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

Comparing:
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 1826 by gezelter, Wed Jan 9 19:41:48 2013 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		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49	+	#include <exception>
50	+	#include <iostream>
51	+	#include <sstream>
52	+	#include <string>
53
50	–	#include <sprng.h>
51	–
54		#include "brains/MoleculeCreator.hpp"
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
58	<	#include "io/parse_me.h"
57	<	#include "UseTheForce/ForceFieldFactory.hpp"
58	>	#include "brains/ForceField.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61	+	#include "math/SeqRandNumGen.hpp"
62	+	#include "mdParser/MDLexer.hpp"
63	+	#include "mdParser/MDParser.hpp"
64	+	#include "mdParser/MDTreeParser.hpp"
65	+	#include "mdParser/SimplePreprocessor.hpp"
66	+	#include "antlr/ANTLRException.hpp"
67	+	#include "antlr/TokenStreamRecognitionException.hpp"
68	+	#include "antlr/TokenStreamIOException.hpp"
69	+	#include "antlr/TokenStreamException.hpp"
70	+	#include "antlr/RecognitionException.hpp"
71	+	#include "antlr/CharStreamException.hpp"
72	+
73	+	#include "antlr/MismatchedCharException.hpp"
74	+	#include "antlr/MismatchedTokenException.hpp"
75	+	#include "antlr/NoViableAltForCharException.hpp"
76	+	#include "antlr/NoViableAltException.hpp"
77	+
78	+	#include "types/DirectionalAdapter.hpp"
79	+	#include "types/MultipoleAdapter.hpp"
80	+	#include "types/EAMAdapter.hpp"
81	+	#include "types/SuttonChenAdapter.hpp"
82	+	#include "types/PolarizableAdapter.hpp"
83	+	#include "types/FixedChargeAdapter.hpp"
84	+	#include "types/FluctuatingChargeAdapter.hpp"
85	+
86		#ifdef IS_MPI
87	<	#include "io/mpiBASS.h"
88	<	#include "math/randomSPRNG.hpp"
87	>	#include "mpi.h"
88	>	#include "math/ParallelRandNumGen.hpp"
89		#endif
90
91	<	namespace oopse {
91	>	namespace OpenMD {
92	>
93	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
94	>	Globals* simParams = NULL;
95	>	try {
96
97	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
97	>	// Create a preprocessor that preprocesses md file into an ostringstream
98	>	std::stringstream ppStream;
99	>	#ifdef IS_MPI
100	>	int streamSize;
101	>	const int masterNode = 0;
102	>	int commStatus;
103	>	if (worldRank == masterNode) {
104	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108	>
109	>	#ifdef IS_MPI
110	>	//brocasting the stream size
111	>	streamSize = ppStream.str().size() +1;
112	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
113
114	<	#ifdef IS_MPI
114	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
115	>
116	>
117	>	} else {
118
119	<	if (worldRank == 0) {
72	<	#endif // is_mpi
119	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
120
121	<	simParams->initalize();
122	<	set_interface_stamps(stamps, simParams);
121	>	//get stream size
122	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
123
124	<	#ifdef IS_MPI
124	>	char* buf = new char[streamSize];
125	>	assert(buf);
126	>
127	>	//receive file content
128	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129	>
130	>	ppStream.str(buf);
131	>	delete [] buf;
132
133	<	mpiEventInit();
133	>	}
134	>	#endif
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139	>
140	>	// Create a parser that reads from the scanner
141	>	MDParser parser(lexer);
142	>	parser.setFilename(filename);
143
144	<	#endif
144	>	// Create an observer that synchorizes file name change
145	>	FilenameObserver observer;
146	>	observer.setLexer(&lexer);
147	>	observer.setParser(&parser);
148	>	lexer.setObserver(&observer);
149	>
150	>	antlr::ASTFactory factory;
151	>	parser.initializeASTFactory(factory);
152	>	parser.setASTFactory(&factory);
153	>	parser.mdfile();
154
155	<	yacc_BASS(mdFileName.c_str());
155	>	// Create a tree parser that reads information into Globals
156	>	MDTreeParser treeParser;
157	>	treeParser.initializeASTFactory(factory);
158	>	treeParser.setASTFactory(&factory);
159	>	simParams = treeParser.walkTree(parser.getAST());
160	>	}
161
162	<	#ifdef IS_MPI
162	>
163	>	catch(antlr::MismatchedCharException& e) {
164	>	sprintf(painCave.errMsg,
165	>	"parser exception: %s %s:%d:%d\n",
166	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>	catch(antlr::MismatchedTokenException &e) {
171	>	sprintf(painCave.errMsg,
172	>	"parser exception: %s %s:%d:%d\n",
173	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	catch(antlr::NoViableAltForCharException &e) {
178	>	sprintf(painCave.errMsg,
179	>	"parser exception: %s %s:%d:%d\n",
180	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184	>	catch(antlr::NoViableAltException &e) {
185	>	sprintf(painCave.errMsg,
186	>	"parser exception: %s %s:%d:%d\n",
187	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	>	painCave.isFatal = 1;
189	>	simError();
190	>	}
191	>
192	>	catch(antlr::TokenStreamRecognitionException& e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s %s:%d:%d\n",
195	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199	>
200	>	catch(antlr::TokenStreamIOException& e) {
201	>	sprintf(painCave.errMsg,
202	>	"parser exception: %s\n",
203	>	e.getMessage().c_str());
204	>	painCave.isFatal = 1;
205	>	simError();
206	>	}
207	>
208	>	catch(antlr::TokenStreamException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s\n",
211	>	e.getMessage().c_str());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>	catch (antlr::RecognitionException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s %s:%d:%d\n",
218	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (antlr::CharStreamException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"parser exception: %s\n",
225	>	e.getMessage().c_str());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (OpenMDException& e) {
230	>	sprintf(painCave.errMsg,
231	>	"%s\n",
232	>	e.getMessage().c_str());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>	catch (std::exception& e) {
237	>	sprintf(painCave.errMsg,
238	>	"parser exception: %s\n",
239	>	e.what());
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243
244	<	throwMPIEvent(NULL);
244	>	simParams->setMDfileVersion(mdFileVersion);
245	>	return simParams;
246	>	}
247	>
248	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
249	>	bool loadInitCoords) {
250	>
251	>	const int bufferSize = 65535;
252	>	char buffer[bufferSize];
253	>	int lineNo = 0;
254	>	std::string mdRawData;
255	>	int metaDataBlockStart = -1;
256	>	int metaDataBlockEnd = -1;
257	>	int i, j;
258	>	streamoff mdOffset;
259	>	int mdFileVersion;
260	>
261	>	// Create a string for embedding the version information in the MetaData
262	>	std::string version;
263	>	version.assign("## Last run using OpenMD Version: ");
264	>	version.append(OPENMD_VERSION_MAJOR);
265	>	version.append(".");
266	>	version.append(OPENMD_VERSION_MINOR);
267	>
268	>	std::string svnrev;
269	>	//convert a macro from compiler to a string in c++
270	>	STR_DEFINE(svnrev, SVN_REV );
271	>	version.append(" Revision: ");
272	>	// If there's no SVN revision, just call this the RELEASE revision.
273	>	if (!svnrev.empty()) {
274	>	version.append(svnrev);
275		} else {
276	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
276	>	version.append("RELEASE");
277		}
278	+
279	+	#ifdef IS_MPI
280	+	const int masterNode = 0;
281	+	if (worldRank == masterNode) {
282	+	#endif
283
284	<	#endif
284	>	std::ifstream mdFile_;
285	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
286	>
287	>	if (mdFile_.fail()) {
288	>	sprintf(painCave.errMsg,
289	>	"SimCreator: Cannot open file: %s\n",
290	>	mdFileName.c_str());
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294
295	<	}
295	>	mdFile_.getline(buffer, bufferSize);
296	>	++lineNo;
297	>	std::string line = trimLeftCopy(buffer);
298	>	i = CaseInsensitiveFind(line, "<OpenMD");
299	>	if (static_cast<size_t>(i) == string::npos) {
300	>	// try the older file strings to see if that works:
301	>	i = CaseInsensitiveFind(line, "<OOPSE");
302	>	}
303	>
304	>	if (static_cast<size_t>(i) == string::npos) {
305	>	// still no luck!
306	>	sprintf(painCave.errMsg,
307	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
308	>	mdFileName.c_str());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>
313	>	// found the correct opening string, now try to get the file
314	>	// format version number.
315
316	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
317	<
318	<	MakeStamps * stamps = new MakeStamps();
316	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
317	>	std::string fileType = tokenizer.nextToken();
318	>	toUpper(fileType);
319
320	<	Globals * simParams = new Globals();
320	>	mdFileVersion = 0;
321
322	<	//parse meta-data file
323	<	parseFile(mdFileName, stamps, simParams);
322	>	if (fileType == "OPENMD") {
323	>	while (tokenizer.hasMoreTokens()) {
324	>	std::string token(tokenizer.nextToken());
325	>	toUpper(token);
326	>	if (token == "VERSION") {
327	>	mdFileVersion = tokenizer.nextTokenAsInt();
328	>	break;
329	>	}
330	>	}
331	>	}
332	>
333	>	//scan through the input stream and find MetaData tag
334	>	while(mdFile_.getline(buffer, bufferSize)) {
335	>	++lineNo;
336	>
337	>	std::string line = trimLeftCopy(buffer);
338	>	if (metaDataBlockStart == -1) {
339	>	i = CaseInsensitiveFind(line, "<MetaData>");
340	>	if (i != string::npos) {
341	>	metaDataBlockStart = lineNo;
342	>	mdOffset = mdFile_.tellg();
343	>	}
344	>	} else {
345	>	i = CaseInsensitiveFind(line, "</MetaData>");
346	>	if (i != string::npos) {
347	>	metaDataBlockEnd = lineNo;
348	>	}
349	>	}
350	>	}
351
352	<	//create the force field
353	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
354	<	simParams->getForceField());
355	<
356	<	if (ff == NULL) {
357	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
358	<	simParams->getForceField());
359	<	painCave.isFatal = 1;
360	<	simError();
352	>	if (metaDataBlockStart == -1) {
353	>	sprintf(painCave.errMsg,
354	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
355	>	mdFileName.c_str());
356	>	painCave.isFatal = 1;
357	>	simError();
358	>	}
359	>	if (metaDataBlockEnd == -1) {
360	>	sprintf(painCave.errMsg,
361	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
362	>	mdFileName.c_str());
363	>	painCave.isFatal = 1;
364	>	simError();
365	>	}
366	>
367	>	mdFile_.clear();
368	>	mdFile_.seekg(0);
369	>	mdFile_.seekg(mdOffset);
370	>
371	>	mdRawData.clear();
372	>
373	>	bool foundVersion = false;
374	>
375	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
376	>	mdFile_.getline(buffer, bufferSize);
377	>	std::string line = trimLeftCopy(buffer);
378	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
379	>	if (static_cast<size_t>(j) != string::npos) {
380	>	foundVersion = true;
381	>	mdRawData += version;
382	>	} else {
383	>	mdRawData += buffer;
384	>	}
385	>	mdRawData += "\n";
386	>	}
387	>
388	>	if (!foundVersion) mdRawData += version + "\n";
389	>
390	>	mdFile_.close();
391	>
392	>	#ifdef IS_MPI
393		}
394	+	#endif
395
396	+	std::stringstream rawMetaDataStream(mdRawData);
397	+
398	+	//parse meta-data file
399	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
400	+	metaDataBlockStart + 1);
401	+
402	+	//create the force field
403	+	ForceField * ff = new ForceField(simParams->getForceField());
404	+
405	+	if (ff == NULL) {
406	+	sprintf(painCave.errMsg,
407	+	"ForceField Factory can not create %s force field\n",
408	+	simParams->getForceField().c_str());
409	+	painCave.isFatal = 1;
410	+	simError();
411	+	}
412	+
413		if (simParams->haveForceFieldFileName()) {
414	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
414	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
415		}
416
417		std::string forcefieldFileName;
418		forcefieldFileName = ff->getForceFieldFileName();
419	<
419	>
420		if (simParams->haveForceFieldVariant()) {
421	<	//If the force field has variant, the variant force field name will be
422	<	//Base.variant.frc. For exampel EAM.u6.frc
423	<
424	<	std::string variant = simParams->getForceFieldVariant();
425	<
426	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
427	<	variant = "." + variant;
428	<	if (pos != std::string::npos) {
429	<	forcefieldFileName.insert(pos, variant);
430	<	} else {
431	<	//If the default force field file name does not containt .frc suffix, just append the .variant
432	<	forcefieldFileName.append(variant);
433	<	}
421	>	//If the force field has variant, the variant force field name will be
422	>	//Base.variant.frc. For exampel EAM.u6.frc
423	>
424	>	std::string variant = simParams->getForceFieldVariant();
425	>
426	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
427	>	variant = "." + variant;
428	>	if (pos != std::string::npos) {
429	>	forcefieldFileName.insert(pos, variant);
430	>	} else {
431	>	//If the default force field file name does not containt .frc suffix, just append the .variant
432	>	forcefieldFileName.append(variant);
433	>	}
434		}
435
436		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
437		//create SimInfo
438	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
438	>	SimInfo * info = new SimInfo(ff, simParams);
439
440	<	//gather parameters (SimCreator only retrieves part of the parameters)
440	>	info->setRawMetaData(mdRawData);
441	>
442	>	//gather parameters (SimCreator only retrieves part of the
443	>	//parameters)
444		gatherParameters(info, mdFileName);
445	<
445	>
446		//divide the molecules and determine the global index of molecules
447		#ifdef IS_MPI
448		divideMolecules(info);
449		#endif
450	<
450	>
451		//create the molecules
452		createMolecules(info);
453	+
454	+	//find the storage layout
455
456	+	int storageLayout = computeStorageLayout(info);
457
458	<	//allocate memory for DataStorage(circular reference, need to break it)
459	<	info->setSnapshotManager(new SimSnapshotManager(info));
458	>	//allocate memory for DataStorage(circular reference, need to
459	>	//break it)
460	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
461
462	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
463	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
464	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
462	>	//set the global index of atoms, rigidbodies and cutoffgroups
463	>	//(only need to be set once, the global index will never change
464	>	//again). Local indices of atoms and rigidbodies are already set
465	>	//by MoleculeCreator class which actually delegates the
466	>	//responsibility to LocalIndexManager.
467		setGlobalIndex(info);
468	<
469	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
470	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
471	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
472	<	//we can determine the beginning global indices of atoms before they get created.
468	>
469	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
470	>	//method, at that point atoms don't have the global index yet
471	>	//(their global index are all initialized to -1).  Therefore we
472	>	//have to call addInteractionPairs explicitly here. A way to work
473	>	//around is that we can determine the beginning global indices of
474	>	//atoms before they get created.
475		SimInfo::MoleculeIterator mi;
476		Molecule* mol;
477		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
478	<	info->addExcludePairs(mol);
478	>	info->addInteractionPairs(mol);
479		}
480
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
481		if (loadInitCoords)
482	<	loadCoordinates(info);
186	<
482	>	loadCoordinates(info, mdFileName);
483		return info;
484	<	}
485	<
486	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
487	<
488	<	//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
484	>	}
485	>
486	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
487	>
488	>	//figure out the output file names
489		std::string prefix;
490	<
490	>
491		#ifdef IS_MPI
492	<
492	>
493		if (worldRank == 0) {
494		#endif // is_mpi
495	<
496	<	if (simParams->haveFinalConfig()) {
497	<	prefix = getPrefix(simParams->getFinalConfig());
498	<	} else {
499	<	prefix = getPrefix(mdfile);
500	<	}
501	<
502	<	info->setFinalConfigFileName(prefix + ".eor");
503	<	info->setDumpFileName(prefix + ".dump");
504	<	info->setStatFileName(prefix + ".stat");
505	<
495	>	Globals * simParams = info->getSimParams();
496	>	if (simParams->haveFinalConfig()) {
497	>	prefix = getPrefix(simParams->getFinalConfig());
498	>	} else {
499	>	prefix = getPrefix(mdfile);
500	>	}
501	>
502	>	info->setFinalConfigFileName(prefix + ".eor");
503	>	info->setDumpFileName(prefix + ".dump");
504	>	info->setStatFileName(prefix + ".stat");
505	>	info->setRestFileName(prefix + ".zang");
506	>
507		#ifdef IS_MPI
508	<
508	>
509		}
510	<
510	>
511		#endif
512	<
513	<	}
514	<
512	>
513	>	}
514	>
515		#ifdef IS_MPI
516	<	void SimCreator::divideMolecules(SimInfo *info) {
517	<	double numerator;
518	<	double denominator;
519	<	double precast;
520	<	double x;
521	<	double y;
522	<	double a;
516	>	void SimCreator::divideMolecules(SimInfo *info) {
517	>	RealType numerator;
518	>	RealType denominator;
519	>	RealType precast;
520	>	RealType x;
521	>	RealType y;
522	>	RealType a;
523		int old_atoms;
524		int add_atoms;
525		int new_atoms;
526		int nTarget;
527		int done;
528		int i;
285	–	int j;
529		int loops;
530		int which_proc;
531		int nProcessors;
532		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
533		int nGlobalMols = info->getNGlobalMolecules();
534		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
535
536	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
537	<
536	>	nProcessors = MPI::COMM_WORLD.Get_size();
537	>
538		if (nProcessors > nGlobalMols) {
539	<	sprintf(painCave.errMsg,
540	<	"nProcessors (%d) > nMol (%d)\n"
541	<	"\tThe number of processors is larger than\n"
542	<	"\tthe number of molecules.  This will not result in a \n"
543	<	"\tusable division of atoms for force decomposition.\n"
544	<	"\tEither try a smaller number of processors, or run the\n"
545	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
546	<
547	<	painCave.isFatal = 1;
548	<	simError();
539	>	sprintf(painCave.errMsg,
540	>	"nProcessors (%d) > nMol (%d)\n"
541	>	"\tThe number of processors is larger than\n"
542	>	"\tthe number of molecules.  This will not result in a \n"
543	>	"\tusable division of atoms for force decomposition.\n"
544	>	"\tEither try a smaller number of processors, or run the\n"
545	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
546	>
547	>	painCave.isFatal = 1;
548	>	simError();
549		}
550	<
550	>
551	>	int seedValue;
552	>	Globals * simParams = info->getSimParams();
553	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
554	>	if (simParams->haveSeed()) {
555	>	seedValue = simParams->getSeed();
556	>	myRandom = new SeqRandNumGen(seedValue);
557	>	}else {
558	>	myRandom = new SeqRandNumGen();
559	>	}
560	>
561	>
562		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
563	<
563	>
564		//initialize atomsPerProc
565		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
566	<
566	>
567		if (worldRank == 0) {
568	<	numerator = info->getNGlobalAtoms();
569	<	denominator = nProcessors;
570	<	precast = numerator / denominator;
571	<	nTarget = (int)(precast + 0.5);
572	<
573	<	for(i = 0; i < nGlobalMols; i++) {
321	<	done = 0;
322	<	loops = 0;
568	>	numerator = info->getNGlobalAtoms();
569	>	denominator = nProcessors;
570	>	precast = numerator / denominator;
571	>	nTarget = (int)(precast + 0.5);
572	>
573	>	for(i = 0; i < nGlobalMols; i++) {
574
575	<	while (!done) {
576	<	loops++;
575	>	done = 0;
576	>	loops = 0;
577	>
578	>	while (!done) {
579	>	loops++;
580	>
581	>	// Pick a processor at random
582	>
583	>	which_proc = (int) (myRandom->rand() * nProcessors);
584	>
585	>	//get the molecule stamp first
586	>	int stampId = info->getMoleculeStampId(i);
587	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
588	>
589	>	// How many atoms does this processor have so far?
590	>	old_atoms = atomsPerProc[which_proc];
591	>	add_atoms = moleculeStamp->getNAtoms();
592	>	new_atoms = old_atoms + add_atoms;
593	>
594	>	// If we've been through this loop too many times, we need
595	>	// to just give up and assign the molecule to this processor
596	>	// and be done with it.
597	>
598	>	if (loops > 100) {
599
600	<	// Pick a processor at random
601	<
602	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
603	<
604	<	//get the molecule stamp first
605	<	int stampId = info->getMoleculeStampId(i);
606	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
607	<
608	<	// How many atoms does this processor have so far?
609	<	old_atoms = atomsPerProc[which_proc];
610	<	add_atoms = moleculeStamp->getNAtoms();
611	<	new_atoms = old_atoms + add_atoms;
612	<
613	<	// If we've been through this loop too many times, we need
614	<	// to just give up and assign the molecule to this processor
615	<	// and be done with it.
616	<
617	<	if (loops > 100) {
618	<	sprintf(painCave.errMsg,
619	<	"I've tried 100 times to assign molecule %d to a "
620	<	" processor, but can't find a good spot.\n"
621	<	"I'm assigning it at random to processor %d.\n",
622	<	i, which_proc);
623	<
624	<	painCave.isFatal = 0;
625	<	simError();
626	<
627	<	molToProcMap[i] = which_proc;
628	<	atomsPerProc[which_proc] += add_atoms;
629	<
630	<	done = 1;
631	<	continue;
632	<	}
633	<
634	<	// If we can add this molecule to this processor without sending
635	<	// it above nTarget, then go ahead and do it:
636	<
637	<	if (new_atoms <= nTarget) {
638	<	molToProcMap[i] = which_proc;
639	<	atomsPerProc[which_proc] += add_atoms;
640	<
641	<	done = 1;
642	<	continue;
643	<	}
644	<
645	<	// The only situation left is when new_atoms > nTarget.  We
646	<	// want to accept this with some probability that dies off the
647	<	// 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	<	}
600	>	sprintf(painCave.errMsg,
601	>	"There have been 100 attempts to assign molecule %d to an\n"
602	>	"\tunderworked processor, but there's no good place to\n"
603	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
604	>	i, which_proc);
605	>
606	>	painCave.isFatal = 0;
607	>	painCave.severity = OPENMD_INFO;
608	>	simError();
609	>
610	>	molToProcMap[i] = which_proc;
611	>	atomsPerProc[which_proc] += add_atoms;
612	>
613	>	done = 1;
614	>	continue;
615	>	}
616	>
617	>	// If we can add this molecule to this processor without sending
618	>	// it above nTarget, then go ahead and do it:
619	>
620	>	if (new_atoms <= nTarget) {
621	>	molToProcMap[i] = which_proc;
622	>	atomsPerProc[which_proc] += add_atoms;
623	>
624	>	done = 1;
625	>	continue;
626	>	}
627	>
628	>	// The only situation left is when new_atoms > nTarget.  We
629	>	// want to accept this with some probability that dies off the
630	>	// farther we are from nTarget
631	>
632	>	// roughly:  x = new_atoms - nTarget
633	>	//           Pacc(x) = exp(- a * x)
634	>	// where a = penalty / (average atoms per molecule)
635	>
636	>	x = (RealType)(new_atoms - nTarget);
637	>	y = myRandom->rand();
638	>
639	>	if (y < exp(- a * x)) {
640	>	molToProcMap[i] = which_proc;
641	>	atomsPerProc[which_proc] += add_atoms;
642	>
643	>	done = 1;
644	>	continue;
645	>	} else {
646	>	continue;
647	>	}
648		}
649	+	}
650	+
651	+	delete myRandom;
652
653	<	// Spray out this nonsense to all other processors:
654	<
397	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
653	>	// Spray out this nonsense to all other processors:
654	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655		} else {
656	+
657	+	// Listen to your marching orders from processor 0:
658	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
659
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
660		}
661	<
661	>
662		info->setMolToProcMap(molToProcMap);
663		sprintf(checkPointMsg,
664		"Successfully divided the molecules among the processors.\n");
665	<	MPIcheckPoint();
666	<	}
667	<
665	>	errorCheckPoint();
666	>	}
667	>
668		#endif
669	<
670	<	void SimCreator::createMolecules(SimInfo *info) {
669	>
670	>	void SimCreator::createMolecules(SimInfo *info) {
671		MoleculeCreator molCreator;
672		int stampId;
673	<
673	>
674		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
675	<
675	>
676		#ifdef IS_MPI
677	<
678	<	if (info->getMolToProc(i) == worldRank) {
677	>
678	>	if (info->getMolToProc(i) == worldRank) {
679		#endif
680	<
681	<	stampId = info->getMoleculeStampId(i);
682	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
683	<	stampId, i, info->getLocalIndexManager());
684	<
685	<	info->addMolecule(mol);
686	<
680	>
681	>	stampId = info->getMoleculeStampId(i);
682	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
683	>	info->getMoleculeStamp(stampId),
684	>	stampId, i,
685	>	info->getLocalIndexManager());
686	>
687	>	info->addMolecule(mol);
688	>
689		#ifdef IS_MPI
690	<
691	<	}
692	<
690	>
691	>	}
692	>
693		#endif
694	<
694	>
695		} //end for(int i=0)
696	<	}
696	>	}
697	>
698	>	int SimCreator::computeStorageLayout(SimInfo* info) {
699
700	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
701	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
702	<	int i;
703	<	char * id;
704	<	MoleculeStamp * currentStamp;
705	<	Component** the_components = simParams->getComponents();
706	<	int n_components = simParams->getNComponents();
700	>	Globals* simParams = info->getSimParams();
701	>	int nRigidBodies = info->getNGlobalRigidBodies();
702	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
703	>	set<AtomType*>::iterator i;
704	>	bool hasDirectionalAtoms = false;
705	>	bool hasFixedCharge = false;
706	>	bool hasDipoles = false;
707	>	bool hasQuadrupoles = false;
708	>	bool hasPolarizable = false;
709	>	bool hasFluctuatingCharge = false;
710	>	bool hasMetallic = false;
711	>	int storageLayout = 0;
712	>	storageLayout |= DataStorage::dslPosition;
713	>	storageLayout |= DataStorage::dslVelocity;
714	>	storageLayout |= DataStorage::dslForce;
715
716	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
716	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717
718	<	for(i = 0; i < n_components; i++) {
719	<	if (!the_components[i]->haveNMol()) {
720	<	// we have a problem
721	<	sprintf(painCave.errMsg,
722	<	"SimCreator Error. No global NMol or component NMol given.\n"
723	<	"\tCannot calculate the number of atoms.\n");
718	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
719	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
720	>	EAMAdapter ea = EAMAdapter( (*i) );
721	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
722	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
723	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
724	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
725
726	<	painCave.isFatal = 1;
727	<	simError();
728	<	}
729	<
730	<	id = the_components[i]->getType();
731	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
732	<
733	<	if (currentStamp == NULL) {
734	<	sprintf(painCave.errMsg,
735	<	"SimCreator error: Component \"%s\" was not found in the "
736	<	"list of declared molecules\n", id);
737	<
738	<	painCave.isFatal = 1;
739	<	simError();
740	<	}
741	<
742	<	moleculeStampPairs.push_back(
743	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
744	<	} //end for (i = 0; i < n_components; i++)
745	<	} else {
746	<	sprintf(painCave.errMsg, "SimSetup error.\n"
747	<	"\tSorry, the ability to specify total"
748	<	" nMols and then give molfractions in the components\n"
749	<	"\tis not currently supported."
750	<	" Please give nMol in the components.\n");
726	>	if (da.isDirectional()){
727	>	hasDirectionalAtoms = true;
728	>	}
729	>	if (ma.isDipole()){
730	>	hasDipoles = true;
731	>	}
732	>	if (ma.isQuadrupole()){
733	>	hasQuadrupoles = true;
734	>	}
735	>	if (ea.isEAM() || sca.isSuttonChen()){
736	>	hasMetallic = true;
737	>	}
738	>	if ( fca.isFixedCharge() ){
739	>	hasFixedCharge = true;
740	>	}
741	>	if ( fqa.isFluctuatingCharge() ){
742	>	hasFluctuatingCharge = true;
743	>	}
744	>	if ( pa.isPolarizable() ){
745	>	hasPolarizable = true;
746	>	}
747	>	}
748	>
749	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
750	>	storageLayout |= DataStorage::dslAmat;
751	>	if(storageLayout & DataStorage::dslVelocity) {
752	>	storageLayout |= DataStorage::dslAngularMomentum;
753	>	}
754	>	if (storageLayout & DataStorage::dslForce) {
755	>	storageLayout |= DataStorage::dslTorque;
756	>	}
757	>	}
758	>	if (hasDipoles) {
759	>	storageLayout |= DataStorage::dslDipole;
760	>	}
761	>	if (hasQuadrupoles) {
762	>	storageLayout |= DataStorage::dslQuadrupole;
763	>	}
764	>	if (hasFixedCharge || hasFluctuatingCharge) {
765	>	storageLayout |= DataStorage::dslSkippedCharge;
766	>	}
767	>	if (hasMetallic) {
768	>	storageLayout |= DataStorage::dslDensity;
769	>	storageLayout |= DataStorage::dslFunctional;
770	>	storageLayout |= DataStorage::dslFunctionalDerivative;
771	>	}
772	>	if (hasPolarizable) {
773	>	storageLayout |= DataStorage::dslElectricField;
774	>	}
775	>	if (hasFluctuatingCharge){
776	>	storageLayout |= DataStorage::dslFlucQPosition;
777	>	if(storageLayout & DataStorage::dslVelocity) {
778	>	storageLayout |= DataStorage::dslFlucQVelocity;
779	>	}
780	>	if (storageLayout & DataStorage::dslForce) {
781	>	storageLayout |= DataStorage::dslFlucQForce;
782	>	}
783	>	}
784	>
785	>	// if the user has asked for them, make sure we've got the memory for the
786	>	// objects defined.
787
788	<	painCave.isFatal = 1;
789	<	simError();
788	>	if (simParams->getOutputParticlePotential()) {
789	>	storageLayout |= DataStorage::dslParticlePot;
790		}
791
792	<	#ifdef IS_MPI
792	>	if (simParams->havePrintHeatFlux()) {
793	>	if (simParams->getPrintHeatFlux()) {
794	>	storageLayout |= DataStorage::dslParticlePot;
795	>	}
796	>	}
797
798	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
799	<	MPIcheckPoint();
798	>	if (simParams->getOutputElectricField()) {
799	>	storageLayout |= DataStorage::dslElectricField;
800	>	}
801
802	<	#endif // is_mpi
802	>	if (simParams->getOutputFluctuatingCharges()) {
803	>	storageLayout |= DataStorage::dslFlucQPosition;
804	>	storageLayout |= DataStorage::dslFlucQVelocity;
805	>	storageLayout |= DataStorage::dslFlucQForce;
806	>	}
807
808	<	}
808	>	return storageLayout;
809	>	}
810
811	<	void SimCreator::setGlobalIndex(SimInfo *info) {
811	>	void SimCreator::setGlobalIndex(SimInfo *info) {
812		SimInfo::MoleculeIterator mi;
813		Molecule::AtomIterator ai;
814		Molecule::RigidBodyIterator ri;
815		Molecule::CutoffGroupIterator ci;
816	+	Molecule::IntegrableObjectIterator  ioi;
817		Molecule * mol;
818		Atom * atom;
819		RigidBody * rb;
#	Line 507 | Line 822 | void SimCreator::setGlobalIndex(SimInfo *info) {
822		int beginRigidBodyIndex;
823		int beginCutoffGroupIndex;
824		int nGlobalAtoms = info->getNGlobalAtoms();
825	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
826
511	–	#ifndef IS_MPI
512	–
827		beginAtomIndex = 0;
828	<	beginRigidBodyIndex = 0;
828	>	//rigidbody's index begins right after atom's
829	>	beginRigidBodyIndex = info->getNGlobalAtoms();
830		beginCutoffGroupIndex = 0;
831
832	<	#else
832	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
833	>
834	>	#ifdef IS_MPI
835	>	if (info->getMolToProc(i) == worldRank) {
836	>	#endif
837	>	// stuff to do if I own this molecule
838	>	mol = info->getMoleculeByGlobalIndex(i);
839
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	–
840		//local index(index in DataStorge) of atom is important
841		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	<	atom->setGlobalIndex(beginAtomIndex++);
842	>	atom->setGlobalIndex(beginAtomIndex++);
843		}
844	<
844	>
845		for(rb = mol->beginRigidBody(ri); rb != NULL;
846		rb = mol->nextRigidBody(ri)) {
847	<	rb->setGlobalIndex(beginRigidBodyIndex++);
847	>	rb->setGlobalIndex(beginRigidBodyIndex++);
848		}
849	<
850	<	//local index of cutoff group is trivial, it only depends on the order of travesing
849	>
850	>	//local index of cutoff group is trivial, it only depends on
851	>	//the order of travesing
852		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
853		cg = mol->nextCutoffGroup(ci)) {
854	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
855	<	}
856	<	}
854	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
855	>	}
856	>
857	>	#ifdef IS_MPI
858	>	}  else {
859
860	+	// stuff to do if I don't own this molecule
861	+
862	+	int stampId = info->getMoleculeStampId(i);
863	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
864	+
865	+	beginAtomIndex += stamp->getNAtoms();
866	+	beginRigidBodyIndex += stamp->getNRigidBodies();
867	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
868	+	}
869	+	#endif
870	+
871	+	} //end for(int i=0)
872	+
873		//fill globalGroupMembership
874		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
875		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
876	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
877	<
878	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
879	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
880	<	}
881	<
882	<	}
876	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
877	>
878	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
879	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
880	>	}
881	>
882	>	}
883		}
884	<
884	>
885		#ifdef IS_MPI
886		// Since the globalGroupMembership has been zero filled and we've only
887		// poked values into the atoms we know, we can do an Allreduce
888		// to get the full globalGroupMembership array (We think).
889		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
890		// docs said we could.
891	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
892	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
893	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
894	<	info->setGlobalGroupMembership(tmpGroupMembership);
891	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
892	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
893	>	&tmpGroupMembership[0], nGlobalAtoms,
894	>	MPI::INT, MPI::SUM);
895	>	info->setGlobalGroupMembership(tmpGroupMembership);
896		#else
897		info->setGlobalGroupMembership(globalGroupMembership);
898		#endif
899	<
899	>
900		//fill molMembership
901	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
901	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
902	>	info->getNGlobalRigidBodies(), 0);
903
904	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
905	<
906	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
908	<	}
904	>	for(mol = info->beginMolecule(mi); mol != NULL;
905	>	mol = info->nextMolecule(mi)) {
906	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
908	>	}
909	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
910	>	rb = mol->nextRigidBody(ri)) {
911	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
912	>	}
913		}
914	<
914	>
915		#ifdef IS_MPI
916	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
917	<
918	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
919	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
916	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
917	>	info->getNGlobalRigidBodies(), 0);
918	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
919	>	nGlobalAtoms + nGlobalRigidBodies,
920	>	MPI::INT, MPI::SUM);
921
922		info->setGlobalMolMembership(tmpMolMembership);
923		#else
924		info->setGlobalMolMembership(globalMolMembership);
925		#endif
926
927	<	}
927	>	// nIOPerMol holds the number of integrable objects per molecule
928	>	// here the molecules are listed by their global indices.
929
930	<	void SimCreator::loadCoordinates(SimInfo* info) {
931	<	Globals* simParams;
932	<	simParams = info->getSimParams();
930	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
931	>	for (mol = info->beginMolecule(mi); mol != NULL;
932	>	mol = info->nextMolecule(mi)) {
933	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
934	>	}
935
936	<	if (!simParams->haveInitialConfig()) {
937	<	sprintf(painCave.errMsg,
938	<	"Cannot intialize a simulation without an initial configuration file.\n");
939	<	painCave.isFatal = 1;;
940	<	simError();
936	>	#ifdef IS_MPI
937	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
938	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
939	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
940	>	#else
941	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
942	>	#endif
943	>
944	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
945	>
946	>	int startingIndex = 0;
947	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
948	>	startingIOIndexForMol[i] = startingIndex;
949	>	startingIndex += numIntegrableObjectsPerMol[i];
950		}
951	<
952	<	DumpReader reader(info, simParams->getInitialConfig());
951	>
952	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
953	>	for (mol = info->beginMolecule(mi); mol != NULL;
954	>	mol = info->nextMolecule(mi)) {
955	>	int myGlobalIndex = mol->getGlobalIndex();
956	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
957	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
958	>	sd = mol->nextIntegrableObject(ioi)) {
959	>	sd->setGlobalIntegrableObjectIndex(globalIO);
960	>	IOIndexToIntegrableObject[globalIO] = sd;
961	>	globalIO++;
962	>	}
963	>	}
964	>
965	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
966	>
967	>	}
968	>
969	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
970	>
971	>	DumpReader reader(info, mdFileName);
972		int nframes = reader.getNFrames();
973	<
973	>
974		if (nframes > 0) {
975	<	reader.readFrame(nframes - 1);
975	>	reader.readFrame(nframes - 1);
976		} else {
977	<	//invalid initial coordinate file
978	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
979	<	simParams->getInitialConfig());
980	<	painCave.isFatal = 1;
981	<	simError();
977	>	//invalid initial coordinate file
978	>	sprintf(painCave.errMsg,
979	>	"Initial configuration file %s should at least contain one frame\n",
980	>	mdFileName.c_str());
981	>	painCave.isFatal = 1;
982	>	simError();
983		}
650	–
984		//copy the current snapshot to previous snapshot
985		info->getSnapshotManager()->advance();
986	<	}
986	>	}
987	>
988	>	} //end namespace OpenMD
989
655	–	} //end namespace oopse
990
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 1826 by gezelter, Wed Jan 9 19:41:48 2013 UTC

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