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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
Revision 1880 by gezelter, Mon Jun 17 18:28:30 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();
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	>	mdRawData.clear();
368	>
369	>	bool foundVersion = false;
370	>
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	>	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());
410	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
411		}
412
413		std::string forcefieldFileName;
414		forcefieldFileName = ff->getForceFieldFileName();
415	<
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	<	}
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);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
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
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
477		if (loadInitCoords)
478	<	loadCoordinates(info);
186	<
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
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
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;
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;
512	>	void SimCreator::divideMolecules(SimInfo *info) {
513	>	RealType a;
514		int nProcessors;
515		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
516		int nGlobalMols = info->getNGlobalMolecules();
517	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
517	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
518	>	// error
519	>	// condition:
520
521	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
522	<
521	>	nProcessors = MPI::COMM_WORLD.Get_size();
522	>
523		if (nProcessors > nGlobalMols) {
524	<	sprintf(painCave.errMsg,
525	<	"nProcessors (%d) > nMol (%d)\n"
526	<	"\tThe number of processors is larger than\n"
527	<	"\tthe number of molecules.  This will not result in a \n"
528	<	"\tusable division of atoms for force decomposition.\n"
529	<	"\tEither try a smaller number of processors, or run the\n"
530	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
531	<
532	<	painCave.isFatal = 1;
533	<	simError();
524	>	sprintf(painCave.errMsg,
525	>	"nProcessors (%d) > nMol (%d)\n"
526	>	"\tThe number of processors is larger than\n"
527	>	"\tthe number of molecules.  This will not result in a \n"
528	>	"\tusable division of atoms for force decomposition.\n"
529	>	"\tEither try a smaller number of processors, or run the\n"
530	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
531	>	nGlobalMols);
532	>
533	>	painCave.isFatal = 1;
534	>	simError();
535		}
536	<
536	>
537	>	Globals * simParams = info->getSimParams();
538	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
539	>	//random number generator
540	>	if (simParams->haveSeed()) {
541	>	int seedValue = simParams->getSeed();
542	>	myRandom = new SeqRandNumGen(seedValue);
543	>	}else {
544	>	myRandom = new SeqRandNumGen();
545	>	}
546	>
547	>
548		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
549	<
549	>
550		//initialize atomsPerProc
551		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
552	<
552	>
553		if (worldRank == 0) {
554	<	numerator = info->getNGlobalAtoms();
555	<	denominator = nProcessors;
556	<	precast = numerator / denominator;
557	<	nTarget = (int)(precast + 0.5);
558	<
559	<	for(i = 0; i < nGlobalMols; i++) {
321	<	done = 0;
322	<	loops = 0;
554	>	RealType numerator = info->getNGlobalAtoms();
555	>	RealType denominator = nProcessors;
556	>	RealType precast = numerator / denominator;
557	>	int nTarget = (int)(precast + 0.5);
558	>
559	>	for(int i = 0; i < nGlobalMols; i++) {
560
561	<	while (!done) {
562	<	loops++;
561	>	int done = 0;
562	>	int loops = 0;
563	>
564	>	while (!done) {
565	>	loops++;
566	>
567	>	// Pick a processor at random
568	>
569	>	int which_proc = (int) (myRandom->rand() * nProcessors);
570	>
571	>	//get the molecule stamp first
572	>	int stampId = info->getMoleculeStampId(i);
573	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
574	>
575	>	// How many atoms does this processor have so far?
576	>	int old_atoms = atomsPerProc[which_proc];
577	>	int add_atoms = moleculeStamp->getNAtoms();
578	>	int new_atoms = old_atoms + add_atoms;
579	>
580	>	// If we've been through this loop too many times, we need
581	>	// to just give up and assign the molecule to this processor
582	>	// and be done with it.
583	>
584	>	if (loops > 100) {
585
586	<	// Pick a processor at random
587	<
588	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
589	<
590	<	//get the molecule stamp first
591	<	int stampId = info->getMoleculeStampId(i);
592	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
593	<
594	<	// How many atoms does this processor have so far?
595	<	old_atoms = atomsPerProc[which_proc];
596	<	add_atoms = moleculeStamp->getNAtoms();
597	<	new_atoms = old_atoms + add_atoms;
598	<
599	<	// If we've been through this loop too many times, we need
600	<	// to just give up and assign the molecule to this processor
601	<	// and be done with it.
602	<
603	<	if (loops > 100) {
604	<	sprintf(painCave.errMsg,
605	<	"I've tried 100 times to assign molecule %d to a "
606	<	" processor, but can't find a good spot.\n"
607	<	"I'm assigning it at random to processor %d.\n",
608	<	i, which_proc);
609	<
610	<	painCave.isFatal = 0;
611	<	simError();
612	<
613	<	molToProcMap[i] = which_proc;
614	<	atomsPerProc[which_proc] += add_atoms;
615	<
616	<	done = 1;
617	<	continue;
618	<	}
619	<
620	<	// If we can add this molecule to this processor without sending
621	<	// it above nTarget, then go ahead and do it:
622	<
623	<	if (new_atoms <= nTarget) {
624	<	molToProcMap[i] = which_proc;
625	<	atomsPerProc[which_proc] += add_atoms;
626	<
627	<	done = 1;
628	<	continue;
629	<	}
630	<
631	<	// The only situation left is when new_atoms > nTarget.  We
632	<	// want to accept this with some probability that dies off the
633	<	// 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	<	}
586	>	sprintf(painCave.errMsg,
587	>	"There have been 100 attempts to assign molecule %d to an\n"
588	>	"\tunderworked processor, but there's no good place to\n"
589	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
590	>	i, which_proc);
591	>
592	>	painCave.isFatal = 0;
593	>	painCave.severity = OPENMD_INFO;
594	>	simError();
595	>
596	>	molToProcMap[i] = which_proc;
597	>	atomsPerProc[which_proc] += add_atoms;
598	>
599	>	done = 1;
600	>	continue;
601	>	}
602	>
603	>	// If we can add this molecule to this processor without sending
604	>	// it above nTarget, then go ahead and do it:
605	>
606	>	if (new_atoms <= nTarget) {
607	>	molToProcMap[i] = which_proc;
608	>	atomsPerProc[which_proc] += add_atoms;
609	>
610	>	done = 1;
611	>	continue;
612	>	}
613	>
614	>	// The only situation left is when new_atoms > nTarget.  We
615	>	// want to accept this with some probability that dies off the
616	>	// farther we are from nTarget
617	>
618	>	// roughly:  x = new_atoms - nTarget
619	>	//           Pacc(x) = exp(- a * x)
620	>	// where a = penalty / (average atoms per molecule)
621	>
622	>	RealType x = (RealType)(new_atoms - nTarget);
623	>	RealType y = myRandom->rand();
624	>
625	>	if (y < exp(- a * x)) {
626	>	molToProcMap[i] = which_proc;
627	>	atomsPerProc[which_proc] += add_atoms;
628	>
629	>	done = 1;
630	>	continue;
631	>	} else {
632	>	continue;
633	>	}
634		}
635	+	}
636	+
637	+	delete myRandom;
638
639	<	// Spray out this nonsense to all other processors:
640	<
397	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
639	>	// Spray out this nonsense to all other processors:
640	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
641		} else {
642	+
643	+	// Listen to your marching orders from processor 0:
644	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
645
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
646		}
647	<
647	>
648		info->setMolToProcMap(molToProcMap);
649		sprintf(checkPointMsg,
650		"Successfully divided the molecules among the processors.\n");
651	<	MPIcheckPoint();
652	<	}
653	<
651	>	errorCheckPoint();
652	>	}
653	>
654		#endif
655	<
656	<	void SimCreator::createMolecules(SimInfo *info) {
655	>
656	>	void SimCreator::createMolecules(SimInfo *info) {
657		MoleculeCreator molCreator;
658		int stampId;
659	<
659	>
660		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
661	<
661	>
662		#ifdef IS_MPI
663	<
664	<	if (info->getMolToProc(i) == worldRank) {
663	>
664	>	if (info->getMolToProc(i) == worldRank) {
665		#endif
666	<
667	<	stampId = info->getMoleculeStampId(i);
668	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
669	<	stampId, i, info->getLocalIndexManager());
670	<
671	<	info->addMolecule(mol);
672	<
666	>
667	>	stampId = info->getMoleculeStampId(i);
668	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
669	>	info->getMoleculeStamp(stampId),
670	>	stampId, i,
671	>	info->getLocalIndexManager());
672	>
673	>	info->addMolecule(mol);
674	>
675		#ifdef IS_MPI
676	<
677	<	}
678	<
676	>
677	>	}
678	>
679		#endif
680	<
680	>
681		} //end for(int i=0)
682	<	}
682	>	}
683	>
684	>	int SimCreator::computeStorageLayout(SimInfo* info) {
685
686	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
687	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
688	<	int i;
689	<	char * id;
690	<	MoleculeStamp * currentStamp;
691	<	Component** the_components = simParams->getComponents();
692	<	int n_components = simParams->getNComponents();
686	>	Globals* simParams = info->getSimParams();
687	>	int nRigidBodies = info->getNGlobalRigidBodies();
688	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
689	>	set<AtomType*>::iterator i;
690	>	bool hasDirectionalAtoms = false;
691	>	bool hasFixedCharge = false;
692	>	bool hasDipoles = false;
693	>	bool hasQuadrupoles = false;
694	>	bool hasPolarizable = false;
695	>	bool hasFluctuatingCharge = false;
696	>	bool hasMetallic = false;
697	>	int storageLayout = 0;
698	>	storageLayout |= DataStorage::dslPosition;
699	>	storageLayout |= DataStorage::dslVelocity;
700	>	storageLayout |= DataStorage::dslForce;
701
702	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
702	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
703
704	<	for(i = 0; i < n_components; i++) {
705	<	if (!the_components[i]->haveNMol()) {
706	<	// we have a problem
707	<	sprintf(painCave.errMsg,
708	<	"SimCreator Error. No global NMol or component NMol given.\n"
709	<	"\tCannot calculate the number of atoms.\n");
704	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
705	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
706	>	EAMAdapter ea = EAMAdapter( (*i) );
707	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
708	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
709	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
710	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
711
712	<	painCave.isFatal = 1;
713	<	simError();
714	<	}
715	<
716	<	id = the_components[i]->getType();
717	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
718	<
719	<	if (currentStamp == NULL) {
720	<	sprintf(painCave.errMsg,
721	<	"SimCreator error: Component \"%s\" was not found in the "
722	<	"list of declared molecules\n", id);
723	<
724	<	painCave.isFatal = 1;
725	<	simError();
726	<	}
727	<
728	<	moleculeStampPairs.push_back(
729	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
730	<	} //end for (i = 0; i < n_components; i++)
731	<	} else {
732	<	sprintf(painCave.errMsg, "SimSetup error.\n"
733	<	"\tSorry, the ability to specify total"
734	<	" nMols and then give molfractions in the components\n"
735	<	"\tis not currently supported."
736	<	" Please give nMol in the components.\n");
712	>	if (da.isDirectional()){
713	>	hasDirectionalAtoms = true;
714	>	}
715	>	if (ma.isDipole()){
716	>	hasDipoles = true;
717	>	}
718	>	if (ma.isQuadrupole()){
719	>	hasQuadrupoles = true;
720	>	}
721	>	if (ea.isEAM() || sca.isSuttonChen()){
722	>	hasMetallic = true;
723	>	}
724	>	if ( fca.isFixedCharge() ){
725	>	hasFixedCharge = true;
726	>	}
727	>	if ( fqa.isFluctuatingCharge() ){
728	>	hasFluctuatingCharge = true;
729	>	}
730	>	if ( pa.isPolarizable() ){
731	>	hasPolarizable = true;
732	>	}
733	>	}
734	>
735	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
736	>	storageLayout |= DataStorage::dslAmat;
737	>	if(storageLayout & DataStorage::dslVelocity) {
738	>	storageLayout |= DataStorage::dslAngularMomentum;
739	>	}
740	>	if (storageLayout & DataStorage::dslForce) {
741	>	storageLayout |= DataStorage::dslTorque;
742	>	}
743	>	}
744	>	if (hasDipoles) {
745	>	storageLayout |= DataStorage::dslDipole;
746	>	}
747	>	if (hasQuadrupoles) {
748	>	storageLayout |= DataStorage::dslQuadrupole;
749	>	}
750	>	if (hasFixedCharge || hasFluctuatingCharge) {
751	>	storageLayout |= DataStorage::dslSkippedCharge;
752	>	}
753	>	if (hasMetallic) {
754	>	storageLayout |= DataStorage::dslDensity;
755	>	storageLayout |= DataStorage::dslFunctional;
756	>	storageLayout |= DataStorage::dslFunctionalDerivative;
757	>	}
758	>	if (hasPolarizable) {
759	>	storageLayout |= DataStorage::dslElectricField;
760	>	}
761	>	if (hasFluctuatingCharge){
762	>	storageLayout |= DataStorage::dslFlucQPosition;
763	>	if(storageLayout & DataStorage::dslVelocity) {
764	>	storageLayout |= DataStorage::dslFlucQVelocity;
765	>	}
766	>	if (storageLayout & DataStorage::dslForce) {
767	>	storageLayout |= DataStorage::dslFlucQForce;
768	>	}
769	>	}
770	>
771	>	// if the user has asked for them, make sure we've got the memory for the
772	>	// objects defined.
773
774	<	painCave.isFatal = 1;
775	<	simError();
774	>	if (simParams->getOutputParticlePotential()) {
775	>	storageLayout |= DataStorage::dslParticlePot;
776		}
777
778	<	#ifdef IS_MPI
778	>	if (simParams->havePrintHeatFlux()) {
779	>	if (simParams->getPrintHeatFlux()) {
780	>	storageLayout |= DataStorage::dslParticlePot;
781	>	}
782	>	}
783
784	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
785	<	MPIcheckPoint();
784	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
785	>	storageLayout |= DataStorage::dslElectricField;
786	>	}
787
788	<	#endif // is_mpi
788	>	if (simParams->getOutputFluctuatingCharges()) {
789	>	storageLayout |= DataStorage::dslFlucQPosition;
790	>	storageLayout |= DataStorage::dslFlucQVelocity;
791	>	storageLayout |= DataStorage::dslFlucQForce;
792	>	}
793
794	<	}
794	>	info->setStorageLayout(storageLayout);
795
796	<	void SimCreator::setGlobalIndex(SimInfo *info) {
796	>	return storageLayout;
797	>	}
798	>
799	>	void SimCreator::setGlobalIndex(SimInfo *info) {
800		SimInfo::MoleculeIterator mi;
801		Molecule::AtomIterator ai;
802		Molecule::RigidBodyIterator ri;
803		Molecule::CutoffGroupIterator ci;
804	+	Molecule::IntegrableObjectIterator  ioi;
805		Molecule * mol;
806		Atom * atom;
807		RigidBody * rb;
#	Line 507 | Line 810 | void SimCreator::setGlobalIndex(SimInfo *info) {
810		int beginRigidBodyIndex;
811		int beginCutoffGroupIndex;
812		int nGlobalAtoms = info->getNGlobalAtoms();
813	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
814
511	–	#ifndef IS_MPI
512	–
815		beginAtomIndex = 0;
816	<	beginRigidBodyIndex = 0;
816	>	//rigidbody's index begins right after atom's
817	>	beginRigidBodyIndex = info->getNGlobalAtoms();
818		beginCutoffGroupIndex = 0;
819
820	<	#else
820	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
821	>
822	>	#ifdef IS_MPI
823	>	if (info->getMolToProc(i) == worldRank) {
824	>	#endif
825	>	// stuff to do if I own this molecule
826	>	mol = info->getMoleculeByGlobalIndex(i);
827
519	–	int nproc;
520	–	int myNode;
521	–
522	–	myNode = worldRank;
523	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524	–
525	–	std::vector < int > tmpAtomsInProc(nproc, 0);
526	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528	–	std::vector < int > NumAtomsInProc(nproc, 0);
529	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
530	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531	–
532	–	tmpAtomsInProc[myNode] = info->getNAtoms();
533	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535	–
536	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538	–	MPI_SUM, MPI_COMM_WORLD);
539	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543	–
544	–	beginAtomIndex = 0;
545	–	beginRigidBodyIndex = 0;
546	–	beginCutoffGroupIndex = 0;
547	–
548	–	for(int i = 0; i < myNode; i++) {
549	–	beginAtomIndex += NumAtomsInProc[i];
550	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
551	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552	–	}
553	–
554	–	//rigidbody's index begins right after atom's
555	–	beginRigidBodyIndex += info->getNGlobalAtoms();
556	–	#endif
557	–
558	–	for(mol = info->beginMolecule(mi); mol != NULL;
559	–	mol = info->nextMolecule(mi)) {
560	–
828		//local index(index in DataStorge) of atom is important
829		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	<	atom->setGlobalIndex(beginAtomIndex++);
830	>	atom->setGlobalIndex(beginAtomIndex++);
831		}
832	<
832	>
833		for(rb = mol->beginRigidBody(ri); rb != NULL;
834		rb = mol->nextRigidBody(ri)) {
835	<	rb->setGlobalIndex(beginRigidBodyIndex++);
835	>	rb->setGlobalIndex(beginRigidBodyIndex++);
836		}
837	<
838	<	//local index of cutoff group is trivial, it only depends on the order of travesing
837	>
838	>	//local index of cutoff group is trivial, it only depends on
839	>	//the order of travesing
840		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
841		cg = mol->nextCutoffGroup(ci)) {
842	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
843	<	}
844	<	}
842	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
843	>	}
844	>
845	>	#ifdef IS_MPI
846	>	}  else {
847
848	+	// stuff to do if I don't own this molecule
849	+
850	+	int stampId = info->getMoleculeStampId(i);
851	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
852	+
853	+	beginAtomIndex += stamp->getNAtoms();
854	+	beginRigidBodyIndex += stamp->getNRigidBodies();
855	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
856	+	}
857	+	#endif
858	+
859	+	} //end for(int i=0)
860	+
861		//fill globalGroupMembership
862		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
863		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
864	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
865	<
866	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
867	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
868	<	}
869	<
870	<	}
864	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
865	>
866	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
867	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
868	>	}
869	>
870	>	}
871		}
872	<
872	>
873		#ifdef IS_MPI
874		// Since the globalGroupMembership has been zero filled and we've only
875		// poked values into the atoms we know, we can do an Allreduce
876		// to get the full globalGroupMembership array (We think).
877		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
878		// docs said we could.
879	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
880	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
881	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
882	<	info->setGlobalGroupMembership(tmpGroupMembership);
879	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
880	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
881	>	&tmpGroupMembership[0], nGlobalAtoms,
882	>	MPI::INT, MPI::SUM);
883	>	info->setGlobalGroupMembership(tmpGroupMembership);
884		#else
885		info->setGlobalGroupMembership(globalGroupMembership);
886		#endif
887	<
887	>
888		//fill molMembership
889	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
889	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
890	>	info->getNGlobalRigidBodies(), 0);
891
892	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
893	<
894	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
896	<	}
892	>	for(mol = info->beginMolecule(mi); mol != NULL;
893	>	mol = info->nextMolecule(mi)) {
894	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
896	>	}
897	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
898	>	rb = mol->nextRigidBody(ri)) {
899	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
900	>	}
901		}
902	<
902	>
903		#ifdef IS_MPI
904	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
905	<
906	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
907	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
904	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
905	>	info->getNGlobalRigidBodies(), 0);
906	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
907	>	nGlobalAtoms + nGlobalRigidBodies,
908	>	MPI::INT, MPI::SUM);
909
910		info->setGlobalMolMembership(tmpMolMembership);
911		#else
912		info->setGlobalMolMembership(globalMolMembership);
913		#endif
914
915	<	}
915	>	// nIOPerMol holds the number of integrable objects per molecule
916	>	// here the molecules are listed by their global indices.
917
918	<	void SimCreator::loadCoordinates(SimInfo* info) {
919	<	Globals* simParams;
920	<	simParams = info->getSimParams();
918	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
919	>	for (mol = info->beginMolecule(mi); mol != NULL;
920	>	mol = info->nextMolecule(mi)) {
921	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
922	>	}
923
924	<	if (!simParams->haveInitialConfig()) {
925	<	sprintf(painCave.errMsg,
926	<	"Cannot intialize a simulation without an initial configuration file.\n");
927	<	painCave.isFatal = 1;;
928	<	simError();
924	>	#ifdef IS_MPI
925	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
926	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
927	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
928	>	#else
929	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
930	>	#endif
931	>
932	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
933	>
934	>	int startingIndex = 0;
935	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
936	>	startingIOIndexForMol[i] = startingIndex;
937	>	startingIndex += numIntegrableObjectsPerMol[i];
938		}
939	<
940	<	DumpReader reader(info, simParams->getInitialConfig());
939	>
940	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
941	>	for (mol = info->beginMolecule(mi); mol != NULL;
942	>	mol = info->nextMolecule(mi)) {
943	>	int myGlobalIndex = mol->getGlobalIndex();
944	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
945	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
946	>	sd = mol->nextIntegrableObject(ioi)) {
947	>	sd->setGlobalIntegrableObjectIndex(globalIO);
948	>	IOIndexToIntegrableObject[globalIO] = sd;
949	>	globalIO++;
950	>	}
951	>	}
952	>
953	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
954	>
955	>	}
956	>
957	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
958	>
959	>	DumpReader reader(info, mdFileName);
960		int nframes = reader.getNFrames();
961	<
961	>
962		if (nframes > 0) {
963	<	reader.readFrame(nframes - 1);
963	>	reader.readFrame(nframes - 1);
964		} else {
965	<	//invalid initial coordinate file
966	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
967	<	simParams->getInitialConfig());
968	<	painCave.isFatal = 1;
969	<	simError();
965	>	//invalid initial coordinate file
966	>	sprintf(painCave.errMsg,
967	>	"Initial configuration file %s should at least contain one frame\n",
968	>	mdFileName.c_str());
969	>	painCave.isFatal = 1;
970	>	simError();
971		}
650	–
972		//copy the current snapshot to previous snapshot
973		info->getSnapshotManager()->advance();
974	<	}
974	>	}
975	>
976	>	} //end namespace OpenMD
977
655	–	} //end namespace oopse
978
657	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
Revision 1880 by gezelter, Mon Jun 17 18:28:30 2013 UTC

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