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

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49
50	<	#include <sprng.h>
50	>	#ifdef IS_MPI
51	>	#include "mpi.h"
52	>	#include "math/ParallelRandNumGen.hpp"
53	>	#endif
54
55	+	#include <exception>
56	+	#include <iostream>
57	+	#include <sstream>
58	+	#include <string>
59	+
60		#include "brains/MoleculeCreator.hpp"
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "io/parse_me.h"
57	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67	<	#ifdef IS_MPI
68	<	#include "io/mpiBASS.h"
69	<	#include "math/randomSPRNG.hpp"
70	<	#endif
67	>	#include "math/SeqRandNumGen.hpp"
68	>	#include "mdParser/MDLexer.hpp"
69	>	#include "mdParser/MDParser.hpp"
70	>	#include "mdParser/MDTreeParser.hpp"
71	>	#include "mdParser/SimplePreprocessor.hpp"
72	>	#include "antlr/ANTLRException.hpp"
73	>	#include "antlr/TokenStreamRecognitionException.hpp"
74	>	#include "antlr/TokenStreamIOException.hpp"
75	>	#include "antlr/TokenStreamException.hpp"
76	>	#include "antlr/RecognitionException.hpp"
77	>	#include "antlr/CharStreamException.hpp"
78
79	<	namespace oopse {
79	>	#include "antlr/MismatchedCharException.hpp"
80	>	#include "antlr/MismatchedTokenException.hpp"
81	>	#include "antlr/NoViableAltForCharException.hpp"
82	>	#include "antlr/NoViableAltException.hpp"
83
84	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
84	>	#include "types/DirectionalAdapter.hpp"
85	>	#include "types/MultipoleAdapter.hpp"
86	>	#include "types/EAMAdapter.hpp"
87	>	#include "types/SuttonChenAdapter.hpp"
88	>	#include "types/PolarizableAdapter.hpp"
89	>	#include "types/FixedChargeAdapter.hpp"
90	>	#include "types/FluctuatingChargeAdapter.hpp"
91
69	–	#ifdef IS_MPI
92
93	<	if (worldRank == 0) {
94	<	#endif // is_mpi
93	>	namespace OpenMD {
94	>
95	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
96	>	Globals* simParams = NULL;
97	>	try {
98
99	<	simParams->initalize();
100	<	set_interface_stamps(stamps, simParams);
99	>	// Create a preprocessor that preprocesses md file into an ostringstream
100	>	std::stringstream ppStream;
101	>	#ifdef IS_MPI
102	>	int streamSize;
103	>	const int masterNode = 0;
104
105	<	#ifdef IS_MPI
105	>	if (worldRank == masterNode) {
106	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
107	>	#endif
108	>	SimplePreprocessor preprocessor;
109	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
110	>
111	>	#ifdef IS_MPI
112	>	//brocasting the stream size
113	>	streamSize = ppStream.str().size() +1;
114	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
115	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
116	>
117	>	} else {
118	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
119
120	<	mpiEventInit();
120	>	//get stream size
121	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
122
123	<	#endif
123	>	char* buf = new char[streamSize];
124	>	assert(buf);
125	>
126	>	//receive file content
127	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
128	>
129	>	ppStream.str(buf);
130	>	delete [] buf;
131	>	}
132	>	#endif
133	>	// Create a scanner that reads from the input stream
134	>	MDLexer lexer(ppStream);
135	>	lexer.setFilename(filename);
136	>	lexer.initDeferredLineCount();
137	>
138	>	// Create a parser that reads from the scanner
139	>	MDParser parser(lexer);
140	>	parser.setFilename(filename);
141
142	<	yacc_BASS(mdFileName.c_str());
142	>	// Create an observer that synchorizes file name change
143	>	FilenameObserver observer;
144	>	observer.setLexer(&lexer);
145	>	observer.setParser(&parser);
146	>	lexer.setObserver(&observer);
147	>
148	>	antlr::ASTFactory factory;
149	>	parser.initializeASTFactory(factory);
150	>	parser.setASTFactory(&factory);
151	>	parser.mdfile();
152
153	<	#ifdef IS_MPI
153	>	// Create a tree parser that reads information into Globals
154	>	MDTreeParser treeParser;
155	>	treeParser.initializeASTFactory(factory);
156	>	treeParser.setASTFactory(&factory);
157	>	simParams = treeParser.walkTree(parser.getAST());
158	>	}
159
160	<	throwMPIEvent(NULL);
161	<	} else {
162	<	set_interface_stamps(stamps, simParams);
163	<	mpiEventInit();
164	<	MPIcheckPoint();
165	<	mpiEventLoop();
160	>
161	>	catch(antlr::MismatchedCharException& e) {
162	>	sprintf(painCave.errMsg,
163	>	"parser exception: %s %s:%d:%d\n",
164	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
165	>	painCave.isFatal = 1;
166	>	simError();
167		}
168	+	catch(antlr::MismatchedTokenException &e) {
169	+	sprintf(painCave.errMsg,
170	+	"parser exception: %s %s:%d:%d\n",
171	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
172	+	painCave.isFatal = 1;
173	+	simError();
174	+	}
175	+	catch(antlr::NoViableAltForCharException &e) {
176	+	sprintf(painCave.errMsg,
177	+	"parser exception: %s %s:%d:%d\n",
178	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
179	+	painCave.isFatal = 1;
180	+	simError();
181	+	}
182	+	catch(antlr::NoViableAltException &e) {
183	+	sprintf(painCave.errMsg,
184	+	"parser exception: %s %s:%d:%d\n",
185	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
186	+	painCave.isFatal = 1;
187	+	simError();
188	+	}
189	+
190	+	catch(antlr::TokenStreamRecognitionException& e) {
191	+	sprintf(painCave.errMsg,
192	+	"parser exception: %s %s:%d:%d\n",
193	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
194	+	painCave.isFatal = 1;
195	+	simError();
196	+	}
197	+
198	+	catch(antlr::TokenStreamIOException& e) {
199	+	sprintf(painCave.errMsg,
200	+	"parser exception: %s\n",
201	+	e.getMessage().c_str());
202	+	painCave.isFatal = 1;
203	+	simError();
204	+	}
205	+
206	+	catch(antlr::TokenStreamException& e) {
207	+	sprintf(painCave.errMsg,
208	+	"parser exception: %s\n",
209	+	e.getMessage().c_str());
210	+	painCave.isFatal = 1;
211	+	simError();
212	+	}
213	+	catch (antlr::RecognitionException& e) {
214	+	sprintf(painCave.errMsg,
215	+	"parser exception: %s %s:%d:%d\n",
216	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
217	+	painCave.isFatal = 1;
218	+	simError();
219	+	}
220	+	catch (antlr::CharStreamException& e) {
221	+	sprintf(painCave.errMsg,
222	+	"parser exception: %s\n",
223	+	e.getMessage().c_str());
224	+	painCave.isFatal = 1;
225	+	simError();
226	+	}
227	+	catch (OpenMDException& e) {
228	+	sprintf(painCave.errMsg,
229	+	"%s\n",
230	+	e.getMessage().c_str());
231	+	painCave.isFatal = 1;
232	+	simError();
233	+	}
234	+	catch (std::exception& e) {
235	+	sprintf(painCave.errMsg,
236	+	"parser exception: %s\n",
237	+	e.what());
238	+	painCave.isFatal = 1;
239	+	simError();
240	+	}
241
242	<	#endif
242	>	simParams->setMDfileVersion(mdFileVersion);
243	>	return simParams;
244	>	}
245	>
246	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
247	>	bool loadInitCoords) {
248	>
249	>	const int bufferSize = 65535;
250	>	char buffer[bufferSize];
251	>	int lineNo = 0;
252	>	std::string mdRawData;
253	>	int metaDataBlockStart = -1;
254	>	int metaDataBlockEnd = -1;
255	>	int i, j;
256	>	streamoff mdOffset;
257	>	int mdFileVersion;
258
259	<	}
259	>	// Create a string for embedding the version information in the MetaData
260	>	std::string version;
261	>	version.assign("## Last run using OpenMD Version: ");
262	>	version.append(OPENMD_VERSION_MAJOR);
263	>	version.append(".");
264	>	version.append(OPENMD_VERSION_MINOR);
265
266	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
267	<
268	<	MakeStamps * stamps = new MakeStamps();
266	>	std::string svnrev;
267	>	//convert a macro from compiler to a string in c++
268	>	STR_DEFINE(svnrev, SVN_REV );
269	>	version.append(" Revision: ");
270	>	// If there's no SVN revision, just call this the RELEASE revision.
271	>	if (!svnrev.empty()) {
272	>	version.append(svnrev);
273	>	} else {
274	>	version.append("RELEASE");
275	>	}
276	>
277	>	#ifdef IS_MPI
278	>	const int masterNode = 0;
279	>	if (worldRank == masterNode) {
280	>	#endif
281
282	<	Globals * simParams = new Globals();
282	>	std::ifstream mdFile_;
283	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
284	>
285	>	if (mdFile_.fail()) {
286	>	sprintf(painCave.errMsg,
287	>	"SimCreator: Cannot open file: %s\n",
288	>	mdFileName.c_str());
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292
293	<	//parse meta-data file
294	<	parseFile(mdFileName, stamps, simParams);
293	>	mdFile_.getline(buffer, bufferSize);
294	>	++lineNo;
295	>	std::string line = trimLeftCopy(buffer);
296	>	i = CaseInsensitiveFind(line, "<OpenMD");
297	>	if (static_cast<size_t>(i) == string::npos) {
298	>	// try the older file strings to see if that works:
299	>	i = CaseInsensitiveFind(line, "<OOPSE");
300	>	}
301	>
302	>	if (static_cast<size_t>(i) == string::npos) {
303	>	// still no luck!
304	>	sprintf(painCave.errMsg,
305	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
306	>	mdFileName.c_str());
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	// found the correct opening string, now try to get the file
312	>	// format version number.
313
314	<	//create the force field
315	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
316	<	simParams->getForceField());
111	<
112	<	if (ff == NULL) {
113	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
114	<	simParams->getForceField());
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
314	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
315	>	std::string fileType = tokenizer.nextToken();
316	>	toUpper(fileType);
317
318	<	std::string forcefieldFileName;
120	<	forcefieldFileName = ff->getForceFieldFileName();
318	>	mdFileVersion = 0;
319
320	<	if (simParams->haveForceFieldVariant()) {
321	<	//If the force field has variant, the variant force field name will be
322	<	//Base.variant.frc. For exampel EAM.u6.frc
320	>	if (fileType == "OPENMD") {
321	>	while (tokenizer.hasMoreTokens()) {
322	>	std::string token(tokenizer.nextToken());
323	>	toUpper(token);
324	>	if (token == "VERSION") {
325	>	mdFileVersion = tokenizer.nextTokenAsInt();
326	>	break;
327	>	}
328	>	}
329	>	}
330	>
331	>	//scan through the input stream and find MetaData tag
332	>	while(mdFile_.getline(buffer, bufferSize)) {
333	>	++lineNo;
334
335	<	std::string variant = simParams->getForceFieldVariant();
336	<
337	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
338	<	variant = "." + variant;
339	<	if (pos != std::string::npos) {
340	<	forcefieldFileName.insert(pos, variant);
335	>	std::string line = trimLeftCopy(buffer);
336	>	if (metaDataBlockStart == -1) {
337	>	i = CaseInsensitiveFind(line, "<MetaData>");
338	>	if (i != string::npos) {
339	>	metaDataBlockStart = lineNo;
340	>	mdOffset = mdFile_.tellg();
341	>	}
342		} else {
343	<	//If the default force field file name does not containt .frc suffix, just append the .variant
344	<	forcefieldFileName.append(variant);
343	>	i = CaseInsensitiveFind(line, "</MetaData>");
344	>	if (i != string::npos) {
345	>	metaDataBlockEnd = lineNo;
346	>	}
347	>	}
348	>	}
349	>
350	>	if (metaDataBlockStart == -1) {
351	>	sprintf(painCave.errMsg,
352	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
353	>	mdFileName.c_str());
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
357	>	if (metaDataBlockEnd == -1) {
358	>	sprintf(painCave.errMsg,
359	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
360	>	mdFileName.c_str());
361	>	painCave.isFatal = 1;
362	>	simError();
363	>	}
364	>
365	>	mdFile_.clear();
366	>	mdFile_.seekg(0);
367	>	mdFile_.seekg(mdOffset);
368	>
369	>	mdRawData.clear();
370	>
371	>	bool foundVersion = false;
372	>
373	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
374	>	mdFile_.getline(buffer, bufferSize);
375	>	std::string line = trimLeftCopy(buffer);
376	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
377	>	if (static_cast<size_t>(j) != string::npos) {
378	>	foundVersion = true;
379	>	mdRawData += version;
380	>	} else {
381	>	mdRawData += buffer;
382		}
383	+	mdRawData += "\n";
384	+	}
385	+
386	+	if (!foundVersion) mdRawData += version + "\n";
387	+
388	+	mdFile_.close();
389	+
390	+	#ifdef IS_MPI
391	+	}
392	+	#endif
393	+
394	+	std::stringstream rawMetaDataStream(mdRawData);
395	+
396	+	//parse meta-data file
397	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
398	+	metaDataBlockStart + 1);
399	+
400	+	//create the force field
401	+	ForceField * ff = new ForceField(simParams->getForceField());
402	+
403	+	if (ff == NULL) {
404	+	sprintf(painCave.errMsg,
405	+	"ForceField Factory can not create %s force field\n",
406	+	simParams->getForceField().c_str());
407	+	painCave.isFatal = 1;
408	+	simError();
409	+	}
410	+
411	+	if (simParams->haveForceFieldFileName()) {
412	+	ff->setForceFieldFileName(simParams->getForceFieldFileName());
413	+	}
414	+
415	+	std::string forcefieldFileName;
416	+	forcefieldFileName = ff->getForceFieldFileName();
417	+
418	+	if (simParams->haveForceFieldVariant()) {
419	+	//If the force field has variant, the variant force field name will be
420	+	//Base.variant.frc. For exampel EAM.u6.frc
421	+
422	+	std::string variant = simParams->getForceFieldVariant();
423	+
424	+	std::string::size_type pos = forcefieldFileName.rfind(".frc");
425	+	variant = "." + variant;
426	+	if (pos != std::string::npos) {
427	+	forcefieldFileName.insert(pos, variant);
428	+	} else {
429	+	//If the default force field file name does not containt .frc suffix, just append the .variant
430	+	forcefieldFileName.append(variant);
431	+	}
432		}
433
434		ff->parse(forcefieldFileName);
139	–
140	–	//extract the molecule stamps
141	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
142	–	compList(stamps, simParams, moleculeStampPairs);
143	–
435		//create SimInfo
436	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
436	>	SimInfo * info = new SimInfo(ff, simParams);
437
438	<	//gather parameters (SimCreator only retrieves part of the parameters)
438	>	info->setRawMetaData(mdRawData);
439	>
440	>	//gather parameters (SimCreator only retrieves part of the
441	>	//parameters)
442		gatherParameters(info, mdFileName);
443	<
443	>
444		//divide the molecules and determine the global index of molecules
445		#ifdef IS_MPI
446		divideMolecules(info);
447		#endif
448	<
448	>
449		//create the molecules
450		createMolecules(info);
451	+
452	+	//find the storage layout
453
454	+	int storageLayout = computeStorageLayout(info);
455
456	<	//allocate memory for DataStorage(circular reference, need to break it)
457	<	info->setSnapshotManager(new SimSnapshotManager(info));
456	>	//allocate memory for DataStorage(circular reference, need to
457	>	//break it)
458	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
459
460	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
461	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
462	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
460	>	//set the global index of atoms, rigidbodies and cutoffgroups
461	>	//(only need to be set once, the global index will never change
462	>	//again). Local indices of atoms and rigidbodies are already set
463	>	//by MoleculeCreator class which actually delegates the
464	>	//responsibility to LocalIndexManager.
465		setGlobalIndex(info);
466	<
467	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
468	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
469	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
470	<	//we can determine the beginning global indices of atoms before they get created.
466	>
467	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
468	>	//method, at that point atoms don't have the global index yet
469	>	//(their global index are all initialized to -1).  Therefore we
470	>	//have to call addInteractionPairs explicitly here. A way to work
471	>	//around is that we can determine the beginning global indices of
472	>	//atoms before they get created.
473		SimInfo::MoleculeIterator mi;
474		Molecule* mol;
475		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
476	<	info->addExcludePairs(mol);
476	>	info->addInteractionPairs(mol);
477		}
478
177	–
178	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
179	–	//eta, chi for NPT integrator)
479		if (loadInitCoords)
480	<	loadCoordinates(info);
182	<
480	>	loadCoordinates(info, mdFileName);
481		return info;
482	<	}
483	<
484	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
485	<
486	<	//setup seed for random number generator
189	<	int seedValue;
190	<	Globals * simParams = info->getSimParams();
191	<
192	<	if (simParams->haveSeed()) {
193	<	seedValue = simParams->getSeed();
194	<
195	<	if (seedValue < 100000000 ) {
196	<	sprintf(painCave.errMsg,
197	<	"Seed for sprng library should contain at least 9 digits\n"
198	<	"OOPSE will generate a seed for user\n");
199	<
200	<	painCave.isFatal = 0;
201	<	simError();
202	<
203	<	//using seed generated by system instead of invalid seed set by user
204	<
205	<	#ifndef IS_MPI
206	<
207	<	seedValue = make_sprng_seed();
208	<
209	<	#else
210	<
211	<	if (worldRank == 0) {
212	<	seedValue = make_sprng_seed();
213	<	}
214	<
215	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
216	<
217	<	#endif
218	<
219	<	} //end if (seedValue /1000000000 == 0)
220	<	} else {
221	<
222	<	#ifndef IS_MPI
223	<
224	<	seedValue = make_sprng_seed();
225	<
226	<	#else
227	<
228	<	if (worldRank == 0) {
229	<	seedValue = make_sprng_seed();
230	<	}
231	<
232	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
233	<
234	<	#endif
235	<
236	<	} //end of simParams->haveSeed()
237	<
238	<	info->setSeed(seedValue);
239	<
240	<
241	<	//figure out the ouput file names
482	>	}
483	>
484	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
485	>
486	>	//figure out the output file names
487		std::string prefix;
488	<
488	>
489		#ifdef IS_MPI
490	<
490	>
491		if (worldRank == 0) {
492		#endif // is_mpi
493	<
494	<	if (simParams->haveFinalConfig()) {
495	<	prefix = getPrefix(simParams->getFinalConfig());
496	<	} else {
497	<	prefix = getPrefix(mdfile);
498	<	}
499	<
500	<	info->setFinalConfigFileName(prefix + ".eor");
501	<	info->setDumpFileName(prefix + ".dump");
502	<	info->setStatFileName(prefix + ".stat");
503	<
493	>	Globals * simParams = info->getSimParams();
494	>	if (simParams->haveFinalConfig()) {
495	>	prefix = getPrefix(simParams->getFinalConfig());
496	>	} else {
497	>	prefix = getPrefix(mdfile);
498	>	}
499	>
500	>	info->setFinalConfigFileName(prefix + ".eor");
501	>	info->setDumpFileName(prefix + ".dump");
502	>	info->setStatFileName(prefix + ".stat");
503	>	info->setRestFileName(prefix + ".zang");
504	>
505		#ifdef IS_MPI
506	<
506	>
507		}
508	<
508	>
509		#endif
510	<
511	<	}
512	<
510	>
511	>	}
512	>
513		#ifdef IS_MPI
514	<	void SimCreator::divideMolecules(SimInfo *info) {
515	<	double numerator;
270	<	double denominator;
271	<	double precast;
272	<	double x;
273	<	double y;
274	<	double a;
275	<	int old_atoms;
276	<	int add_atoms;
277	<	int new_atoms;
278	<	int nTarget;
279	<	int done;
280	<	int i;
281	<	int j;
282	<	int loops;
283	<	int which_proc;
514	>	void SimCreator::divideMolecules(SimInfo *info) {
515	>	RealType a;
516		int nProcessors;
517		std::vector<int> atomsPerProc;
286	–	randomSPRNG myRandom(info->getSeed());
518		int nGlobalMols = info->getNGlobalMolecules();
519	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
519	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
520	>	// error
521	>	// condition:
522
523	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
524	<
523	>	nProcessors = MPI::COMM_WORLD.Get_size();
524	>
525		if (nProcessors > nGlobalMols) {
526	<	sprintf(painCave.errMsg,
527	<	"nProcessors (%d) > nMol (%d)\n"
528	<	"\tThe number of processors is larger than\n"
529	<	"\tthe number of molecules.  This will not result in a \n"
530	<	"\tusable division of atoms for force decomposition.\n"
531	<	"\tEither try a smaller number of processors, or run the\n"
532	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
533	<
534	<	painCave.isFatal = 1;
535	<	simError();
526	>	sprintf(painCave.errMsg,
527	>	"nProcessors (%d) > nMol (%d)\n"
528	>	"\tThe number of processors is larger than\n"
529	>	"\tthe number of molecules.  This will not result in a \n"
530	>	"\tusable division of atoms for force decomposition.\n"
531	>	"\tEither try a smaller number of processors, or run the\n"
532	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
533	>	nGlobalMols);
534	>
535	>	painCave.isFatal = 1;
536	>	simError();
537		}
538	<
538	>
539	>	Globals * simParams = info->getSimParams();
540	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
541	>	//random number generator
542	>	if (simParams->haveSeed()) {
543	>	int seedValue = simParams->getSeed();
544	>	myRandom = new SeqRandNumGen(seedValue);
545	>	}else {
546	>	myRandom = new SeqRandNumGen();
547	>	}
548	>
549	>
550		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
551	<
551	>
552		//initialize atomsPerProc
553		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
554	<
554	>
555		if (worldRank == 0) {
556	<	numerator = info->getNGlobalAtoms();
557	<	denominator = nProcessors;
558	<	precast = numerator / denominator;
559	<	nTarget = (int)(precast + 0.5);
556	>	RealType numerator = info->getNGlobalAtoms();
557	>	RealType denominator = nProcessors;
558	>	RealType precast = numerator / denominator;
559	>	int nTarget = (int)(precast + 0.5);
560	>
561	>	for(int i = 0; i < nGlobalMols; i++) {
562
563	<	for(i = 0; i < nGlobalMols; i++) {
564	<	done = 0;
565	<	loops = 0;
566	<
567	<	while (!done) {
568	<	loops++;
569	<
570	<	// Pick a processor at random
571	<
572	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
573	<
574	<	//get the molecule stamp first
575	<	int stampId = info->getMoleculeStampId(i);
576	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
577	<
578	<	// How many atoms does this processor have so far?
579	<	old_atoms = atomsPerProc[which_proc];
580	<	add_atoms = moleculeStamp->getNAtoms();
581	<	new_atoms = old_atoms + add_atoms;
582	<
583	<	// If we've been through this loop too many times, we need
584	<	// to just give up and assign the molecule to this processor
585	<	// and be done with it.
563	>	int done = 0;
564	>	int loops = 0;
565	>
566	>	while (!done) {
567	>	loops++;
568	>
569	>	// Pick a processor at random
570	>
571	>	int which_proc = (int) (myRandom->rand() * nProcessors);
572	>
573	>	//get the molecule stamp first
574	>	int stampId = info->getMoleculeStampId(i);
575	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
576	>
577	>	// How many atoms does this processor have so far?
578	>	int old_atoms = atomsPerProc[which_proc];
579	>	int add_atoms = moleculeStamp->getNAtoms();
580	>	int new_atoms = old_atoms + add_atoms;
581	>
582	>	// If we've been through this loop too many times, we need
583	>	// to just give up and assign the molecule to this processor
584	>	// and be done with it.
585	>
586	>	if (loops > 100) {
587
588	<	if (loops > 100) {
589	<	sprintf(painCave.errMsg,
590	<	"I've tried 100 times to assign molecule %d to a "
591	<	" processor, but can't find a good spot.\n"
592	<	"I'm assigning it at random to processor %d.\n",
593	<	i, which_proc);
594	<
595	<	painCave.isFatal = 0;
596	<	simError();
597	<
598	<	molToProcMap[i] = which_proc;
599	<	atomsPerProc[which_proc] += add_atoms;
600	<
601	<	done = 1;
602	<	continue;
603	<	}
604	<
605	<	// If we can add this molecule to this processor without sending
606	<	// it above nTarget, then go ahead and do it:
607	<
608	<	if (new_atoms <= nTarget) {
609	<	molToProcMap[i] = which_proc;
610	<	atomsPerProc[which_proc] += add_atoms;
611	<
612	<	done = 1;
613	<	continue;
614	<	}
615	<
616	<	// The only situation left is when new_atoms > nTarget.  We
617	<	// want to accept this with some probability that dies off the
618	<	// farther we are from nTarget
619	<
620	<	// roughly:  x = new_atoms - nTarget
621	<	//           Pacc(x) = exp(- a * x)
622	<	// where a = penalty / (average atoms per molecule)
623	<
624	<	x = (double)(new_atoms - nTarget);
625	<	y = myRandom.getRandom();
626	<
627	<	if (y < exp(- a * x)) {
628	<	molToProcMap[i] = which_proc;
629	<	atomsPerProc[which_proc] += add_atoms;
630	<
631	<	done = 1;
632	<	continue;
633	<	} else {
634	<	continue;
635	<	}
388	<	}
588	>	sprintf(painCave.errMsg,
589	>	"There have been 100 attempts to assign molecule %d to an\n"
590	>	"\tunderworked processor, but there's no good place to\n"
591	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
592	>	i, which_proc);
593	>
594	>	painCave.isFatal = 0;
595	>	painCave.severity = OPENMD_INFO;
596	>	simError();
597	>
598	>	molToProcMap[i] = which_proc;
599	>	atomsPerProc[which_proc] += add_atoms;
600	>
601	>	done = 1;
602	>	continue;
603	>	}
604	>
605	>	// If we can add this molecule to this processor without sending
606	>	// it above nTarget, then go ahead and do it:
607	>
608	>	if (new_atoms <= nTarget) {
609	>	molToProcMap[i] = which_proc;
610	>	atomsPerProc[which_proc] += add_atoms;
611	>
612	>	done = 1;
613	>	continue;
614	>	}
615	>
616	>	// The only situation left is when new_atoms > nTarget.  We
617	>	// want to accept this with some probability that dies off the
618	>	// farther we are from nTarget
619	>
620	>	// roughly:  x = new_atoms - nTarget
621	>	//           Pacc(x) = exp(- a * x)
622	>	// where a = penalty / (average atoms per molecule)
623	>
624	>	RealType x = (RealType)(new_atoms - nTarget);
625	>	RealType y = myRandom->rand();
626	>
627	>	if (y < exp(- a * x)) {
628	>	molToProcMap[i] = which_proc;
629	>	atomsPerProc[which_proc] += add_atoms;
630	>
631	>	done = 1;
632	>	continue;
633	>	} else {
634	>	continue;
635	>	}
636		}
637	+	}
638	+
639	+	delete myRandom;
640
641	<	// Spray out this nonsense to all other processors:
642	<
393	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
641	>	// Spray out this nonsense to all other processors:
642	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
643		} else {
644	+
645	+	// Listen to your marching orders from processor 0:
646	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
647
396	–	// Listen to your marching orders from processor 0:
397	–
398	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
648		}
649	<
649	>
650		info->setMolToProcMap(molToProcMap);
651		sprintf(checkPointMsg,
652		"Successfully divided the molecules among the processors.\n");
653	<	MPIcheckPoint();
654	<	}
655	<
653	>	errorCheckPoint();
654	>	}
655	>
656		#endif
657	<
658	<	void SimCreator::createMolecules(SimInfo *info) {
657	>
658	>	void SimCreator::createMolecules(SimInfo *info) {
659		MoleculeCreator molCreator;
660		int stampId;
661	<
661	>
662		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
663	<
663	>
664		#ifdef IS_MPI
665	<
666	<	if (info->getMolToProc(i) == worldRank) {
665	>
666	>	if (info->getMolToProc(i) == worldRank) {
667		#endif
668	<
669	<	stampId = info->getMoleculeStampId(i);
670	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
671	<	stampId, i, info->getLocalIndexManager());
672	<
673	<	info->addMolecule(mol);
674	<
668	>
669	>	stampId = info->getMoleculeStampId(i);
670	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
671	>	info->getMoleculeStamp(stampId),
672	>	stampId, i,
673	>	info->getLocalIndexManager());
674	>
675	>	info->addMolecule(mol);
676	>
677		#ifdef IS_MPI
678	<
679	<	}
680	<
678	>
679	>	}
680	>
681		#endif
682	<
682	>
683		} //end for(int i=0)
684	<	}
684	>	}
685	>
686	>	int SimCreator::computeStorageLayout(SimInfo* info) {
687
688	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
689	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
690	<	int i;
691	<	char * id;
692	<	MoleculeStamp * currentStamp;
693	<	Component** the_components = simParams->getComponents();
694	<	int n_components = simParams->getNComponents();
688	>	Globals* simParams = info->getSimParams();
689	>	int nRigidBodies = info->getNGlobalRigidBodies();
690	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
691	>	set<AtomType*>::iterator i;
692	>	bool hasDirectionalAtoms = false;
693	>	bool hasFixedCharge = false;
694	>	bool hasDipoles = false;
695	>	bool hasQuadrupoles = false;
696	>	bool hasPolarizable = false;
697	>	bool hasFluctuatingCharge = false;
698	>	bool hasMetallic = false;
699	>	int storageLayout = 0;
700	>	storageLayout |= DataStorage::dslPosition;
701	>	storageLayout |= DataStorage::dslVelocity;
702	>	storageLayout |= DataStorage::dslForce;
703
704	<	if (!simParams->haveNMol()) {
444	<	// we don't have the total number of molecules, so we assume it is
445	<	// given in each component
704	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
705
706	<	for(i = 0; i < n_components; i++) {
707	<	if (!the_components[i]->haveNMol()) {
708	<	// we have a problem
709	<	sprintf(painCave.errMsg,
710	<	"SimCreator Error. No global NMol or component NMol given.\n"
711	<	"\tCannot calculate the number of atoms.\n");
706	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
707	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
708	>	EAMAdapter ea = EAMAdapter( (*i) );
709	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
710	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
711	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
712	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
713
714	<	painCave.isFatal = 1;
715	<	simError();
716	<	}
714	>	if (da.isDirectional()){
715	>	hasDirectionalAtoms = true;
716	>	}
717	>	if (ma.isDipole()){
718	>	hasDipoles = true;
719	>	}
720	>	if (ma.isQuadrupole()){
721	>	hasQuadrupoles = true;
722	>	}
723	>	if (ea.isEAM() || sca.isSuttonChen()){
724	>	hasMetallic = true;
725	>	}
726	>	if ( fca.isFixedCharge() ){
727	>	hasFixedCharge = true;
728	>	}
729	>	if ( fqa.isFluctuatingCharge() ){
730	>	hasFluctuatingCharge = true;
731	>	}
732	>	if ( pa.isPolarizable() ){
733	>	hasPolarizable = true;
734	>	}
735	>	}
736	>
737	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
738	>	storageLayout |= DataStorage::dslAmat;
739	>	if(storageLayout & DataStorage::dslVelocity) {
740	>	storageLayout |= DataStorage::dslAngularMomentum;
741	>	}
742	>	if (storageLayout & DataStorage::dslForce) {
743	>	storageLayout |= DataStorage::dslTorque;
744	>	}
745	>	}
746	>	if (hasDipoles) {
747	>	storageLayout |= DataStorage::dslDipole;
748	>	}
749	>	if (hasQuadrupoles) {
750	>	storageLayout |= DataStorage::dslQuadrupole;
751	>	}
752	>	if (hasFixedCharge || hasFluctuatingCharge) {
753	>	storageLayout |= DataStorage::dslSkippedCharge;
754	>	}
755	>	if (hasMetallic) {
756	>	storageLayout |= DataStorage::dslDensity;
757	>	storageLayout |= DataStorage::dslFunctional;
758	>	storageLayout |= DataStorage::dslFunctionalDerivative;
759	>	}
760	>	if (hasPolarizable) {
761	>	storageLayout |= DataStorage::dslElectricField;
762	>	}
763	>	if (hasFluctuatingCharge){
764	>	storageLayout |= DataStorage::dslFlucQPosition;
765	>	if(storageLayout & DataStorage::dslVelocity) {
766	>	storageLayout |= DataStorage::dslFlucQVelocity;
767	>	}
768	>	if (storageLayout & DataStorage::dslForce) {
769	>	storageLayout |= DataStorage::dslFlucQForce;
770	>	}
771	>	}
772	>
773	>	// if the user has asked for them, make sure we've got the memory for the
774	>	// objects defined.
775
776	<	id = the_components[i]->getType();
777	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
776	>	if (simParams->getOutputParticlePotential()) {
777	>	storageLayout |= DataStorage::dslParticlePot;
778	>	}
779
780	<	if (currentStamp == NULL) {
781	<	sprintf(painCave.errMsg,
782	<	"SimCreator error: Component \"%s\" was not found in the "
783	<	"list of declared molecules\n", id);
780	>	if (simParams->havePrintHeatFlux()) {
781	>	if (simParams->getPrintHeatFlux()) {
782	>	storageLayout |= DataStorage::dslParticlePot;
783	>	}
784	>	}
785
786	<	painCave.isFatal = 1;
787	<	simError();
468	<	}
469	<
470	<	moleculeStampPairs.push_back(
471	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
472	<	} //end for (i = 0; i < n_components; i++)
473	<	} else {
474	<	sprintf(painCave.errMsg, "SimSetup error.\n"
475	<	"\tSorry, the ability to specify total"
476	<	" nMols and then give molfractions in the components\n"
477	<	"\tis not currently supported."
478	<	" Please give nMol in the components.\n");
479	<
480	<	painCave.isFatal = 1;
481	<	simError();
786	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
787	>	storageLayout |= DataStorage::dslElectricField;
788		}
789
790	<	#ifdef IS_MPI
790	>	if (simParams->getOutputFluctuatingCharges()) {
791	>	storageLayout |= DataStorage::dslFlucQPosition;
792	>	storageLayout |= DataStorage::dslFlucQVelocity;
793	>	storageLayout |= DataStorage::dslFlucQForce;
794	>	}
795
796	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
487	<	MPIcheckPoint();
796	>	info->setStorageLayout(storageLayout);
797
798	<	#endif // is_mpi
798	>	return storageLayout;
799	>	}
800
801	<	}
492	<
493	<	void SimCreator::setGlobalIndex(SimInfo *info) {
801	>	void SimCreator::setGlobalIndex(SimInfo *info) {
802		SimInfo::MoleculeIterator mi;
803		Molecule::AtomIterator ai;
804		Molecule::RigidBodyIterator ri;
805		Molecule::CutoffGroupIterator ci;
806	<	Molecule * mol;
807	<	Atom * atom;
808	<	RigidBody * rb;
809	<	CutoffGroup * cg;
806	>	Molecule::BondIterator boi;
807	>	Molecule::BendIterator bei;
808	>	Molecule::TorsionIterator ti;
809	>	Molecule::InversionIterator ii;
810	>	Molecule::IntegrableObjectIterator  ioi;
811	>	Molecule* mol;
812	>	Atom* atom;
813	>	RigidBody* rb;
814	>	CutoffGroup* cg;
815	>	Bond* bond;
816	>	Bend* bend;
817	>	Torsion* torsion;
818	>	Inversion* inversion;
819		int beginAtomIndex;
820		int beginRigidBodyIndex;
821		int beginCutoffGroupIndex;
822	+	int beginBondIndex;
823	+	int beginBendIndex;
824	+	int beginTorsionIndex;
825	+	int beginInversionIndex;
826		int nGlobalAtoms = info->getNGlobalAtoms();
827	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
828
507	–	#ifndef IS_MPI
508	–
829		beginAtomIndex = 0;
830	<	beginRigidBodyIndex = 0;
830	>	// The rigid body indices begin immediately after the atom indices:
831	>	beginRigidBodyIndex = info->getNGlobalAtoms();
832		beginCutoffGroupIndex = 0;
833	+	beginBondIndex = 0;
834	+	beginBendIndex = 0;
835	+	beginTorsionIndex = 0;
836	+	beginInversionIndex = 0;
837	+
838	+	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
839	+
840	+	#ifdef IS_MPI
841	+	if (info->getMolToProc(i) == worldRank) {
842	+	#endif
843	+	// stuff to do if I own this molecule
844	+	mol = info->getMoleculeByGlobalIndex(i);
845
846	<	#else
847	<
848	<	int nproc;
849	<	int myNode;
517	<
518	<	myNode = worldRank;
519	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
520	<
521	<	std::vector < int > tmpAtomsInProc(nproc, 0);
522	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
523	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
524	<	std::vector < int > NumAtomsInProc(nproc, 0);
525	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
526	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
527	<
528	<	tmpAtomsInProc[myNode] = info->getNAtoms();
529	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
530	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
531	<
532	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
533	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
534	<	MPI_SUM, MPI_COMM_WORLD);
535	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
536	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
537	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
538	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
539	<
540	<	beginAtomIndex = 0;
541	<	beginRigidBodyIndex = 0;
542	<	beginCutoffGroupIndex = 0;
543	<
544	<	for(int i = 0; i < myNode; i++) {
545	<	beginAtomIndex += NumAtomsInProc[i];
546	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
547	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
548	<	}
549	<
550	<	#endif
551	<
552	<	for(mol = info->beginMolecule(mi); mol != NULL;
553	<	mol = info->nextMolecule(mi)) {
554	<
555	<	//local index(index in DataStorge) of atom is important
556	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
557	<	atom->setGlobalIndex(beginAtomIndex++);
846	>	// The local index(index in DataStorge) of the atom is important:
847	>	for(atom = mol->beginAtom(ai); atom != NULL;
848	>	atom = mol->nextAtom(ai)) {
849	>	atom->setGlobalIndex(beginAtomIndex++);
850		}
851	<
851	>
852		for(rb = mol->beginRigidBody(ri); rb != NULL;
853		rb = mol->nextRigidBody(ri)) {
854	<	rb->setGlobalIndex(beginRigidBodyIndex++);
854	>	rb->setGlobalIndex(beginRigidBodyIndex++);
855		}
856	<
857	<	//local index of cutoff group is trivial, it only depends on the order of travesing
856	>
857	>	// The local index of other objects only depends on the order
858	>	// of traversal:
859		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
860		cg = mol->nextCutoffGroup(ci)) {
861	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
862	<	}
863	<	}
861	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
862	>	}
863	>	for(bond = mol->beginBond(boi); bond != NULL;
864	>	bond = mol->nextBond(boi)) {
865	>	bond->setGlobalIndex(beginBondIndex++);
866	>	}
867	>	for(bend = mol->beginBend(bei); bend != NULL;
868	>	bend = mol->nextBend(bei)) {
869	>	bend->setGlobalIndex(beginBendIndex++);
870	>	}
871	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
872	>	torsion = mol->nextTorsion(ti)) {
873	>	torsion->setGlobalIndex(beginTorsionIndex++);
874	>	}
875	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
876	>	inversion = mol->nextInversion(ii)) {
877	>	inversion->setGlobalIndex(beginInversionIndex++);
878	>	}
879	>
880	>	#ifdef IS_MPI
881	>	}  else {
882
883	<	//fill globalGroupMembership
884	<	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
885	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
886	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
883	>	// stuff to do if I don't own this molecule
884	>
885	>	int stampId = info->getMoleculeStampId(i);
886	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
887
888	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
889	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
890	<	}
888	>	beginAtomIndex += stamp->getNAtoms();
889	>	beginRigidBodyIndex += stamp->getNRigidBodies();
890	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
891	>	beginBondIndex += stamp->getNBonds();
892	>	beginBendIndex += stamp->getNBends();
893	>	beginTorsionIndex += stamp->getNTorsions();
894	>	beginInversionIndex += stamp->getNInversions();
895	>	}
896	>	#endif
897
898	<	}
582	<	}
898	>	} //end for(int i=0)
899
900	+	//fill globalGroupMembership
901	+	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
902	+	for(mol = info->beginMolecule(mi); mol != NULL;
903	+	mol = info->nextMolecule(mi)) {
904	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
905	+	cg = mol->nextCutoffGroup(ci)) {
906	+	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
907	+	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
908	+	}
909	+
910	+	}
911	+	}
912	+
913		#ifdef IS_MPI
914		// Since the globalGroupMembership has been zero filled and we've only
915		// poked values into the atoms we know, we can do an Allreduce
916		// to get the full globalGroupMembership array (We think).
917		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
918		// docs said we could.
919	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
920	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
921	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
922	<	info->setGlobalGroupMembership(tmpGroupMembership);
919	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
920	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
921	>	&tmpGroupMembership[0], nGlobalAtoms,
922	>	MPI::INT, MPI::SUM);
923	>	info->setGlobalGroupMembership(tmpGroupMembership);
924		#else
925		info->setGlobalGroupMembership(globalGroupMembership);
926		#endif
927	<
927	>
928		//fill molMembership
929	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
929	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
930	>	info->getNGlobalRigidBodies(), 0);
931
932	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
933	<
934	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
935	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
936	<	}
932	>	for(mol = info->beginMolecule(mi); mol != NULL;
933	>	mol = info->nextMolecule(mi)) {
934	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
935	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
936	>	}
937	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
938	>	rb = mol->nextRigidBody(ri)) {
939	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
940	>	}
941		}
942	<
942	>
943		#ifdef IS_MPI
944	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
945	<
946	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
947	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
944	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
945	>	info->getNGlobalRigidBodies(), 0);
946	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
947	>	nGlobalAtoms + nGlobalRigidBodies,
948	>	MPI::INT, MPI::SUM);
949
950		info->setGlobalMolMembership(tmpMolMembership);
951		#else
952		info->setGlobalMolMembership(globalMolMembership);
953		#endif
954
955	<	}
955	>	// nIOPerMol holds the number of integrable objects per molecule
956	>	// here the molecules are listed by their global indices.
957
958	<	void SimCreator::loadCoordinates(SimInfo* info) {
959	<	Globals* simParams;
960	<	simParams = info->getSimParams();
958	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
959	>	for (mol = info->beginMolecule(mi); mol != NULL;
960	>	mol = info->nextMolecule(mi)) {
961	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
962	>	}
963
964	<	if (!simParams->haveInitialConfig()) {
965	<	sprintf(painCave.errMsg,
966	<	"Cannot intialize a simulation without an initial configuration file.\n");
967	<	painCave.isFatal = 1;;
968	<	simError();
964	>	#ifdef IS_MPI
965	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
966	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
967	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
968	>	#else
969	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
970	>	#endif
971	>
972	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
973	>
974	>	int startingIndex = 0;
975	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
976	>	startingIOIndexForMol[i] = startingIndex;
977	>	startingIndex += numIntegrableObjectsPerMol[i];
978		}
979	<
980	<	DumpReader reader(info, simParams->getInitialConfig());
979	>
980	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
981	>	for (mol = info->beginMolecule(mi); mol != NULL;
982	>	mol = info->nextMolecule(mi)) {
983	>	int myGlobalIndex = mol->getGlobalIndex();
984	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
985	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
986	>	sd = mol->nextIntegrableObject(ioi)) {
987	>	sd->setGlobalIntegrableObjectIndex(globalIO);
988	>	IOIndexToIntegrableObject[globalIO] = sd;
989	>	globalIO++;
990	>	}
991	>	}
992	>
993	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
994	>
995	>	}
996	>
997	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
998	>
999	>	DumpReader reader(info, mdFileName);
1000		int nframes = reader.getNFrames();
1001	<
1001	>
1002		if (nframes > 0) {
1003	<	reader.readFrame(nframes - 1);
1003	>	reader.readFrame(nframes - 1);
1004		} else {
1005	<	//invalid initial coordinate file
1006	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
1007	<	simParams->getInitialConfig());
1008	<	painCave.isFatal = 1;
1009	<	simError();
1005	>	//invalid initial coordinate file
1006	>	sprintf(painCave.errMsg,
1007	>	"Initial configuration file %s should at least contain one frame\n",
1008	>	mdFileName.c_str());
1009	>	painCave.isFatal = 1;
1010	>	simError();
1011		}
644	–
1012		//copy the current snapshot to previous snapshot
1013		info->getSnapshotManager()->advance();
1014	<	}
1014	>	}
1015	>
1016	>	} //end namespace OpenMD
1017
649	–	} //end namespace oopse
1018
651	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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