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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 1983 by gezelter, Tue Apr 15 20:36:19 2014 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 "utils/Revision.hpp"
68	>	#include "math/SeqRandNumGen.hpp"
69	>	#include "mdParser/MDLexer.hpp"
70	>	#include "mdParser/MDParser.hpp"
71	>	#include "mdParser/MDTreeParser.hpp"
72	>	#include "mdParser/SimplePreprocessor.hpp"
73	>	#include "antlr/ANTLRException.hpp"
74	>	#include "antlr/TokenStreamRecognitionException.hpp"
75	>	#include "antlr/TokenStreamIOException.hpp"
76	>	#include "antlr/TokenStreamException.hpp"
77	>	#include "antlr/RecognitionException.hpp"
78	>	#include "antlr/CharStreamException.hpp"
79
80	<	namespace oopse {
80	>	#include "antlr/MismatchedCharException.hpp"
81	>	#include "antlr/MismatchedTokenException.hpp"
82	>	#include "antlr/NoViableAltForCharException.hpp"
83	>	#include "antlr/NoViableAltException.hpp"
84
85	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
85	>	#include "types/DirectionalAdapter.hpp"
86	>	#include "types/MultipoleAdapter.hpp"
87	>	#include "types/EAMAdapter.hpp"
88	>	#include "types/SuttonChenAdapter.hpp"
89	>	#include "types/PolarizableAdapter.hpp"
90	>	#include "types/FixedChargeAdapter.hpp"
91	>	#include "types/FluctuatingChargeAdapter.hpp"
92
69	–	#ifdef IS_MPI
93
94	<	if (worldRank == 0) {
95	<	#endif // is_mpi
94	>	namespace OpenMD {
95	>
96	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
97	>	Globals* simParams = NULL;
98	>	try {
99
100	<	simParams->initalize();
101	<	set_interface_stamps(stamps, simParams);
100	>	// Create a preprocessor that preprocesses md file into an ostringstream
101	>	std::stringstream ppStream;
102	>	#ifdef IS_MPI
103	>	int streamSize;
104	>	const int masterNode = 0;
105
106	<	#ifdef IS_MPI
106	>	if (worldRank == masterNode) {
107	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
108	>	#endif
109	>	SimplePreprocessor preprocessor;
110	>	preprocessor.preprocess(rawMetaDataStream, filename,
111	>	startOfMetaDataBlock, ppStream);
112	>
113	>	#ifdef IS_MPI
114	>	//broadcasting the stream size
115	>	streamSize = ppStream.str().size() +1;
116	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
117	>	MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
118	>	streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
119	>	} else {
120
121	<	mpiEventInit();
121	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
122
123	<	#endif
123	>	//get stream size
124	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127	>
128	>	//receive file content
129	>	MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
130
131	<	yacc_BASS(mdFileName.c_str());
131	>	ppStream.str(buf);
132	>	delete [] buf;
133	>	}
134	>	#endif
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139	>
140	>	// Create a parser that reads from the scanner
141	>	MDParser parser(lexer);
142	>	parser.setFilename(filename);
143
144	<	#ifdef IS_MPI
144	>	// Create an observer that synchorizes file name change
145	>	FilenameObserver observer;
146	>	observer.setLexer(&lexer);
147	>	observer.setParser(&parser);
148	>	lexer.setObserver(&observer);
149	>
150	>	antlr::ASTFactory factory;
151	>	parser.initializeASTFactory(factory);
152	>	parser.setASTFactory(&factory);
153	>	parser.mdfile();
154	>	// Create a tree parser that reads information into Globals
155	>	MDTreeParser treeParser;
156	>	treeParser.initializeASTFactory(factory);
157	>	treeParser.setASTFactory(&factory);
158	>	simParams = treeParser.walkTree(parser.getAST());
159	>	}
160
161	<	throwMPIEvent(NULL);
161	>
162	>	catch(antlr::MismatchedCharException& e) {
163	>	sprintf(painCave.errMsg,
164	>	"parser exception: %s %s:%d:%d\n",
165	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	>	painCave.isFatal = 1;
167	>	simError();
168	>	}
169	>	catch(antlr::MismatchedTokenException &e) {
170	>	sprintf(painCave.errMsg,
171	>	"parser exception: %s %s:%d:%d\n",
172	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	>	painCave.isFatal = 1;
174	>	simError();
175	>	}
176	>	catch(antlr::NoViableAltForCharException &e) {
177	>	sprintf(painCave.errMsg,
178	>	"parser exception: %s %s:%d:%d\n",
179	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	>	painCave.isFatal = 1;
181	>	simError();
182	>	}
183	>	catch(antlr::NoViableAltException &e) {
184	>	sprintf(painCave.errMsg,
185	>	"parser exception: %s %s:%d:%d\n",
186	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
187	>	painCave.isFatal = 1;
188	>	simError();
189	>	}
190	>
191	>	catch(antlr::TokenStreamRecognitionException& e) {
192	>	sprintf(painCave.errMsg,
193	>	"parser exception: %s %s:%d:%d\n",
194	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
195	>	painCave.isFatal = 1;
196	>	simError();
197	>	}
198	>
199	>	catch(antlr::TokenStreamIOException& e) {
200	>	sprintf(painCave.errMsg,
201	>	"parser exception: %s\n",
202	>	e.getMessage().c_str());
203	>	painCave.isFatal = 1;
204	>	simError();
205	>	}
206	>
207	>	catch(antlr::TokenStreamException& e) {
208	>	sprintf(painCave.errMsg,
209	>	"parser exception: %s\n",
210	>	e.getMessage().c_str());
211	>	painCave.isFatal = 1;
212	>	simError();
213	>	}
214	>	catch (antlr::RecognitionException& e) {
215	>	sprintf(painCave.errMsg,
216	>	"parser exception: %s %s:%d:%d\n",
217	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
218	>	painCave.isFatal = 1;
219	>	simError();
220	>	}
221	>	catch (antlr::CharStreamException& e) {
222	>	sprintf(painCave.errMsg,
223	>	"parser exception: %s\n",
224	>	e.getMessage().c_str());
225	>	painCave.isFatal = 1;
226	>	simError();
227	>	}
228	>	catch (OpenMDException& e) {
229	>	sprintf(painCave.errMsg,
230	>	"%s\n",
231	>	e.getMessage().c_str());
232	>	painCave.isFatal = 1;
233	>	simError();
234	>	}
235	>	catch (std::exception& e) {
236	>	sprintf(painCave.errMsg,
237	>	"parser exception: %s\n",
238	>	e.what());
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242	>
243	>	simParams->setMDfileVersion(mdFileVersion);
244	>	return simParams;
245	>	}
246	>
247	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
248	>	bool loadInitCoords) {
249	>
250	>	const int bufferSize = 65535;
251	>	char buffer[bufferSize];
252	>	int lineNo = 0;
253	>	std::string mdRawData;
254	>	int metaDataBlockStart = -1;
255	>	int metaDataBlockEnd = -1;
256	>	int i, j;
257	>	streamoff mdOffset;
258	>	int mdFileVersion;
259	>
260	>	// Create a string for embedding the version information in the MetaData
261	>	std::string version;
262	>	version.assign("## Last run using OpenMD Version: ");
263	>	version.append(OPENMD_VERSION_MAJOR);
264	>	version.append(".");
265	>	version.append(OPENMD_VERSION_MINOR);
266	>
267	>	std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
268	>	//convert a macro from compiler to a string in c++
269	>	// STR_DEFINE(svnrev, SVN_REV );
270	>	version.append(" Revision: ");
271	>	// If there's no SVN revision, just call this the RELEASE revision.
272	>	if (!svnrev.empty()) {
273	>	version.append(svnrev);
274		} else {
275	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
275	>	version.append("RELEASE");
276		}
277	+
278	+	#ifdef IS_MPI
279	+	const int masterNode = 0;
280	+	if (worldRank == masterNode) {
281	+	#endif
282
283	<	#endif
283	>	std::ifstream mdFile_;
284	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
285	>
286	>	if (mdFile_.fail()) {
287	>	sprintf(painCave.errMsg,
288	>	"SimCreator: Cannot open file: %s\n",
289	>	mdFileName.c_str());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293
294	<	}
294	>	mdFile_.getline(buffer, bufferSize);
295	>	++lineNo;
296	>	std::string line = trimLeftCopy(buffer);
297	>	i = CaseInsensitiveFind(line, "<OpenMD");
298	>	if (static_cast<size_t>(i) == string::npos) {
299	>	// try the older file strings to see if that works:
300	>	i = CaseInsensitiveFind(line, "<OOPSE");
301	>	}
302	>
303	>	if (static_cast<size_t>(i) == string::npos) {
304	>	// still no luck!
305	>	sprintf(painCave.errMsg,
306	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
307	>	mdFileName.c_str());
308	>	painCave.isFatal = 1;
309	>	simError();
310	>	}
311	>
312	>	// found the correct opening string, now try to get the file
313	>	// format version number.
314
315	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
316	<
317	<	MakeStamps * stamps = new MakeStamps();
315	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
316	>	std::string fileType = tokenizer.nextToken();
317	>	toUpper(fileType);
318
319	<	Globals * simParams = new Globals();
319	>	mdFileVersion = 0;
320
321	<	//parse meta-data file
322	<	parseFile(mdFileName, stamps, simParams);
321	>	if (fileType == "OPENMD") {
322	>	while (tokenizer.hasMoreTokens()) {
323	>	std::string token(tokenizer.nextToken());
324	>	toUpper(token);
325	>	if (token == "VERSION") {
326	>	mdFileVersion = tokenizer.nextTokenAsInt();
327	>	break;
328	>	}
329	>	}
330	>	}
331	>
332	>	//scan through the input stream and find MetaData tag
333	>	while(mdFile_.getline(buffer, bufferSize)) {
334	>	++lineNo;
335	>
336	>	std::string line = trimLeftCopy(buffer);
337	>	if (metaDataBlockStart == -1) {
338	>	i = CaseInsensitiveFind(line, "<MetaData>");
339	>	if (i != string::npos) {
340	>	metaDataBlockStart = lineNo;
341	>	mdOffset = mdFile_.tellg();
342	>	}
343	>	} else {
344	>	i = CaseInsensitiveFind(line, "</MetaData>");
345	>	if (i != string::npos) {
346	>	metaDataBlockEnd = lineNo;
347	>	}
348	>	}
349	>	}
350
351	<	//create the force field
352	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
353	<	simParams->getForceField());
354	<
355	<	if (ff == NULL) {
356	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
357	<	simParams->getForceField());
358	<	painCave.isFatal = 1;
359	<	simError();
351	>	if (metaDataBlockStart == -1) {
352	>	sprintf(painCave.errMsg,
353	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
354	>	mdFileName.c_str());
355	>	painCave.isFatal = 1;
356	>	simError();
357	>	}
358	>	if (metaDataBlockEnd == -1) {
359	>	sprintf(painCave.errMsg,
360	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
361	>	mdFileName.c_str());
362	>	painCave.isFatal = 1;
363	>	simError();
364	>	}
365	>
366	>	mdFile_.clear();
367	>	mdFile_.seekg(0);
368	>	mdFile_.seekg(mdOffset);
369	>
370	>	mdRawData.clear();
371	>
372	>	bool foundVersion = false;
373	>
374	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
375	>	mdFile_.getline(buffer, bufferSize);
376	>	std::string line = trimLeftCopy(buffer);
377	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
378	>	if (static_cast<size_t>(j) != string::npos) {
379	>	foundVersion = true;
380	>	mdRawData += version;
381	>	} else {
382	>	mdRawData += buffer;
383	>	}
384	>	mdRawData += "\n";
385	>	}
386	>
387	>	if (!foundVersion) mdRawData += version + "\n";
388	>
389	>	mdFile_.close();
390	>
391	>	#ifdef IS_MPI
392		}
393	+	#endif
394
395	+	std::stringstream rawMetaDataStream(mdRawData);
396	+
397	+	//parse meta-data file
398	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
399	+	metaDataBlockStart + 1);
400	+
401	+	//create the force field
402	+	ForceField * ff = new ForceField(simParams->getForceField());
403	+
404	+	if (ff == NULL) {
405	+	sprintf(painCave.errMsg,
406	+	"ForceField Factory can not create %s force field\n",
407	+	simParams->getForceField().c_str());
408	+	painCave.isFatal = 1;
409	+	simError();
410	+	}
411	+
412		if (simParams->haveForceFieldFileName()) {
413	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
413	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
414		}
415
416		std::string forcefieldFileName;
417		forcefieldFileName = ff->getForceFieldFileName();
418	<
418	>
419		if (simParams->haveForceFieldVariant()) {
420	<	//If the force field has variant, the variant force field name will be
421	<	//Base.variant.frc. For exampel EAM.u6.frc
422	<
423	<	std::string variant = simParams->getForceFieldVariant();
424	<
425	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
426	<	variant = "." + variant;
427	<	if (pos != std::string::npos) {
428	<	forcefieldFileName.insert(pos, variant);
429	<	} else {
430	<	//If the default force field file name does not containt .frc suffix, just append the .variant
431	<	forcefieldFileName.append(variant);
432	<	}
420	>	//If the force field has variant, the variant force field name will be
421	>	//Base.variant.frc. For exampel EAM.u6.frc
422	>
423	>	std::string variant = simParams->getForceFieldVariant();
424	>
425	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
426	>	variant = "." + variant;
427	>	if (pos != std::string::npos) {
428	>	forcefieldFileName.insert(pos, variant);
429	>	} else {
430	>	//If the default force field file name does not containt .frc suffix, just append the .variant
431	>	forcefieldFileName.append(variant);
432	>	}
433		}
434
435		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
436		//create SimInfo
437	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
437	>	SimInfo * info = new SimInfo(ff, simParams);
438
439	<	//gather parameters (SimCreator only retrieves part of the parameters)
439	>	info->setRawMetaData(mdRawData);
440	>
441	>	//gather parameters (SimCreator only retrieves part of the
442	>	//parameters)
443		gatherParameters(info, mdFileName);
444	<
444	>
445		//divide the molecules and determine the global index of molecules
446		#ifdef IS_MPI
447		divideMolecules(info);
448		#endif
449	<
449	>
450		//create the molecules
451		createMolecules(info);
452	+
453	+	//find the storage layout
454
455	+	int storageLayout = computeStorageLayout(info);
456
457	<	//allocate memory for DataStorage(circular reference, need to break it)
458	<	info->setSnapshotManager(new SimSnapshotManager(info));
457	>	//allocate memory for DataStorage(circular reference, need to
458	>	//break it)
459	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
460
461	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
462	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
463	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
461	>	//set the global index of atoms, rigidbodies and cutoffgroups
462	>	//(only need to be set once, the global index will never change
463	>	//again). Local indices of atoms and rigidbodies are already set
464	>	//by MoleculeCreator class which actually delegates the
465	>	//responsibility to LocalIndexManager.
466		setGlobalIndex(info);
467	<
468	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
469	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
470	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
471	<	//we can determine the beginning global indices of atoms before they get created.
467	>
468	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
469	>	//method, at that point atoms don't have the global index yet
470	>	//(their global index are all initialized to -1).  Therefore we
471	>	//have to call addInteractionPairs explicitly here. A way to work
472	>	//around is that we can determine the beginning global indices of
473	>	//atoms before they get created.
474		SimInfo::MoleculeIterator mi;
475		Molecule* mol;
476		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
477	<	info->addExcludePairs(mol);
477	>	info->addInteractionPairs(mol);
478		}
479
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
480		if (loadInitCoords)
481	<	loadCoordinates(info);
186	<
481	>	loadCoordinates(info, mdFileName);
482		return info;
483	<	}
484	<
485	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
486	<
487	<	//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
483	>	}
484	>
485	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
486	>
487	>	//figure out the output file names
488		std::string prefix;
489	<
489	>
490		#ifdef IS_MPI
491	<
491	>
492		if (worldRank == 0) {
493		#endif // is_mpi
494	<
495	<	if (simParams->haveFinalConfig()) {
496	<	prefix = getPrefix(simParams->getFinalConfig());
497	<	} else {
498	<	prefix = getPrefix(mdfile);
499	<	}
500	<
501	<	info->setFinalConfigFileName(prefix + ".eor");
502	<	info->setDumpFileName(prefix + ".dump");
503	<	info->setStatFileName(prefix + ".stat");
504	<
494	>	Globals * simParams = info->getSimParams();
495	>	if (simParams->haveFinalConfig()) {
496	>	prefix = getPrefix(simParams->getFinalConfig());
497	>	} else {
498	>	prefix = getPrefix(mdfile);
499	>	}
500	>
501	>	info->setFinalConfigFileName(prefix + ".eor");
502	>	info->setDumpFileName(prefix + ".dump");
503	>	info->setStatFileName(prefix + ".stat");
504	>	info->setRestFileName(prefix + ".zang");
505	>
506		#ifdef IS_MPI
507	<
507	>
508		}
509	<
509	>
510		#endif
511	<
512	<	}
513	<
511	>
512	>	}
513	>
514		#ifdef IS_MPI
515	<	void SimCreator::divideMolecules(SimInfo *info) {
516	<	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;
515	>	void SimCreator::divideMolecules(SimInfo *info) {
516	>	RealType a;
517		int nProcessors;
518		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
519		int nGlobalMols = info->getNGlobalMolecules();
520	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
520	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
521	>	// error
522	>	// condition:
523
524	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
525	<
524	>	MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
525	>
526		if (nProcessors > nGlobalMols) {
527	<	sprintf(painCave.errMsg,
528	<	"nProcessors (%d) > nMol (%d)\n"
529	<	"\tThe number of processors is larger than\n"
530	<	"\tthe number of molecules.  This will not result in a \n"
531	<	"\tusable division of atoms for force decomposition.\n"
532	<	"\tEither try a smaller number of processors, or run the\n"
533	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
534	<
535	<	painCave.isFatal = 1;
536	<	simError();
527	>	sprintf(painCave.errMsg,
528	>	"nProcessors (%d) > nMol (%d)\n"
529	>	"\tThe number of processors is larger than\n"
530	>	"\tthe number of molecules.  This will not result in a \n"
531	>	"\tusable division of atoms for force decomposition.\n"
532	>	"\tEither try a smaller number of processors, or run the\n"
533	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
534	>	nGlobalMols);
535	>
536	>	painCave.isFatal = 1;
537	>	simError();
538		}
539	<
539	>
540	>	Globals * simParams = info->getSimParams();
541	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
542	>	//random number generator
543	>	if (simParams->haveSeed()) {
544	>	int seedValue = simParams->getSeed();
545	>	myRandom = new SeqRandNumGen(seedValue);
546	>	}else {
547	>	myRandom = new SeqRandNumGen();
548	>	}
549	>
550	>
551		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
552	<
552	>
553		//initialize atomsPerProc
554		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
555	<
555	>
556		if (worldRank == 0) {
557	<	numerator = info->getNGlobalAtoms();
558	<	denominator = nProcessors;
559	<	precast = numerator / denominator;
560	<	nTarget = (int)(precast + 0.5);
557	>	RealType numerator = info->getNGlobalAtoms();
558	>	RealType denominator = nProcessors;
559	>	RealType precast = numerator / denominator;
560	>	int nTarget = (int)(precast + 0.5);
561	>
562	>	for(int i = 0; i < nGlobalMols; i++) {
563
564	<	for(i = 0; i < nGlobalMols; i++) {
565	<	done = 0;
566	<	loops = 0;
567	<
568	<	while (!done) {
569	<	loops++;
570	<
571	<	// Pick a processor at random
572	<
573	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
574	<
575	<	//get the molecule stamp first
576	<	int stampId = info->getMoleculeStampId(i);
577	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
578	<
579	<	// How many atoms does this processor have so far?
580	<	old_atoms = atomsPerProc[which_proc];
581	<	add_atoms = moleculeStamp->getNAtoms();
582	<	new_atoms = old_atoms + add_atoms;
583	<
584	<	// If we've been through this loop too many times, we need
585	<	// to just give up and assign the molecule to this processor
586	<	// and be done with it.
564	>	int done = 0;
565	>	int loops = 0;
566	>
567	>	while (!done) {
568	>	loops++;
569	>
570	>	// Pick a processor at random
571	>
572	>	int which_proc = (int) (myRandom->rand() * nProcessors);
573	>
574	>	//get the molecule stamp first
575	>	int stampId = info->getMoleculeStampId(i);
576	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
577	>
578	>	// How many atoms does this processor have so far?
579	>	int old_atoms = atomsPerProc[which_proc];
580	>	int add_atoms = moleculeStamp->getNAtoms();
581	>	int new_atoms = old_atoms + add_atoms;
582	>
583	>	// If we've been through this loop too many times, we need
584	>	// to just give up and assign the molecule to this processor
585	>	// and be done with it.
586	>
587	>	if (loops > 100) {
588
589	<	if (loops > 100) {
590	<	sprintf(painCave.errMsg,
591	<	"I've tried 100 times to assign molecule %d to a "
592	<	" processor, but can't find a good spot.\n"
593	<	"I'm assigning it at random to processor %d.\n",
594	<	i, which_proc);
595	<
596	<	painCave.isFatal = 0;
597	<	simError();
598	<
599	<	molToProcMap[i] = which_proc;
600	<	atomsPerProc[which_proc] += add_atoms;
601	<
602	<	done = 1;
603	<	continue;
604	<	}
605	<
606	<	// If we can add this molecule to this processor without sending
607	<	// it above nTarget, then go ahead and do it:
608	<
609	<	if (new_atoms <= nTarget) {
610	<	molToProcMap[i] = which_proc;
611	<	atomsPerProc[which_proc] += add_atoms;
612	<
613	<	done = 1;
614	<	continue;
615	<	}
616	<
617	<	// The only situation left is when new_atoms > nTarget.  We
618	<	// want to accept this with some probability that dies off the
619	<	// farther we are from nTarget
620	<
621	<	// roughly:  x = new_atoms - nTarget
622	<	//           Pacc(x) = exp(- a * x)
623	<	// where a = penalty / (average atoms per molecule)
624	<
625	<	x = (double)(new_atoms - nTarget);
626	<	y = myRandom.getRandom();
627	<
628	<	if (y < exp(- a * x)) {
629	<	molToProcMap[i] = which_proc;
630	<	atomsPerProc[which_proc] += add_atoms;
631	<
632	<	done = 1;
633	<	continue;
634	<	} else {
635	<	continue;
636	<	}
392	<	}
589	>	sprintf(painCave.errMsg,
590	>	"There have been 100 attempts to assign molecule %d to an\n"
591	>	"\tunderworked processor, but there's no good place to\n"
592	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
593	>	i, which_proc);
594	>
595	>	painCave.isFatal = 0;
596	>	painCave.severity = OPENMD_INFO;
597	>	simError();
598	>
599	>	molToProcMap[i] = which_proc;
600	>	atomsPerProc[which_proc] += add_atoms;
601	>
602	>	done = 1;
603	>	continue;
604	>	}
605	>
606	>	// If we can add this molecule to this processor without sending
607	>	// it above nTarget, then go ahead and do it:
608	>
609	>	if (new_atoms <= nTarget) {
610	>	molToProcMap[i] = which_proc;
611	>	atomsPerProc[which_proc] += add_atoms;
612	>
613	>	done = 1;
614	>	continue;
615	>	}
616	>
617	>	// The only situation left is when new_atoms > nTarget.  We
618	>	// want to accept this with some probability that dies off the
619	>	// farther we are from nTarget
620	>
621	>	// roughly:  x = new_atoms - nTarget
622	>	//           Pacc(x) = exp(- a * x)
623	>	// where a = penalty / (average atoms per molecule)
624	>
625	>	RealType x = (RealType)(new_atoms - nTarget);
626	>	RealType y = myRandom->rand();
627	>
628	>	if (y < exp(- a * x)) {
629	>	molToProcMap[i] = which_proc;
630	>	atomsPerProc[which_proc] += add_atoms;
631	>
632	>	done = 1;
633	>	continue;
634	>	} else {
635	>	continue;
636	>	}
637		}
638	+	}
639	+
640	+	delete myRandom;
641
642	<	// Spray out this nonsense to all other processors:
642	>	// Spray out this nonsense to all other processors:
643	>	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644
397	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
645		} else {
646	+
647	+	// Listen to your marching orders from processor 0:
648	+	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
649
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
650		}
651	<
651	>
652		info->setMolToProcMap(molToProcMap);
653		sprintf(checkPointMsg,
654		"Successfully divided the molecules among the processors.\n");
655	<	MPIcheckPoint();
656	<	}
657	<
655	>	errorCheckPoint();
656	>	}
657	>
658		#endif
659	<
660	<	void SimCreator::createMolecules(SimInfo *info) {
659	>
660	>	void SimCreator::createMolecules(SimInfo *info) {
661		MoleculeCreator molCreator;
662		int stampId;
663	<
663	>
664		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
665	<
665	>
666		#ifdef IS_MPI
667	<
668	<	if (info->getMolToProc(i) == worldRank) {
667	>
668	>	if (info->getMolToProc(i) == worldRank) {
669		#endif
670	<
671	<	stampId = info->getMoleculeStampId(i);
672	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
673	<	stampId, i, info->getLocalIndexManager());
674	<
675	<	info->addMolecule(mol);
676	<
670	>
671	>	stampId = info->getMoleculeStampId(i);
672	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
673	>	info->getMoleculeStamp(stampId),
674	>	stampId, i,
675	>	info->getLocalIndexManager());
676	>
677	>	info->addMolecule(mol);
678	>
679		#ifdef IS_MPI
680	<
681	<	}
682	<
680	>
681	>	}
682	>
683		#endif
684	<
684	>
685		} //end for(int i=0)
686	<	}
686	>	}
687	>
688	>	int SimCreator::computeStorageLayout(SimInfo* info) {
689
690	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
691	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
692	<	int i;
693	<	char * id;
694	<	MoleculeStamp * currentStamp;
695	<	Component** the_components = simParams->getComponents();
696	<	int n_components = simParams->getNComponents();
690	>	Globals* simParams = info->getSimParams();
691	>	int nRigidBodies = info->getNGlobalRigidBodies();
692	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
693	>	set<AtomType*>::iterator i;
694	>	bool hasDirectionalAtoms = false;
695	>	bool hasFixedCharge = false;
696	>	bool hasDipoles = false;
697	>	bool hasQuadrupoles = false;
698	>	bool hasPolarizable = false;
699	>	bool hasFluctuatingCharge = false;
700	>	bool hasMetallic = false;
701	>	int storageLayout = 0;
702	>	storageLayout |= DataStorage::dslPosition;
703	>	storageLayout |= DataStorage::dslVelocity;
704	>	storageLayout |= DataStorage::dslForce;
705
706	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
706	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
707
708	<	for(i = 0; i < n_components; i++) {
709	<	if (!the_components[i]->haveNMol()) {
710	<	// we have a problem
711	<	sprintf(painCave.errMsg,
712	<	"SimCreator Error. No global NMol or component NMol given.\n"
713	<	"\tCannot calculate the number of atoms.\n");
708	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
709	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
710	>	EAMAdapter ea = EAMAdapter( (*i) );
711	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
712	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
713	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
714	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
715
716	<	painCave.isFatal = 1;
717	<	simError();
718	<	}
716	>	if (da.isDirectional()){
717	>	hasDirectionalAtoms = true;
718	>	}
719	>	if (ma.isDipole()){
720	>	hasDipoles = true;
721	>	}
722	>	if (ma.isQuadrupole()){
723	>	hasQuadrupoles = true;
724	>	}
725	>	if (ea.isEAM() || sca.isSuttonChen()){
726	>	hasMetallic = true;
727	>	}
728	>	if ( fca.isFixedCharge() ){
729	>	hasFixedCharge = true;
730	>	}
731	>	if ( fqa.isFluctuatingCharge() ){
732	>	hasFluctuatingCharge = true;
733	>	}
734	>	if ( pa.isPolarizable() ){
735	>	hasPolarizable = true;
736	>	}
737	>	}
738	>
739	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
740	>	storageLayout |= DataStorage::dslAmat;
741	>	if(storageLayout & DataStorage::dslVelocity) {
742	>	storageLayout |= DataStorage::dslAngularMomentum;
743	>	}
744	>	if (storageLayout & DataStorage::dslForce) {
745	>	storageLayout |= DataStorage::dslTorque;
746	>	}
747	>	}
748	>	if (hasDipoles) {
749	>	storageLayout |= DataStorage::dslDipole;
750	>	}
751	>	if (hasQuadrupoles) {
752	>	storageLayout |= DataStorage::dslQuadrupole;
753	>	}
754	>	if (hasFixedCharge || hasFluctuatingCharge) {
755	>	storageLayout |= DataStorage::dslSkippedCharge;
756	>	}
757	>	if (hasMetallic) {
758	>	storageLayout |= DataStorage::dslDensity;
759	>	storageLayout |= DataStorage::dslFunctional;
760	>	storageLayout |= DataStorage::dslFunctionalDerivative;
761	>	}
762	>	if (hasPolarizable) {
763	>	storageLayout |= DataStorage::dslElectricField;
764	>	}
765	>	if (hasFluctuatingCharge){
766	>	storageLayout |= DataStorage::dslFlucQPosition;
767	>	if(storageLayout & DataStorage::dslVelocity) {
768	>	storageLayout |= DataStorage::dslFlucQVelocity;
769	>	}
770	>	if (storageLayout & DataStorage::dslForce) {
771	>	storageLayout |= DataStorage::dslFlucQForce;
772	>	}
773	>	}
774	>
775	>	// if the user has asked for them, make sure we've got the memory for the
776	>	// objects defined.
777
778	<	id = the_components[i]->getType();
779	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
778	>	if (simParams->getOutputParticlePotential()) {
779	>	storageLayout |= DataStorage::dslParticlePot;
780	>	}
781
782	<	if (currentStamp == NULL) {
783	<	sprintf(painCave.errMsg,
784	<	"SimCreator error: Component \"%s\" was not found in the "
785	<	"list of declared molecules\n", id);
782	>	if (simParams->havePrintHeatFlux()) {
783	>	if (simParams->getPrintHeatFlux()) {
784	>	storageLayout |= DataStorage::dslParticlePot;
785	>	}
786	>	}
787
788	<	painCave.isFatal = 1;
789	<	simError();
472	<	}
473	<
474	<	moleculeStampPairs.push_back(
475	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
476	<	} //end for (i = 0; i < n_components; i++)
477	<	} else {
478	<	sprintf(painCave.errMsg, "SimSetup error.\n"
479	<	"\tSorry, the ability to specify total"
480	<	" nMols and then give molfractions in the components\n"
481	<	"\tis not currently supported."
482	<	" Please give nMol in the components.\n");
483	<
484	<	painCave.isFatal = 1;
485	<	simError();
788	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
789	>	storageLayout |= DataStorage::dslElectricField;
790		}
791
792	<	#ifdef IS_MPI
793	<
794	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
795	<	MPIcheckPoint();
792	>	if (simParams->getOutputFluctuatingCharges()) {
793	>	storageLayout |= DataStorage::dslFlucQPosition;
794	>	storageLayout |= DataStorage::dslFlucQVelocity;
795	>	storageLayout |= DataStorage::dslFlucQForce;
796	>	}
797
798	<	#endif // is_mpi
798	>	info->setStorageLayout(storageLayout);
799
800	<	}
800	>	return storageLayout;
801	>	}
802
803	<	void SimCreator::setGlobalIndex(SimInfo *info) {
803	>	void SimCreator::setGlobalIndex(SimInfo *info) {
804		SimInfo::MoleculeIterator mi;
805		Molecule::AtomIterator ai;
806		Molecule::RigidBodyIterator ri;
807		Molecule::CutoffGroupIterator ci;
808	<	Molecule * mol;
809	<	Atom * atom;
810	<	RigidBody * rb;
811	<	CutoffGroup * cg;
808	>	Molecule::BondIterator boi;
809	>	Molecule::BendIterator bei;
810	>	Molecule::TorsionIterator ti;
811	>	Molecule::InversionIterator ii;
812	>	Molecule::IntegrableObjectIterator  ioi;
813	>	Molecule* mol;
814	>	Atom* atom;
815	>	RigidBody* rb;
816	>	CutoffGroup* cg;
817	>	Bond* bond;
818	>	Bend* bend;
819	>	Torsion* torsion;
820	>	Inversion* inversion;
821		int beginAtomIndex;
822		int beginRigidBodyIndex;
823		int beginCutoffGroupIndex;
824	+	int beginBondIndex;
825	+	int beginBendIndex;
826	+	int beginTorsionIndex;
827	+	int beginInversionIndex;
828		int nGlobalAtoms = info->getNGlobalAtoms();
829	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
830
511	–	#ifndef IS_MPI
512	–
831		beginAtomIndex = 0;
832	<	beginRigidBodyIndex = 0;
832	>	// The rigid body indices begin immediately after the atom indices:
833	>	beginRigidBodyIndex = info->getNGlobalAtoms();
834		beginCutoffGroupIndex = 0;
835	+	beginBondIndex = 0;
836	+	beginBendIndex = 0;
837	+	beginTorsionIndex = 0;
838	+	beginInversionIndex = 0;
839	+
840	+	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
841	+
842	+	#ifdef IS_MPI
843	+	if (info->getMolToProc(i) == worldRank) {
844	+	#endif
845	+	// stuff to do if I own this molecule
846	+	mol = info->getMoleculeByGlobalIndex(i);
847
848	<	#else
849	<
850	<	int nproc;
851	<	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	<
561	<	//local index(index in DataStorge) of atom is important
562	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
563	<	atom->setGlobalIndex(beginAtomIndex++);
848	>	// The local index(index in DataStorge) of the atom is important:
849	>	for(atom = mol->beginAtom(ai); atom != NULL;
850	>	atom = mol->nextAtom(ai)) {
851	>	atom->setGlobalIndex(beginAtomIndex++);
852		}
853	<
853	>
854		for(rb = mol->beginRigidBody(ri); rb != NULL;
855		rb = mol->nextRigidBody(ri)) {
856	<	rb->setGlobalIndex(beginRigidBodyIndex++);
856	>	rb->setGlobalIndex(beginRigidBodyIndex++);
857		}
858	<
859	<	//local index of cutoff group is trivial, it only depends on the order of travesing
858	>
859	>	// The local index of other objects only depends on the order
860	>	// of traversal:
861		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
862		cg = mol->nextCutoffGroup(ci)) {
863	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
864	<	}
865	<	}
863	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
864	>	}
865	>	for(bond = mol->beginBond(boi); bond != NULL;
866	>	bond = mol->nextBond(boi)) {
867	>	bond->setGlobalIndex(beginBondIndex++);
868	>	}
869	>	for(bend = mol->beginBend(bei); bend != NULL;
870	>	bend = mol->nextBend(bei)) {
871	>	bend->setGlobalIndex(beginBendIndex++);
872	>	}
873	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
874	>	torsion = mol->nextTorsion(ti)) {
875	>	torsion->setGlobalIndex(beginTorsionIndex++);
876	>	}
877	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
878	>	inversion = mol->nextInversion(ii)) {
879	>	inversion->setGlobalIndex(beginInversionIndex++);
880	>	}
881	>
882	>	#ifdef IS_MPI
883	>	}  else {
884
885	<	//fill globalGroupMembership
886	<	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
887	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
888	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
885	>	// stuff to do if I don't own this molecule
886	>
887	>	int stampId = info->getMoleculeStampId(i);
888	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
889
890	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
891	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
892	<	}
890	>	beginAtomIndex += stamp->getNAtoms();
891	>	beginRigidBodyIndex += stamp->getNRigidBodies();
892	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
893	>	beginBondIndex += stamp->getNBonds();
894	>	beginBendIndex += stamp->getNBends();
895	>	beginTorsionIndex += stamp->getNTorsions();
896	>	beginInversionIndex += stamp->getNInversions();
897	>	}
898	>	#endif
899
900	<	}
588	<	}
900	>	} //end for(int i=0)
901
902	+	//fill globalGroupMembership
903	+	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
904	+	for(mol = info->beginMolecule(mi); mol != NULL;
905	+	mol = info->nextMolecule(mi)) {
906	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
907	+	cg = mol->nextCutoffGroup(ci)) {
908	+	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
909	+	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
910	+	}
911	+
912	+	}
913	+	}
914	+
915		#ifdef IS_MPI
916		// Since the globalGroupMembership has been zero filled and we've only
917		// poked values into the atoms we know, we can do an Allreduce
918		// to get the full globalGroupMembership array (We think).
919		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
920		// docs said we could.
921	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
922	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
921	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
922	>	MPI_Allreduce(&globalGroupMembership[0],
923	>	&tmpGroupMembership[0], nGlobalAtoms,
924		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
925	<	info->setGlobalGroupMembership(tmpGroupMembership);
925	>
926	>	info->setGlobalGroupMembership(tmpGroupMembership);
927		#else
928		info->setGlobalGroupMembership(globalGroupMembership);
929		#endif
930	<
930	>
931		//fill molMembership
932	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
932	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
933	>	info->getNGlobalRigidBodies(), 0);
934
935	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
936	<
937	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
938	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
939	<	}
935	>	for(mol = info->beginMolecule(mi); mol != NULL;
936	>	mol = info->nextMolecule(mi)) {
937	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
938	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
939	>	}
940	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
941	>	rb = mol->nextRigidBody(ri)) {
942	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
943	>	}
944		}
945	<
945	>
946		#ifdef IS_MPI
947	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
948	<
949	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
947	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
948	>	info->getNGlobalRigidBodies(), 0);
949	>	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
950	>	nGlobalAtoms + nGlobalRigidBodies,
951		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
952
953		info->setGlobalMolMembership(tmpMolMembership);
#	Line 622 | Line 955 | void SimCreator::setGlobalIndex(SimInfo *info) {
955		info->setGlobalMolMembership(globalMolMembership);
956		#endif
957
958	<	}
958	>	// nIOPerMol holds the number of integrable objects per molecule
959	>	// here the molecules are listed by their global indices.
960
961	<	void SimCreator::loadCoordinates(SimInfo* info) {
962	<	Globals* simParams;
963	<	simParams = info->getSimParams();
961	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
962	>	for (mol = info->beginMolecule(mi); mol != NULL;
963	>	mol = info->nextMolecule(mi)) {
964	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
965	>	}
966
967	<	if (!simParams->haveInitialConfig()) {
968	<	sprintf(painCave.errMsg,
969	<	"Cannot intialize a simulation without an initial configuration file.\n");
970	<	painCave.isFatal = 1;;
971	<	simError();
967	>	#ifdef IS_MPI
968	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
969	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
970	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
971	>	#else
972	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
973	>	#endif
974	>
975	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
976	>
977	>	int startingIndex = 0;
978	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
979	>	startingIOIndexForMol[i] = startingIndex;
980	>	startingIndex += numIntegrableObjectsPerMol[i];
981		}
982	<
983	<	DumpReader reader(info, simParams->getInitialConfig());
982	>
983	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
984	>	for (mol = info->beginMolecule(mi); mol != NULL;
985	>	mol = info->nextMolecule(mi)) {
986	>	int myGlobalIndex = mol->getGlobalIndex();
987	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
988	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
989	>	sd = mol->nextIntegrableObject(ioi)) {
990	>	sd->setGlobalIntegrableObjectIndex(globalIO);
991	>	IOIndexToIntegrableObject[globalIO] = sd;
992	>	globalIO++;
993	>	}
994	>	}
995	>
996	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
997	>
998	>	}
999	>
1000	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
1001	>
1002	>	DumpReader reader(info, mdFileName);
1003		int nframes = reader.getNFrames();
1004	<
1004	>
1005		if (nframes > 0) {
1006	<	reader.readFrame(nframes - 1);
1006	>	reader.readFrame(nframes - 1);
1007		} else {
1008	<	//invalid initial coordinate file
1009	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
1010	<	simParams->getInitialConfig());
1011	<	painCave.isFatal = 1;
1012	<	simError();
1008	>	//invalid initial coordinate file
1009	>	sprintf(painCave.errMsg,
1010	>	"Initial configuration file %s should at least contain one frame\n",
1011	>	mdFileName.c_str());
1012	>	painCave.isFatal = 1;
1013	>	simError();
1014		}
650	–
1015		//copy the current snapshot to previous snapshot
1016		info->getSnapshotManager()->advance();
1017	<	}
1017	>	}
1018	>
1019	>	} //end namespace OpenMD
1020
655	–	} //end namespace oopse
1021
657	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

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