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root/group/trunk/OOPSE-3.0/src/applications/nanoRodBuilder/nanorodBuilder.cpp
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Comparing trunk/OOPSE-3.0/src/applications/nanoRodBuilder/nanorodBuilder.cpp (file contents):
Revision 2215 by chuckv, Thu Apr 28 00:24:11 2005 UTC vs.
Revision 2218 by chuckv, Tue May 3 17:55:28 2005 UTC

# Line 103 | Line 103 | int main(int argc, char *argv []) {
103    std::vector<Vector3d> latticePos;
104    std::vector<Vector3d> latticeOrt;
105    int numMolPerCell;
106 –  int curMolIndex;
106    DumpWriter *writer;
107    
108    // parse command line arguments
# Line 209 | Line 208 | int main(int argc, char *argv []) {
208    
209    // Create geometry for nanocrystal
210   #ifdef HAVE_CGAL
211 <  GeometryBuilder myGeometry(rodLength,rodDiameter);
211 >  GeometryBuilder *myGeometry;
212 >  // GeometryBuilder myGeometry(rodLength,rodDiameter);
213 >  if (args_info.twinnedCrystal_flag){
214 >     myGeometry = new GeometryBuilder(rodLength,rodDiameter);
215 >  }
216 >  else{
217 >     myGeometry = new GeometryBuilder(rodLength,rodDiameter);
218 >  }
219 >  
220    if (args_info.genGeomview_given){
221       if (args_info.genGeomview_flag){
222          outGeomFileName = getPrefix(inputFileName.c_str()) + ".off";
223 <        myGeometry.dumpGeometry(outGeomFileName);
223 >        myGeometry->dumpGeometry(outGeomFileName);
224       }
225    }
226 <
226 >  
227   #endif
228    
229    /*
# Line 227 | Line 234 | int main(int argc, char *argv []) {
234    
235    //place the molecules
236    
237 <  curMolIndex = 0;
237 >
238    
239    //get the orientation of the cell sites
240    //for the same type of molecule in same lattice, it will not change
241    latticeOrt = simpleLat->getLatticePointsOrt();
242    
243    
237 –  /*
238 –    void BaseLattice::getLatticePointsPos(std::vector<Vector3d>&
239 –    latticePos, int nx, int ny, int nz){
240 –    
241 –    latticePos.resize(nCellSites);
242 –                        
243 –    for( int i=0;i < nCellSites;i++){
244 –    
245 –    latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5);
246 –    latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5);
247 –    latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5);    
248 –    }
249 –    
250 –  */
244    
252 –  
253 –  
254 –  
245    numMol = 0;
246    for(int i = -nx; i < nx; i++) {    
247      for(int j = -ny; j < ny; j++) {      
# Line 266 | Line 256 | int main(int argc, char *argv []) {
256          for(int l = 0; l < numMolPerCell; l++) {
257  
258   #ifdef HAVE_CGAL
259 <          if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
259 >          if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
260              numMol++;
261            }
262 + #else
263 +           numMol++;
264   #endif
265          }
266        }
267      }
268    }
269 <  std::cerr << "numMol before is " << numMol << std::endl;
269 >
270    
271    // needed for writing out new md file.
272    
# Line 299 | Line 291 | int main(int argc, char *argv []) {
291    Molecule* mol;
292    SimInfo::MoleculeIterator mi;
293    mol = NewInfo->beginMolecule(mi);
294 <  numMol = 0;
295 <  int countMol = 0;
294 >
295 >
296    for(int i = -nx; i < nx; i++) {
297       for(int j = -ny; j < ny; j++) {
298          for(int k = -nz; k < nz; k++) {
# Line 309 | Line 301 | int main(int argc, char *argv []) {
301             simpleLat->getLatticePointsPos(latticePos, i, j, k);
302            
303             for(int l = 0; l < numMolPerCell; l++) {
304 <              if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
305 <                 countMol++;              
304 > #ifdef HAVE_CGAL              
305 >              if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
306 > #endif                              
307                   if (mol != NULL) {
308                      locator->placeMol(latticePos[l], latticeOrt[l], mol);
316 –                    numMol++;
309                   } else {
310 <                    std::cerr<<"Error in placing molecule " << countMol << std::endl;                    
310 >                    std::cerr<<"Error in placing molecule " << std::endl;                    
311                   }
312                   mol = NewInfo->nextMolecule(mi);
313 + #ifdef HAVE_CGAL                
314                }
315 <              
315 > #endif              
316             }
317          }
318       }
319    }
320    
321 <  std::cerr << "numMol after is " << numMol << std::endl;
321 >
322    
323    //fill Hmat
324    hmat(0, 0)= nx * latticeConstant;

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