--- trunk/mdtools/md_code/Thermo.cpp	2003/01/28 22:16:55	252
+++ trunk/mdtools/md_code/Thermo.cpp	2003/01/30 20:03:37	254
@@ -1,8 +1,9 @@
 #include <cmath>
 #include <iostream>
+using namespace std;
 
-
 #ifdef IS_MPI
+#include <mpi.h>
 #include <mpi++.h>
 #endif //is_mpi
 
@@ -16,7 +17,10 @@ Thermo::Thermo( SimInfo* the_entry_plug ) { 
 Thermo::Thermo( SimInfo* the_entry_plug ) { 
   entry_plug = the_entry_plug;
   int baseSeed = BASE_SEED;
+  
+  cerr << "creating thermo stream\n";
   gaussStream = new gaussianSPRNG( baseSeed );
+  cerr << "created thermo stream\n";
 }
 
 Thermo::~Thermo(){
@@ -65,7 +69,7 @@ double Thermo::getKinetic(){
     }
   }
 #ifdef IS_MPI
-  MPI_COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
+  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
   kinetic = kinetic_global;
 #endif //is_mpi
 
@@ -96,7 +100,7 @@ double Thermo::getPotential(){
 
   // Get total potential for entire system from MPI.
 #ifdef IS_MPI
-  MPI_COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
+  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
   potential = potential_global;
 #endif // is_mpi
 
@@ -164,7 +168,6 @@ void Thermo::velocitize() {
   ndf = ndfRaw - n_constraints - 3;
   kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
   
-  printf("Entered Velocitize\n");
   for(vr = 0; vr < n_atoms; vr++){
     
     // uses equipartition theory to solve for vbar in angstrom/fs
@@ -188,7 +191,7 @@ void Thermo::velocitize() {
 #ifdef IS_MPI
 #error "SPRNG random number generator must be used for MPI"
 #else
-#warning "Using drand48 for random number generation"
+    // warning "Using drand48 for random number generation"
 #endif  // is_mpi 
 
     x = drand48();
@@ -202,7 +205,7 @@ void Thermo::velocitize() {
     x = drand48();
     y = drand48();
     vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
-    printf("Setting new velocities vx: %f\n",vx);
+
 #endif // use_spring
 
 #ifdef USE_SPRNG
@@ -264,7 +267,7 @@ void Thermo::velocitize() {
 #ifdef IS_MPI
 #error "SPRNG random number generator must be used for MPI"
 #else  // is_mpi
-#warning "Using drand48 for random number generation"
+	//warning "Using drand48 for random number generation"
 #endif   // is_MPI
 	
 	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );