--- trunk/mdtools/md_code/Thermo.cpp	2002/09/24 22:10:55	117
+++ trunk/mdtools/md_code/Thermo.cpp	2003/02/03 21:15:59	261
@@ -1,11 +1,30 @@
 #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;
+  
+  gaussStream = new gaussianSPRNG( baseSeed );
+}
+
+Thermo::~Thermo(){
+  delete gaussStream;
+}
+
 double Thermo::getKinetic(){
 
   const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
@@ -17,12 +36,15 @@ double Thermo::getKinetic(){
   DirectionalAtom *dAtom;
 
   int n_atoms;
+  double kinetic_global;
   Atom** atoms;
+
   
   n_atoms = entry_plug->n_atoms;
   atoms = entry_plug->atoms;
 
   kinetic = 0.0;
+  kinetic_global = 0.0;
   for( kl=0; kl < n_atoms; kl++ ){
 
     vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
@@ -44,7 +66,11 @@ double Thermo::getKinetic(){
 	+ (jz2 / dAtom->getIzz());
     }
   }
-  
+#ifdef IS_MPI
+  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
+  kinetic = kinetic_global;
+#endif //is_mpi
+
   kinetic = kinetic * 0.5 / e_convert;
 
   return kinetic;
@@ -53,6 +79,7 @@ double Thermo::getPotential(){
 double Thermo::getPotential(){
   
   double potential;
+  double potential_global;
   int el, nSRI;
   SRI** sris;
 
@@ -60,16 +87,21 @@ double Thermo::getPotential(){
   nSRI = entry_plug->n_SRI;
 
   potential = 0.0;
+  potential_global = 0.0;
+  potential += entry_plug->lrPot;
 
-  potential += entry_plug->longRange->get_potential();;
-
   // std::cerr << "long range potential: " << potential << "\n";
-
   for( el=0; el<nSRI; el++ ){
     
     potential += sris[el]->get_potential();
   }
 
+  // Get total potential for entire system from MPI.
+#ifdef IS_MPI
+  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
+  potential = potential_global;
+#endif // is_mpi
+
   return potential;
 }
 
@@ -145,7 +177,21 @@ void Thermo::velocitize() {
     
     // picks random velocities from a gaussian distribution
     // centered on vbar
-    
+#ifndef USE_SPRNG
+    /* If we are using mpi, we need to use the SPRNG random
+       generator. The non drand48 generator will just repeat
+       the same numbers for every node creating a non-gaussian
+       distribution for the simulation. drand48 is fine for the
+       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  // is_mpi 
+
     x = drand48();
     y = drand48();
     vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
@@ -157,7 +203,15 @@ void Thermo::velocitize() {
     x = drand48();
     y = drand48();
     vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
-    
+
+#endif // use_spring
+
+#ifdef USE_SPRNG
+    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 );
     atoms[vr]->set_vz( vz );
@@ -205,6 +259,14 @@ 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  // is_mpi
+	//warning "Using drand48 for random number generation"
+#endif   // is_MPI
 	
 	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
 	x = drand48();
@@ -220,6 +282,18 @@ void Thermo::velocitize() {
 	x = drand48();
 	y = drand48();
 	jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
+
+#else //use_sprng
+
+	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
+	jx = vbar * gaussStream->getGaussian();
+
+	vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
+	jy = vbar * gaussStream->getGaussian();
+
+	vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
+	jz = vbar * gaussStream->getGaussian();
+#endif //use_sprng
 	
 	dAtom->setJx( jx );
 	dAtom->setJy( jy );