--- trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp	2015/03/07 21:41:51	2071
@@ -35,8 +35,9 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include <cstdlib>
@@ -71,26 +72,17 @@ int main(int argc, char *argv []) {
 
 int main(int argc, char *argv []) {
   
-  //register force fields
-  registerForceFields();
   registerLattice();
   
   gengetopt_args_info args_info;
   std::string latticeType;
   std::string inputFileName;
   std::string outputFileName;
-
   MoLocator* locator;
   int nComponents;
   double latticeConstant;
-  std::vector<double> lc;
-
   RealType particleRadius;
-
   Mat3x3d hmat;
-  std::vector<Vector3d> latticePos;
-  std::vector<Vector3d> latticeOrt;
- 
   DumpWriter *writer;
   
   // Parse Command Line Arguments
@@ -126,18 +118,21 @@ int main(int argc, char *argv []) {
   /* Build a lattice and get lattice points for this lattice constant */
   vector<Vector3d> sites = nanoParticle.getSites();
   vector<Vector3d> orientations = nanoParticle.getOrientations();
-  std::vector<int> vacancyTargets;
+
+
+  std::vector<std::size_t> vacancyTargets;
   vector<bool> isVacancy;
   
   Vector3d myLoc;
   RealType myR;
  
-  for (int i = 0; i < sites.size(); i++) 
+  for (unsigned int i = 0; i < sites.size(); i++) 
     isVacancy.push_back(false);
 
   if (args_info.vacancyPercent_given) {
     if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
-      sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
+      sprintf(painCave.errMsg, 
+	      "vacancyPercent was set to a non-sensical value.");
       painCave.isFatal = 1;
       simError();
     } else {
@@ -156,7 +151,7 @@ int main(int argc, char *argv []) {
       }
       if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
         
-        for (int i = 0; i < sites.size(); i++) {
+        for (std::size_t i = 0; i < sites.size(); i++) {
           myLoc = sites[i];
           myR = myLoc.length();
           if (myR >= vIR && myR <= vOR) {
@@ -173,12 +168,13 @@ int main(int argc, char *argv []) {
                 "\tsites between %lf and %lf.", (int) vacancyTargets.size(), 
                 vIR, vOR); 
         painCave.isFatal = 0;
+        painCave.severity = OPENMD_INFO;
         simError();
 
         isVacancy.clear();
-        for (int i = 0; i < sites.size(); i++) {
+        for (std::size_t i = 0; i < sites.size(); i++) {
           bool vac = false;
-          for (int j = 0; j < vacancyTargets.size(); j++) {
+          for (std::size_t j = 0; j < vacancyTargets.size(); j++) {
             if (i == vacancyTargets[j]) vac = true;
           }
           isVacancy.push_back(vac);
@@ -194,12 +190,11 @@ int main(int argc, char *argv []) {
   }
 
   /* Get number of lattice sites */
-  int nSites = sites.size() - vacancyTargets.size();
+  std::size_t nSites = sites.size() - vacancyTargets.size();
 
   std::vector<Component*> components = simParams->getComponents();
   std::vector<RealType> molFractions;
   std::vector<RealType> shellRadii;
-  std::vector<RealType> molecularMasses;
   std::vector<int> nMol;
   std::map<int, int> componentFromSite;
   nComponents = components.size();
@@ -276,7 +271,8 @@ int main(int argc, char *argv []) {
       totalFraction += molFractions.at(i);
     }
     if (abs(totalFraction - 1.0) > 1e-6) {
-      sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
+      sprintf(painCave.errMsg, 
+	      "The sum of molFractions was not close enough to 1.0");
       painCave.isFatal = 1;
       simError();
     }
@@ -290,28 +286,31 @@ int main(int argc, char *argv []) {
     
     // recompute actual mol fractions and perform final sanity check:
     
-    int totalMolecules = 0;
+    std::size_t totalMolecules = 0;
     for (int i=0; i < nComponents; i++) {
       molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
       totalMolecules += nMol.at(i);
     }
     
     if (totalMolecules != nSites) {
-      sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
+      sprintf(painCave.errMsg, 
+	      "Computed total number of molecules is not equal "
               "to the number of lattice sites!");
       painCave.isFatal = 1;
       simError();
     }
   } else {
 
-    for (int i = 0; i < shellRadii.size(); i++) {
+    for (unsigned int i = 0; i < shellRadii.size(); i++) {
       if (shellRadii.at(i) > particleRadius + 1e-6 ) {
-        sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
+        sprintf(painCave.errMsg, 
+		"One of the shellRadius values exceeds the particle Radius.");
         painCave.isFatal = 1;
         simError();
       } 
       if (shellRadii.at(i) <= 0.0 ) {
-        sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
+        sprintf(painCave.errMsg, 
+		"One of the shellRadius values is smaller than zero!");
         painCave.isFatal = 1;
         simError();
       }
@@ -322,10 +321,11 @@ int main(int argc, char *argv []) {
   if ((int)args_info.molFraction_given){
     sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
     painCave.isFatal = 0;
+    painCave.severity = OPENMD_INFO;
     simError();
     /* Random particle is the default case*/
 
-    for (int i = 0; i < sites.size(); i++) 
+    for (unsigned int i = 0; i < sites.size(); i++) 
       if (!isVacancy[i]) ids.push_back(i);
     
     std::random_shuffle(ids.begin(), ids.end());
@@ -333,6 +333,7 @@ int main(int argc, char *argv []) {
   } else{ 
     sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
     painCave.isFatal = 0;
+    painCave.severity = OPENMD_INFO;
     simError();
 
     RealType smallestSoFar;
@@ -340,7 +341,7 @@ int main(int argc, char *argv []) {
     nMol.clear();
     nMol.resize(nComponents);
 
-    for (int i = 0; i < sites.size(); i++) {
+    for (unsigned int i = 0; i < sites.size(); i++) {
       myLoc = sites[i];
       myR = myLoc.length();
       smallestSoFar = particleRadius;      
@@ -364,8 +365,7 @@ int main(int argc, char *argv []) {
   //creat new .md file on fly which corrects the number of molecule     
   createMdFile(inputFileName, outputFileName, nMol);
   
-  if (oldInfo != NULL)
-    delete oldInfo;
+  delete oldInfo;
   
   SimCreator newCreator;
   SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
@@ -376,14 +376,13 @@ int main(int argc, char *argv []) {
   mol = NewInfo->beginMolecule(mi);
 
   int l = 0;
-  int whichSite = 0;
 
   for (int i = 0; i < nComponents; i++){
     locator = new MoLocator(NewInfo->getMoleculeStamp(i), 
                             NewInfo->getForceField());
     
     if (!args_info.molFraction_given) {
-      for (int n = 0; n < sites.size(); n++) {
+      for (unsigned int n = 0; n < sites.size(); n++) {
         if (!isVacancy[n]) {
           if (componentFromSite[n] == i) {
             mol = NewInfo->getMoleculeByGlobalIndex(l);
@@ -437,6 +436,7 @@ int main(int argc, char *argv []) {
   sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
           "generated.\n", outputFileName.c_str());
   painCave.isFatal = 0;
+  painCave.severity = OPENMD_INFO;
   simError();
   return 0;
 }
@@ -454,7 +454,7 @@ void createMdFile(const std::string&oldMdFileName, 
   newMdFile.open(newMdFileName.c_str());
   oldMdFile.getline(buffer, MAXLEN);
 
-  int i = 0;
+  unsigned int i = 0;
   while (!oldMdFile.eof()) {
 
     //correct molecule number