ViewVC Help

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

root/OpenMD/branches/development/src/brains/SimCreator.cpp

Comparing:
trunk/src/brains/SimCreator.cpp (file contents), Revision 832 by tim, Fri Dec 30 15:32:55 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1838 by gezelter, Tue Jan 22 16:20:11 2013 UTC

#	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, 24107 (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	<
49	>	#include <exception>
50		#include <iostream>
51		#include <sstream>
52		#include <string>
#	Line 55 | Line 55
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
58	<	#include "UseTheForce/ForceFieldFactory.hpp"
58	>	#include "brains/ForceField.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 75
75		#include "antlr/NoViableAltForCharException.hpp"
76		#include "antlr/NoViableAltException.hpp"
77
78	+	#include "types/DirectionalAdapter.hpp"
79	+	#include "types/MultipoleAdapter.hpp"
80	+	#include "types/EAMAdapter.hpp"
81	+	#include "types/SuttonChenAdapter.hpp"
82	+	#include "types/PolarizableAdapter.hpp"
83	+	#include "types/FixedChargeAdapter.hpp"
84	+	#include "types/FluctuatingChargeAdapter.hpp"
85	+
86		#ifdef IS_MPI
87	+	#include "mpi.h"
88		#include "math/ParallelRandNumGen.hpp"
89		#endif
90
91	<	namespace oopse {
91	>	namespace OpenMD {
92
93	<	Globals* SimCreator::parseFile(const std::string mdFileName){
94	<	Globals* simParams = NULL;
95	<	try {
93	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
94	>	Globals* simParams = NULL;
95	>	try {
96
97	<	// Create a preprocessor that preprocesses md file into an ostringstream
98	<	std::stringstream ppStream;
97	>	// Create a preprocessor that preprocesses md file into an ostringstream
98	>	std::stringstream ppStream;
99		#ifdef IS_MPI
100	<	int streamSize;
101	<	const int masterNode = 0;
102	<	int commStatus;
103	<	if (worldRank == masterNode) {
104	<	#endif
100	>	int streamSize;
101	>	const int masterNode = 0;
102	>
103	>	if (worldRank == masterNode) {
104	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108
97	–	SimplePreprocessor preprocessor;
98	–	preprocessor.preprocess(mdFileName, ppStream);
99	–
109		#ifdef IS_MPI
110	<	//brocasting the stream size
111	<	streamSize = ppStream.str().size() +1;
112	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
110	>	//brocasting the stream size
111	>	streamSize = ppStream.str().size() +1;
112	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
113	>	MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode);
114	>
115	>	} else {
116	>	MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
117
118	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
119	<
118	>	//get stream size
119	>	MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
120	>
121	>	char* buf = new char[streamSize];
122	>	assert(buf);
123
124	<	} else {
125	<	//get stream size
110	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
124	>	//receive file content
125	>	MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
126
127	<	char* buf = new char[streamSize];
128	<	assert(buf);
129	<
115	<	//receive file content
116	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
117	<
118	<	ppStream.str(buf);
119	<	delete buf;
120	<
121	<	}
127	>	ppStream.str(buf);
128	>	delete [] buf;
129	>	}
130		#endif
131	<	// Create a scanner that reads from the input stream
132	<	MDLexer lexer(ppStream);
133	<	lexer.setFilename(mdFileName);
134	<	lexer.initDeferredLineCount();
131	>	// Create a scanner that reads from the input stream
132	>	MDLexer lexer(ppStream);
133	>	lexer.setFilename(filename);
134	>	lexer.initDeferredLineCount();
135
136	<	// Create a parser that reads from the scanner
137	<	MDParser parser(lexer);
138	<	parser.setFilename(mdFileName);
136	>	// Create a parser that reads from the scanner
137	>	MDParser parser(lexer);
138	>	parser.setFilename(filename);
139
140	<	// Create an observer that synchorizes file name change
141	<	FilenameObserver observer;
142	<	observer.setLexer(&lexer);
143	<	observer.setParser(&parser);
144	<	lexer.setObserver(&observer);
140	>	// Create an observer that synchorizes file name change
141	>	FilenameObserver observer;
142	>	observer.setLexer(&lexer);
143	>	observer.setParser(&parser);
144	>	lexer.setObserver(&observer);
145
146	<	antlr::ASTFactory factory;
147	<	parser.initializeASTFactory(factory);
148	<	parser.setASTFactory(&factory);
149	<	parser.mdfile();
146	>	antlr::ASTFactory factory;
147	>	parser.initializeASTFactory(factory);
148	>	parser.setASTFactory(&factory);
149	>	parser.mdfile();
150
151	<	// Create a tree parser that reads information into Globals
152	<	MDTreeParser treeParser;
153	<	treeParser.initializeASTFactory(factory);
154	<	treeParser.setASTFactory(&factory);
155	<	simParams = treeParser.walkTree(parser.getAST());
151	>	// Create a tree parser that reads information into Globals
152	>	MDTreeParser treeParser;
153	>	treeParser.initializeASTFactory(factory);
154	>	treeParser.setASTFactory(&factory);
155	>	simParams = treeParser.walkTree(parser.getAST());
156	>	}
157
149	–	}
158
159	<	catch(antlr::MismatchedCharException& e) {
160	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
161	<	}
162	<	catch(antlr::MismatchedTokenException &e) {
163	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
164	<	}
165	<	catch(antlr::NoViableAltForCharException &e) {
166	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
167	<	}
168	<	catch(antlr::NoViableAltException &e) {
169	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
170	<	}
171	<	catch(antlr::TokenStreamRecognitionException& e) {
172	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
173	<	}
174	<	catch(antlr::TokenStreamIOException& e) {
175	<	cerr<< "parser exception: " << e.getMessage() << endl;
176	<	}
177	<	catch(antlr::TokenStreamException& e) {
178	<	cerr<< "parser exception: " << e.getMessage() << endl;
179	<	}
180	<	catch (antlr::RecognitionException& e) {
181	<	cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
182	<	}
183	<	catch (antlr::CharStreamException& e) {
184	<	cerr << "parser exception: " << e.getMessage() << endl;
185	<	}
186	<	catch (exception& e) {
187	<	cerr << "parser exception: " << e.what() << endl;
188	<	}
159	>	catch(antlr::MismatchedCharException& e) {
160	>	sprintf(painCave.errMsg,
161	>	"parser exception: %s %s:%d:%d\n",
162	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
163	>	painCave.isFatal = 1;
164	>	simError();
165	>	}
166	>	catch(antlr::MismatchedTokenException &e) {
167	>	sprintf(painCave.errMsg,
168	>	"parser exception: %s %s:%d:%d\n",
169	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
170	>	painCave.isFatal = 1;
171	>	simError();
172	>	}
173	>	catch(antlr::NoViableAltForCharException &e) {
174	>	sprintf(painCave.errMsg,
175	>	"parser exception: %s %s:%d:%d\n",
176	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
177	>	painCave.isFatal = 1;
178	>	simError();
179	>	}
180	>	catch(antlr::NoViableAltException &e) {
181	>	sprintf(painCave.errMsg,
182	>	"parser exception: %s %s:%d:%d\n",
183	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187	>
188	>	catch(antlr::TokenStreamRecognitionException& e) {
189	>	sprintf(painCave.errMsg,
190	>	"parser exception: %s %s:%d:%d\n",
191	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
192	>	painCave.isFatal = 1;
193	>	simError();
194	>	}
195	>
196	>	catch(antlr::TokenStreamIOException& e) {
197	>	sprintf(painCave.errMsg,
198	>	"parser exception: %s\n",
199	>	e.getMessage().c_str());
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>
204	>	catch(antlr::TokenStreamException& e) {
205	>	sprintf(painCave.errMsg,
206	>	"parser exception: %s\n",
207	>	e.getMessage().c_str());
208	>	painCave.isFatal = 1;
209	>	simError();
210	>	}
211	>	catch (antlr::RecognitionException& e) {
212	>	sprintf(painCave.errMsg,
213	>	"parser exception: %s %s:%d:%d\n",
214	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218	>	catch (antlr::CharStreamException& e) {
219	>	sprintf(painCave.errMsg,
220	>	"parser exception: %s\n",
221	>	e.getMessage().c_str());
222	>	painCave.isFatal = 1;
223	>	simError();
224	>	}
225	>	catch (OpenMDException& e) {
226	>	sprintf(painCave.errMsg,
227	>	"%s\n",
228	>	e.getMessage().c_str());
229	>	painCave.isFatal = 1;
230	>	simError();
231	>	}
232	>	catch (std::exception& e) {
233	>	sprintf(painCave.errMsg,
234	>	"parser exception: %s\n",
235	>	e.what());
236	>	painCave.isFatal = 1;
237	>	simError();
238	>	}
239
240	<	return simParams;
240	>	simParams->setMDfileVersion(mdFileVersion);
241	>	return simParams;
242		}
243
244		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
245		bool loadInitCoords) {
246	+
247	+	const int bufferSize = 65535;
248	+	char buffer[bufferSize];
249	+	int lineNo = 0;
250	+	std::string mdRawData;
251	+	int metaDataBlockStart = -1;
252	+	int metaDataBlockEnd = -1;
253	+	int i, j;
254	+	streamoff mdOffset;
255	+	int mdFileVersion;
256
257	+	// Create a string for embedding the version information in the MetaData
258	+	std::string version;
259	+	version.assign("## Last run using OpenMD Version: ");
260	+	version.append(OPENMD_VERSION_MAJOR);
261	+	version.append(".");
262	+	version.append(OPENMD_VERSION_MINOR);
263	+
264	+	std::string svnrev;
265	+	//convert a macro from compiler to a string in c++
266	+	STR_DEFINE(svnrev, SVN_REV );
267	+	version.append(" Revision: ");
268	+	// If there's no SVN revision, just call this the RELEASE revision.
269	+	if (!svnrev.empty()) {
270	+	version.append(svnrev);
271	+	} else {
272	+	version.append("RELEASE");
273	+	}
274	+
275	+	#ifdef IS_MPI
276	+	const int masterNode = 0;
277	+	if (worldRank == masterNode) {
278	+	#endif
279	+
280	+	std::ifstream mdFile_;
281	+	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
282	+
283	+	if (mdFile_.fail()) {
284	+	sprintf(painCave.errMsg,
285	+	"SimCreator: Cannot open file: %s\n",
286	+	mdFileName.c_str());
287	+	painCave.isFatal = 1;
288	+	simError();
289	+	}
290	+
291	+	mdFile_.getline(buffer, bufferSize);
292	+	++lineNo;
293	+	std::string line = trimLeftCopy(buffer);
294	+	i = CaseInsensitiveFind(line, "<OpenMD");
295	+	if (static_cast<size_t>(i) == string::npos) {
296	+	// try the older file strings to see if that works:
297	+	i = CaseInsensitiveFind(line, "<OOPSE");
298	+	}
299	+
300	+	if (static_cast<size_t>(i) == string::npos) {
301	+	// still no luck!
302	+	sprintf(painCave.errMsg,
303	+	"SimCreator: File: %s is not a valid OpenMD file!\n",
304	+	mdFileName.c_str());
305	+	painCave.isFatal = 1;
306	+	simError();
307	+	}
308	+
309	+	// found the correct opening string, now try to get the file
310	+	// format version number.
311	+
312	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
313	+	std::string fileType = tokenizer.nextToken();
314	+	toUpper(fileType);
315	+
316	+	mdFileVersion = 0;
317	+
318	+	if (fileType == "OPENMD") {
319	+	while (tokenizer.hasMoreTokens()) {
320	+	std::string token(tokenizer.nextToken());
321	+	toUpper(token);
322	+	if (token == "VERSION") {
323	+	mdFileVersion = tokenizer.nextTokenAsInt();
324	+	break;
325	+	}
326	+	}
327	+	}
328	+
329	+	//scan through the input stream and find MetaData tag
330	+	while(mdFile_.getline(buffer, bufferSize)) {
331	+	++lineNo;
332	+
333	+	std::string line = trimLeftCopy(buffer);
334	+	if (metaDataBlockStart == -1) {
335	+	i = CaseInsensitiveFind(line, "<MetaData>");
336	+	if (i != string::npos) {
337	+	metaDataBlockStart = lineNo;
338	+	mdOffset = mdFile_.tellg();
339	+	}
340	+	} else {
341	+	i = CaseInsensitiveFind(line, "</MetaData>");
342	+	if (i != string::npos) {
343	+	metaDataBlockEnd = lineNo;
344	+	}
345	+	}
346	+	}
347	+
348	+	if (metaDataBlockStart == -1) {
349	+	sprintf(painCave.errMsg,
350	+	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
351	+	mdFileName.c_str());
352	+	painCave.isFatal = 1;
353	+	simError();
354	+	}
355	+	if (metaDataBlockEnd == -1) {
356	+	sprintf(painCave.errMsg,
357	+	"SimCreator: File: %s did not contain a closed MetaData block!\n",
358	+	mdFileName.c_str());
359	+	painCave.isFatal = 1;
360	+	simError();
361	+	}
362	+
363	+	mdFile_.clear();
364	+	mdFile_.seekg(0);
365	+	mdFile_.seekg(mdOffset);
366	+
367	+	mdRawData.clear();
368	+
369	+	bool foundVersion = false;
370	+
371	+	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
372	+	mdFile_.getline(buffer, bufferSize);
373	+	std::string line = trimLeftCopy(buffer);
374	+	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
375	+	if (static_cast<size_t>(j) != string::npos) {
376	+	foundVersion = true;
377	+	mdRawData += version;
378	+	} else {
379	+	mdRawData += buffer;
380	+	}
381	+	mdRawData += "\n";
382	+	}
383	+
384	+	if (!foundVersion) mdRawData += version + "\n";
385	+
386	+	mdFile_.close();
387	+
388	+	#ifdef IS_MPI
389	+	}
390	+	#endif
391	+
392	+	std::stringstream rawMetaDataStream(mdRawData);
393	+
394		//parse meta-data file
395	<	Globals* simParams = parseFile(mdFileName);
395	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
396	>	metaDataBlockStart + 1);
397
398		//create the force field
399	<	ForceField * ff = ForceFieldFactory::getInstance()
400	<	->createForceField(simParams->getForceField());
194	<
399	>	ForceField * ff = new ForceField(simParams->getForceField());
400	>
401		if (ff == NULL) {
402		sprintf(painCave.errMsg,
403		"ForceField Factory can not create %s force field\n",
#	Line 224 | Line 430 | Globals* SimCreator::parseFile(const std::string mdFil
430		}
431
432		ff->parse(forcefieldFileName);
227	–	ff->setFortranForceOptions();
433		//create SimInfo
434		SimInfo * info = new SimInfo(ff, simParams);
435	+
436	+	info->setRawMetaData(mdRawData);
437
438	<	//gather parameters (SimCreator only retrieves part of the parameters)
438	>	//gather parameters (SimCreator only retrieves part of the
439	>	//parameters)
440		gatherParameters(info, mdFileName);
441
442		//divide the molecules and determine the global index of molecules
#	Line 239 | Line 447 | Globals* SimCreator::parseFile(const std::string mdFil
447		//create the molecules
448		createMolecules(info);
449
450	+	//find the storage layout
451	+
452	+	int storageLayout = computeStorageLayout(info);
453	+
454	+	//allocate memory for DataStorage(circular reference, need to
455	+	//break it)
456	+	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
457
458	<	//allocate memory for DataStorage(circular reference, need to break it)
459	<	info->setSnapshotManager(new SimSnapshotManager(info));
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
248	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
458	>	//set the global index of atoms, rigidbodies and cutoffgroups
459	>	//(only need to be set once, the global index will never change
460	>	//again). Local indices of atoms and rigidbodies are already set
461	>	//by MoleculeCreator class which actually delegates the
462	>	//responsibility to LocalIndexManager.
463		setGlobalIndex(info);
464
465	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
466	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
467	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
468	<	//we can determine the beginning global indices of atoms before they get created.
465	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
466	>	//method, at that point atoms don't have the global index yet
467	>	//(their global index are all initialized to -1).  Therefore we
468	>	//have to call addInteractionPairs explicitly here. A way to work
469	>	//around is that we can determine the beginning global indices of
470	>	//atoms before they get created.
471		SimInfo::MoleculeIterator mi;
472		Molecule* mol;
473		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
474	<	info->addExcludePairs(mol);
474	>	info->addInteractionPairs(mol);
475		}
476
477		if (loadInitCoords)
478	<	loadCoordinates(info);
263	<
478	>	loadCoordinates(info, mdFileName);
479		return info;
480		}
481
#	Line 295 | Line 510 | Globals* SimCreator::parseFile(const std::string mdFil
510
511		#ifdef IS_MPI
512		void SimCreator::divideMolecules(SimInfo *info) {
513	<	double numerator;
514	<	double denominator;
515	<	double precast;
516	<	double x;
517	<	double y;
518	<	double a;
513	>	RealType numerator;
514	>	RealType denominator;
515	>	RealType precast;
516	>	RealType x;
517	>	RealType y;
518	>	RealType a;
519		int old_atoms;
520		int add_atoms;
521		int new_atoms;
522		int nTarget;
523		int done;
524		int i;
310	–	int j;
525		int loops;
526		int which_proc;
527		int nProcessors;
#	Line 315 | Line 529 | Globals* SimCreator::parseFile(const std::string mdFil
529		int nGlobalMols = info->getNGlobalMolecules();
530		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
531
532	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
532	>	nProcessors = MPI::COMM_WORLD.Get_size();
533
534		if (nProcessors > nGlobalMols) {
535		sprintf(painCave.errMsg,
#	Line 324 | Line 538 | Globals* SimCreator::parseFile(const std::string mdFil
538		"\tthe number of molecules.  This will not result in a \n"
539		"\tusable division of atoms for force decomposition.\n"
540		"\tEither try a smaller number of processors, or run the\n"
541	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
541	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
542
543		painCave.isFatal = 1;
544		simError();
#	Line 353 | Line 567 | Globals* SimCreator::parseFile(const std::string mdFil
567		nTarget = (int)(precast + 0.5);
568
569		for(i = 0; i < nGlobalMols; i++) {
570	+
571		done = 0;
572		loops = 0;
573
#	Line 377 | Line 592 | Globals* SimCreator::parseFile(const std::string mdFil
592		// and be done with it.
593
594		if (loops > 100) {
595	+
596		sprintf(painCave.errMsg,
597	<	"I've tried 100 times to assign molecule %d to a "
598	<	" processor, but can't find a good spot.\n"
599	<	"I'm assigning it at random to processor %d.\n",
597	>	"There have been 100 attempts to assign molecule %d to an\n"
598	>	"\tunderworked processor, but there's no good place to\n"
599	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
600		i, which_proc);
601	<
601	>
602		painCave.isFatal = 0;
603	+	painCave.severity = OPENMD_INFO;
604		simError();
605
606		molToProcMap[i] = which_proc;
#	Line 412 | Line 629 | Globals* SimCreator::parseFile(const std::string mdFil
629		//           Pacc(x) = exp(- a * x)
630		// where a = penalty / (average atoms per molecule)
631
632	<	x = (double)(new_atoms - nTarget);
632	>	x = (RealType)(new_atoms - nTarget);
633		y = myRandom->rand();
634
635		if (y < exp(- a * x)) {
#	Line 428 | Line 645 | Globals* SimCreator::parseFile(const std::string mdFil
645		}
646
647		delete myRandom;
648	<
648	>
649		// Spray out this nonsense to all other processors:
650	<
434	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
650	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
651		} else {
652
653		// Listen to your marching orders from processor 0:
654	<
655	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
654	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
655	>
656		}
657
658		info->setMolToProcMap(molToProcMap);
659		sprintf(checkPointMsg,
660		"Successfully divided the molecules among the processors.\n");
661	<	MPIcheckPoint();
661	>	errorCheckPoint();
662		}
663
664		#endif
#	Line 459 | Line 675 | Globals* SimCreator::parseFile(const std::string mdFil
675		#endif
676
677		stampId = info->getMoleculeStampId(i);
678	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
679	<	stampId, i, info->getLocalIndexManager());
678	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
679	>	info->getMoleculeStamp(stampId),
680	>	stampId, i,
681	>	info->getLocalIndexManager());
682
683		info->addMolecule(mol);
684
#	Line 472 | Line 690 | Globals* SimCreator::parseFile(const std::string mdFil
690
691		} //end for(int i=0)
692		}
693	+
694	+	int SimCreator::computeStorageLayout(SimInfo* info) {
695	+
696	+	Globals* simParams = info->getSimParams();
697	+	int nRigidBodies = info->getNGlobalRigidBodies();
698	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
699	+	set<AtomType*>::iterator i;
700	+	bool hasDirectionalAtoms = false;
701	+	bool hasFixedCharge = false;
702	+	bool hasDipoles = false;
703	+	bool hasQuadrupoles = false;
704	+	bool hasPolarizable = false;
705	+	bool hasFluctuatingCharge = false;
706	+	bool hasMetallic = false;
707	+	int storageLayout = 0;
708	+	storageLayout |= DataStorage::dslPosition;
709	+	storageLayout |= DataStorage::dslVelocity;
710	+	storageLayout |= DataStorage::dslForce;
711	+
712	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
713	+
714	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
715	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
716	+	EAMAdapter ea = EAMAdapter( (*i) );
717	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
718	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
719	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
720	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
721	+
722	+	if (da.isDirectional()){
723	+	hasDirectionalAtoms = true;
724	+	}
725	+	if (ma.isDipole()){
726	+	hasDipoles = true;
727	+	}
728	+	if (ma.isQuadrupole()){
729	+	hasQuadrupoles = true;
730	+	}
731	+	if (ea.isEAM() || sca.isSuttonChen()){
732	+	hasMetallic = true;
733	+	}
734	+	if ( fca.isFixedCharge() ){
735	+	hasFixedCharge = true;
736	+	}
737	+	if ( fqa.isFluctuatingCharge() ){
738	+	hasFluctuatingCharge = true;
739	+	}
740	+	if ( pa.isPolarizable() ){
741	+	hasPolarizable = true;
742	+	}
743	+	}
744
745	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
746	+	storageLayout |= DataStorage::dslAmat;
747	+	if(storageLayout & DataStorage::dslVelocity) {
748	+	storageLayout |= DataStorage::dslAngularMomentum;
749	+	}
750	+	if (storageLayout & DataStorage::dslForce) {
751	+	storageLayout |= DataStorage::dslTorque;
752	+	}
753	+	}
754	+	if (hasDipoles) {
755	+	storageLayout |= DataStorage::dslDipole;
756	+	}
757	+	if (hasQuadrupoles) {
758	+	storageLayout |= DataStorage::dslQuadrupole;
759	+	}
760	+	if (hasFixedCharge || hasFluctuatingCharge) {
761	+	storageLayout |= DataStorage::dslSkippedCharge;
762	+	}
763	+	if (hasMetallic) {
764	+	storageLayout |= DataStorage::dslDensity;
765	+	storageLayout |= DataStorage::dslFunctional;
766	+	storageLayout |= DataStorage::dslFunctionalDerivative;
767	+	}
768	+	if (hasPolarizable) {
769	+	storageLayout |= DataStorage::dslElectricField;
770	+	}
771	+	if (hasFluctuatingCharge){
772	+	storageLayout |= DataStorage::dslFlucQPosition;
773	+	if(storageLayout & DataStorage::dslVelocity) {
774	+	storageLayout |= DataStorage::dslFlucQVelocity;
775	+	}
776	+	if (storageLayout & DataStorage::dslForce) {
777	+	storageLayout |= DataStorage::dslFlucQForce;
778	+	}
779	+	}
780	+
781	+	// if the user has asked for them, make sure we've got the memory for the
782	+	// objects defined.
783	+
784	+	if (simParams->getOutputParticlePotential()) {
785	+	storageLayout |= DataStorage::dslParticlePot;
786	+	}
787	+
788	+	if (simParams->havePrintHeatFlux()) {
789	+	if (simParams->getPrintHeatFlux()) {
790	+	storageLayout |= DataStorage::dslParticlePot;
791	+	}
792	+	}
793	+
794	+	if (simParams->getOutputElectricField()) {
795	+	storageLayout |= DataStorage::dslElectricField;
796	+	}
797	+
798	+	if (simParams->getOutputFluctuatingCharges()) {
799	+	storageLayout |= DataStorage::dslFlucQPosition;
800	+	storageLayout |= DataStorage::dslFlucQVelocity;
801	+	storageLayout |= DataStorage::dslFlucQForce;
802	+	}
803	+
804	+	info->setStorageLayout(storageLayout);
805	+
806	+	return storageLayout;
807	+	}
808	+
809		void SimCreator::setGlobalIndex(SimInfo *info) {
810		SimInfo::MoleculeIterator mi;
811		Molecule::AtomIterator ai;
812		Molecule::RigidBodyIterator ri;
813		Molecule::CutoffGroupIterator ci;
814	+	Molecule::IntegrableObjectIterator  ioi;
815		Molecule * mol;
816		Atom * atom;
817		RigidBody * rb;
#	Line 486 | Line 820 | Globals* SimCreator::parseFile(const std::string mdFil
820		int beginRigidBodyIndex;
821		int beginCutoffGroupIndex;
822		int nGlobalAtoms = info->getNGlobalAtoms();
823	<
490	<	#ifndef IS_MPI
823	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
824
825		beginAtomIndex = 0;
493	–	beginRigidBodyIndex = 0;
494	–	beginCutoffGroupIndex = 0;
495	–
496	–	#else
497	–
498	–	int nproc;
499	–	int myNode;
500	–
501	–	myNode = worldRank;
502	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
503	–
504	–	std::vector < int > tmpAtomsInProc(nproc, 0);
505	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
506	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
507	–	std::vector < int > NumAtomsInProc(nproc, 0);
508	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
509	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
510	–
511	–	tmpAtomsInProc[myNode] = info->getNAtoms();
512	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
513	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
514	–
515	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
516	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
517	–	MPI_SUM, MPI_COMM_WORLD);
518	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
519	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
520	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
521	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
522	–
523	–	beginAtomIndex = 0;
524	–	beginRigidBodyIndex = 0;
525	–	beginCutoffGroupIndex = 0;
526	–
527	–	for(int i = 0; i < myNode; i++) {
528	–	beginAtomIndex += NumAtomsInProc[i];
529	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
530	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
531	–	}
532	–
533	–	#endif
534	–
826		//rigidbody's index begins right after atom's
827	<	beginRigidBodyIndex += info->getNGlobalAtoms();
828	<
829	<	for(mol = info->beginMolecule(mi); mol != NULL;
830	<	mol = info->nextMolecule(mi)) {
827	>	beginRigidBodyIndex = info->getNGlobalAtoms();
828	>	beginCutoffGroupIndex = 0;
829	>
830	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
831
832	<	//local index(index in DataStorge) of atom is important
833	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
834	<	atom->setGlobalIndex(beginAtomIndex++);
832	>	#ifdef IS_MPI
833	>	if (info->getMolToProc(i) == worldRank) {
834	>	#endif
835	>	// stuff to do if I own this molecule
836	>	mol = info->getMoleculeByGlobalIndex(i);
837	>
838	>	//local index(index in DataStorge) of atom is important
839	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
840	>	atom->setGlobalIndex(beginAtomIndex++);
841	>	}
842	>
843	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
844	>	rb = mol->nextRigidBody(ri)) {
845	>	rb->setGlobalIndex(beginRigidBodyIndex++);
846	>	}
847	>
848	>	//local index of cutoff group is trivial, it only depends on
849	>	//the order of travesing
850	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
851	>	cg = mol->nextCutoffGroup(ci)) {
852	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
853	>	}
854	>
855	>	#ifdef IS_MPI
856	>	}  else {
857	>
858	>	// stuff to do if I don't own this molecule
859	>
860	>	int stampId = info->getMoleculeStampId(i);
861	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
862	>
863	>	beginAtomIndex += stamp->getNAtoms();
864	>	beginRigidBodyIndex += stamp->getNRigidBodies();
865	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
866		}
867	<
868	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
869	<	rb = mol->nextRigidBody(ri)) {
870	<	rb->setGlobalIndex(beginRigidBodyIndex++);
549	<	}
550	<
551	<	//local index of cutoff group is trivial, it only depends on the order of travesing
552	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
553	<	cg = mol->nextCutoffGroup(ci)) {
554	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
555	<	}
556	<	}
557	<
867	>	#endif
868	>
869	>	} //end for(int i=0)
870	>
871		//fill globalGroupMembership
872		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
873		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
#	Line 566 | Line 879 | Globals* SimCreator::parseFile(const std::string mdFil
879
880		}
881		}
882	<
882	>
883		#ifdef IS_MPI
884		// Since the globalGroupMembership has been zero filled and we've only
885		// poked values into the atoms we know, we can do an Allreduce
886		// to get the full globalGroupMembership array (We think).
887		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
888		// docs said we could.
889	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
890	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
891	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
889	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
890	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
891	>	&tmpGroupMembership[0], nGlobalAtoms,
892	>	MPI::INT, MPI::SUM);
893		info->setGlobalGroupMembership(tmpGroupMembership);
894		#else
895		info->setGlobalGroupMembership(globalGroupMembership);
896		#endif
897
898		//fill molMembership
899	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
899	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
900	>	info->getNGlobalRigidBodies(), 0);
901
902	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
903	<
902	>	for(mol = info->beginMolecule(mi); mol != NULL;
903	>	mol = info->nextMolecule(mi)) {
904		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
905		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
906		}
907	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
908	+	rb = mol->nextRigidBody(ri)) {
909	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
910	+	}
911		}
912
913		#ifdef IS_MPI
914	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
914	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
915	>	info->getNGlobalRigidBodies(), 0);
916	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
917	>	nGlobalAtoms + nGlobalRigidBodies,
918	>	MPI::INT, MPI::SUM);
919
597	–	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
598	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
599	–
920		info->setGlobalMolMembership(tmpMolMembership);
921		#else
922		info->setGlobalMolMembership(globalMolMembership);
923		#endif
924	+
925	+	// nIOPerMol holds the number of integrable objects per molecule
926	+	// here the molecules are listed by their global indices.
927	+
928	+	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
929	+	for (mol = info->beginMolecule(mi); mol != NULL;
930	+	mol = info->nextMolecule(mi)) {
931	+	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
932	+	}
933
934	<	}
935	<
936	<	void SimCreator::loadCoordinates(SimInfo* info) {
937	<	Globals* simParams;
938	<	simParams = info->getSimParams();
934	>	#ifdef IS_MPI
935	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
936	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
937	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
938	>	#else
939	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
940	>	#endif
941	>
942	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
943
944	<	if (!simParams->haveInitialConfig()) {
945	<	sprintf(painCave.errMsg,
946	<	"Cannot intialize a simulation without an initial configuration file.\n");
947	<	painCave.isFatal = 1;;
615	<	simError();
944	>	int startingIndex = 0;
945	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
946	>	startingIOIndexForMol[i] = startingIndex;
947	>	startingIndex += numIntegrableObjectsPerMol[i];
948		}
949
950	<	DumpReader reader(info, simParams->getInitialConfig());
950	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
951	>	for (mol = info->beginMolecule(mi); mol != NULL;
952	>	mol = info->nextMolecule(mi)) {
953	>	int myGlobalIndex = mol->getGlobalIndex();
954	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
955	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
956	>	sd = mol->nextIntegrableObject(ioi)) {
957	>	sd->setGlobalIntegrableObjectIndex(globalIO);
958	>	IOIndexToIntegrableObject[globalIO] = sd;
959	>	globalIO++;
960	>	}
961	>	}
962	>
963	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
964	>
965	>	}
966	>
967	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
968	>
969	>	DumpReader reader(info, mdFileName);
970		int nframes = reader.getNFrames();
971
972		if (nframes > 0) {
#	Line 624 | Line 975 | Globals* SimCreator::parseFile(const std::string mdFil
975		//invalid initial coordinate file
976		sprintf(painCave.errMsg,
977		"Initial configuration file %s should at least contain one frame\n",
978	<	simParams->getInitialConfig().c_str());
978	>	mdFileName.c_str());
979		painCave.isFatal = 1;
980		simError();
981		}
631	–
982		//copy the current snapshot to previous snapshot
983		info->getSnapshotManager()->advance();
984		}
985
986	<	} //end namespace oopse
986	>	} //end namespace OpenMD
987
988

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 832 by tim, Fri Dec 30 15:32:55 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1838 by gezelter, Tue Jan 22 16:20:11 2013 UTC

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

Diff Legend

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