not result in a \n"
517	<	"\tusable division of atoms for force decomposition.\n"
518	<	"\tEither try a smaller number of processors, or run the\n"
519	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
520	<
521	<	painCave.isFatal = 1;
522	<	simError();
513	>	sprintf(painCave.errMsg,
514	>	"nProcessors (%d) > nMol (%d)\n"
515	>	"\tThe number of processors is larger than\n"
516	>	"\tthe number of molecules.  This will not result in a \n"
517	>	"\tusable division of atoms for force decomposition.\n"
518	>	"\tEither try a smaller number of processors, or run the\n"
519	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
520	>
521	>	painCave.isFatal = 1;
522	>	simError();
523		}
524	<
524	>
525	>	int seedValue;
526	>	Globals * simParams = info->getSimParams();
527	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
528	>	if (simParams->haveSeed()) {
529	>	seedValue = simParams->getSeed();
530	>	myRandom = new SeqRandNumGen(seedValue);
531	>	}else {
532	>	myRandom = new SeqRandNumGen();
533	>	}
534	>
535	>
536		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
537	<
537	>
538		//initialize atomsPerProc
539		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
540	<
540	>
541		if (worldRank == 0) {
542	<	numerator = info->getNGlobalAtoms();
543	<	denominator = nProcessors;
544	<	precast = numerator / denominator;
545	<	nTarget = (int)(precast + 0.5);
542	>	numerator = info->getNGlobalAtoms();
543	>	denominator = nProcessors;
544	>	precast = numerator / denominator;
545	>	nTarget = (int)(precast + 0.5);
546	>
547	>	for(i = 0; i < nGlobalMols; i++) {
548
549	<	for(i = 0; i < nGlobalMols; i++) {
550	<	done = 0;
551	<	loops = 0;
552	<
553	<	while (!done) {
554	<	loops++;
549	>	done = 0;
550	>	loops = 0;
551	>
552	>	while (!done) {
553	>	loops++;
554	>
555	>	// Pick a processor at random
556	>
557	>	which_proc = (int) (myRandom->rand() * nProcessors);
558	>
559	>	//get the molecule stamp first
560	>	int stampId = info->getMoleculeStampId(i);
561	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
562	>
563	>	// How many atoms does this processor have so far?
564	>	old_atoms = atomsPerProc[which_proc];
565	>	add_atoms = moleculeStamp->getNAtoms();
566	>	new_atoms = old_atoms + add_atoms;
567	>
568	>	// If we've been through this loop too many times, we need
569	>	// to just give up and assign the molecule to this processor
570	>	// and be done with it.
571	>
572	>	if (loops > 100) {
573
574	<	// Pick a processor at random
575	<
576	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
577	<
578	<	//get the molecule stamp first
579	<	int stampId = info->getMoleculeStampId(i);
580	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
581	<
582	<	// How many atoms does this processor have so far?
583	<	old_atoms = atomsPerProc[which_proc];
584	<	add_atoms = moleculeStamp->getNAtoms();
585	<	new_atoms = old_atoms + add_atoms;
586	<
587	<	// If we've been through this loop too many times, we need
588	<	// to just give up and assign the molecule to this processor
589	<	// and be done with it.
590	<
591	<	if (loops > 100) {
592	<	sprintf(painCave.errMsg,
593	<	"I've tried 100 times to assign molecule %d to a "
594	<	" processor, but can't find a good spot.\n"
595	<	"I'm assigning it at random to processor %d.\n",
596	<	i, which_proc);
597	<
598	<	painCave.isFatal = 0;
599	<	simError();
600	<
601	<	molToProcMap[i] = which_proc;
602	<	atomsPerProc[which_proc] += add_atoms;
603	<
604	<	done = 1;
605	<	continue;
606	<	}
607	<
608	<	// If we can add this molecule to this processor without sending
609	<	// it above nTarget, then go ahead and do it:
610	<
611	<	if (new_atoms <= nTarget) {
612	<	molToProcMap[i] = which_proc;
613	<	atomsPerProc[which_proc] += add_atoms;
614	<
615	<	done = 1;
616	<	continue;
617	<	}
618	<
619	<	// The only situation left is when new_atoms > nTarget.  We
620	<	// want to accept this with some probability that dies off the
621	<	// farther we are from nTarget
375	<
376	<	// roughly:  x = new_atoms - nTarget
377	<	//           Pacc(x) = exp(- a * x)
378	<	// where a = penalty / (average atoms per molecule)
379	<
380	<	x = (double)(new_atoms - nTarget);
381	<	y = myRandom.getRandom();
382	<
383	<	if (y < exp(- a * x)) {
384	<	molToProcMap[i] = which_proc;
385	<	atomsPerProc[which_proc] += add_atoms;
386	<
387	<	done = 1;
388	<	continue;
389	<	} else {
390	<	continue;
391	<	}
392	<	}
574	>	sprintf(painCave.errMsg,
575	>	"There have been 100 attempts to assign molecule %d to an\n"
576	>	"\tunderworked processor, but there's no good place to\n"
577	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
578	>	i, which_proc);
579	>
580	>	painCave.isFatal = 0;
581	>	painCave.severity = OPENMD_INFO;
582	>	simError();
583	>
584	>	molToProcMap[i] = which_proc;
585	>	atomsPerProc[which_proc] += add_atoms;
586	>
587	>	done = 1;
588	>	continue;
589	>	}
590	>
591	>	// If we can add this molecule to this processor without sending
592	>	// it above nTarget, then go ahead and do it:
593	>
594	>	if (new_atoms <= nTarget) {
595	>	molToProcMap[i] = which_proc;
596	>	atomsPerProc[which_proc] += add_atoms;
597	>
598	>	done = 1;
599	>	continue;
600	>	}
601	>
602	>	// The only situation left is when new_atoms > nTarget.  We
603	>	// want to accept this with some probability that dies off the
604	>	// farther we are from nTarget
605	>
606	>	// roughly:  x = new_atoms - nTarget
607	>	//           Pacc(x) = exp(- a * x)
608	>	// where a = penalty / (average atoms per molecule)
609	>
610	>	x = (RealType)(new_atoms - nTarget);
611	>	y = myRandom->rand();
612	>
613	>	if (y < exp(- a * x)) {
614	>	molToProcMap[i] = which_proc;
615	>	atomsPerProc[which_proc] += add_atoms;
616	>
617	>	done = 1;
618	>	continue;
619	>	} else {
620	>	continue;
621	>	}
622		}
623	+	}
624	+
625	+	delete myRandom;
626
627	<	// Spray out this nonsense to all other processors:
628	<
397	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
627	>	// Spray out this nonsense to all other processors:
628	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
629		} else {
630	+
631	+	// Listen to your marching orders from processor 0:
632	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
633
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
634		}
635	<
635	>
636		info->setMolToProcMap(molToProcMap);
637		sprintf(checkPointMsg,
638		"Successfully divided the molecules among the processors.\n");
639	<	MPIcheckPoint();
640	<	}
641	<
639	>	errorCheckPoint();
640	>	}
641	>
642		#endif
643	<
644	<	void SimCreator::createMolecules(SimInfo *info) {
643	>
644	>	void SimCreator::createMolecules(SimInfo *info) {
645		MoleculeCreator molCreator;
646		int stampId;
647	<
647	>
648		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
649	<
649	>
650		#ifdef IS_MPI
651	<
652	<	if (info->getMolToProc(i) == worldRank) {
651	>
652	>	if (info->getMolToProc(i) == worldRank) {
653		#endif
654	<
655	<	stampId = info->getMoleculeStampId(i);
656	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
657	<	stampId, i, info->getLocalIndexManager());
658	<
659	<	info->addMolecule(mol);
660	<
654	>
655	>	stampId = info->getMoleculeStampId(i);
656	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
657	>	info->getMoleculeStamp(stampId),
658	>	stampId, i,
659	>	info->getLocalIndexManager());
660	>
661	>	info->addMolecule(mol);
662	>
663		#ifdef IS_MPI
664	<
665	<	}
666	<
664	>
665	>	}
666	>
667		#endif
668	<
668	>
669		} //end for(int i=0)
670	<	}
670	>	}
671	>
672	>	int SimCreator::computeStorageLayout(SimInfo* info) {
673
674	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
675	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
676	<	int i;
677	<	char * id;
678	<	MoleculeStamp * currentStamp;
679	<	Component** the_components = simParams->getComponents();
680	<	int n_components = simParams->getNComponents();
674	>	Globals* simParams = info->getSimParams();
675	>	int nRigidBodies = info->getNGlobalRigidBodies();
676	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
677	>	set<AtomType*>::iterator i;
678	>	bool hasDirectionalAtoms = false;
679	>	bool hasFixedCharge = false;
680	>	bool hasDipoles = false;
681	>	bool hasQuadrupoles = false;
682	>	bool hasPolarizable = false;
683	>	bool hasFluctuatingCharge = false;
684	>	bool hasMetallic = false;
685	>	int storageLayout = 0;
686	>	storageLayout |= DataStorage::dslPosition;
687	>	storageLayout |= DataStorage::dslVelocity;
688	>	storageLayout |= DataStorage::dslForce;
689
690	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
690	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
691
692	<	for(i = 0; i < n_components; i++) {
693	<	if (!the_components[i]->haveNMol()) {
694	<	// we have a problem
695	<	sprintf(painCave.errMsg,
696	<	"SimCreator Error. No global NMol or component NMol given.\n"
697	<	"\tCannot calculate the number of atoms.\n");
692	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
693	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
694	>	EAMAdapter ea = EAMAdapter( (*i) );
695	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
696	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
697	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
698	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
699
700	<	painCave.isFatal = 1;
701	<	simError();
702	<	}
703	<
704	<	id = the_components[i]->getType();
705	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
706	<
707	<	if (currentStamp == NULL) {
708	<	sprintf(painCave.errMsg,
709	<	"SimCreator error: Component \"%s\" was not found in the "
710	<	"list of declared molecules\n", id);
711	<
712	<	painCave.isFatal = 1;
713	<	simError();
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");
700	>	if (da.isDirectional()){
701	>	hasDirectionalAtoms = true;
702	>	}
703	>	if (ma.isDipole()){
704	>	hasDipoles = true;
705	>	}
706	>	if (ma.isQuadrupole()){
707	>	hasQuadrupoles = true;
708	>	}
709	>	if (ea.isEAM() || sca.isSuttonChen()){
710	>	hasMetallic = true;
711	>	}
712	>	if ( fca.isFixedCharge() ){
713	>	hasFixedCharge = true;
714	>	}
715	>	if ( fqa.isFluctuatingCharge() ){
716	>	hasFluctuatingCharge = true;
717	>	}
718	>	if ( pa.isPolarizable() ){
719	>	hasPolarizable = true;
720	>	}
721	>	}
722	>
723	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
724	>	storageLayout |= DataStorage::dslAmat;
725	>	if(storageLayout & DataStorage::dslVelocity) {
726	>	storageLayout |= DataStorage::dslAngularMomentum;
727	>	}
728	>	if (storageLayout & DataStorage::dslForce) {
729	>	storageLayout |= DataStorage::dslTorque;
730	>	}
731	>	}
732	>	if (hasDipoles) {
733	>	storageLayout |= DataStorage::dslDipole;
734	>	}
735	>	if (hasQuadrupoles) {
736	>	storageLayout |= DataStorage::dslQuadrupole;
737	>	}
738	>	if (hasFixedCharge || hasFluctuatingCharge) {
739	>	storageLayout |= DataStorage::dslSkippedCharge;
740	>	}
741	>	if (hasMetallic) {
742	>	storageLayout |= DataStorage::dslDensity;
743	>	storageLayout |= DataStorage::dslFunctional;
744	>	storageLayout |= DataStorage::dslFunctionalDerivative;
745	>	}
746	>	if (hasPolarizable) {
747	>	storageLayout |= DataStorage::dslElectricField;
748	>	}
749	>	if (hasFluctuatingCharge){
750	>	storageLayout |= DataStorage::dslFlucQPosition;
751	>	if(storageLayout & DataStorage::dslVelocity) {
752	>	storageLayout |= DataStorage::dslFlucQVelocity;
753	>	}
754	>	if (storageLayout & DataStorage::dslForce) {
755	>	storageLayout |= DataStorage::dslFlucQForce;
756	>	}
757	>	}
758	>
759	>	// if the user has asked for them, make sure we've got the memory for the
760	>	// objects defined.
761
762	<	painCave.isFatal = 1;
763	<	simError();
762	>	if (simParams->getOutputParticlePotential()) {
763	>	storageLayout |= DataStorage::dslParticlePot;
764		}
765
766	<	#ifdef IS_MPI
766	>	if (simParams->havePrintHeatFlux()) {
767	>	if (simParams->getPrintHeatFlux()) {
768	>	storageLayout |= DataStorage::dslParticlePot;
769	>	}
770	>	}
771
772	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
773	<	MPIcheckPoint();
772	>	if (simParams->getOutputElectricField()) {
773	>	storageLayout |= DataStorage::dslElectricField;
774	>	}
775
776	<	#endif // is_mpi
776	>	if (simParams->getOutputFluctuatingCharges()) {
777	>	storageLayout |= DataStorage::dslFlucQPosition;
778	>	storageLayout |= DataStorage::dslFlucQVelocity;
779	>	storageLayout |= DataStorage::dslFlucQForce;
780	>	}
781
782	<	}
782	>	return storageLayout;
783	>	}
784
785	<	void SimCreator::setGlobalIndex(SimInfo *info) {
785	>	void SimCreator::setGlobalIndex(SimInfo *info) {
786		SimInfo::MoleculeIterator mi;
787		Molecule::AtomIterator ai;
788		Molecule::RigidBodyIterator ri;
789		Molecule::CutoffGroupIterator ci;
790	+	Molecule::IntegrableObjectIterator  ioi;
791		Molecule * mol;
792		Atom * atom;
793		RigidBody * rb;
#	Line 507 | Line 796 | void SimCreator::setGlobalIndex(SimInfo *info) {
796		int beginRigidBodyIndex;
797		int beginCutoffGroupIndex;
798		int nGlobalAtoms = info->getNGlobalAtoms();
799	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
800
511	–	#ifndef IS_MPI
512	–
801		beginAtomIndex = 0;
802	<	beginRigidBodyIndex = 0;
802	>	//rigidbody's index begins right after atom's
803	>	beginRigidBodyIndex = info->getNGlobalAtoms();
804		beginCutoffGroupIndex = 0;
805
806	<	#else
806	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
807	>
808	>	#ifdef IS_MPI
809	>	if (info->getMolToProc(i) == worldRank) {
810	>	#endif
811	>	// stuff to do if I own this molecule
812	>	mol = info->getMoleculeByGlobalIndex(i);
813
519	–	int nproc;
520	–	int myNode;
521	–
522	–	myNode = worldRank;
523	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524	–
525	–	std::vector < int > tmpAtomsInProc(nproc, 0);
526	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528	–	std::vector < int > NumAtomsInProc(nproc, 0);
529	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
530	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531	–
532	–	tmpAtomsInProc[myNode] = info->getNAtoms();
533	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535	–
536	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538	–	MPI_SUM, MPI_COMM_WORLD);
539	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543	–
544	–	beginAtomIndex = 0;
545	–	beginRigidBodyIndex = 0;
546	–	beginCutoffGroupIndex = 0;
547	–
548	–	for(int i = 0; i < myNode; i++) {
549	–	beginAtomIndex += NumAtomsInProc[i];
550	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
551	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552	–	}
553	–
554	–	//rigidbody's index begins right after atom's
555	–	beginRigidBodyIndex += info->getNGlobalAtoms();
556	–	#endif
557	–
558	–	for(mol = info->beginMolecule(mi); mol != NULL;
559	–	mol = info->nextMolecule(mi)) {
560	–
814		//local index(index in DataStorge) of atom is important
815		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
816	<	atom->setGlobalIndex(beginAtomIndex++);
816	>	atom->setGlobalIndex(beginAtomIndex++);
817		}
818	<
818	>
819		for(rb = mol->beginRigidBody(ri); rb != NULL;
820		rb = mol->nextRigidBody(ri)) {
821	<	rb->setGlobalIndex(beginRigidBodyIndex++);
821	>	rb->setGlobalIndex(beginRigidBodyIndex++);
822		}
823	<
824	<	//local index of cutoff group is trivial, it only depends on the order of travesing
823	>
824	>	//local index of cutoff group is trivial, it only depends on
825	>	//the order of travesing
826		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
827		cg = mol->nextCutoffGroup(ci)) {
828	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
829	<	}
830	<	}
828	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
829	>	}
830	>
831	>	#ifdef IS_MPI
832	>	}  else {
833
834	+	// stuff to do if I don't own this molecule
835	+
836	+	int stampId = info->getMoleculeStampId(i);
837	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
838	+
839	+	beginAtomIndex += stamp->getNAtoms();
840	+	beginRigidBodyIndex += stamp->getNRigidBodies();
841	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
842	+	}
843	+	#endif
844	+
845	+	} //end for(int i=0)
846	+
847		//fill globalGroupMembership
848		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
849		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
850	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
851	<
852	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
853	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
854	<	}
855	<
856	<	}
850	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
851	>
852	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
853	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
854	>	}
855	>
856	>	}
857		}
858	<
858	>
859		#ifdef IS_MPI
860		// Since the globalGroupMembership has been zero filled and we've only
861		// poked values into the atoms we know, we can do an Allreduce
862		// to get the full globalGroupMembership array (We think).
863		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
864		// docs said we could.
865	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
866	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
867	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
868	<	info->setGlobalGroupMembership(tmpGroupMembership);
865	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
866	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
867	>	&tmpGroupMembership[0], nGlobalAtoms,
868	>	MPI::INT, MPI::SUM);
869	>	info->setGlobalGroupMembership(tmpGroupMembership);
870		#else
871		info->setGlobalGroupMembership(globalGroupMembership);
872		#endif
873	<
873	>
874		//fill molMembership
875	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
875	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
876	>	info->getNGlobalRigidBodies(), 0);
877
878	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
879	<
880	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
882	<	}
878	>	for(mol = info->beginMolecule(mi); mol != NULL;
879	>	mol = info->nextMolecule(mi)) {
880	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
882	>	}
883	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
884	>	rb = mol->nextRigidBody(ri)) {
885	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
886	>	}
887		}
888	<
888	>
889		#ifdef IS_MPI
890	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
891	<
892	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
893	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
890	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
891	>	info->getNGlobalRigidBodies(), 0);
892	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
893	>	nGlobalAtoms + nGlobalRigidBodies,
894	>	MPI::INT, MPI::SUM);
895
896		info->setGlobalMolMembership(tmpMolMembership);
897		#else
898		info->setGlobalMolMembership(globalMolMembership);
899		#endif
900
901	<	}
901	>	// nIOPerMol holds the number of integrable objects per molecule
902	>	// here the molecules are listed by their global indices.
903
904	<	void SimCreator::loadCoordinates(SimInfo* info) {
904	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
905	>	for (mol = info->beginMolecule(mi); mol != NULL;
906	>	mol = info->nextMolecule(mi)) {
907	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
908	>	}
909	>
910	>	#ifdef IS_MPI
911	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
912	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
913	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
914	>	#else
915	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
916	>	#endif
917	>
918	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
919	>
920	>	int startingIndex = 0;
921	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
922	>	startingIOIndexForMol[i] = startingIndex;
923	>	startingIndex += numIntegrableObjectsPerMol[i];
924	>	}
925	>
926	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
927	>	for (mol = info->beginMolecule(mi); mol != NULL;
928	>	mol = info->nextMolecule(mi)) {
929	>	int myGlobalIndex = mol->getGlobalIndex();
930	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
931	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
932	>	sd = mol->nextIntegrableObject(ioi)) {
933	>	sd->setGlobalIntegrableObjectIndex(globalIO);
934	>	IOIndexToIntegrableObject[globalIO] = sd;
935	>	globalIO++;
936	>	}
937	>	}
938	>
939	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
940	>
941	>	}
942	>
943	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
944		Globals* simParams;
945	+
946		simParams = info->getSimParams();
947
948	<	if (!simParams->haveInitialConfig()) {
632	<	sprintf(painCave.errMsg,
633	<	"Cannot intialize a simulation without an initial configuration file.\n");
634	<	painCave.isFatal = 1;;
635	<	simError();
636	<	}
637	<
638	<	DumpReader reader(info, simParams->getInitialConfig());
948	>	DumpReader reader(info, mdFileName);
949		int nframes = reader.getNFrames();
950
951		if (nframes > 0) {
952	<	reader.readFrame(nframes - 1);
952	>	reader.readFrame(nframes - 1);
953		} else {
954	<	//invalid initial coordinate file
955	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
956	<	simParams->getInitialConfig());
957	<	painCave.isFatal = 1;
958	<	simError();
954	>	//invalid initial coordinate file
955	>	sprintf(painCave.errMsg,
956	>	"Initial configuration file %s should at least contain one frame\n",
957	>	mdFileName.c_str());
958	>	painCave.isFatal = 1;
959	>	simError();
960		}
650	–
961		//copy the current snapshot to previous snapshot
962		info->getSnapshotManager()->advance();
963	<	}
963	>	}
964	>
965	>	} //end namespace OpenMD
966
655	–	} //end namespace oopse
967
657	–

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

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