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root/group/trunk/mdtools/interface_implementation/SimSetup.cpp
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Comparing trunk/mdtools/interface_implementation/SimSetup.cpp (file contents):
Revision 189 by mmeineke, Tue Nov 26 21:04:43 2002 UTC vs.
Revision 202 by mmeineke, Tue Dec 10 21:41:26 2002 UTC

# Line 73 | Line 73 | void SimSetup::createSim( void ){
73  
74    MakeStamps *the_stamps;
75    Globals* the_globals;
76 <  int i;
76 >  int i, j;
77  
78    // get the stamps and globals;
79    the_stamps = stamps;
# Line 161 | Line 161 | void SimSetup::createSim( void ){
161   #endif // is_mpi
162  
163    // make an array of molecule stamps that match the components used.
164 +  // also extract the used stamps out into a separate linked list
165  
166 +  simnfo->nComponents = n_components;
167 +  simnfo->componentsNmol = components_nmol;
168 +  simnfo->compStamps = comp_stamps;
169 +  simnfo->headStamp = new LinkedMolStamp();
170 +  
171 +  char* id;
172 +  LinkedMolStamp* headStamp = simnfo->headStamp;
173 +  LinkedMolStamp* currentStamp = NULL;
174    for( i=0; i<n_components; i++ ){
175  
176 <    comp_stamps[i] =
177 <      the_stamps->getMolecule( the_components[i]->getType() );
176 >    id = the_components[i]->getType();
177 >    comp_stamps[i] = NULL;
178 >    
179 >    // check to make sure the component isn't already in the list
180 >
181 >    comp_stamps[i] = headStamp->match( id );
182 >    if( comp_stamps[i] == NULL ){
183 >      
184 >      // extract the component from the list;
185 >      
186 >      currentStamp = the_stamps->extractMolStamp( id );
187 >      if( currentStamp == NULL ){
188 >        sprintf( painCave.errMsg,
189 >                 "SimSetup error: Component \"%s\" was not found in the "
190 >                 "list of declared molecules\n"
191 >                 id );
192 >        painCave.isFatal = 1;
193 >        simError();
194 >      }
195 >      
196 >      headStamp->add( currentStamp );
197 >      comp_stamps[i] = headStamp->match( id );
198 >    }
199    }
200  
201 + #ifdef IS_MPI
202 +  strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203 +  MPIcheckPoint();
204 + #endif // is_mpi
205 +  
206  
207  
208 +
209    // caclulate the number of atoms, bonds, bends and torsions
210  
211    tot_atoms = 0;
# Line 177 | Line 213 | void SimSetup::createSim( void ){
213    tot_bends = 0;
214    tot_torsions = 0;
215    for( i=0; i<n_components; i++ ){
216 <
217 <    tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
218 <    tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
219 <    tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
216 >    
217 >    tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218 >    tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219 >    tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221    }
222  
# Line 191 | Line 227 | void SimSetup::createSim( void ){
227    simnfo->n_bends = tot_bends;
228    simnfo->n_torsions = tot_torsions;
229    simnfo->n_SRI = tot_SRI;
230 +  simnfo->n_mol = tot_nmol;
231  
232 +  
233 + #ifdef IS_MPI
234 +
235 +  // divide the molecules among processors here.
236 +  
237 +  mpiSimulation* mpiSim = new mpiSimulation( simnfo );
238 +  
239 +  mpiSim->divideLabor();
240 +
241 +  // set up the local variables
242 +  
243 +  int localMol;
244 +  int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
245 +  
246 +  localMol = 0;
247 +  local_atoms = 0;
248 +  local_bonds = 0;
249 +  local_bends = 0;
250 +  local_torsions = 0;
251 +  for( i=0; i<n_components; i++ ){
252 +
253 +    for( j=0; j<components_nmol[i]; j++ ){
254 +      
255 +      if( mpiSim->getMyMolStart() <= j &&
256 +          j <= mpiSim->getMyMolEnd() ){
257 +        
258 +        local_atoms +=    comp_stamps[i]->getNAtoms();
259 +        local_bonds +=    comp_stamps[i]->getNBonds();
260 +        local_bends +=    comp_stamps[i]->getNBends();
261 +        local_torsions += comp_stamps[i]->getNTorsions();
262 +        localMol++;
263 +      }      
264 +    }
265 +  }
266 +
267 +  
268 +
269 +  simnfo->n_atoms = mpiSim->getMyNlocal();  
270 +  
271 +
272 + #endif // is_mpi
273 +  
274 +
275    // create the atom and short range interaction arrays
276  
277 <  Atom::createArrays(tot_atoms);
278 <  the_atoms = new Atom*[tot_atoms];
279 <  the_molecules = new Molecule[tot_nmol];
277 >  Atom::createArrays(simnfo->n_atoms);
278 >  the_atoms = new Atom*[simnfo->n_atoms];
279 >  the_molecules = new Molecule[simnfo->n_mol];
280  
281  
282 <  if( tot_SRI ){
283 <    the_sris = new SRI*[tot_SRI];
284 <    the_excludes = new ex_pair[tot_SRI];
282 >  if( simnfo->n_SRI ){
283 >    the_sris = new SRI*[simnfo->n_SRI];
284 >    the_excludes = new ex_pair[simnfo->n_SRI];
285    }
286  
287    // set the arrays into the SimInfo object
# Line 230 | Line 310 | void SimSetup::createSim( void ){
310      makeTorsions();
311    }
312  
233 –  //  makeMolecules();
313  
314    // get some of the tricky things that may still be in the globals
315  
# Line 314 | Line 393 | void SimSetup::createSim( void ){
393   //     delete fileInit;
394   //   }
395   //   else{
396 +
397 + #ifdef IS_MPI
398 +
399 +  // no init from bass
400 +  
401 +  sprintf( painCave.errMsg,
402 +           "Cannot intialize a parallel simulation without an initial configuration file.\n" );
403 +  painCave.isFatal;
404 +  simError();
405 +  
406 + #else
407  
408    initFromBass();
409 +
410 + #endif // is_mpi
411  
412   #ifdef IS_MPI
413 <  strcpy( checkPointMsg, "initFromBass successfully created the lattice" );
413 >  strcpy( checkPointMsg, "Successfully read in the initial configuration" );
414    MPIcheckPoint();
415   #endif // is_mpi
416  
# Line 501 | Line 593 | void SimSetup::makeAtoms( void ){
593        the_molecules[molIndex].setNMembers( nMemb );
594        the_molecules[molIndex].setStartAtom( molStart );
595        the_molecules[molIndex].setEndAtom( molEnd );
596 +      the_molecules[molIndex].setStampID( i );
597        molIndex++;
598  
599      }

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