--- trunk/src/applications/staticProps/BondOrderParameter.cpp	2006/12/20 21:03:11	1100
+++ trunk/src/applications/staticProps/BondOrderParameter.cpp	2011/08/12 14:37:25	1610
@@ -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.
@@ -38,12 +29,18 @@
  * University of Notre Dame has been advised of the possibility of
  * such damages.
  *
- *  BondOrderParameter.cpp
- *  OOPSE-4
+ * 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).                        
  *
  *  Created by J. Daniel Gezelter on 09/26/06.
  *  @author  J. Daniel Gezelter
- *  @version $Id: BondOrderParameter.cpp,v 1.22 2006-12-20 21:03:11 gezelter Exp $
+ *  @version $Id$
  *
  */
  
@@ -53,7 +50,7 @@
 #include "primitives/Molecule.hpp"
 #include "utils/NumericConstant.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   BondOrderParameter::BondOrderParameter(SimInfo* info, 
                                          const std::string& filename, 
@@ -110,7 +107,7 @@ namespace oopse {
         Wigner3jm(&lPass, &lPass, &lPass, 
                   &m1Pass, &m2m, &m2M, 
                   THRCOF, &mSize, &error);
-        
+       
         m2Min[lm] = (int)floor(m2m);
         m2Max[lm] = (int)floor(m2M);
         
@@ -253,6 +250,7 @@ namespace oopse {
                   for(int m = -l; m <= l; m++){
                     sphericalHarmonic.setM(m);
                     q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
+
                   }
                 }
                 nBonds++;
@@ -266,6 +264,7 @@ namespace oopse {
           q2[l] = 0.0;
           for (int m = -l; m <= l; m++){
             q[std::make_pair(l,m)] /= (RealType)nBonds;            
+
             q2[l] += norm(q[std::make_pair(l,m)]);
           }
           q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
@@ -347,7 +346,7 @@ namespace oopse {
       } else {
         sprintf( painCave.errMsg,
                  "q_l value outside reasonable range\n");
-        painCave.severity = OOPSE_ERROR;
+        painCave.severity = OPENMD_ERROR;
         painCave.isFatal = 1;
         simError();  
       }
@@ -361,7 +360,7 @@ namespace oopse {
       } else {
         sprintf( painCave.errMsg,
                  "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
-        painCave.severity = OOPSE_ERROR;
+        painCave.severity = OPENMD_ERROR;
         painCave.isFatal = 1;
         simError();  
       }