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Comparing trunk/OOPSE-2.0/src/brains/SimCreator.cpp (file contents):
Revision 1981 by tim, Mon Feb 7 19:14:26 2005 UTC vs.
Revision 2544 by tim, Wed Jan 11 19:01:20 2006 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 46 | Line 46
46   * @time 13:51am
47   * @version 1.0
48   */
49 + #include <exception>
50 + #include <iostream>
51 + #include <sstream>
52 + #include <string>
53  
50 – #include <sprng.h>
51 –
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 + #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 + #include "antlr/ANTLRException.hpp"
67 + #include "antlr/TokenStreamRecognitionException.hpp"
68 + #include "antlr/TokenStreamIOException.hpp"
69 + #include "antlr/TokenStreamException.hpp"
70 + #include "antlr/RecognitionException.hpp"
71 + #include "antlr/CharStreamException.hpp"
72 +
73 + #include "antlr/MismatchedCharException.hpp"
74 + #include "antlr/MismatchedTokenException.hpp"
75 + #include "antlr/NoViableAltForCharException.hpp"
76 + #include "antlr/NoViableAltException.hpp"
77 +
78   #ifdef IS_MPI
79 < #include "io/mpiBASS.h"
62 < #include "math/randomSPRNG.hpp"
79 > #include "math/ParallelRandNumGen.hpp"
80   #endif
81  
82   namespace oopse {
83 +  
84 + Globals* SimCreator::parseFile(const std::string mdFileName){
85 +        Globals* simParams = NULL;
86 +        try {
87  
88 < void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
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) {
95 > #endif
96 >                
97 >                SimplePreprocessor preprocessor;
98 >                preprocessor.preprocess(mdFileName, 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);                  
104  
105 < #ifdef IS_MPI
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);  
111 >                
112 >                  char* buf = new char[streamSize];
113 >                  assert(buf);
114 >                
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 <    if (worldRank == 0) {
122 < #endif // is_mpi
121 >            }
122 > #endif            
123 >            // Create a scanner that reads from the input stream
124 >            MDLexer lexer(ppStream);
125 >            lexer.setFilename(mdFileName);
126 >            lexer.initDeferredLineCount();
127 >    
128 >            // Create a parser that reads from the scanner
129 >            MDParser parser(lexer);
130 >            parser.setFilename(mdFileName);
131  
132 <        simParams->initalize();
133 <        set_interface_stamps(stamps, simParams);
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();
142  
143 < #ifdef IS_MPI
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 <        mpiEventInit();
149 >        }
150  
151 < #endif
151 >      
152 >      catch(antlr::MismatchedCharException& e) {
153 >          sprintf(painCave.errMsg,
154 >                  "parser exception: %s %s:%d:%d\n",
155 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
156 >          painCave.isFatal = 1;
157 >          simError();          
158 >      }
159 >      catch(antlr::MismatchedTokenException &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::NoViableAltForCharException &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::NoViableAltException &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 >      
181 >        catch(antlr::TokenStreamRecognitionException& e) {
182 >          sprintf(painCave.errMsg,
183 >                  "parser exception: %s %s:%d:%d\n",
184 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
185 >          painCave.isFatal = 1;
186 >          simError();  
187 >        }
188 >        
189 >        catch(antlr::TokenStreamIOException& e) {
190 >          sprintf(painCave.errMsg,
191 >                  "parser exception: %s\n",
192 >                  e.getMessage().c_str());
193 >          painCave.isFatal = 1;
194 >          simError();
195 >        }
196 >        
197 >        catch(antlr::TokenStreamException& e) {
198 >          sprintf(painCave.errMsg,
199 >                  "parser exception: %s\n",
200 >                  e.getMessage().c_str());
201 >          painCave.isFatal = 1;
202 >          simError();
203 >        }        
204 >       catch (antlr::RecognitionException& e) {
205 >          sprintf(painCave.errMsg,
206 >                  "parser exception: %s %s:%d:%d\n",
207 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
208 >          painCave.isFatal = 1;
209 >          simError();          
210 >       }
211 >       catch (antlr::CharStreamException& e) {
212 >          sprintf(painCave.errMsg,
213 >                  "parser exception: %s\n",
214 >                  e.getMessage().c_str());
215 >          painCave.isFatal = 1;
216 >          simError();        
217 >       }
218 >       catch (OOPSEException& e) {
219 >          sprintf(painCave.errMsg,
220 >                  "%s\n",
221 >                  e.getMessage().c_str());
222 >          painCave.isFatal = 1;
223 >          simError();
224 >       }
225 >       catch (std::exception& e) {
226 >          sprintf(painCave.errMsg,
227 >                  "parser exception: %s\n",
228 >                  e.what());
229 >          painCave.isFatal = 1;
230 >          simError();
231 >       }
232  
233 <        yacc_BASS(mdFileName.c_str());
233 >        return simParams;
234 >  }
235 >  
236 >  SimInfo*  SimCreator::createSim(const std::string & mdFileName,
237 >                                  bool loadInitCoords) {
238  
85 – #ifdef IS_MPI
86 –
87 –        throwMPIEvent(NULL);
88 –    } else {
89 –        set_interface_stamps(stamps, simParams);
90 –        mpiEventInit();
91 –        MPIcheckPoint();
92 –        mpiEventLoop();
93 –    }
94 –
95 – #endif
96 –
97 – }
98 –
99 – SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
100 –    
101 –    MakeStamps * stamps = new MakeStamps();
102 –
103 –    Globals * simParams = new Globals();
104 –
239      //parse meta-data file
240 <    parseFile(mdFileName, stamps, simParams);
241 <
240 >    Globals* simParams = parseFile(mdFileName);
241 >    
242      //create the force field
243 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
244 <                          simParams->getForceField());
243 >    ForceField * ff = ForceFieldFactory::getInstance()
244 >      ->createForceField(simParams->getForceField());
245      
246      if (ff == NULL) {
247 <        sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
248 <                simParams->getForceField());
249 <        painCave.isFatal = 1;
250 <        simError();
247 >      sprintf(painCave.errMsg,
248 >              "ForceField Factory can not create %s force field\n",
249 >              simParams->getForceField().c_str());
250 >      painCave.isFatal = 1;
251 >      simError();
252      }
253 <
253 >    
254      if (simParams->haveForceFieldFileName()) {
255 <        ff->setForceFieldFileName(simParams->getForceFieldFileName());
255 >      ff->setForceFieldFileName(simParams->getForceFieldFileName());
256      }
257      
258      std::string forcefieldFileName;
259      forcefieldFileName = ff->getForceFieldFileName();
260 <
260 >    
261      if (simParams->haveForceFieldVariant()) {
262 <        //If the force field has variant, the variant force field name will be
263 <        //Base.variant.frc. For exampel EAM.u6.frc
264 <        
265 <        std::string variant = simParams->getForceFieldVariant();
266 <
267 <        std::string::size_type pos = forcefieldFileName.rfind(".frc");
268 <        variant = "." + variant;
269 <        if (pos != std::string::npos) {
270 <            forcefieldFileName.insert(pos, variant);
271 <        } else {
272 <            //If the default force field file name does not containt .frc suffix, just append the .variant
273 <            forcefieldFileName.append(variant);
274 <        }
262 >      //If the force field has variant, the variant force field name will be
263 >      //Base.variant.frc. For exampel EAM.u6.frc
264 >      
265 >      std::string variant = simParams->getForceFieldVariant();
266 >      
267 >      std::string::size_type pos = forcefieldFileName.rfind(".frc");
268 >      variant = "." + variant;
269 >      if (pos != std::string::npos) {
270 >        forcefieldFileName.insert(pos, variant);
271 >      } else {
272 >        //If the default force field file name does not containt .frc suffix, just append the .variant
273 >        forcefieldFileName.append(variant);
274 >      }
275      }
276      
277      ff->parse(forcefieldFileName);
278 <    
144 <    //extract the molecule stamps
145 <    std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146 <    compList(stamps, simParams, moleculeStampPairs);
147 <
278 >    ff->setFortranForceOptions();
279      //create SimInfo
280 <    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
281 <
280 >    SimInfo * info = new SimInfo(ff, simParams);
281 >    
282      //gather parameters (SimCreator only retrieves part of the parameters)
283      gatherParameters(info, mdFileName);
284 <
284 >    
285      //divide the molecules and determine the global index of molecules
286   #ifdef IS_MPI
287      divideMolecules(info);
288   #endif
289 <
289 >    
290      //create the molecules
291      createMolecules(info);
292 <
293 <
292 >    
293 >    
294      //allocate memory for DataStorage(circular reference, need to break it)
295      info->setSnapshotManager(new SimSnapshotManager(info));
296      
# Line 167 | Line 298 | SimInfo*  SimCreator::createSim(const std::string & md
298      //global index will never change again). Local indices of atoms and rigidbodies are already set by
299      //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
300      setGlobalIndex(info);
301 <
301 >    
302      //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
303      //atoms don't have the global index yet  (their global index are all initialized to -1).
304      //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
# Line 175 | Line 306 | SimInfo*  SimCreator::createSim(const std::string & md
306      SimInfo::MoleculeIterator mi;
307      Molecule* mol;
308      for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
309 <        info->addExcludePairs(mol);
309 >      info->addExcludePairs(mol);
310      }
311      
181 –
182 –    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183 –    //eta, chi for NPT integrator)
312      if (loadInitCoords)
313 <        loadCoordinates(info);    
313 >      loadCoordinates(info);    
314      
315      return info;
316 < }
317 <
318 < void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
319 <
320 <    //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
316 >  }
317 >  
318 >  void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
319 >    
320 >    //figure out the output file names
321      std::string prefix;
322 <
322 >    
323   #ifdef IS_MPI
324 <
324 >    
325      if (worldRank == 0) {
326   #endif // is_mpi
327 <
328 <        if (simParams->haveFinalConfig()) {
329 <            prefix = getPrefix(simParams->getFinalConfig());
330 <        } else {
331 <            prefix = getPrefix(mdfile);
332 <        }
333 <
334 <        info->setFinalConfigFileName(prefix + ".eor");
335 <        info->setDumpFileName(prefix + ".dump");
336 <        info->setStatFileName(prefix + ".stat");
337 <
327 >      Globals * simParams = info->getSimParams();
328 >      if (simParams->haveFinalConfig()) {
329 >        prefix = getPrefix(simParams->getFinalConfig());
330 >      } else {
331 >        prefix = getPrefix(mdfile);
332 >      }
333 >      
334 >      info->setFinalConfigFileName(prefix + ".eor");
335 >      info->setDumpFileName(prefix + ".dump");
336 >      info->setStatFileName(prefix + ".stat");
337 >      info->setRestFileName(prefix + ".zang");
338 >      
339   #ifdef IS_MPI
340 <
340 >      
341      }
342 <
342 >    
343   #endif
344 <
345 < }
346 <
344 >    
345 >  }
346 >  
347   #ifdef IS_MPI
348 < void SimCreator::divideMolecules(SimInfo *info) {
348 >  void SimCreator::divideMolecules(SimInfo *info) {
349      double numerator;
350      double denominator;
351      double precast;
# Line 287 | Line 363 | void SimCreator::divideMolecules(SimInfo *info) {
363      int which_proc;
364      int nProcessors;
365      std::vector<int> atomsPerProc;
290 –    randomSPRNG myRandom(info->getSeed());
366      int nGlobalMols = info->getNGlobalMolecules();
367      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
368      
369      MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
370 <
370 >    
371      if (nProcessors > nGlobalMols) {
372 <        sprintf(painCave.errMsg,
373 <                "nProcessors (%d) > nMol (%d)\n"
374 <                    "\tThe number of processors is larger than\n"
375 <                    "\tthe number of molecules.  This will not result in a \n"
376 <                    "\tusable division of atoms for force decomposition.\n"
377 <                    "\tEither try a smaller number of processors, or run the\n"
378 <                    "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
379 <
380 <        painCave.isFatal = 1;
381 <        simError();
372 >      sprintf(painCave.errMsg,
373 >              "nProcessors (%d) > nMol (%d)\n"
374 >              "\tThe number of processors is larger than\n"
375 >              "\tthe number of molecules.  This will not result in a \n"
376 >              "\tusable division of atoms for force decomposition.\n"
377 >              "\tEither try a smaller number of processors, or run the\n"
378 >              "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
379 >      
380 >      painCave.isFatal = 1;
381 >      simError();
382      }
383 <
383 >    
384 >    int seedValue;
385 >    Globals * simParams = info->getSimParams();
386 >    SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
387 >    if (simParams->haveSeed()) {
388 >      seedValue = simParams->getSeed();
389 >      myRandom = new SeqRandNumGen(seedValue);
390 >    }else {
391 >      myRandom = new SeqRandNumGen();
392 >    }  
393 >    
394 >    
395      a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
396 <
396 >    
397      //initialize atomsPerProc
398      atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
399 <
399 >    
400      if (worldRank == 0) {
401 <        numerator = info->getNGlobalAtoms();
402 <        denominator = nProcessors;
403 <        precast = numerator / denominator;
404 <        nTarget = (int)(precast + 0.5);
405 <
406 <        for(i = 0; i < nGlobalMols; i++) {
407 <            done = 0;
408 <            loops = 0;
409 <
410 <            while (!done) {
411 <                loops++;
412 <
413 <                // Pick a processor at random
414 <
415 <                which_proc = (int) (myRandom.getRandom() * nProcessors);
416 <
417 <                //get the molecule stamp first
418 <                int stampId = info->getMoleculeStampId(i);
419 <                MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
420 <
421 <                // How many atoms does this processor have so far?
422 <                old_atoms = atomsPerProc[which_proc];
423 <                add_atoms = moleculeStamp->getNAtoms();
424 <                new_atoms = old_atoms + add_atoms;
425 <
426 <                // If we've been through this loop too many times, we need
427 <                // to just give up and assign the molecule to this processor
428 <                // and be done with it.
429 <
430 <                if (loops > 100) {
431 <                    sprintf(painCave.errMsg,
432 <                            "I've tried 100 times to assign molecule %d to a "
433 <                                " processor, but can't find a good spot.\n"
434 <                                "I'm assigning it at random to processor %d.\n",
435 <                            i, which_proc);
436 <
437 <                    painCave.isFatal = 0;
438 <                    simError();
439 <
440 <                    molToProcMap[i] = which_proc;
441 <                    atomsPerProc[which_proc] += add_atoms;
442 <
443 <                    done = 1;
444 <                    continue;
445 <                }
446 <
447 <                // If we can add this molecule to this processor without sending
448 <                // it above nTarget, then go ahead and do it:
449 <
450 <                if (new_atoms <= nTarget) {
451 <                    molToProcMap[i] = which_proc;
452 <                    atomsPerProc[which_proc] += add_atoms;
453 <
454 <                    done = 1;
455 <                    continue;
456 <                }
457 <
458 <                // The only situation left is when new_atoms > nTarget.  We
459 <                // want to accept this with some probability that dies off the
460 <                // farther we are from nTarget
461 <
462 <                // roughly:  x = new_atoms - nTarget
463 <                //           Pacc(x) = exp(- a * x)
464 <                // where a = penalty / (average atoms per molecule)
465 <
466 <                x = (double)(new_atoms - nTarget);
467 <                y = myRandom.getRandom();
468 <
469 <                if (y < exp(- a * x)) {
470 <                    molToProcMap[i] = which_proc;
471 <                    atomsPerProc[which_proc] += add_atoms;
472 <
473 <                    done = 1;
474 <                    continue;
475 <                } else {
476 <                    continue;
477 <                }
392 <            }
401 >      numerator = info->getNGlobalAtoms();
402 >      denominator = nProcessors;
403 >      precast = numerator / denominator;
404 >      nTarget = (int)(precast + 0.5);
405 >      
406 >      for(i = 0; i < nGlobalMols; i++) {
407 >        done = 0;
408 >        loops = 0;
409 >        
410 >        while (!done) {
411 >          loops++;
412 >          
413 >          // Pick a processor at random
414 >          
415 >          which_proc = (int) (myRandom->rand() * nProcessors);
416 >          
417 >          //get the molecule stamp first
418 >          int stampId = info->getMoleculeStampId(i);
419 >          MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
420 >          
421 >          // How many atoms does this processor have so far?
422 >          old_atoms = atomsPerProc[which_proc];
423 >          add_atoms = moleculeStamp->getNAtoms();
424 >          new_atoms = old_atoms + add_atoms;
425 >          
426 >          // If we've been through this loop too many times, we need
427 >          // to just give up and assign the molecule to this processor
428 >          // and be done with it.
429 >          
430 >          if (loops > 100) {
431 >            sprintf(painCave.errMsg,
432 >                    "I've tried 100 times to assign molecule %d to a "
433 >                    " processor, but can't find a good spot.\n"
434 >                    "I'm assigning it at random to processor %d.\n",
435 >                    i, which_proc);
436 >            
437 >            painCave.isFatal = 0;
438 >            simError();
439 >            
440 >            molToProcMap[i] = which_proc;
441 >            atomsPerProc[which_proc] += add_atoms;
442 >            
443 >            done = 1;
444 >            continue;
445 >          }
446 >          
447 >          // If we can add this molecule to this processor without sending
448 >          // it above nTarget, then go ahead and do it:
449 >          
450 >          if (new_atoms <= nTarget) {
451 >            molToProcMap[i] = which_proc;
452 >            atomsPerProc[which_proc] += add_atoms;
453 >            
454 >            done = 1;
455 >            continue;
456 >          }
457 >          
458 >          // The only situation left is when new_atoms > nTarget.  We
459 >          // want to accept this with some probability that dies off the
460 >          // farther we are from nTarget
461 >          
462 >          // roughly:  x = new_atoms - nTarget
463 >          //           Pacc(x) = exp(- a * x)
464 >          // where a = penalty / (average atoms per molecule)
465 >          
466 >          x = (double)(new_atoms - nTarget);
467 >          y = myRandom->rand();
468 >          
469 >          if (y < exp(- a * x)) {
470 >            molToProcMap[i] = which_proc;
471 >            atomsPerProc[which_proc] += add_atoms;
472 >            
473 >            done = 1;
474 >            continue;
475 >          } else {
476 >            continue;
477 >          }
478          }
479 <
480 <        // Spray out this nonsense to all other processors:
481 <
482 <        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
479 >      }
480 >      
481 >      delete myRandom;
482 >      
483 >      // Spray out this nonsense to all other processors:
484 >      
485 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
486      } else {
487 <
488 <        // Listen to your marching orders from processor 0:
489 <
490 <        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
487 >      
488 >      // Listen to your marching orders from processor 0:
489 >      
490 >      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
491      }
492 <
492 >    
493      info->setMolToProcMap(molToProcMap);
494      sprintf(checkPointMsg,
495              "Successfully divided the molecules among the processors.\n");
496      MPIcheckPoint();
497 < }
498 <
497 >  }
498 >  
499   #endif
500 <
501 < void SimCreator::createMolecules(SimInfo *info) {
500 >  
501 >  void SimCreator::createMolecules(SimInfo *info) {
502      MoleculeCreator molCreator;
503      int stampId;
504 <
504 >    
505      for(int i = 0; i < info->getNGlobalMolecules(); i++) {
506 <
506 >      
507   #ifdef IS_MPI
508 <
509 <        if (info->getMolToProc(i) == worldRank) {
508 >      
509 >      if (info->getMolToProc(i) == worldRank) {
510   #endif
511 <
512 <            stampId = info->getMoleculeStampId(i);
513 <            Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
514 <                                                                                    stampId, i, info->getLocalIndexManager());
515 <
516 <            info->addMolecule(mol);
517 <
511 >        
512 >        stampId = info->getMoleculeStampId(i);
513 >        Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
514 >                                                   stampId, i, info->getLocalIndexManager());
515 >        
516 >        info->addMolecule(mol);
517 >        
518   #ifdef IS_MPI
519 <
520 <        }
521 <
519 >        
520 >      }
521 >      
522   #endif
523 <
523 >      
524      } //end for(int i=0)  
525 < }
526 <
527 < 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) {
525 >  }
526 >    
527 >  void SimCreator::setGlobalIndex(SimInfo *info) {
528      SimInfo::MoleculeIterator mi;
529      Molecule::AtomIterator ai;
530      Molecule::RigidBodyIterator ri;
# Line 509 | Line 539 | void SimCreator::setGlobalIndex(SimInfo *info) {
539      int nGlobalAtoms = info->getNGlobalAtoms();
540      
541   #ifndef IS_MPI
542 <
542 >    
543      beginAtomIndex = 0;
544      beginRigidBodyIndex = 0;
545      beginCutoffGroupIndex = 0;
546 <
546 >    
547   #else
548 <
548 >    
549      int nproc;
550      int myNode;
551 <
551 >    
552      myNode = worldRank;
553      MPI_Comm_size(MPI_COMM_WORLD, &nproc);
554 <
554 >    
555      std::vector < int > tmpAtomsInProc(nproc, 0);
556      std::vector < int > tmpRigidBodiesInProc(nproc, 0);
557      std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
558      std::vector < int > NumAtomsInProc(nproc, 0);
559      std::vector < int > NumRigidBodiesInProc(nproc, 0);
560      std::vector < int > NumCutoffGroupsInProc(nproc, 0);
561 <
561 >    
562      tmpAtomsInProc[myNode] = info->getNAtoms();
563      tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
564      tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
565 <
565 >    
566      //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
567      MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
568                    MPI_SUM, MPI_COMM_WORLD);
# Line 540 | Line 570 | void SimCreator::setGlobalIndex(SimInfo *info) {
570                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
571      MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
572                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
573 <
573 >    
574      beginAtomIndex = 0;
575      beginRigidBodyIndex = 0;
576      beginCutoffGroupIndex = 0;
577 <
577 >    
578      for(int i = 0; i < myNode; i++) {
579 <        beginAtomIndex += NumAtomsInProc[i];
580 <        beginRigidBodyIndex += NumRigidBodiesInProc[i];
581 <        beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
579 >      beginAtomIndex += NumAtomsInProc[i];
580 >      beginRigidBodyIndex += NumRigidBodiesInProc[i];
581 >      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
582      }
583 <
583 >    
584   #endif
585 <
585 >    
586      //rigidbody's index begins right after atom's
587      beginRigidBodyIndex += info->getNGlobalAtoms();
588 <
588 >    
589      for(mol = info->beginMolecule(mi); mol != NULL;
590          mol = info->nextMolecule(mi)) {
591 <
592 <        //local index(index in DataStorge) of atom is important
593 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
594 <            atom->setGlobalIndex(beginAtomIndex++);
595 <        }
596 <
597 <        for(rb = mol->beginRigidBody(ri); rb != NULL;
598 <            rb = mol->nextRigidBody(ri)) {
599 <            rb->setGlobalIndex(beginRigidBodyIndex++);
600 <        }
601 <
602 <        //local index of cutoff group is trivial, it only depends on the order of travesing
603 <        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
604 <            cg = mol->nextCutoffGroup(ci)) {
605 <            cg->setGlobalIndex(beginCutoffGroupIndex++);
606 <        }
591 >      
592 >      //local index(index in DataStorge) of atom is important
593 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
594 >        atom->setGlobalIndex(beginAtomIndex++);
595 >      }
596 >      
597 >      for(rb = mol->beginRigidBody(ri); rb != NULL;
598 >          rb = mol->nextRigidBody(ri)) {
599 >        rb->setGlobalIndex(beginRigidBodyIndex++);
600 >      }
601 >      
602 >      //local index of cutoff group is trivial, it only depends on the order of travesing
603 >      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
604 >          cg = mol->nextCutoffGroup(ci)) {
605 >        cg->setGlobalIndex(beginCutoffGroupIndex++);
606 >      }
607      }
608 <
608 >    
609      //fill globalGroupMembership
610      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
611      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
612 <        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
613 <
614 <            for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
615 <                globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
616 <            }
617 <
618 <        }      
612 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
613 >        
614 >        for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
615 >          globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
616 >        }
617 >        
618 >      }      
619      }
620 <
620 >    
621   #ifdef IS_MPI    
622      // Since the globalGroupMembership has been zero filled and we've only
623      // poked values into the atoms we know, we can do an Allreduce
# Line 597 | Line 627 | void SimCreator::setGlobalIndex(SimInfo *info) {
627      std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
628      MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
629                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
630 <     info->setGlobalGroupMembership(tmpGroupMembership);
630 >    info->setGlobalGroupMembership(tmpGroupMembership);
631   #else
632      info->setGlobalGroupMembership(globalGroupMembership);
633   #endif
634 <
634 >    
635      //fill molMembership
636      std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
637      
638      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
639 <
640 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
641 <            globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
642 <        }
639 >      
640 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
641 >        globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
642 >      }
643      }
644 <
644 >    
645   #ifdef IS_MPI
646      std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
647 <
647 >    
648      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
649                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
650      
# Line 622 | Line 652 | void SimCreator::setGlobalIndex(SimInfo *info) {
652   #else
653      info->setGlobalMolMembership(globalMolMembership);
654   #endif
655 <
656 < }
657 <
658 < void SimCreator::loadCoordinates(SimInfo* info) {
655 >    
656 >  }
657 >  
658 >  void SimCreator::loadCoordinates(SimInfo* info) {
659      Globals* simParams;
660      simParams = info->getSimParams();
661      
662      if (!simParams->haveInitialConfig()) {
663 <        sprintf(painCave.errMsg,
664 <                "Cannot intialize a simulation without an initial configuration file.\n");
665 <        painCave.isFatal = 1;;
666 <        simError();
663 >      sprintf(painCave.errMsg,
664 >              "Cannot intialize a simulation without an initial configuration file.\n");
665 >      painCave.isFatal = 1;;
666 >      simError();
667      }
668 <        
668 >    
669      DumpReader reader(info, simParams->getInitialConfig());
670      int nframes = reader.getNFrames();
671 <
671 >    
672      if (nframes > 0) {
673 <        reader.readFrame(nframes - 1);
673 >      reader.readFrame(nframes - 1);
674      } else {
675 <        //invalid initial coordinate file
676 <        sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
677 <                simParams->getInitialConfig());
678 <        painCave.isFatal = 1;
679 <        simError();
675 >      //invalid initial coordinate file
676 >      sprintf(painCave.errMsg,
677 >              "Initial configuration file %s should at least contain one frame\n",
678 >              simParams->getInitialConfig().c_str());
679 >      painCave.isFatal = 1;
680 >      simError();
681      }
682 <
682 >    
683      //copy the current snapshot to previous snapshot
684      info->getSnapshotManager()->advance();
685 < }
686 <
685 >  }
686 >  
687   } //end namespace oopse
688  
689  

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