--- trunk/src/applications/dynamicProps/DynamicProps.cpp	2011/05/19 18:12:09	1566
+++ trunk/src/applications/dynamicProps/DynamicProps.cpp	2012/11/16 15:12:21	1811
@@ -36,19 +36,21 @@
  * [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).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include <iostream>
 #include <fstream>
 #include <string>
 
-#include "brains/Register.hpp"
 #include "brains/SimCreator.hpp"
 #include "brains/SimInfo.hpp"
+#include "utils/StringUtils.hpp"
 #include "utils/simError.h"
 
 #include "applications/dynamicProps/DynamicPropsCmd.h"
+#include "applications/dynamicProps/SelectionCorrFunc.hpp"
 #include "applications/dynamicProps/DipoleCorrFunc.hpp"
 #include "applications/dynamicProps/RCorrFunc.hpp"
 #include "applications/dynamicProps/VCorrFunc.hpp"
@@ -58,15 +60,13 @@
 #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
 #include "applications/dynamicProps/EnergyCorrFunc.hpp"
 #include "applications/dynamicProps/StressCorrFunc.hpp"
+#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
+#include "applications/dynamicProps/MomentumCorrFunc.hpp"
 
-
 using namespace OpenMD;
 
 int main(int argc, char* argv[]){
   
-  //register force fields
-  registerForceFields();
-
   gengetopt_args_info args_info;
 
   //parse the command line option
@@ -98,7 +98,7 @@ int main(int argc, char* argv[]){
     
   if (args_info.sele2_given) {
     sele2 = args_info.sele2_arg;
-  }else {
+  } else {
     char* sele2Env = getenv("SELECTION2");
     if (sele2Env) {
       sele2 = sele2Env;            
@@ -107,28 +107,42 @@ int main(int argc, char* argv[]){
     }
   }
 
+  // use the memory string to figure out how much memory we can use:
+  char *end;
+  long long int memSize = memparse(args_info.memory_arg, &end);
+  sprintf( painCave.errMsg,
+           "Amount of memory being used: %llu bytes\n", memSize);
+  painCave.severity = OPENMD_INFO;
+  painCave.isFatal = 0;
+  simError();     
+
   //parse md file and set up the system
   SimCreator creator;
   SimInfo* info = creator.createSim(dumpFileName, false);
 
-
   TimeCorrFunc* corrFunc;
-  if (args_info.dcorr_given){
-    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
+  if(args_info.sdcorr_given){
+    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
+  } else if (args_info.selecorr_given){
+    corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
+  } else if (args_info.dcorr_given){
+    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.rcorr_given) {
-    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
+    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.r_rcorr_given) {
-    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
+    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.thetacorr_given) {
-    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
+    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.drcorr_given) {
-    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
+    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.vcorr_given) {
-    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2); 
+    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); 
   } else if (args_info.helfandEcorr_given){
-    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);
+    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
   } else if (args_info.stresscorr_given){
-    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2);
+    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.lcorr_given) {
     int order;
     if (args_info.order_given)
@@ -141,7 +155,7 @@ int main(int argc, char* argv[]){
       simError();
     }
         
-    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order); 
+    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); 
   }
 
   if (args_info.output_given) {