--- trunk/src/applications/hydrodynamics/BeadModel.cpp	2006/04/25 02:06:12	944
+++ trunk/src/applications/hydrodynamics/BeadModel.cpp	2012/08/22 02:28:28	1782
@@ -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.
@@ -37,18 +28,29 @@
  * 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include "applications/hydrodynamics/BeadModel.hpp"
+#include "types/LennardJonesAdapter.hpp"
 
-namespace oopse {
+namespace OpenMD {
   bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
     
     if (sd_->isAtom()) {
       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 = OOPSE_ERROR;
+        painCave.severity = OPENMD_ERROR;
         painCave.isFatal = 1;
         simError();    
         return false;
@@ -62,7 +64,7 @@ namespace oopse {
         if (!createSingleBead(atom, beads)) {
           sprintf( painCave.errMsg,
                    "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
-          painCave.severity = OOPSE_ERROR;
+          painCave.severity = OPENMD_ERROR;
           painCave.isFatal = 1;
           simError();    
           return false;
@@ -74,49 +76,32 @@ namespace oopse {
   
   bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
     AtomType* atomType = atom->getAtomType();
-    
+    LennardJonesAdapter lja = LennardJonesAdapter(atomType);
     if (atomType->isGayBerne()) {
       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);
-        } else {
-          sprintf( painCave.errMsg,
-                   "Can not cast GenericData to LJParam\n");
-          painCave.severity = OOPSE_ERROR;
-          painCave.isFatal = 1;
-          simError();          
-        }       
+    } else if (lja.isLennardJones()){
+      BeadParam currBead;
+      currBead.atomName = atom->getType();
+      currBead.pos = atom->getPos();
+      currBead.radius = lja.getSigma()/2.0;
+      beads.push_back(currBead);
+    } 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();          
       }
-    } else if (atomType->isEAM()) {
-      GenericData* data = atomType->getPropertyByName("EAM");
-      if (data != NULL) {
-        EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);          
-        if (eamData != NULL) {
-          EAMParam eamParam = eamData->getData();
-          BeadParam currBead;
-          currBead.atomName = atom->getType();
-          currBead.pos = atom->getPos();
-          currBead.radius = eamParam.rcut;
-          beads.push_back(currBead);
-        } else {
-          sprintf( painCave.errMsg,
-                   "Can not cast GenericData to EAMParam\n");
-          painCave.severity = OOPSE_ERROR;
-          painCave.isFatal = 1;
-          simError();          
-        }       
-      }
-      return true;
-    }   
+    }
+    return true;    
   }
 }