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Comparing branches/development/src/applications/nanoparticleBuilder/nanorodBuilder.cpp (file contents):
Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   *  Created by Kelsey M. Stocker on 2/9/12.
# Line 55 | Line 55
55  
56   #include "config.h"
57   #include "shapedLatticeRod.hpp"
58 + #include "shapedLatticeEllipsoid.hpp"
59   #include "nanorodBuilderCmd.h"
60   #include "lattice/LatticeFactory.hpp"
61   #include "utils/MoLocator.hpp"
# Line 123 | Line 124 | int main(int argc, char *argv []) {
124    rodLength = args_info.length_arg;
125    Globals* simParams = oldInfo->getSimParams();
126    
127 <  /* Create nanorod */
128 <  shapedLatticeRod nanoRod(latticeConstant, latticeType,
129 <                           rodRadius, rodLength);
130 <  
131 <  /* Build a lattice and get lattice points for this lattice constant */
132 <  vector<Vector3d> sites = nanoRod.getSites();
133 <  vector<Vector3d> orientations = nanoRod.getOrientations();
127 >  vector<Vector3d> sites;
128 >  vector<Vector3d> orientations;
129 >
130 >  if (args_info.ellipsoid_flag) {
131 >    shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType,
132 >                                         rodLength, rodRadius);
133 >    sites = nanoEllipsoid.getSites();
134 >    orientations = nanoEllipsoid.getOrientations();
135 >  } else {
136 >    
137 >    /* Create nanorod */
138 >    shapedLatticeRod nanoRod(latticeConstant, latticeType,
139 >                             rodRadius, rodLength);
140 >    /* Build a lattice and get lattice points for this lattice constant */
141 >    sites = nanoRod.getSites();
142 >    orientations = nanoRod.getOrientations();
143 >  }
144 >
145    std::vector<int> vacancyTargets;
146    vector<bool> isVacancy;
147    
# Line 347 | Line 359 | int main(int argc, char *argv []) {
359      painCave.isFatal = 0;
360      simError();
361  
362 <    RealType smallestSoFar;
362 >    // RealType smallestSoFar;
363      int myComponent = -1;
364      nMol.clear();
365      nMol.resize(nComponents);
366  
367      // cerr << "shellRadii[0] " << shellRadii[0] << "\n";
368 <    //  cerr << "rodRadius " << rodRadius << "\n";
368 >    // cerr << "rodRadius " << rodRadius << "\n";
369  
370      for (int i = 0; i < sites.size(); i++) {
371        myLoc = sites[i];
372        myR = myLoc.length();
373 <      smallestSoFar = rodRadius;  
374 <      //cerr << "vac = " << isVacancy[i]<< "\n";
373 >      // smallestSoFar = rodRadius;  
374 >      // cerr << "vac = " << isVacancy[i]<< "\n";
375      
376        if (!isVacancy[i]) {
377  
# Line 387 | Line 399 | int main(int argc, char *argv []) {
399  
400    createMdFile(inputFileName, outputFileName, nMol);
401    
402 <  if (oldInfo != NULL)
391 <    delete oldInfo;
402 >  delete oldInfo;
403    
404    SimCreator newCreator;
405    SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
# Line 399 | Line 410 | int main(int argc, char *argv []) {
410    mol = NewInfo->beginMolecule(mi);
411  
412    int l = 0;
402 –  int whichSite = 0;
413  
414    for (int i = 0; i < nComponents; i++){
415      locator = new MoLocator(NewInfo->getMoleculeStamp(i),

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