--- trunk/OOPSE/libmdtools/NPTi.cpp	2003/07/09 22:14:06	586
+++ trunk/OOPSE/libmdtools/NPTi.cpp	2003/09/19 16:01:07	772
@@ -9,6 +9,9 @@
 #include "Integrator.hpp"
 #include "simError.h" 
 
+#ifdef IS_MPI
+#include "mpiSimulation.hpp"
+#endif
 
 // Basic isotropic thermostating and barostating via the Melchionna
 // modification of the Hoover algorithm:
@@ -20,184 +23,300 @@ NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
 // 
 //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
 
-NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
-  Integrator( theInfo, the_ff )
+template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
+  T( theInfo, the_ff )
 {
   chi = 0.0;
   eta = 0.0;
+  integralOfChidt = 0.0;
   have_tau_thermostat = 0;
   have_tau_barostat = 0;
   have_target_temp = 0;
   have_target_pressure = 0;
+  have_chi_tolerance = 0;
+  have_eta_tolerance = 0;
+  have_pos_iter_tolerance = 0;
+
+  oldPos = new double[3*nAtoms];
+  oldVel = new double[3*nAtoms];
+  oldJi = new double[3*nAtoms];
+#ifdef IS_MPI
+  Nparticles = mpiSim->getTotAtoms();
+#else
+  Nparticles = theInfo->n_atoms;
+#endif
+
 }
 
-void NPTi::moveA() {
-  
-  int i,j,k;
-  int atomIndex, aMatIndex;
+template<typename T> NPTi<T>::~NPTi() {
+  delete[] oldPos;
+  delete[] oldVel;
+  delete[] oldJi;
+}
+
+template<typename T> void NPTi<T>::moveA() {
+ 
+  //new version of NPTi
+  int i, j, k;
   DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
+  double Tb[3], ji[3];
+  double A[3][3], I[3][3];
+  double angle, mass;
+  double vel[3], pos[3], frc[3];
+
   double rj[3];
   double instaTemp, instaPress, instaVol;
-  double tt2, tb2;
-  double angle;
+  double tt2, tb2, scaleFactor;
+  double COM[3];
 
-
   tt2 = tauThermostat * tauThermostat;
   tb2 = tauBarostat * tauBarostat;
 
   instaTemp = tStats->getTemperature();
   instaPress = tStats->getPressure();
   instaVol = tStats->getVolume();
-   
-   // first evolve chi a half step
   
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
-		 (p_convert*NkBT*tb2));
-
+  tStats->getCOM(COM);
+  
+  //evolve velocity half step
   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+eta));
 
-    // position whole step    
+    atoms[i]->getVel( vel );
+    atoms[i]->getFrc( frc );
 
-    rj[0] = pos[atomIndex];
-    rj[1] = pos[atomIndex+1];
-    rj[2] = pos[atomIndex+2];
-    
-    info->wrapVector(rj);
+    mass = atoms[i]->getMass();
 
-    pos[atomIndex] += dt * (vel[atomIndex] + eta*rj[0]);
-    pos[atomIndex+1] += dt * (vel[atomIndex+1] + eta*rj[1]);
-    pos[atomIndex+2] += dt * (vel[atomIndex+2] + eta*rj[2]);
+    for (j=0; j < 3; j++) {
+      // velocity half step 
+      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
+    }
+
+    atoms[i]->setVel( vel );
    
     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->getTrq( Tb );
       dAtom->lab2Body( Tb );
       
       // get the angular momentum, and propagate a half step
 
-      ji[0] = dAtom->getJx();
-      ji[1] = dAtom->getJy();
-      ji[2] = dAtom->getJz();
+      dAtom->getJ( ji );
+
+      for (j=0; j < 3; j++) 
+        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
       
-      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
-      
+
+      dAtom->getA(A);
+      dAtom->getI(I);
+    
       // rotate about the x-axis      
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); 
-      
+      angle = dt2 * ji[0] / I[0][0];
+      this->rotate( 1, 2, angle, ji, A ); 
+
       // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[1] / I[1][1];
+      this->rotate( 2, 0, angle, ji, A );
       
       // rotate about the z-axis
-      angle = dt * ji[2] / dAtom->getIzz();
-      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
+      angle = dt * ji[2] / I[2][2];
+      this->rotate( 0, 1, angle, ji, A);
       
       // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[1] / I[1][1];
+      this->rotate( 2, 0, angle, ji, A );
       
        // rotate about the x-axis
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[0] / I[0][0];
+      this->rotate( 1, 2, angle, ji, A );
       
-      dAtom->setJx( ji[0] );
-      dAtom->setJy( ji[1] );
-      dAtom->setJz( ji[2] );
+      dAtom->setJ( ji );
+      dAtom->setA( A  );    
+    }    
+  }
+
+  // advance chi half step
+  
+  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
+
+  // calculate the integral of chidt
+
+  integralOfChidt += dt2*chi;
+
+  // advance eta half step
+
+  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2));
+
+  //save the old positions
+  for(i = 0; i < nAtoms; i++){
+    atoms[i]->getPos(pos);
+    for(j = 0; j < 3; j++)
+      oldPos[i*3 + j] = pos[j];
+  }
+  
+  //the first estimation of r(t+dt) is equal to  r(t) 
+    
+  for(k = 0; k < 4; k ++){
+
+    for(i =0 ; i < nAtoms; i++){
+
+      atoms[i]->getVel(vel);
+      atoms[i]->getPos(pos);
+
+      for(j = 0; j < 3; j++)
+        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];     
+      
+      for(j = 0; j < 3; j++)
+        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]);
+
+      atoms[i]->setPos( pos );
     }
     
+    if (nConstrained){
+      constrainA();
+    }
   }
+    
+
   // Scale the box after all the positions have been moved:
+  
+  scaleFactor = exp(dt*eta);
 
-  cerr << "eta = " << eta 
-       << "; exp(dt*eta) = " << exp(eta*dt) << "\n";
+  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
+    sprintf( painCave.errMsg,
+             "NPTi error: Attempting a Box scaling of more than 10 percent"
+             " check your tauBarostat, as it is probably too small!\n"
+             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
+             );
+    painCave.isFatal = 1;
+    simError();
+  } else {         
+    info->scaleBox(scaleFactor);      
+  }  
 
-  info->scaleBox(exp(dt*eta));
-
 }
 
-void NPTi::moveB( void ){
-  int i,j,k;
-  int atomIndex;
+template<typename T> void NPTi<T>::moveB( void ){
+  
+  //new version of NPTi
+  int i, j, k;
   DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
+  double Tb[3], ji[3];
+  double vel[3], frc[3];
+  double mass;
+
   double instaTemp, instaPress, instaVol;
   double tt2, tb2;
+  double oldChi, prevChi;
+  double oldEta, prevEta;
   
   tt2 = tauThermostat * tauThermostat;
   tb2 = tauBarostat * tauBarostat;
 
-  instaTemp = tStats->getTemperature();
-  instaPress = tStats->getPressure();
-  instaVol = tStats->getVolume();
+  // Set things up for the iteration:
 
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
-		 (p_convert*NkBT*tb2));
-  
+  oldChi = chi;
+  oldEta = eta;
+
   for( i=0; i<nAtoms; i++ ){
-    atomIndex = i * 3;
-    
-    // velocity half step
-    for( j=atomIndex; j<(atomIndex+3); j++ )
-    for( j=atomIndex; j<(atomIndex+3); j++ )
-      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert 
-                       - vel[j]*(chi+eta));
-    
+
+    atoms[i]->getVel( vel );
+
+    for (j=0; j < 3; j++)
+      oldVel[3*i + j]  = vel[j];
+
     if( atoms[i]->isDirectional() ){
-      
+
       dAtom = (DirectionalAtom *)atoms[i];
+
+      dAtom->getJ( ji );
+
+      for (j=0; j < 3; j++)
+        oldJi[3*i + j] = ji[j];
+
+    }
+  }
+
+  // do the iteration:
+
+  instaVol = tStats->getVolume();
+  
+  for (k=0; k < 4; k++) {
+    
+    instaTemp = tStats->getTemperature();
+    instaPress = tStats->getPressure();
+
+    // evolve chi another half step using the temperature at t + dt/2
+
+    prevChi = chi;
+    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
+
+    prevEta = eta;
+
+    // advance eta half step and calculate scale factor for velocity
+
+    eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / 
+       (p_convert*NkBT*tb2));
+
+  
+    for( i=0; i<nAtoms; i++ ){
+
+      atoms[i]->getFrc( frc );
+      atoms[i]->getVel(vel);
       
-      // get and convert the torque to body frame
+      mass = atoms[i]->getMass();
       
-      Tb[0] = dAtom->getTx();
-      Tb[1] = dAtom->getTy();
-      Tb[2] = dAtom->getTz();
+      // 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 + eta));
       
-      dAtom->lab2Body( Tb );
+      atoms[i]->setVel( vel );
       
-      // get the angular momentum, and complete the angular momentum
-      // half step
+      if( atoms[i]->isDirectional() ){
+
+        dAtom = (DirectionalAtom *)atoms[i];
+  
+        // get and convert the torque to body frame      
+  
+        dAtom->getTrq( Tb );
+        dAtom->lab2Body( Tb );       
+             
+        for (j=0; j < 3; j++) 
+          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
       
-      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] );
+          dAtom->setJ( ji );
+      }
     }
+    
+    if (nConstrained){
+      constrainB();
+    }    
+    
+    if (fabs(prevChi - chi) <= 
+	chiTolerance && fabs(prevEta -eta) <= etaTolerance) 
+      break;
   }
+
+  //calculate integral of chidt
+  integralOfChidt += dt2*chi;
+
 }
 
-int NPTi::readyCheck() {
+template<typename T> void NPTi<T>::resetIntegrator() {
+  chi = 0.0;
+  eta = 0.0;
+}
+
+template<typename T> int NPTi<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. 
@@ -244,9 +363,75 @@ int NPTi::readyCheck() {
     return -1;
   }    
 
-  // We need NkBT a lot, so just set it here:
+  if (!have_chi_tolerance) {
+    sprintf( painCave.errMsg,
+             "NPTi warning: setting chi tolerance to 1e-6\n");
+    chiTolerance = 1e-6;
+    have_chi_tolerance = 1;
+    painCave.isFatal = 0;
+    simError();
+  } 
 
-  NkBT = (double)info->ndf * kB * targetTemp;
+  if (!have_eta_tolerance) {
+    sprintf( painCave.errMsg,
+             "NPTi warning: setting eta tolerance to 1e-6\n");
+    etaTolerance = 1e-6;
+    have_eta_tolerance = 1;
+    painCave.isFatal = 0;
+    simError();
+  } 
+  
+  
+  // We need NkBT a lot, so just set it here: This is the RAW number
+  // of particles, so no subtraction or addition of constraints or
+  // orientational degrees of freedom:
+  
+  NkBT = (double)Nparticles * kB * targetTemp;
+  
+  // fkBT is used because the thermostat operates on more degrees of freedom
+  // than the barostat (when there are particles with orientational degrees
+  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
+  
+  fkBT = (double)info->ndf * kB * targetTemp;
 
   return 1;
 }
+
+template<typename T> double NPTi<T>::getConservedQuantity(void){
+
+  double conservedQuantity;
+  double Three_NkBT;
+  double Energy;
+  double thermostat_kinetic;
+  double thermostat_potential;
+  double barostat_kinetic;
+  double barostat_potential;
+  double tb2;
+  double eta2; 
+
+  Energy = tStats->getTotalE();
+
+  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / 
+    (2.0 * eConvert);
+
+  thermostat_potential = fkBT* integralOfChidt / eConvert;
+
+
+  barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta / 
+    (2.0 * eConvert);
+  
+  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / 
+    eConvert;
+
+  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
+    barostat_kinetic + barostat_potential;
+  
+  cout.width(8);
+  cout.precision(8);
+
+  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << 
+      "\t" << thermostat_potential << "\t" << barostat_kinetic << 
+      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
+
+  return conservedQuantity; 
+}