--- trunk/mdtools/md_code/Thermo.cpp	2003/01/02 20:14:08	221
+++ trunk/mdtools/md_code/Thermo.cpp	2003/01/30 20:03:37	254
@@ -1,12 +1,32 @@
 #include <cmath>
+#include <iostream>
+using namespace std;
+
+#ifdef IS_MPI
+#include <mpi.h>
 #include <mpi++.h>
+#endif //is_mpi
 
 #include "Thermo.hpp"
 #include "SRI.hpp"
 #include "LRI.hpp"
 #include "Integrator.hpp"
 
+#define BASE_SEED 123456789
 
+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(){
+  delete gaussStream;
+}
+
 double Thermo::getKinetic(){
 
   const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
@@ -49,9 +69,9 @@ 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
+#endif //is_mpi
 
   kinetic = kinetic * 0.5 / e_convert;
 
@@ -70,7 +90,7 @@ double Thermo::getPotential(){
 
   potential = 0.0;
   potential_global = 0.0;
-  potential += entry_plug->longRange->get_potential();;
+  potential += entry_plug->lrPot;
 
   // std::cerr << "long range potential: " << potential << "\n";
   for( el=0; el<nSRI; el++ ){
@@ -80,9 +100,9 @@ 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
+#endif // is_mpi
 
   return potential;
 }
@@ -167,11 +187,13 @@ void Thermo::velocitize() {
        single processor version of the code, but SPRNG should
        still be preferred for consistency.
     */
+
 #ifdef IS_MPI
 #error "SPRNG random number generator must be used for MPI"
 #else
-#warning "Using drand48 for random number generation"
-#endif   
+    // warning "Using drand48 for random number generation"
+#endif  // is_mpi 
+
     x = drand48();
     y = drand48();
     vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
@@ -183,13 +205,14 @@ void Thermo::velocitize() {
     x = drand48();
     y = drand48();
     vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
-#endif
 
+#endif // use_spring
+
 #ifdef USE_SPRNG
-    vx = vbar * entry_plug->gaussStream->getGaussian();
-    vy = vbar * entry_plug->gaussStream->getGaussian();
-    vz = vbar * entry_plug->gaussStream->getGaussian();
-#endif
+    vx = vbar * gaussStream->getGaussian();
+    vy = vbar * gaussStream->getGaussian();
+    vz = vbar * gaussStream->getGaussian();
+#endif // use_spring
 
     atoms[vr]->set_vx( vx ); 
     atoms[vr]->set_vy( vy );
@@ -238,11 +261,14 @@ void Thermo::velocitize() {
       if( atoms[i]->isDirectional() ){
 	
 	dAtom = (DirectionalAtom *)atoms[i];
+
+#ifndef USE_SPRNG
+
 #ifdef IS_MPI
 #error "SPRNG random number generator must be used for MPI"
-#else
-#warning "Using drand48 for random number generation"
-#endif   
+#else  // is_mpi
+	//warning "Using drand48 for random number generation"
+#endif   // is_MPI
 	
 	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
 	x = drand48();
@@ -258,17 +284,18 @@ void Thermo::velocitize() {
 	x = drand48();
 	y = drand48();
 	jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
-#endif
-#ifdef USE_SPRNG
+
+#else //use_sprng
+
 	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
-	jx = vbar * entry_plug->gaussStream->getGaussian();
+	jx = vbar * gaussStream->getGaussian();
 
 	vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
-	jy = vbar * entry_plug->gaussStream->getGaussian();
+	jy = vbar * gaussStream->getGaussian();
 
 	vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
-	jz = vbar * entry_plug->gaussStream->getGaussian();
-#endif
+	jz = vbar * gaussStream->getGaussian();
+#endif //use_sprng
 	
 	dAtom->setJx( jx );
 	dAtom->setJy( jy );