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Comparing branches/new_design/OOPSE-3.0/src/brains/SimCreator.cpp (file contents):
Revision 1724 by tim, Fri Nov 5 23:38:27 2004 UTC vs.
Revision 1725 by tim, Wed Nov 10 22:01:06 2004 UTC

# Line 22 | Line 22
22   * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
23   *
24   */
25 –
26 – /**
27 –  * @file SimCreator.cpp
28 –  * @author tlin
29 –  * @date 11/03/2004
30 –  * @time 13:51am
31 –  * @version 1.0
32 –  */
25  
26 < #include "brains/SimCreator.hpp"  
26 > /**
27 > * @file SimCreator.cpp
28 > * @author tlin
29 > * @date 11/03/2004
30 > * @time 13:51am
31 > * @version 1.0
32 > */
33 >
34 > #include "brains/SimCreator.hpp"
35   namespace oopse {
36  
37   void SimSetup::parseFile(char* mdfile,  MakeStamps* stamps, Globals* globals){
# Line 72 | Line 72 | SimInfo* SimCreator::createSim(const std::string& mdfi
72      parseFile(mdfile, stamps, globals);
73  
74      //create the force field
75 <    ForceFiled* ff = ForceFieldFactory::getInstance()->createForceField(globals->getForceField());
75 >    ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField());
76      
77      //create SimInfo
78      SimInfo* info = new SimInfo();
# Line 91 | Line 91 | SimInfo* SimCreator::createSim(const std::string& mdfi
91      //create the molecules
92      createMolecules(info);
93  
94 +    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
95 +    //global index will never change again). Local indices of atoms and rigidbodies are already set by
96 +    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
97 +    setGlobalIndices(info);
98 +    
99      //allocate memory for DataStorage(circular reference, need to break it)
100      info->setSnapshotManager(new SimSnapshotManager(info);
101      
102 <    //load initial coordinates
102 >    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
103 >    //eta, chi for NPT integrator)
104      DumpReader reader(info->getInitFilename());
105      int nframes = reader->getNframes();
106  
# Line 111 | Line 117 | void SimCreator::gatherParameters(SimModel* model) {
117      return info;
118   }    
119  
120 < void SimCreator::gatherParameters(SimModel* model) {
121 <    model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
122 <    model->addProperty(new DoubleGenericData("dt"), globals->getDt());
120 > void SimCreator::gatherParameters(SimInfo* info) {
121 >    //model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
122 >    //model->addProperty(new DoubleGenericData("dt"), globals->getDt());
123 >
124 >    //setup seed for random number generator
125 >    int seedValue;
126 >    Globals* globals = info->getGlobals();
127 >    
128 >    if (globals->haveSeed()){
129 >        seedValue = globals->getSeed();
130 >
131 >        if(seedValue / 1000000000 == 0){
132 >            sprintf(painCave.errMsg,
133 >            "Seed for sprng library should contain at least 9 digits\n"
134 >            "OOPSE will generate a seed for user\n");
135 >            painCave.isFatal = 0;
136 >            simError();
137 >
138 >    //using seed generated by system instead of invalid seed set by user
139 > #ifndef IS_MPI
140 >            seedValue = make_sprng_seed();
141 > #else
142 >            if (worldRank == 0){
143 >                seedValue = make_sprng_seed();
144 >            }
145 >            MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);  
146 > #endif      
147 >        } //end if (seedValue /1000000000 == 0)
148 >    } else{
149 >    
150 > #ifndef IS_MPI
151 >        seedValue = make_sprng_seed();
152 > #else
153 >        if (worldRank == 0){
154 >            seedValue = make_sprng_seed();
155 >        }
156 >        MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);  
157 > #endif
158 >    }//end of globals->haveSeed()
159 >    info->setSeed(seedValue);
160 >
161 >    //
162 >    std::string prefix;
163 > #ifdef IS_MPI
164 >    if (worldRank == 0){
165 > #endif // is_mpi
166 >      
167 >        if(globals->haveFinalConfig()) {
168 >            prefix = getPrefix(globals->getFinalConfig());  
169 >        } else {
170 >            prefix = getPrefix(mdfile_);
171 >        }
172 >        
173 >        info->setFinalConfFileName(prefix + ".eor");
174 >        info->setDumpFileName(prefix + ".dump");
175 >        info->setStatFileName(prefix + ".stat");
176 >
177 > #ifdef IS_MPI
178 >    }
179 > #endif    
180 >
181 >
182 >
183   }
184  
185   #ifdef IS_MPI
# Line 123 | Line 189 | void SimCreator::mpiMolDivide(){
189  
190      mpiSim->divideLabor();
191  
126 –    strcpy(checkPointMsg, "Passed nlocal consistency check.");
127 –    MPIcheckPoint();
192   }
193   #endif
194  
195   Molecule* SimCreator::createMolecules(SimInfo* info) {
196 +    MoleculeCreator molCreator;
197 +    int stampId;
198  
133 –
199      
200 <    for (i = 0; i < mpiSim->getNMolGlobal(); i++){
201 <        if (mol2proc[i] == worldRank){
200 >    for (int i = 0; i < info->getNGlobalMolecules(); i++){
201 >        if (info->getMolToProc(i) == worldRank){
202  
203 <            Molecule* mol = MoleculeCreator.createMolecule(molStamp, stampID, globalIndex);
203 >            stampId = info->getMoleculeStampId(i);
204 >            Molecule* mol = molCreator.createMolecule(info->getForceField(),
205 >                                                                                info->getMoleculeStamp(stampId), stampId, i);
206                          
207              info->addMolecule(mol);
208          }
# Line 176 | Line 243 | void SimSetup::compList(MakeStamps* stamps,SimInfo* in
243                  simError();
244              }      
245  
246 <            info.moleculeStamps.push_back(make_pair(currentStamp, the_components[i]->getNMol()));
246 >            info->addMoleculeStamp(currentStamp, the_components[i]->getNMol);
247            
248          } //end for (i = 0; i < n_components; i++)
249          
# Line 197 | Line 264 | void SimSetup::compList(MakeStamps* stamps,SimInfo* in
264   #endif // is_mpi
265   }
266  
267 + void SimCreator::setGlobalIndices(SimInfo* info) {
268 +    typename SimInfo::MoleculeIterator mi;
269 +    typename Molecule::AtomIterator ai;
270 +    typename Molecule::RigidBodyIterator ri;
271 +    typename Molecule::CutoffGroupIterator ci;
272 +    Molecule* mol;
273 +    Atom* atom;
274 +    RigidBody* rb;
275 +    CutoffGroup* cg;
276 +    int beginAtomIndex;
277 +    int beginRigidBodyIndex;
278 +    int beginCutoffGroupIndex;
279  
280 + #ifdef IS_MPI
281 +    beginAtomIndex = 0;
282 +    beginRigidBodyIndex = 0;
283 +    beginCutoffGroupIndex = 0;
284 + #else
285 +    int nproc;
286 +    int myNode;
287 +
288 +    myNode = worldRank;
289 +    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
290 +    
291 +    std::vector<int> tmpAtomsInProc(nproc, 0);
292 +    std::vector<int> tmpRigidBodiesInProc(nproc, 0);
293 +    std::vector<int> tmpCutoffGroupsInProc(nproc, 0);    
294 +    std::vector<int> NumAtomsInProc(nproc, 0);
295 +    std::vector<int> NumRigidBodiesInProc(nproc, 0);
296 +    std::vector<int> NumCutoffGroupsInProc(nproc, 0);
297 +
298 +    tmpAtomInProc[myNode] = info->getNAtoms();
299 +    tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess();
300 +    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss();
301 +    
302 +    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
303 +    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
304 +    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
305 +    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
306 +
307 +    beginAtomIndex = 0;
308 +    beginRigidBodyIndex = 0;
309 +    beginCutoffGroupIndex = 0;
310 +
311 +    for (int i = 0; i < nproc; i++) {
312 +        beginAtomIndex += NumAtomsInProc[i];
313 +        beginRigidBodyIndex += NumRigidBodiesInProc[i];
314 +        beginCutoffGroupIndex += NumCutoffGroupsInProc[i];        
315 +    }
316 +    
317 + #endif
318 +    
319 +    for (mol = info->beginMolecule(mi); mol != NULL; mol  = info->nextMolecule(mi)) {
320 +
321 +        //local index(index in DataStorge) of atom is important
322 +        for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
323 +            atom->setGlobalIndex(beginAtomIndex++);
324 +        }
325 +
326 +        for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
327 +            rb->setGlobalIndex(beginRigidBodyIndex++);
328 +        }
329 +        
330 +        //local index of cutoff group is trivial, it only depends on the order of travesing
331 +        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
332 +            cg->setGlobalIndex(beginCutoffGroupIndex++);
333 +        }        
334 +        
335 +    }
336 + }
337 +
338   } //end namespace oopse

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