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Comparing branches/development/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
42  
43   #include <cstdlib>
# Line 71 | Line 72 | int main(int argc, char *argv []) {
72  
73   int main(int argc, char *argv []) {
74    
74 –  //register force fields
75 –  registerForceFields();
75    registerLattice();
76    
77    gengetopt_args_info args_info;
# Line 126 | Line 125 | int main(int argc, char *argv []) {
125    /* Build a lattice and get lattice points for this lattice constant */
126    vector<Vector3d> sites = nanoParticle.getSites();
127    vector<Vector3d> orientations = nanoParticle.getOrientations();
128 +
129 +
130    std::vector<int> vacancyTargets;
131    vector<bool> isVacancy;
132    
133    Vector3d myLoc;
134    RealType myR;
135  
136 <  for (int i = 0; i < sites.size(); i++)
136 >  for (unsigned int i = 0; i < sites.size(); i++)
137      isVacancy.push_back(false);
138  
139    if (args_info.vacancyPercent_given) {
# Line 156 | Line 157 | int main(int argc, char *argv []) {
157        }
158        if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
159          
160 <        for (int i = 0; i < sites.size(); i++) {
160 >        for (unsigned int i = 0; i < sites.size(); i++) {
161            myLoc = sites[i];
162            myR = myLoc.length();
163            if (myR >= vIR && myR <= vOR) {
# Line 176 | Line 177 | int main(int argc, char *argv []) {
177          simError();
178  
179          isVacancy.clear();
180 <        for (int i = 0; i < sites.size(); i++) {
180 >        for (unsigned int i = 0; i < sites.size(); i++) {
181            bool vac = false;
182 <          for (int j = 0; j < vacancyTargets.size(); j++) {
182 >          for (unsigned int j = 0; j < vacancyTargets.size(); j++) {
183              if (i == vacancyTargets[j]) vac = true;
184            }
185            isVacancy.push_back(vac);
# Line 304 | Line 305 | int main(int argc, char *argv []) {
305      }
306    } else {
307  
308 <    for (int i = 0; i < shellRadii.size(); i++) {
308 >    for (unsigned int i = 0; i < shellRadii.size(); i++) {
309        if (shellRadii.at(i) > particleRadius + 1e-6 ) {
310          sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
311          painCave.isFatal = 1;
# Line 325 | Line 326 | int main(int argc, char *argv []) {
326      simError();
327      /* Random particle is the default case*/
328  
329 <    for (int i = 0; i < sites.size(); i++)
329 >    for (unsigned int i = 0; i < sites.size(); i++)
330        if (!isVacancy[i]) ids.push_back(i);
331      
332      std::random_shuffle(ids.begin(), ids.end());
# Line 340 | Line 341 | int main(int argc, char *argv []) {
341      nMol.clear();
342      nMol.resize(nComponents);
343  
344 <    for (int i = 0; i < sites.size(); i++) {
344 >    for (unsigned int i = 0; i < sites.size(); i++) {
345        myLoc = sites[i];
346        myR = myLoc.length();
347        smallestSoFar = particleRadius;      
# Line 364 | Line 365 | int main(int argc, char *argv []) {
365    //creat new .md file on fly which corrects the number of molecule    
366    createMdFile(inputFileName, outputFileName, nMol);
367    
368 <  if (oldInfo != NULL)
368 <    delete oldInfo;
368 >  delete oldInfo;
369    
370    SimCreator newCreator;
371    SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
# Line 376 | Line 376 | int main(int argc, char *argv []) {
376    mol = NewInfo->beginMolecule(mi);
377  
378    int l = 0;
379 –  int whichSite = 0;
379  
380    for (int i = 0; i < nComponents; i++){
381      locator = new MoLocator(NewInfo->getMoleculeStamp(i),
382                              NewInfo->getForceField());
383      
384      if (!args_info.molFraction_given) {
385 <      for (int n = 0; n < sites.size(); n++) {
385 >      for (unsigned int n = 0; n < sites.size(); n++) {
386          if (!isVacancy[n]) {
387            if (componentFromSite[n] == i) {
388              mol = NewInfo->getMoleculeByGlobalIndex(l);
# Line 454 | Line 453 | void createMdFile(const std::string&oldMdFileName,
453    newMdFile.open(newMdFileName.c_str());
454    oldMdFile.getline(buffer, MAXLEN);
455  
456 <  int i = 0;
456 >  unsigned int i = 0;
457    while (!oldMdFile.eof()) {
458  
459      //correct molecule number

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