--- trunk/src/profiling/mdProfile.cpp	2005/01/12 22:41:40	246
+++ trunk/src/profiling/mdProfile.cpp	2009/11/25 20:02:06	1390
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -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 <sys/time.h>
@@ -67,10 +67,10 @@ namespace mdProfileSpace {
   struct timeval startTime[N_PROFILES];
   struct timeval endTime[N_PROFILES];
     
-  double accumTime[N_PROFILES];
+  RealType accumTime[N_PROFILES];
   
 #ifdef IS_MPI
-  double globalTime[N_PROFILES];
+  RealType globalTime[N_PROFILES];
 #endif //is_mpi
 
   
@@ -78,8 +78,8 @@ extern "C"{
 
 extern "C"{
   
-  void F90_FUNC(gettimes, GETTIMES)(double* forceTime, 
-				    double* commTime);
+  void FC_FUNC(gettimes, GETTIMES)(RealType* forceTime, 
+				    RealType* commTime);
 }
 
 
@@ -118,15 +118,15 @@ void endProfile( proNames theProfile ){
 
 void endProfile( proNames theProfile ){
   struct timezone tz;
-  double startVal, endVal;
+  RealType startVal, endVal;
 
   gettimeofday( &endTime[theProfile], &tz );
 
-  startVal = (double)startTime[theProfile].tv_sec 
-    + (double)startTime[theProfile].tv_usec / 1000000.0;
+  startVal = (RealType)startTime[theProfile].tv_sec 
+    + (RealType)startTime[theProfile].tv_usec / 1000000.0;
 
-  endVal = (double)endTime[theProfile].tv_sec 
-    + (double)endTime[theProfile].tv_usec / 1000000.0;
+  endVal = (RealType)endTime[theProfile].tv_sec 
+    + (RealType)endTime[theProfile].tv_usec / 1000000.0;
   
   accumTime[theProfile] += endVal - startVal;
 }
@@ -135,25 +135,25 @@ void writeProfiles( void ){
 void writeProfiles( void ){
  
   int i;
-  double totalTime;
-  double percentTime[N_PROFILES];
+  RealType totalTime;
+  RealType percentTime[N_PROFILES];
   int days, hours, minutes, secs, msecs;
-  double donkey;
+  RealType donkey;
   
-  double forceTime, commTime;
+  RealType forceTime, commTime;
   
 #ifdef IS_MPI
   int j;
 
   MPI_Status istatus;    
 
-  double nodeTime, nodeForceTime, nodeCommTime;
-  double nodeAccum[N_PROFILES];
-  double nodePercent[N_PROFILES];
+  RealType nodeTime, nodeForceTime, nodeCommTime;
+  RealType nodeAccum[N_PROFILES];
+  RealType nodePercent[N_PROFILES];
 
-  double globalTime, globalForceTime, globalCommTime;
-  double globalAccum[N_PROFILES];
-  double globalPercent[N_PROFILES];
+  RealType globalTime, globalForceTime, globalCommTime;
+  RealType globalAccum[N_PROFILES];
+  RealType globalPercent[N_PROFILES];
 #endif // is_mpi
 
 
@@ -191,7 +191,7 @@ void writeProfiles( void ){
   secs = (int)donkey;
   msecs = (int)( (donkey - secs) * 1000 );
 
-  F90_FUNC(gettimes, GETTIMES)(&forceTime, &commTime);
+  FC_FUNC(gettimes, GETTIMES)(&forceTime, &commTime);
 
   fprintf( stdout,
 	   "----------------------------------------------------------------------------\n"
@@ -211,8 +211,8 @@ void writeProfiles( void ){
 
   if( worldRank == 0 ){
     
-    double *nodeTots = new double[mpiSim->getNProcessors()];
-    double *nodePercentTots = new double[mpiSim->getNProcessors()];
+    RealType *nodeTots = new RealType[mpiSim->getNProcessors()];
+    RealType *nodePercentTots = new RealType[mpiSim->getNProcessors()];
     
     totalTime = 0.0;
     for(i=0;i<N_PROFILES;i++)
@@ -250,7 +250,7 @@ void writeProfiles( void ){
     secs = (int)donkey;
     msecs = (int)( (donkey - secs) * 1000 );
     
-    F90_FUNC(gettimes, GETTIMES)(&forceTime, &commTime);
+    FC_FUNC(gettimes, GETTIMES)(&forceTime, &commTime);
 
     fprintf( stdout,
 	     "----------------------------------------------------------------------------\n"
@@ -281,12 +281,12 @@ void writeProfiles( void ){
       
       nodeTime = 0.0;
      
-      MPI_Recv(nodeAccum, N_PROFILES, MPI_DOUBLE, j,
+      MPI_Recv(nodeAccum, N_PROFILES, MPI_REALTYPE, j,
 	       1, MPI_COMM_WORLD, &istatus );
 
-      MPI_Recv(&nodeForceTime, 1, MPI_DOUBLE, j,
+      MPI_Recv(&nodeForceTime, 1, MPI_REALTYPE, j,
 	       1, MPI_COMM_WORLD, &istatus );
-      MPI_Recv(&nodeCommTime, 1, MPI_DOUBLE, j,
+      MPI_Recv(&nodeCommTime, 1, MPI_REALTYPE, j,
 	       1, MPI_COMM_WORLD, &istatus );
 
       for(i=0;i<N_PROFILES;i++){
@@ -419,11 +419,11 @@ void writeProfiles( void ){
       
       if( worldRank == j ){
 	
-	F90_FUNC(gettimes, GETTIMES)(&forceTime, &commTime);
+	FC_FUNC(gettimes, GETTIMES)(&forceTime, &commTime);
 
-	MPI_Send( accumTime, N_PROFILES, MPI_DOUBLE, 0, 1, MPI_COMM_WORLD );
-	MPI_Send( &forceTime, 1, MPI_DOUBLE, 0, 1, MPI_COMM_WORLD );
-	MPI_Send( &commTime, 1, MPI_DOUBLE, 0, 1, MPI_COMM_WORLD );
+	MPI_Send( accumTime, N_PROFILES, MPI_REALTYPE, 0, 1, MPI_COMM_WORLD );
+	MPI_Send( &forceTime, 1, MPI_REALTYPE, 0, 1, MPI_COMM_WORLD );
+	MPI_Send( &commTime, 1, MPI_REALTYPE, 0, 1, MPI_COMM_WORLD );
       }
     }
   }