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

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trunk/src/brains/SimCreator.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 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, 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, ppStream);
108	>
109	>	#ifdef IS_MPI
110	>	//brocasting the stream size
111	>	streamSize = ppStream.str().size() +1;
112	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
113	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
114	>
115	>	} else {
116	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
117
118	<	if (worldRank == 0) {
119	<	#endif // is_mpi
118	>	//get stream size
119	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
120
121	<	simParams->initalize();
122	<	set_interface_stamps(stamps, simParams);
121	>	char* buf = new char[streamSize];
122	>	assert(buf);
123	>
124	>	//receive file content
125	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
126	>
127	>	ppStream.str(buf);
128	>	delete [] buf;
129	>	}
130	>	#endif
131	>	// Create a scanner that reads from the input stream
132	>	MDLexer lexer(ppStream);
133	>	lexer.setFilename(filename);
134	>	lexer.initDeferredLineCount();
135	>
136	>	// Create a parser that reads from the scanner
137	>	MDParser parser(lexer);
138	>	parser.setFilename(filename);
139
140	<	#ifdef IS_MPI
140	>	// Create an observer that synchorizes file name change
141	>	FilenameObserver observer;
142	>	observer.setLexer(&lexer);
143	>	observer.setParser(&parser);
144	>	lexer.setObserver(&observer);
145	>
146	>	antlr::ASTFactory factory;
147	>	parser.initializeASTFactory(factory);
148	>	parser.setASTFactory(&factory);
149	>	parser.mdfile();
150
151	<	mpiEventInit();
151	>	// Create a tree parser that reads information into Globals
152	>	MDTreeParser treeParser;
153	>	treeParser.initializeASTFactory(factory);
154	>	treeParser.setASTFactory(&factory);
155	>	simParams = treeParser.walkTree(parser.getAST());
156	>	}
157
158	<	#endif
158	>
159	>	catch(antlr::MismatchedCharException& e) {
160	>	sprintf(painCave.errMsg,
161	>	"parser exception: %s %s:%d:%d\n",
162	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
163	>	painCave.isFatal = 1;
164	>	simError();
165	>	}
166	>	catch(antlr::MismatchedTokenException &e) {
167	>	sprintf(painCave.errMsg,
168	>	"parser exception: %s %s:%d:%d\n",
169	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
170	>	painCave.isFatal = 1;
171	>	simError();
172	>	}
173	>	catch(antlr::NoViableAltForCharException &e) {
174	>	sprintf(painCave.errMsg,
175	>	"parser exception: %s %s:%d:%d\n",
176	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
177	>	painCave.isFatal = 1;
178	>	simError();
179	>	}
180	>	catch(antlr::NoViableAltException &e) {
181	>	sprintf(painCave.errMsg,
182	>	"parser exception: %s %s:%d:%d\n",
183	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187	>
188	>	catch(antlr::TokenStreamRecognitionException& e) {
189	>	sprintf(painCave.errMsg,
190	>	"parser exception: %s %s:%d:%d\n",
191	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
192	>	painCave.isFatal = 1;
193	>	simError();
194	>	}
195	>
196	>	catch(antlr::TokenStreamIOException& e) {
197	>	sprintf(painCave.errMsg,
198	>	"parser exception: %s\n",
199	>	e.getMessage().c_str());
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>
204	>	catch(antlr::TokenStreamException& e) {
205	>	sprintf(painCave.errMsg,
206	>	"parser exception: %s\n",
207	>	e.getMessage().c_str());
208	>	painCave.isFatal = 1;
209	>	simError();
210	>	}
211	>	catch (antlr::RecognitionException& e) {
212	>	sprintf(painCave.errMsg,
213	>	"parser exception: %s %s:%d:%d\n",
214	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218	>	catch (antlr::CharStreamException& e) {
219	>	sprintf(painCave.errMsg,
220	>	"parser exception: %s\n",
221	>	e.getMessage().c_str());
222	>	painCave.isFatal = 1;
223	>	simError();
224	>	}
225	>	catch (OpenMDException& e) {
226	>	sprintf(painCave.errMsg,
227	>	"%s\n",
228	>	e.getMessage().c_str());
229	>	painCave.isFatal = 1;
230	>	simError();
231	>	}
232	>	catch (std::exception& e) {
233	>	sprintf(painCave.errMsg,
234	>	"parser exception: %s\n",
235	>	e.what());
236	>	painCave.isFatal = 1;
237	>	simError();
238	>	}
239
240	<	yacc_BASS(mdFileName.c_str());
240	>	simParams->setMDfileVersion(mdFileVersion);
241	>	return simParams;
242	>	}
243	>
244	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
245	>	bool loadInitCoords) {
246	>
247	>	const int bufferSize = 65535;
248	>	char buffer[bufferSize];
249	>	int lineNo = 0;
250	>	std::string mdRawData;
251	>	int metaDataBlockStart = -1;
252	>	int metaDataBlockEnd = -1;
253	>	int i, j;
254	>	streamoff mdOffset;
255	>	int mdFileVersion;
256
257	<	#ifdef IS_MPI
257	>	// Create a string for embedding the version information in the MetaData
258	>	std::string version;
259	>	version.assign("## Last run using OpenMD Version: ");
260	>	version.append(OPENMD_VERSION_MAJOR);
261	>	version.append(".");
262	>	version.append(OPENMD_VERSION_MINOR);
263
264	<	throwMPIEvent(NULL);
264	>	std::string svnrev;
265	>	//convert a macro from compiler to a string in c++
266	>	STR_DEFINE(svnrev, SVN_REV );
267	>	version.append(" Revision: ");
268	>	// If there's no SVN revision, just call this the RELEASE revision.
269	>	if (!svnrev.empty()) {
270	>	version.append(svnrev);
271		} else {
272	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
272	>	version.append("RELEASE");
273		}
274	+
275	+	#ifdef IS_MPI
276	+	const int masterNode = 0;
277	+	if (worldRank == masterNode) {
278	+	#endif
279
280	<	#endif
280	>	std::ifstream mdFile_;
281	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
282	>
283	>	if (mdFile_.fail()) {
284	>	sprintf(painCave.errMsg,
285	>	"SimCreator: Cannot open file: %s\n",
286	>	mdFileName.c_str());
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290
291	<	}
291	>	mdFile_.getline(buffer, bufferSize);
292	>	++lineNo;
293	>	std::string line = trimLeftCopy(buffer);
294	>	i = CaseInsensitiveFind(line, "<OpenMD");
295	>	if (static_cast<size_t>(i) == string::npos) {
296	>	// try the older file strings to see if that works:
297	>	i = CaseInsensitiveFind(line, "<OOPSE");
298	>	}
299	>
300	>	if (static_cast<size_t>(i) == string::npos) {
301	>	// still no luck!
302	>	sprintf(painCave.errMsg,
303	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
304	>	mdFileName.c_str());
305	>	painCave.isFatal = 1;
306	>	simError();
307	>	}
308	>
309	>	// found the correct opening string, now try to get the file
310	>	// format version number.
311
312	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
313	<
314	<	MakeStamps * stamps = new MakeStamps();
312	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
313	>	std::string fileType = tokenizer.nextToken();
314	>	toUpper(fileType);
315
316	<	Globals * simParams = new Globals();
316	>	mdFileVersion = 0;
317
318	<	//parse meta-data file
319	<	parseFile(mdFileName, stamps, simParams);
318	>	if (fileType == "OPENMD") {
319	>	while (tokenizer.hasMoreTokens()) {
320	>	std::string token(tokenizer.nextToken());
321	>	toUpper(token);
322	>	if (token == "VERSION") {
323	>	mdFileVersion = tokenizer.nextTokenAsInt();
324	>	break;
325	>	}
326	>	}
327	>	}
328	>
329	>	//scan through the input stream and find MetaData tag
330	>	while(mdFile_.getline(buffer, bufferSize)) {
331	>	++lineNo;
332	>
333	>	std::string line = trimLeftCopy(buffer);
334	>	if (metaDataBlockStart == -1) {
335	>	i = CaseInsensitiveFind(line, "<MetaData>");
336	>	if (i != string::npos) {
337	>	metaDataBlockStart = lineNo;
338	>	mdOffset = mdFile_.tellg();
339	>	}
340	>	} else {
341	>	i = CaseInsensitiveFind(line, "</MetaData>");
342	>	if (i != string::npos) {
343	>	metaDataBlockEnd = lineNo;
344	>	}
345	>	}
346	>	}
347
348	<	//create the force field
349	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
350	<	simParams->getForceField());
351	<
352	<	if (ff == NULL) {
353	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
354	<	simParams->getForceField());
355	<	painCave.isFatal = 1;
356	<	simError();
357	<	}
348	>	if (metaDataBlockStart == -1) {
349	>	sprintf(painCave.errMsg,
350	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
351	>	mdFileName.c_str());
352	>	painCave.isFatal = 1;
353	>	simError();
354	>	}
355	>	if (metaDataBlockEnd == -1) {
356	>	sprintf(painCave.errMsg,
357	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
358	>	mdFileName.c_str());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	}
362	>
363	>	mdFile_.clear();
364	>	mdFile_.seekg(0);
365	>	mdFile_.seekg(mdOffset);
366
367	<	std::string forcefieldFileName;
120	<	forcefieldFileName = ff->getForceFieldFileName();
367	>	mdRawData.clear();
368
369	<	if (simParams->haveForceFieldVariant()) {
123	<	//If the force field has variant, the variant force field name will be
124	<	//Base.variant.frc. For exampel EAM.u6.frc
125	<
126	<	std::string variant = simParams->getForceFieldVariant();
369	>	bool foundVersion = false;
370
371	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
372	<	variant = "." + variant;
373	<	if (pos != std::string::npos) {
374	<	forcefieldFileName.insert(pos, variant);
371	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
372	>	mdFile_.getline(buffer, bufferSize);
373	>	std::string line = trimLeftCopy(buffer);
374	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
375	>	if (static_cast<size_t>(j) != string::npos) {
376	>	foundVersion = true;
377	>	mdRawData += version;
378		} else {
379	<	//If the default force field file name does not containt .frc suffix, just append the .variant
134	<	forcefieldFileName.append(variant);
379	>	mdRawData += buffer;
380		}
381	+	mdRawData += "\n";
382	+	}
383	+
384	+	if (!foundVersion) mdRawData += version + "\n";
385	+
386	+	mdFile_.close();
387	+
388	+	#ifdef IS_MPI
389	+	}
390	+	#endif
391	+
392	+	std::stringstream rawMetaDataStream(mdRawData);
393	+
394	+	//parse meta-data file
395	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
396	+	metaDataBlockStart + 1);
397	+
398	+	//create the force field
399	+	ForceField * ff = new ForceField(simParams->getForceField());
400	+
401	+	if (ff == NULL) {
402	+	sprintf(painCave.errMsg,
403	+	"ForceField Factory can not create %s force field\n",
404	+	simParams->getForceField().c_str());
405	+	painCave.isFatal = 1;
406	+	simError();
407	+	}
408	+
409	+	if (simParams->haveForceFieldFileName()) {
410	+	ff->setForceFieldFileName(simParams->getForceFieldFileName());
411	+	}
412	+
413	+	std::string forcefieldFileName;
414	+	forcefieldFileName = ff->getForceFieldFileName();
415	+
416	+	if (simParams->haveForceFieldVariant()) {
417	+	//If the force field has variant, the variant force field name will be
418	+	//Base.variant.frc. For exampel EAM.u6.frc
419	+
420	+	std::string variant = simParams->getForceFieldVariant();
421	+
422	+	std::string::size_type pos = forcefieldFileName.rfind(".frc");
423	+	variant = "." + variant;
424	+	if (pos != std::string::npos) {
425	+	forcefieldFileName.insert(pos, variant);
426	+	} else {
427	+	//If the default force field file name does not containt .frc suffix, just append the .variant
428	+	forcefieldFileName.append(variant);
429	+	}
430		}
431
432		ff->parse(forcefieldFileName);
139	–
140	–	//extract the molecule stamps
141	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
142	–	compList(stamps, simParams, moleculeStampPairs);
143	–
433		//create SimInfo
434	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
434	>	SimInfo * info = new SimInfo(ff, simParams);
435
436	<	//gather parameters (SimCreator only retrieves part of the parameters)
436	>	info->setRawMetaData(mdRawData);
437	>
438	>	//gather parameters (SimCreator only retrieves part of the
439	>	//parameters)
440		gatherParameters(info, mdFileName);
441	<
441	>
442		//divide the molecules and determine the global index of molecules
443		#ifdef IS_MPI
444		divideMolecules(info);
445		#endif
446	<
446	>
447		//create the molecules
448		createMolecules(info);
449	+
450	+	//find the storage layout
451
452	+	int storageLayout = computeStorageLayout(info);
453
454	<	//allocate memory for DataStorage(circular reference, need to break it)
455	<	info->setSnapshotManager(new SimSnapshotManager(info));
454	>	//allocate memory for DataStorage(circular reference, need to
455	>	//break it)
456	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
457
458	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
459	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
460	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
458	>	//set the global index of atoms, rigidbodies and cutoffgroups
459	>	//(only need to be set once, the global index will never change
460	>	//again). Local indices of atoms and rigidbodies are already set
461	>	//by MoleculeCreator class which actually delegates the
462	>	//responsibility to LocalIndexManager.
463		setGlobalIndex(info);
464	<
465	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
466	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
467	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
468	<	//we can determine the beginning global indices of atoms before they get created.
464	>
465	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
466	>	//method, at that point atoms don't have the global index yet
467	>	//(their global index are all initialized to -1).  Therefore we
468	>	//have to call addInteractionPairs explicitly here. A way to work
469	>	//around is that we can determine the beginning global indices of
470	>	//atoms before they get created.
471		SimInfo::MoleculeIterator mi;
472		Molecule* mol;
473		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
474	<	info->addExcludePairs(mol);
474	>	info->addInteractionPairs(mol);
475		}
476
177	–
178	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
179	–	//eta, chi for NPT integrator)
477		if (loadInitCoords)
478	<	loadCoordinates(info);
182	<
478	>	loadCoordinates(info, mdFileName);
479		return info;
480	<	}
481	<
482	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
483	<
484	<	//setup seed for random number generator
189	<	int seedValue;
190	<	Globals * simParams = info->getSimParams();
191	<
192	<	if (simParams->haveSeed()) {
193	<	seedValue = simParams->getSeed();
194	<
195	<	if (seedValue < 100000000 ) {
196	<	sprintf(painCave.errMsg,
197	<	"Seed for sprng library should contain at least 9 digits\n"
198	<	"OOPSE will generate a seed for user\n");
199	<
200	<	painCave.isFatal = 0;
201	<	simError();
202	<
203	<	//using seed generated by system instead of invalid seed set by user
204	<
205	<	#ifndef IS_MPI
206	<
207	<	seedValue = make_sprng_seed();
208	<
209	<	#else
210	<
211	<	if (worldRank == 0) {
212	<	seedValue = make_sprng_seed();
213	<	}
214	<
215	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
216	<
217	<	#endif
218	<
219	<	} //end if (seedValue /1000000000 == 0)
220	<	} else {
221	<
222	<	#ifndef IS_MPI
223	<
224	<	seedValue = make_sprng_seed();
225	<
226	<	#else
227	<
228	<	if (worldRank == 0) {
229	<	seedValue = make_sprng_seed();
230	<	}
231	<
232	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
233	<
234	<	#endif
235	<
236	<	} //end of simParams->haveSeed()
237	<
238	<	info->setSeed(seedValue);
239	<
240	<
241	<	//figure out the ouput file names
480	>	}
481	>
482	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
483	>
484	>	//figure out the output file names
485		std::string prefix;
486	<
486	>
487		#ifdef IS_MPI
488	<
488	>
489		if (worldRank == 0) {
490		#endif // is_mpi
491	<
492	<	if (simParams->haveFinalConfig()) {
493	<	prefix = getPrefix(simParams->getFinalConfig());
494	<	} else {
495	<	prefix = getPrefix(mdfile);
496	<	}
497	<
498	<	info->setFinalConfigFileName(prefix + ".eor");
499	<	info->setDumpFileName(prefix + ".dump");
500	<	info->setStatFileName(prefix + ".stat");
501	<
491	>	Globals * simParams = info->getSimParams();
492	>	if (simParams->haveFinalConfig()) {
493	>	prefix = getPrefix(simParams->getFinalConfig());
494	>	} else {
495	>	prefix = getPrefix(mdfile);
496	>	}
497	>
498	>	info->setFinalConfigFileName(prefix + ".eor");
499	>	info->setDumpFileName(prefix + ".dump");
500	>	info->setStatFileName(prefix + ".stat");
501	>	info->setRestFileName(prefix + ".zang");
502	>
503		#ifdef IS_MPI
504	<
504	>
505		}
506	<
506	>
507		#endif
508	<
509	<	}
510	<
508	>
509	>	}
510	>
511		#ifdef IS_MPI
512	<	void SimCreator::divideMolecules(SimInfo *info) {
513	<	double numerator;
514	<	double denominator;
515	<	double precast;
516	<	double x;
517	<	double y;
518	<	double a;
275	<	int old_atoms;
276	<	int add_atoms;
277	<	int new_atoms;
278	<	int nTarget;
279	<	int done;
280	<	int i;
281	<	int j;
282	<	int loops;
283	<	int which_proc;
512	>	void SimCreator::divideMolecules(SimInfo *info) {
513	>	RealType numerator;
514	>	RealType denominator;
515	>	RealType precast;
516	>	RealType x;
517	>	RealType y;
518	>	RealType a;
519		int nProcessors;
520		std::vector<int> atomsPerProc;
286	–	randomSPRNG myRandom(info->getSeed());
521		int nGlobalMols = info->getNGlobalMolecules();
522	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
522	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
523	>	// error
524	>	// condition:
525
526	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
527	<
526	>	nProcessors = MPI::COMM_WORLD.Get_size();
527	>
528		if (nProcessors > nGlobalMols) {
529	<	sprintf(painCave.errMsg,
530	<	"nProcessors (%d) > nMol (%d)\n"
531	<	"\tThe number of processors is larger than\n"
532	<	"\tthe number of molecules.  This will not result in a \n"
533	<	"\tusable division of atoms for force decomposition.\n"
534	<	"\tEither try a smaller number of processors, or run the\n"
535	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
536	<
537	<	painCave.isFatal = 1;
538	<	simError();
529	>	sprintf(painCave.errMsg,
530	>	"nProcessors (%d) > nMol (%d)\n"
531	>	"\tThe number of processors is larger than\n"
532	>	"\tthe number of molecules.  This will not result in a \n"
533	>	"\tusable division of atoms for force decomposition.\n"
534	>	"\tEither try a smaller number of processors, or run the\n"
535	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
536	>	nGlobalMols);
537	>
538	>	painCave.isFatal = 1;
539	>	simError();
540		}
541	<
541	>
542	>	Globals * simParams = info->getSimParams();
543	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
544	>	//random number generator
545	>	if (simParams->haveSeed()) {
546	>	int seedValue = simParams->getSeed();
547	>	myRandom = new SeqRandNumGen(seedValue);
548	>	}else {
549	>	myRandom = new SeqRandNumGen();
550	>	}
551	>
552	>
553		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
554	<
554	>
555		//initialize atomsPerProc
556		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
557	<
557	>
558		if (worldRank == 0) {
559	<	numerator = info->getNGlobalAtoms();
560	<	denominator = nProcessors;
561	<	precast = numerator / denominator;
562	<	nTarget = (int)(precast + 0.5);
559	>	numerator = info->getNGlobalAtoms();
560	>	denominator = nProcessors;
561	>	precast = numerator / denominator;
562	>	int nTarget = (int)(precast + 0.5);
563	>
564	>	for(int i = 0; i < nGlobalMols; i++) {
565
566	<	for(i = 0; i < nGlobalMols; i++) {
567	<	done = 0;
568	<	loops = 0;
566	>	int done = 0;
567	>	int loops = 0;
568	>
569	>	while (!done) {
570	>	loops++;
571	>
572	>	// Pick a processor at random
573	>
574	>	int which_proc = (int) (myRandom->rand() * nProcessors);
575	>
576	>	//get the molecule stamp first
577	>	int stampId = info->getMoleculeStampId(i);
578	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
579	>
580	>	// How many atoms does this processor have so far?
581	>	int old_atoms = atomsPerProc[which_proc];
582	>	int add_atoms = moleculeStamp->getNAtoms();
583	>	int new_atoms = old_atoms + add_atoms;
584	>
585	>	// If we've been through this loop too many times, we need
586	>	// to just give up and assign the molecule to this processor
587	>	// and be done with it.
588	>
589	>	if (loops > 100) {
590
591	<	while (!done) {
592	<	loops++;
593	<
594	<	// Pick a processor at random
595	<
596	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
597	<
598	<	//get the molecule stamp first
599	<	int stampId = info->getMoleculeStampId(i);
600	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
601	<
602	<	// How many atoms does this processor have so far?
603	<	old_atoms = atomsPerProc[which_proc];
604	<	add_atoms = moleculeStamp->getNAtoms();
605	<	new_atoms = old_atoms + add_atoms;
606	<
607	<	// If we've been through this loop too many times, we need
608	<	// to just give up and assign the molecule to this processor
609	<	// and be done with it.
610	<
611	<	if (loops > 100) {
612	<	sprintf(painCave.errMsg,
613	<	"I've tried 100 times to assign molecule %d to a "
614	<	" processor, but can't find a good spot.\n"
615	<	"I'm assigning it at random to processor %d.\n",
616	<	i, which_proc);
617	<
618	<	painCave.isFatal = 0;
619	<	simError();
620	<
621	<	molToProcMap[i] = which_proc;
622	<	atomsPerProc[which_proc] += add_atoms;
623	<
624	<	done = 1;
625	<	continue;
626	<	}
627	<
628	<	// If we can add this molecule to this processor without sending
629	<	// it above nTarget, then go ahead and do it:
630	<
631	<	if (new_atoms <= nTarget) {
632	<	molToProcMap[i] = which_proc;
633	<	atomsPerProc[which_proc] += add_atoms;
634	<
635	<	done = 1;
636	<	continue;
637	<	}
638	<
368	<	// The only situation left is when new_atoms > nTarget.  We
369	<	// want to accept this with some probability that dies off the
370	<	// farther we are from nTarget
371	<
372	<	// roughly:  x = new_atoms - nTarget
373	<	//           Pacc(x) = exp(- a * x)
374	<	// where a = penalty / (average atoms per molecule)
375	<
376	<	x = (double)(new_atoms - nTarget);
377	<	y = myRandom.getRandom();
378	<
379	<	if (y < exp(- a * x)) {
380	<	molToProcMap[i] = which_proc;
381	<	atomsPerProc[which_proc] += add_atoms;
382	<
383	<	done = 1;
384	<	continue;
385	<	} else {
386	<	continue;
387	<	}
388	<	}
591	>	sprintf(painCave.errMsg,
592	>	"There have been 100 attempts to assign molecule %d to an\n"
593	>	"\tunderworked processor, but there's no good place to\n"
594	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
595	>	i, which_proc);
596	>
597	>	painCave.isFatal = 0;
598	>	painCave.severity = OPENMD_INFO;
599	>	simError();
600	>
601	>	molToProcMap[i] = which_proc;
602	>	atomsPerProc[which_proc] += add_atoms;
603	>
604	>	done = 1;
605	>	continue;
606	>	}
607	>
608	>	// If we can add this molecule to this processor without sending
609	>	// it above nTarget, then go ahead and do it:
610	>
611	>	if (new_atoms <= nTarget) {
612	>	molToProcMap[i] = which_proc;
613	>	atomsPerProc[which_proc] += add_atoms;
614	>
615	>	done = 1;
616	>	continue;
617	>	}
618	>
619	>	// The only situation left is when new_atoms > nTarget.  We
620	>	// want to accept this with some probability that dies off the
621	>	// farther we are from nTarget
622	>
623	>	// roughly:  x = new_atoms - nTarget
624	>	//           Pacc(x) = exp(- a * x)
625	>	// where a = penalty / (average atoms per molecule)
626	>
627	>	x = (RealType)(new_atoms - nTarget);
628	>	y = myRandom->rand();
629	>
630	>	if (y < exp(- a * x)) {
631	>	molToProcMap[i] = which_proc;
632	>	atomsPerProc[which_proc] += add_atoms;
633	>
634	>	done = 1;
635	>	continue;
636	>	} else {
637	>	continue;
638	>	}
639		}
640	+	}
641	+
642	+	delete myRandom;
643
644	<	// Spray out this nonsense to all other processors:
645	<
393	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644	>	// Spray out this nonsense to all other processors:
645	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
646		} else {
647	+
648	+	// Listen to your marching orders from processor 0:
649	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
650
396	–	// Listen to your marching orders from processor 0:
397	–
398	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
651		}
652	<
652	>
653		info->setMolToProcMap(molToProcMap);
654		sprintf(checkPointMsg,
655		"Successfully divided the molecules among the processors.\n");
656	<	MPIcheckPoint();
657	<	}
658	<
656	>	errorCheckPoint();
657	>	}
658	>
659		#endif
660	<
661	<	void SimCreator::createMolecules(SimInfo *info) {
660	>
661	>	void SimCreator::createMolecules(SimInfo *info) {
662		MoleculeCreator molCreator;
663		int stampId;
664	<
664	>
665		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
666	<
666	>
667		#ifdef IS_MPI
668	<
669	<	if (info->getMolToProc(i) == worldRank) {
668	>
669	>	if (info->getMolToProc(i) == worldRank) {
670		#endif
671	<
672	<	stampId = info->getMoleculeStampId(i);
673	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
674	<	stampId, i, info->getLocalIndexManager());
675	<
676	<	info->addMolecule(mol);
677	<
671	>
672	>	stampId = info->getMoleculeStampId(i);
673	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
674	>	info->getMoleculeStamp(stampId),
675	>	stampId, i,
676	>	info->getLocalIndexManager());
677	>
678	>	info->addMolecule(mol);
679	>
680		#ifdef IS_MPI
681	<
682	<	}
683	<
681	>
682	>	}
683	>
684		#endif
685	<
685	>
686		} //end for(int i=0)
687	<	}
687	>	}
688	>
689	>	int SimCreator::computeStorageLayout(SimInfo* info) {
690
691	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
692	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
693	<	int i;
694	<	char * id;
695	<	MoleculeStamp * currentStamp;
696	<	Component** the_components = simParams->getComponents();
697	<	int n_components = simParams->getNComponents();
691	>	Globals* simParams = info->getSimParams();
692	>	int nRigidBodies = info->getNGlobalRigidBodies();
693	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
694	>	set<AtomType*>::iterator i;
695	>	bool hasDirectionalAtoms = false;
696	>	bool hasFixedCharge = false;
697	>	bool hasDipoles = false;
698	>	bool hasQuadrupoles = false;
699	>	bool hasPolarizable = false;
700	>	bool hasFluctuatingCharge = false;
701	>	bool hasMetallic = false;
702	>	int storageLayout = 0;
703	>	storageLayout |= DataStorage::dslPosition;
704	>	storageLayout |= DataStorage::dslVelocity;
705	>	storageLayout |= DataStorage::dslForce;
706
707	<	if (!simParams->haveNMol()) {
444	<	// we don't have the total number of molecules, so we assume it is
445	<	// given in each component
707	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
708
709	<	for(i = 0; i < n_components; i++) {
710	<	if (!the_components[i]->haveNMol()) {
711	<	// we have a problem
712	<	sprintf(painCave.errMsg,
713	<	"SimCreator Error. No global NMol or component NMol given.\n"
714	<	"\tCannot calculate the number of atoms.\n");
709	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
710	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
711	>	EAMAdapter ea = EAMAdapter( (*i) );
712	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
713	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
714	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
715	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
716
717	<	painCave.isFatal = 1;
718	<	simError();
719	<	}
720	<
721	<	id = the_components[i]->getType();
722	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
723	<
724	<	if (currentStamp == NULL) {
725	<	sprintf(painCave.errMsg,
726	<	"SimCreator error: Component \"%s\" was not found in the "
727	<	"list of declared molecules\n", id);
728	<
729	<	painCave.isFatal = 1;
730	<	simError();
731	<	}
732	<
733	<	moleculeStampPairs.push_back(
734	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
735	<	} //end for (i = 0; i < n_components; i++)
736	<	} else {
737	<	sprintf(painCave.errMsg, "SimSetup error.\n"
738	<	"\tSorry, the ability to specify total"
739	<	" nMols and then give molfractions in the components\n"
740	<	"\tis not currently supported."
741	<	" Please give nMol in the components.\n");
717	>	if (da.isDirectional()){
718	>	hasDirectionalAtoms = true;
719	>	}
720	>	if (ma.isDipole()){
721	>	hasDipoles = true;
722	>	}
723	>	if (ma.isQuadrupole()){
724	>	hasQuadrupoles = true;
725	>	}
726	>	if (ea.isEAM() || sca.isSuttonChen()){
727	>	hasMetallic = true;
728	>	}
729	>	if ( fca.isFixedCharge() ){
730	>	hasFixedCharge = true;
731	>	}
732	>	if ( fqa.isFluctuatingCharge() ){
733	>	hasFluctuatingCharge = true;
734	>	}
735	>	if ( pa.isPolarizable() ){
736	>	hasPolarizable = true;
737	>	}
738	>	}
739	>
740	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
741	>	storageLayout |= DataStorage::dslAmat;
742	>	if(storageLayout & DataStorage::dslVelocity) {
743	>	storageLayout |= DataStorage::dslAngularMomentum;
744	>	}
745	>	if (storageLayout & DataStorage::dslForce) {
746	>	storageLayout |= DataStorage::dslTorque;
747	>	}
748	>	}
749	>	if (hasDipoles) {
750	>	storageLayout |= DataStorage::dslDipole;
751	>	}
752	>	if (hasQuadrupoles) {
753	>	storageLayout |= DataStorage::dslQuadrupole;
754	>	}
755	>	if (hasFixedCharge || hasFluctuatingCharge) {
756	>	storageLayout |= DataStorage::dslSkippedCharge;
757	>	}
758	>	if (hasMetallic) {
759	>	storageLayout |= DataStorage::dslDensity;
760	>	storageLayout |= DataStorage::dslFunctional;
761	>	storageLayout |= DataStorage::dslFunctionalDerivative;
762	>	}
763	>	if (hasPolarizable) {
764	>	storageLayout |= DataStorage::dslElectricField;
765	>	}
766	>	if (hasFluctuatingCharge){
767	>	storageLayout |= DataStorage::dslFlucQPosition;
768	>	if(storageLayout & DataStorage::dslVelocity) {
769	>	storageLayout |= DataStorage::dslFlucQVelocity;
770	>	}
771	>	if (storageLayout & DataStorage::dslForce) {
772	>	storageLayout |= DataStorage::dslFlucQForce;
773	>	}
774	>	}
775	>
776	>	// if the user has asked for them, make sure we've got the memory for the
777	>	// objects defined.
778
779	<	painCave.isFatal = 1;
780	<	simError();
779	>	if (simParams->getOutputParticlePotential()) {
780	>	storageLayout |= DataStorage::dslParticlePot;
781		}
782
783	<	#ifdef IS_MPI
783	>	if (simParams->havePrintHeatFlux()) {
784	>	if (simParams->getPrintHeatFlux()) {
785	>	storageLayout |= DataStorage::dslParticlePot;
786	>	}
787	>	}
788
789	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
790	<	MPIcheckPoint();
789	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
790	>	storageLayout |= DataStorage::dslElectricField;
791	>	}
792
793	<	#endif // is_mpi
793	>	if (simParams->getOutputFluctuatingCharges()) {
794	>	storageLayout |= DataStorage::dslFlucQPosition;
795	>	storageLayout |= DataStorage::dslFlucQVelocity;
796	>	storageLayout |= DataStorage::dslFlucQForce;
797	>	}
798
799	<	}
799	>	info->setStorageLayout(storageLayout);
800
801	<	void SimCreator::setGlobalIndex(SimInfo *info) {
801	>	return storageLayout;
802	>	}
803	>
804	>	void SimCreator::setGlobalIndex(SimInfo *info) {
805		SimInfo::MoleculeIterator mi;
806		Molecule::AtomIterator ai;
807		Molecule::RigidBodyIterator ri;
808		Molecule::CutoffGroupIterator ci;
809	+	Molecule::IntegrableObjectIterator  ioi;
810		Molecule * mol;
811		Atom * atom;
812		RigidBody * rb;
#	Line 503 | Line 815 | void SimCreator::setGlobalIndex(SimInfo *info) {
815		int beginRigidBodyIndex;
816		int beginCutoffGroupIndex;
817		int nGlobalAtoms = info->getNGlobalAtoms();
818	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
819
507	–	#ifndef IS_MPI
508	–
820		beginAtomIndex = 0;
821	<	beginRigidBodyIndex = 0;
821	>	//rigidbody's index begins right after atom's
822	>	beginRigidBodyIndex = info->getNGlobalAtoms();
823		beginCutoffGroupIndex = 0;
824
825	<	#else
825	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
826	>
827	>	#ifdef IS_MPI
828	>	if (info->getMolToProc(i) == worldRank) {
829	>	#endif
830	>	// stuff to do if I own this molecule
831	>	mol = info->getMoleculeByGlobalIndex(i);
832
515	–	int nproc;
516	–	int myNode;
517	–
518	–	myNode = worldRank;
519	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
520	–
521	–	std::vector < int > tmpAtomsInProc(nproc, 0);
522	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
523	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
524	–	std::vector < int > NumAtomsInProc(nproc, 0);
525	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
526	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
527	–
528	–	tmpAtomsInProc[myNode] = info->getNAtoms();
529	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
530	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
531	–
532	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
533	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
534	–	MPI_SUM, MPI_COMM_WORLD);
535	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
536	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
537	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
538	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
539	–
540	–	beginAtomIndex = 0;
541	–	beginRigidBodyIndex = 0;
542	–	beginCutoffGroupIndex = 0;
543	–
544	–	for(int i = 0; i < myNode; i++) {
545	–	beginAtomIndex += NumAtomsInProc[i];
546	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
547	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
548	–	}
549	–
550	–	#endif
551	–
552	–	for(mol = info->beginMolecule(mi); mol != NULL;
553	–	mol = info->nextMolecule(mi)) {
554	–
833		//local index(index in DataStorge) of atom is important
834		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
835	<	atom->setGlobalIndex(beginAtomIndex++);
835	>	atom->setGlobalIndex(beginAtomIndex++);
836		}
837	<
837	>
838		for(rb = mol->beginRigidBody(ri); rb != NULL;
839		rb = mol->nextRigidBody(ri)) {
840	<	rb->setGlobalIndex(beginRigidBodyIndex++);
840	>	rb->setGlobalIndex(beginRigidBodyIndex++);
841		}
842	<
843	<	//local index of cutoff group is trivial, it only depends on the order of travesing
842	>
843	>	//local index of cutoff group is trivial, it only depends on
844	>	//the order of travesing
845		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
846		cg = mol->nextCutoffGroup(ci)) {
847	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
848	<	}
849	<	}
847	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
848	>	}
849	>
850	>	#ifdef IS_MPI
851	>	}  else {
852
853	+	// stuff to do if I don't own this molecule
854	+
855	+	int stampId = info->getMoleculeStampId(i);
856	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
857	+
858	+	beginAtomIndex += stamp->getNAtoms();
859	+	beginRigidBodyIndex += stamp->getNRigidBodies();
860	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
861	+	}
862	+	#endif
863	+
864	+	} //end for(int i=0)
865	+
866		//fill globalGroupMembership
867		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
868		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
869	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
870	<
871	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
872	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
873	<	}
874	<
875	<	}
869	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
870	>
871	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
872	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
873	>	}
874	>
875	>	}
876		}
877	<
877	>
878		#ifdef IS_MPI
879		// Since the globalGroupMembership has been zero filled and we've only
880		// poked values into the atoms we know, we can do an Allreduce
881		// to get the full globalGroupMembership array (We think).
882		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
883		// docs said we could.
884	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
885	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
886	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
887	<	info->setGlobalGroupMembership(tmpGroupMembership);
884	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
885	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
886	>	&tmpGroupMembership[0], nGlobalAtoms,
887	>	MPI::INT, MPI::SUM);
888	>	info->setGlobalGroupMembership(tmpGroupMembership);
889		#else
890		info->setGlobalGroupMembership(globalGroupMembership);
891		#endif
892	<
892	>
893		//fill molMembership
894	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
894	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
895	>	info->getNGlobalRigidBodies(), 0);
896
897	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
898	<
899	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
900	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
901	<	}
897	>	for(mol = info->beginMolecule(mi); mol != NULL;
898	>	mol = info->nextMolecule(mi)) {
899	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
900	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
901	>	}
902	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
903	>	rb = mol->nextRigidBody(ri)) {
904	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
905	>	}
906		}
907	<
907	>
908		#ifdef IS_MPI
909	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
910	<
911	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
912	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
909	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
910	>	info->getNGlobalRigidBodies(), 0);
911	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
912	>	nGlobalAtoms + nGlobalRigidBodies,
913	>	MPI::INT, MPI::SUM);
914
915		info->setGlobalMolMembership(tmpMolMembership);
916		#else
917		info->setGlobalMolMembership(globalMolMembership);
918		#endif
919
920	<	}
920	>	// nIOPerMol holds the number of integrable objects per molecule
921	>	// here the molecules are listed by their global indices.
922
923	<	void SimCreator::loadCoordinates(SimInfo* info) {
924	<	Globals* simParams;
925	<	simParams = info->getSimParams();
923	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
924	>	for (mol = info->beginMolecule(mi); mol != NULL;
925	>	mol = info->nextMolecule(mi)) {
926	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
927	>	}
928
929	<	if (!simParams->haveInitialConfig()) {
930	<	sprintf(painCave.errMsg,
931	<	"Cannot intialize a simulation without an initial configuration file.\n");
932	<	painCave.isFatal = 1;;
933	<	simError();
929	>	#ifdef IS_MPI
930	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
931	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
932	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
933	>	#else
934	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
935	>	#endif
936	>
937	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
938	>
939	>	int startingIndex = 0;
940	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
941	>	startingIOIndexForMol[i] = startingIndex;
942	>	startingIndex += numIntegrableObjectsPerMol[i];
943		}
944	<
945	<	DumpReader reader(info, simParams->getInitialConfig());
944	>
945	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
946	>	for (mol = info->beginMolecule(mi); mol != NULL;
947	>	mol = info->nextMolecule(mi)) {
948	>	int myGlobalIndex = mol->getGlobalIndex();
949	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
950	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
951	>	sd = mol->nextIntegrableObject(ioi)) {
952	>	sd->setGlobalIntegrableObjectIndex(globalIO);
953	>	IOIndexToIntegrableObject[globalIO] = sd;
954	>	globalIO++;
955	>	}
956	>	}
957	>
958	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
959	>
960	>	}
961	>
962	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
963	>
964	>	DumpReader reader(info, mdFileName);
965		int nframes = reader.getNFrames();
966	<
966	>
967		if (nframes > 0) {
968	<	reader.readFrame(nframes - 1);
968	>	reader.readFrame(nframes - 1);
969		} else {
970	<	//invalid initial coordinate file
971	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
972	<	simParams->getInitialConfig());
973	<	painCave.isFatal = 1;
974	<	simError();
970	>	//invalid initial coordinate file
971	>	sprintf(painCave.errMsg,
972	>	"Initial configuration file %s should at least contain one frame\n",
973	>	mdFileName.c_str());
974	>	painCave.isFatal = 1;
975	>	simError();
976		}
644	–
977		//copy the current snapshot to previous snapshot
978		info->getSnapshotManager()->advance();
979	<	}
979	>	}
980	>
981	>	} //end namespace OpenMD
982
649	–	} //end namespace oopse
983
651	–

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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