--- trunk/src/applications/dynamicProps/DynamicProps.cpp	2007/01/03 20:47:00	1112
+++ trunk/src/applications/dynamicProps/DynamicProps.cpp	2011/05/19 14:28:04	1565
@@ -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 <iostream>
@@ -55,9 +55,12 @@
 #include "applications/dynamicProps/LegendreCorrFunc.hpp"
 #include "applications/dynamicProps/RadialRCorrFunc.hpp"
 #include "applications/dynamicProps/ThetaCorrFunc.hpp"
+#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
+#include "applications/dynamicProps/EnergyCorrFunc.hpp"
+#include "applications/dynamicProps/StressCorrFunc.hpp"
 
 
-using namespace oopse;
+using namespace OpenMD;
 
 int main(int argc, char* argv[]){
   
@@ -81,13 +84,13 @@ int main(int argc, char* argv[]){
   if (args_info.sele1_given) {
     sele1 = args_info.sele1_arg;
   }else {
-    char*  sele1Env= getenv("OOPSE_SELE1");
+    char*  sele1Env= getenv("SELECTION1");
     if (sele1Env) {
       sele1 = sele1Env;
     }else {
       sprintf( painCave.errMsg,
-               "neither --sele1 option nor $OOPSE_SELE1 is set");
-      painCave.severity = OOPSE_ERROR;
+               "neither --sele1 option nor $SELECTION1 is set");
+      painCave.severity = OPENMD_ERROR;
       painCave.isFatal = 1;
       simError();
     }
@@ -96,7 +99,7 @@ int main(int argc, char* argv[]){
   if (args_info.sele2_given) {
     sele2 = args_info.sele2_arg;
   }else {
-    char* sele2Env = getenv("OOPSE_SELE2");
+    char* sele2Env = getenv("SELECTION2");
     if (sele2Env) {
       sele2 = sele2Env;            
     } else {
@@ -118,9 +121,14 @@ int main(int argc, char* argv[]){
     corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
   } else if (args_info.thetacorr_given) {
     corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
-  }
-  else if (args_info.vcorr_given) {
+  } else if (args_info.drcorr_given) {
+    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
+  } else if (args_info.vcorr_given) {
     corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2); 
+  } else if (args_info.helfandEcorr_given){
+    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);
+  } else if (args_info.StresCorrFunc_given){
+    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2);
   } else if (args_info.lcorr_given) {
     int order;
     if (args_info.order_given)
@@ -128,7 +136,7 @@ int main(int argc, char* argv[]){
     else {
       sprintf( painCave.errMsg,
                "--order must be set if --lcoor is set\n");
-      painCave.severity = OOPSE_ERROR;
+      painCave.severity = OPENMD_ERROR;
       painCave.isFatal = 1;
       simError();
     }