--- trunk/src/applications/hydrodynamics/BeadModel.cpp	2006/03/15 15:51:44	898
+++ trunk/src/applications/hydrodynamics/BeadModel.cpp	2009/11/25 20:02:06	1390
@@ -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.
@@ -37,57 +28,92 @@
  * 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, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
 
 #include "applications/hydrodynamics/BeadModel.hpp"
 
-namespace oopse {
-bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
-
+namespace OpenMD {
+  bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
+    
     if (sd_->isAtom()) {
-        createSingleBead(static_cast<Atom*>(sd_), beads);
+      if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
+        sprintf( painCave.errMsg,
+                 "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
+        painCave.severity = OPENMD_ERROR;
+        painCave.isFatal = 1;
+        simError();    
+        return false;
+      }
     }
     else if (sd_->isRigidBody()) {
-        RigidBody* rb = static_cast<RigidBody*>(sd_);
-        std::vector<Atom*>::iterator ai; 
-        Atom* atom;
-        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
-            if (!createSingleBead(atom, beads))
-                return false;
+      RigidBody* rb = static_cast<RigidBody*>(sd_);
+      std::vector<Atom*>::iterator ai; 
+      Atom* atom;
+      for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
+        if (!createSingleBead(atom, beads)) {
+          sprintf( painCave.errMsg,
+                   "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
+          painCave.severity = OPENMD_ERROR;
+          painCave.isFatal = 1;
+          simError();    
+          return false;
         }
-    }
-
+      }
+    }    
     return true;
-}
-
-bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
+  }
+  
+  bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
     AtomType* atomType = atom->getAtomType();
-
+    
     if (atomType->isGayBerne()) {
-        return false;
+      return false;
     } else if (atomType->isLennardJones()){
-        GenericData* data = atomType->getPropertyByName("LennardJones");
-        if (data != NULL) {
-            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
-
-            if (ljData != NULL) {
-                LJParam ljParam = ljData->getData();
-                BeadParam currBead;
-                currBead.atomName = atom->getType();
-                currBead.pos = atom->getPos();
-                currBead.radius = ljParam.sigma/2.0;
-                beads.push_back(currBead);
+      GenericData* data = atomType->getPropertyByName("LennardJones");
+      if (data != NULL) {
+        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
+        
+        if (ljData != NULL) {
+          LJParam ljParam = ljData->getData();
+          BeadParam currBead;
+          currBead.atomName = atom->getType();
+          currBead.pos = atom->getPos();
+          currBead.radius = ljParam.sigma/2.0;
+          beads.push_back(currBead);
         } else {
-            sprintf( painCave.errMsg,
-            "Can not cast GenericData to LJParam\n");
-            painCave.severity = OOPSE_ERROR;
-            painCave.isFatal = 1;
-            simError();          
-            }       
-        }
+          sprintf( painCave.errMsg,
+                   "Can not cast GenericData to LJParam\n");
+          painCave.severity = OPENMD_ERROR;
+          painCave.isFatal = 1;
+          simError();          
+        }       
+      }
+    } else {
+      int obanum = etab.GetAtomicNum((atom->getType()).c_str());
+      if (obanum != 0) {
+        BeadParam currBead;      
+        currBead.atomName = atom->getType();
+        currBead.pos = atom->getPos();        
+        currBead.radius = etab.GetVdwRad(obanum);
+        std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n";
+        beads.push_back(currBead);
+      } else {
+        sprintf( painCave.errMsg,
+                 "Could not find atom type in default element.txt\n");
+        painCave.severity = OPENMD_ERROR;
+        painCave.isFatal = 1;
+        simError();          
+      }
     }
-
-    return true;
+    return true;    
+  }
 }
-
-}