--- trunk/OOPSE/libmdtools/NPTi.cpp	2003/09/15 16:52:02	763
+++ trunk/OOPSE/libmdtools/NPTi.cpp	2003/11/06 19:11:38	853
@@ -1,4 +1,4 @@
-#include <cmath>
+#include <math.h>
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -7,297 +7,96 @@
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
 #include "Integrator.hpp"
-#include "simError.h" 
+#include "simError.h"
 
 #ifdef IS_MPI
 #include "mpiSimulation.hpp"
 #endif
 
-
 // Basic isotropic thermostating and barostating via the Melchionna
 // modification of the Hoover algorithm:
 //
 //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
-//       Molec. Phys., 78, 533. 
+//       Molec. Phys., 78, 533.
 //
 //           and
-// 
+//
 //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
 
 template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
   T( theInfo, the_ff )
 {
-  chi = 0.0;
+  GenericData* data;
+  DoubleArrayData * etaValue;
+  vector<double> etaArray;
+
   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;
+  oldEta = 0.0;
 
-  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
+  // retrieve eta from simInfo if
+  data = info->getProperty(ETAVALUE_ID);
+  if(data){
+    etaValue = dynamic_cast<DoubleArrayData*>(data);
 
+    if(etaValue){
+      etaArray = etaValue->getData();
+      eta = etaArray[0];
+      oldEta = eta;
+    }
+  }
+
 }
 
 template<typename T> NPTi<T>::~NPTi() {
-  delete[] oldPos;
-  delete[] oldVel;
-  delete[] oldJi;
+  //nothing for now
 }
 
-template<typename T> void NPTi<T>::moveA() {
+template<typename T> void NPTi<T>::resetIntegrator() {
+  eta = 0.0;
+  T::resetIntegrator();
+}
 
- 
-//   int i, j;
-//   DirectionalAtom* dAtom;
-//   double Tb[3], ji[3];
-//   double A[3][3], I[3][3];
-//   double angle, mass;
-//   double vel[3], pos[3], frc[3];
+template<typename T> void NPTi<T>::evolveEtaA() {
+  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
+		 (p_convert*NkBT*tb2));
+  oldEta = eta;
+}
 
-//   double rj[3];
-//   double instaTemp, instaPress, instaVol;
-//   double tt2, tb2, scaleFactor;
+template<typename T> void NPTi<T>::evolveEtaB() {
 
-//   tt2 = tauThermostat * tauThermostat;
-//   tb2 = tauBarostat * tauBarostat;
+  prevEta = eta;
+  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
+		 (p_convert*NkBT*tb2));
+}
 
-//   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));
+template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
+  int i;
 
-//   integralOfChidt += dt2* chi;
+  for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
+}
 
-//   for( i=0; i<nAtoms; i++ ){
-//     atoms[i]->getVel( vel );
-//     atoms[i]->getPos( pos );
-//     atoms[i]->getFrc( frc );
+template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
+  int i;
 
-//     mass = atoms[i]->getMass();
+  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
+}
 
-//     for (j=0; j < 3; j++) {
-//       vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
-//       rj[j] = pos[j];
-//     }
 
-//     atoms[i]->setVel( vel );
+template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
+					       int index, double sc[3]){
+  int j;
 
-//     info->wrapVector(rj);
+  for(j=0; j<3; j++)
+    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
 
-//     for (j = 0; j < 3; j++) 
-//       pos[j] += dt * (vel[j] + eta*rj[j]);
+  for(j=0; j<3; j++)
+    sc[j] *= eta;
+}
 
-//     atoms[i]->setPos( pos );
+template<typename T> void NPTi<T>::scaleSimBox( void ){
 
-//     if( atoms[i]->isDirectional() ){
+  double scaleFactor;
 
-//       dAtom = (DirectionalAtom *)atoms[i];
-	  
-//       // get and convert the torque to body frame
-      
-//       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);
-      
-//       // 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] / I[0][0];
-//       this->rotate( 1, 2, angle, ji, A ); 
-
-//       // rotate about the y-axis
-//       angle = dt2 * ji[1] / I[1][1];
-//       this->rotate( 2, 0, angle, ji, A );
-      
-//       // rotate about the z-axis
-//       angle = dt * ji[2] / I[2][2];
-//       this->rotate( 0, 1, angle, ji, A);
-      
-//       // rotate about the y-axis
-//       angle = dt2 * ji[1] / I[1][1];
-//       this->rotate( 2, 0, angle, ji, A );
-      
-//        // rotate about the x-axis
-//       angle = dt2 * ji[0] / I[0][0];
-//       this->rotate( 1, 2, angle, ji, A );
-      
-//       dAtom->setJ( ji );
-//       dAtom->setA( A  );    
-//     }                
-
-//   }
-
-//   // Scale the box after all the positions have been moved:
-  
-//   scaleFactor = exp(dt*eta);
-
-//   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(exp(dt*eta));      
-//   }
-  
- 
-  //new version of NPTi
-  int i, j, k;
-  DirectionalAtom* dAtom;
-  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, scaleFactor;
-  double COM[3];
-
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
-
-  instaTemp = tStats->getTemperature();
-  instaPress = tStats->getPressure();
-  instaVol = tStats->getVolume();
-  
-  tStats->getCOM(COM);
-  
-  //evolve velocity half step
-  for( i=0; i<nAtoms; i++ ){
-
-    atoms[i]->getVel( vel );
-    atoms[i]->getFrc( frc );
-
-    mass = atoms[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 + eta));
-  
-    }
-
-    atoms[i]->setVel( vel );
-   
-    if( atoms[i]->isDirectional() ){
-
-      dAtom = (DirectionalAtom *)atoms[i];
-
-      // get and convert the torque to body frame
-      
-      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);
-      
-      // 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] / I[0][0];
-      this->rotate( 1, 2, angle, ji, A ); 
-
-      // rotate about the y-axis
-      angle = dt2 * ji[1] / I[1][1];
-      this->rotate( 2, 0, angle, ji, A );
-      
-      // rotate about the z-axis
-      angle = dt * ji[2] / I[2][2];
-      this->rotate( 0, 1, angle, ji, A);
-      
-      // rotate about the y-axis
-      angle = dt2 * ji[1] / I[1][1];
-      this->rotate( 2, 0, angle, ji, A );
-      
-       // rotate about the x-axis
-      angle = dt2 * ji[0] / I[0][0];
-      this->rotate( 1, 2, angle, ji, A );
-      
-      dAtom->setJ( ji );
-      dAtom->setA( A  );    
-    }    
-  }
-
-  // evolve chi and eta  half step
-  
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2));
-
-  //calculate the integral of chidt
-  integralOfChidt += dt2*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(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];
-
-      
-      //wrapVector(r(t)) = r(t)-R0
-      //info->wrapVector(rj);
-      
-      for(j = 0; j < 3; j++)
-        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]);
-
-      atoms[i]->setPos( pos );
-
-    }
-
-  }
-    
-
-  // Scale the box after all the positions have been moved:
-  
   scaleFactor = exp(dt*eta);
 
   if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
@@ -308,326 +107,69 @@ template<typename T> void NPTi<T>::moveA() {
              );
     painCave.isFatal = 1;
     simError();
-  } else {         
-    info->scaleBox(scaleFactor);      
-  }  
+  } else {
+    info->scaleBox(scaleFactor);
+  }
 
-  //advance volume;
-  volume = volume * exp(dt*eta);
 }
 
-template<typename T> void NPTi<T>::moveB( void ){
+template<typename T> bool NPTi<T>::etaConverged() {
 
-/*
-  int i, j;
-  DirectionalAtom* dAtom;
-  double Tb[3], ji[3];
-  double vel[3], frc[3];
-  double mass;
-
-  double instaTemp, instaPress, instaVol;
-  double tt2, tb2;
-  
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
-
-  instaTemp = tStats->getTemperature();
-  instaPress = tStats->getPressure();
-  instaVol = tStats->getVolume();
+  return ( fabs(prevEta - eta) <= etaTolerance );
+}
 
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
-		 (p_convert*NkBT*tb2));
-  integralOfChidt += dt2*chi;
-  
-  for( i=0; i<nAtoms; i++ ){
+template<typename T> double NPTi<T>::getConservedQuantity(void){
 
-    atoms[i]->getVel( vel );
-    atoms[i]->getFrc( frc );
+  double conservedQuantity;
+  double Energy;
+  double thermostat_kinetic;
+  double thermostat_potential;
+  double barostat_kinetic;
+  double barostat_potential;
 
-    mass = atoms[i]->getMass();
+  Energy = tStats->getTotalE();
 
-    // velocity half step
-    for (j=0; j < 3; j++) 
-      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
-    
-    atoms[i]->setVel( vel );
+  thermostat_kinetic = fkBT* tt2 * chi * chi /
+    (2.0 * eConvert);
 
-    if( atoms[i]->isDirectional() ){
+  thermostat_potential = fkBT* integralOfChidt / eConvert;
 
-      dAtom = (DirectionalAtom *)atoms[i];
 
-      // get and convert the torque to body frame      
+  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
+    (2.0 * eConvert);
 
-      dAtom->getTrq( Tb );
-      dAtom->lab2Body( Tb );
+  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
+    eConvert;
 
-      // get the angular momentum, and propagate a half step
+  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
+    barostat_kinetic + barostat_potential;
 
-      dAtom->getJ( ji );
+//   cout.width(8);
+//   cout.precision(8);
 
-      for (j=0; j < 3; j++) 
-        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);     
-
-      dAtom->setJ( ji );
-    }
-  }
- 
-*/
-  
-  //new version of NPTi
-  int i, j, k;
-  DirectionalAtom* dAtom;
-  double Tb[3], ji[3];
-  double vel[3], frc[3];
-  double mass;
-
-  double instTemp, instPress, instVol;
-  double tt2, tb2;
-  double oldChi, prevChi;
-  double oldEta, preEta;
-  
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
-
-
-  // Set things up for the iteration:
-
-  oldChi = chi;
-  oldEta = eta;
-
-  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:
-
-  instVol = tStats->getVolume();
-  
-  for (k=0; k < 4; k++) {
-    
-    instTemp = tStats->getTemperature();
-    instPress = tStats->getPressure();
-
-    // evolve chi another half step using the temperature at t + dt/2
-
-    prevChi = chi;
-    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / 
-      (tauThermostat*tauThermostat);
-
-    preEta = eta;
-    eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) / 
-       (p_convert*NkBT*tb2));
-
-  
-    for( i=0; i<nAtoms; i++ ){
-
-      atoms[i]->getFrc( frc );
-      atoms[i]->getVel(vel);
-      
-      mass = atoms[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 + eta));
-      
-      atoms[i]->setVel( vel );
-      
-      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);
-      
-          dAtom->setJ( ji );
-      }
-    }
-
-    if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) 
-      break;
-  }
-
-  //calculate integral of chida
-  integralOfChidt += dt2*chi;
-
-
+//   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
+//       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
+//       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
+  return conservedQuantity;
 }
 
-template<typename T> void NPTi<T>::resetIntegrator() {
-  chi = 0.0;
-  eta = 0.0;
-}
+template<typename T> string NPTi<T>::getAdditionalParameters(void){
+  string parameters;
+  const int BUFFERSIZE = 2000; // size of the read buffer
+  char buffer[BUFFERSIZE];
 
-template<typename T> int NPTi<T>::readyCheck() {
+  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
+  parameters += buffer;
 
-  //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,
-             "NPTi error: You can't use the NPTi integrator\n"
-             "   without a targetTemp!\n"
-             );
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }
+  sprintf(buffer,"\t%G\t0\t0;", eta);
+  parameters += buffer;
 
-  if (!have_target_pressure) {
-    sprintf( painCave.errMsg,
-             "NPTi error: You can't use the NPTi integrator\n"
-             "   without a targetPressure!\n"
-             );
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }
-  
-  // We must set tauThermostat.
-   
-  if (!have_tau_thermostat) {
-    sprintf( painCave.errMsg,
-             "NPTi error: If you use the NPTi\n"
-             "   integrator, you must set tauThermostat.\n");
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }    
+  sprintf(buffer,"\t0\t%G\t0;", eta);
+  parameters += buffer;
 
-  // We must set tauBarostat.
-   
-  if (!have_tau_barostat) {
-    sprintf( painCave.errMsg,
-             "NPTi error: If you use the NPTi\n"
-             "   integrator, you must set tauBarostat.\n");
-    painCave.isFatal = 1;
-    simError();
-    return -1;
-  }    
+  sprintf(buffer,"\t0\t0\t%G;", eta);
+  parameters += buffer;
 
-  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();
-  } 
+  return parameters;
 
-    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:
-
-  NkBT = (double)Nparticles * kB * targetTemp;
-  fkBT = (double)info->ndf * kB * targetTemp;
-
-  return 1;
 }
-
-template<typename T> double NPTi<T>::getConservedQuantity(void){
-
-  double conservedQuantity;
-  double tb2;
-  double eta2;  
-  double E_NPT;
-  double U;
-  double TS;
-  double PV;
-  double extra;
-
-  static double pre_U;
-  static double pre_TS;
-  static double pre_PV;
-  static double pre_extra;
-  static int hackCount = 0;
-
-  double delta_U;
-  double delta_TS;
-  double delta_PV;
-  double delta_extra;
-
-  U = tStats->getTotalE();
-
-  TS = fkBT * 
-    (integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert;
-
-  PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert;
-
-  tb2 = tauBarostat * tauBarostat;
-  eta2 = eta * eta;
-
-  extra = (fkBT * tb2 * eta2 / 2.0 ) / eConvert;
-  /*
-  if(hackCount == 0){
-    pre_U = U;
-    pre_TS =TS;
-    pre_PV = PV;
-    pre_extra =extra;
-    hackCount ++;
-  }
-
-  delta_U = U - pre_U;
-  delta_TS = TS - pre_TS;
-  delta_PV = PV - pre_PV;
-  delta_extra = extra - pre_extra;
-*/
-  cout.width(8);
-  cout.precision(8);
-
-  
-  cout << info->getTime() << "\t" 
-       << chi << "\t"
-       << eta << "\t"
-       << U << "\t" 
-       << TS << "\t"
-       << PV << "\t"
-       << extra << "\t"
-       << U+TS+PV+extra << endl;
-
-/*
-    pre_U = U;
-    pre_TS =TS;
-    pre_PV = PV;
-    pre_extra =extra;
-
-
-  cout << info->getTime() << "\t" 
-       << U << "\t" 
-       << U+TS << "\t"
-       << U+TS+PV << "\t"
-       << U+TS+PV+extra << endl;
-*/
-  conservedQuantity = U+TS+PV+extra;
-  return conservedQuantity; 
-}