--- trunk/OOPSE/libmdtools/NPTf.cpp	2003/09/19 20:00:27	778
+++ trunk/OOPSE/libmdtools/NPTf.cpp	2003/09/22 21:23:25	780
@@ -26,69 +26,77 @@ template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo,
 template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
   T( theInfo, the_ff )
 {
-  int i, j;
-  chi = 0.0;
-  integralOfChidt = 0.0;
-
-  for(i = 0; i < 3; i++) 
-    for (j = 0; j < 3; j++) 
+  
+  int i,j;
+  
+  for(i = 0; i < 3; i++){
+    for (j = 0; j < 3; j++){
+      
       eta[i][j] = 0.0;
+      oldEta[i][j] = 0.0;
+    }
+  }
+}
 
-  have_tau_thermostat = 0;
-  have_tau_barostat = 0;
-  have_target_temp = 0;
-  have_target_pressure = 0;
+template<typename T> NPTf<T>::~NPTf() {
 
-  have_chi_tolerance = 0;
-  have_eta_tolerance = 0;
-  have_pos_iter_tolerance = 0;
+  // empty for now
+}
 
-  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
-
+template<typename T> void NPTf<T>::resetIntegrator() {
+  
+  int i, j;
+  
+  for(i = 0; i < 3; i++)
+    for (j = 0; j < 3; j++)
+      eta[i][j] = 0.0;
+  
+  T::resetIntegrator();
 }
 
-template<typename T> NPTf<T>::~NPTf() {
-  delete[] oldPos;
-  delete[] oldVel;
-  delete[] oldJi;
+template<typename T> void NPTf<T>::evolveEtaA() {
+  
+  int i, j;
+  
+  for(i = 0; i < 3; i ++){
+    for(j = 0; j < 3; j++){
+      if( i == j)
+        eta[i][j] += dt2 *  instaVol * 
+	  (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
+      else
+        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
+    }
+  }
+  
+  for(i = 0; i < 3; i++)
+    for (j = 0; j < 3; j++)
+      oldEta[i][j] = eta[i][j];
 }
 
-template<typename T> void NPTf<T>::moveA() {
+template<typename T> void NPTf<T>::evolveEtaB() {
+  
+  int i,j;
 
-  // new version of NPTf
-  int i, j, k;
-  DirectionalAtom* dAtom;
-  double Tb[3], ji[3];
+  for(i = 0; i < 3; i++)
+    for (j = 0; j < 3; j++)
+      prevEta[i][j] = eta[i][j];
 
-  double mass;
-  double vel[3], pos[3], frc[3];
+  for(i = 0; i < 3; i ++){
+    for(j = 0; j < 3; j++){
+      if( i == j) {
+	eta[i][j] = oldEta[i][j] + dt2 *  instaVol * 
+	  (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
+      } else {
+	eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
+      }
+    }
+  }
+}
 
-  double rj[3];
-  double instaTemp, instaPress, instaVol;
-  double tt2, tb2;
-  double sc[3];
-  double eta2ij;
-  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
-  double bigScale, smallScale, offDiagMax;
-  double COM[3];
+template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
+  int i,j;
+  double vScale[3][3];
 
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
-
-  instaTemp = tStats->getTemperature();
-  tStats->getPressureTensor(press);
-  instaVol = tStats->getVolume();
-  
-  tStats->getCOM(COM);
-
-  //calculate scale factor of veloity
   for (i = 0; i < 3; i++ ) {
     for (j = 0; j < 3; j++ ) {
       vScale[i][j] = eta[i][j];
@@ -99,96 +107,51 @@ template<typename T> void NPTf<T>::moveA() {
     }
   }
   
-  //evolve velocity half step
-  for( i=0; i<nAtoms; i++ ){
+  info->matVecMul3( vScale, vel, sc );
+}
 
-    atoms[i]->getVel( vel );
-    atoms[i]->getFrc( frc );
+template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
+  int i,j;
+  double myVel[3];
+  double vScale[3][3];
 
-    mass = atoms[i]->getMass();
-    
-    info->matVecMul3( vScale, vel, sc );
-
-    for (j=0; j < 3; j++) {
-      // velocity half step 
-      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
-    }
-
-    atoms[i]->setVel( vel );
-   
-    if( atoms[i]->isDirectional() ){
-
-      dAtom = (DirectionalAtom *)atoms[i];
-
-      // get and convert the torque to body frame
+  for (i = 0; i < 3; i++ ) {
+    for (j = 0; j < 3; j++ ) {
+      vScale[i][j] = eta[i][j];
       
-      dAtom->getTrq( Tb );
-      dAtom->lab2Body( Tb );
-      
-      // get the angular momentum, and propagate a half step
-
-      dAtom->getJ( ji );
-
-      for (j=0; j < 3; j++) 
-        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
-      
-      this->rotationPropagation( dAtom, ji );
-   
-      dAtom->setJ( ji );
-    }    
-  }
-
-  // advance chi half step
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-
-  // calculate the integral of chidt
-  integralOfChidt += dt2*chi;
-
-  // advance eta half step
-
-  for(i = 0; i < 3; i ++)
-    for(j = 0; j < 3; j++){
-      if( i == j)
-        eta[i][j] += dt2 *  instaVol * 
-	  (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
-      else
-        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
+      if (i == j) {
+        vScale[i][j] += chi;          
+      }               
     }
-    
-  //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 (j = 0; j < 3; j++)
+    myVel[j] = oldVel[3*index + j];
 
-    for(i =0 ; i < nAtoms; i++){
+  info->matVecMul3( vScale, myVel, sc );
+}
 
-      atoms[i]->getVel(vel);
-      atoms[i]->getPos(pos);
+template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], 
+					       int index, double sc[3]){
+  int j;
+  double rj[3];
 
-      for(j = 0; j < 3; j++)
-        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; 
-      
-      info->matVecMul3( eta, rj, sc );
-      
-      for(j = 0; j < 3; j++)
-        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
+  for(j=0; j<3; j++)
+    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
 
-      atoms[i]->setPos( pos );
+  info->matVecMul3( eta, rj, sc );
+}
 
-    }
+template<typename T> void NPTf<T>::scaleSimBox( void ){
 
-    if (nConstrained) {
-      constrainA();
-    }
-  }  
+  int i,j,k;
+  double scaleMat[3][3];
+  double eta2ij;
+  double bigScale, smallScale, offDiagMax;
+  double hm[3][3], hmnew[3][3];
+  
 
- 
+
   // Scale the box after all the positions have been moved:
   
   // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
@@ -253,220 +216,23 @@ template<typename T> void NPTf<T>::moveA() {
     info->matMul3(hm, scaleMat, hmnew);
     info->setBoxM(hmnew);
   }
-  
 }
 
-template<typename T> void NPTf<T>::moveB( void ){
-
-  //new version of NPTf
-  int i, j, k;
-  DirectionalAtom* dAtom;
-  double Tb[3], ji[3];
-  double vel[3], myVel[3], frc[3];
-  double mass;
+template<typename T> bool NPTf<T>::etaConverged() {
+  int i;
+  double diffEta, sumEta;
 
-  double instaTemp, instaPress, instaVol;
-  double tt2, tb2;
-  double sc[3];
-  double press[3][3], vScale[3][3];
-  double oldChi, prevChi;
-  double oldEta[3][3], prevEta[3][3], diffEta;
-  
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
-
-  // Set things up for the iteration:
-
-  oldChi = chi;
-  
+  sumEta = 0;
   for(i = 0; i < 3; i++)
-    for(j = 0; j < 3; j++)
-      oldEta[i][j] = eta[i][j];
-
-  for( i=0; i<nAtoms; i++ ){
-
-    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();
+    sumEta += pow(prevEta[i][i] - eta[i][i], 2);    
   
-  for (k=0; k < 4; k++) {
-    
-    instaTemp = tStats->getTemperature();
-    tStats->getPressureTensor(press);
-
-    // evolve chi another half step using the temperature at t + dt/2
-
-    prevChi = chi;
-    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-    
-    for(i = 0; i < 3; i++)
-      for(j = 0; j < 3; j++)
-        prevEta[i][j] = eta[i][j];
-
-    //advance eta half step and calculate scale factor for velocity
-
-    for(i = 0; i < 3; i ++)
-      for(j = 0; j < 3; j++){
-        if( i == j) {
-          eta[i][j] = oldEta[i][j] + dt2 *  instaVol * 
-            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
-          vScale[i][j] = eta[i][j] + chi;
-        } else {
-          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
-          vScale[i][j] = eta[i][j];
-        }
-      }  
-    
-    for( i=0; i<nAtoms; i++ ){
-
-      atoms[i]->getFrc( frc );
-      atoms[i]->getVel(vel);
-      
-      mass = atoms[i]->getMass();
-     
-      for (j = 0; j < 3; j++)
-        myVel[j] = oldVel[3*i + j];
-      
-      info->matVecMul3( vScale, myVel, sc );
-      
-      // velocity half step
-      for (j=0; j < 3; j++) {
-        // velocity half step  (use chi from previous step here):
-        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
-      }
-      
-      atoms[i]->setVel( vel );
-      
-      if( atoms[i]->isDirectional() ){
-
-        dAtom = (DirectionalAtom *)atoms[i];
+  diffEta = sqrt( sumEta / 3.0 );
   
-        // 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);
-      
-          dAtom->setJ( ji );
-      }
-    }
-
-    if (nConstrained) {
-      constrainB();
-    }
-    
-    diffEta = 0;
-    for(i = 0; i < 3; i++)
-      diffEta += pow(prevEta[i][i] - eta[i][i], 2);    
-    
-    if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) 
-      break;
-  }
-
-  //calculate integral of chidt
-  integralOfChidt += dt2*chi;
-  
+  return ( diffEta <= etaTolerance );
 }
 
-template<typename T> void NPTf<T>::resetIntegrator() {
-  int i,j;
-  
-  chi = 0.0;
-
-  for(i = 0; i < 3; i++) 
-    for (j = 0; j < 3; j++) 
-      eta[i][j] = 0.0;
-
-}
-
-template<typename T> int NPTf<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,
-             "NPTf error: You can't use the NPTf integrator\n"
-             "   without a targetTemp!\n"
-             );
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }
-
-  if (!have_target_pressure) {
-    sprintf( painCave.errMsg,
-             "NPTf error: You can't use the NPTf integrator\n"
-             "   without a targetPressure!\n"
-             );
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }
-  
-  // We must set tauThermostat.
-   
-  if (!have_tau_thermostat) {
-    sprintf( painCave.errMsg,
-             "NPTf error: If you use the NPTf\n"
-             "   integrator, you must set tauThermostat.\n");
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }    
-
-  // We must set tauBarostat.
-   
-  if (!have_tau_barostat) {
-    sprintf( painCave.errMsg,
-             "NPTf error: If you use the NPTf\n"
-             "   integrator, you must set tauBarostat.\n");
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }    
-
-  
-  // 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 NPTf<T>::getConservedQuantity(void){
-
+  
   double conservedQuantity;
   double Energy;
   double thermostat_kinetic;
@@ -478,7 +244,7 @@ template<typename T> double NPTf<T>::getConservedQuant
 
   Energy = tStats->getTotalE();
 
-  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / 
+  thermostat_kinetic = fkBT* tt2 * chi * chi / 
     (2.0 * eConvert);
 
   thermostat_potential = fkBT* integralOfChidt / eConvert;
@@ -487,7 +253,7 @@ template<typename T> double NPTf<T>::getConservedQuant
   info->matMul3(a, eta, b);
   trEta = info->matTrace3(b);
 
-  barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / 
+  barostat_kinetic = NkBT * tb2 * trEta / 
     (2.0 * eConvert);
   
   barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / 
@@ -496,12 +262,13 @@ template<typename T> double NPTf<T>::getConservedQuant
   conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
     barostat_kinetic + barostat_potential;
   
-  cout.width(8);
-  cout.precision(8);
+//   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;
+//   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << 
+//       "\t" << thermostat_potential << "\t" << barostat_kinetic << 
+//       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
 
   return conservedQuantity; 
+  
 }