# | Line 1 | Line 1 | |
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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 47 | Line 47 | |
47 | * @version 1.0 | |
48 | */ | |
49 | ||
50 | < | #include <sprng.h> |
50 | > | #include <iostream> |
51 | > | #include <sstream> |
52 | > | #include <string> |
53 | ||
54 | #include "brains/MoleculeCreator.hpp" | |
55 | #include "brains/SimCreator.hpp" | |
56 | #include "brains/SimSnapshotManager.hpp" | |
57 | #include "io/DumpReader.hpp" | |
56 | – | #include "io/parse_me.h" |
58 | #include "UseTheForce/ForceFieldFactory.hpp" | |
59 | #include "utils/simError.h" | |
60 | #include "utils/StringUtils.hpp" | |
61 | < | #ifdef IS_MPI |
62 | < | #include "io/mpiBASS.h" |
63 | < | #include "math/randomSPRNG.hpp" |
64 | < | #endif |
61 | > | #include "math/SeqRandNumGen.hpp" |
62 | > | #include "mdParser/MDLexer.hpp" |
63 | > | #include "mdParser/MDParser.hpp" |
64 | > | #include "mdParser/MDTreeParser.hpp" |
65 | > | #include "mdParser/SimplePreprocessor.hpp" |
66 | ||
65 | – | namespace oopse { |
67 | ||
67 | – | void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
68 | – | |
68 | #ifdef IS_MPI | |
69 | < | |
71 | < | if (worldRank == 0) { |
72 | < | #endif // is_mpi |
73 | < | |
74 | < | simParams->initalize(); |
75 | < | set_interface_stamps(stamps, simParams); |
76 | < | |
77 | < | #ifdef IS_MPI |
78 | < | |
79 | < | mpiEventInit(); |
80 | < | |
69 | > | #include "math/ParallelRandNumGen.hpp" |
70 | #endif | |
71 | ||
72 | < | yacc_BASS(mdFileName.c_str()); |
72 | > | namespace oopse { |
73 | > | |
74 | > | Globals* SimCreator::parseFile(const std::string mdFileName){ |
75 | > | Globals* simParams = NULL; |
76 | > | try { |
77 | ||
78 | < | #ifdef IS_MPI |
78 | > | // Create a preprocessor that preprocesses md file into an ostringstream |
79 | > | std::stringstream ppStream; |
80 | > | #ifdef IS_MPI |
81 | > | int streamSize; |
82 | > | const int masterNode = 0; |
83 | > | int commStatus; |
84 | > | if (worldRank == masterNode) { |
85 | > | #endif |
86 | > | |
87 | > | SimplePreprocessor preprocessor; |
88 | > | preprocessor.preprocess(mdFileName, ppStream); |
89 | > | |
90 | > | #ifdef IS_MPI |
91 | > | //brocasting the stream size |
92 | > | streamSize = ppStream.str().size() +1; |
93 | > | commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
94 | ||
95 | < | throwMPIEvent(NULL); |
96 | < | } else { |
97 | < | set_interface_stamps(stamps, simParams); |
98 | < | mpiEventInit(); |
99 | < | MPIcheckPoint(); |
100 | < | mpiEventLoop(); |
101 | < | } |
95 | > | commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
96 | > | |
97 | > | |
98 | > | } else { |
99 | > | //get stream size |
100 | > | commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
101 | > | |
102 | > | char* buf = new char[streamSize]; |
103 | > | assert(buf); |
104 | > | |
105 | > | //receive file content |
106 | > | commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
107 | > | |
108 | > | ppStream.str(buf); |
109 | > | delete buf; |
110 | ||
111 | < | #endif |
111 | > | } |
112 | > | #endif |
113 | > | // Create a scanner that reads from the input stream |
114 | > | MDLexer lexer(ppStream); |
115 | > | lexer.setFilename(mdFileName); |
116 | > | lexer.initDeferredLineCount(); |
117 | > | |
118 | > | // Create a parser that reads from the scanner |
119 | > | MDParser parser(lexer); |
120 | > | parser.setFilename(mdFileName); |
121 | ||
122 | < | } |
123 | < | |
124 | < | SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
122 | > | // Create an observer that synchorizes file name change |
123 | > | FilenameObserver observer; |
124 | > | observer.setLexer(&lexer); |
125 | > | observer.setParser(&parser); |
126 | > | lexer.setObserver(&observer); |
127 | ||
128 | < | MakeStamps * stamps = new MakeStamps(); |
128 | > | antlr::ASTFactory factory; |
129 | > | parser.initializeASTFactory(factory); |
130 | > | parser.setASTFactory(&factory); |
131 | > | parser.mdfile(); |
132 | ||
133 | < | Globals * simParams = new Globals(); |
133 | > | // Create a tree parser that reads information into Globals |
134 | > | MDTreeParser treeParser; |
135 | > | treeParser.initializeASTFactory(factory); |
136 | > | treeParser.setASTFactory(&factory); |
137 | > | simParams = treeParser.walkTree(parser.getAST()); |
138 | ||
139 | < | //parse meta-data file |
140 | < | parseFile(mdFileName, stamps, simParams); |
139 | > | } |
140 | > | catch (exception& e) { |
141 | > | cerr << "parser exception: " << e.what() << endl; |
142 | > | } |
143 | ||
144 | + | return simParams; |
145 | + | } |
146 | + | |
147 | + | SimInfo* SimCreator::createSim(const std::string & mdFileName, |
148 | + | bool loadInitCoords) { |
149 | + | |
150 | + | //parse meta-data file |
151 | + | Globals* simParams = parseFile(mdFileName); |
152 | + | |
153 | //create the force field | |
154 | < | ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
155 | < | simParams->getForceField()); |
154 | > | ForceField * ff = ForceFieldFactory::getInstance() |
155 | > | ->createForceField(simParams->getForceField()); |
156 | ||
157 | if (ff == NULL) { | |
158 | < | sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
159 | < | simParams->getForceField()); |
160 | < | painCave.isFatal = 1; |
161 | < | simError(); |
158 | > | sprintf(painCave.errMsg, |
159 | > | "ForceField Factory can not create %s force field\n", |
160 | > | simParams->getForceField().c_str()); |
161 | > | painCave.isFatal = 1; |
162 | > | simError(); |
163 | } | |
164 | < | |
164 | > | |
165 | if (simParams->haveForceFieldFileName()) { | |
166 | < | ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
166 | > | ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
167 | } | |
168 | ||
169 | std::string forcefieldFileName; | |
170 | forcefieldFileName = ff->getForceFieldFileName(); | |
171 | < | |
171 | > | |
172 | if (simParams->haveForceFieldVariant()) { | |
173 | < | //If the force field has variant, the variant force field name will be |
174 | < | //Base.variant.frc. For exampel EAM.u6.frc |
175 | < | |
176 | < | std::string variant = simParams->getForceFieldVariant(); |
177 | < | |
178 | < | std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
179 | < | variant = "." + variant; |
180 | < | if (pos != std::string::npos) { |
181 | < | forcefieldFileName.insert(pos, variant); |
182 | < | } else { |
183 | < | //If the default force field file name does not containt .frc suffix, just append the .variant |
184 | < | forcefieldFileName.append(variant); |
185 | < | } |
173 | > | //If the force field has variant, the variant force field name will be |
174 | > | //Base.variant.frc. For exampel EAM.u6.frc |
175 | > | |
176 | > | std::string variant = simParams->getForceFieldVariant(); |
177 | > | |
178 | > | std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
179 | > | variant = "." + variant; |
180 | > | if (pos != std::string::npos) { |
181 | > | forcefieldFileName.insert(pos, variant); |
182 | > | } else { |
183 | > | //If the default force field file name does not containt .frc suffix, just append the .variant |
184 | > | forcefieldFileName.append(variant); |
185 | > | } |
186 | } | |
187 | ||
188 | ff->parse(forcefieldFileName); | |
189 | < | |
144 | < | //extract the molecule stamps |
145 | < | std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
146 | < | compList(stamps, simParams, moleculeStampPairs); |
147 | < | |
189 | > | |
190 | //create SimInfo | |
191 | < | SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
192 | < | |
191 | > | SimInfo * info = new SimInfo(ff, simParams); |
192 | > | |
193 | //gather parameters (SimCreator only retrieves part of the parameters) | |
194 | gatherParameters(info, mdFileName); | |
195 | < | |
195 | > | |
196 | //divide the molecules and determine the global index of molecules | |
197 | #ifdef IS_MPI | |
198 | divideMolecules(info); | |
199 | #endif | |
200 | < | |
200 | > | |
201 | //create the molecules | |
202 | createMolecules(info); | |
203 | < | |
204 | < | |
203 | > | |
204 | > | |
205 | //allocate memory for DataStorage(circular reference, need to break it) | |
206 | info->setSnapshotManager(new SimSnapshotManager(info)); | |
207 | ||
# | Line 167 | Line 209 | SimInfo* SimCreator::createSim(const std::string & md | |
209 | //global index will never change again). Local indices of atoms and rigidbodies are already set by | |
210 | //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. | |
211 | setGlobalIndex(info); | |
212 | < | |
212 | > | |
213 | //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point | |
214 | //atoms don't have the global index yet (their global index are all initialized to -1). | |
215 | //Therefore we have to call addExcludePairs explicitly here. A way to work around is that | |
# | Line 175 | Line 217 | SimInfo* SimCreator::createSim(const std::string & md | |
217 | SimInfo::MoleculeIterator mi; | |
218 | Molecule* mol; | |
219 | for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { | |
220 | < | info->addExcludePairs(mol); |
220 | > | info->addExcludePairs(mol); |
221 | } | |
222 | ||
181 | – | |
182 | – | //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
183 | – | //eta, chi for NPT integrator) |
223 | if (loadInitCoords) | |
224 | < | loadCoordinates(info); |
224 | > | loadCoordinates(info); |
225 | ||
226 | return info; | |
227 | < | } |
228 | < | |
229 | < | void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
230 | < | |
231 | < | //setup seed for random number generator |
193 | < | int seedValue; |
194 | < | Globals * simParams = info->getSimParams(); |
195 | < | |
196 | < | if (simParams->haveSeed()) { |
197 | < | seedValue = simParams->getSeed(); |
198 | < | |
199 | < | if (seedValue < 100000000 ) { |
200 | < | sprintf(painCave.errMsg, |
201 | < | "Seed for sprng library should contain at least 9 digits\n" |
202 | < | "OOPSE will generate a seed for user\n"); |
203 | < | |
204 | < | painCave.isFatal = 0; |
205 | < | simError(); |
206 | < | |
207 | < | //using seed generated by system instead of invalid seed set by user |
208 | < | |
209 | < | #ifndef IS_MPI |
210 | < | |
211 | < | seedValue = make_sprng_seed(); |
212 | < | |
213 | < | #else |
214 | < | |
215 | < | if (worldRank == 0) { |
216 | < | seedValue = make_sprng_seed(); |
217 | < | } |
218 | < | |
219 | < | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
220 | < | |
221 | < | #endif |
222 | < | |
223 | < | } //end if (seedValue /1000000000 == 0) |
224 | < | } else { |
225 | < | |
226 | < | #ifndef IS_MPI |
227 | < | |
228 | < | seedValue = make_sprng_seed(); |
229 | < | |
230 | < | #else |
231 | < | |
232 | < | if (worldRank == 0) { |
233 | < | seedValue = make_sprng_seed(); |
234 | < | } |
235 | < | |
236 | < | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
237 | < | |
238 | < | #endif |
239 | < | |
240 | < | } //end of simParams->haveSeed() |
241 | < | |
242 | < | info->setSeed(seedValue); |
243 | < | |
244 | < | |
245 | < | //figure out the ouput file names |
227 | > | } |
228 | > | |
229 | > | void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
230 | > | |
231 | > | //figure out the output file names |
232 | std::string prefix; | |
233 | < | |
233 | > | |
234 | #ifdef IS_MPI | |
235 | < | |
235 | > | |
236 | if (worldRank == 0) { | |
237 | #endif // is_mpi | |
238 | < | |
239 | < | if (simParams->haveFinalConfig()) { |
240 | < | prefix = getPrefix(simParams->getFinalConfig()); |
241 | < | } else { |
242 | < | prefix = getPrefix(mdfile); |
243 | < | } |
244 | < | |
245 | < | info->setFinalConfigFileName(prefix + ".eor"); |
246 | < | info->setDumpFileName(prefix + ".dump"); |
247 | < | info->setStatFileName(prefix + ".stat"); |
248 | < | |
238 | > | Globals * simParams = info->getSimParams(); |
239 | > | if (simParams->haveFinalConfig()) { |
240 | > | prefix = getPrefix(simParams->getFinalConfig()); |
241 | > | } else { |
242 | > | prefix = getPrefix(mdfile); |
243 | > | } |
244 | > | |
245 | > | info->setFinalConfigFileName(prefix + ".eor"); |
246 | > | info->setDumpFileName(prefix + ".dump"); |
247 | > | info->setStatFileName(prefix + ".stat"); |
248 | > | info->setRestFileName(prefix + ".zang"); |
249 | > | |
250 | #ifdef IS_MPI | |
251 | < | |
251 | > | |
252 | } | |
253 | < | |
253 | > | |
254 | #endif | |
255 | < | |
256 | < | } |
257 | < | |
255 | > | |
256 | > | } |
257 | > | |
258 | #ifdef IS_MPI | |
259 | < | void SimCreator::divideMolecules(SimInfo *info) { |
259 | > | void SimCreator::divideMolecules(SimInfo *info) { |
260 | double numerator; | |
261 | double denominator; | |
262 | double precast; | |
# | Line 287 | Line 274 | void SimCreator::divideMolecules(SimInfo *info) { | |
274 | int which_proc; | |
275 | int nProcessors; | |
276 | std::vector<int> atomsPerProc; | |
290 | – | randomSPRNG myRandom(info->getSeed()); |
277 | int nGlobalMols = info->getNGlobalMolecules(); | |
278 | std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: | |
279 | ||
280 | MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); | |
281 | < | |
281 | > | |
282 | if (nProcessors > nGlobalMols) { | |
283 | < | sprintf(painCave.errMsg, |
284 | < | "nProcessors (%d) > nMol (%d)\n" |
285 | < | "\tThe number of processors is larger than\n" |
286 | < | "\tthe number of molecules. This will not result in a \n" |
287 | < | "\tusable division of atoms for force decomposition.\n" |
288 | < | "\tEither try a smaller number of processors, or run the\n" |
289 | < | "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
290 | < | |
291 | < | painCave.isFatal = 1; |
292 | < | simError(); |
283 | > | sprintf(painCave.errMsg, |
284 | > | "nProcessors (%d) > nMol (%d)\n" |
285 | > | "\tThe number of processors is larger than\n" |
286 | > | "\tthe number of molecules. This will not result in a \n" |
287 | > | "\tusable division of atoms for force decomposition.\n" |
288 | > | "\tEither try a smaller number of processors, or run the\n" |
289 | > | "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
290 | > | |
291 | > | painCave.isFatal = 1; |
292 | > | simError(); |
293 | } | |
294 | < | |
294 | > | |
295 | > | int seedValue; |
296 | > | Globals * simParams = info->getSimParams(); |
297 | > | SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
298 | > | if (simParams->haveSeed()) { |
299 | > | seedValue = simParams->getSeed(); |
300 | > | myRandom = new SeqRandNumGen(seedValue); |
301 | > | }else { |
302 | > | myRandom = new SeqRandNumGen(); |
303 | > | } |
304 | > | |
305 | > | |
306 | a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); | |
307 | < | |
307 | > | |
308 | //initialize atomsPerProc | |
309 | atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); | |
310 | < | |
310 | > | |
311 | if (worldRank == 0) { | |
312 | < | numerator = info->getNGlobalAtoms(); |
313 | < | denominator = nProcessors; |
314 | < | precast = numerator / denominator; |
315 | < | nTarget = (int)(precast + 0.5); |
316 | < | |
317 | < | for(i = 0; i < nGlobalMols; i++) { |
318 | < | done = 0; |
319 | < | loops = 0; |
320 | < | |
321 | < | while (!done) { |
322 | < | loops++; |
323 | < | |
324 | < | // Pick a processor at random |
325 | < | |
326 | < | which_proc = (int) (myRandom.getRandom() * nProcessors); |
327 | < | |
328 | < | //get the molecule stamp first |
329 | < | int stampId = info->getMoleculeStampId(i); |
330 | < | MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
331 | < | |
332 | < | // How many atoms does this processor have so far? |
333 | < | old_atoms = atomsPerProc[which_proc]; |
334 | < | add_atoms = moleculeStamp->getNAtoms(); |
335 | < | new_atoms = old_atoms + add_atoms; |
336 | < | |
337 | < | // If we've been through this loop too many times, we need |
338 | < | // to just give up and assign the molecule to this processor |
339 | < | // and be done with it. |
340 | < | |
341 | < | if (loops > 100) { |
342 | < | sprintf(painCave.errMsg, |
343 | < | "I've tried 100 times to assign molecule %d to a " |
344 | < | " processor, but can't find a good spot.\n" |
345 | < | "I'm assigning it at random to processor %d.\n", |
346 | < | i, which_proc); |
347 | < | |
348 | < | painCave.isFatal = 0; |
349 | < | simError(); |
350 | < | |
351 | < | molToProcMap[i] = which_proc; |
352 | < | atomsPerProc[which_proc] += add_atoms; |
353 | < | |
354 | < | done = 1; |
355 | < | continue; |
356 | < | } |
357 | < | |
358 | < | // If we can add this molecule to this processor without sending |
359 | < | // it above nTarget, then go ahead and do it: |
360 | < | |
361 | < | if (new_atoms <= nTarget) { |
362 | < | molToProcMap[i] = which_proc; |
363 | < | atomsPerProc[which_proc] += add_atoms; |
364 | < | |
365 | < | done = 1; |
366 | < | continue; |
367 | < | } |
368 | < | |
369 | < | // The only situation left is when new_atoms > nTarget. We |
370 | < | // want to accept this with some probability that dies off the |
371 | < | // farther we are from nTarget |
372 | < | |
373 | < | // roughly: x = new_atoms - nTarget |
374 | < | // Pacc(x) = exp(- a * x) |
375 | < | // where a = penalty / (average atoms per molecule) |
376 | < | |
377 | < | x = (double)(new_atoms - nTarget); |
378 | < | y = myRandom.getRandom(); |
379 | < | |
380 | < | if (y < exp(- a * x)) { |
381 | < | molToProcMap[i] = which_proc; |
382 | < | atomsPerProc[which_proc] += add_atoms; |
383 | < | |
384 | < | done = 1; |
385 | < | continue; |
386 | < | } else { |
387 | < | continue; |
388 | < | } |
392 | < | } |
312 | > | numerator = info->getNGlobalAtoms(); |
313 | > | denominator = nProcessors; |
314 | > | precast = numerator / denominator; |
315 | > | nTarget = (int)(precast + 0.5); |
316 | > | |
317 | > | for(i = 0; i < nGlobalMols; i++) { |
318 | > | done = 0; |
319 | > | loops = 0; |
320 | > | |
321 | > | while (!done) { |
322 | > | loops++; |
323 | > | |
324 | > | // Pick a processor at random |
325 | > | |
326 | > | which_proc = (int) (myRandom->rand() * nProcessors); |
327 | > | |
328 | > | //get the molecule stamp first |
329 | > | int stampId = info->getMoleculeStampId(i); |
330 | > | MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
331 | > | |
332 | > | // How many atoms does this processor have so far? |
333 | > | old_atoms = atomsPerProc[which_proc]; |
334 | > | add_atoms = moleculeStamp->getNAtoms(); |
335 | > | new_atoms = old_atoms + add_atoms; |
336 | > | |
337 | > | // If we've been through this loop too many times, we need |
338 | > | // to just give up and assign the molecule to this processor |
339 | > | // and be done with it. |
340 | > | |
341 | > | if (loops > 100) { |
342 | > | sprintf(painCave.errMsg, |
343 | > | "I've tried 100 times to assign molecule %d to a " |
344 | > | " processor, but can't find a good spot.\n" |
345 | > | "I'm assigning it at random to processor %d.\n", |
346 | > | i, which_proc); |
347 | > | |
348 | > | painCave.isFatal = 0; |
349 | > | simError(); |
350 | > | |
351 | > | molToProcMap[i] = which_proc; |
352 | > | atomsPerProc[which_proc] += add_atoms; |
353 | > | |
354 | > | done = 1; |
355 | > | continue; |
356 | > | } |
357 | > | |
358 | > | // If we can add this molecule to this processor without sending |
359 | > | // it above nTarget, then go ahead and do it: |
360 | > | |
361 | > | if (new_atoms <= nTarget) { |
362 | > | molToProcMap[i] = which_proc; |
363 | > | atomsPerProc[which_proc] += add_atoms; |
364 | > | |
365 | > | done = 1; |
366 | > | continue; |
367 | > | } |
368 | > | |
369 | > | // The only situation left is when new_atoms > nTarget. We |
370 | > | // want to accept this with some probability that dies off the |
371 | > | // farther we are from nTarget |
372 | > | |
373 | > | // roughly: x = new_atoms - nTarget |
374 | > | // Pacc(x) = exp(- a * x) |
375 | > | // where a = penalty / (average atoms per molecule) |
376 | > | |
377 | > | x = (double)(new_atoms - nTarget); |
378 | > | y = myRandom->rand(); |
379 | > | |
380 | > | if (y < exp(- a * x)) { |
381 | > | molToProcMap[i] = which_proc; |
382 | > | atomsPerProc[which_proc] += add_atoms; |
383 | > | |
384 | > | done = 1; |
385 | > | continue; |
386 | > | } else { |
387 | > | continue; |
388 | > | } |
389 | } | |
390 | < | |
391 | < | // Spray out this nonsense to all other processors: |
392 | < | |
393 | < | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
390 | > | } |
391 | > | |
392 | > | delete myRandom; |
393 | > | |
394 | > | // Spray out this nonsense to all other processors: |
395 | > | |
396 | > | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
397 | } else { | |
398 | < | |
399 | < | // Listen to your marching orders from processor 0: |
400 | < | |
401 | < | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
398 | > | |
399 | > | // Listen to your marching orders from processor 0: |
400 | > | |
401 | > | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
402 | } | |
403 | < | |
403 | > | |
404 | info->setMolToProcMap(molToProcMap); | |
405 | sprintf(checkPointMsg, | |
406 | "Successfully divided the molecules among the processors.\n"); | |
407 | MPIcheckPoint(); | |
408 | < | } |
409 | < | |
408 | > | } |
409 | > | |
410 | #endif | |
411 | < | |
412 | < | void SimCreator::createMolecules(SimInfo *info) { |
411 | > | |
412 | > | void SimCreator::createMolecules(SimInfo *info) { |
413 | MoleculeCreator molCreator; | |
414 | int stampId; | |
415 | < | |
415 | > | |
416 | for(int i = 0; i < info->getNGlobalMolecules(); i++) { | |
417 | < | |
417 | > | |
418 | #ifdef IS_MPI | |
419 | < | |
420 | < | if (info->getMolToProc(i) == worldRank) { |
419 | > | |
420 | > | if (info->getMolToProc(i) == worldRank) { |
421 | #endif | |
422 | < | |
423 | < | stampId = info->getMoleculeStampId(i); |
424 | < | Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
425 | < | stampId, i, info->getLocalIndexManager()); |
426 | < | |
427 | < | info->addMolecule(mol); |
428 | < | |
422 | > | |
423 | > | stampId = info->getMoleculeStampId(i); |
424 | > | Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
425 | > | stampId, i, info->getLocalIndexManager()); |
426 | > | |
427 | > | info->addMolecule(mol); |
428 | > | |
429 | #ifdef IS_MPI | |
430 | < | |
431 | < | } |
432 | < | |
430 | > | |
431 | > | } |
432 | > | |
433 | #endif | |
434 | < | |
434 | > | |
435 | } //end for(int i=0) | |
436 | < | } |
437 | < | |
438 | < | void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
440 | < | std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
441 | < | int i; |
442 | < | char * id; |
443 | < | MoleculeStamp * currentStamp; |
444 | < | Component** the_components = simParams->getComponents(); |
445 | < | int n_components = simParams->getNComponents(); |
446 | < | |
447 | < | if (!simParams->haveNMol()) { |
448 | < | // we don't have the total number of molecules, so we assume it is |
449 | < | // given in each component |
450 | < | |
451 | < | for(i = 0; i < n_components; i++) { |
452 | < | if (!the_components[i]->haveNMol()) { |
453 | < | // we have a problem |
454 | < | sprintf(painCave.errMsg, |
455 | < | "SimCreator Error. No global NMol or component NMol given.\n" |
456 | < | "\tCannot calculate the number of atoms.\n"); |
457 | < | |
458 | < | painCave.isFatal = 1; |
459 | < | simError(); |
460 | < | } |
461 | < | |
462 | < | id = the_components[i]->getType(); |
463 | < | currentStamp = (stamps->extractMolStamp(id))->getStamp(); |
464 | < | |
465 | < | if (currentStamp == NULL) { |
466 | < | sprintf(painCave.errMsg, |
467 | < | "SimCreator error: Component \"%s\" was not found in the " |
468 | < | "list of declared molecules\n", id); |
469 | < | |
470 | < | painCave.isFatal = 1; |
471 | < | simError(); |
472 | < | } |
473 | < | |
474 | < | moleculeStampPairs.push_back( |
475 | < | std::make_pair(currentStamp, the_components[i]->getNMol())); |
476 | < | } //end for (i = 0; i < n_components; i++) |
477 | < | } else { |
478 | < | sprintf(painCave.errMsg, "SimSetup error.\n" |
479 | < | "\tSorry, the ability to specify total" |
480 | < | " nMols and then give molfractions in the components\n" |
481 | < | "\tis not currently supported." |
482 | < | " Please give nMol in the components.\n"); |
483 | < | |
484 | < | painCave.isFatal = 1; |
485 | < | simError(); |
486 | < | } |
487 | < | |
488 | < | #ifdef IS_MPI |
489 | < | |
490 | < | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
491 | < | MPIcheckPoint(); |
492 | < | |
493 | < | #endif // is_mpi |
494 | < | |
495 | < | } |
496 | < | |
497 | < | void SimCreator::setGlobalIndex(SimInfo *info) { |
436 | > | } |
437 | > | |
438 | > | void SimCreator::setGlobalIndex(SimInfo *info) { |
439 | SimInfo::MoleculeIterator mi; | |
440 | Molecule::AtomIterator ai; | |
441 | Molecule::RigidBodyIterator ri; | |
# | Line 509 | Line 450 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
450 | int nGlobalAtoms = info->getNGlobalAtoms(); | |
451 | ||
452 | #ifndef IS_MPI | |
453 | < | |
453 | > | |
454 | beginAtomIndex = 0; | |
455 | beginRigidBodyIndex = 0; | |
456 | beginCutoffGroupIndex = 0; | |
457 | < | |
457 | > | |
458 | #else | |
459 | < | |
459 | > | |
460 | int nproc; | |
461 | int myNode; | |
462 | < | |
462 | > | |
463 | myNode = worldRank; | |
464 | MPI_Comm_size(MPI_COMM_WORLD, &nproc); | |
465 | < | |
465 | > | |
466 | std::vector < int > tmpAtomsInProc(nproc, 0); | |
467 | std::vector < int > tmpRigidBodiesInProc(nproc, 0); | |
468 | std::vector < int > tmpCutoffGroupsInProc(nproc, 0); | |
469 | std::vector < int > NumAtomsInProc(nproc, 0); | |
470 | std::vector < int > NumRigidBodiesInProc(nproc, 0); | |
471 | std::vector < int > NumCutoffGroupsInProc(nproc, 0); | |
472 | < | |
472 | > | |
473 | tmpAtomsInProc[myNode] = info->getNAtoms(); | |
474 | tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); | |
475 | tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); | |
476 | < | |
476 | > | |
477 | //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups | |
478 | MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, | |
479 | MPI_SUM, MPI_COMM_WORLD); | |
# | Line 540 | Line 481 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
481 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
482 | MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, | |
483 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
484 | < | |
484 | > | |
485 | beginAtomIndex = 0; | |
486 | beginRigidBodyIndex = 0; | |
487 | beginCutoffGroupIndex = 0; | |
488 | < | |
488 | > | |
489 | for(int i = 0; i < myNode; i++) { | |
490 | < | beginAtomIndex += NumAtomsInProc[i]; |
491 | < | beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
492 | < | beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
490 | > | beginAtomIndex += NumAtomsInProc[i]; |
491 | > | beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
492 | > | beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
493 | } | |
494 | < | |
494 | > | |
495 | > | #endif |
496 | > | |
497 | //rigidbody's index begins right after atom's | |
498 | beginRigidBodyIndex += info->getNGlobalAtoms(); | |
499 | < | #endif |
557 | < | |
499 | > | |
500 | for(mol = info->beginMolecule(mi); mol != NULL; | |
501 | mol = info->nextMolecule(mi)) { | |
502 | < | |
503 | < | //local index(index in DataStorge) of atom is important |
504 | < | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
505 | < | atom->setGlobalIndex(beginAtomIndex++); |
506 | < | } |
507 | < | |
508 | < | for(rb = mol->beginRigidBody(ri); rb != NULL; |
509 | < | rb = mol->nextRigidBody(ri)) { |
510 | < | rb->setGlobalIndex(beginRigidBodyIndex++); |
511 | < | } |
512 | < | |
513 | < | //local index of cutoff group is trivial, it only depends on the order of travesing |
514 | < | for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
515 | < | cg = mol->nextCutoffGroup(ci)) { |
516 | < | cg->setGlobalIndex(beginCutoffGroupIndex++); |
517 | < | } |
502 | > | |
503 | > | //local index(index in DataStorge) of atom is important |
504 | > | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
505 | > | atom->setGlobalIndex(beginAtomIndex++); |
506 | > | } |
507 | > | |
508 | > | for(rb = mol->beginRigidBody(ri); rb != NULL; |
509 | > | rb = mol->nextRigidBody(ri)) { |
510 | > | rb->setGlobalIndex(beginRigidBodyIndex++); |
511 | > | } |
512 | > | |
513 | > | //local index of cutoff group is trivial, it only depends on the order of travesing |
514 | > | for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
515 | > | cg = mol->nextCutoffGroup(ci)) { |
516 | > | cg->setGlobalIndex(beginCutoffGroupIndex++); |
517 | > | } |
518 | } | |
519 | < | |
519 | > | |
520 | //fill globalGroupMembership | |
521 | std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); | |
522 | for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { | |
523 | < | for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
524 | < | |
525 | < | for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
526 | < | globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
527 | < | } |
528 | < | |
529 | < | } |
523 | > | for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
524 | > | |
525 | > | for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
526 | > | globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
527 | > | } |
528 | > | |
529 | > | } |
530 | } | |
531 | < | |
531 | > | |
532 | #ifdef IS_MPI | |
533 | // Since the globalGroupMembership has been zero filled and we've only | |
534 | // poked values into the atoms we know, we can do an Allreduce | |
# | Line 596 | Line 538 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
538 | std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); | |
539 | MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, | |
540 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
541 | < | info->setGlobalGroupMembership(tmpGroupMembership); |
541 | > | info->setGlobalGroupMembership(tmpGroupMembership); |
542 | #else | |
543 | info->setGlobalGroupMembership(globalGroupMembership); | |
544 | #endif | |
545 | < | |
545 | > | |
546 | //fill molMembership | |
547 | std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); | |
548 | ||
549 | for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { | |
550 | < | |
551 | < | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
552 | < | globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
553 | < | } |
550 | > | |
551 | > | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
552 | > | globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
553 | > | } |
554 | } | |
555 | < | |
555 | > | |
556 | #ifdef IS_MPI | |
557 | std::vector<int> tmpMolMembership(nGlobalAtoms, 0); | |
558 | < | |
558 | > | |
559 | MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, | |
560 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
561 | ||
# | Line 621 | Line 563 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
563 | #else | |
564 | info->setGlobalMolMembership(globalMolMembership); | |
565 | #endif | |
566 | < | |
567 | < | } |
568 | < | |
569 | < | void SimCreator::loadCoordinates(SimInfo* info) { |
566 | > | |
567 | > | } |
568 | > | |
569 | > | void SimCreator::loadCoordinates(SimInfo* info) { |
570 | Globals* simParams; | |
571 | simParams = info->getSimParams(); | |
572 | ||
573 | if (!simParams->haveInitialConfig()) { | |
574 | < | sprintf(painCave.errMsg, |
575 | < | "Cannot intialize a simulation without an initial configuration file.\n"); |
576 | < | painCave.isFatal = 1;; |
577 | < | simError(); |
574 | > | sprintf(painCave.errMsg, |
575 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
576 | > | painCave.isFatal = 1;; |
577 | > | simError(); |
578 | } | |
579 | < | |
579 | > | |
580 | DumpReader reader(info, simParams->getInitialConfig()); | |
581 | int nframes = reader.getNFrames(); | |
582 | < | |
582 | > | |
583 | if (nframes > 0) { | |
584 | < | reader.readFrame(nframes - 1); |
584 | > | reader.readFrame(nframes - 1); |
585 | } else { | |
586 | < | //invalid initial coordinate file |
587 | < | sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
588 | < | simParams->getInitialConfig()); |
589 | < | painCave.isFatal = 1; |
590 | < | simError(); |
586 | > | //invalid initial coordinate file |
587 | > | sprintf(painCave.errMsg, |
588 | > | "Initial configuration file %s should at least contain one frame\n", |
589 | > | simParams->getInitialConfig().c_str()); |
590 | > | painCave.isFatal = 1; |
591 | > | simError(); |
592 | } | |
593 | < | |
593 | > | |
594 | //copy the current snapshot to previous snapshot | |
595 | info->getSnapshotManager()->advance(); | |
596 | < | } |
597 | < | |
596 | > | } |
597 | > | |
598 | } //end namespace oopse | |
599 | ||
600 |
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