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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1976 by gezelter, Wed Mar 12 20:01:15 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	>	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
109	>	#endif
110	>	SimplePreprocessor preprocessor;
111	>	preprocessor.preprocess(rawMetaDataStream, filename,
112	>	startOfMetaDataBlock, ppStream);
113	>
114	>	#ifdef IS_MPI
115	>	//broadcasting the stream size
116	>	streamSize = ppStream.str().size() +1;
117	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
118	>	MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
119	>	streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
120
121	<	mpiEventInit();
121	>	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
122	>	// MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
123	>	//                       streamSize, MPI::CHAR, masterNode);
124	>
125	>	} else {
126
127	<	#endif
127	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
128	>	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
129
130	<	yacc_BASS(mdFileName.c_str());
130	>	//get stream size
131	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
132	>	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
133	>	char* buf = new char[streamSize];
134	>	assert(buf);
135	>
136	>	//receive file content
137	>	MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
138	>	// MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
139
140	<	#ifdef IS_MPI
140	>	ppStream.str(buf);
141	>	delete [] buf;
142	>	}
143	>	#endif
144	>	// Create a scanner that reads from the input stream
145	>	MDLexer lexer(ppStream);
146	>	lexer.setFilename(filename);
147	>	lexer.initDeferredLineCount();
148	>
149	>	// Create a parser that reads from the scanner
150	>	MDParser parser(lexer);
151	>	parser.setFilename(filename);
152
153	<	throwMPIEvent(NULL);
153	>	// Create an observer that synchorizes file name change
154	>	FilenameObserver observer;
155	>	observer.setLexer(&lexer);
156	>	observer.setParser(&parser);
157	>	lexer.setObserver(&observer);
158	>
159	>	antlr::ASTFactory factory;
160	>	parser.initializeASTFactory(factory);
161	>	parser.setASTFactory(&factory);
162	>	parser.mdfile();
163	>	// Create a tree parser that reads information into Globals
164	>	MDTreeParser treeParser;
165	>	treeParser.initializeASTFactory(factory);
166	>	treeParser.setASTFactory(&factory);
167	>	simParams = treeParser.walkTree(parser.getAST());
168	>	}
169	>
170	>
171	>	catch(antlr::MismatchedCharException& e) {
172	>	sprintf(painCave.errMsg,
173	>	"parser exception: %s %s:%d:%d\n",
174	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	catch(antlr::MismatchedTokenException &e) {
179	>	sprintf(painCave.errMsg,
180	>	"parser exception: %s %s:%d:%d\n",
181	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
185	>	catch(antlr::NoViableAltForCharException &e) {
186	>	sprintf(painCave.errMsg,
187	>	"parser exception: %s %s:%d:%d\n",
188	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
189	>	painCave.isFatal = 1;
190	>	simError();
191	>	}
192	>	catch(antlr::NoViableAltException &e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s %s:%d:%d\n",
195	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199	>
200	>	catch(antlr::TokenStreamRecognitionException& e) {
201	>	sprintf(painCave.errMsg,
202	>	"parser exception: %s %s:%d:%d\n",
203	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
204	>	painCave.isFatal = 1;
205	>	simError();
206	>	}
207	>
208	>	catch(antlr::TokenStreamIOException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s\n",
211	>	e.getMessage().c_str());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>
216	>	catch(antlr::TokenStreamException& e) {
217	>	sprintf(painCave.errMsg,
218	>	"parser exception: %s\n",
219	>	e.getMessage().c_str());
220	>	painCave.isFatal = 1;
221	>	simError();
222	>	}
223	>	catch (antlr::RecognitionException& e) {
224	>	sprintf(painCave.errMsg,
225	>	"parser exception: %s %s:%d:%d\n",
226	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
227	>	painCave.isFatal = 1;
228	>	simError();
229	>	}
230	>	catch (antlr::CharStreamException& e) {
231	>	sprintf(painCave.errMsg,
232	>	"parser exception: %s\n",
233	>	e.getMessage().c_str());
234	>	painCave.isFatal = 1;
235	>	simError();
236	>	}
237	>	catch (OpenMDException& e) {
238	>	sprintf(painCave.errMsg,
239	>	"%s\n",
240	>	e.getMessage().c_str());
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>	catch (std::exception& e) {
245	>	sprintf(painCave.errMsg,
246	>	"parser exception: %s\n",
247	>	e.what());
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>
252	>	simParams->setMDfileVersion(mdFileVersion);
253	>	return simParams;
254	>	}
255	>
256	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
257	>	bool loadInitCoords) {
258	>
259	>	const int bufferSize = 65535;
260	>	char buffer[bufferSize];
261	>	int lineNo = 0;
262	>	std::string mdRawData;
263	>	int metaDataBlockStart = -1;
264	>	int metaDataBlockEnd = -1;
265	>	int i, j;
266	>	streamoff mdOffset;
267	>	int mdFileVersion;
268	>
269	>	// Create a string for embedding the version information in the MetaData
270	>	std::string version;
271	>	version.assign("## Last run using OpenMD Version: ");
272	>	version.append(OPENMD_VERSION_MAJOR);
273	>	version.append(".");
274	>	version.append(OPENMD_VERSION_MINOR);
275	>
276	>	std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
277	>	//convert a macro from compiler to a string in c++
278	>	// STR_DEFINE(svnrev, SVN_REV );
279	>	version.append(" Revision: ");
280	>	// If there's no SVN revision, just call this the RELEASE revision.
281	>	if (!svnrev.empty()) {
282	>	version.append(svnrev);
283		} else {
284	<	set_interface_stamps(stamps, simParams);
90	<	mpiEventInit();
91	<	MPIcheckPoint();
92	<	mpiEventLoop();
284	>	version.append("RELEASE");
285		}
286	+
287	+	#ifdef IS_MPI
288	+	const int masterNode = 0;
289	+	if (worldRank == masterNode) {
290	+	#endif
291
292	<	#endif
292	>	std::ifstream mdFile_;
293	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
294	>
295	>	if (mdFile_.fail()) {
296	>	sprintf(painCave.errMsg,
297	>	"SimCreator: Cannot open file: %s\n",
298	>	mdFileName.c_str());
299	>	painCave.isFatal = 1;
300	>	simError();
301	>	}
302
303	<	}
303	>	mdFile_.getline(buffer, bufferSize);
304	>	++lineNo;
305	>	std::string line = trimLeftCopy(buffer);
306	>	i = CaseInsensitiveFind(line, "<OpenMD");
307	>	if (static_cast<size_t>(i) == string::npos) {
308	>	// try the older file strings to see if that works:
309	>	i = CaseInsensitiveFind(line, "<OOPSE");
310	>	}
311	>
312	>	if (static_cast<size_t>(i) == string::npos) {
313	>	// still no luck!
314	>	sprintf(painCave.errMsg,
315	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
316	>	mdFileName.c_str());
317	>	painCave.isFatal = 1;
318	>	simError();
319	>	}
320	>
321	>	// found the correct opening string, now try to get the file
322	>	// format version number.
323
324	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
325	<
326	<	MakeStamps * stamps = new MakeStamps();
324	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
325	>	std::string fileType = tokenizer.nextToken();
326	>	toUpper(fileType);
327
328	<	Globals * simParams = new Globals();
328	>	mdFileVersion = 0;
329
330	<	//parse meta-data file
331	<	parseFile(mdFileName, stamps, simParams);
330	>	if (fileType == "OPENMD") {
331	>	while (tokenizer.hasMoreTokens()) {
332	>	std::string token(tokenizer.nextToken());
333	>	toUpper(token);
334	>	if (token == "VERSION") {
335	>	mdFileVersion = tokenizer.nextTokenAsInt();
336	>	break;
337	>	}
338	>	}
339	>	}
340	>
341	>	//scan through the input stream and find MetaData tag
342	>	while(mdFile_.getline(buffer, bufferSize)) {
343	>	++lineNo;
344	>
345	>	std::string line = trimLeftCopy(buffer);
346	>	if (metaDataBlockStart == -1) {
347	>	i = CaseInsensitiveFind(line, "<MetaData>");
348	>	if (i != string::npos) {
349	>	metaDataBlockStart = lineNo;
350	>	mdOffset = mdFile_.tellg();
351	>	}
352	>	} else {
353	>	i = CaseInsensitiveFind(line, "</MetaData>");
354	>	if (i != string::npos) {
355	>	metaDataBlockEnd = lineNo;
356	>	}
357	>	}
358	>	}
359
360	<	//create the force field
361	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
362	<	simParams->getForceField());
363	<
364	<	if (ff == NULL) {
365	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
366	<	simParams->getForceField());
367	<	painCave.isFatal = 1;
368	<	simError();
360	>	if (metaDataBlockStart == -1) {
361	>	sprintf(painCave.errMsg,
362	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
363	>	mdFileName.c_str());
364	>	painCave.isFatal = 1;
365	>	simError();
366	>	}
367	>	if (metaDataBlockEnd == -1) {
368	>	sprintf(painCave.errMsg,
369	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
370	>	mdFileName.c_str());
371	>	painCave.isFatal = 1;
372	>	simError();
373	>	}
374	>
375	>	mdFile_.clear();
376	>	mdFile_.seekg(0);
377	>	mdFile_.seekg(mdOffset);
378	>
379	>	mdRawData.clear();
380	>
381	>	bool foundVersion = false;
382	>
383	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
384	>	mdFile_.getline(buffer, bufferSize);
385	>	std::string line = trimLeftCopy(buffer);
386	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
387	>	if (static_cast<size_t>(j) != string::npos) {
388	>	foundVersion = true;
389	>	mdRawData += version;
390	>	} else {
391	>	mdRawData += buffer;
392	>	}
393	>	mdRawData += "\n";
394	>	}
395	>
396	>	if (!foundVersion) mdRawData += version + "\n";
397	>
398	>	mdFile_.close();
399	>
400	>	#ifdef IS_MPI
401		}
402	+	#endif
403
404	+	std::stringstream rawMetaDataStream(mdRawData);
405	+
406	+	//parse meta-data file
407	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
408	+	metaDataBlockStart + 1);
409	+
410	+	//create the force field
411	+	ForceField * ff = new ForceField(simParams->getForceField());
412	+
413	+	if (ff == NULL) {
414	+	sprintf(painCave.errMsg,
415	+	"ForceField Factory can not create %s force field\n",
416	+	simParams->getForceField().c_str());
417	+	painCave.isFatal = 1;
418	+	simError();
419	+	}
420	+
421		if (simParams->haveForceFieldFileName()) {
422	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
422	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
423		}
424
425		std::string forcefieldFileName;
426		forcefieldFileName = ff->getForceFieldFileName();
427	<
427	>
428		if (simParams->haveForceFieldVariant()) {
429	<	//If the force field has variant, the variant force field name will be
430	<	//Base.variant.frc. For exampel EAM.u6.frc
431	<
432	<	std::string variant = simParams->getForceFieldVariant();
433	<
434	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
435	<	variant = "." + variant;
436	<	if (pos != std::string::npos) {
437	<	forcefieldFileName.insert(pos, variant);
438	<	} else {
439	<	//If the default force field file name does not containt .frc suffix, just append the .variant
440	<	forcefieldFileName.append(variant);
441	<	}
429	>	//If the force field has variant, the variant force field name will be
430	>	//Base.variant.frc. For exampel EAM.u6.frc
431	>
432	>	std::string variant = simParams->getForceFieldVariant();
433	>
434	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
435	>	variant = "." + variant;
436	>	if (pos != std::string::npos) {
437	>	forcefieldFileName.insert(pos, variant);
438	>	} else {
439	>	//If the default force field file name does not containt .frc suffix, just append the .variant
440	>	forcefieldFileName.append(variant);
441	>	}
442		}
443
444		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
445		//create SimInfo
446	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
446	>	SimInfo * info = new SimInfo(ff, simParams);
447
448	<	//gather parameters (SimCreator only retrieves part of the parameters)
448	>	info->setRawMetaData(mdRawData);
449	>
450	>	//gather parameters (SimCreator only retrieves part of the
451	>	//parameters)
452		gatherParameters(info, mdFileName);
453	<
453	>
454		//divide the molecules and determine the global index of molecules
455		#ifdef IS_MPI
456		divideMolecules(info);
457		#endif
458	<
458	>
459		//create the molecules
460		createMolecules(info);
461	+
462	+	//find the storage layout
463
464	+	int storageLayout = computeStorageLayout(info);
465
466	<	//allocate memory for DataStorage(circular reference, need to break it)
467	<	info->setSnapshotManager(new SimSnapshotManager(info));
466	>	//allocate memory for DataStorage(circular reference, need to
467	>	//break it)
468	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
469
470	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
471	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
472	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
470	>	//set the global index of atoms, rigidbodies and cutoffgroups
471	>	//(only need to be set once, the global index will never change
472	>	//again). Local indices of atoms and rigidbodies are already set
473	>	//by MoleculeCreator class which actually delegates the
474	>	//responsibility to LocalIndexManager.
475		setGlobalIndex(info);
476	<
477	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
478	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
479	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
480	<	//we can determine the beginning global indices of atoms before they get created.
476	>
477	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
478	>	//method, at that point atoms don't have the global index yet
479	>	//(their global index are all initialized to -1).  Therefore we
480	>	//have to call addInteractionPairs explicitly here. A way to work
481	>	//around is that we can determine the beginning global indices of
482	>	//atoms before they get created.
483		SimInfo::MoleculeIterator mi;
484		Molecule* mol;
485		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
486	<	info->addExcludePairs(mol);
486	>	info->addInteractionPairs(mol);
487		}
488
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
489		if (loadInitCoords)
490	<	loadCoordinates(info);
186	<
490	>	loadCoordinates(info, mdFileName);
491		return info;
492	<	}
493	<
494	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
495	<
496	<	//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
492	>	}
493	>
494	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
495	>
496	>	//figure out the output file names
497		std::string prefix;
498	<
498	>
499		#ifdef IS_MPI
500	<
500	>
501		if (worldRank == 0) {
502		#endif // is_mpi
503	<
504	<	if (simParams->haveFinalConfig()) {
505	<	prefix = getPrefix(simParams->getFinalConfig());
506	<	} else {
507	<	prefix = getPrefix(mdfile);
508	<	}
509	<
510	<	info->setFinalConfigFileName(prefix + ".eor");
511	<	info->setDumpFileName(prefix + ".dump");
512	<	info->setStatFileName(prefix + ".stat");
513	<
503	>	Globals * simParams = info->getSimParams();
504	>	if (simParams->haveFinalConfig()) {
505	>	prefix = getPrefix(simParams->getFinalConfig());
506	>	} else {
507	>	prefix = getPrefix(mdfile);
508	>	}
509	>
510	>	info->setFinalConfigFileName(prefix + ".eor");
511	>	info->setDumpFileName(prefix + ".dump");
512	>	info->setStatFileName(prefix + ".stat");
513	>	info->setRestFileName(prefix + ".zang");
514	>
515		#ifdef IS_MPI
516	<
516	>
517		}
518	<
518	>
519		#endif
520	<
521	<	}
522	<
520	>
521	>	}
522	>
523		#ifdef IS_MPI
524	<	void SimCreator::divideMolecules(SimInfo *info) {
525	<	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;
524	>	void SimCreator::divideMolecules(SimInfo *info) {
525	>	RealType a;
526		int nProcessors;
527		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
528		int nGlobalMols = info->getNGlobalMolecules();
529	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
529	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
530	>	// error
531	>	// condition:
532
533	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
534	<
533	>	MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
534	>	//nProcessors = MPI::COMM_WORLD.Get_size();
535	>
536		if (nProcessors > nGlobalMols) {
537	<	sprintf(painCave.errMsg,
538	<	"nProcessors (%d) > nMol (%d)\n"
539	<	"\tThe number of processors is larger than\n"
540	<	"\tthe number of molecules.  This will not result in a \n"
541	<	"\tusable division of atoms for force decomposition.\n"
542	<	"\tEither try a smaller number of processors, or run the\n"
543	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
544	<
545	<	painCave.isFatal = 1;
546	<	simError();
537	>	sprintf(painCave.errMsg,
538	>	"nProcessors (%d) > nMol (%d)\n"
539	>	"\tThe number of processors is larger than\n"
540	>	"\tthe number of molecules.  This will not result in a \n"
541	>	"\tusable division of atoms for force decomposition.\n"
542	>	"\tEither try a smaller number of processors, or run the\n"
543	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
544	>	nGlobalMols);
545	>
546	>	painCave.isFatal = 1;
547	>	simError();
548		}
549	<
549	>
550	>	Globals * simParams = info->getSimParams();
551	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
552	>	//random number generator
553	>	if (simParams->haveSeed()) {
554	>	int seedValue = simParams->getSeed();
555	>	myRandom = new SeqRandNumGen(seedValue);
556	>	}else {
557	>	myRandom = new SeqRandNumGen();
558	>	}
559	>
560	>
561		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
562	<
562	>
563		//initialize atomsPerProc
564		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
565	<
565	>
566		if (worldRank == 0) {
567	<	numerator = info->getNGlobalAtoms();
568	<	denominator = nProcessors;
569	<	precast = numerator / denominator;
570	<	nTarget = (int)(precast + 0.5);
567	>	RealType numerator = info->getNGlobalAtoms();
568	>	RealType denominator = nProcessors;
569	>	RealType precast = numerator / denominator;
570	>	int nTarget = (int)(precast + 0.5);
571	>
572	>	for(int i = 0; i < nGlobalMols; i++) {
573
574	<	for(i = 0; i < nGlobalMols; i++) {
575	<	done = 0;
576	<	loops = 0;
577	<
578	<	while (!done) {
579	<	loops++;
580	<
581	<	// Pick a processor at random
582	<
583	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
584	<
585	<	//get the molecule stamp first
586	<	int stampId = info->getMoleculeStampId(i);
587	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
588	<
589	<	// How many atoms does this processor have so far?
590	<	old_atoms = atomsPerProc[which_proc];
591	<	add_atoms = moleculeStamp->getNAtoms();
592	<	new_atoms = old_atoms + add_atoms;
593	<
594	<	// If we've been through this loop too many times, we need
595	<	// to just give up and assign the molecule to this processor
596	<	// and be done with it.
574	>	int done = 0;
575	>	int loops = 0;
576	>
577	>	while (!done) {
578	>	loops++;
579	>
580	>	// Pick a processor at random
581	>
582	>	int which_proc = (int) (myRandom->rand() * 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	>	int old_atoms = atomsPerProc[which_proc];
590	>	int add_atoms = moleculeStamp->getNAtoms();
591	>	int 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.
596	>
597	>	if (loops > 100) {
598
599	<	if (loops > 100) {
600	<	sprintf(painCave.errMsg,
601	<	"I've tried 100 times to assign molecule %d to a "
602	<	" processor, but can't find a good spot.\n"
603	<	"I'm assigning it at random to processor %d.\n",
604	<	i, which_proc);
605	<
606	<	painCave.isFatal = 0;
607	<	simError();
608	<
609	<	molToProcMap[i] = which_proc;
610	<	atomsPerProc[which_proc] += add_atoms;
611	<
612	<	done = 1;
613	<	continue;
614	<	}
615	<
616	<	// If we can add this molecule to this processor without sending
617	<	// it above nTarget, then go ahead and do it:
618	<
619	<	if (new_atoms <= nTarget) {
620	<	molToProcMap[i] = which_proc;
621	<	atomsPerProc[which_proc] += add_atoms;
622	<
623	<	done = 1;
624	<	continue;
625	<	}
626	<
627	<	// The only situation left is when new_atoms > nTarget.  We
628	<	// want to accept this with some probability that dies off the
629	<	// farther we are from nTarget
630	<
631	<	// roughly:  x = new_atoms - nTarget
632	<	//           Pacc(x) = exp(- a * x)
633	<	// where a = penalty / (average atoms per molecule)
634	<
635	<	x = (double)(new_atoms - nTarget);
636	<	y = myRandom.getRandom();
637	<
638	<	if (y < exp(- a * x)) {
639	<	molToProcMap[i] = which_proc;
640	<	atomsPerProc[which_proc] += add_atoms;
641	<
642	<	done = 1;
643	<	continue;
644	<	} else {
645	<	continue;
646	<	}
392	<	}
599	>	sprintf(painCave.errMsg,
600	>	"There have been 100 attempts to assign molecule %d to an\n"
601	>	"\tunderworked processor, but there's no good place to\n"
602	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
603	>	i, which_proc);
604	>
605	>	painCave.isFatal = 0;
606	>	painCave.severity = OPENMD_INFO;
607	>	simError();
608	>
609	>	molToProcMap[i] = which_proc;
610	>	atomsPerProc[which_proc] += add_atoms;
611	>
612	>	done = 1;
613	>	continue;
614	>	}
615	>
616	>	// If we can add this molecule to this processor without sending
617	>	// it above nTarget, then go ahead and do it:
618	>
619	>	if (new_atoms <= nTarget) {
620	>	molToProcMap[i] = which_proc;
621	>	atomsPerProc[which_proc] += add_atoms;
622	>
623	>	done = 1;
624	>	continue;
625	>	}
626	>
627	>	// The only situation left is when new_atoms > nTarget.  We
628	>	// want to accept this with some probability that dies off the
629	>	// farther we are from nTarget
630	>
631	>	// roughly:  x = new_atoms - nTarget
632	>	//           Pacc(x) = exp(- a * x)
633	>	// where a = penalty / (average atoms per molecule)
634	>
635	>	RealType x = (RealType)(new_atoms - nTarget);
636	>	RealType y = myRandom->rand();
637	>
638	>	if (y < exp(- a * x)) {
639	>	molToProcMap[i] = which_proc;
640	>	atomsPerProc[which_proc] += add_atoms;
641	>
642	>	done = 1;
643	>	continue;
644	>	} else {
645	>	continue;
646	>	}
647		}
648	+	}
649	+
650	+	delete myRandom;
651
652	<	// Spray out this nonsense to all other processors:
653	<
654	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
652	>	// Spray out this nonsense to all other processors:
653	>	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
654	>	// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655		} else {
656	+
657	+	// Listen to your marching orders from processor 0:
658	+	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
659	+	// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
660
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
661		}
662	<
662	>
663		info->setMolToProcMap(molToProcMap);
664		sprintf(checkPointMsg,
665		"Successfully divided the molecules among the processors.\n");
666	<	MPIcheckPoint();
667	<	}
668	<
666	>	errorCheckPoint();
667	>	}
668	>
669		#endif
670	<
671	<	void SimCreator::createMolecules(SimInfo *info) {
670	>
671	>	void SimCreator::createMolecules(SimInfo *info) {
672		MoleculeCreator molCreator;
673		int stampId;
674	<
674	>
675		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
676	<
676	>
677		#ifdef IS_MPI
678	<
679	<	if (info->getMolToProc(i) == worldRank) {
678	>
679	>	if (info->getMolToProc(i) == worldRank) {
680		#endif
681	<
682	<	stampId = info->getMoleculeStampId(i);
683	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
684	<	stampId, i, info->getLocalIndexManager());
685	<
686	<	info->addMolecule(mol);
687	<
681	>
682	>	stampId = info->getMoleculeStampId(i);
683	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
684	>	info->getMoleculeStamp(stampId),
685	>	stampId, i,
686	>	info->getLocalIndexManager());
687	>
688	>	info->addMolecule(mol);
689	>
690		#ifdef IS_MPI
691	<
692	<	}
693	<
691	>
692	>	}
693	>
694		#endif
695	<
695	>
696		} //end for(int i=0)
697	<	}
697	>	}
698	>
699	>	int SimCreator::computeStorageLayout(SimInfo* info) {
700
701	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
702	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
703	<	int i;
704	<	char * id;
705	<	MoleculeStamp * currentStamp;
706	<	Component** the_components = simParams->getComponents();
707	<	int n_components = simParams->getNComponents();
701	>	Globals* simParams = info->getSimParams();
702	>	int nRigidBodies = info->getNGlobalRigidBodies();
703	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
704	>	set<AtomType*>::iterator i;
705	>	bool hasDirectionalAtoms = false;
706	>	bool hasFixedCharge = false;
707	>	bool hasDipoles = false;
708	>	bool hasQuadrupoles = false;
709	>	bool hasPolarizable = false;
710	>	bool hasFluctuatingCharge = false;
711	>	bool hasMetallic = false;
712	>	int storageLayout = 0;
713	>	storageLayout |= DataStorage::dslPosition;
714	>	storageLayout |= DataStorage::dslVelocity;
715	>	storageLayout |= DataStorage::dslForce;
716
717	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
717	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
718
719	<	for(i = 0; i < n_components; i++) {
720	<	if (!the_components[i]->haveNMol()) {
721	<	// we have a problem
722	<	sprintf(painCave.errMsg,
723	<	"SimCreator Error. No global NMol or component NMol given.\n"
724	<	"\tCannot calculate the number of atoms.\n");
719	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
720	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
721	>	EAMAdapter ea = EAMAdapter( (*i) );
722	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
723	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
724	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
725	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
726
727	<	painCave.isFatal = 1;
728	<	simError();
729	<	}
727	>	if (da.isDirectional()){
728	>	hasDirectionalAtoms = true;
729	>	}
730	>	if (ma.isDipole()){
731	>	hasDipoles = true;
732	>	}
733	>	if (ma.isQuadrupole()){
734	>	hasQuadrupoles = true;
735	>	}
736	>	if (ea.isEAM() || sca.isSuttonChen()){
737	>	hasMetallic = true;
738	>	}
739	>	if ( fca.isFixedCharge() ){
740	>	hasFixedCharge = true;
741	>	}
742	>	if ( fqa.isFluctuatingCharge() ){
743	>	hasFluctuatingCharge = true;
744	>	}
745	>	if ( pa.isPolarizable() ){
746	>	hasPolarizable = true;
747	>	}
748	>	}
749	>
750	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
751	>	storageLayout |= DataStorage::dslAmat;
752	>	if(storageLayout & DataStorage::dslVelocity) {
753	>	storageLayout |= DataStorage::dslAngularMomentum;
754	>	}
755	>	if (storageLayout & DataStorage::dslForce) {
756	>	storageLayout |= DataStorage::dslTorque;
757	>	}
758	>	}
759	>	if (hasDipoles) {
760	>	storageLayout |= DataStorage::dslDipole;
761	>	}
762	>	if (hasQuadrupoles) {
763	>	storageLayout |= DataStorage::dslQuadrupole;
764	>	}
765	>	if (hasFixedCharge || hasFluctuatingCharge) {
766	>	storageLayout |= DataStorage::dslSkippedCharge;
767	>	}
768	>	if (hasMetallic) {
769	>	storageLayout |= DataStorage::dslDensity;
770	>	storageLayout |= DataStorage::dslFunctional;
771	>	storageLayout |= DataStorage::dslFunctionalDerivative;
772	>	}
773	>	if (hasPolarizable) {
774	>	storageLayout |= DataStorage::dslElectricField;
775	>	}
776	>	if (hasFluctuatingCharge){
777	>	storageLayout |= DataStorage::dslFlucQPosition;
778	>	if(storageLayout & DataStorage::dslVelocity) {
779	>	storageLayout |= DataStorage::dslFlucQVelocity;
780	>	}
781	>	if (storageLayout & DataStorage::dslForce) {
782	>	storageLayout |= DataStorage::dslFlucQForce;
783	>	}
784	>	}
785	>
786	>	// if the user has asked for them, make sure we've got the memory for the
787	>	// objects defined.
788
789	<	id = the_components[i]->getType();
790	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
789	>	if (simParams->getOutputParticlePotential()) {
790	>	storageLayout |= DataStorage::dslParticlePot;
791	>	}
792
793	<	if (currentStamp == NULL) {
794	<	sprintf(painCave.errMsg,
795	<	"SimCreator error: Component \"%s\" was not found in the "
796	<	"list of declared molecules\n", id);
793	>	if (simParams->havePrintHeatFlux()) {
794	>	if (simParams->getPrintHeatFlux()) {
795	>	storageLayout |= DataStorage::dslParticlePot;
796	>	}
797	>	}
798
799	<	painCave.isFatal = 1;
800	<	simError();
801	<	}
799	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
800	>	storageLayout |= DataStorage::dslElectricField;
801	>	}
802
803	<	moleculeStampPairs.push_back(
804	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
805	<	} //end for (i = 0; i < n_components; i++)
806	<	} 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();
803	>	if (simParams->getOutputFluctuatingCharges()) {
804	>	storageLayout |= DataStorage::dslFlucQPosition;
805	>	storageLayout |= DataStorage::dslFlucQVelocity;
806	>	storageLayout |= DataStorage::dslFlucQForce;
807		}
808
809	<	#ifdef IS_MPI
809	>	info->setStorageLayout(storageLayout);
810
811	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
812	<	MPIcheckPoint();
811	>	return storageLayout;
812	>	}
813
814	<	#endif // is_mpi
494	<
495	<	}
496	<
497	<	void SimCreator::setGlobalIndex(SimInfo *info) {
814	>	void SimCreator::setGlobalIndex(SimInfo *info) {
815		SimInfo::MoleculeIterator mi;
816		Molecule::AtomIterator ai;
817		Molecule::RigidBodyIterator ri;
818		Molecule::CutoffGroupIterator ci;
819	<	Molecule * mol;
820	<	Atom * atom;
821	<	RigidBody * rb;
822	<	CutoffGroup * cg;
819	>	Molecule::BondIterator boi;
820	>	Molecule::BendIterator bei;
821	>	Molecule::TorsionIterator ti;
822	>	Molecule::InversionIterator ii;
823	>	Molecule::IntegrableObjectIterator  ioi;
824	>	Molecule* mol;
825	>	Atom* atom;
826	>	RigidBody* rb;
827	>	CutoffGroup* cg;
828	>	Bond* bond;
829	>	Bend* bend;
830	>	Torsion* torsion;
831	>	Inversion* inversion;
832		int beginAtomIndex;
833		int beginRigidBodyIndex;
834		int beginCutoffGroupIndex;
835	+	int beginBondIndex;
836	+	int beginBendIndex;
837	+	int beginTorsionIndex;
838	+	int beginInversionIndex;
839		int nGlobalAtoms = info->getNGlobalAtoms();
840	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
841
511	–	#ifndef IS_MPI
512	–
842		beginAtomIndex = 0;
843	<	beginRigidBodyIndex = 0;
843	>	// The rigid body indices begin immediately after the atom indices:
844	>	beginRigidBodyIndex = info->getNGlobalAtoms();
845		beginCutoffGroupIndex = 0;
846	+	beginBondIndex = 0;
847	+	beginBendIndex = 0;
848	+	beginTorsionIndex = 0;
849	+	beginInversionIndex = 0;
850	+
851	+	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
852	+
853	+	#ifdef IS_MPI
854	+	if (info->getMolToProc(i) == worldRank) {
855	+	#endif
856	+	// stuff to do if I own this molecule
857	+	mol = info->getMoleculeByGlobalIndex(i);
858
859	<	#else
860	<
861	<	int nproc;
862	<	int myNode;
521	<
522	<	myNode = worldRank;
523	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524	<
525	<	std::vector < int > tmpAtomsInProc(nproc, 0);
526	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528	<	std::vector < int > NumAtomsInProc(nproc, 0);
529	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
530	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531	<
532	<	tmpAtomsInProc[myNode] = info->getNAtoms();
533	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535	<
536	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538	<	MPI_SUM, MPI_COMM_WORLD);
539	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543	<
544	<	beginAtomIndex = 0;
545	<	beginRigidBodyIndex = 0;
546	<	beginCutoffGroupIndex = 0;
547	<
548	<	for(int i = 0; i < myNode; i++) {
549	<	beginAtomIndex += NumAtomsInProc[i];
550	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
551	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552	<	}
553	<
554	<	#endif
555	<
556	<	for(mol = info->beginMolecule(mi); mol != NULL;
557	<	mol = info->nextMolecule(mi)) {
558	<
559	<	//local index(index in DataStorge) of atom is important
560	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
561	<	atom->setGlobalIndex(beginAtomIndex++);
859	>	// The local index(index in DataStorge) of the atom is important:
860	>	for(atom = mol->beginAtom(ai); atom != NULL;
861	>	atom = mol->nextAtom(ai)) {
862	>	atom->setGlobalIndex(beginAtomIndex++);
863		}
864	<
864	>
865		for(rb = mol->beginRigidBody(ri); rb != NULL;
866		rb = mol->nextRigidBody(ri)) {
867	<	rb->setGlobalIndex(beginRigidBodyIndex++);
867	>	rb->setGlobalIndex(beginRigidBodyIndex++);
868		}
869	<
870	<	//local index of cutoff group is trivial, it only depends on the order of travesing
869	>
870	>	// The local index of other objects only depends on the order
871	>	// of traversal:
872		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
873		cg = mol->nextCutoffGroup(ci)) {
874	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
875	<	}
876	<	}
874	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
875	>	}
876	>	for(bond = mol->beginBond(boi); bond != NULL;
877	>	bond = mol->nextBond(boi)) {
878	>	bond->setGlobalIndex(beginBondIndex++);
879	>	}
880	>	for(bend = mol->beginBend(bei); bend != NULL;
881	>	bend = mol->nextBend(bei)) {
882	>	bend->setGlobalIndex(beginBendIndex++);
883	>	}
884	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
885	>	torsion = mol->nextTorsion(ti)) {
886	>	torsion->setGlobalIndex(beginTorsionIndex++);
887	>	}
888	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
889	>	inversion = mol->nextInversion(ii)) {
890	>	inversion->setGlobalIndex(beginInversionIndex++);
891	>	}
892	>
893	>	#ifdef IS_MPI
894	>	}  else {
895
896	<	//fill globalGroupMembership
897	<	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
898	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
899	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
896	>	// stuff to do if I don't own this molecule
897	>
898	>	int stampId = info->getMoleculeStampId(i);
899	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
900
901	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
903	<	}
901	>	beginAtomIndex += stamp->getNAtoms();
902	>	beginRigidBodyIndex += stamp->getNRigidBodies();
903	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
904	>	beginBondIndex += stamp->getNBonds();
905	>	beginBendIndex += stamp->getNBends();
906	>	beginTorsionIndex += stamp->getNTorsions();
907	>	beginInversionIndex += stamp->getNInversions();
908	>	}
909	>	#endif
910
911	<	}
586	<	}
911	>	} //end for(int i=0)
912
913	+	//fill globalGroupMembership
914	+	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
915	+	for(mol = info->beginMolecule(mi); mol != NULL;
916	+	mol = info->nextMolecule(mi)) {
917	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
918	+	cg = mol->nextCutoffGroup(ci)) {
919	+	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
920	+	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
921	+	}
922	+
923	+	}
924	+	}
925	+
926		#ifdef IS_MPI
927		// Since the globalGroupMembership has been zero filled and we've only
928		// poked values into the atoms we know, we can do an Allreduce
929		// to get the full globalGroupMembership array (We think).
930		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
931		// docs said we could.
932	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
933	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
932	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
933	>	MPI_Allreduce(&globalGroupMembership[0],
934	>	&tmpGroupMembership[0], nGlobalAtoms,
935		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
936	<	info->setGlobalGroupMembership(tmpGroupMembership);
936	>	// MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
937	>	//                           &tmpGroupMembership[0], nGlobalAtoms,
938	>	//                           MPI::INT, MPI::SUM);
939	>	info->setGlobalGroupMembership(tmpGroupMembership);
940		#else
941		info->setGlobalGroupMembership(globalGroupMembership);
942		#endif
943	<
943	>
944		//fill molMembership
945	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
945	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
946	>	info->getNGlobalRigidBodies(), 0);
947
948	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
949	<
950	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
951	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
952	<	}
948	>	for(mol = info->beginMolecule(mi); mol != NULL;
949	>	mol = info->nextMolecule(mi)) {
950	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
951	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
952	>	}
953	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
954	>	rb = mol->nextRigidBody(ri)) {
955	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
956	>	}
957		}
958	<
958	>
959		#ifdef IS_MPI
960	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
961	<
962	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
960	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
961	>	info->getNGlobalRigidBodies(), 0);
962	>	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
963	>	nGlobalAtoms + nGlobalRigidBodies,
964		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
965	+	// MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
966	+	//                           nGlobalAtoms + nGlobalRigidBodies,
967	+	//                           MPI::INT, MPI::SUM);
968
969		info->setGlobalMolMembership(tmpMolMembership);
970		#else
971		info->setGlobalMolMembership(globalMolMembership);
972		#endif
973
974	<	}
974	>	// nIOPerMol holds the number of integrable objects per molecule
975	>	// here the molecules are listed by their global indices.
976
977	<	void SimCreator::loadCoordinates(SimInfo* info) {
978	<	Globals* simParams;
979	<	simParams = info->getSimParams();
977	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
978	>	for (mol = info->beginMolecule(mi); mol != NULL;
979	>	mol = info->nextMolecule(mi)) {
980	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
981	>	}
982
983	<	if (!simParams->haveInitialConfig()) {
984	<	sprintf(painCave.errMsg,
985	<	"Cannot intialize a simulation without an initial configuration file.\n");
986	<	painCave.isFatal = 1;;
987	<	simError();
983	>	#ifdef IS_MPI
984	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
985	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
986	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
987	>	// MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
988	>	//                           info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
989	>	#else
990	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
991	>	#endif
992	>
993	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
994	>
995	>	int startingIndex = 0;
996	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
997	>	startingIOIndexForMol[i] = startingIndex;
998	>	startingIndex += numIntegrableObjectsPerMol[i];
999		}
1000	<
1001	<	DumpReader reader(info, simParams->getInitialConfig());
1000	>
1001	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
1002	>	for (mol = info->beginMolecule(mi); mol != NULL;
1003	>	mol = info->nextMolecule(mi)) {
1004	>	int myGlobalIndex = mol->getGlobalIndex();
1005	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
1006	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
1007	>	sd = mol->nextIntegrableObject(ioi)) {
1008	>	sd->setGlobalIntegrableObjectIndex(globalIO);
1009	>	IOIndexToIntegrableObject[globalIO] = sd;
1010	>	globalIO++;
1011	>	}
1012	>	}
1013	>
1014	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
1015	>
1016	>	}
1017	>
1018	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
1019	>
1020	>	DumpReader reader(info, mdFileName);
1021		int nframes = reader.getNFrames();
1022	<
1022	>
1023		if (nframes > 0) {
1024	<	reader.readFrame(nframes - 1);
1024	>	reader.readFrame(nframes - 1);
1025		} else {
1026	<	//invalid initial coordinate file
1027	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
1028	<	simParams->getInitialConfig());
1029	<	painCave.isFatal = 1;
1030	<	simError();
1026	>	//invalid initial coordinate file
1027	>	sprintf(painCave.errMsg,
1028	>	"Initial configuration file %s should at least contain one frame\n",
1029	>	mdFileName.c_str());
1030	>	painCave.isFatal = 1;
1031	>	simError();
1032		}
648	–
1033		//copy the current snapshot to previous snapshot
1034		info->getSnapshotManager()->advance();
1035	<	}
1035	>	}
1036	>
1037	>	} //end namespace OpenMD
1038
653	–	} //end namespace oopse
1039
655	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1976 by gezelter, Wed Mar 12 20:01:15 2014 UTC

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