--- trunk/src/applications/hydrodynamics/ShapeBuilder.cpp	2006/04/25 02:06:12	944
+++ trunk/src/applications/hydrodynamics/ShapeBuilder.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.
@@ -37,12 +28,21 @@
  * 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/ShapeBuilder.hpp"
-#include "applications/hydrodynamics/Spheric.hpp"
-#include "applications/hydrodynamics/Ellipsoid.hpp"
+#include "hydrodynamics/Sphere.hpp"
+#include "hydrodynamics/Ellipsoid.hpp"
 #include "applications/hydrodynamics/CompositeShape.hpp"
-namespace oopse {
+namespace OpenMD {
   
   Shape* ShapeBuilder::createShape(StuntDouble* sd) {
     Shape* currShape = NULL;
@@ -66,32 +66,27 @@ namespace oopse {
         
         if (ljData != NULL) {
           LJParam ljParam = ljData->getData();
-          currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
+          currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
         } else {
           sprintf( painCave.errMsg,
                    "Can not cast GenericData to LJParam\n");
-          painCave.severity = OOPSE_ERROR;
+          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();
-          currShape = new Spheric(atom->getPos(), eamParam.rcut);
-        } else {
-          sprintf( painCave.errMsg,
-                   "Can not cast GenericData to EAMParam\n");
-          painCave.severity = OOPSE_ERROR;
-          painCave.isFatal = 1;
-          simError();          
-        }       
+    } else {
+      int obanum = etab.GetAtomicNum((atom->getType()).c_str());
+      if (obanum != 0) {
+        currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
+      } else {
+        sprintf( painCave.errMsg,
+                 "Could not find atom type in default element.txt\n");
+        painCave.severity = OPENMD_ERROR;
+        painCave.isFatal = 1;
+        simError();          
       }
-    }    
+    }
     return currShape;
   }
   
@@ -107,17 +102,18 @@ namespace oopse {
         
         if (gayBerneData != NULL) {  
           GayBerneParam gayBerneParam = gayBerneData->getData();
-          currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
+          currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0, 
+				    gayBerneParam.GB_d/2.0, datom->getA());
         } else {
           sprintf( painCave.errMsg,
                    "Can not cast GenericData to GayBerneParam\n");
-          painCave.severity = OOPSE_ERROR;
+          painCave.severity = OPENMD_ERROR;
           painCave.isFatal = 1;
           simError();   
         }
       } else {
         sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
-        painCave.severity = OOPSE_ERROR;
+        painCave.severity = OPENMD_ERROR;
         painCave.isFatal = 1;
         simError();    
       }            
@@ -128,30 +124,26 @@ namespace oopse {
         
         if (ljData != NULL) {
           LJParam ljParam = ljData->getData();
-          currShape = new Spheric(datom->getPos(), ljParam.sigma/2.0);
+          currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0);
         } else {
           sprintf( painCave.errMsg,
                    "Can not cast GenericData to LJParam\n");
-          painCave.severity = OOPSE_ERROR;
+          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();
-            currShape = new Spheric(datom->getPos(), eamParam.rcut);
-          } else {
-            sprintf( painCave.errMsg,
-                     "Can not cast GenericData to EAMParam\n");
-            painCave.severity = OOPSE_ERROR;
-            painCave.isFatal = 1;
-            simError();          
-          }       
+      } else {
+        int obanum = etab.GetAtomicNum((datom->getType()).c_str());
+        if (obanum != 0) {
+          currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
+        } else {
+          sprintf( painCave.errMsg,
+                   "Could not find atom type in default element.txt\n");
+          painCave.severity = OPENMD_ERROR;
+          painCave.isFatal = 1;
+          simError();          
         }
-      }
+      }      
     }
     return currShape;
   }