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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 1436 by tim, Thu Jul 29 19:12:00 2004 UTC

# Line 31 | Line 31 | int main( int argc, char* argv[]){
31    string outMdFileName;
32    string outInitFileName;
33    SimInfo* oldInfo;
34 –  SimInfo* newInfo;
34    SimSetup* oldSimSetup;
36 –  SimSetup* newSimSetup;
35    BaseLattice* simpleLat;
36    int numMol;
37    double latticeConstant;
# Line 53 | Line 51 | int main( int argc, char* argv[]){
51    // parse command line arguments
52    if (cmdline_parser (argc, argv, &args_info) != 0)
53      exit(1) ;
54 +  
55 +  density = args_info.density_arg;
56  
57 –  //process density
58 –  if(!args_info.density_given && !args_info.ndensity_given){
59 –    cerr << "SimpleBuilder Error: density or number density must be given" << endl;
60 –    cmdline_parser_print_help();
61 –    exit(1);
62 –  }
63 –  else if(args_info.density_given){
64 –    if( args_info.ndensity_given)
65 –      cerr << "SimpleBuilder Warning: both of density and number density are given, use density" << endl;
66 –    
67 –    density = args_info.density_arg;
68 –  }
69 –  else if(args_info.ndensity_given){
70 –    //convert number density to density
71 –  }
72 –
73 –
57    //get lattice type
58    latticeType = UpperCase(args_info.latticetype_arg);
59    if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
# Line 107 | Line 90 | int main( int argc, char* argv[]){
90      exit(1);
91    }
92  
110 –  //determine the output file names
93    
112 –  if (args_info.output_given){
113 –    outPrefix = args_info.output_arg;
114 –  }
115 –  else
116 –    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
117 –  
118 –  outMdFileName = outPrefix + ".md";
119 –  outInitFileName = outPrefix + ".in";
120 –
94    //parse md file and set up the system
95    oldInfo = new SimInfo;
96    if(oldInfo == NULL){
# Line 130 | Line 103 | int main( int argc, char* argv[]){
103       cerr << "error in creating SimSetup" << endl;
104       exit(1);
105    }
106 <    
106 >
107 >  oldSimSetup->suspendInit();
108    oldSimSetup->setSimInfo(oldInfo );
109    oldSimSetup->parseFile(&inputFileName[0] );
110    oldSimSetup->createSim();
111 +  
112    if(oldInfo->nComponents >=2){
113        cerr << "can not build the system with more than two components" << endl;
114        exit(1);
115    }
141 –
116    
117    //get mass of molecule.
118    //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
# Line 161 | Line 135 | int main( int argc, char* argv[]){
135    simpleLat->setLatticeConstant(lc);
136    
137    //calculate the total number of molecules
138 <  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);
138 >  numMol = nx * ny * nz * numMolPerCell;
139  
140 <  //parse new .md file and set up the system
170 <  newInfo = new SimInfo;
171 <  if(newInfo == NULL){
172 <     cerr << "error in creating SimInfo" << endl;
173 <     exit(1);
174 <  }
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();
140 >  if (oldInfo->n_mol != numMol){
141  
142 +    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
143 +    outMdFileName = outPrefix + ".md";
144 +
145 +    //creat new .md file on fly which corrects the number of molecule    
146 +    createMdFile(inputFileName, outMdFileName, numMol);
147 +    cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl;
148 +    cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl;
149 +    exit(1);
150 +  }
151 +  
152 +  //determine the output file names  
153 +  if (args_info.output_given)
154 +    outInitFileName = args_info.output_arg;
155 +  else
156 +    outInitFileName = getPrefix(inputFileName.c_str())  + ".in";
157 +  
158 +  
159    //allocat memory for storing pos, vel and etc
160 <  newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
161 <  for (int i = 0; i < newInfo->n_atoms; i++)
162 <    newInfo->atoms[i]->setCoords();  
160 >  oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
161 >  for (int i = 0; i < oldInfo->n_atoms; i++)
162 >    oldInfo->atoms[i]->setCoords();  
163  
164    //creat Molocator
165 <  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
165 >  locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField());
166  
167    //fill Hmat
168    Hmat[0][0] = nx * latticeConstant;
169    Hmat[0][1] = 0.0;
170    Hmat[0][2] = 0.0;
171  
172 <  Hmat[1][0] = ny * latticeConstant;
173 <  Hmat[1][1] = 0.0;
172 >  Hmat[1][0] = 0.0;
173 >  Hmat[1][1] = ny * latticeConstant;
174    Hmat[1][2] = 0.0;
175  
176 <  Hmat[2][0] = nz * latticeConstant;
176 >  Hmat[2][0] = 0.0;
177    Hmat[2][1] = 0.0;
178 <  Hmat[2][2] = 0.0;
178 >  Hmat[2][2] = nz * latticeConstant ;
179  
180    //set Hmat
181 <  newInfo->setBoxM(Hmat);
181 >  oldInfo->setBoxM(Hmat);
182    
183    //place the molecules
184  
# Line 223 | Line 196 | int main( int argc, char* argv[]){
196            simpleLat->getLatticePointsPos(latticePos, i, j, k);
197  
198            for(int l = 0; l < numMolPerCell; l++)
199 <            locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
199 >            locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++]));
200         }
201      }
202    }
203  
204    //create dumpwriter and write out the coordinates
205 <  writer = new DumpWriter( newInfo );
205 >  oldInfo->finalName = outInitFileName;
206 >  writer = new DumpWriter( oldInfo );
207    if(writer == NULL){
208      cerr << "error in creating DumpWriter" << endl;
209      exit(1);    
210    }
211    writer->writeFinal(0);
212 <  
212 >  cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl;
213    //delete objects
214 <  if(!oldInfo)
214 >
215 >  //delete oldInfo and oldSimSetup
216 >  if(oldInfo != NULL)
217       delete oldInfo;
218    
219 <  if(!oldSimSetup)
220 <     delete oldSimSetup;
245 <
246 <  if(!newInfo)
247 <     delete newInfo;
219 >  if(oldSimSetup != NULL)
220 >     delete oldSimSetup;
221    
249 –  if(!newSimSetup)
250 –     delete newSimSetup;
251 –
222    if (writer != NULL)
223      delete writer;
224    return 0;
# Line 259 | Line 229 | void createMdFile(const string& oldMdFileName, const s
229    ofstream newMdFile;
230    const int MAXLEN = 65535;
231    char buffer[MAXLEN];
262 –  string line;
232  
233    //create new .md file based on old .md file
234    oldMdFile.open(oldMdFileName.c_str());
# Line 268 | Line 237 | void createMdFile(const string& oldMdFileName, const s
237    oldMdFile.getline(buffer, MAXLEN);
238    while(!oldMdFile.eof()){
239  
240 <    if(line.find("nMol") < line.size()){
241 <      
240 >    //correct molecule number
241 >    if(strstr(buffer, "nMol") !=NULL){      
242        sprintf(buffer, "\t\tnMol = %d;", numMol);
243        newMdFile << buffer << endl;
244      }

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