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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49	+	#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
103	<	#ifdef IS_MPI
103	>	if (worldRank == masterNode) {
104	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock,
108	>	ppStream);
109	>
110	>	#ifdef IS_MPI
111	>	//brocasting the stream size
112	>	streamSize = ppStream.str().size() +1;
113	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
114	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
115	>
116	>	} else {
117	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
118
119	<	if (worldRank == 0) {
120	<	#endif // is_mpi
119	>	//get stream size
120	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121
122	<	simParams->initalize();
123	<	set_interface_stamps(stamps, simParams);
122	>	char* buf = new char[streamSize];
123	>	assert(buf);
124	>
125	>	//receive file content
126	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
127	>
128	>	ppStream.str(buf);
129	>	delete [] buf;
130	>	}
131	>	#endif
132	>	// Create a scanner that reads from the input stream
133	>	MDLexer lexer(ppStream);
134	>	lexer.setFilename(filename);
135	>	lexer.initDeferredLineCount();
136	>
137	>	// Create a parser that reads from the scanner
138	>	MDParser parser(lexer);
139	>	parser.setFilename(filename);
140
141	<	#ifdef IS_MPI
141	>	// Create an observer that synchorizes file name change
142	>	FilenameObserver observer;
143	>	observer.setLexer(&lexer);
144	>	observer.setParser(&parser);
145	>	lexer.setObserver(&observer);
146	>
147	>	antlr::ASTFactory factory;
148	>	parser.initializeASTFactory(factory);
149	>	parser.setASTFactory(&factory);
150	>	parser.mdfile();
151
152	<	mpiEventInit();
152	>	// Create a tree parser that reads information into Globals
153	>	MDTreeParser treeParser;
154	>	treeParser.initializeASTFactory(factory);
155	>	treeParser.setASTFactory(&factory);
156	>	simParams = treeParser.walkTree(parser.getAST());
157	>	}
158
159	<	#endif
159	>
160	>	catch(antlr::MismatchedCharException& e) {
161	>	sprintf(painCave.errMsg,
162	>	"parser exception: %s %s:%d:%d\n",
163	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
164	>	painCave.isFatal = 1;
165	>	simError();
166	>	}
167	>	catch(antlr::MismatchedTokenException &e) {
168	>	sprintf(painCave.errMsg,
169	>	"parser exception: %s %s:%d:%d\n",
170	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
171	>	painCave.isFatal = 1;
172	>	simError();
173	>	}
174	>	catch(antlr::NoViableAltForCharException &e) {
175	>	sprintf(painCave.errMsg,
176	>	"parser exception: %s %s:%d:%d\n",
177	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
178	>	painCave.isFatal = 1;
179	>	simError();
180	>	}
181	>	catch(antlr::NoViableAltException &e) {
182	>	sprintf(painCave.errMsg,
183	>	"parser exception: %s %s:%d:%d\n",
184	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
185	>	painCave.isFatal = 1;
186	>	simError();
187	>	}
188	>
189	>	catch(antlr::TokenStreamRecognitionException& e) {
190	>	sprintf(painCave.errMsg,
191	>	"parser exception: %s %s:%d:%d\n",
192	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
193	>	painCave.isFatal = 1;
194	>	simError();
195	>	}
196	>
197	>	catch(antlr::TokenStreamIOException& e) {
198	>	sprintf(painCave.errMsg,
199	>	"parser exception: %s\n",
200	>	e.getMessage().c_str());
201	>	painCave.isFatal = 1;
202	>	simError();
203	>	}
204	>
205	>	catch(antlr::TokenStreamException& e) {
206	>	sprintf(painCave.errMsg,
207	>	"parser exception: %s\n",
208	>	e.getMessage().c_str());
209	>	painCave.isFatal = 1;
210	>	simError();
211	>	}
212	>	catch (antlr::RecognitionException& e) {
213	>	sprintf(painCave.errMsg,
214	>	"parser exception: %s %s:%d:%d\n",
215	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
216	>	painCave.isFatal = 1;
217	>	simError();
218	>	}
219	>	catch (antlr::CharStreamException& e) {
220	>	sprintf(painCave.errMsg,
221	>	"parser exception: %s\n",
222	>	e.getMessage().c_str());
223	>	painCave.isFatal = 1;
224	>	simError();
225	>	}
226	>	catch (OpenMDException& e) {
227	>	sprintf(painCave.errMsg,
228	>	"%s\n",
229	>	e.getMessage().c_str());
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	catch (std::exception& e) {
234	>	sprintf(painCave.errMsg,
235	>	"parser exception: %s\n",
236	>	e.what());
237	>	painCave.isFatal = 1;
238	>	simError();
239	>	}
240
241	<	yacc_BASS(mdFileName.c_str());
241	>	simParams->setMDfileVersion(mdFileVersion);
242	>	return simParams;
243	>	}
244	>
245	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
246	>	bool loadInitCoords) {
247	>
248	>	const int bufferSize = 65535;
249	>	char buffer[bufferSize];
250	>	int lineNo = 0;
251	>	std::string mdRawData;
252	>	int metaDataBlockStart = -1;
253	>	int metaDataBlockEnd = -1;
254	>	int i, j;
255	>	streamoff mdOffset;
256	>	int mdFileVersion;
257
258	<	#ifdef IS_MPI
258	>	// Create a string for embedding the version information in the MetaData
259	>	std::string version;
260	>	version.assign("## Last run using OpenMD Version: ");
261	>	version.append(OPENMD_VERSION_MAJOR);
262	>	version.append(".");
263	>	version.append(OPENMD_VERSION_MINOR);
264
265	<	throwMPIEvent(NULL);
265	>	std::string svnrev;
266	>	//convert a macro from compiler to a string in c++
267	>	STR_DEFINE(svnrev, SVN_REV );
268	>	version.append(" Revision: ");
269	>	// If there's no SVN revision, just call this the RELEASE revision.
270	>	if (!svnrev.empty()) {
271	>	version.append(svnrev);
272		} else {
273	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
273	>	version.append("RELEASE");
274		}
275	+
276	+	#ifdef IS_MPI
277	+	const int masterNode = 0;
278	+	if (worldRank == masterNode) {
279	+	#endif
280
281	<	#endif
281	>	std::ifstream mdFile_;
282	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
283	>
284	>	if (mdFile_.fail()) {
285	>	sprintf(painCave.errMsg,
286	>	"SimCreator: Cannot open file: %s\n",
287	>	mdFileName.c_str());
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291
292	<	}
292	>	mdFile_.getline(buffer, bufferSize);
293	>	++lineNo;
294	>	std::string line = trimLeftCopy(buffer);
295	>	i = CaseInsensitiveFind(line, "<OpenMD");
296	>	if (static_cast<size_t>(i) == string::npos) {
297	>	// try the older file strings to see if that works:
298	>	i = CaseInsensitiveFind(line, "<OOPSE");
299	>	}
300	>
301	>	if (static_cast<size_t>(i) == string::npos) {
302	>	// still no luck!
303	>	sprintf(painCave.errMsg,
304	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
305	>	mdFileName.c_str());
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	// found the correct opening string, now try to get the file
311	>	// format version number.
312
313	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
314	<
315	<	MakeStamps * stamps = new MakeStamps();
313	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
314	>	std::string fileType = tokenizer.nextToken();
315	>	toUpper(fileType);
316
317	<	Globals * simParams = new Globals();
317	>	mdFileVersion = 0;
318
319	<	//parse meta-data file
320	<	parseFile(mdFileName, stamps, simParams);
319	>	if (fileType == "OPENMD") {
320	>	while (tokenizer.hasMoreTokens()) {
321	>	std::string token(tokenizer.nextToken());
322	>	toUpper(token);
323	>	if (token == "VERSION") {
324	>	mdFileVersion = tokenizer.nextTokenAsInt();
325	>	break;
326	>	}
327	>	}
328	>	}
329	>
330	>	//scan through the input stream and find MetaData tag
331	>	while(mdFile_.getline(buffer, bufferSize)) {
332	>	++lineNo;
333	>
334	>	std::string line = trimLeftCopy(buffer);
335	>	if (metaDataBlockStart == -1) {
336	>	i = CaseInsensitiveFind(line, "<MetaData>");
337	>	if (i != string::npos) {
338	>	metaDataBlockStart = lineNo;
339	>	mdOffset = mdFile_.tellg();
340	>	}
341	>	} else {
342	>	i = CaseInsensitiveFind(line, "</MetaData>");
343	>	if (i != string::npos) {
344	>	metaDataBlockEnd = lineNo;
345	>	}
346	>	}
347	>	}
348
349	<	//create the force field
350	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
351	<	simParams->getForceField());
352	<
353	<	if (ff == NULL) {
354	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
355	<	simParams->getForceField());
356	<	painCave.isFatal = 1;
357	<	simError();
349	>	if (metaDataBlockStart == -1) {
350	>	sprintf(painCave.errMsg,
351	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
352	>	mdFileName.c_str());
353	>	painCave.isFatal = 1;
354	>	simError();
355	>	}
356	>	if (metaDataBlockEnd == -1) {
357	>	sprintf(painCave.errMsg,
358	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
359	>	mdFileName.c_str());
360	>	painCave.isFatal = 1;
361	>	simError();
362	>	}
363	>
364	>	mdFile_.clear();
365	>	mdFile_.seekg(0);
366	>	mdFile_.seekg(mdOffset);
367	>
368	>	mdRawData.clear();
369	>
370	>	bool foundVersion = false;
371	>
372	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
373	>	mdFile_.getline(buffer, bufferSize);
374	>	std::string line = trimLeftCopy(buffer);
375	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
376	>	if (static_cast<size_t>(j) != string::npos) {
377	>	foundVersion = true;
378	>	mdRawData += version;
379	>	} else {
380	>	mdRawData += buffer;
381	>	}
382	>	mdRawData += "\n";
383	>	}
384	>
385	>	if (!foundVersion) mdRawData += version + "\n";
386	>
387	>	mdFile_.close();
388	>
389	>	#ifdef IS_MPI
390		}
391	+	#endif
392
393	+	std::stringstream rawMetaDataStream(mdRawData);
394	+
395	+	//parse meta-data file
396	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
397	+	metaDataBlockStart + 1);
398	+
399	+	//create the force field
400	+	ForceField * ff = new ForceField(simParams->getForceField());
401	+
402	+	if (ff == NULL) {
403	+	sprintf(painCave.errMsg,
404	+	"ForceField Factory can not create %s force field\n",
405	+	simParams->getForceField().c_str());
406	+	painCave.isFatal = 1;
407	+	simError();
408	+	}
409	+
410		if (simParams->haveForceFieldFileName()) {
411	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
411	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
412		}
413
414		std::string forcefieldFileName;
415		forcefieldFileName = ff->getForceFieldFileName();
416	<
416	>
417		if (simParams->haveForceFieldVariant()) {
418	<	//If the force field has variant, the variant force field name will be
419	<	//Base.variant.frc. For exampel EAM.u6.frc
420	<
421	<	std::string variant = simParams->getForceFieldVariant();
422	<
423	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
424	<	variant = "." + variant;
425	<	if (pos != std::string::npos) {
426	<	forcefieldFileName.insert(pos, variant);
427	<	} else {
428	<	//If the default force field file name does not containt .frc suffix, just append the .variant
429	<	forcefieldFileName.append(variant);
430	<	}
418	>	//If the force field has variant, the variant force field name will be
419	>	//Base.variant.frc. For exampel EAM.u6.frc
420	>
421	>	std::string variant = simParams->getForceFieldVariant();
422	>
423	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
424	>	variant = "." + variant;
425	>	if (pos != std::string::npos) {
426	>	forcefieldFileName.insert(pos, variant);
427	>	} else {
428	>	//If the default force field file name does not containt .frc suffix, just append the .variant
429	>	forcefieldFileName.append(variant);
430	>	}
431		}
432
433		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
434		//create SimInfo
435	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
435	>	SimInfo * info = new SimInfo(ff, simParams);
436
437	<	//gather parameters (SimCreator only retrieves part of the parameters)
437	>	info->setRawMetaData(mdRawData);
438	>
439	>	//gather parameters (SimCreator only retrieves part of the
440	>	//parameters)
441		gatherParameters(info, mdFileName);
442	<
442	>
443		//divide the molecules and determine the global index of molecules
444		#ifdef IS_MPI
445		divideMolecules(info);
446		#endif
447	<
447	>
448		//create the molecules
449		createMolecules(info);
450	+
451	+	//find the storage layout
452
453	+	int storageLayout = computeStorageLayout(info);
454
455	<	//allocate memory for DataStorage(circular reference, need to break it)
456	<	info->setSnapshotManager(new SimSnapshotManager(info));
455	>	//allocate memory for DataStorage(circular reference, need to
456	>	//break it)
457	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
458
459	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
460	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
461	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
459	>	//set the global index of atoms, rigidbodies and cutoffgroups
460	>	//(only need to be set once, the global index will never change
461	>	//again). Local indices of atoms and rigidbodies are already set
462	>	//by MoleculeCreator class which actually delegates the
463	>	//responsibility to LocalIndexManager.
464		setGlobalIndex(info);
465	<
466	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
467	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
468	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
469	<	//we can determine the beginning global indices of atoms before they get created.
465	>
466	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
467	>	//method, at that point atoms don't have the global index yet
468	>	//(their global index are all initialized to -1).  Therefore we
469	>	//have to call addInteractionPairs explicitly here. A way to work
470	>	//around is that we can determine the beginning global indices of
471	>	//atoms before they get created.
472		SimInfo::MoleculeIterator mi;
473		Molecule* mol;
474		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
475	<	info->addExcludePairs(mol);
475	>	info->addInteractionPairs(mol);
476		}
477
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
478		if (loadInitCoords)
479	<	loadCoordinates(info);
186	<
479	>	loadCoordinates(info, mdFileName);
480		return info;
481	<	}
482	<
483	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
484	<
485	<	//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
481	>	}
482	>
483	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
484	>
485	>	//figure out the output file names
486		std::string prefix;
487	<
487	>
488		#ifdef IS_MPI
489	<
489	>
490		if (worldRank == 0) {
491		#endif // is_mpi
492	<
493	<	if (simParams->haveFinalConfig()) {
494	<	prefix = getPrefix(simParams->getFinalConfig());
495	<	} else {
496	<	prefix = getPrefix(mdfile);
497	<	}
498	<
499	<	info->setFinalConfigFileName(prefix + ".eor");
500	<	info->setDumpFileName(prefix + ".dump");
501	<	info->setStatFileName(prefix + ".stat");
502	<
492	>	Globals * simParams = info->getSimParams();
493	>	if (simParams->haveFinalConfig()) {
494	>	prefix = getPrefix(simParams->getFinalConfig());
495	>	} else {
496	>	prefix = getPrefix(mdfile);
497	>	}
498	>
499	>	info->setFinalConfigFileName(prefix + ".eor");
500	>	info->setDumpFileName(prefix + ".dump");
501	>	info->setStatFileName(prefix + ".stat");
502	>	info->setRestFileName(prefix + ".zang");
503	>
504		#ifdef IS_MPI
505	<
505	>
506		}
507	<
507	>
508		#endif
509	<
510	<	}
511	<
509	>
510	>	}
511	>
512		#ifdef IS_MPI
513	<	void SimCreator::divideMolecules(SimInfo *info) {
514	<	double numerator;
274	<	double denominator;
275	<	double precast;
276	<	double x;
277	<	double y;
278	<	double a;
279	<	int old_atoms;
280	<	int add_atoms;
281	<	int new_atoms;
282	<	int nTarget;
283	<	int done;
284	<	int i;
285	<	int j;
286	<	int loops;
287	<	int which_proc;
513	>	void SimCreator::divideMolecules(SimInfo *info) {
514	>	RealType a;
515		int nProcessors;
516		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
517		int nGlobalMols = info->getNGlobalMolecules();
518	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
518	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
519	>	// error
520	>	// condition:
521
522	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
523	<
522	>	nProcessors = MPI::COMM_WORLD.Get_size();
523	>
524		if (nProcessors > nGlobalMols) {
525	<	sprintf(painCave.errMsg,
526	<	"nProcessors (%d) > nMol (%d)\n"
527	<	"\tThe number of processors is larger than\n"
528	<	"\tthe number of molecules.  This will not result in a \n"
529	<	"\tusable division of atoms for force decomposition.\n"
530	<	"\tEither try a smaller number of processors, or run the\n"
531	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
532	<
533	<	painCave.isFatal = 1;
534	<	simError();
525	>	sprintf(painCave.errMsg,
526	>	"nProcessors (%d) > nMol (%d)\n"
527	>	"\tThe number of processors is larger than\n"
528	>	"\tthe number of molecules.  This will not result in a \n"
529	>	"\tusable division of atoms for force decomposition.\n"
530	>	"\tEither try a smaller number of processors, or run the\n"
531	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
532	>	nGlobalMols);
533	>
534	>	painCave.isFatal = 1;
535	>	simError();
536		}
537	<
537	>
538	>	Globals * simParams = info->getSimParams();
539	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
540	>	//random number generator
541	>	if (simParams->haveSeed()) {
542	>	int seedValue = simParams->getSeed();
543	>	myRandom = new SeqRandNumGen(seedValue);
544	>	}else {
545	>	myRandom = new SeqRandNumGen();
546	>	}
547	>
548	>
549		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
550	<
550	>
551		//initialize atomsPerProc
552		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
553	<
553	>
554		if (worldRank == 0) {
555	<	numerator = info->getNGlobalAtoms();
556	<	denominator = nProcessors;
557	<	precast = numerator / denominator;
558	<	nTarget = (int)(precast + 0.5);
555	>	RealType numerator = info->getNGlobalAtoms();
556	>	RealType denominator = nProcessors;
557	>	RealType precast = numerator / denominator;
558	>	int nTarget = (int)(precast + 0.5);
559	>
560	>	for(int i = 0; i < nGlobalMols; i++) {
561
562	<	for(i = 0; i < nGlobalMols; i++) {
563	<	done = 0;
564	<	loops = 0;
562	>	int done = 0;
563	>	int loops = 0;
564	>
565	>	while (!done) {
566	>	loops++;
567	>
568	>	// Pick a processor at random
569	>
570	>	int which_proc = (int) (myRandom->rand() * nProcessors);
571	>
572	>	//get the molecule stamp first
573	>	int stampId = info->getMoleculeStampId(i);
574	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
575	>
576	>	// How many atoms does this processor have so far?
577	>	int old_atoms = atomsPerProc[which_proc];
578	>	int add_atoms = moleculeStamp->getNAtoms();
579	>	int new_atoms = old_atoms + add_atoms;
580	>
581	>	// If we've been through this loop too many times, we need
582	>	// to just give up and assign the molecule to this processor
583	>	// and be done with it.
584	>
585	>	if (loops > 100) {
586
587	<	while (!done) {
588	<	loops++;
589	<
590	<	// Pick a processor at random
591	<
592	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
593	<
594	<	//get the molecule stamp first
595	<	int stampId = info->getMoleculeStampId(i);
596	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
597	<
598	<	// How many atoms does this processor have so far?
599	<	old_atoms = atomsPerProc[which_proc];
600	<	add_atoms = moleculeStamp->getNAtoms();
601	<	new_atoms = old_atoms + add_atoms;
602	<
603	<	// If we've been through this loop too many times, we need
604	<	// to just give up and assign the molecule to this processor
605	<	// and be done with it.
606	<
607	<	if (loops > 100) {
608	<	sprintf(painCave.errMsg,
609	<	"I've tried 100 times to assign molecule %d to a "
610	<	" processor, but can't find a good spot.\n"
611	<	"I'm assigning it at random to processor %d.\n",
612	<	i, which_proc);
613	<
614	<	painCave.isFatal = 0;
615	<	simError();
616	<
617	<	molToProcMap[i] = which_proc;
618	<	atomsPerProc[which_proc] += add_atoms;
619	<
620	<	done = 1;
621	<	continue;
622	<	}
623	<
624	<	// If we can add this molecule to this processor without sending
625	<	// it above nTarget, then go ahead and do it:
626	<
627	<	if (new_atoms <= nTarget) {
628	<	molToProcMap[i] = which_proc;
629	<	atomsPerProc[which_proc] += add_atoms;
630	<
631	<	done = 1;
632	<	continue;
633	<	}
634	<
372	<	// The only situation left is when new_atoms > nTarget.  We
373	<	// want to accept this with some probability that dies off the
374	<	// 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	<	}
587	>	sprintf(painCave.errMsg,
588	>	"There have been 100 attempts to assign molecule %d to an\n"
589	>	"\tunderworked processor, but there's no good place to\n"
590	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
591	>	i, which_proc);
592	>
593	>	painCave.isFatal = 0;
594	>	painCave.severity = OPENMD_INFO;
595	>	simError();
596	>
597	>	molToProcMap[i] = which_proc;
598	>	atomsPerProc[which_proc] += add_atoms;
599	>
600	>	done = 1;
601	>	continue;
602	>	}
603	>
604	>	// If we can add this molecule to this processor without sending
605	>	// it above nTarget, then go ahead and do it:
606	>
607	>	if (new_atoms <= nTarget) {
608	>	molToProcMap[i] = which_proc;
609	>	atomsPerProc[which_proc] += add_atoms;
610	>
611	>	done = 1;
612	>	continue;
613	>	}
614	>
615	>	// The only situation left is when new_atoms > nTarget.  We
616	>	// want to accept this with some probability that dies off the
617	>	// farther we are from nTarget
618	>
619	>	// roughly:  x = new_atoms - nTarget
620	>	//           Pacc(x) = exp(- a * x)
621	>	// where a = penalty / (average atoms per molecule)
622	>
623	>	RealType x = (RealType)(new_atoms - nTarget);
624	>	RealType y = myRandom->rand();
625	>
626	>	if (y < exp(- a * x)) {
627	>	molToProcMap[i] = which_proc;
628	>	atomsPerProc[which_proc] += add_atoms;
629	>
630	>	done = 1;
631	>	continue;
632	>	} else {
633	>	continue;
634	>	}
635		}
636	+	}
637	+
638	+	delete myRandom;
639
640	<	// Spray out this nonsense to all other processors:
641	<
397	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
640	>	// Spray out this nonsense to all other processors:
641	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
642		} else {
643	+
644	+	// Listen to your marching orders from processor 0:
645	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
646
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
647		}
648	<
648	>
649		info->setMolToProcMap(molToProcMap);
650		sprintf(checkPointMsg,
651		"Successfully divided the molecules among the processors.\n");
652	<	MPIcheckPoint();
653	<	}
654	<
652	>	errorCheckPoint();
653	>	}
654	>
655		#endif
656	<
657	<	void SimCreator::createMolecules(SimInfo *info) {
656	>
657	>	void SimCreator::createMolecules(SimInfo *info) {
658		MoleculeCreator molCreator;
659		int stampId;
660	<
660	>
661		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
662	<
662	>
663		#ifdef IS_MPI
664	<
665	<	if (info->getMolToProc(i) == worldRank) {
664	>
665	>	if (info->getMolToProc(i) == worldRank) {
666		#endif
667	<
668	<	stampId = info->getMoleculeStampId(i);
669	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
670	<	stampId, i, info->getLocalIndexManager());
671	<
672	<	info->addMolecule(mol);
673	<
667	>
668	>	stampId = info->getMoleculeStampId(i);
669	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
670	>	info->getMoleculeStamp(stampId),
671	>	stampId, i,
672	>	info->getLocalIndexManager());
673	>
674	>	info->addMolecule(mol);
675	>
676		#ifdef IS_MPI
677	<
678	<	}
679	<
677	>
678	>	}
679	>
680		#endif
681	<
681	>
682		} //end for(int i=0)
683	<	}
683	>	}
684	>
685	>	int SimCreator::computeStorageLayout(SimInfo* info) {
686
687	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
688	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
689	<	int i;
690	<	char * id;
691	<	MoleculeStamp * currentStamp;
692	<	Component** the_components = simParams->getComponents();
693	<	int n_components = simParams->getNComponents();
687	>	Globals* simParams = info->getSimParams();
688	>	int nRigidBodies = info->getNGlobalRigidBodies();
689	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
690	>	set<AtomType*>::iterator i;
691	>	bool hasDirectionalAtoms = false;
692	>	bool hasFixedCharge = false;
693	>	bool hasDipoles = false;
694	>	bool hasQuadrupoles = false;
695	>	bool hasPolarizable = false;
696	>	bool hasFluctuatingCharge = false;
697	>	bool hasMetallic = false;
698	>	int storageLayout = 0;
699	>	storageLayout |= DataStorage::dslPosition;
700	>	storageLayout |= DataStorage::dslVelocity;
701	>	storageLayout |= DataStorage::dslForce;
702
703	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
703	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
704
705	<	for(i = 0; i < n_components; i++) {
706	<	if (!the_components[i]->haveNMol()) {
707	<	// we have a problem
708	<	sprintf(painCave.errMsg,
709	<	"SimCreator Error. No global NMol or component NMol given.\n"
710	<	"\tCannot calculate the number of atoms.\n");
705	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
706	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
707	>	EAMAdapter ea = EAMAdapter( (*i) );
708	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
709	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
710	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
711	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
712
713	<	painCave.isFatal = 1;
714	<	simError();
715	<	}
716	<
717	<	id = the_components[i]->getType();
718	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
719	<
720	<	if (currentStamp == NULL) {
721	<	sprintf(painCave.errMsg,
722	<	"SimCreator error: Component \"%s\" was not found in the "
723	<	"list of declared molecules\n", id);
724	<
725	<	painCave.isFatal = 1;
726	<	simError();
727	<	}
728	<
729	<	moleculeStampPairs.push_back(
730	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
731	<	} //end for (i = 0; i < n_components; i++)
732	<	} else {
733	<	sprintf(painCave.errMsg, "SimSetup error.\n"
734	<	"\tSorry, the ability to specify total"
735	<	" nMols and then give molfractions in the components\n"
736	<	"\tis not currently supported."
737	<	" Please give nMol in the components.\n");
713	>	if (da.isDirectional()){
714	>	hasDirectionalAtoms = true;
715	>	}
716	>	if (ma.isDipole()){
717	>	hasDipoles = true;
718	>	}
719	>	if (ma.isQuadrupole()){
720	>	hasQuadrupoles = true;
721	>	}
722	>	if (ea.isEAM() || sca.isSuttonChen()){
723	>	hasMetallic = true;
724	>	}
725	>	if ( fca.isFixedCharge() ){
726	>	hasFixedCharge = true;
727	>	}
728	>	if ( fqa.isFluctuatingCharge() ){
729	>	hasFluctuatingCharge = true;
730	>	}
731	>	if ( pa.isPolarizable() ){
732	>	hasPolarizable = true;
733	>	}
734	>	}
735	>
736	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
737	>	storageLayout |= DataStorage::dslAmat;
738	>	if(storageLayout & DataStorage::dslVelocity) {
739	>	storageLayout |= DataStorage::dslAngularMomentum;
740	>	}
741	>	if (storageLayout & DataStorage::dslForce) {
742	>	storageLayout |= DataStorage::dslTorque;
743	>	}
744	>	}
745	>	if (hasDipoles) {
746	>	storageLayout |= DataStorage::dslDipole;
747	>	}
748	>	if (hasQuadrupoles) {
749	>	storageLayout |= DataStorage::dslQuadrupole;
750	>	}
751	>	if (hasFixedCharge || hasFluctuatingCharge) {
752	>	storageLayout |= DataStorage::dslSkippedCharge;
753	>	}
754	>	if (hasMetallic) {
755	>	storageLayout |= DataStorage::dslDensity;
756	>	storageLayout |= DataStorage::dslFunctional;
757	>	storageLayout |= DataStorage::dslFunctionalDerivative;
758	>	}
759	>	if (hasPolarizable) {
760	>	storageLayout |= DataStorage::dslElectricField;
761	>	}
762	>	if (hasFluctuatingCharge){
763	>	storageLayout |= DataStorage::dslFlucQPosition;
764	>	if(storageLayout & DataStorage::dslVelocity) {
765	>	storageLayout |= DataStorage::dslFlucQVelocity;
766	>	}
767	>	if (storageLayout & DataStorage::dslForce) {
768	>	storageLayout |= DataStorage::dslFlucQForce;
769	>	}
770	>	}
771	>
772	>	// if the user has asked for them, make sure we've got the memory for the
773	>	// objects defined.
774
775	<	painCave.isFatal = 1;
776	<	simError();
775	>	if (simParams->getOutputParticlePotential()) {
776	>	storageLayout |= DataStorage::dslParticlePot;
777		}
778
779	<	#ifdef IS_MPI
779	>	if (simParams->havePrintHeatFlux()) {
780	>	if (simParams->getPrintHeatFlux()) {
781	>	storageLayout |= DataStorage::dslParticlePot;
782	>	}
783	>	}
784
785	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
786	<	MPIcheckPoint();
785	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
786	>	storageLayout |= DataStorage::dslElectricField;
787	>	}
788
789	<	#endif // is_mpi
789	>	if (simParams->getOutputFluctuatingCharges()) {
790	>	storageLayout |= DataStorage::dslFlucQPosition;
791	>	storageLayout |= DataStorage::dslFlucQVelocity;
792	>	storageLayout |= DataStorage::dslFlucQForce;
793	>	}
794
795	<	}
795	>	info->setStorageLayout(storageLayout);
796
797	<	void SimCreator::setGlobalIndex(SimInfo *info) {
797	>	return storageLayout;
798	>	}
799	>
800	>	void SimCreator::setGlobalIndex(SimInfo *info) {
801		SimInfo::MoleculeIterator mi;
802		Molecule::AtomIterator ai;
803		Molecule::RigidBodyIterator ri;
804		Molecule::CutoffGroupIterator ci;
805	+	Molecule::IntegrableObjectIterator  ioi;
806		Molecule * mol;
807		Atom * atom;
808		RigidBody * rb;
#	Line 507 | Line 811 | void SimCreator::setGlobalIndex(SimInfo *info) {
811		int beginRigidBodyIndex;
812		int beginCutoffGroupIndex;
813		int nGlobalAtoms = info->getNGlobalAtoms();
814	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
815
511	–	#ifndef IS_MPI
512	–
816		beginAtomIndex = 0;
817	<	beginRigidBodyIndex = 0;
817	>	//rigidbody's index begins right after atom's
818	>	beginRigidBodyIndex = info->getNGlobalAtoms();
819		beginCutoffGroupIndex = 0;
820
821	<	#else
821	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
822	>
823	>	#ifdef IS_MPI
824	>	if (info->getMolToProc(i) == worldRank) {
825	>	#endif
826	>	// stuff to do if I own this molecule
827	>	mol = info->getMoleculeByGlobalIndex(i);
828
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	–	#endif
555	–
556	–	for(mol = info->beginMolecule(mi); mol != NULL;
557	–	mol = info->nextMolecule(mi)) {
558	–
829		//local index(index in DataStorge) of atom is important
830		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
831	<	atom->setGlobalIndex(beginAtomIndex++);
831	>	atom->setGlobalIndex(beginAtomIndex++);
832		}
833	<
833	>
834		for(rb = mol->beginRigidBody(ri); rb != NULL;
835		rb = mol->nextRigidBody(ri)) {
836	<	rb->setGlobalIndex(beginRigidBodyIndex++);
836	>	rb->setGlobalIndex(beginRigidBodyIndex++);
837		}
838	<
839	<	//local index of cutoff group is trivial, it only depends on the order of travesing
838	>
839	>	//local index of cutoff group is trivial, it only depends on
840	>	//the order of travesing
841		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
842		cg = mol->nextCutoffGroup(ci)) {
843	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
844	<	}
845	<	}
843	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
844	>	}
845	>
846	>	#ifdef IS_MPI
847	>	}  else {
848
849	+	// stuff to do if I don't own this molecule
850	+
851	+	int stampId = info->getMoleculeStampId(i);
852	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
853	+
854	+	beginAtomIndex += stamp->getNAtoms();
855	+	beginRigidBodyIndex += stamp->getNRigidBodies();
856	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
857	+	}
858	+	#endif
859	+
860	+	} //end for(int i=0)
861	+
862		//fill globalGroupMembership
863		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
864		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
865	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
866	<
867	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
868	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
869	<	}
870	<
871	<	}
865	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
866	>
867	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
868	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
869	>	}
870	>
871	>	}
872		}
873	<
873	>
874		#ifdef IS_MPI
875		// Since the globalGroupMembership has been zero filled and we've only
876		// poked values into the atoms we know, we can do an Allreduce
877		// to get the full globalGroupMembership array (We think).
878		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
879		// docs said we could.
880	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
881	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
882	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
883	<	info->setGlobalGroupMembership(tmpGroupMembership);
880	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
881	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
882	>	&tmpGroupMembership[0], nGlobalAtoms,
883	>	MPI::INT, MPI::SUM);
884	>	info->setGlobalGroupMembership(tmpGroupMembership);
885		#else
886		info->setGlobalGroupMembership(globalGroupMembership);
887		#endif
888	<
888	>
889		//fill molMembership
890	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
890	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
891	>	info->getNGlobalRigidBodies(), 0);
892
893	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
894	<
895	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
897	<	}
893	>	for(mol = info->beginMolecule(mi); mol != NULL;
894	>	mol = info->nextMolecule(mi)) {
895	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
897	>	}
898	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
899	>	rb = mol->nextRigidBody(ri)) {
900	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
901	>	}
902		}
903	<
903	>
904		#ifdef IS_MPI
905	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
906	<
907	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
908	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
905	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
906	>	info->getNGlobalRigidBodies(), 0);
907	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
908	>	nGlobalAtoms + nGlobalRigidBodies,
909	>	MPI::INT, MPI::SUM);
910
911		info->setGlobalMolMembership(tmpMolMembership);
912		#else
913		info->setGlobalMolMembership(globalMolMembership);
914		#endif
915
916	<	}
916	>	// nIOPerMol holds the number of integrable objects per molecule
917	>	// here the molecules are listed by their global indices.
918
919	<	void SimCreator::loadCoordinates(SimInfo* info) {
920	<	Globals* simParams;
921	<	simParams = info->getSimParams();
919	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
920	>	for (mol = info->beginMolecule(mi); mol != NULL;
921	>	mol = info->nextMolecule(mi)) {
922	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
923	>	}
924
925	<	if (!simParams->haveInitialConfig()) {
926	<	sprintf(painCave.errMsg,
927	<	"Cannot intialize a simulation without an initial configuration file.\n");
928	<	painCave.isFatal = 1;;
929	<	simError();
925	>	#ifdef IS_MPI
926	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
927	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
928	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
929	>	#else
930	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
931	>	#endif
932	>
933	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
934	>
935	>	int startingIndex = 0;
936	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
937	>	startingIOIndexForMol[i] = startingIndex;
938	>	startingIndex += numIntegrableObjectsPerMol[i];
939		}
940	<
941	<	DumpReader reader(info, simParams->getInitialConfig());
940	>
941	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
942	>	for (mol = info->beginMolecule(mi); mol != NULL;
943	>	mol = info->nextMolecule(mi)) {
944	>	int myGlobalIndex = mol->getGlobalIndex();
945	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
946	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
947	>	sd = mol->nextIntegrableObject(ioi)) {
948	>	sd->setGlobalIntegrableObjectIndex(globalIO);
949	>	IOIndexToIntegrableObject[globalIO] = sd;
950	>	globalIO++;
951	>	}
952	>	}
953	>
954	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
955	>
956	>	}
957	>
958	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
959	>
960	>	DumpReader reader(info, mdFileName);
961		int nframes = reader.getNFrames();
962	<
962	>
963		if (nframes > 0) {
964	<	reader.readFrame(nframes - 1);
964	>	reader.readFrame(nframes - 1);
965		} else {
966	<	//invalid initial coordinate file
967	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
968	<	simParams->getInitialConfig());
969	<	painCave.isFatal = 1;
970	<	simError();
966	>	//invalid initial coordinate file
967	>	sprintf(painCave.errMsg,
968	>	"Initial configuration file %s should at least contain one frame\n",
969	>	mdFileName.c_str());
970	>	painCave.isFatal = 1;
971	>	simError();
972		}
648	–
973		//copy the current snapshot to previous snapshot
974		info->getSnapshotManager()->advance();
975	<	}
975	>	}
976	>
977	>	} //end namespace OpenMD
978
653	–	} //end namespace oopse
979
655	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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