--- trunk/src/applications/dynamicProps/DynamicProps.cpp	2012/11/16 15:12:21	1811
+++ trunk/src/applications/dynamicProps/DynamicProps.cpp	2014/10/16 19:13:51	2024
@@ -35,7 +35,7 @@
  *                                                                      
  * [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).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
  * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
  * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
@@ -55,6 +55,7 @@
 #include "applications/dynamicProps/RCorrFunc.hpp"
 #include "applications/dynamicProps/VCorrFunc.hpp"
 #include "applications/dynamicProps/LegendreCorrFunc.hpp"
+#include "applications/dynamicProps/LegendreCorrFuncZ.hpp"
 #include "applications/dynamicProps/RadialRCorrFunc.hpp"
 #include "applications/dynamicProps/ThetaCorrFunc.hpp"
 #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
@@ -62,6 +63,9 @@
 #include "applications/dynamicProps/StressCorrFunc.hpp"
 #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
 #include "applications/dynamicProps/MomentumCorrFunc.hpp"
+#include "applications/dynamicProps/cOHz.hpp"
+#include "applications/dynamicProps/BondCorrFunc.hpp"
+#include "applications/dynamicProps/FreqFlucCorrFunc.hpp"
 
 using namespace OpenMD;
 
@@ -74,35 +78,38 @@ int main(int argc, char* argv[]){
     exit(1) ;
   }
 
-
   //get the dumpfile name and meta-data file name
   std::string dumpFileName = args_info.input_arg;
     
   std::string sele1;
   std::string sele2;
-
+  
+  // check the first selection argument, or set it to the environment
+  // variable, or failing that, set it to "select all"
+  
   if (args_info.sele1_given) {
     sele1 = args_info.sele1_arg;
-  }else {
+  } else {
     char*  sele1Env= getenv("SELECTION1");
     if (sele1Env) {
       sele1 = sele1Env;
-    }else {
-      sprintf( painCave.errMsg,
-               "neither --sele1 option nor $SELECTION1 is set");
-      painCave.severity = OPENMD_ERROR;
-      painCave.isFatal = 1;
-      simError();
+    } else {
+      sele1 = "select all";
     }
   }
-    
+  
+  // check the second selection argument, or set it to the environment
+  // variable, or failing that, set it to the first selection
+  
   if (args_info.sele2_given) {
     sele2 = args_info.sele2_arg;
   } else {
     char* sele2Env = getenv("SELECTION2");
     if (sele2Env) {
       sele2 = sele2Env;            
-    } else {
+    } else { 
+      //If sele2 is not specified, then the default behavior
+      //should be what is already intended for sele1
       sele2 = sele1;
     }
   }
@@ -137,27 +144,64 @@ int main(int argc, char* argv[]){
     corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.vcorr_given) {
     corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); 
+  } else if (args_info.vcorrZ_given) {
+    corrFunc = new VCorrFuncZ(info, dumpFileName, sele1, sele2, memSize); 
+  } else if (args_info.vcorrR_given) {
+    corrFunc = new VCorrFuncR(info, dumpFileName, sele1, sele2, memSize); 
+  } else if (args_info.bondcorr_given) {
+    corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize); 
   } else if (args_info.helfandEcorr_given){
     corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.stresscorr_given){
     corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.momentum_given){
     corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
+  } else if (args_info.freqfluccorr_given){
+    corrFunc = new FreqFlucCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.lcorr_given) {
     int order;
     if (args_info.order_given)
         order = args_info.order_arg;
     else {
       sprintf( painCave.errMsg,
-               "--order must be set if --lcoor is set\n");
+               "--order must be set if --lcorr is set\n");
       painCave.severity = OPENMD_ERROR;
       painCave.isFatal = 1;
       simError();
     }
         
     corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); 
+  } else if (args_info.lcorrZ_given) {
+    int order;
+    if (args_info.order_given)
+        order = args_info.order_arg;
+    else {
+      sprintf( painCave.errMsg,
+               "--order must be set if --lcorrZ is set\n");
+      painCave.severity = OPENMD_ERROR;
+      painCave.isFatal = 1;
+      simError();
+    }
+        
+    corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); 
+
+  } else if (args_info.cohZ_given) {
+    int order;
+    if (args_info.order_given)
+        order = args_info.order_arg;
+    else {
+      sprintf( painCave.errMsg,
+               "--order must be set if --cohZ is set\n");
+      painCave.severity = OPENMD_ERROR;
+      painCave.isFatal = 1;
+      simError();
+    }
+        
+    corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); 
+
   }
 
+
   if (args_info.output_given) {
     corrFunc->setOutputName(args_info.output_arg);
   }