--- trunk/src/applications/staticProps/BondOrderParameter.cpp	2006/11/21 20:44:54	1094
+++ trunk/src/applications/staticProps/BondOrderParameter.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.
@@ -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 1.21 2006-11-21 20:44:54 gezelter Exp $
+ *  @version $Id: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $
  *
  */
  
@@ -53,7 +50,7 @@
 #include "primitives/Molecule.hpp"
 #include "utils/NumericConstant.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   BondOrderParameter::BondOrderParameter(SimInfo* info, 
                                          const std::string& filename, 
@@ -83,8 +80,8 @@ namespace oopse {
     // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
     // use values for MinW_ and MaxW_ that are slightly larger than this:
 
-    MinW_ = -0.25;
-    MaxW_ = 0.25;
+    MinW_ = -1.1;
+    MaxW_ = 1.1;
     deltaW_ = (MaxW_ - MinW_) / nbins;
 
     // Make arrays for Wigner3jm
@@ -105,7 +102,7 @@ namespace oopse {
         for (int ii = 0; ii < 2*l + 1; ii++){
           THRCOF[ii] = 0.0;
         }
-            
+
         // Get Wigner coefficients
         Wigner3jm(&lPass, &lPass, &lPass, 
                   &m1Pass, &m2m, &m2M, 
@@ -114,7 +111,7 @@ namespace oopse {
         m2Min[lm] = (int)floor(m2m);
         m2Max[lm] = (int)floor(m2M);
         
-        for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
+        for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
           w3j[lm].push_back(THRCOF[mmm]);
         }
       }
@@ -277,7 +274,7 @@ namespace oopse {
           w[l] = 0.0;
           for (int m1 = -l; m1 <= l; m1++) {
             std::pair<int,int> lm = std::make_pair(l, m1);
-            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
+            for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
               int m2 = m2Min[lm] + mmm;
               int m3 = -m1-m2;
               w[l] += w3j[lm][mmm] * q[lm] * 
@@ -322,7 +319,7 @@ namespace oopse {
       W[l] = 0.0;
       for (int m1 = -l; m1 <= l; m1++) {
         std::pair<int,int> lm = std::make_pair(l, m1);
-        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
+        for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
           int m2 = m2Min[lm] + mmm;
           int m3 = -m1-m2;
           W[l] += w3j[lm][mmm] * QBar[lm] * 
@@ -347,7 +344,7 @@ 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 +358,7 @@ 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();  
       }