--- trunk/src/applications/randomBuilder/randomBuilder.cpp	2006/10/10 18:34:12	1067
+++ trunk/src/applications/randomBuilder/randomBuilder.cpp	2014/03/13 13:03:11	1978
@@ -5,19 +5,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,12 +28,21 @@
  * University of Notre Dame has been advised of the possibility of
  * such damages.
  *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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, 234107 (2008).          
+ * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
  *
  *  randomBuilder.cpp
  *
  *  Created by Charles F. Vardeman II on 10 Apr 2006.
  *  @author  Charles F. Vardeman II
- *  @version $Id: randomBuilder.cpp,v 1.6 2006-10-10 18:34:12 gezelter Exp $
+ *  @version $Id$
  *
  */
 
@@ -69,7 +69,7 @@ using namespace std;
 #include "utils/StringUtils.hpp"
 
 using namespace std;
-using namespace oopse;
+using namespace OpenMD;
 
 void createMdFile(const std::string&oldMdFileName, 
                   const std::string&newMdFileName,
@@ -77,8 +77,6 @@ int main(int argc, char *argv []) {
 
 int main(int argc, char *argv []) {
 
-  // register force fields
-  registerForceFields();
   registerLattice();
     
   gengetopt_args_info args_info;
@@ -233,8 +231,8 @@ int main(int argc, char *argv []) {
   for (int i=0; i < nComponents; i++) {
     molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
     totalMolecules += nMol.at(i);
-    molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i),
-                                         oldInfo->getForceField()));
+    molecularMasses.push_back(MoLocator::getMolMass(oldInfo->getMoleculeStamp(i),
+                                                    oldInfo->getForceField()));
     totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
   }
   RealType avgMass = totalMass / (RealType) totalMolecules;
@@ -285,8 +283,7 @@ int main(int argc, char *argv []) {
 
   createMdFile(inputFileName, outputFileName, nMol);
 
-  if (oldInfo != NULL)
-    delete oldInfo;
+  delete oldInfo;
 
   // We need to read in the new SimInfo object, then Parse the 
   // md file and set up the system
@@ -317,7 +314,7 @@ int main(int argc, char *argv []) {
   // Randomize a vector of ints:
 
   vector<int> ids;
-  for (int i = 0; i < sites.size(); i++) ids.push_back(i);
+  for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i);
   std::random_shuffle(ids.begin(), ids.end());
 
   Molecule* mol;
@@ -348,9 +345,10 @@ int main(int argc, char *argv []) {
 
   delete writer;
 
-  sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
+  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;
 }
@@ -370,12 +368,12 @@ void createMdFile(const std::string&oldMdFileName, 
   
   oldMdFile.getline(buffer, MAXLEN);
  
-  int i = 0;
+  unsigned int i = 0;
   while (!oldMdFile.eof()) {
     
     //correct molecule number
     if (strstr(buffer, "nMol") != NULL) {
-      if(i<nMol.size()){
+      if (i<nMol.size()){
 	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
 	newMdFile << buffer << std::endl;
 	i++;
@@ -388,5 +386,14 @@ void createMdFile(const std::string&oldMdFileName, 
   
   oldMdFile.close();
   newMdFile.close();
+
+  if (i != nMol.size()) {
+    sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
+            "\tstatements in component blocks.  Make sure that all\n"
+            "\tcomponents in the template file have nMol=1");
+    painCave.isFatal = 1;
+    simError();
+  }
+
 }