ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49
50	<	#include <sprng.h>
50	>	#ifdef IS_MPI
51	>	#include "mpi.h"
52	>	#include "math/ParallelRandNumGen.hpp"
53	>	#endif
54
55	+	#include <exception>
56	+	#include <iostream>
57	+	#include <sstream>
58	+	#include <string>
59	+
60		#include "brains/MoleculeCreator.hpp"
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "io/parse_me.h"
57	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67	<	#ifdef IS_MPI
68	<	#include "io/mpiBASS.h"
69	<	#include "math/randomSPRNG.hpp"
70	<	#endif
67	>	#include "utils/Revision.hpp"
68	>	#include "math/SeqRandNumGen.hpp"
69	>	#include "mdParser/MDLexer.hpp"
70	>	#include "mdParser/MDParser.hpp"
71	>	#include "mdParser/MDTreeParser.hpp"
72	>	#include "mdParser/SimplePreprocessor.hpp"
73	>	#include "antlr/ANTLRException.hpp"
74	>	#include "antlr/TokenStreamRecognitionException.hpp"
75	>	#include "antlr/TokenStreamIOException.hpp"
76	>	#include "antlr/TokenStreamException.hpp"
77	>	#include "antlr/RecognitionException.hpp"
78	>	#include "antlr/CharStreamException.hpp"
79
80	<	namespace oopse {
80	>	#include "antlr/MismatchedCharException.hpp"
81	>	#include "antlr/MismatchedTokenException.hpp"
82	>	#include "antlr/NoViableAltForCharException.hpp"
83	>	#include "antlr/NoViableAltException.hpp"
84
85	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
85	>	#include "types/DirectionalAdapter.hpp"
86	>	#include "types/MultipoleAdapter.hpp"
87	>	#include "types/EAMAdapter.hpp"
88	>	#include "types/SuttonChenAdapter.hpp"
89	>	#include "types/PolarizableAdapter.hpp"
90	>	#include "types/FixedChargeAdapter.hpp"
91	>	#include "types/FluctuatingChargeAdapter.hpp"
92
69	–	#ifdef IS_MPI
93
94	<	if (worldRank == 0) {
95	<	#endif // is_mpi
94	>	namespace OpenMD {
95	>
96	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
97	>	Globals* simParams = NULL;
98	>	try {
99
100	<	simParams->initalize();
101	<	set_interface_stamps(stamps, simParams);
100	>	// Create a preprocessor that preprocesses md file into an ostringstream
101	>	std::stringstream ppStream;
102	>	#ifdef IS_MPI
103	>	int streamSize;
104	>	const int masterNode = 0;
105
106	<	#ifdef IS_MPI
106	>	if (worldRank == masterNode) {
107	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
108	>	#endif
109	>	SimplePreprocessor preprocessor;
110	>	preprocessor.preprocess(rawMetaDataStream, filename,
111	>	startOfMetaDataBlock, ppStream);
112	>
113	>	#ifdef IS_MPI
114	>	//broadcasting the stream size
115	>	streamSize = ppStream.str().size() +1;
116	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
117	>	MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
118	>	streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
119	>	} else {
120
121	<	mpiEventInit();
121	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
122
123	<	#endif
123	>	//get stream size
124	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
125	>	char* buf = new char[streamSize];
126	>	assert(buf);
127	>
128	>	//receive file content
129	>	MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
130
131	<	yacc_BASS(mdFileName.c_str());
131	>	ppStream.str(buf);
132	>	delete [] buf;
133	>	}
134	>	#endif
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139	>
140	>	// Create a parser that reads from the scanner
141	>	MDParser parser(lexer);
142	>	parser.setFilename(filename);
143
144	<	#ifdef IS_MPI
144	>	// Create an observer that synchorizes file name change
145	>	FilenameObserver observer;
146	>	observer.setLexer(&lexer);
147	>	observer.setParser(&parser);
148	>	lexer.setObserver(&observer);
149	>
150	>	antlr::ASTFactory factory;
151	>	parser.initializeASTFactory(factory);
152	>	parser.setASTFactory(&factory);
153	>	parser.mdfile();
154	>	// Create a tree parser that reads information into Globals
155	>	MDTreeParser treeParser;
156	>	treeParser.initializeASTFactory(factory);
157	>	treeParser.setASTFactory(&factory);
158	>	simParams = treeParser.walkTree(parser.getAST());
159	>	}
160
161	<	throwMPIEvent(NULL);
162	<	} else {
163	<	set_interface_stamps(stamps, simParams);
164	<	mpiEventInit();
165	<	MPIcheckPoint();
166	<	mpiEventLoop();
161	>
162	>	catch(antlr::MismatchedCharException& e) {
163	>	sprintf(painCave.errMsg,
164	>	"parser exception: %s %s:%d:%d\n",
165	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
166	>	painCave.isFatal = 1;
167	>	simError();
168		}
169	+	catch(antlr::MismatchedTokenException &e) {
170	+	sprintf(painCave.errMsg,
171	+	"parser exception: %s %s:%d:%d\n",
172	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
173	+	painCave.isFatal = 1;
174	+	simError();
175	+	}
176	+	catch(antlr::NoViableAltForCharException &e) {
177	+	sprintf(painCave.errMsg,
178	+	"parser exception: %s %s:%d:%d\n",
179	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
180	+	painCave.isFatal = 1;
181	+	simError();
182	+	}
183	+	catch(antlr::NoViableAltException &e) {
184	+	sprintf(painCave.errMsg,
185	+	"parser exception: %s %s:%d:%d\n",
186	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
187	+	painCave.isFatal = 1;
188	+	simError();
189	+	}
190	+
191	+	catch(antlr::TokenStreamRecognitionException& e) {
192	+	sprintf(painCave.errMsg,
193	+	"parser exception: %s %s:%d:%d\n",
194	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
195	+	painCave.isFatal = 1;
196	+	simError();
197	+	}
198	+
199	+	catch(antlr::TokenStreamIOException& e) {
200	+	sprintf(painCave.errMsg,
201	+	"parser exception: %s\n",
202	+	e.getMessage().c_str());
203	+	painCave.isFatal = 1;
204	+	simError();
205	+	}
206	+
207	+	catch(antlr::TokenStreamException& e) {
208	+	sprintf(painCave.errMsg,
209	+	"parser exception: %s\n",
210	+	e.getMessage().c_str());
211	+	painCave.isFatal = 1;
212	+	simError();
213	+	}
214	+	catch (antlr::RecognitionException& e) {
215	+	sprintf(painCave.errMsg,
216	+	"parser exception: %s %s:%d:%d\n",
217	+	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
218	+	painCave.isFatal = 1;
219	+	simError();
220	+	}
221	+	catch (antlr::CharStreamException& e) {
222	+	sprintf(painCave.errMsg,
223	+	"parser exception: %s\n",
224	+	e.getMessage().c_str());
225	+	painCave.isFatal = 1;
226	+	simError();
227	+	}
228	+	catch (OpenMDException& e) {
229	+	sprintf(painCave.errMsg,
230	+	"%s\n",
231	+	e.getMessage().c_str());
232	+	painCave.isFatal = 1;
233	+	simError();
234	+	}
235	+	catch (std::exception& e) {
236	+	sprintf(painCave.errMsg,
237	+	"parser exception: %s\n",
238	+	e.what());
239	+	painCave.isFatal = 1;
240	+	simError();
241	+	}
242
243	<	#endif
243	>	simParams->setMDfileVersion(mdFileVersion);
244	>	return simParams;
245	>	}
246	>
247	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
248	>	bool loadInitCoords) {
249	>
250	>	const int bufferSize = 65535;
251	>	char buffer[bufferSize];
252	>	int lineNo = 0;
253	>	std::string mdRawData;
254	>	int metaDataBlockStart = -1;
255	>	int metaDataBlockEnd = -1;
256	>	int i, j;
257	>	streamoff mdOffset;
258	>	int mdFileVersion;
259
260	<	}
260	>	// Create a string for embedding the version information in the MetaData
261	>	std::string version;
262	>	version.assign("## Last run using OpenMD Version: ");
263	>	version.append(OPENMD_VERSION_MAJOR);
264	>	version.append(".");
265	>	version.append(OPENMD_VERSION_MINOR);
266
267	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
268	<
269	<	MakeStamps * stamps = new MakeStamps();
267	>	std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
268	>	//convert a macro from compiler to a string in c++
269	>	// STR_DEFINE(svnrev, SVN_REV );
270	>	version.append(" Revision: ");
271	>	// If there's no SVN revision, just call this the RELEASE revision.
272	>	if (!svnrev.empty()) {
273	>	version.append(svnrev);
274	>	} else {
275	>	version.append("RELEASE");
276	>	}
277	>
278	>	#ifdef IS_MPI
279	>	const int masterNode = 0;
280	>	if (worldRank == masterNode) {
281	>	#endif
282
283	<	Globals * simParams = new Globals();
283	>	std::ifstream mdFile_;
284	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
285	>
286	>	if (mdFile_.fail()) {
287	>	sprintf(painCave.errMsg,
288	>	"SimCreator: Cannot open file: %s\n",
289	>	mdFileName.c_str());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293
294	<	//parse meta-data file
295	<	parseFile(mdFileName, stamps, simParams);
294	>	mdFile_.getline(buffer, bufferSize);
295	>	++lineNo;
296	>	std::string line = trimLeftCopy(buffer);
297	>	i = CaseInsensitiveFind(line, "<OpenMD");
298	>	if (static_cast<size_t>(i) == string::npos) {
299	>	// try the older file strings to see if that works:
300	>	i = CaseInsensitiveFind(line, "<OOPSE");
301	>	}
302	>
303	>	if (static_cast<size_t>(i) == string::npos) {
304	>	// still no luck!
305	>	sprintf(painCave.errMsg,
306	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
307	>	mdFileName.c_str());
308	>	painCave.isFatal = 1;
309	>	simError();
310	>	}
311	>
312	>	// found the correct opening string, now try to get the file
313	>	// format version number.
314
315	<	//create the force field
316	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
317	<	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	<	}
315	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
316	>	std::string fileType = tokenizer.nextToken();
317	>	toUpper(fileType);
318
319	<	std::string forcefieldFileName;
120	<	forcefieldFileName = ff->getForceFieldFileName();
319	>	mdFileVersion = 0;
320
321	<	if (simParams->haveForceFieldVariant()) {
322	<	//If the force field has variant, the variant force field name will be
323	<	//Base.variant.frc. For exampel EAM.u6.frc
321	>	if (fileType == "OPENMD") {
322	>	while (tokenizer.hasMoreTokens()) {
323	>	std::string token(tokenizer.nextToken());
324	>	toUpper(token);
325	>	if (token == "VERSION") {
326	>	mdFileVersion = tokenizer.nextTokenAsInt();
327	>	break;
328	>	}
329	>	}
330	>	}
331	>
332	>	//scan through the input stream and find MetaData tag
333	>	while(mdFile_.getline(buffer, bufferSize)) {
334	>	++lineNo;
335
336	<	std::string variant = simParams->getForceFieldVariant();
337	<
338	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
339	<	variant = "." + variant;
340	<	if (pos != std::string::npos) {
341	<	forcefieldFileName.insert(pos, variant);
336	>	std::string line = trimLeftCopy(buffer);
337	>	if (metaDataBlockStart == -1) {
338	>	i = CaseInsensitiveFind(line, "<MetaData>");
339	>	if (i != string::npos) {
340	>	metaDataBlockStart = lineNo;
341	>	mdOffset = mdFile_.tellg();
342	>	}
343		} else {
344	<	//If the default force field file name does not containt .frc suffix, just append the .variant
345	<	forcefieldFileName.append(variant);
344	>	i = CaseInsensitiveFind(line, "</MetaData>");
345	>	if (i != string::npos) {
346	>	metaDataBlockEnd = lineNo;
347	>	}
348		}
349	+	}
350	+
351	+	if (metaDataBlockStart == -1) {
352	+	sprintf(painCave.errMsg,
353	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
354	+	mdFileName.c_str());
355	+	painCave.isFatal = 1;
356	+	simError();
357	+	}
358	+	if (metaDataBlockEnd == -1) {
359	+	sprintf(painCave.errMsg,
360	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
361	+	mdFileName.c_str());
362	+	painCave.isFatal = 1;
363	+	simError();
364	+	}
365	+
366	+	mdFile_.clear();
367	+	mdFile_.seekg(0);
368	+	mdFile_.seekg(mdOffset);
369	+
370	+	mdRawData.clear();
371	+
372	+	bool foundVersion = false;
373	+
374	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
375	+	mdFile_.getline(buffer, bufferSize);
376	+	std::string line = trimLeftCopy(buffer);
377	+	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
378	+	if (static_cast<size_t>(j) != string::npos) {
379	+	foundVersion = true;
380	+	mdRawData += version;
381	+	} else {
382	+	mdRawData += buffer;
383	+	}
384	+	mdRawData += "\n";
385	+	}
386	+
387	+	if (!foundVersion) mdRawData += version + "\n";
388	+
389	+	mdFile_.close();
390	+
391	+	#ifdef IS_MPI
392	+	}
393	+	#endif
394	+
395	+	std::stringstream rawMetaDataStream(mdRawData);
396	+
397	+	//parse meta-data file
398	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
399	+	metaDataBlockStart + 1);
400	+
401	+	//create the force field
402	+	ForceField * ff = new ForceField(simParams->getForceField());
403	+
404	+	if (ff == NULL) {
405	+	sprintf(painCave.errMsg,
406	+	"ForceField Factory can not create %s force field\n",
407	+	simParams->getForceField().c_str());
408	+	painCave.isFatal = 1;
409	+	simError();
410	+	}
411	+
412	+	if (simParams->haveForceFieldFileName()) {
413	+	ff->setForceFieldFileName(simParams->getForceFieldFileName());
414	+	}
415	+
416	+	std::string forcefieldFileName;
417	+	forcefieldFileName = ff->getForceFieldFileName();
418	+
419	+	if (simParams->haveForceFieldVariant()) {
420	+	//If the force field has variant, the variant force field name will be
421	+	//Base.variant.frc. For exampel EAM.u6.frc
422	+
423	+	std::string variant = simParams->getForceFieldVariant();
424	+
425	+	std::string::size_type pos = forcefieldFileName.rfind(".frc");
426	+	variant = "." + variant;
427	+	if (pos != std::string::npos) {
428	+	forcefieldFileName.insert(pos, variant);
429	+	} else {
430	+	//If the default force field file name does not containt .frc suffix, just append the .variant
431	+	forcefieldFileName.append(variant);
432	+	}
433		}
434
435		ff->parse(forcefieldFileName);
139	–
140	–	//extract the molecule stamps
141	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
142	–	compList(stamps, simParams, moleculeStampPairs);
143	–
436		//create SimInfo
437	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
437	>	SimInfo * info = new SimInfo(ff, simParams);
438
439	<	//gather parameters (SimCreator only retrieves part of the parameters)
439	>	info->setRawMetaData(mdRawData);
440	>
441	>	//gather parameters (SimCreator only retrieves part of the
442	>	//parameters)
443		gatherParameters(info, mdFileName);
444	<
444	>
445		//divide the molecules and determine the global index of molecules
446		#ifdef IS_MPI
447		divideMolecules(info);
448		#endif
449	<
449	>
450		//create the molecules
451		createMolecules(info);
452	+
453	+	//find the storage layout
454
455	+	int storageLayout = computeStorageLayout(info);
456
457	<	//allocate memory for DataStorage(circular reference, need to break it)
458	<	info->setSnapshotManager(new SimSnapshotManager(info));
457	>	//allocate memory for DataStorage(circular reference, need to
458	>	//break it)
459	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
460
461	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
462	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
463	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
461	>	//set the global index of atoms, rigidbodies and cutoffgroups
462	>	//(only need to be set once, the global index will never change
463	>	//again). Local indices of atoms and rigidbodies are already set
464	>	//by MoleculeCreator class which actually delegates the
465	>	//responsibility to LocalIndexManager.
466		setGlobalIndex(info);
467	<
468	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
469	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
470	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
471	<	//we can determine the beginning global indices of atoms before they get created.
467	>
468	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
469	>	//method, at that point atoms don't have the global index yet
470	>	//(their global index are all initialized to -1).  Therefore we
471	>	//have to call addInteractionPairs explicitly here. A way to work
472	>	//around is that we can determine the beginning global indices of
473	>	//atoms before they get created.
474		SimInfo::MoleculeIterator mi;
475		Molecule* mol;
476		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
477	<	info->addExcludePairs(mol);
477	>	info->addInteractionPairs(mol);
478		}
479
177	–
178	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
179	–	//eta, chi for NPT integrator)
480		if (loadInitCoords)
481	<	loadCoordinates(info);
182	<
481	>	loadCoordinates(info, mdFileName);
482		return info;
483	<	}
484	<
485	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
486	<
487	<	//setup seed for random number generator
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
483	>	}
484	>
485	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
486	>
487	>	//figure out the output file names
488		std::string prefix;
489	<
489	>
490		#ifdef IS_MPI
491	<
491	>
492		if (worldRank == 0) {
493		#endif // is_mpi
494	<
495	<	if (simParams->haveFinalConfig()) {
496	<	prefix = getPrefix(simParams->getFinalConfig());
497	<	} else {
498	<	prefix = getPrefix(mdfile);
499	<	}
500	<
501	<	info->setFinalConfigFileName(prefix + ".eor");
502	<	info->setDumpFileName(prefix + ".dump");
503	<	info->setStatFileName(prefix + ".stat");
504	<
494	>	Globals * simParams = info->getSimParams();
495	>	if (simParams->haveFinalConfig()) {
496	>	prefix = getPrefix(simParams->getFinalConfig());
497	>	} else {
498	>	prefix = getPrefix(mdfile);
499	>	}
500	>
501	>	info->setFinalConfigFileName(prefix + ".eor");
502	>	info->setDumpFileName(prefix + ".dump");
503	>	info->setStatFileName(prefix + ".stat");
504	>	info->setRestFileName(prefix + ".zang");
505	>
506		#ifdef IS_MPI
507	<
507	>
508		}
509	<
509	>
510		#endif
511	<
512	<	}
513	<
511	>
512	>	}
513	>
514		#ifdef IS_MPI
515	<	void SimCreator::divideMolecules(SimInfo *info) {
516	<	double numerator;
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;
515	>	void SimCreator::divideMolecules(SimInfo *info) {
516	>	RealType a;
517		int nProcessors;
518		std::vector<int> atomsPerProc;
286	–	randomSPRNG myRandom(info->getSeed());
519		int nGlobalMols = info->getNGlobalMolecules();
520	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
520	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
521	>	// error
522	>	// condition:
523
524	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
525	<
524	>	MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
525	>
526		if (nProcessors > nGlobalMols) {
527	<	sprintf(painCave.errMsg,
528	<	"nProcessors (%d) > nMol (%d)\n"
529	<	"\tThe number of processors is larger than\n"
530	<	"\tthe number of molecules.  This will not result in a \n"
531	<	"\tusable division of atoms for force decomposition.\n"
532	<	"\tEither try a smaller number of processors, or run the\n"
533	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
534	<
535	<	painCave.isFatal = 1;
536	<	simError();
527	>	sprintf(painCave.errMsg,
528	>	"nProcessors (%d) > nMol (%d)\n"
529	>	"\tThe number of processors is larger than\n"
530	>	"\tthe number of molecules.  This will not result in a \n"
531	>	"\tusable division of atoms for force decomposition.\n"
532	>	"\tEither try a smaller number of processors, or run the\n"
533	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
534	>	nGlobalMols);
535	>
536	>	painCave.isFatal = 1;
537	>	simError();
538		}
539	<
539	>
540	>	Globals * simParams = info->getSimParams();
541	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
542	>	//random number generator
543	>	if (simParams->haveSeed()) {
544	>	int seedValue = simParams->getSeed();
545	>	myRandom = new SeqRandNumGen(seedValue);
546	>	}else {
547	>	myRandom = new SeqRandNumGen();
548	>	}
549	>
550	>
551		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
552	<
552	>
553		//initialize atomsPerProc
554		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
555	<
555	>
556		if (worldRank == 0) {
557	<	numerator = info->getNGlobalAtoms();
558	<	denominator = nProcessors;
559	<	precast = numerator / denominator;
560	<	nTarget = (int)(precast + 0.5);
557	>	RealType numerator = info->getNGlobalAtoms();
558	>	RealType denominator = nProcessors;
559	>	RealType precast = numerator / denominator;
560	>	int nTarget = (int)(precast + 0.5);
561	>
562	>	for(int i = 0; i < nGlobalMols; i++) {
563
564	<	for(i = 0; i < nGlobalMols; i++) {
565	<	done = 0;
566	<	loops = 0;
567	<
568	<	while (!done) {
569	<	loops++;
570	<
571	<	// Pick a processor at random
572	<
573	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
574	<
575	<	//get the molecule stamp first
576	<	int stampId = info->getMoleculeStampId(i);
577	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
578	<
579	<	// How many atoms does this processor have so far?
580	<	old_atoms = atomsPerProc[which_proc];
581	<	add_atoms = moleculeStamp->getNAtoms();
582	<	new_atoms = old_atoms + add_atoms;
583	<
584	<	// If we've been through this loop too many times, we need
585	<	// to just give up and assign the molecule to this processor
586	<	// and be done with it.
564	>	int done = 0;
565	>	int loops = 0;
566	>
567	>	while (!done) {
568	>	loops++;
569	>
570	>	// Pick a processor at random
571	>
572	>	int which_proc = (int) (myRandom->rand() * nProcessors);
573	>
574	>	//get the molecule stamp first
575	>	int stampId = info->getMoleculeStampId(i);
576	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
577	>
578	>	// How many atoms does this processor have so far?
579	>	int old_atoms = atomsPerProc[which_proc];
580	>	int add_atoms = moleculeStamp->getNAtoms();
581	>	int new_atoms = old_atoms + add_atoms;
582	>
583	>	// If we've been through this loop too many times, we need
584	>	// to just give up and assign the molecule to this processor
585	>	// and be done with it.
586	>
587	>	if (loops > 100) {
588
589	<	if (loops > 100) {
590	<	sprintf(painCave.errMsg,
591	<	"I've tried 100 times to assign molecule %d to a "
592	<	" processor, but can't find a good spot.\n"
593	<	"I'm assigning it at random to processor %d.\n",
594	<	i, which_proc);
595	<
596	<	painCave.isFatal = 0;
597	<	simError();
598	<
599	<	molToProcMap[i] = which_proc;
600	<	atomsPerProc[which_proc] += add_atoms;
601	<
602	<	done = 1;
603	<	continue;
604	<	}
605	<
606	<	// If we can add this molecule to this processor without sending
607	<	// it above nTarget, then go ahead and do it:
608	<
609	<	if (new_atoms <= nTarget) {
610	<	molToProcMap[i] = which_proc;
611	<	atomsPerProc[which_proc] += add_atoms;
612	<
613	<	done = 1;
614	<	continue;
615	<	}
616	<
617	<	// The only situation left is when new_atoms > nTarget.  We
618	<	// want to accept this with some probability that dies off the
619	<	// farther we are from nTarget
620	<
621	<	// roughly:  x = new_atoms - nTarget
622	<	//           Pacc(x) = exp(- a * x)
623	<	// where a = penalty / (average atoms per molecule)
624	<
625	<	x = (double)(new_atoms - nTarget);
626	<	y = myRandom.getRandom();
627	<
628	<	if (y < exp(- a * x)) {
629	<	molToProcMap[i] = which_proc;
630	<	atomsPerProc[which_proc] += add_atoms;
631	<
632	<	done = 1;
633	<	continue;
634	<	} else {
635	<	continue;
636	<	}
388	<	}
589	>	sprintf(painCave.errMsg,
590	>	"There have been 100 attempts to assign molecule %d to an\n"
591	>	"\tunderworked processor, but there's no good place to\n"
592	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
593	>	i, which_proc);
594	>
595	>	painCave.isFatal = 0;
596	>	painCave.severity = OPENMD_INFO;
597	>	simError();
598	>
599	>	molToProcMap[i] = which_proc;
600	>	atomsPerProc[which_proc] += add_atoms;
601	>
602	>	done = 1;
603	>	continue;
604	>	}
605	>
606	>	// If we can add this molecule to this processor without sending
607	>	// it above nTarget, then go ahead and do it:
608	>
609	>	if (new_atoms <= nTarget) {
610	>	molToProcMap[i] = which_proc;
611	>	atomsPerProc[which_proc] += add_atoms;
612	>
613	>	done = 1;
614	>	continue;
615	>	}
616	>
617	>	// The only situation left is when new_atoms > nTarget.  We
618	>	// want to accept this with some probability that dies off the
619	>	// farther we are from nTarget
620	>
621	>	// roughly:  x = new_atoms - nTarget
622	>	//           Pacc(x) = exp(- a * x)
623	>	// where a = penalty / (average atoms per molecule)
624	>
625	>	RealType x = (RealType)(new_atoms - nTarget);
626	>	RealType y = myRandom->rand();
627	>
628	>	if (y < exp(- a * x)) {
629	>	molToProcMap[i] = which_proc;
630	>	atomsPerProc[which_proc] += add_atoms;
631	>
632	>	done = 1;
633	>	continue;
634	>	} else {
635	>	continue;
636	>	}
637		}
638	+	}
639	+
640	+	delete myRandom;
641
642	<	// Spray out this nonsense to all other processors:
642	>	// Spray out this nonsense to all other processors:
643	>	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644
393	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
645		} else {
646	+
647	+	// Listen to your marching orders from processor 0:
648	+	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
649
396	–	// Listen to your marching orders from processor 0:
397	–
398	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
650		}
651	<
651	>
652		info->setMolToProcMap(molToProcMap);
653		sprintf(checkPointMsg,
654		"Successfully divided the molecules among the processors.\n");
655	<	MPIcheckPoint();
656	<	}
657	<
655	>	errorCheckPoint();
656	>	}
657	>
658		#endif
659	<
660	<	void SimCreator::createMolecules(SimInfo *info) {
659	>
660	>	void SimCreator::createMolecules(SimInfo *info) {
661		MoleculeCreator molCreator;
662		int stampId;
663	<
663	>
664		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
665	<
665	>
666		#ifdef IS_MPI
667	<
668	<	if (info->getMolToProc(i) == worldRank) {
667	>
668	>	if (info->getMolToProc(i) == worldRank) {
669		#endif
670	<
671	<	stampId = info->getMoleculeStampId(i);
672	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
673	<	stampId, i, info->getLocalIndexManager());
674	<
675	<	info->addMolecule(mol);
676	<
670	>
671	>	stampId = info->getMoleculeStampId(i);
672	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
673	>	info->getMoleculeStamp(stampId),
674	>	stampId, i,
675	>	info->getLocalIndexManager());
676	>
677	>	info->addMolecule(mol);
678	>
679		#ifdef IS_MPI
680	<
681	<	}
682	<
680	>
681	>	}
682	>
683		#endif
684	<
684	>
685		} //end for(int i=0)
686	<	}
686	>	}
687	>
688	>	int SimCreator::computeStorageLayout(SimInfo* info) {
689
690	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
691	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
692	<	int i;
693	<	char * id;
694	<	MoleculeStamp * currentStamp;
695	<	Component** the_components = simParams->getComponents();
696	<	int n_components = simParams->getNComponents();
690	>	Globals* simParams = info->getSimParams();
691	>	int nRigidBodies = info->getNGlobalRigidBodies();
692	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
693	>	set<AtomType*>::iterator i;
694	>	bool hasDirectionalAtoms = false;
695	>	bool hasFixedCharge = false;
696	>	bool hasDipoles = false;
697	>	bool hasQuadrupoles = false;
698	>	bool hasPolarizable = false;
699	>	bool hasFluctuatingCharge = false;
700	>	bool hasMetallic = false;
701	>	int storageLayout = 0;
702	>	storageLayout |= DataStorage::dslPosition;
703	>	storageLayout |= DataStorage::dslVelocity;
704	>	storageLayout |= DataStorage::dslForce;
705
706	<	if (!simParams->haveNMol()) {
444	<	// we don't have the total number of molecules, so we assume it is
445	<	// given in each component
706	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
707
708	<	for(i = 0; i < n_components; i++) {
709	<	if (!the_components[i]->haveNMol()) {
710	<	// we have a problem
711	<	sprintf(painCave.errMsg,
712	<	"SimCreator Error. No global NMol or component NMol given.\n"
713	<	"\tCannot calculate the number of atoms.\n");
708	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
709	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
710	>	EAMAdapter ea = EAMAdapter( (*i) );
711	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
712	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
713	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
714	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
715
716	<	painCave.isFatal = 1;
717	<	simError();
718	<	}
716	>	if (da.isDirectional()){
717	>	hasDirectionalAtoms = true;
718	>	}
719	>	if (ma.isDipole()){
720	>	hasDipoles = true;
721	>	}
722	>	if (ma.isQuadrupole()){
723	>	hasQuadrupoles = true;
724	>	}
725	>	if (ea.isEAM() || sca.isSuttonChen()){
726	>	hasMetallic = true;
727	>	}
728	>	if ( fca.isFixedCharge() ){
729	>	hasFixedCharge = true;
730	>	}
731	>	if ( fqa.isFluctuatingCharge() ){
732	>	hasFluctuatingCharge = true;
733	>	}
734	>	if ( pa.isPolarizable() ){
735	>	hasPolarizable = true;
736	>	}
737	>	}
738	>
739	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
740	>	storageLayout |= DataStorage::dslAmat;
741	>	if(storageLayout & DataStorage::dslVelocity) {
742	>	storageLayout |= DataStorage::dslAngularMomentum;
743	>	}
744	>	if (storageLayout & DataStorage::dslForce) {
745	>	storageLayout |= DataStorage::dslTorque;
746	>	}
747	>	}
748	>	if (hasDipoles) {
749	>	storageLayout |= DataStorage::dslDipole;
750	>	}
751	>	if (hasQuadrupoles) {
752	>	storageLayout |= DataStorage::dslQuadrupole;
753	>	}
754	>	if (hasFixedCharge || hasFluctuatingCharge) {
755	>	storageLayout |= DataStorage::dslSkippedCharge;
756	>	}
757	>	if (hasMetallic) {
758	>	storageLayout |= DataStorage::dslDensity;
759	>	storageLayout |= DataStorage::dslFunctional;
760	>	storageLayout |= DataStorage::dslFunctionalDerivative;
761	>	}
762	>	if (hasPolarizable) {
763	>	storageLayout |= DataStorage::dslElectricField;
764	>	}
765	>	if (hasFluctuatingCharge){
766	>	storageLayout |= DataStorage::dslFlucQPosition;
767	>	if(storageLayout & DataStorage::dslVelocity) {
768	>	storageLayout |= DataStorage::dslFlucQVelocity;
769	>	}
770	>	if (storageLayout & DataStorage::dslForce) {
771	>	storageLayout |= DataStorage::dslFlucQForce;
772	>	}
773	>	}
774	>
775	>	// if the user has asked for them, make sure we've got the memory for the
776	>	// objects defined.
777
778	<	id = the_components[i]->getType();
779	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
778	>	if (simParams->getOutputParticlePotential()) {
779	>	storageLayout |= DataStorage::dslParticlePot;
780	>	}
781
782	<	if (currentStamp == NULL) {
783	<	sprintf(painCave.errMsg,
784	<	"SimCreator error: Component \"%s\" was not found in the "
785	<	"list of declared molecules\n", id);
782	>	if (simParams->havePrintHeatFlux()) {
783	>	if (simParams->getPrintHeatFlux()) {
784	>	storageLayout |= DataStorage::dslParticlePot;
785	>	}
786	>	}
787
788	<	painCave.isFatal = 1;
789	<	simError();
790	<	}
788	>	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
789	>	storageLayout |= DataStorage::dslElectricField;
790	>	}
791
792	<	moleculeStampPairs.push_back(
793	<	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();
792	>	if (simParams->getOutputSitePotential() ) {
793	>	storageLayout |= DataStorage::dslSitePotential;
794		}
795
796	<	#ifdef IS_MPI
796	>	if (simParams->getOutputFluctuatingCharges()) {
797	>	storageLayout |= DataStorage::dslFlucQPosition;
798	>	storageLayout |= DataStorage::dslFlucQVelocity;
799	>	storageLayout |= DataStorage::dslFlucQForce;
800	>	}
801
802	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
487	<	MPIcheckPoint();
802	>	info->setStorageLayout(storageLayout);
803
804	<	#endif // is_mpi
804	>	return storageLayout;
805	>	}
806
807	<	}
492	<
493	<	void SimCreator::setGlobalIndex(SimInfo *info) {
807	>	void SimCreator::setGlobalIndex(SimInfo *info) {
808		SimInfo::MoleculeIterator mi;
809		Molecule::AtomIterator ai;
810		Molecule::RigidBodyIterator ri;
811		Molecule::CutoffGroupIterator ci;
812	<	Molecule * mol;
813	<	Atom * atom;
814	<	RigidBody * rb;
815	<	CutoffGroup * cg;
812	>	Molecule::BondIterator boi;
813	>	Molecule::BendIterator bei;
814	>	Molecule::TorsionIterator ti;
815	>	Molecule::InversionIterator ii;
816	>	Molecule::IntegrableObjectIterator  ioi;
817	>	Molecule* mol;
818	>	Atom* atom;
819	>	RigidBody* rb;
820	>	CutoffGroup* cg;
821	>	Bond* bond;
822	>	Bend* bend;
823	>	Torsion* torsion;
824	>	Inversion* inversion;
825		int beginAtomIndex;
826		int beginRigidBodyIndex;
827		int beginCutoffGroupIndex;
828	+	int beginBondIndex;
829	+	int beginBendIndex;
830	+	int beginTorsionIndex;
831	+	int beginInversionIndex;
832		int nGlobalAtoms = info->getNGlobalAtoms();
833	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
834
507	–	#ifndef IS_MPI
508	–
835		beginAtomIndex = 0;
836	<	beginRigidBodyIndex = 0;
836	>	// The rigid body indices begin immediately after the atom indices:
837	>	beginRigidBodyIndex = info->getNGlobalAtoms();
838		beginCutoffGroupIndex = 0;
839	+	beginBondIndex = 0;
840	+	beginBendIndex = 0;
841	+	beginTorsionIndex = 0;
842	+	beginInversionIndex = 0;
843	+
844	+	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
845	+
846	+	#ifdef IS_MPI
847	+	if (info->getMolToProc(i) == worldRank) {
848	+	#endif
849	+	// stuff to do if I own this molecule
850	+	mol = info->getMoleculeByGlobalIndex(i);
851
852	<	#else
853	<
854	<	int nproc;
855	<	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++);
852	>	// The local index(index in DataStorge) of the atom is important:
853	>	for(atom = mol->beginAtom(ai); atom != NULL;
854	>	atom = mol->nextAtom(ai)) {
855	>	atom->setGlobalIndex(beginAtomIndex++);
856		}
857	<
857	>
858		for(rb = mol->beginRigidBody(ri); rb != NULL;
859		rb = mol->nextRigidBody(ri)) {
860	<	rb->setGlobalIndex(beginRigidBodyIndex++);
860	>	rb->setGlobalIndex(beginRigidBodyIndex++);
861		}
862	<
863	<	//local index of cutoff group is trivial, it only depends on the order of travesing
862	>
863	>	// The local index of other objects only depends on the order
864	>	// of traversal:
865		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
866		cg = mol->nextCutoffGroup(ci)) {
867	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
868	<	}
869	<	}
867	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
868	>	}
869	>	for(bond = mol->beginBond(boi); bond != NULL;
870	>	bond = mol->nextBond(boi)) {
871	>	bond->setGlobalIndex(beginBondIndex++);
872	>	}
873	>	for(bend = mol->beginBend(bei); bend != NULL;
874	>	bend = mol->nextBend(bei)) {
875	>	bend->setGlobalIndex(beginBendIndex++);
876	>	}
877	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
878	>	torsion = mol->nextTorsion(ti)) {
879	>	torsion->setGlobalIndex(beginTorsionIndex++);
880	>	}
881	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
882	>	inversion = mol->nextInversion(ii)) {
883	>	inversion->setGlobalIndex(beginInversionIndex++);
884	>	}
885	>
886	>	#ifdef IS_MPI
887	>	}  else {
888
889	<	//fill globalGroupMembership
890	<	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
891	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
892	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
889	>	// stuff to do if I don't own this molecule
890	>
891	>	int stampId = info->getMoleculeStampId(i);
892	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
893
894	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
895	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
896	<	}
894	>	beginAtomIndex += stamp->getNAtoms();
895	>	beginRigidBodyIndex += stamp->getNRigidBodies();
896	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
897	>	beginBondIndex += stamp->getNBonds();
898	>	beginBendIndex += stamp->getNBends();
899	>	beginTorsionIndex += stamp->getNTorsions();
900	>	beginInversionIndex += stamp->getNInversions();
901	>	}
902	>	#endif
903
904	<	}
582	<	}
904	>	} //end for(int i=0)
905
906	+	//fill globalGroupMembership
907	+	std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
908	+	for(mol = info->beginMolecule(mi); mol != NULL;
909	+	mol = info->nextMolecule(mi)) {
910	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
911	+	cg = mol->nextCutoffGroup(ci)) {
912	+	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
913	+	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
914	+	}
915	+
916	+	}
917	+	}
918	+
919		#ifdef IS_MPI
920		// Since the globalGroupMembership has been zero filled and we've only
921		// poked values into the atoms we know, we can do an Allreduce
922		// to get the full globalGroupMembership array (We think).
923		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
924		// docs said we could.
925	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
926	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
925	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
926	>	MPI_Allreduce(&globalGroupMembership[0],
927	>	&tmpGroupMembership[0], nGlobalAtoms,
928		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
929	<	info->setGlobalGroupMembership(tmpGroupMembership);
929	>
930	>	info->setGlobalGroupMembership(tmpGroupMembership);
931		#else
932		info->setGlobalGroupMembership(globalGroupMembership);
933		#endif
934	<
934	>
935		//fill molMembership
936	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
936	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
937	>	info->getNGlobalRigidBodies(), 0);
938
939	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
940	<
941	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
942	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
943	<	}
939	>	for(mol = info->beginMolecule(mi); mol != NULL;
940	>	mol = info->nextMolecule(mi)) {
941	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
942	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
943	>	}
944	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
945	>	rb = mol->nextRigidBody(ri)) {
946	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
947	>	}
948		}
949	<
949	>
950		#ifdef IS_MPI
951	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
952	<
953	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
951	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
952	>	info->getNGlobalRigidBodies(), 0);
953	>	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
954	>	nGlobalAtoms + nGlobalRigidBodies,
955		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
956
957		info->setGlobalMolMembership(tmpMolMembership);
#	Line 616 | Line 959 | void SimCreator::setGlobalIndex(SimInfo *info) {
959		info->setGlobalMolMembership(globalMolMembership);
960		#endif
961
962	<	}
962	>	// nIOPerMol holds the number of integrable objects per molecule
963	>	// here the molecules are listed by their global indices.
964
965	<	void SimCreator::loadCoordinates(SimInfo* info) {
966	<	Globals* simParams;
967	<	simParams = info->getSimParams();
965	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
966	>	for (mol = info->beginMolecule(mi); mol != NULL;
967	>	mol = info->nextMolecule(mi)) {
968	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
969	>	}
970
971	<	if (!simParams->haveInitialConfig()) {
972	<	sprintf(painCave.errMsg,
973	<	"Cannot intialize a simulation without an initial configuration file.\n");
974	<	painCave.isFatal = 1;;
975	<	simError();
971	>	#ifdef IS_MPI
972	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
973	>	MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
974	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
975	>	#else
976	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
977	>	#endif
978	>
979	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
980	>
981	>	int startingIndex = 0;
982	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
983	>	startingIOIndexForMol[i] = startingIndex;
984	>	startingIndex += numIntegrableObjectsPerMol[i];
985		}
986	<
987	<	DumpReader reader(info, simParams->getInitialConfig());
986	>
987	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
988	>	for (mol = info->beginMolecule(mi); mol != NULL;
989	>	mol = info->nextMolecule(mi)) {
990	>	int myGlobalIndex = mol->getGlobalIndex();
991	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
992	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
993	>	sd = mol->nextIntegrableObject(ioi)) {
994	>	sd->setGlobalIntegrableObjectIndex(globalIO);
995	>	IOIndexToIntegrableObject[globalIO] = sd;
996	>	globalIO++;
997	>	}
998	>	}
999	>
1000	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
1001	>
1002	>	}
1003	>
1004	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
1005	>
1006	>	DumpReader reader(info, mdFileName);
1007		int nframes = reader.getNFrames();
1008	<
1008	>
1009		if (nframes > 0) {
1010	<	reader.readFrame(nframes - 1);
1010	>	reader.readFrame(nframes - 1);
1011		} else {
1012	<	//invalid initial coordinate file
1013	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
1014	<	simParams->getInitialConfig());
1015	<	painCave.isFatal = 1;
1016	<	simError();
1012	>	//invalid initial coordinate file
1013	>	sprintf(painCave.errMsg,
1014	>	"Initial configuration file %s should at least contain one frame\n",
1015	>	mdFileName.c_str());
1016	>	painCave.isFatal = 1;
1017	>	simError();
1018		}
644	–
1019		//copy the current snapshot to previous snapshot
1020		info->getSnapshotManager()->advance();
1021	<	}
1021	>	}
1022	>
1023	>	} //end namespace OpenMD
1024
649	–	} //end namespace oopse
1025
651	–

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines