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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 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
50	<	#include <sprng.h>
50	>	#ifdef IS_MPI
51	>	#include "mpi.h"
52	>	#include "math/ParallelRandNumGen.hpp"
53	>	#endif
54
55	+	#include <exception>
56	+	#include <iostream>
57	+	#include <sstream>
58	+	#include <string>
59	+
60		#include "brains/MoleculeCreator.hpp"
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "io/parse_me.h"
57	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67	<	#ifdef IS_MPI
68	<	#include "io/mpiBASS.h"
69	<	#include "math/randomSPRNG.hpp"
70	<	#endif
67	>	#include "math/SeqRandNumGen.hpp"
68	>	#include "mdParser/MDLexer.hpp"
69	>	#include "mdParser/MDParser.hpp"
70	>	#include "mdParser/MDTreeParser.hpp"
71	>	#include "mdParser/SimplePreprocessor.hpp"
72	>	#include "antlr/ANTLRException.hpp"
73	>	#include "antlr/TokenStreamRecognitionException.hpp"
74	>	#include "antlr/TokenStreamIOException.hpp"
75	>	#include "antlr/TokenStreamException.hpp"
76	>	#include "antlr/RecognitionException.hpp"
77	>	#include "antlr/CharStreamException.hpp"
78
79	<	namespace oopse {
79	>	#include "antlr/MismatchedCharException.hpp"
80	>	#include "antlr/MismatchedTokenException.hpp"
81	>	#include "antlr/NoViableAltForCharException.hpp"
82	>	#include "antlr/NoViableAltException.hpp"
83
84	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
84	>	#include "types/DirectionalAdapter.hpp"
85	>	#include "types/MultipoleAdapter.hpp"
86	>	#include "types/EAMAdapter.hpp"
87	>	#include "types/SuttonChenAdapter.hpp"
88	>	#include "types/PolarizableAdapter.hpp"
89	>	#include "types/FixedChargeAdapter.hpp"
90	>	#include "types/FluctuatingChargeAdapter.hpp"
91
69	–	#ifdef IS_MPI
92
93	<	if (worldRank == 0) {
94	<	#endif // is_mpi
93	>	namespace OpenMD {
94	>
95	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
96	>	Globals* simParams = NULL;
97	>	try {
98
99	<	simParams->initalize();
100	<	set_interface_stamps(stamps, simParams);
99	>	// Create a preprocessor that preprocesses md file into an ostringstream
100	>	std::stringstream ppStream;
101	>	#ifdef IS_MPI
102	>	int streamSize;
103	>	const int masterNode = 0;
104
105	<	#ifdef IS_MPI
105	>	if (worldRank == masterNode) {
106	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
107	>	#endif
108	>	SimplePreprocessor preprocessor;
109	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
110	>
111	>	#ifdef IS_MPI
112	>	//brocasting the stream size
113	>	streamSize = ppStream.str().size() +1;
114	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
115	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
116	>
117	>	} else {
118	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
119
120	<	mpiEventInit();
120	>	//get stream size
121	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
122
123	<	#endif
123	>	char* buf = new char[streamSize];
124	>	assert(buf);
125	>
126	>	//receive file content
127	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
128	>
129	>	ppStream.str(buf);
130	>	delete [] buf;
131	>	}
132	>	#endif
133	>	// Create a scanner that reads from the input stream
134	>	MDLexer lexer(ppStream);
135	>	lexer.setFilename(filename);
136	>	lexer.initDeferredLineCount();
137	>
138	>	// Create a parser that reads from the scanner
139	>	MDParser parser(lexer);
140	>	parser.setFilename(filename);
141
142	<	yacc_BASS(mdFileName.c_str());
142	>	// Create an observer that synchorizes file name change
143	>	FilenameObserver observer;
144	>	observer.setLexer(&lexer);
145	>	observer.setParser(&parser);
146	>	lexer.setObserver(&observer);
147	>
148	>	antlr::ASTFactory factory;
149	>	parser.initializeASTFactory(factory);
150	>	parser.setASTFactory(&factory);
151	>	parser.mdfile();
152
153	<	#ifdef IS_MPI
153	>	// Create a tree parser that reads information into Globals
154	>	MDTreeParser treeParser;
155	>	treeParser.initializeASTFactory(factory);
156	>	treeParser.setASTFactory(&factory);
157	>	simParams = treeParser.walkTree(parser.getAST());
158	>	}
159
160	<	throwMPIEvent(NULL);
160	>
161	>	catch(antlr::MismatchedCharException& e) {
162	>	sprintf(painCave.errMsg,
163	>	"parser exception: %s %s:%d:%d\n",
164	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
165	>	painCave.isFatal = 1;
166	>	simError();
167	>	}
168	>	catch(antlr::MismatchedTokenException &e) {
169	>	sprintf(painCave.errMsg,
170	>	"parser exception: %s %s:%d:%d\n",
171	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
172	>	painCave.isFatal = 1;
173	>	simError();
174	>	}
175	>	catch(antlr::NoViableAltForCharException &e) {
176	>	sprintf(painCave.errMsg,
177	>	"parser exception: %s %s:%d:%d\n",
178	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
179	>	painCave.isFatal = 1;
180	>	simError();
181	>	}
182	>	catch(antlr::NoViableAltException &e) {
183	>	sprintf(painCave.errMsg,
184	>	"parser exception: %s %s:%d:%d\n",
185	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
186	>	painCave.isFatal = 1;
187	>	simError();
188	>	}
189	>
190	>	catch(antlr::TokenStreamRecognitionException& e) {
191	>	sprintf(painCave.errMsg,
192	>	"parser exception: %s %s:%d:%d\n",
193	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
194	>	painCave.isFatal = 1;
195	>	simError();
196	>	}
197	>
198	>	catch(antlr::TokenStreamIOException& e) {
199	>	sprintf(painCave.errMsg,
200	>	"parser exception: %s\n",
201	>	e.getMessage().c_str());
202	>	painCave.isFatal = 1;
203	>	simError();
204	>	}
205	>
206	>	catch(antlr::TokenStreamException& e) {
207	>	sprintf(painCave.errMsg,
208	>	"parser exception: %s\n",
209	>	e.getMessage().c_str());
210	>	painCave.isFatal = 1;
211	>	simError();
212	>	}
213	>	catch (antlr::RecognitionException& e) {
214	>	sprintf(painCave.errMsg,
215	>	"parser exception: %s %s:%d:%d\n",
216	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
217	>	painCave.isFatal = 1;
218	>	simError();
219	>	}
220	>	catch (antlr::CharStreamException& e) {
221	>	sprintf(painCave.errMsg,
222	>	"parser exception: %s\n",
223	>	e.getMessage().c_str());
224	>	painCave.isFatal = 1;
225	>	simError();
226	>	}
227	>	catch (OpenMDException& e) {
228	>	sprintf(painCave.errMsg,
229	>	"%s\n",
230	>	e.getMessage().c_str());
231	>	painCave.isFatal = 1;
232	>	simError();
233	>	}
234	>	catch (std::exception& e) {
235	>	sprintf(painCave.errMsg,
236	>	"parser exception: %s\n",
237	>	e.what());
238	>	painCave.isFatal = 1;
239	>	simError();
240	>	}
241	>
242	>	simParams->setMDfileVersion(mdFileVersion);
243	>	return simParams;
244	>	}
245	>
246	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
247	>	bool loadInitCoords) {
248	>
249	>	const int bufferSize = 65535;
250	>	char buffer[bufferSize];
251	>	int lineNo = 0;
252	>	std::string mdRawData;
253	>	int metaDataBlockStart = -1;
254	>	int metaDataBlockEnd = -1;
255	>	int i, j;
256	>	streamoff mdOffset;
257	>	int mdFileVersion;
258	>
259	>	// Create a string for embedding the version information in the MetaData
260	>	std::string version;
261	>	version.assign("## Last run using OpenMD Version: ");
262	>	version.append(OPENMD_VERSION_MAJOR);
263	>	version.append(".");
264	>	version.append(OPENMD_VERSION_MINOR);
265	>
266	>	std::string svnrev;
267	>	//convert a macro from compiler to a string in c++
268	>	STR_DEFINE(svnrev, SVN_REV );
269	>	version.append(" Revision: ");
270	>	// If there's no SVN revision, just call this the RELEASE revision.
271	>	if (!svnrev.empty()) {
272	>	version.append(svnrev);
273		} else {
274	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
274	>	version.append("RELEASE");
275		}
276	+
277	+	#ifdef IS_MPI
278	+	const int masterNode = 0;
279	+	if (worldRank == masterNode) {
280	+	#endif
281
282	<	#endif
282	>	std::ifstream mdFile_;
283	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
284	>
285	>	if (mdFile_.fail()) {
286	>	sprintf(painCave.errMsg,
287	>	"SimCreator: Cannot open file: %s\n",
288	>	mdFileName.c_str());
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292
293	<	}
293	>	mdFile_.getline(buffer, bufferSize);
294	>	++lineNo;
295	>	std::string line = trimLeftCopy(buffer);
296	>	i = CaseInsensitiveFind(line, "<OpenMD");
297	>	if (static_cast<size_t>(i) == string::npos) {
298	>	// try the older file strings to see if that works:
299	>	i = CaseInsensitiveFind(line, "<OOPSE");
300	>	}
301	>
302	>	if (static_cast<size_t>(i) == string::npos) {
303	>	// still no luck!
304	>	sprintf(painCave.errMsg,
305	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
306	>	mdFileName.c_str());
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	// found the correct opening string, now try to get the file
312	>	// format version number.
313
314	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
315	<
316	<	MakeStamps * stamps = new MakeStamps();
314	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
315	>	std::string fileType = tokenizer.nextToken();
316	>	toUpper(fileType);
317
318	<	Globals * simParams = new Globals();
318	>	mdFileVersion = 0;
319
320	<	//parse meta-data file
321	<	parseFile(mdFileName, stamps, simParams);
320	>	if (fileType == "OPENMD") {
321	>	while (tokenizer.hasMoreTokens()) {
322	>	std::string token(tokenizer.nextToken());
323	>	toUpper(token);
324	>	if (token == "VERSION") {
325	>	mdFileVersion = tokenizer.nextTokenAsInt();
326	>	break;
327	>	}
328	>	}
329	>	}
330	>
331	>	//scan through the input stream and find MetaData tag
332	>	while(mdFile_.getline(buffer, bufferSize)) {
333	>	++lineNo;
334	>
335	>	std::string line = trimLeftCopy(buffer);
336	>	if (metaDataBlockStart == -1) {
337	>	i = CaseInsensitiveFind(line, "<MetaData>");
338	>	if (i != string::npos) {
339	>	metaDataBlockStart = lineNo;
340	>	mdOffset = mdFile_.tellg();
341	>	}
342	>	} else {
343	>	i = CaseInsensitiveFind(line, "</MetaData>");
344	>	if (i != string::npos) {
345	>	metaDataBlockEnd = lineNo;
346	>	}
347	>	}
348	>	}
349
350	<	//create the force field
351	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
352	<	simParams->getForceField());
353	<
354	<	if (ff == NULL) {
355	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
356	<	simParams->getForceField());
357	<	painCave.isFatal = 1;
358	<	simError();
350	>	if (metaDataBlockStart == -1) {
351	>	sprintf(painCave.errMsg,
352	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
353	>	mdFileName.c_str());
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
357	>	if (metaDataBlockEnd == -1) {
358	>	sprintf(painCave.errMsg,
359	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
360	>	mdFileName.c_str());
361	>	painCave.isFatal = 1;
362	>	simError();
363	>	}
364	>
365	>	mdFile_.clear();
366	>	mdFile_.seekg(0);
367	>	mdFile_.seekg(mdOffset);
368	>
369	>	mdRawData.clear();
370	>
371	>	bool foundVersion = false;
372	>
373	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
374	>	mdFile_.getline(buffer, bufferSize);
375	>	std::string line = trimLeftCopy(buffer);
376	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
377	>	if (static_cast<size_t>(j) != string::npos) {
378	>	foundVersion = true;
379	>	mdRawData += version;
380	>	} else {
381	>	mdRawData += buffer;
382	>	}
383	>	mdRawData += "\n";
384	>	}
385	>
386	>	if (!foundVersion) mdRawData += version + "\n";
387	>
388	>	mdFile_.close();
389	>
390	>	#ifdef IS_MPI
391		}
392	+	#endif
393
394	+	std::stringstream rawMetaDataStream(mdRawData);
395	+
396	+	//parse meta-data file
397	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
398	+	metaDataBlockStart + 1);
399	+
400	+	//create the force field
401	+	ForceField * ff = new ForceField(simParams->getForceField());
402	+
403	+	if (ff == NULL) {
404	+	sprintf(painCave.errMsg,
405	+	"ForceField Factory can not create %s force field\n",
406	+	simParams->getForceField().c_str());
407	+	painCave.isFatal = 1;
408	+	simError();
409	+	}
410	+
411		if (simParams->haveForceFieldFileName()) {
412	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
412	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
413		}
414
415		std::string forcefieldFileName;
416		forcefieldFileName = ff->getForceFieldFileName();
417	<
417	>
418		if (simParams->haveForceFieldVariant()) {
419	<	//If the force field has variant, the variant force field name will be
420	<	//Base.variant.frc. For exampel EAM.u6.frc
421	<
422	<	std::string variant = simParams->getForceFieldVariant();
423	<
424	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
425	<	variant = "." + variant;
426	<	if (pos != std::string::npos) {
427	<	forcefieldFileName.insert(pos, variant);
428	<	} else {
429	<	//If the default force field file name does not containt .frc suffix, just append the .variant
430	<	forcefieldFileName.append(variant);
431	<	}
419	>	//If the force field has variant, the variant force field name will be
420	>	//Base.variant.frc. For exampel EAM.u6.frc
421	>
422	>	std::string variant = simParams->getForceFieldVariant();
423	>
424	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
425	>	variant = "." + variant;
426	>	if (pos != std::string::npos) {
427	>	forcefieldFileName.insert(pos, variant);
428	>	} else {
429	>	//If the default force field file name does not containt .frc suffix, just append the .variant
430	>	forcefieldFileName.append(variant);
431	>	}
432		}
433
434		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
435		//create SimInfo
436	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
436	>	SimInfo * info = new SimInfo(ff, simParams);
437
438	<	//gather parameters (SimCreator only retrieves part of the parameters)
438	>	info->setRawMetaData(mdRawData);
439	>
440	>	//gather parameters (SimCreator only retrieves part of the
441	>	//parameters)
442		gatherParameters(info, mdFileName);
443	<
443	>
444		//divide the molecules and determine the global index of molecules
445		#ifdef IS_MPI
446		divideMolecules(info);
447		#endif
448	<
448	>
449		//create the molecules
450		createMolecules(info);
451	+
452	+	//find the storage layout
453
454	+	int storageLayout = computeStorageLayout(info);
455
456	<	//allocate memory for DataStorage(circular reference, need to break it)
457	<	info->setSnapshotManager(new SimSnapshotManager(info));
456	>	//allocate memory for DataStorage(circular reference, need to
457	>	//break it)
458	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
459
460	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
461	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
462	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
460	>	//set the global index of atoms, rigidbodies and cutoffgroups
461	>	//(only need to be set once, the global index will never change
462	>	//again). Local indices of atoms and rigidbodies are already set
463	>	//by MoleculeCreator class which actually delegates the
464	>	//responsibility to LocalIndexManager.
465		setGlobalIndex(info);
466	<
467	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
468	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
469	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
470	<	//we can determine the beginning global indices of atoms before they get created.
466	>
467	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
468	>	//method, at that point atoms don't have the global index yet
469	>	//(their global index are all initialized to -1).  Therefore we
470	>	//have to call addInteractionPairs explicitly here. A way to work
471	>	//around is that we can determine the beginning global indices of
472	>	//atoms before they get created.
473		SimInfo::MoleculeIterator mi;
474		Molecule* mol;
475		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
476	<	info->addExcludePairs(mol);
476	>	info->addInteractionPairs(mol);
477		}
478
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
479		if (loadInitCoords)
480	<	loadCoordinates(info);
186	<
480	>	loadCoordinates(info, mdFileName);
481		return info;
482	<	}
483	<
484	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
485	<
486	<	//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
482	>	}
483	>
484	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
485	>
486	>	//figure out the output file names
487		std::string prefix;
488	<
488	>
489		#ifdef IS_MPI
490	<
490	>
491		if (worldRank == 0) {
492		#endif // is_mpi
493	<
494	<	if (simParams->haveFinalConfig()) {
495	<	prefix = getPrefix(simParams->getFinalConfig());
496	<	} else {
497	<	prefix = getPrefix(mdfile);
498	<	}
499	<
500	<	info->setFinalConfigFileName(prefix + ".eor");
501	<	info->setDumpFileName(prefix + ".dump");
502	<	info->setStatFileName(prefix + ".stat");
503	<
493	>	Globals * simParams = info->getSimParams();
494	>	if (simParams->haveFinalConfig()) {
495	>	prefix = getPrefix(simParams->getFinalConfig());
496	>	} else {
497	>	prefix = getPrefix(mdfile);
498	>	}
499	>
500	>	info->setFinalConfigFileName(prefix + ".eor");
501	>	info->setDumpFileName(prefix + ".dump");
502	>	info->setStatFileName(prefix + ".stat");
503	>	info->setRestFileName(prefix + ".zang");
504	>
505		#ifdef IS_MPI
506	<
506	>
507		}
508	<
508	>
509		#endif
510	<
511	<	}
512	<
510	>
511	>	}
512	>
513		#ifdef IS_MPI
514	<	void SimCreator::divideMolecules(SimInfo *info) {
515	<	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;
514	>	void SimCreator::divideMolecules(SimInfo *info) {
515	>	RealType a;
516		int nProcessors;
517		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
518		int nGlobalMols = info->getNGlobalMolecules();
519	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
519	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
520	>	// error
521	>	// condition:
522
523	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
524	<
523	>	nProcessors = MPI::COMM_WORLD.Get_size();
524	>
525		if (nProcessors > nGlobalMols) {
526	<	sprintf(painCave.errMsg,
527	<	"nProcessors (%d) > nMol (%d)\n"
528	<	"\tThe number of processors is larger than\n"
529	<	"\tthe number of molecules.  This will not result in a \n"
530	<	"\tusable division of atoms for force decomposition.\n"
531	<	"\tEither try a smaller number of processors, or run the\n"
532	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
533	<
534	<	painCave.isFatal = 1;
535	<	simError();
526	>	sprintf(painCave.errMsg,
527	>	"nProcessors (%d) > nMol (%d)\n"
528	>	"\tThe number of processors is larger than\n"
529	>	"\tthe number of molecules.  This will not result in a \n"
530	>	"\tusable division of atoms for force decomposition.\n"
531	>	"\tEither try a smaller number of processors, or run the\n"
532	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
533	>	nGlobalMols);
534	>
535	>	painCave.isFatal = 1;
536	>	simError();
537		}
538	<
538	>
539	>	Globals * simParams = info->getSimParams();
540	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
541	>	//random number generator
542	>	if (simParams->haveSeed()) {
543	>	int seedValue = simParams->getSeed();
544	>	myRandom = new SeqRandNumGen(seedValue);
545	>	}else {
546	>	myRandom = new SeqRandNumGen();
547	>	}
548	>
549	>
550		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
551	<
551	>
552		//initialize atomsPerProc
553		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
554	<
554	>
555		if (worldRank == 0) {
556	<	numerator = info->getNGlobalAtoms();
557	<	denominator = nProcessors;
558	<	precast = numerator / denominator;
559	<	nTarget = (int)(precast + 0.5);
556	>	RealType numerator = info->getNGlobalAtoms();
557	>	RealType denominator = nProcessors;
558	>	RealType precast = numerator / denominator;
559	>	int nTarget = (int)(precast + 0.5);
560	>
561	>	for(int i = 0; i < nGlobalMols; i++) {
562
563	<	for(i = 0; i < nGlobalMols; i++) {
564	<	done = 0;
565	<	loops = 0;
563	>	int done = 0;
564	>	int loops = 0;
565	>
566	>	while (!done) {
567	>	loops++;
568	>
569	>	// Pick a processor at random
570	>
571	>	int which_proc = (int) (myRandom->rand() * nProcessors);
572	>
573	>	//get the molecule stamp first
574	>	int stampId = info->getMoleculeStampId(i);
575	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
576	>
577	>	// How many atoms does this processor have so far?
578	>	int old_atoms = atomsPerProc[which_proc];
579	>	int add_atoms = moleculeStamp->getNAtoms();
580	>	int new_atoms = old_atoms + add_atoms;
581	>
582	>	// If we've been through this loop too many times, we need
583	>	// to just give up and assign the molecule to this processor
584	>	// and be done with it.
585	>
586	>	if (loops > 100) {
587
588	<	while (!done) {
589	<	loops++;
590	<
591	<	// Pick a processor at random
592	<
593	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
594	<
595	<	//get the molecule stamp first
596	<	int stampId = info->getMoleculeStampId(i);
597	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
598	<
599	<	// How many atoms does this processor have so far?
600	<	old_atoms = atomsPerProc[which_proc];
601	<	add_atoms = moleculeStamp->getNAtoms();
602	<	new_atoms = old_atoms + add_atoms;
603	<
604	<	// If we've been through this loop too many times, we need
605	<	// to just give up and assign the molecule to this processor
606	<	// and be done with it.
607	<
608	<	if (loops > 100) {
609	<	sprintf(painCave.errMsg,
610	<	"I've tried 100 times to assign molecule %d to a "
611	<	" processor, but can't find a good spot.\n"
612	<	"I'm assigning it at random to processor %d.\n",
613	<	i, which_proc);
614	<
615	<	painCave.isFatal = 0;
616	<	simError();
617	<
618	<	molToProcMap[i] = which_proc;
619	<	atomsPerProc[which_proc] += add_atoms;
620	<
621	<	done = 1;
622	<	continue;
623	<	}
624	<
625	<	// If we can add this molecule to this processor without sending
626	<	// it above nTarget, then go ahead and do it:
627	<
628	<	if (new_atoms <= nTarget) {
629	<	molToProcMap[i] = which_proc;
630	<	atomsPerProc[which_proc] += add_atoms;
631	<
632	<	done = 1;
633	<	continue;
634	<	}
635	<
372	<	// The only situation left is when new_atoms > nTarget.  We
373	<	// want to accept this with some probability that dies off the
374	<	// farther we are from nTarget
375	<
376	<	// roughly:  x = new_atoms - nTarget
377	<	//           Pacc(x) = exp(- a * x)
378	<	// where a = penalty / (average atoms per molecule)
379	<
380	<	x = (double)(new_atoms - nTarget);
381	<	y = myRandom.getRandom();
382	<
383	<	if (y < exp(- a * x)) {
384	<	molToProcMap[i] = which_proc;
385	<	atomsPerProc[which_proc] += add_atoms;
386	<
387	<	done = 1;
388	<	continue;
389	<	} else {
390	<	continue;
391	<	}
392	<	}
588	>	sprintf(painCave.errMsg,
589	>	"There have been 100 attempts to assign molecule %d to an\n"
590	>	"\tunderworked processor, but there's no good place to\n"
591	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
592	>	i, which_proc);
593	>
594	>	painCave.isFatal = 0;
595	>	painCave.severity = OPENMD_INFO;
596	>	simError();
597	>
598	>	molToProcMap[i] = which_proc;
599	>	atomsPerProc[which_proc] += add_atoms;
600	>
601	>	done = 1;
602	>	continue;
603	>	}
604	>
605	>	// If we can add this molecule to this processor without sending
606	>	// it above nTarget, then go ahead and do it:
607	>
608	>	if (new_atoms <= nTarget) {
609	>	molToProcMap[i] = which_proc;
610	>	atomsPerProc[which_proc] += add_atoms;
611	>
612	>	done = 1;
613	>	continue;
614	>	}
615	>
616	>	// The only situation left is when new_atoms > nTarget.  We
617	>	// want to accept this with some probability that dies off the
618	>	// farther we are from nTarget
619	>
620	>	// roughly:  x = new_atoms - nTarget
621	>	//           Pacc(x) = exp(- a * x)
622	>	// where a = penalty / (average atoms per molecule)
623	>
624	>	RealType x = (RealType)(new_atoms - nTarget);
625	>	RealType y = myRandom->rand();
626	>
627	>	if (y < exp(- a * x)) {
628	>	molToProcMap[i] = which_proc;
629	>	atomsPerProc[which_proc] += add_atoms;
630	>
631	>	done = 1;
632	>	continue;
633	>	} else {
634	>	continue;
635	>	}
636		}
637	+	}
638	+
639	+	delete myRandom;
640
641	<	// Spray out this nonsense to all other processors:
642	<
397	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
641	>	// Spray out this nonsense to all other processors:
642	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
643		} else {
644	+
645	+	// Listen to your marching orders from processor 0:
646	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
647
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
648		}
649	<
649	>
650		info->setMolToProcMap(molToProcMap);
651		sprintf(checkPointMsg,
652		"Successfully divided the molecules among the processors.\n");
653	<	MPIcheckPoint();
654	<	}
655	<
653	>	errorCheckPoint();
654	>	}
655	>
656		#endif
657	<
658	<	void SimCreator::createMolecules(SimInfo *info) {
657	>
658	>	void SimCreator::createMolecules(SimInfo *info) {
659		MoleculeCreator molCreator;
660		int stampId;
661	<
661	>
662		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
663	<
663	>
664		#ifdef IS_MPI
665	<
666	<	if (info->getMolToProc(i) == worldRank) {
665	>
666	>	if (info->getMolToProc(i) == worldRank) {
667		#endif
668	<
669	<	stampId = info->getMoleculeStampId(i);
670	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
671	<	stampId, i, info->getLocalIndexManager());
672	<
673	<	info->addMolecule(mol);
674	<
668	>
669	>	stampId = info->getMoleculeStampId(i);
670	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
671	>	info->getMoleculeStamp(stampId),
672	>	stampId, i,
673	>	info->getLocalIndexManager());
674	>
675	>	info->addMolecule(mol);
676	>
677		#ifdef IS_MPI
678	<
679	<	}
680	<
678	>
679	>	}
680	>
681		#endif
682	<
682	>
683		} //end for(int i=0)
684	<	}
684	>	}
685	>
686	>	int SimCreator::computeStorageLayout(SimInfo* info) {
687
688	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
689	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
690	<	int i;
691	<	char * id;
692	<	MoleculeStamp * currentStamp;
693	<	Component** the_components = simParams->getComponents();
694	<	int n_components = simParams->getNComponents();
688	>	Globals* simParams = info->getSimParams();
689	>	int nRigidBodies = info->getNGlobalRigidBodies();
690	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
691	>	set<AtomType*>::iterator i;
692	>	bool hasDirectionalAtoms = false;
693	>	bool hasFixedCharge = false;
694	>	bool hasDipoles = false;
695	>	bool hasQuadrupoles = false;
696	>	bool hasPolarizable = false;
697	>	bool hasFluctuatingCharge = false;
698	>	bool hasMetallic = false;
699	>	int storageLayout = 0;
700	>	storageLayout |= DataStorage::dslPosition;
701	>	storageLayout |= DataStorage::dslVelocity;
702	>	storageLayout |= DataStorage::dslForce;
703
704	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
704	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
705
706	<	for(i = 0; i < n_components; i++) {
707	<	if (!the_components[i]->haveNMol()) {
708	<	// we have a problem
709	<	sprintf(painCave.errMsg,
710	<	"SimCreator Error. No global NMol or component NMol given.\n"
711	<	"\tCannot calculate the number of atoms.\n");
706	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
707	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
708	>	EAMAdapter ea = EAMAdapter( (*i) );
709	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
710	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
711	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
712	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
713
714	<	painCave.isFatal = 1;
715	<	simError();
716	<	}
717	<
718	<	id = the_components[i]->getType();
719	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
720	<
721	<	if (currentStamp == NULL) {
722	<	sprintf(painCave.errMsg,
723	<	"SimCreator error: Component \"%s\" was not found in the "
724	<	"list of declared molecules\n", id);
725	<
726	<	painCave.isFatal = 1;
727	<	simError();
728	<	}
729	<
730	<	moleculeStampPairs.push_back(
731	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
732	<	} //end for (i = 0; i < n_components; i++)
733	<	} else {
734	<	sprintf(painCave.errMsg, "SimSetup error.\n"
735	<	"\tSorry, the ability to specify total"
736	<	" nMols and then give molfractions in the components\n"
737	<	"\tis not currently supported."
738	<	" Please give nMol in the components.\n");
714	>	if (da.isDirectional()){
715	>	hasDirectionalAtoms = true;
716	>	}
717	>	if (ma.isDipole()){
718	>	hasDipoles = true;
719	>	}
720	>	if (ma.isQuadrupole()){
721	>	hasQuadrupoles = true;
722	>	}
723	>	if (ea.isEAM() || sca.isSuttonChen()){
724	>	hasMetallic = true;
725	>	}
726	>	if ( fca.isFixedCharge() ){
727	>	hasFixedCharge = true;
728	>	}
729	>	if ( fqa.isFluctuatingCharge() ){
730	>	hasFluctuatingCharge = true;
731	>	}
732	>	if ( pa.isPolarizable() ){
733	>	hasPolarizable = true;
734	>	}
735	>	}
736	>
737	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
738	>	storageLayout |= DataStorage::dslAmat;
739	>	if(storageLayout & DataStorage::dslVelocity) {
740	>	storageLayout |= DataStorage::dslAngularMomentum;
741	>	}
742	>	if (storageLayout & DataStorage::dslForce) {
743	>	storageLayout |= DataStorage::dslTorque;
744	>	}
745	>	}
746	>	if (hasDipoles) {
747	>	storageLayout |= DataStorage::dslDipole;
748	>	}
749	>	if (hasQuadrupoles) {
750	>	storageLayout |= DataStorage::dslQuadrupole;
751	>	}
752	>	if (hasFixedCharge || hasFluctuatingCharge) {
753	>	storageLayout |= DataStorage::dslSkippedCharge;
754	>	}
755	>	if (hasMetallic) {
756	>	storageLayout |= DataStorage::dslDensity;
757	>	storageLayout |= DataStorage::dslFunctional;
758	>	storageLayout |= DataStorage::dslFunctionalDerivative;
759	>	}
760	>	if (hasPolarizable) {
761	>	storageLayout |= DataStorage::dslElectricField;
762	>	}
763	>	if (hasFluctuatingCharge){
764	>	storageLayout |= DataStorage::dslFlucQPosition;
765	>	if(storageLayout & DataStorage::dslVelocity) {
766	>	storageLayout |= DataStorage::dslFlucQVelocity;
767	>	}
768	>	if (storageLayout & DataStorage::dslForce) {
769	>	storageLayout |= DataStorage::dslFlucQForce;
770	>	}
771	>	}
772	>
773	>	// if the user has asked for them, make sure we've got the memory for the
774	>	// objects defined.
775
776	<	painCave.isFatal = 1;
777	<	simError();
776	>	if (simParams->getOutputParticlePotential()) {
777	>	storageLayout |= DataStorage::dslParticlePot;
778		}
779
780	<	#ifdef IS_MPI
780	>	if (simParams->havePrintHeatFlux()) {
781	>	if (simParams->getPrintHeatFlux()) {
782	>	storageLayout |= DataStorage::dslParticlePot;
783	>	}
784	>	}
785
786	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
787	<	MPIcheckPoint();
786	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
787	>	storageLayout |= DataStorage::dslElectricField;
788	>	}
789
790	<	#endif // is_mpi
790	>	if (simParams->getOutputFluctuatingCharges()) {
791	>	storageLayout |= DataStorage::dslFlucQPosition;
792	>	storageLayout |= DataStorage::dslFlucQVelocity;
793	>	storageLayout |= DataStorage::dslFlucQForce;
794	>	}
795
796	<	}
796	>	info->setStorageLayout(storageLayout);
797
798	<	void SimCreator::setGlobalIndex(SimInfo *info) {
798	>	return storageLayout;
799	>	}
800	>
801	>	void SimCreator::setGlobalIndex(SimInfo *info) {
802		SimInfo::MoleculeIterator mi;
803		Molecule::AtomIterator ai;
804		Molecule::RigidBodyIterator ri;
805		Molecule::CutoffGroupIterator ci;
806	+	Molecule::IntegrableObjectIterator  ioi;
807		Molecule * mol;
808		Atom * atom;
809		RigidBody * rb;
#	Line 507 | Line 812 | void SimCreator::setGlobalIndex(SimInfo *info) {
812		int beginRigidBodyIndex;
813		int beginCutoffGroupIndex;
814		int nGlobalAtoms = info->getNGlobalAtoms();
815	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
816
511	–	#ifndef IS_MPI
512	–
817		beginAtomIndex = 0;
818	<	beginRigidBodyIndex = 0;
818	>	//rigidbody's index begins right after atom's
819	>	beginRigidBodyIndex = info->getNGlobalAtoms();
820		beginCutoffGroupIndex = 0;
821
822	<	#else
822	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
823	>
824	>	#ifdef IS_MPI
825	>	if (info->getMolToProc(i) == worldRank) {
826	>	#endif
827	>	// stuff to do if I own this molecule
828	>	mol = info->getMoleculeByGlobalIndex(i);
829
519	–	int nproc;
520	–	int myNode;
521	–
522	–	myNode = worldRank;
523	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524	–
525	–	std::vector < int > tmpAtomsInProc(nproc, 0);
526	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528	–	std::vector < int > NumAtomsInProc(nproc, 0);
529	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
530	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531	–
532	–	tmpAtomsInProc[myNode] = info->getNAtoms();
533	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535	–
536	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538	–	MPI_SUM, MPI_COMM_WORLD);
539	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543	–
544	–	beginAtomIndex = 0;
545	–	beginRigidBodyIndex = 0;
546	–	beginCutoffGroupIndex = 0;
547	–
548	–	for(int i = 0; i < myNode; i++) {
549	–	beginAtomIndex += NumAtomsInProc[i];
550	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
551	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552	–	}
553	–
554	–	#endif
555	–
556	–	for(mol = info->beginMolecule(mi); mol != NULL;
557	–	mol = info->nextMolecule(mi)) {
558	–
830		//local index(index in DataStorge) of atom is important
831		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
832	<	atom->setGlobalIndex(beginAtomIndex++);
832	>	atom->setGlobalIndex(beginAtomIndex++);
833		}
834	<
834	>
835		for(rb = mol->beginRigidBody(ri); rb != NULL;
836		rb = mol->nextRigidBody(ri)) {
837	<	rb->setGlobalIndex(beginRigidBodyIndex++);
837	>	rb->setGlobalIndex(beginRigidBodyIndex++);
838		}
839	<
840	<	//local index of cutoff group is trivial, it only depends on the order of travesing
839	>
840	>	//local index of cutoff group is trivial, it only depends on
841	>	//the order of travesing
842		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
843		cg = mol->nextCutoffGroup(ci)) {
844	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
845	<	}
846	<	}
844	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
845	>	}
846	>
847	>	#ifdef IS_MPI
848	>	}  else {
849
850	+	// stuff to do if I don't own this molecule
851	+
852	+	int stampId = info->getMoleculeStampId(i);
853	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
854	+
855	+	beginAtomIndex += stamp->getNAtoms();
856	+	beginRigidBodyIndex += stamp->getNRigidBodies();
857	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
858	+	}
859	+	#endif
860	+
861	+	} //end for(int i=0)
862	+
863		//fill globalGroupMembership
864		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
865		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
866	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
867	<
868	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
869	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
870	<	}
871	<
872	<	}
866	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
867	>
868	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
869	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
870	>	}
871	>
872	>	}
873		}
874	<
874	>
875		#ifdef IS_MPI
876		// Since the globalGroupMembership has been zero filled and we've only
877		// poked values into the atoms we know, we can do an Allreduce
878		// to get the full globalGroupMembership array (We think).
879		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
880		// docs said we could.
881	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
882	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
883	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
884	<	info->setGlobalGroupMembership(tmpGroupMembership);
881	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
882	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
883	>	&tmpGroupMembership[0], nGlobalAtoms,
884	>	MPI::INT, MPI::SUM);
885	>	info->setGlobalGroupMembership(tmpGroupMembership);
886		#else
887		info->setGlobalGroupMembership(globalGroupMembership);
888		#endif
889	<
889	>
890		//fill molMembership
891	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
891	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
892	>	info->getNGlobalRigidBodies(), 0);
893
894	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
895	<
896	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
898	<	}
894	>	for(mol = info->beginMolecule(mi); mol != NULL;
895	>	mol = info->nextMolecule(mi)) {
896	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
898	>	}
899	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
900	>	rb = mol->nextRigidBody(ri)) {
901	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
902	>	}
903		}
904	<
904	>
905		#ifdef IS_MPI
906	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
907	<
908	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
909	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
906	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
907	>	info->getNGlobalRigidBodies(), 0);
908	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
909	>	nGlobalAtoms + nGlobalRigidBodies,
910	>	MPI::INT, MPI::SUM);
911
912		info->setGlobalMolMembership(tmpMolMembership);
913		#else
914		info->setGlobalMolMembership(globalMolMembership);
915		#endif
916
917	<	}
917	>	// nIOPerMol holds the number of integrable objects per molecule
918	>	// here the molecules are listed by their global indices.
919
920	<	void SimCreator::loadCoordinates(SimInfo* info) {
921	<	Globals* simParams;
922	<	simParams = info->getSimParams();
920	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
921	>	for (mol = info->beginMolecule(mi); mol != NULL;
922	>	mol = info->nextMolecule(mi)) {
923	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
924	>	}
925
926	<	if (!simParams->haveInitialConfig()) {
927	<	sprintf(painCave.errMsg,
928	<	"Cannot intialize a simulation without an initial configuration file.\n");
929	<	painCave.isFatal = 1;;
930	<	simError();
926	>	#ifdef IS_MPI
927	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
928	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
929	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
930	>	#else
931	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
932	>	#endif
933	>
934	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
935	>
936	>	int startingIndex = 0;
937	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
938	>	startingIOIndexForMol[i] = startingIndex;
939	>	startingIndex += numIntegrableObjectsPerMol[i];
940		}
941	<
942	<	DumpReader reader(info, simParams->getInitialConfig());
941	>
942	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
943	>	for (mol = info->beginMolecule(mi); mol != NULL;
944	>	mol = info->nextMolecule(mi)) {
945	>	int myGlobalIndex = mol->getGlobalIndex();
946	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
947	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
948	>	sd = mol->nextIntegrableObject(ioi)) {
949	>	sd->setGlobalIntegrableObjectIndex(globalIO);
950	>	IOIndexToIntegrableObject[globalIO] = sd;
951	>	globalIO++;
952	>	}
953	>	}
954	>
955	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
956	>
957	>	}
958	>
959	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
960	>
961	>	DumpReader reader(info, mdFileName);
962		int nframes = reader.getNFrames();
963	<
963	>
964		if (nframes > 0) {
965	<	reader.readFrame(nframes - 1);
965	>	reader.readFrame(nframes - 1);
966		} else {
967	<	//invalid initial coordinate file
968	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
969	<	simParams->getInitialConfig());
970	<	painCave.isFatal = 1;
971	<	simError();
967	>	//invalid initial coordinate file
968	>	sprintf(painCave.errMsg,
969	>	"Initial configuration file %s should at least contain one frame\n",
970	>	mdFileName.c_str());
971	>	painCave.isFatal = 1;
972	>	simError();
973		}
648	–
974		//copy the current snapshot to previous snapshot
975		info->getSnapshotManager()->advance();
976	<	}
976	>	}
977	>
978	>	} //end namespace OpenMD
979
653	–	} //end namespace oopse
980
655	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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