--- trunk/OOPSE/libmdtools/Thermo.cpp	2003/03/25 22:54:16	401
+++ trunk/OOPSE/libmdtools/Thermo.cpp	2004/04/22 21:33:55	1131
@@ -1,23 +1,25 @@
-#include <cmath>
+#include <math.h>
 #include <iostream>
 using namespace std;
 
 #ifdef IS_MPI
 #include <mpi.h>
-#include <mpi++.h>
 #endif //is_mpi
 
 #include "Thermo.hpp"
 #include "SRI.hpp"
 #include "Integrator.hpp"
+#include "simError.h"
+#include "MatVec3.h"
+
+#ifdef IS_MPI
 #define __C
-//#include "mpiSimulation.hpp"
+#include "mpiSimulation.hpp"
+#endif // is_mpi
 
-#define BASE_SEED 123456789
-
-Thermo::Thermo( SimInfo* the_entry_plug ) { 
-  entry_plug = the_entry_plug;
-  int baseSeed = BASE_SEED;
+Thermo::Thermo( SimInfo* the_info ) { 
+  info = the_info;
+  int baseSeed = the_info->getSeed();
   
   gaussStream = new gaussianSPRNG( baseSeed );
 }
\ No newline at end of file
@@ -29,49 +31,46 @@ double Thermo::getKinetic(){
 double Thermo::getKinetic(){
 
   const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
-  double vx2, vy2, vz2;
-  double kinetic, v_sqr;
-  int kl;
-  double jx2, jy2, jz2; // the square of the angular momentums
+  double kinetic;
+  double amass;
+  double aVel[3], aJ[3], I[3][3];
+  int i, j, k, kl;
 
-  DirectionalAtom *dAtom;
-
-  int n_atoms;
   double kinetic_global;
-  Atom** atoms;
-
+  vector<StuntDouble *> integrableObjects = info->integrableObjects;
   
-  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();
-    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
-    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
+  for (kl=0; kl<integrableObjects.size(); kl++) {
+    integrableObjects[kl]->getVel(aVel);
+    amass = integrableObjects[kl]->getMass();
 
-    v_sqr = vx2 + vy2 + vz2;
-    kinetic += atoms[kl]->getMass() * v_sqr;
+   for(j=0; j<3; j++) 
+      kinetic += amass*aVel[j]*aVel[j];
 
-    if( atoms[kl]->isDirectional() ){
-            
-      dAtom = (DirectionalAtom *)atoms[kl];
-      
-      jx2 = dAtom->getJx() * dAtom->getJx();	
-      jy2 = dAtom->getJy() * dAtom->getJy();
-      jz2 = dAtom->getJz() * dAtom->getJz();
-      
-      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) 
-	+ (jz2 / dAtom->getIzz());
-    }
+   if (integrableObjects[kl]->isDirectional()){
+ 
+      integrableObjects[kl]->getJ( aJ );
+      integrableObjects[kl]->getI( I );
+
+      if (integrableObjects[kl]->isLinear()) {
+        i = integrableObjects[kl]->linearAxis();
+        j = (i+1)%3;
+        k = (i+2)%3;
+        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
+      } else {
+        for (j=0; j<3; j++) 
+          kinetic += aJ[j]*aJ[j] / I[j][j];
+      }
+   }
   }
 #ifdef IS_MPI
-  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
+  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
+		MPI_SUM, MPI_COMM_WORLD);
   kinetic = kinetic_global;
 #endif //is_mpi
-
+  
   kinetic = kinetic * 0.5 / e_convert;
 
   return kinetic;
\ No newline at end of file
@@ -82,21 +81,23 @@ double Thermo::getPotential(){
   double potential_local;
   double potential;
   int el, nSRI;
-  SRI** sris;
+  Molecule* molecules;
 
-  sris = entry_plug->sr_interactions;
-  nSRI = entry_plug->n_SRI;
+  molecules = info->molecules;
+  nSRI = info->n_SRI;
 
   potential_local = 0.0;
-  potential_local += entry_plug->lrPot;
+  potential = 0.0;
+  potential_local += info->lrPot;
 
-  for( el=0; el<nSRI; el++ ){    
-    potential_local += sris[el]->get_potential();
+  for( el=0; el<info->n_mol; el++ ){    
+    potential_local += molecules[el].getPotential();
   }
 
   // Get total potential for entire system from MPI.
 #ifdef IS_MPI
-  MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM);
+  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
+		MPI_SUM, MPI_COMM_WORLD);
 #else
   potential = potential_local; 
 #endif // is_mpi
\ No newline at end of file
@@ -114,164 +115,263 @@ double Thermo::getTemperature(){
 
 double Thermo::getTemperature(){
 
-  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
+  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
   double temperature;
-  int ndf_local, ndf;
+
+  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
+  return temperature;
+}
+
+double Thermo::getVolume() {
+
+  return info->boxVol;
+}
+
+double Thermo::getPressure() {
+
+  // Relies on the calculation of the full molecular pressure tensor
   
-  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
-    - entry_plug->n_constraints;
+  const double p_convert = 1.63882576e8;
+  double press[3][3];
+  double pressure;
 
-#ifdef IS_MPI
-  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
-#else
-  ndf = ndf_local;
-#endif
+  this->getPressureTensor(press);
 
-  ndf = ndf - 3;
+  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
+
+  return pressure;
+}
+
+double Thermo::getPressureX() {
+
+  // Relies on the calculation of the full molecular pressure tensor
   
-  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
-  return temperature;
+  const double p_convert = 1.63882576e8;
+  double press[3][3];
+  double pressureX;
+
+  this->getPressureTensor(press);
+
+  pressureX = p_convert * press[0][0];
+
+  return pressureX;
 }
 
-double Thermo::getPressure(){
+double Thermo::getPressureY() {
 
-//  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
-// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
-//  const double conv_A_m = 1.0E-10; //convert A -> m
+  // Relies on the calculation of the full molecular pressure tensor
+  
+  const double p_convert = 1.63882576e8;
+  double press[3][3];
+  double pressureY;
 
-  return 0.0;
+  this->getPressureTensor(press);
+
+  pressureY = p_convert * press[1][1];
+
+  return pressureY;
+}
+
+double Thermo::getPressureZ() {
+
+  // Relies on the calculation of the full molecular pressure tensor
+  
+  const double p_convert = 1.63882576e8;
+  double press[3][3];
+  double pressureZ;
+
+  this->getPressureTensor(press);
+
+  pressureZ = p_convert * press[2][2];
+
+  return pressureZ;
+}
+
+
+void Thermo::getPressureTensor(double press[3][3]){
+  // returns pressure tensor in units amu*fs^-2*Ang^-1
+  // routine derived via viral theorem description in:
+  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
+
+  const double e_convert = 4.184e-4;
+
+  double molmass, volume;
+  double vcom[3], pcom[3], fcom[3], scaled[3];
+  double p_local[9], p_global[9];
+  int i, j, k, nMols;
+  Molecule* molecules;
+
+  nMols = info->n_mol;
+  molecules = info->molecules;
+  //tau = info->tau;
+
+  // use velocities of molecular centers of mass and molecular masses:
+  for (i=0; i < 9; i++) {    
+    p_local[i] = 0.0;
+    p_global[i] = 0.0;
+  }
+
+  for (i=0; i < info->integrableObjects.size(); i++) {
+
+    molmass = info->integrableObjects[i]->getMass();
+    
+    info->integrableObjects[i]->getVel(vcom);
+    info->integrableObjects[i]->getPos(pcom);
+    info->integrableObjects[i]->getFrc(fcom);
+
+    matVecMul3(info->HmatInv, pcom, scaled);
+  
+    for(j=0; j<3; j++)
+      scaled[j] -= roundMe(scaled[j]);
+
+    // calc the wrapped real coordinates from the wrapped scaled coordinates
+  
+    matVecMul3(info->Hmat, scaled, pcom);
+    
+    p_local[0] += molmass * (vcom[0] * vcom[0]) + fcom[0]*pcom[0]*eConvert; 
+    p_local[1] += molmass * (vcom[0] * vcom[1]) + fcom[0]*pcom[1]*eConvert; 
+    p_local[2] += molmass * (vcom[0] * vcom[2]) + fcom[0]*pcom[2]*eConvert; 
+    p_local[3] += molmass * (vcom[1] * vcom[0]) + fcom[1]*pcom[0]*eConvert; 
+    p_local[4] += molmass * (vcom[1] * vcom[1]) + fcom[1]*pcom[1]*eConvert; 
+    p_local[5] += molmass * (vcom[1] * vcom[2]) + fcom[1]*pcom[2]*eConvert; 
+    p_local[6] += molmass * (vcom[2] * vcom[0]) + fcom[2]*pcom[0]*eConvert; 
+    p_local[7] += molmass * (vcom[2] * vcom[1]) + fcom[2]*pcom[1]*eConvert; 
+    p_local[8] += molmass * (vcom[2] * vcom[2]) + fcom[2]*pcom[2]*eConvert; 
+    
+  }
+
+  // Get total for entire system from MPI.
+
+#ifdef IS_MPI
+  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
+#else
+  for (i=0; i<9; i++) {
+    p_global[i] = p_local[i]; 
+  }
+#endif // is_mpi
+
+  volume = this->getVolume();
+
+  for(i = 0; i < 3; i++) {
+    for (j = 0; j < 3; j++) {
+      k = 3*i + j;
+      press[i][j] = p_global[k] /  volume;
+
+    }
+  }
 }
 
 void Thermo::velocitize() {
   
-  double x,y;
-  double vx, vy, vz;
-  double jx, jy, jz;
-  int i, vr, vd; // velocity randomizer loop counters
-  double *vdrift;
+  double aVel[3], aJ[3], I[3][3];
+  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
+  double vdrift[3];
   double vbar;
   const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
   double av2;
   double kebar;
-  int ndf; // number of degrees of freedom
-  int ndfRaw; // the raw number of degrees of freedom
-  int n_atoms;
-  Atom** atoms;
-  DirectionalAtom* dAtom;
   double temperature;
-  int n_oriented;
-  int n_constraints;
+  int nobj;
 
-  atoms         = entry_plug->atoms;
-  n_atoms       = entry_plug->n_atoms;
-  temperature   = entry_plug->target_temp;
-  n_oriented    = entry_plug->n_oriented;
-  n_constraints = entry_plug->n_constraints;
+  nobj = info->integrableObjects.size();
   
-
-  ndfRaw = 3 * n_atoms + 3 * n_oriented;
-  ndf = ndfRaw - n_constraints - 3;
-  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
+  temperature   = info->target_temp;
   
-  for(vr = 0; vr < n_atoms; vr++){
+  kebar = kb * temperature * (double)info->ndfRaw / 
+    ( 2.0 * (double)info->ndf );
+  
+  for(vr = 0; vr < nobj; vr++){
     
     // uses equipartition theory to solve for vbar in angstrom/fs
 
-    av2 = 2.0 * kebar / atoms[vr]->getMass();
+    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
     vbar = sqrt( av2 );
 
-//     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
-    
     // picks random velocities from a gaussian distribution
     // centered on vbar
 
-    vx = vbar * gaussStream->getGaussian();
-    vy = vbar * gaussStream->getGaussian();
-    vz = vbar * gaussStream->getGaussian();
+    for (j=0; j<3; j++) 
+      aVel[j] = vbar * gaussStream->getGaussian();
+    
+    info->integrableObjects[vr]->setVel( aVel );
+    
+    if(info->integrableObjects[vr]->isDirectional()){
 
-    atoms[vr]->set_vx( vx ); 
-    atoms[vr]->set_vy( vy );
-    atoms[vr]->set_vz( vz );
+      info->integrableObjects[vr]->getI( I );
+
+      if (info->integrableObjects[vr]->isLinear()) {
+
+        l= info->integrableObjects[vr]->linearAxis();
+        m = (l+1)%3;
+        n = (l+2)%3;
+
+        aJ[l] = 0.0;
+        vbar = sqrt( 2.0 * kebar * I[m][m] );
+        aJ[m] = vbar * gaussStream->getGaussian();
+        vbar = sqrt( 2.0 * kebar * I[n][n] );
+        aJ[n] = vbar * gaussStream->getGaussian();
+        
+      } else {
+        for (j = 0 ; j < 3; j++) {
+          vbar = sqrt( 2.0 * kebar * I[j][j] );
+          aJ[j] = vbar * gaussStream->getGaussian();
+        }	
+      } // else isLinear
+
+      info->integrableObjects[vr]->setJ( aJ ); 
+      
+    }//isDirectional 
+
   }
 
   // Get the Center of Mass drift velocity.
 
-  vdrift = getCOMVel();
+  getCOMVel(vdrift);
   
   //  Corrects for the center of mass drift.
   // sums all the momentum and divides by total mass.
 
-  for(vd = 0; vd < n_atoms; vd++){
+  for(vd = 0; vd < nobj; vd++){
     
-    vx = atoms[vd]->get_vx();
-    vy = atoms[vd]->get_vy();
-    vz = atoms[vd]->get_vz();
-        
-    vx -= vdrift[0];
-    vy -= vdrift[1];
-    vz -= vdrift[2];
+    info->integrableObjects[vd]->getVel(aVel);
     
-    atoms[vd]->set_vx(vx);
-    atoms[vd]->set_vy(vy);
-    atoms[vd]->set_vz(vz);
+    for (j=0; j < 3; j++) 
+      aVel[j] -= vdrift[j];
+        
+    info->integrableObjects[vd]->setVel( aVel );
   }
-  if( n_oriented ){
-  
-    for( i=0; i<n_atoms; i++ ){
-      
-      if( atoms[i]->isDirectional() ){
-	
-	dAtom = (DirectionalAtom *)atoms[i];
 
-	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();
-	
-	dAtom->setJx( jx );
-	dAtom->setJy( jy );
-	dAtom->setJz( jz );
-      }
-    }	
-  }
 }
 
-double* Thermo::getCOMVel(){
+void Thermo::getCOMVel(double vdrift[3]){
 
   double mtot, mtot_local;
-  double* vdrift;
+  double aVel[3], amass;
   double vdrift_local[3];
-  int vd, n_atoms;
-  Atom** atoms;
+  int vd, j;
+  int nobj;
 
-  vdrift = new double[3];
-  // We are very careless here with the distinction between n_atoms and n_local
-  // We should really fix this before someone pokes an eye out.
+  nobj   = info->integrableObjects.size();
 
-  n_atoms = entry_plug->n_atoms;  
-  atoms   = entry_plug->atoms;
-
   mtot_local = 0.0;
   vdrift_local[0] = 0.0;
   vdrift_local[1] = 0.0;
   vdrift_local[2] = 0.0;
   
-  for(vd = 0; vd < n_atoms; vd++){
+  for(vd = 0; vd < nobj; vd++){
     
-    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
-    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
-    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
+    amass = info->integrableObjects[vd]->getMass();
+    info->integrableObjects[vd]->getVel( aVel );
+
+    for(j = 0; j < 3; j++) 
+      vdrift_local[j] += aVel[j] * amass;
     
-    mtot_local += atoms[vd]->getMass();
+    mtot_local += amass;
   }
 
 #ifdef IS_MPI
-  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
-  MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM);
+  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
 #else
   mtot = mtot_local;
   for(vd = 0; vd < 3; vd++) {
\ No newline at end of file
@@ -283,6 +383,68 @@ double* Thermo::getCOMVel(){
     vdrift[vd] = vdrift[vd] / mtot;
   }
   
-  return vdrift;
 }
 
+void Thermo::getCOM(double COM[3]){
+
+  double mtot, mtot_local;
+  double aPos[3], amass;
+  double COM_local[3];
+  int i, j;
+  int nobj;
+
+  mtot_local = 0.0;
+  COM_local[0] = 0.0;
+  COM_local[1] = 0.0;
+  COM_local[2] = 0.0;
+
+  nobj = info->integrableObjects.size();
+  for(i = 0; i < nobj; i++){
+    
+    amass = info->integrableObjects[i]->getMass();
+    info->integrableObjects[i]->getPos( aPos );
+
+    for(j = 0; j < 3; j++) 
+      COM_local[j] += aPos[j] * amass;
+    
+    mtot_local += amass;
+  }
+
+#ifdef IS_MPI
+  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+#else
+  mtot = mtot_local;
+  for(i = 0; i < 3; i++) {
+    COM[i] = COM_local[i];
+  }
+#endif
+    
+  for (i = 0; i < 3; i++) {
+    COM[i] = COM[i] / mtot;
+  }
+}
+
+void Thermo::removeCOMdrift() {
+  double vdrift[3], aVel[3];
+  int vd, j, nobj;
+
+  nobj = info->integrableObjects.size();
+
+  // Get the Center of Mass drift velocity.
+
+  getCOMVel(vdrift);
+  
+  //  Corrects for the center of mass drift.
+  // sums all the momentum and divides by total mass.
+
+  for(vd = 0; vd < nobj; vd++){
+    
+    info->integrableObjects[vd]->getVel(aVel);
+    
+    for (j=0; j < 3; j++) 
+      aVel[j] -= vdrift[j];
+        
+    info->integrableObjects[vd]->setVel( aVel );
+  }
+}
\ No newline at end of file