| 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. |
| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
/** |
| 46 |
|
* @time 13:51am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
< |
|
| 49 |
> |
#include <exception> |
| 50 |
|
#include <iostream> |
| 51 |
|
#include <sstream> |
| 52 |
|
#include <string> |
| 79 |
|
#include "math/ParallelRandNumGen.hpp" |
| 80 |
|
#endif |
| 81 |
|
|
| 82 |
< |
namespace oopse { |
| 82 |
> |
namespace OpenMD { |
| 83 |
|
|
| 84 |
< |
Globals* SimCreator::parseFile(const std::string mdFileName){ |
| 85 |
< |
Globals* simParams = NULL; |
| 86 |
< |
try { |
| 84 |
> |
Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){ |
| 85 |
> |
Globals* simParams = NULL; |
| 86 |
> |
try { |
| 87 |
|
|
| 88 |
< |
// Create a preprocessor that preprocesses md file into an ostringstream |
| 89 |
< |
std::stringstream ppStream; |
| 88 |
> |
// Create a preprocessor that preprocesses md file into an ostringstream |
| 89 |
> |
std::stringstream ppStream; |
| 90 |
|
#ifdef IS_MPI |
| 91 |
< |
int streamSize; |
| 92 |
< |
const int masterNode = 0; |
| 93 |
< |
int commStatus; |
| 94 |
< |
if (worldRank == masterNode) { |
| 91 |
> |
int streamSize; |
| 92 |
> |
const int masterNode = 0; |
| 93 |
> |
int commStatus; |
| 94 |
> |
if (worldRank == masterNode) { |
| 95 |
|
#endif |
| 96 |
|
|
| 97 |
< |
SimplePreprocessor preprocessor; |
| 98 |
< |
preprocessor.preprocess(mdFileName, ppStream); |
| 97 |
> |
SimplePreprocessor preprocessor; |
| 98 |
> |
preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); |
| 99 |
|
|
| 100 |
|
#ifdef IS_MPI |
| 101 |
< |
//brocasting the stream size |
| 102 |
< |
streamSize = ppStream.str().size() +1; |
| 103 |
< |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 101 |
> |
//brocasting the stream size |
| 102 |
> |
streamSize = ppStream.str().size() +1; |
| 103 |
> |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 104 |
|
|
| 105 |
< |
commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 105 |
> |
commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 106 |
|
|
| 107 |
|
|
| 108 |
< |
} else { |
| 109 |
< |
//get stream size |
| 110 |
< |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 108 |
> |
} else { |
| 109 |
> |
//get stream size |
| 110 |
> |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 111 |
> |
|
| 112 |
> |
char* buf = new char[streamSize]; |
| 113 |
> |
assert(buf); |
| 114 |
|
|
| 115 |
< |
char* buf = new char[streamSize]; |
| 116 |
< |
assert(buf); |
| 115 |
> |
//receive file content |
| 116 |
> |
commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 117 |
|
|
| 118 |
< |
//receive file content |
| 119 |
< |
commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 117 |
< |
|
| 118 |
< |
ppStream.str(buf); |
| 119 |
< |
delete buf; |
| 118 |
> |
ppStream.str(buf); |
| 119 |
> |
delete [] buf; |
| 120 |
|
|
| 121 |
< |
} |
| 121 |
> |
} |
| 122 |
|
#endif |
| 123 |
< |
// Create a scanner that reads from the input stream |
| 124 |
< |
MDLexer lexer(ppStream); |
| 125 |
< |
lexer.setFilename(mdFileName); |
| 126 |
< |
lexer.initDeferredLineCount(); |
| 123 |
> |
// Create a scanner that reads from the input stream |
| 124 |
> |
MDLexer lexer(ppStream); |
| 125 |
> |
lexer.setFilename(filename); |
| 126 |
> |
lexer.initDeferredLineCount(); |
| 127 |
|
|
| 128 |
< |
// Create a parser that reads from the scanner |
| 129 |
< |
MDParser parser(lexer); |
| 130 |
< |
parser.setFilename(mdFileName); |
| 128 |
> |
// Create a parser that reads from the scanner |
| 129 |
> |
MDParser parser(lexer); |
| 130 |
> |
parser.setFilename(filename); |
| 131 |
|
|
| 132 |
< |
// Create an observer that synchorizes file name change |
| 133 |
< |
FilenameObserver observer; |
| 134 |
< |
observer.setLexer(&lexer); |
| 135 |
< |
observer.setParser(&parser); |
| 136 |
< |
lexer.setObserver(&observer); |
| 132 |
> |
// Create an observer that synchorizes file name change |
| 133 |
> |
FilenameObserver observer; |
| 134 |
> |
observer.setLexer(&lexer); |
| 135 |
> |
observer.setParser(&parser); |
| 136 |
> |
lexer.setObserver(&observer); |
| 137 |
|
|
| 138 |
< |
antlr::ASTFactory factory; |
| 139 |
< |
parser.initializeASTFactory(factory); |
| 140 |
< |
parser.setASTFactory(&factory); |
| 141 |
< |
parser.mdfile(); |
| 138 |
> |
antlr::ASTFactory factory; |
| 139 |
> |
parser.initializeASTFactory(factory); |
| 140 |
> |
parser.setASTFactory(&factory); |
| 141 |
> |
parser.mdfile(); |
| 142 |
|
|
| 143 |
< |
// Create a tree parser that reads information into Globals |
| 144 |
< |
MDTreeParser treeParser; |
| 145 |
< |
treeParser.initializeASTFactory(factory); |
| 146 |
< |
treeParser.setASTFactory(&factory); |
| 147 |
< |
simParams = treeParser.walkTree(parser.getAST()); |
| 143 |
> |
// Create a tree parser that reads information into Globals |
| 144 |
> |
MDTreeParser treeParser; |
| 145 |
> |
treeParser.initializeASTFactory(factory); |
| 146 |
> |
treeParser.setASTFactory(&factory); |
| 147 |
> |
simParams = treeParser.walkTree(parser.getAST()); |
| 148 |
> |
} |
| 149 |
|
|
| 149 |
– |
} |
| 150 |
|
|
| 151 |
< |
catch(antlr::MismatchedCharException& e) { |
| 152 |
< |
cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
| 153 |
< |
} |
| 154 |
< |
catch(antlr::MismatchedTokenException &e) { |
| 155 |
< |
cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
| 156 |
< |
} |
| 157 |
< |
catch(antlr::NoViableAltForCharException &e) { |
| 158 |
< |
cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
| 159 |
< |
} |
| 160 |
< |
catch(antlr::NoViableAltException &e) { |
| 161 |
< |
cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
| 162 |
< |
} |
| 163 |
< |
catch(antlr::TokenStreamRecognitionException& e) { |
| 164 |
< |
cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
| 165 |
< |
} |
| 166 |
< |
catch(antlr::TokenStreamIOException& e) { |
| 167 |
< |
cerr<< "parser exception: " << e.getMessage() << endl; |
| 168 |
< |
} |
| 169 |
< |
catch(antlr::TokenStreamException& e) { |
| 170 |
< |
cerr<< "parser exception: " << e.getMessage() << endl; |
| 171 |
< |
} |
| 172 |
< |
catch (antlr::RecognitionException& e) { |
| 173 |
< |
cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; |
| 174 |
< |
} |
| 175 |
< |
catch (antlr::CharStreamException& e) { |
| 176 |
< |
cerr << "parser exception: " << e.getMessage() << endl; |
| 177 |
< |
} |
| 178 |
< |
catch (exception& e) { |
| 179 |
< |
cerr << "parser exception: " << e.what() << endl; |
| 180 |
< |
} |
| 151 |
> |
catch(antlr::MismatchedCharException& e) { |
| 152 |
> |
sprintf(painCave.errMsg, |
| 153 |
> |
"parser exception: %s %s:%d:%d\n", |
| 154 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 155 |
> |
painCave.isFatal = 1; |
| 156 |
> |
simError(); |
| 157 |
> |
} |
| 158 |
> |
catch(antlr::MismatchedTokenException &e) { |
| 159 |
> |
sprintf(painCave.errMsg, |
| 160 |
> |
"parser exception: %s %s:%d:%d\n", |
| 161 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 162 |
> |
painCave.isFatal = 1; |
| 163 |
> |
simError(); |
| 164 |
> |
} |
| 165 |
> |
catch(antlr::NoViableAltForCharException &e) { |
| 166 |
> |
sprintf(painCave.errMsg, |
| 167 |
> |
"parser exception: %s %s:%d:%d\n", |
| 168 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 169 |
> |
painCave.isFatal = 1; |
| 170 |
> |
simError(); |
| 171 |
> |
} |
| 172 |
> |
catch(antlr::NoViableAltException &e) { |
| 173 |
> |
sprintf(painCave.errMsg, |
| 174 |
> |
"parser exception: %s %s:%d:%d\n", |
| 175 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 176 |
> |
painCave.isFatal = 1; |
| 177 |
> |
simError(); |
| 178 |
> |
} |
| 179 |
> |
|
| 180 |
> |
catch(antlr::TokenStreamRecognitionException& 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::TokenStreamIOException& e) { |
| 189 |
> |
sprintf(painCave.errMsg, |
| 190 |
> |
"parser exception: %s\n", |
| 191 |
> |
e.getMessage().c_str()); |
| 192 |
> |
painCave.isFatal = 1; |
| 193 |
> |
simError(); |
| 194 |
> |
} |
| 195 |
> |
|
| 196 |
> |
catch(antlr::TokenStreamException& e) { |
| 197 |
> |
sprintf(painCave.errMsg, |
| 198 |
> |
"parser exception: %s\n", |
| 199 |
> |
e.getMessage().c_str()); |
| 200 |
> |
painCave.isFatal = 1; |
| 201 |
> |
simError(); |
| 202 |
> |
} |
| 203 |
> |
catch (antlr::RecognitionException& e) { |
| 204 |
> |
sprintf(painCave.errMsg, |
| 205 |
> |
"parser exception: %s %s:%d:%d\n", |
| 206 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 207 |
> |
painCave.isFatal = 1; |
| 208 |
> |
simError(); |
| 209 |
> |
} |
| 210 |
> |
catch (antlr::CharStreamException& e) { |
| 211 |
> |
sprintf(painCave.errMsg, |
| 212 |
> |
"parser exception: %s\n", |
| 213 |
> |
e.getMessage().c_str()); |
| 214 |
> |
painCave.isFatal = 1; |
| 215 |
> |
simError(); |
| 216 |
> |
} |
| 217 |
> |
catch (OpenMDException& e) { |
| 218 |
> |
sprintf(painCave.errMsg, |
| 219 |
> |
"%s\n", |
| 220 |
> |
e.getMessage().c_str()); |
| 221 |
> |
painCave.isFatal = 1; |
| 222 |
> |
simError(); |
| 223 |
> |
} |
| 224 |
> |
catch (std::exception& e) { |
| 225 |
> |
sprintf(painCave.errMsg, |
| 226 |
> |
"parser exception: %s\n", |
| 227 |
> |
e.what()); |
| 228 |
> |
painCave.isFatal = 1; |
| 229 |
> |
simError(); |
| 230 |
> |
} |
| 231 |
|
|
| 232 |
< |
return simParams; |
| 232 |
> |
return simParams; |
| 233 |
|
} |
| 234 |
|
|
| 235 |
|
SimInfo* SimCreator::createSim(const std::string & mdFileName, |
| 236 |
|
bool loadInitCoords) { |
| 237 |
|
|
| 238 |
+ |
const int bufferSize = 65535; |
| 239 |
+ |
char buffer[bufferSize]; |
| 240 |
+ |
int lineNo = 0; |
| 241 |
+ |
std::string mdRawData; |
| 242 |
+ |
int metaDataBlockStart = -1; |
| 243 |
+ |
int metaDataBlockEnd = -1; |
| 244 |
+ |
int i; |
| 245 |
+ |
int mdOffset; |
| 246 |
+ |
|
| 247 |
+ |
#ifdef IS_MPI |
| 248 |
+ |
const int masterNode = 0; |
| 249 |
+ |
if (worldRank == masterNode) { |
| 250 |
+ |
#endif |
| 251 |
+ |
|
| 252 |
+ |
std::ifstream mdFile_(mdFileName.c_str()); |
| 253 |
+ |
|
| 254 |
+ |
if (mdFile_.fail()) { |
| 255 |
+ |
sprintf(painCave.errMsg, |
| 256 |
+ |
"SimCreator: Cannot open file: %s\n", |
| 257 |
+ |
mdFileName.c_str()); |
| 258 |
+ |
painCave.isFatal = 1; |
| 259 |
+ |
simError(); |
| 260 |
+ |
} |
| 261 |
+ |
|
| 262 |
+ |
mdFile_.getline(buffer, bufferSize); |
| 263 |
+ |
++lineNo; |
| 264 |
+ |
std::string line = trimLeftCopy(buffer); |
| 265 |
+ |
i = CaseInsensitiveFind(line, "<OpenMD"); |
| 266 |
+ |
if (static_cast<size_t>(i) == string::npos) { |
| 267 |
+ |
// try the older file strings to see if that works: |
| 268 |
+ |
i = CaseInsensitiveFind(line, "<OOPSE"); |
| 269 |
+ |
} |
| 270 |
+ |
|
| 271 |
+ |
if (static_cast<size_t>(i) == string::npos) { |
| 272 |
+ |
// still no luck! |
| 273 |
+ |
sprintf(painCave.errMsg, |
| 274 |
+ |
"SimCreator: File: %s is not a valid OpenMD file!\n", |
| 275 |
+ |
mdFileName.c_str()); |
| 276 |
+ |
painCave.isFatal = 1; |
| 277 |
+ |
simError(); |
| 278 |
+ |
} |
| 279 |
+ |
|
| 280 |
+ |
//scan through the input stream and find MetaData tag |
| 281 |
+ |
while(mdFile_.getline(buffer, bufferSize)) { |
| 282 |
+ |
++lineNo; |
| 283 |
+ |
|
| 284 |
+ |
std::string line = trimLeftCopy(buffer); |
| 285 |
+ |
if (metaDataBlockStart == -1) { |
| 286 |
+ |
i = CaseInsensitiveFind(line, "<MetaData>"); |
| 287 |
+ |
if (i != string::npos) { |
| 288 |
+ |
metaDataBlockStart = lineNo; |
| 289 |
+ |
mdOffset = mdFile_.tellg(); |
| 290 |
+ |
} |
| 291 |
+ |
} else { |
| 292 |
+ |
i = CaseInsensitiveFind(line, "</MetaData>"); |
| 293 |
+ |
if (i != string::npos) { |
| 294 |
+ |
metaDataBlockEnd = lineNo; |
| 295 |
+ |
} |
| 296 |
+ |
} |
| 297 |
+ |
} |
| 298 |
+ |
|
| 299 |
+ |
if (metaDataBlockStart == -1) { |
| 300 |
+ |
sprintf(painCave.errMsg, |
| 301 |
+ |
"SimCreator: File: %s did not contain a <MetaData> tag!\n", |
| 302 |
+ |
mdFileName.c_str()); |
| 303 |
+ |
painCave.isFatal = 1; |
| 304 |
+ |
simError(); |
| 305 |
+ |
} |
| 306 |
+ |
if (metaDataBlockEnd == -1) { |
| 307 |
+ |
sprintf(painCave.errMsg, |
| 308 |
+ |
"SimCreator: File: %s did not contain a closed MetaData block!\n", |
| 309 |
+ |
mdFileName.c_str()); |
| 310 |
+ |
painCave.isFatal = 1; |
| 311 |
+ |
simError(); |
| 312 |
+ |
} |
| 313 |
+ |
|
| 314 |
+ |
mdFile_.clear(); |
| 315 |
+ |
mdFile_.seekg(0); |
| 316 |
+ |
mdFile_.seekg(mdOffset); |
| 317 |
+ |
|
| 318 |
+ |
mdRawData.clear(); |
| 319 |
+ |
|
| 320 |
+ |
for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
| 321 |
+ |
mdFile_.getline(buffer, bufferSize); |
| 322 |
+ |
mdRawData += buffer; |
| 323 |
+ |
mdRawData += "\n"; |
| 324 |
+ |
} |
| 325 |
+ |
|
| 326 |
+ |
mdFile_.close(); |
| 327 |
+ |
|
| 328 |
+ |
#ifdef IS_MPI |
| 329 |
+ |
} |
| 330 |
+ |
#endif |
| 331 |
+ |
|
| 332 |
+ |
std::stringstream rawMetaDataStream(mdRawData); |
| 333 |
+ |
|
| 334 |
|
//parse meta-data file |
| 335 |
< |
Globals* simParams = parseFile(mdFileName); |
| 335 |
> |
Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1); |
| 336 |
|
|
| 337 |
|
//create the force field |
| 338 |
< |
ForceField * ff = ForceFieldFactory::getInstance() |
| 339 |
< |
->createForceField(simParams->getForceField()); |
| 194 |
< |
|
| 338 |
> |
ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField()); |
| 339 |
> |
|
| 340 |
|
if (ff == NULL) { |
| 341 |
|
sprintf(painCave.errMsg, |
| 342 |
|
"ForceField Factory can not create %s force field\n", |
| 369 |
|
} |
| 370 |
|
|
| 371 |
|
ff->parse(forcefieldFileName); |
| 372 |
< |
|
| 372 |
> |
ff->setFortranForceOptions(); |
| 373 |
|
//create SimInfo |
| 374 |
|
SimInfo * info = new SimInfo(ff, simParams); |
| 375 |
+ |
|
| 376 |
+ |
info->setRawMetaData(mdRawData); |
| 377 |
|
|
| 378 |
< |
//gather parameters (SimCreator only retrieves part of the parameters) |
| 378 |
> |
//gather parameters (SimCreator only retrieves part of the |
| 379 |
> |
//parameters) |
| 380 |
|
gatherParameters(info, mdFileName); |
| 381 |
|
|
| 382 |
|
//divide the molecules and determine the global index of molecules |
| 388 |
|
createMolecules(info); |
| 389 |
|
|
| 390 |
|
|
| 391 |
< |
//allocate memory for DataStorage(circular reference, need to break it) |
| 391 |
> |
//allocate memory for DataStorage(circular reference, need to |
| 392 |
> |
//break it) |
| 393 |
|
info->setSnapshotManager(new SimSnapshotManager(info)); |
| 394 |
|
|
| 395 |
< |
//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
| 396 |
< |
//global index will never change again). Local indices of atoms and rigidbodies are already set by |
| 397 |
< |
//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
| 395 |
> |
//set the global index of atoms, rigidbodies and cutoffgroups |
| 396 |
> |
//(only need to be set once, the global index will never change |
| 397 |
> |
//again). Local indices of atoms and rigidbodies are already set |
| 398 |
> |
//by MoleculeCreator class which actually delegates the |
| 399 |
> |
//responsibility to LocalIndexManager. |
| 400 |
|
setGlobalIndex(info); |
| 401 |
|
|
| 402 |
< |
//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point |
| 403 |
< |
//atoms don't have the global index yet (their global index are all initialized to -1). |
| 404 |
< |
//Therefore we have to call addExcludePairs explicitly here. A way to work around is that |
| 405 |
< |
//we can determine the beginning global indices of atoms before they get created. |
| 402 |
> |
//Although addInteractionPairs is called inside SimInfo's addMolecule |
| 403 |
> |
//method, at that point atoms don't have the global index yet |
| 404 |
> |
//(their global index are all initialized to -1). Therefore we |
| 405 |
> |
//have to call addInteractionPairs explicitly here. A way to work |
| 406 |
> |
//around is that we can determine the beginning global indices of |
| 407 |
> |
//atoms before they get created. |
| 408 |
|
SimInfo::MoleculeIterator mi; |
| 409 |
|
Molecule* mol; |
| 410 |
|
for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 411 |
< |
info->addExcludePairs(mol); |
| 411 |
> |
info->addInteractionPairs(mol); |
| 412 |
|
} |
| 413 |
|
|
| 414 |
|
if (loadInitCoords) |
| 415 |
< |
loadCoordinates(info); |
| 415 |
> |
loadCoordinates(info, mdFileName); |
| 416 |
|
|
| 417 |
|
return info; |
| 418 |
|
} |
| 448 |
|
|
| 449 |
|
#ifdef IS_MPI |
| 450 |
|
void SimCreator::divideMolecules(SimInfo *info) { |
| 451 |
< |
double numerator; |
| 452 |
< |
double denominator; |
| 453 |
< |
double precast; |
| 454 |
< |
double x; |
| 455 |
< |
double y; |
| 456 |
< |
double a; |
| 451 |
> |
RealType numerator; |
| 452 |
> |
RealType denominator; |
| 453 |
> |
RealType precast; |
| 454 |
> |
RealType x; |
| 455 |
> |
RealType y; |
| 456 |
> |
RealType a; |
| 457 |
|
int old_atoms; |
| 458 |
|
int add_atoms; |
| 459 |
|
int new_atoms; |
| 477 |
|
"\tthe number of molecules. This will not result in a \n" |
| 478 |
|
"\tusable division of atoms for force decomposition.\n" |
| 479 |
|
"\tEither try a smaller number of processors, or run the\n" |
| 480 |
< |
"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
| 480 |
> |
"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
| 481 |
|
|
| 482 |
|
painCave.isFatal = 1; |
| 483 |
|
simError(); |
| 565 |
|
// Pacc(x) = exp(- a * x) |
| 566 |
|
// where a = penalty / (average atoms per molecule) |
| 567 |
|
|
| 568 |
< |
x = (double)(new_atoms - nTarget); |
| 568 |
> |
x = (RealType)(new_atoms - nTarget); |
| 569 |
|
y = myRandom->rand(); |
| 570 |
|
|
| 571 |
|
if (y < exp(- a * x)) { |
| 595 |
|
info->setMolToProcMap(molToProcMap); |
| 596 |
|
sprintf(checkPointMsg, |
| 597 |
|
"Successfully divided the molecules among the processors.\n"); |
| 598 |
< |
MPIcheckPoint(); |
| 598 |
> |
errorCheckPoint(); |
| 599 |
|
} |
| 600 |
|
|
| 601 |
|
#endif |
| 631 |
|
Molecule::AtomIterator ai; |
| 632 |
|
Molecule::RigidBodyIterator ri; |
| 633 |
|
Molecule::CutoffGroupIterator ci; |
| 634 |
+ |
Molecule::IntegrableObjectIterator ioi; |
| 635 |
|
Molecule * mol; |
| 636 |
|
Atom * atom; |
| 637 |
|
RigidBody * rb; |
| 640 |
|
int beginRigidBodyIndex; |
| 641 |
|
int beginCutoffGroupIndex; |
| 642 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 643 |
< |
|
| 643 |
> |
|
| 644 |
> |
/**@todo fixme */ |
| 645 |
|
#ifndef IS_MPI |
| 646 |
|
|
| 647 |
|
beginAtomIndex = 0; |
| 728 |
|
// to get the full globalGroupMembership array (We think). |
| 729 |
|
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 730 |
|
// docs said we could. |
| 731 |
< |
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
| 731 |
> |
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 732 |
|
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 733 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 734 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 740 |
|
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 741 |
|
|
| 742 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 588 |
– |
|
| 743 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 744 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 745 |
|
} |
| 746 |
|
} |
| 747 |
|
|
| 748 |
|
#ifdef IS_MPI |
| 749 |
< |
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
| 749 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 750 |
|
|
| 751 |
|
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 752 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 755 |
|
#else |
| 756 |
|
info->setGlobalMolMembership(globalMolMembership); |
| 757 |
|
#endif |
| 758 |
+ |
|
| 759 |
+ |
// nIOPerMol holds the number of integrable objects per molecule |
| 760 |
+ |
// here the molecules are listed by their global indices. |
| 761 |
+ |
|
| 762 |
+ |
std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
| 763 |
+ |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 764 |
+ |
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
| 765 |
+ |
} |
| 766 |
|
|
| 767 |
+ |
#ifdef IS_MPI |
| 768 |
+ |
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
| 769 |
+ |
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 770 |
+ |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 771 |
+ |
#else |
| 772 |
+ |
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 773 |
+ |
#endif |
| 774 |
+ |
|
| 775 |
+ |
std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules()); |
| 776 |
+ |
|
| 777 |
+ |
int startingIndex = 0; |
| 778 |
+ |
for (int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 779 |
+ |
startingIOIndexForMol[i] = startingIndex; |
| 780 |
+ |
startingIndex += numIntegrableObjectsPerMol[i]; |
| 781 |
+ |
} |
| 782 |
+ |
|
| 783 |
+ |
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 784 |
+ |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 785 |
+ |
int myGlobalIndex = mol->getGlobalIndex(); |
| 786 |
+ |
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 787 |
+ |
for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL; |
| 788 |
+ |
integrableObject = mol->nextIntegrableObject(ioi)) { |
| 789 |
+ |
integrableObject->setGlobalIntegrableObjectIndex(globalIO); |
| 790 |
+ |
IOIndexToIntegrableObject[globalIO] = integrableObject; |
| 791 |
+ |
globalIO++; |
| 792 |
+ |
} |
| 793 |
+ |
} |
| 794 |
+ |
|
| 795 |
+ |
info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); |
| 796 |
+ |
|
| 797 |
|
} |
| 798 |
|
|
| 799 |
< |
void SimCreator::loadCoordinates(SimInfo* info) { |
| 799 |
> |
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 800 |
|
Globals* simParams; |
| 801 |
|
simParams = info->getSimParams(); |
| 802 |
|
|
| 611 |
– |
if (!simParams->haveInitialConfig()) { |
| 612 |
– |
sprintf(painCave.errMsg, |
| 613 |
– |
"Cannot intialize a simulation without an initial configuration file.\n"); |
| 614 |
– |
painCave.isFatal = 1;; |
| 615 |
– |
simError(); |
| 616 |
– |
} |
| 803 |
|
|
| 804 |
< |
DumpReader reader(info, simParams->getInitialConfig()); |
| 804 |
> |
DumpReader reader(info, mdFileName); |
| 805 |
|
int nframes = reader.getNFrames(); |
| 806 |
|
|
| 807 |
|
if (nframes > 0) { |
| 810 |
|
//invalid initial coordinate file |
| 811 |
|
sprintf(painCave.errMsg, |
| 812 |
|
"Initial configuration file %s should at least contain one frame\n", |
| 813 |
< |
simParams->getInitialConfig().c_str()); |
| 813 |
> |
mdFileName.c_str()); |
| 814 |
|
painCave.isFatal = 1; |
| 815 |
|
simError(); |
| 816 |
|
} |
| 819 |
|
info->getSnapshotManager()->advance(); |
| 820 |
|
} |
| 821 |
|
|
| 822 |
< |
} //end namespace oopse |
| 822 |
> |
} //end namespace OpenMD |
| 823 |
|
|
| 824 |
|
|
