--- trunk/src/restraints/RestraintForceManager.cpp	2009/10/07 20:49:50	1364
+++ trunk/src/restraints/RestraintForceManager.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.
@@ -37,6 +28,15 @@
  * 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 <cmath>
@@ -45,7 +45,7 @@
 #include "restraints/ObjectRestraint.hpp"
 #include "io/RestReader.hpp"
 #include "utils/simError.h"
-#include "utils/OOPSEConstant.hpp"
+#include "utils/PhysicalConstants.hpp"
 #include "utils/StringUtils.hpp"
 #include "selection/SelectionEvaluator.hpp"
 #include "selection/SelectionManager.hpp"
@@ -54,7 +54,7 @@
 #endif
 
 
-namespace oopse {
+namespace OpenMD {
 
   RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) {
 
@@ -109,17 +109,46 @@ namespace oopse {
           molIndex = stamp[i]->getMolIndex();
         }
         
-        Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex);
-        
-        if (mol == NULL) {
+        if (molIndex < 0) {
           sprintf(painCave.errMsg,
-                  "Restraint Error: A molecular restraint was specified, but\n"
-                  "\tno molecule was found with global index %d.\n",
-                  molIndex);
+                  "Restraint Error: A molecular restraint was specified\n"
+                  "\twith a molIndex that was less than 0\n");
           painCave.isFatal = 1;
           simError();      
         }
+        if (molIndex >= info_->getNGlobalMolecules()) {
+          sprintf(painCave.errMsg,
+                  "Restraint Error: A molecular restraint was specified with\n"
+                  "\ta molIndex that was greater than the total number of molecules\n");
+          painCave.isFatal = 1;
+          simError();      
+        }
+       
+        Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex);
         
+        if (mol == NULL) {
+#ifdef IS_MPI
+          // getMoleculeByGlobalIndex returns a NULL in parallel if
+          // this proc doesn't have the molecule.  Do a quick check to
+          // make sure another processor is supposed to have it.
+         
+          int myrank = MPI::COMM_WORLD.Get_rank();
+          if (info_->getMolToProc(molIndex) == myrank) {
+            // If we were supposed to have it but got a null, then freak out.
+#endif
+
+            sprintf(painCave.errMsg,
+                    "Restraint Error: A molecular restraint was specified, but\n"
+                    "\tno molecule was found with global index %d.\n",
+                    molIndex);
+            painCave.isFatal = 1;
+            simError();     
+
+#ifdef IS_MPI
+          }
+#endif
+        }
+        
         MolecularRestraint* rest = new MolecularRestraint();
 
         std::string restPre("mol_");
@@ -318,20 +347,20 @@ namespace oopse {
           if (mRest == NULL) {
             sprintf( painCave.errMsg,
                      "Can not cast RestraintData to MolecularRestraint\n");
-            painCave.severity = OOPSE_ERROR;
+            painCave.severity = OPENMD_ERROR;
             painCave.isFatal = 1;
             simError();                      
           }
         } else {
           sprintf( painCave.errMsg,
                    "Can not cast GenericData to RestraintData\n");
-          painCave.severity = OOPSE_ERROR;
+          painCave.severity = OPENMD_ERROR;
           painCave.isFatal = 1;
           simError();       
         }
       } else {
         sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
-        painCave.severity = OOPSE_ERROR;
+        painCave.severity = OPENMD_ERROR;
         painCave.isFatal = 1;
         simError();          
       }
@@ -383,20 +412,20 @@ namespace oopse {
           if (oRest == NULL) {
             sprintf( painCave.errMsg,
                      "Can not cast RestraintData to ObjectRestraint\n");
-            painCave.severity = OOPSE_ERROR;
+            painCave.severity = OPENMD_ERROR;
             painCave.isFatal = 1;
             simError();                      
           }
         } else {
           sprintf( painCave.errMsg,
                    "Can not cast GenericData to RestraintData\n");
-          painCave.severity = OOPSE_ERROR;
+          painCave.severity = OPENMD_ERROR;
           painCave.isFatal = 1;
           simError();       
         }
       } else {
         sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
-        painCave.severity = OOPSE_ERROR;
+        painCave.severity = OPENMD_ERROR;
         painCave.isFatal = 1;
         simError();          
       }