--- trunk/src/brains/MoleculeCreator.cpp	2008/09/10 19:51:45	1290
+++ trunk/src/brains/MoleculeCreator.cpp	2013/07/19 21:25:45	1908
@@ -6,19 +6,10 @@
  * 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.
@@ -37,13 +28,22 @@
  * arising out of the use of or inability to use software, even if the
  * 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).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
   
 /**
  * @file MoleculeCreator.cpp
  * @author tlin
  * @date 11/04/2004
- * @time 13:44am
  * @version 1.0
  */
 
@@ -54,19 +54,20 @@
 #include "brains/MoleculeCreator.hpp"
 #include "primitives/GhostBend.hpp"
 #include "primitives/GhostTorsion.hpp"
-#include "types/DirectionalAtomType.hpp"
+#include "types/AtomType.hpp"
 #include "types/FixedBondType.hpp"
 #include "utils/simError.h"
 #include "utils/StringUtils.hpp"
 
-namespace oopse {
+namespace OpenMD {
   
   Molecule* MoleculeCreator::createMolecule(ForceField* ff, 
                                             MoleculeStamp *molStamp,
 					    int stampId, int globalIndex, 
                                             LocalIndexManager* localIndexMan) {
-    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
-    
+    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), 
+                                 molStamp->getRegion() );
+
     //create atoms
     Atom* atom;
     AtomStamp* currentAtomStamp;
@@ -138,7 +139,7 @@ namespace oopse {
     int nCutoffGroups = molStamp->getNCutoffGroups();
     for (int i = 0; i < nCutoffGroups; ++i) {
       currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
-      cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
+      cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan);
       mol->addCutoffGroup(cutoffGroup);
     }
 
@@ -169,13 +170,20 @@ namespace oopse {
     // every single free atom
     
     for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
-      cutoffGroup = createCutoffGroup(mol, *fai);
+      cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
       mol->addCutoffGroup(cutoffGroup);
     }
     //create constraints
     createConstraintPair(mol);
     createConstraintElem(mol);
     
+    // Does this molecule stamp define a total constrained charge value?
+    // If so, let the created molecule know about it.
+
+    if (molStamp->haveConstrainTotalCharge() ) {
+      mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
+    }
+
     //the construction of this molecule is finished
     mol->complete();
     
@@ -198,21 +206,12 @@ namespace oopse {
       painCave.isFatal = 1;
       simError();
     }
-    
+
     //below code still have some kind of hard-coding smell
     if (atomType->isDirectional()){
-     
-      DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
-        
-      if (dAtomType == NULL) {
-	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
 
-	painCave.isFatal = 1;
-	simError();
-      }
-
       DirectionalAtom* dAtom;
-      dAtom = new DirectionalAtom(dAtomType);
+      dAtom = new DirectionalAtom(atomType);
       atom = dAtom;    
     }
     else{
@@ -257,7 +256,7 @@ namespace oopse {
     //The third part is the index of the rigidbody defined in meta-data file
     //For example, Butane_RB_0 is a valid rigid body name of butane molecule
     /**@todo replace itoa by lexi_cast */
-    std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
+    std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
     rb->setType(mol->getType() + "_RB_" + s.c_str());
 
     return rb;
@@ -438,7 +437,7 @@ namespace oopse {
               atomD->getType().c_str());
       
       painCave.isFatal = 0;
-      painCave.severity = OOPSE_INFO;
+      painCave.severity = OPENMD_INFO;
       simError();
       return NULL;
     } else {
@@ -449,7 +448,9 @@ namespace oopse {
   }
   
 
-  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
+  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, 
+                                                  CutoffGroupStamp* stamp,
+                                                  LocalIndexManager* localIndexMan) {
     int nAtoms;
     CutoffGroup* cg;
     Atom* atom;
@@ -461,14 +462,22 @@ namespace oopse {
       assert(atom);
       cg->addAtom(atom);
     }
-
+    
+    //set the local index of this cutoffGroup, global index will be set later
+    cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
+    
     return cg;
   }    
-
-  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
+  
+  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
+                                                  LocalIndexManager* localIndexMan) {
     CutoffGroup* cg;
     cg  = new CutoffGroup();
     cg->addAtom(atom);
+
+    //set the local index of this cutoffGroup, global index will be set later
+    cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
+
     return cg;
   }