--- trunk/OOPSE/libmdtools/NVT.cpp	2003/06/24 22:51:57	565
+++ trunk/OOPSE/libmdtools/NVT.cpp	2004/06/11 17:16:21	1268
@@ -1,3 +1,5 @@
+#include <math.h>
+
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -6,173 +8,277 @@
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
 #include "Integrator.hpp"
-#include "simError.h" 
+#include "simError.h"
 
 
 // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
 
-NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
-  Integrator( theInfo, the_ff )
+template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
+  T( theInfo, the_ff )
 {
+  GenericData* data;
+  DoubleData * chiValue;
+  DoubleData * integralOfChidtValue;
+
+  chiValue = NULL;
+  integralOfChidtValue = NULL;
+
   chi = 0.0;
   have_tau_thermostat = 0;
   have_target_temp = 0;
+  have_chi_tolerance = 0;
+  integralOfChidt = 0.0;
+
+
+  if( theInfo->useInitXSstate ){
+
+    // retrieve chi and integralOfChidt from simInfo
+    data = info->getProperty(CHIVALUE_ID);
+    if(data){
+      chiValue = dynamic_cast<DoubleData*>(data);
+    }
+    
+    data = info->getProperty(INTEGRALOFCHIDT_ID);
+    if(data){
+      integralOfChidtValue = dynamic_cast<DoubleData*>(data);
+    }
+    
+    // chi and integralOfChidt should appear by pair
+    if(chiValue && integralOfChidtValue){
+      chi = chiValue->getData();
+      integralOfChidt = integralOfChidtValue->getData();
+    }
+  }
+
+  oldVel = new double[3*integrableObjects.size()];
+  oldJi = new double[3*integrableObjects.size()];
 }
 
-void NVT::moveA() {
-  
-  int i,j,k;
-  int atomIndex, aMatIndex;
+template<typename T> NVT<T>::~NVT() {
+  delete[] oldVel;
+  delete[] oldJi;
+}
+
+template<typename T> void NVT<T>::moveA() {
+
+  int i, j;
   DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
+  double Tb[3], ji[3];
+  double mass;
+  double vel[3], pos[3], frc[3];
+
   double instTemp;
-  double angle;
 
+  // We need the temperature at time = t for the chi update below:
+
   instTemp = tStats->getTemperature();
 
-  // first evolve chi a half step
-  
-  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
+  for( i=0; i < integrableObjects.size(); i++ ){
 
-  for( i=0; i<nAtoms; i++ ){
-    atomIndex = i * 3;
-    aMatIndex = i * 9;
-    
-    // velocity half step
-    for( j=atomIndex; j<(atomIndex+3); j++ )
-      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
+    integrableObjects[i]->getVel( vel );
+    integrableObjects[i]->getPos( pos );
+    integrableObjects[i]->getFrc( frc );
 
-    // position whole step    
-    for( j=atomIndex; j<(atomIndex+3); j++ )
+    mass = integrableObjects[i]->getMass();
+
+    for (j=0; j < 3; j++) {
+      // velocity half step  (use chi from previous step here):
+      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
+      // position whole step
       pos[j] += dt * vel[j];
+    }
 
-   
-    if( atoms[i]->isDirectional() ){
+    integrableObjects[i]->setVel( vel );
+    integrableObjects[i]->setPos( pos );
 
-      dAtom = (DirectionalAtom *)atoms[i];
-	  
+    if( integrableObjects[i]->isDirectional() ){
+
       // get and convert the torque to body frame
-      
-      Tb[0] = dAtom->getTx();
-      Tb[1] = dAtom->getTy();
-      Tb[2] = dAtom->getTz();
-      
-      dAtom->lab2Body( Tb );
-      
+
+      integrableObjects[i]->getTrq( Tb );
+      integrableObjects[i]->lab2Body( Tb );
+
       // get the angular momentum, and propagate a half step
 
-      ji[0] = dAtom->getJx();
-      ji[1] = dAtom->getJy();
-      ji[2] = dAtom->getJz();
-      
-      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
-      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
-      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
-      
-      // use the angular velocities to propagate the rotation matrix a
-      // full time step
-      
-      // rotate about the x-axis      
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); 
-      
-      // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
-      
-      // rotate about the z-axis
-      angle = dt * ji[2] / dAtom->getIzz();
-      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
-      
-      // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
-      
-       // rotate about the x-axis
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
-      
-      dAtom->setJx( ji[0] );
-      dAtom->setJy( ji[1] );
-      dAtom->setJz( ji[2] );
+      integrableObjects[i]->getJ( ji );
+
+      for (j=0; j < 3; j++)
+        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
+
+      this->rotationPropagation( integrableObjects[i], ji );
+
+      integrableObjects[i]->setJ( ji );
     }
-    
   }
-}
 
-void NVT::moveB( void ){
-  int i,j,k;
-  int atomIndex;
-  DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
-  double instTemp;
+  consFramework->doConstrainA();
+
+  // Finally, evolve chi a half step (just like a velocity) using
+  // temperature at time t, not time t+dt/2
+
+  //std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
   
-  instTemp = tStats->getTemperature();
   chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
-  
-  for( i=0; i<nAtoms; i++ ){
-    atomIndex = i * 3;
-    
-    // velocity half step
-    for( j=atomIndex; j<(atomIndex+3); j++ )
-      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
-    
-    if( atoms[i]->isDirectional() ){
-      
-      dAtom = (DirectionalAtom *)atoms[i];
-      
-      // get and convert the torque to body frame
-      
-      Tb[0] = dAtom->getTx();
-      Tb[1] = dAtom->getTy();
-      Tb[2] = dAtom->getTz();
-      
-      dAtom->lab2Body( Tb );
-      
-      // get the angular momentum, and complete the angular momentum
-      // half step
-      
-      ji[0] = dAtom->getJx();
-      ji[1] = dAtom->getJy();
-      ji[2] = dAtom->getJz();
-      
-      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
-      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
-      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
-      
-      dAtom->setJx( ji[0] );
-      dAtom->setJy( ji[1] );
-      dAtom->setJz( ji[2] );
+  integralOfChidt += chi*dt2;
+
+}
+
+template<typename T> void NVT<T>::moveB( void ){
+  int i, j, k;
+  double Tb[3], ji[3];
+  double vel[3], frc[3];
+  double mass;
+  double instTemp;
+  double oldChi, prevChi;
+
+  // Set things up for the iteration:
+
+  oldChi = chi;
+
+  for( i=0; i < integrableObjects.size(); i++ ){
+
+    integrableObjects[i]->getVel( vel );
+
+    for (j=0; j < 3; j++)
+      oldVel[3*i + j]  = vel[j];
+
+    if( integrableObjects[i]->isDirectional() ){
+
+      integrableObjects[i]->getJ( ji );
+
+      for (j=0; j < 3; j++)
+        oldJi[3*i + j] = ji[j];
+
     }
   }
+
+  // do the iteration:
+
+  for (k=0; k < 4; k++) {
+
+    instTemp = tStats->getTemperature();
+
+    // evolve chi another half step using the temperature at t + dt/2
+
+    prevChi = chi;
+    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
+      (tauThermostat*tauThermostat);
+
+    for( i=0; i < integrableObjects.size(); i++ ){
+
+      integrableObjects[i]->getFrc( frc );
+      integrableObjects[i]->getVel(vel);
+
+      mass = integrableObjects[i]->getMass();
+
+      // velocity half step
+      for (j=0; j < 3; j++)
+	vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
+
+      integrableObjects[i]->setVel( vel );
+
+      if( integrableObjects[i]->isDirectional() ){
+
+	// get and convert the torque to body frame
+
+	integrableObjects[i]->getTrq( Tb );
+	integrableObjects[i]->lab2Body( Tb );
+
+	for (j=0; j < 3; j++)
+	  ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
+
+	integrableObjects[i]->setJ( ji );
+      }
+    }
+
+    consFramework->doConstrainB();
+
+    if (fabs(prevChi - chi) <= chiTolerance) break;
+  }
+
+  integralOfChidt += dt2*chi;
 }
 
-int NVT::readyCheck() {
- 
-  // First check to see if we have a target temperature. 
-  // Not having one is fatal. 
-  
+template<typename T> void NVT<T>::resetIntegrator( void ){
+
+  chi = 0.0;
+  integralOfChidt = 0.0;
+}
+
+template<typename T> int NVT<T>::readyCheck() {
+
+  //check parent's readyCheck() first
+  if (T::readyCheck() == -1)
+    return -1;
+
+  // First check to see if we have a target temperature.
+  // Not having one is fatal.
+
   if (!have_target_temp) {
     sprintf( painCave.errMsg,
-             "NVT error: You can't use the NVT integrator without a targetTemp!\n"
+             "You can't use the NVT integrator without a targetTemp!\n"
              );
     painCave.isFatal = 1;
+    painCave.severity = OOPSE_ERROR;
     simError();
     return -1;
   }
-  
+
   // We must set tauThermostat.
-   
+
   if (!have_tau_thermostat) {
     sprintf( painCave.errMsg,
-             "NVT error: If you use the constant temperature\n"
-             "   integrator, you must set tauThermostat.\n");
+             "If you use the constant temperature\n"
+             "\tintegrator, you must set tauThermostat.\n");
+    painCave.severity = OOPSE_ERROR;
     painCave.isFatal = 1;
     simError();
     return -1;
-  }    
+  }
+
+  if (!have_chi_tolerance) {
+    sprintf( painCave.errMsg,
+             "In NVT integrator: setting chi tolerance to 1e-6\n");
+    chiTolerance = 1e-6;
+    have_chi_tolerance = 1;
+    painCave.severity = OOPSE_INFO;
+    painCave.isFatal = 0;
+    simError();
+  }
+
   return 1;
+
 }
 
+template<typename T> double NVT<T>::getConservedQuantity(void){
+
+  double conservedQuantity;
+  double fkBT;
+  double Energy;
+  double thermostat_kinetic;
+  double thermostat_potential;
+
+  fkBT = (double)(info->ndf) * kB * targetTemp;
+
+  Energy = tStats->getTotalE();
+
+  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
+    (2.0 * eConvert);
+
+  thermostat_potential = fkBT * integralOfChidt / eConvert;
+
+  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
+
+  return conservedQuantity;
+}
+
+template<typename T> string NVT<T>::getAdditionalParameters(void){
+  string parameters;
+  const int BUFFERSIZE = 2000; // size of the read buffer
+  char buffer[BUFFERSIZE];
+
+  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
+  parameters += buffer;
+
+  return parameters;
+}