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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 297 by tim, Mon Feb 7 19:14:26 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 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 "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_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
107	>	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
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_LONG, 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
120	<	mpiEventInit();
120	>	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121	>	// MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
122	>	//                       streamSize, MPI::CHAR, masterNode);
123	>
124	>	} else {
125
126	<	#endif
126	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
127	>	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
128
129	<	yacc_BASS(mdFileName.c_str());
129	>	//get stream size
130	>	MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
131	>	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
132	>	char* buf = new char[streamSize];
133	>	assert(buf);
134	>
135	>	//receive file content
136	>	MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
137	>	// MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
138
139	<	#ifdef IS_MPI
139	>	ppStream.str(buf);
140	>	delete [] buf;
141	>	}
142	>	#endif
143	>	// Create a scanner that reads from the input stream
144	>	MDLexer lexer(ppStream);
145	>	lexer.setFilename(filename);
146	>	lexer.initDeferredLineCount();
147	>
148	>	// Create a parser that reads from the scanner
149	>	MDParser parser(lexer);
150	>	parser.setFilename(filename);
151
152	<	throwMPIEvent(NULL);
152	>	// Create an observer that synchorizes file name change
153	>	FilenameObserver observer;
154	>	observer.setLexer(&lexer);
155	>	observer.setParser(&parser);
156	>	lexer.setObserver(&observer);
157	>
158	>	antlr::ASTFactory factory;
159	>	parser.initializeASTFactory(factory);
160	>	parser.setASTFactory(&factory);
161	>	parser.mdfile();
162	>	// Create a tree parser that reads information into Globals
163	>	MDTreeParser treeParser;
164	>	treeParser.initializeASTFactory(factory);
165	>	treeParser.setASTFactory(&factory);
166	>	simParams = treeParser.walkTree(parser.getAST());
167	>	}
168	>
169	>
170	>	catch(antlr::MismatchedCharException& e) {
171	>	sprintf(painCave.errMsg,
172	>	"parser exception: %s %s:%d:%d\n",
173	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	catch(antlr::MismatchedTokenException &e) {
178	>	sprintf(painCave.errMsg,
179	>	"parser exception: %s %s:%d:%d\n",
180	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184	>	catch(antlr::NoViableAltForCharException &e) {
185	>	sprintf(painCave.errMsg,
186	>	"parser exception: %s %s:%d:%d\n",
187	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	>	painCave.isFatal = 1;
189	>	simError();
190	>	}
191	>	catch(antlr::NoViableAltException &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::TokenStreamRecognitionException& e) {
200	>	sprintf(painCave.errMsg,
201	>	"parser exception: %s %s:%d:%d\n",
202	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
203	>	painCave.isFatal = 1;
204	>	simError();
205	>	}
206	>
207	>	catch(antlr::TokenStreamIOException& e) {
208	>	sprintf(painCave.errMsg,
209	>	"parser exception: %s\n",
210	>	e.getMessage().c_str());
211	>	painCave.isFatal = 1;
212	>	simError();
213	>	}
214	>
215	>	catch(antlr::TokenStreamException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s\n",
218	>	e.getMessage().c_str());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (antlr::RecognitionException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"parser exception: %s %s:%d:%d\n",
225	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (antlr::CharStreamException& e) {
230	>	sprintf(painCave.errMsg,
231	>	"parser exception: %s\n",
232	>	e.getMessage().c_str());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>	catch (OpenMDException& e) {
237	>	sprintf(painCave.errMsg,
238	>	"%s\n",
239	>	e.getMessage().c_str());
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>	catch (std::exception& e) {
244	>	sprintf(painCave.errMsg,
245	>	"parser exception: %s\n",
246	>	e.what());
247	>	painCave.isFatal = 1;
248	>	simError();
249	>	}
250	>
251	>	simParams->setMDfileVersion(mdFileVersion);
252	>	return simParams;
253	>	}
254	>
255	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
256	>	bool loadInitCoords) {
257	>
258	>	const int bufferSize = 65535;
259	>	char buffer[bufferSize];
260	>	int lineNo = 0;
261	>	std::string mdRawData;
262	>	int metaDataBlockStart = -1;
263	>	int metaDataBlockEnd = -1;
264	>	int i, j;
265	>	streamoff mdOffset;
266	>	int mdFileVersion;
267	>
268	>	// Create a string for embedding the version information in the MetaData
269	>	std::string version;
270	>	version.assign("## Last run using OpenMD Version: ");
271	>	version.append(OPENMD_VERSION_MAJOR);
272	>	version.append(".");
273	>	version.append(OPENMD_VERSION_MINOR);
274	>
275	>	std::string svnrev;
276	>	//convert a macro from compiler to a string in c++
277	>	STR_DEFINE(svnrev, SVN_REV );
278	>	version.append(" Revision: ");
279	>	// If there's no SVN revision, just call this the RELEASE revision.
280	>	if (!svnrev.empty()) {
281	>	version.append(svnrev);
282		} else {
283	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
283	>	version.append("RELEASE");
284		}
285	+
286	+	#ifdef IS_MPI
287	+	const int masterNode = 0;
288	+	if (worldRank == masterNode) {
289	+	#endif
290
291	<	#endif
291	>	std::ifstream mdFile_;
292	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
293	>
294	>	if (mdFile_.fail()) {
295	>	sprintf(painCave.errMsg,
296	>	"SimCreator: Cannot open file: %s\n",
297	>	mdFileName.c_str());
298	>	painCave.isFatal = 1;
299	>	simError();
300	>	}
301
302	<	}
302	>	mdFile_.getline(buffer, bufferSize);
303	>	++lineNo;
304	>	std::string line = trimLeftCopy(buffer);
305	>	i = CaseInsensitiveFind(line, "<OpenMD");
306	>	if (static_cast<size_t>(i) == string::npos) {
307	>	// try the older file strings to see if that works:
308	>	i = CaseInsensitiveFind(line, "<OOPSE");
309	>	}
310	>
311	>	if (static_cast<size_t>(i) == string::npos) {
312	>	// still no luck!
313	>	sprintf(painCave.errMsg,
314	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
315	>	mdFileName.c_str());
316	>	painCave.isFatal = 1;
317	>	simError();
318	>	}
319	>
320	>	// found the correct opening string, now try to get the file
321	>	// format version number.
322
323	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
324	<
325	<	MakeStamps * stamps = new MakeStamps();
323	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
324	>	std::string fileType = tokenizer.nextToken();
325	>	toUpper(fileType);
326
327	<	Globals * simParams = new Globals();
327	>	mdFileVersion = 0;
328
329	<	//parse meta-data file
330	<	parseFile(mdFileName, stamps, simParams);
329	>	if (fileType == "OPENMD") {
330	>	while (tokenizer.hasMoreTokens()) {
331	>	std::string token(tokenizer.nextToken());
332	>	toUpper(token);
333	>	if (token == "VERSION") {
334	>	mdFileVersion = tokenizer.nextTokenAsInt();
335	>	break;
336	>	}
337	>	}
338	>	}
339	>
340	>	//scan through the input stream and find MetaData tag
341	>	while(mdFile_.getline(buffer, bufferSize)) {
342	>	++lineNo;
343	>
344	>	std::string line = trimLeftCopy(buffer);
345	>	if (metaDataBlockStart == -1) {
346	>	i = CaseInsensitiveFind(line, "<MetaData>");
347	>	if (i != string::npos) {
348	>	metaDataBlockStart = lineNo;
349	>	mdOffset = mdFile_.tellg();
350	>	}
351	>	} else {
352	>	i = CaseInsensitiveFind(line, "</MetaData>");
353	>	if (i != string::npos) {
354	>	metaDataBlockEnd = lineNo;
355	>	}
356	>	}
357	>	}
358
359	<	//create the force field
360	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
361	<	simParams->getForceField());
362	<
363	<	if (ff == NULL) {
364	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
365	<	simParams->getForceField());
366	<	painCave.isFatal = 1;
367	<	simError();
359	>	if (metaDataBlockStart == -1) {
360	>	sprintf(painCave.errMsg,
361	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
362	>	mdFileName.c_str());
363	>	painCave.isFatal = 1;
364	>	simError();
365	>	}
366	>	if (metaDataBlockEnd == -1) {
367	>	sprintf(painCave.errMsg,
368	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
369	>	mdFileName.c_str());
370	>	painCave.isFatal = 1;
371	>	simError();
372	>	}
373	>
374	>	mdFile_.clear();
375	>	mdFile_.seekg(0);
376	>	mdFile_.seekg(mdOffset);
377	>
378	>	mdRawData.clear();
379	>
380	>	bool foundVersion = false;
381	>
382	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
383	>	mdFile_.getline(buffer, bufferSize);
384	>	std::string line = trimLeftCopy(buffer);
385	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
386	>	if (static_cast<size_t>(j) != string::npos) {
387	>	foundVersion = true;
388	>	mdRawData += version;
389	>	} else {
390	>	mdRawData += buffer;
391	>	}
392	>	mdRawData += "\n";
393	>	}
394	>
395	>	if (!foundVersion) mdRawData += version + "\n";
396	>
397	>	mdFile_.close();
398	>
399	>	#ifdef IS_MPI
400		}
401	+	#endif
402
403	+	std::stringstream rawMetaDataStream(mdRawData);
404	+
405	+	//parse meta-data file
406	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
407	+	metaDataBlockStart + 1);
408	+
409	+	//create the force field
410	+	ForceField * ff = new ForceField(simParams->getForceField());
411	+
412	+	if (ff == NULL) {
413	+	sprintf(painCave.errMsg,
414	+	"ForceField Factory can not create %s force field\n",
415	+	simParams->getForceField().c_str());
416	+	painCave.isFatal = 1;
417	+	simError();
418	+	}
419	+
420		if (simParams->haveForceFieldFileName()) {
421	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
421	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
422		}
423
424		std::string forcefieldFileName;
425		forcefieldFileName = ff->getForceFieldFileName();
426	<
426	>
427		if (simParams->haveForceFieldVariant()) {
428	<	//If the force field has variant, the variant force field name will be
429	<	//Base.variant.frc. For exampel EAM.u6.frc
430	<
431	<	std::string variant = simParams->getForceFieldVariant();
432	<
433	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
434	<	variant = "." + variant;
435	<	if (pos != std::string::npos) {
436	<	forcefieldFileName.insert(pos, variant);
437	<	} else {
438	<	//If the default force field file name does not containt .frc suffix, just append the .variant
439	<	forcefieldFileName.append(variant);
440	<	}
428	>	//If the force field has variant, the variant force field name will be
429	>	//Base.variant.frc. For exampel EAM.u6.frc
430	>
431	>	std::string variant = simParams->getForceFieldVariant();
432	>
433	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
434	>	variant = "." + variant;
435	>	if (pos != std::string::npos) {
436	>	forcefieldFileName.insert(pos, variant);
437	>	} else {
438	>	//If the default force field file name does not containt .frc suffix, just append the .variant
439	>	forcefieldFileName.append(variant);
440	>	}
441		}
442
443		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
444		//create SimInfo
445	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
445	>	SimInfo * info = new SimInfo(ff, simParams);
446
447	<	//gather parameters (SimCreator only retrieves part of the parameters)
447	>	info->setRawMetaData(mdRawData);
448	>
449	>	//gather parameters (SimCreator only retrieves part of the
450	>	//parameters)
451		gatherParameters(info, mdFileName);
452	<
452	>
453		//divide the molecules and determine the global index of molecules
454		#ifdef IS_MPI
455		divideMolecules(info);
456		#endif
457	<
457	>
458		//create the molecules
459		createMolecules(info);
460	+
461	+	//find the storage layout
462
463	+	int storageLayout = computeStorageLayout(info);
464
465	<	//allocate memory for DataStorage(circular reference, need to break it)
466	<	info->setSnapshotManager(new SimSnapshotManager(info));
465	>	//allocate memory for DataStorage(circular reference, need to
466	>	//break it)
467	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
468
469	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
470	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
471	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
469	>	//set the global index of atoms, rigidbodies and cutoffgroups
470	>	//(only need to be set once, the global index will never change
471	>	//again). Local indices of atoms and rigidbodies are already set
472	>	//by MoleculeCreator class which actually delegates the
473	>	//responsibility to LocalIndexManager.
474		setGlobalIndex(info);
475	<
476	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
477	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
478	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
479	<	//we can determine the beginning global indices of atoms before they get created.
475	>
476	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
477	>	//method, at that point atoms don't have the global index yet
478	>	//(their global index are all initialized to -1).  Therefore we
479	>	//have to call addInteractionPairs explicitly here. A way to work
480	>	//around is that we can determine the beginning global indices of
481	>	//atoms before they get created.
482		SimInfo::MoleculeIterator mi;
483		Molecule* mol;
484		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
485	<	info->addExcludePairs(mol);
485	>	info->addInteractionPairs(mol);
486		}
487
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
488		if (loadInitCoords)
489	<	loadCoordinates(info);
186	<
489	>	loadCoordinates(info, mdFileName);
490		return info;
491	<	}
492	<
493	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
494	<
495	<	//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
491	>	}
492	>
493	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
494	>
495	>	//figure out the output file names
496		std::string prefix;
497	<
497	>
498		#ifdef IS_MPI
499	<
499	>
500		if (worldRank == 0) {
501		#endif // is_mpi
502	<
503	<	if (simParams->haveFinalConfig()) {
504	<	prefix = getPrefix(simParams->getFinalConfig());
505	<	} else {
506	<	prefix = getPrefix(mdfile);
507	<	}
508	<
509	<	info->setFinalConfigFileName(prefix + ".eor");
510	<	info->setDumpFileName(prefix + ".dump");
511	<	info->setStatFileName(prefix + ".stat");
512	<
502	>	Globals * simParams = info->getSimParams();
503	>	if (simParams->haveFinalConfig()) {
504	>	prefix = getPrefix(simParams->getFinalConfig());
505	>	} else {
506	>	prefix = getPrefix(mdfile);
507	>	}
508	>
509	>	info->setFinalConfigFileName(prefix + ".eor");
510	>	info->setDumpFileName(prefix + ".dump");
511	>	info->setStatFileName(prefix + ".stat");
512	>	info->setRestFileName(prefix + ".zang");
513	>
514		#ifdef IS_MPI
515	<
515	>
516		}
517	<
517	>
518		#endif
519	<
520	<	}
521	<
519	>
520	>	}
521	>
522		#ifdef IS_MPI
523	<	void SimCreator::divideMolecules(SimInfo *info) {
524	<	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;
523	>	void SimCreator::divideMolecules(SimInfo *info) {
524	>	RealType a;
525		int nProcessors;
526		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
527		int nGlobalMols = info->getNGlobalMolecules();
528	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
528	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
529	>	// error
530	>	// condition:
531
532	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
533	<
532	>	MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
533	>	//nProcessors = MPI::COMM_WORLD.Get_size();
534	>
535		if (nProcessors > nGlobalMols) {
536	<	sprintf(painCave.errMsg,
537	<	"nProcessors (%d) > nMol (%d)\n"
538	<	"\tThe number of processors is larger than\n"
539	<	"\tthe number of molecules.  This will not result in a \n"
540	<	"\tusable division of atoms for force decomposition.\n"
541	<	"\tEither try a smaller number of processors, or run the\n"
542	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
543	<
544	<	painCave.isFatal = 1;
545	<	simError();
536	>	sprintf(painCave.errMsg,
537	>	"nProcessors (%d) > nMol (%d)\n"
538	>	"\tThe number of processors is larger than\n"
539	>	"\tthe number of molecules.  This will not result in a \n"
540	>	"\tusable division of atoms for force decomposition.\n"
541	>	"\tEither try a smaller number of processors, or run the\n"
542	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
543	>	nGlobalMols);
544	>
545	>	painCave.isFatal = 1;
546	>	simError();
547		}
548	<
548	>
549	>	Globals * simParams = info->getSimParams();
550	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
551	>	//random number generator
552	>	if (simParams->haveSeed()) {
553	>	int seedValue = simParams->getSeed();
554	>	myRandom = new SeqRandNumGen(seedValue);
555	>	}else {
556	>	myRandom = new SeqRandNumGen();
557	>	}
558	>
559	>
560		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
561	<
561	>
562		//initialize atomsPerProc
563		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
564	<
564	>
565		if (worldRank == 0) {
566	<	numerator = info->getNGlobalAtoms();
567	<	denominator = nProcessors;
568	<	precast = numerator / denominator;
569	<	nTarget = (int)(precast + 0.5);
566	>	RealType numerator = info->getNGlobalAtoms();
567	>	RealType denominator = nProcessors;
568	>	RealType precast = numerator / denominator;
569	>	int nTarget = (int)(precast + 0.5);
570	>
571	>	for(int i = 0; i < nGlobalMols; i++) {
572
573	<	for(i = 0; i < nGlobalMols; i++) {
574	<	done = 0;
575	<	loops = 0;
576	<
577	<	while (!done) {
578	<	loops++;
579	<
580	<	// Pick a processor at random
581	<
582	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
583	<
584	<	//get the molecule stamp first
585	<	int stampId = info->getMoleculeStampId(i);
586	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
587	<
588	<	// How many atoms does this processor have so far?
589	<	old_atoms = atomsPerProc[which_proc];
590	<	add_atoms = moleculeStamp->getNAtoms();
591	<	new_atoms = old_atoms + add_atoms;
592	<
593	<	// If we've been through this loop too many times, we need
594	<	// to just give up and assign the molecule to this processor
595	<	// and be done with it.
573	>	int done = 0;
574	>	int loops = 0;
575	>
576	>	while (!done) {
577	>	loops++;
578	>
579	>	// Pick a processor at random
580	>
581	>	int which_proc = (int) (myRandom->rand() * nProcessors);
582	>
583	>	//get the molecule stamp first
584	>	int stampId = info->getMoleculeStampId(i);
585	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
586	>
587	>	// How many atoms does this processor have so far?
588	>	int old_atoms = atomsPerProc[which_proc];
589	>	int add_atoms = moleculeStamp->getNAtoms();
590	>	int new_atoms = old_atoms + add_atoms;
591	>
592	>	// If we've been through this loop too many times, we need
593	>	// to just give up and assign the molecule to this processor
594	>	// and be done with it.
595	>
596	>	if (loops > 100) {
597
598	<	if (loops > 100) {
599	<	sprintf(painCave.errMsg,
600	<	"I've tried 100 times to assign molecule %d to a "
601	<	" processor, but can't find a good spot.\n"
602	<	"I'm assigning it at random to processor %d.\n",
603	<	i, which_proc);
604	<
605	<	painCave.isFatal = 0;
606	<	simError();
607	<
608	<	molToProcMap[i] = which_proc;
609	<	atomsPerProc[which_proc] += add_atoms;
610	<
611	<	done = 1;
612	<	continue;
613	<	}
614	<
615	<	// If we can add this molecule to this processor without sending
616	<	// it above nTarget, then go ahead and do it:
617	<
618	<	if (new_atoms <= nTarget) {
619	<	molToProcMap[i] = which_proc;
620	<	atomsPerProc[which_proc] += add_atoms;
621	<
622	<	done = 1;
623	<	continue;
624	<	}
625	<
626	<	// The only situation left is when new_atoms > nTarget.  We
627	<	// want to accept this with some probability that dies off the
628	<	// farther we are from nTarget
629	<
630	<	// roughly:  x = new_atoms - nTarget
631	<	//           Pacc(x) = exp(- a * x)
632	<	// where a = penalty / (average atoms per molecule)
633	<
634	<	x = (double)(new_atoms - nTarget);
635	<	y = myRandom.getRandom();
636	<
637	<	if (y < exp(- a * x)) {
638	<	molToProcMap[i] = which_proc;
639	<	atomsPerProc[which_proc] += add_atoms;
640	<
641	<	done = 1;
642	<	continue;
643	<	} else {
644	<	continue;
645	<	}
392	<	}
598	>	sprintf(painCave.errMsg,
599	>	"There have been 100 attempts to assign molecule %d to an\n"
600	>	"\tunderworked processor, but there's no good place to\n"
601	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
602	>	i, which_proc);
603	>
604	>	painCave.isFatal = 0;
605	>	painCave.severity = OPENMD_INFO;
606	>	simError();
607	>
608	>	molToProcMap[i] = which_proc;
609	>	atomsPerProc[which_proc] += add_atoms;
610	>
611	>	done = 1;
612	>	continue;
613	>	}
614	>
615	>	// If we can add this molecule to this processor without sending
616	>	// it above nTarget, then go ahead and do it:
617	>
618	>	if (new_atoms <= nTarget) {
619	>	molToProcMap[i] = which_proc;
620	>	atomsPerProc[which_proc] += add_atoms;
621	>
622	>	done = 1;
623	>	continue;
624	>	}
625	>
626	>	// The only situation left is when new_atoms > nTarget.  We
627	>	// want to accept this with some probability that dies off the
628	>	// farther we are from nTarget
629	>
630	>	// roughly:  x = new_atoms - nTarget
631	>	//           Pacc(x) = exp(- a * x)
632	>	// where a = penalty / (average atoms per molecule)
633	>
634	>	RealType x = (RealType)(new_atoms - nTarget);
635	>	RealType y = myRandom->rand();
636	>
637	>	if (y < exp(- a * x)) {
638	>	molToProcMap[i] = which_proc;
639	>	atomsPerProc[which_proc] += add_atoms;
640	>
641	>	done = 1;
642	>	continue;
643	>	} else {
644	>	continue;
645	>	}
646		}
647	+	}
648	+
649	+	delete myRandom;
650
651	<	// Spray out this nonsense to all other processors:
652	<
653	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
651	>	// Spray out this nonsense to all other processors:
652	>	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
653	>	// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
654		} else {
655	+
656	+	// Listen to your marching orders from processor 0:
657	+	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
658	+	// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
659
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
660		}
661	<
661	>
662		info->setMolToProcMap(molToProcMap);
663		sprintf(checkPointMsg,
664		"Successfully divided the molecules among the processors.\n");
665	<	MPIcheckPoint();
666	<	}
667	<
665	>	errorCheckPoint();
666	>	}
667	>
668		#endif
669	<
670	<	void SimCreator::createMolecules(SimInfo *info) {
669	>
670	>	void SimCreator::createMolecules(SimInfo *info) {
671		MoleculeCreator molCreator;
672		int stampId;
673	<
673	>
674		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
675	<
675	>
676		#ifdef IS_MPI
677	<
678	<	if (info->getMolToProc(i) == worldRank) {
677	>
678	>	if (info->getMolToProc(i) == worldRank) {
679		#endif
680	<
681	<	stampId = info->getMoleculeStampId(i);
682	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
683	<	stampId, i, info->getLocalIndexManager());
684	<
685	<	info->addMolecule(mol);
686	<
680	>
681	>	stampId = info->getMoleculeStampId(i);
682	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
683	>	info->getMoleculeStamp(stampId),
684	>	stampId, i,
685	>	info->getLocalIndexManager());
686	>
687	>	info->addMolecule(mol);
688	>
689		#ifdef IS_MPI
690	<
691	<	}
692	<
690	>
691	>	}
692	>
693		#endif
694	<
694	>
695		} //end for(int i=0)
696	<	}
696	>	}
697	>
698	>	int SimCreator::computeStorageLayout(SimInfo* info) {
699
700	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
701	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
702	<	int i;
703	<	char * id;
704	<	MoleculeStamp * currentStamp;
705	<	Component** the_components = simParams->getComponents();
706	<	int n_components = simParams->getNComponents();
700	>	Globals* simParams = info->getSimParams();
701	>	int nRigidBodies = info->getNGlobalRigidBodies();
702	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
703	>	set<AtomType*>::iterator i;
704	>	bool hasDirectionalAtoms = false;
705	>	bool hasFixedCharge = false;
706	>	bool hasDipoles = false;
707	>	bool hasQuadrupoles = false;
708	>	bool hasPolarizable = false;
709	>	bool hasFluctuatingCharge = false;
710	>	bool hasMetallic = false;
711	>	int storageLayout = 0;
712	>	storageLayout |= DataStorage::dslPosition;
713	>	storageLayout |= DataStorage::dslVelocity;
714	>	storageLayout |= DataStorage::dslForce;
715
716	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
716	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717
718	<	for(i = 0; i < n_components; i++) {
719	<	if (!the_components[i]->haveNMol()) {
720	<	// we have a problem
721	<	sprintf(painCave.errMsg,
722	<	"SimCreator Error. No global NMol or component NMol given.\n"
723	<	"\tCannot calculate the number of atoms.\n");
718	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
719	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
720	>	EAMAdapter ea = EAMAdapter( (*i) );
721	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
722	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
723	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
724	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
725
726	<	painCave.isFatal = 1;
727	<	simError();
728	<	}
726	>	if (da.isDirectional()){
727	>	hasDirectionalAtoms = true;
728	>	}
729	>	if (ma.isDipole()){
730	>	hasDipoles = true;
731	>	}
732	>	if (ma.isQuadrupole()){
733	>	hasQuadrupoles = true;
734	>	}
735	>	if (ea.isEAM() || sca.isSuttonChen()){
736	>	hasMetallic = true;
737	>	}
738	>	if ( fca.isFixedCharge() ){
739	>	hasFixedCharge = true;
740	>	}
741	>	if ( fqa.isFluctuatingCharge() ){
742	>	hasFluctuatingCharge = true;
743	>	}
744	>	if ( pa.isPolarizable() ){
745	>	hasPolarizable = true;
746	>	}
747	>	}
748	>
749	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
750	>	storageLayout |= DataStorage::dslAmat;
751	>	if(storageLayout & DataStorage::dslVelocity) {
752	>	storageLayout |= DataStorage::dslAngularMomentum;
753	>	}
754	>	if (storageLayout & DataStorage::dslForce) {
755	>	storageLayout |= DataStorage::dslTorque;
756	>	}
757	>	}
758	>	if (hasDipoles) {
759	>	storageLayout |= DataStorage::dslDipole;
760	>	}
761	>	if (hasQuadrupoles) {
762	>	storageLayout |= DataStorage::dslQuadrupole;
763	>	}
764	>	if (hasFixedCharge || hasFluctuatingCharge) {
765	>	storageLayout |= DataStorage::dslSkippedCharge;
766	>	}
767	>	if (hasMetallic) {
768	>	storageLayout |= DataStorage::dslDensity;
769	>	storageLayout |= DataStorage::dslFunctional;
770	>	storageLayout |= DataStorage::dslFunctionalDerivative;
771	>	}
772	>	if (hasPolarizable) {
773	>	storageLayout |= DataStorage::dslElectricField;
774	>	}
775	>	if (hasFluctuatingCharge){
776	>	storageLayout |= DataStorage::dslFlucQPosition;
777	>	if(storageLayout & DataStorage::dslVelocity) {
778	>	storageLayout |= DataStorage::dslFlucQVelocity;
779	>	}
780	>	if (storageLayout & DataStorage::dslForce) {
781	>	storageLayout |= DataStorage::dslFlucQForce;
782	>	}
783	>	}
784	>
785	>	// if the user has asked for them, make sure we've got the memory for the
786	>	// objects defined.
787
788	<	id = the_components[i]->getType();
789	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
788	>	if (simParams->getOutputParticlePotential()) {
789	>	storageLayout |= DataStorage::dslParticlePot;
790	>	}
791
792	<	if (currentStamp == NULL) {
793	<	sprintf(painCave.errMsg,
794	<	"SimCreator error: Component \"%s\" was not found in the "
795	<	"list of declared molecules\n", id);
792	>	if (simParams->havePrintHeatFlux()) {
793	>	if (simParams->getPrintHeatFlux()) {
794	>	storageLayout |= DataStorage::dslParticlePot;
795	>	}
796	>	}
797
798	<	painCave.isFatal = 1;
799	<	simError();
800	<	}
798	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
799	>	storageLayout |= DataStorage::dslElectricField;
800	>	}
801
802	<	moleculeStampPairs.push_back(
803	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
804	<	} //end for (i = 0; i < n_components; i++)
805	<	} 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();
802	>	if (simParams->getOutputFluctuatingCharges()) {
803	>	storageLayout |= DataStorage::dslFlucQPosition;
804	>	storageLayout |= DataStorage::dslFlucQVelocity;
805	>	storageLayout |= DataStorage::dslFlucQForce;
806		}
807
808	<	#ifdef IS_MPI
489	<
490	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
491	<	MPIcheckPoint();
808	>	info->setStorageLayout(storageLayout);
809
810	<	#endif // is_mpi
810	>	return storageLayout;
811	>	}
812
813	<	}
496	<
497	<	void SimCreator::setGlobalIndex(SimInfo *info) {
813	>	void SimCreator::setGlobalIndex(SimInfo *info) {
814		SimInfo::MoleculeIterator mi;
815		Molecule::AtomIterator ai;
816		Molecule::RigidBodyIterator ri;
817		Molecule::CutoffGroupIterator ci;
818	<	Molecule * mol;
819	<	Atom * atom;
820	<	RigidBody * rb;
821	<	CutoffGroup * cg;
818	>	Molecule::BondIterator boi;
819	>	Molecule::BendIterator bei;
820	>	Molecule::TorsionIterator ti;
821	>	Molecule::InversionIterator ii;
822	>	Molecule::IntegrableObjectIterator  ioi;
823	>	Molecule* mol;
824	>	Atom* atom;
825	>	RigidBody* rb;
826	>	CutoffGroup* cg;
827	>	Bond* bond;
828	>	Bend* bend;
829	>	Torsion* torsion;
830	>	Inversion* inversion;
831		int beginAtomIndex;
832		int beginRigidBodyIndex;
833		int beginCutoffGroupIndex;
834	+	int beginBondIndex;
835	+	int beginBendIndex;
836	+	int beginTorsionIndex;
837	+	int beginInversionIndex;
838		int nGlobalAtoms = info->getNGlobalAtoms();
839	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
840
511	–	#ifndef IS_MPI
512	–
841		beginAtomIndex = 0;
842	<	beginRigidBodyIndex = 0;
842	>	// The rigid body indices begin immediately after the atom indices:
843	>	beginRigidBodyIndex = info->getNGlobalAtoms();
844		beginCutoffGroupIndex = 0;
845	+	beginBondIndex = 0;
846	+	beginBendIndex = 0;
847	+	beginTorsionIndex = 0;
848	+	beginInversionIndex = 0;
849	+
850	+	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
851	+
852	+	#ifdef IS_MPI
853	+	if (info->getMolToProc(i) == worldRank) {
854	+	#endif
855	+	// stuff to do if I own this molecule
856	+	mol = info->getMoleculeByGlobalIndex(i);
857
858	<	#else
859	<
860	<	int nproc;
861	<	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	<	//rigidbody's index begins right after atom's
557	<	beginRigidBodyIndex += info->getNGlobalAtoms();
558	<
559	<	for(mol = info->beginMolecule(mi); mol != NULL;
560	<	mol = info->nextMolecule(mi)) {
561	<
562	<	//local index(index in DataStorge) of atom is important
563	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
564	<	atom->setGlobalIndex(beginAtomIndex++);
858	>	// The local index(index in DataStorge) of the atom is important:
859	>	for(atom = mol->beginAtom(ai); atom != NULL;
860	>	atom = mol->nextAtom(ai)) {
861	>	atom->setGlobalIndex(beginAtomIndex++);
862		}
863	<
863	>
864		for(rb = mol->beginRigidBody(ri); rb != NULL;
865		rb = mol->nextRigidBody(ri)) {
866	<	rb->setGlobalIndex(beginRigidBodyIndex++);
866	>	rb->setGlobalIndex(beginRigidBodyIndex++);
867		}
868	<
869	<	//local index of cutoff group is trivial, it only depends on the order of travesing
868	>
869	>	// The local index of other objects only depends on the order
870	>	// of traversal:
871		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
872		cg = mol->nextCutoffGroup(ci)) {
873	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
874	<	}
875	<	}
873	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
874	>	}
875	>	for(bond = mol->beginBond(boi); bond != NULL;
876	>	bond = mol->nextBond(boi)) {
877	>	bond->setGlobalIndex(beginBondIndex++);
878	>	}
879	>	for(bend = mol->beginBend(bei); bend != NULL;
880	>	bend = mol->nextBend(bei)) {
881	>	bend->setGlobalIndex(beginBendIndex++);
882	>	}
883	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
884	>	torsion = mol->nextTorsion(ti)) {
885	>	torsion->setGlobalIndex(beginTorsionIndex++);
886	>	}
887	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
888	>	inversion = mol->nextInversion(ii)) {
889	>	inversion->setGlobalIndex(beginInversionIndex++);
890	>	}
891	>
892	>	#ifdef IS_MPI
893	>	}  else {
894
895	<	//fill globalGroupMembership
896	<	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
897	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
898	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
895	>	// stuff to do if I don't own this molecule
896	>
897	>	int stampId = info->getMoleculeStampId(i);
898	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
899
900	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
902	<	}
900	>	beginAtomIndex += stamp->getNAtoms();
901	>	beginRigidBodyIndex += stamp->getNRigidBodies();
902	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
903	>	beginBondIndex += stamp->getNBonds();
904	>	beginBendIndex += stamp->getNBends();
905	>	beginTorsionIndex += stamp->getNTorsions();
906	>	beginInversionIndex += stamp->getNInversions();
907	>	}
908	>	#endif
909
910	<	}
589	<	}
910	>	} //end for(int i=0)
911
912	+	//fill globalGroupMembership
913	+	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
914	+	for(mol = info->beginMolecule(mi); mol != NULL;
915	+	mol = info->nextMolecule(mi)) {
916	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
917	+	cg = mol->nextCutoffGroup(ci)) {
918	+	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
919	+	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
920	+	}
921	+
922	+	}
923	+	}
924	+
925		#ifdef IS_MPI
926		// Since the globalGroupMembership has been zero filled and we've only
927		// poked values into the atoms we know, we can do an Allreduce
928		// to get the full globalGroupMembership array (We think).
929		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
930		// docs said we could.
931	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
932	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
931	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
932	>	MPI_Allreduce(&globalGroupMembership[0],
933	>	&tmpGroupMembership[0], nGlobalAtoms,
934		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
935	<	info->setGlobalGroupMembership(tmpGroupMembership);
935	>	// MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
936	>	//                           &tmpGroupMembership[0], nGlobalAtoms,
937	>	//                           MPI::INT, MPI::SUM);
938	>	info->setGlobalGroupMembership(tmpGroupMembership);
939		#else
940		info->setGlobalGroupMembership(globalGroupMembership);
941		#endif
942	<
942	>
943		//fill molMembership
944	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
944	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
945	>	info->getNGlobalRigidBodies(), 0);
946
947	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
948	<
949	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
950	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
951	<	}
947	>	for(mol = info->beginMolecule(mi); mol != NULL;
948	>	mol = info->nextMolecule(mi)) {
949	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
950	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
951	>	}
952	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
953	>	rb = mol->nextRigidBody(ri)) {
954	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
955	>	}
956		}
957	<
957	>
958		#ifdef IS_MPI
959	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
960	<
961	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
959	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
960	>	info->getNGlobalRigidBodies(), 0);
961	>	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
962	>	nGlobalAtoms + nGlobalRigidBodies,
963		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
964	+	// MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
965	+	//                           nGlobalAtoms + nGlobalRigidBodies,
966	+	//                           MPI::INT, MPI::SUM);
967
968		info->setGlobalMolMembership(tmpMolMembership);
969		#else
970		info->setGlobalMolMembership(globalMolMembership);
971		#endif
972
973	<	}
973	>	// nIOPerMol holds the number of integrable objects per molecule
974	>	// here the molecules are listed by their global indices.
975
976	<	void SimCreator::loadCoordinates(SimInfo* info) {
977	<	Globals* simParams;
978	<	simParams = info->getSimParams();
976	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
977	>	for (mol = info->beginMolecule(mi); mol != NULL;
978	>	mol = info->nextMolecule(mi)) {
979	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
980	>	}
981
982	<	if (!simParams->haveInitialConfig()) {
983	<	sprintf(painCave.errMsg,
984	<	"Cannot intialize a simulation without an initial configuration file.\n");
985	<	painCave.isFatal = 1;;
986	<	simError();
982	>	#ifdef IS_MPI
983	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
984	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
985	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
986	>	// MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
987	>	//                           info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
988	>	#else
989	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
990	>	#endif
991	>
992	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
993	>
994	>	int startingIndex = 0;
995	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
996	>	startingIOIndexForMol[i] = startingIndex;
997	>	startingIndex += numIntegrableObjectsPerMol[i];
998		}
999	<
1000	<	DumpReader reader(info, simParams->getInitialConfig());
999	>
1000	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
1001	>	for (mol = info->beginMolecule(mi); mol != NULL;
1002	>	mol = info->nextMolecule(mi)) {
1003	>	int myGlobalIndex = mol->getGlobalIndex();
1004	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
1005	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
1006	>	sd = mol->nextIntegrableObject(ioi)) {
1007	>	sd->setGlobalIntegrableObjectIndex(globalIO);
1008	>	IOIndexToIntegrableObject[globalIO] = sd;
1009	>	globalIO++;
1010	>	}
1011	>	}
1012	>
1013	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
1014	>
1015	>	}
1016	>
1017	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
1018	>
1019	>	DumpReader reader(info, mdFileName);
1020		int nframes = reader.getNFrames();
1021	<
1021	>
1022		if (nframes > 0) {
1023	<	reader.readFrame(nframes - 1);
1023	>	reader.readFrame(nframes - 1);
1024		} else {
1025	<	//invalid initial coordinate file
1026	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
1027	<	simParams->getInitialConfig());
1028	<	painCave.isFatal = 1;
1029	<	simError();
1025	>	//invalid initial coordinate file
1026	>	sprintf(painCave.errMsg,
1027	>	"Initial configuration file %s should at least contain one frame\n",
1028	>	mdFileName.c_str());
1029	>	painCave.isFatal = 1;
1030	>	simError();
1031		}
651	–
1032		//copy the current snapshot to previous snapshot
1033		info->getSnapshotManager()->advance();
1034	<	}
1034	>	}
1035	>
1036	>	} //end namespace OpenMD
1037
656	–	} //end namespace oopse
1038
658	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 297 by tim, Mon Feb 7 19:14:26 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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