--- trunk/src/brains/Snapshot.cpp	2005/04/15 22:04:00	507
+++ trunk/src/brains/Snapshot.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).                        
  */
   
 /**
@@ -51,26 +51,26 @@
 #include "utils/NumericConstant.hpp"
 #include "utils/simError.h"
 #include "utils/Utility.hpp"
-namespace oopse {
+namespace OpenMD {
 
   void  Snapshot::setHmat(const Mat3x3d& m) {
-    const double orthoTolerance = NumericConstant::epsilon;
     hmat_ = m;
     invHmat_ = hmat_.inverse();
     
+
     //prepare fortran Hmat 
-    double fortranHmat[9];
-    double fortranInvHmat[9];
+    RealType fortranHmat[9];
+    RealType fortranInvHmat[9];
     hmat_.getArray(fortranHmat);
     invHmat_.getArray(fortranInvHmat);
 
     //determine whether the box is orthoTolerance or not
     int oldOrthoRhombic = orthoRhombic_;
     
-    double smallDiag = fabs(hmat_(0, 0));
+    RealType smallDiag = fabs(hmat_(0, 0));
     if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
     if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));    
-    double tol = smallDiag * orthoTolerance;
+    RealType tol = smallDiag * orthoTolerance_;
 
     orthoRhombic_ = 1;
 
@@ -89,25 +89,25 @@ namespace oopse {
 
       if( orthoRhombic_ ) {
 	sprintf( painCave.errMsg,
-		 "OOPSE is switching from the default Non-Orthorhombic\n"
+		 "OpenMD is switching from the default Non-Orthorhombic\n"
 		 "\tto the faster Orthorhombic periodic boundary computations.\n"
-		 "\tThis is usually a good thing, but if you wan't the\n"
+		 "\tThis is usually a good thing, but if you want the\n"
 		 "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
 		 "\tvariable ( currently set to %G ) smaller.\n",
-		 orthoTolerance);
-	painCave.severity = OOPSE_INFO;
+		 orthoTolerance_);
+	painCave.severity = OPENMD_INFO;
 	simError();
       }
       else {
 	sprintf( painCave.errMsg,
-		 "OOPSE is switching from the faster Orthorhombic to the more\n"
+		 "OpenMD is switching from the faster Orthorhombic to the more\n"
 		 "\tflexible Non-Orthorhombic periodic boundary computations.\n"
 		 "\tThis is usually because the box has deformed under\n"
-		 "\tNPTf integration. If you wan't to live on the edge with\n"
+		 "\tNPTf integration. If you want to live on the edge with\n"
 		 "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
 		 "\tvariable ( currently set to %G ) larger.\n",
-		 orthoTolerance);
-	painCave.severity = OOPSE_WARNING;
+		 orthoTolerance_);
+	painCave.severity = OPENMD_WARNING;
 	simError();
       }
     }    
@@ -156,5 +156,32 @@ namespace oopse {
 
   }
 
+  Vector3d Snapshot::getCOM() {
+    if( !hasCOM_ ) {
+      sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
+      painCave.severity = OPENMD_ERROR;
+      simError();
+    }
+    return COM_;
+  }
+  
+  Vector3d Snapshot::getCOMvel() {
+    if( !hasCOM_ ) {
+      sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
+      painCave.severity = OPENMD_ERROR;
+      simError();
+    }
+    return COMvel_;
+  }
+  
+  Vector3d Snapshot::getCOMw() {
+    if( !hasCOM_ ) {
+      sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
+      painCave.severity = OPENMD_ERROR;
+      simError();
+    }
+    return COMw_;
+  }
+ 
 }