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root/group/trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp
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Comparing trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp (file contents):
Revision 1432 by tim, Thu Jul 29 03:31:50 2004 UTC vs.
Revision 1435 by tim, Thu Jul 29 18:16:16 2004 UTC

# Line 29 | Line 29 | int main( int argc, char* argv[]){
29    string inputFileName;
30    string outPrefix;
31    string outMdFileName;
32 –  string outInitFileName;
32    SimInfo* oldInfo;
34 –  SimInfo* newInfo;
33    SimSetup* oldSimSetup;
36 –  SimSetup* newSimSetup;
34    BaseLattice* simpleLat;
35    int numMol;
36    double latticeConstant;
# Line 116 | Line 113 | int main( int argc, char* argv[]){
113      outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
114    
115    outMdFileName = outPrefix + ".md";
119 –  outInitFileName = outPrefix + ".in";
116  
117    //parse md file and set up the system
118    oldInfo = new SimInfo;
# Line 130 | Line 126 | int main( int argc, char* argv[]){
126       cerr << "error in creating SimSetup" << endl;
127       exit(1);
128    }
129 <    
129 >
130 >  oldSimSetup->suspendInit();
131    oldSimSetup->setSimInfo(oldInfo );
132    oldSimSetup->parseFile(&inputFileName[0] );
133    oldSimSetup->createSim();
134 +  
135    if(oldInfo->nComponents >=2){
136        cerr << "can not build the system with more than two components" << endl;
137        exit(1);
138    }
141 –
139    
140    //get mass of molecule.
141    //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
# Line 161 | Line 158 | int main( int argc, char* argv[]){
158    simpleLat->setLatticeConstant(lc);
159    
160    //calculate the total number of molecules
161 <  numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
165 <  
166 <  //creat new .md file on fly
167 <  createMdFile(inputFileName, outMdFileName, numMol);
161 >  numMol = nx * ny * nz * numMolPerCell;
162  
163 <  //parse new .md file and set up the system
164 <  newInfo = new SimInfo;
165 <  if(newInfo == NULL){
166 <     cerr << "error in creating SimInfo" << endl;
167 <     exit(1);
163 >  if (oldInfo->n_mol != numMol){
164 >    //creat new .md file on fly which corrects the number of molecule
165 >    createMdFile(inputFileName, outMdFileName, numMol);
166 >    cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl;
167 >    cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl;
168 >    exit(1);
169    }
175 –  
176 –  newSimSetup = new SimSetup();  
177 –  if(newSimSetup == NULL){
178 –     cerr << "error in creating SimSetup" << endl;
179 –     exit(1);
180 –  }
181 –    
182 –  newSimSetup->setSimInfo(newInfo );
183 –  newSimSetup->parseFile(&outMdFileName[0] );
184 –  newSimSetup->createSim();
170  
171    //allocat memory for storing pos, vel and etc
172 <  newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
173 <  for (int i = 0; i < newInfo->n_atoms; i++)
174 <    newInfo->atoms[i]->setCoords();  
172 >  oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
173 >  for (int i = 0; i < oldInfo->n_atoms; i++)
174 >    oldInfo->atoms[i]->setCoords();  
175  
176    //creat Molocator
177 <  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
177 >  locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField());
178  
179    //fill Hmat
180    Hmat[0][0] = nx * latticeConstant;
181    Hmat[0][1] = 0.0;
182    Hmat[0][2] = 0.0;
183  
184 <  Hmat[1][0] = ny * latticeConstant;
185 <  Hmat[1][1] = 0.0;
184 >  Hmat[1][0] = 0.0;
185 >  Hmat[1][1] = ny * latticeConstant;
186    Hmat[1][2] = 0.0;
187  
188 <  Hmat[2][0] = nz * latticeConstant;
188 >  Hmat[2][0] = 0.0;
189    Hmat[2][1] = 0.0;
190 <  Hmat[2][2] = 0.0;
190 >  Hmat[2][2] = nz * latticeConstant ;
191  
192    //set Hmat
193 <  newInfo->setBoxM(Hmat);
193 >  oldInfo->setBoxM(Hmat);
194    
195    //place the molecules
196  
# Line 223 | Line 208 | int main( int argc, char* argv[]){
208            simpleLat->getLatticePointsPos(latticePos, i, j, k);
209  
210            for(int l = 0; l < numMolPerCell; l++)
211 <            locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
211 >            locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++]));
212         }
213      }
214    }
215  
216    //create dumpwriter and write out the coordinates
217 <  writer = new DumpWriter( newInfo );
217 >  writer = new DumpWriter( oldInfo );
218    if(writer == NULL){
219      cerr << "error in creating DumpWriter" << endl;
220      exit(1);    
# Line 237 | Line 222 | int main( int argc, char* argv[]){
222    writer->writeFinal(0);
223    
224    //delete objects
225 <  if(!oldInfo)
225 >
226 >  //delete oldInfo and oldSimSetup
227 >  if(oldInfo != NULL)
228       delete oldInfo;
229    
230 <  if(!oldSimSetup)
231 <     delete oldSimSetup;
245 <
246 <  if(!newInfo)
247 <     delete newInfo;
230 >  if(oldSimSetup != NULL)
231 >     delete oldSimSetup;
232    
249 –  if(!newSimSetup)
250 –     delete newSimSetup;
251 –
233    if (writer != NULL)
234      delete writer;
235    return 0;
# Line 259 | Line 240 | void createMdFile(const string& oldMdFileName, const s
240    ofstream newMdFile;
241    const int MAXLEN = 65535;
242    char buffer[MAXLEN];
262 –  string line;
243  
244    //create new .md file based on old .md file
245    oldMdFile.open(oldMdFileName.c_str());
# Line 268 | Line 248 | void createMdFile(const string& oldMdFileName, const s
248    oldMdFile.getline(buffer, MAXLEN);
249    while(!oldMdFile.eof()){
250  
251 <    if(line.find("nMol") < line.size()){
252 <      
251 >    //correct molecule number
252 >    if(strstr(buffer, "nMol") !=NULL){      
253        sprintf(buffer, "\t\tnMol = %d;", numMol);
254        newMdFile << buffer << endl;
255      }

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