--- trunk/OOPSE/libmdtools/NPTi.cpp	2003/09/19 16:01:07	772
+++ trunk/OOPSE/libmdtools/NPTi.cpp	2003/11/07 17:09:48	857
@@ -1,4 +1,4 @@
-#include <cmath>
+#include <math.h>
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -7,7 +7,7 @@
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
 #include "Integrator.hpp"
-#include "simError.h" 
+#include "simError.h"
 
 #ifdef IS_MPI
 #include "mpiSimulation.hpp"
@@ -17,174 +17,91 @@
 // 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
-
+  if( theInfo->useInitXSstate ){
+    // 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() {
- 
-  //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];
+template<typename T> void NPTi<T>::resetIntegrator() {
+  eta = 0.0;
+  T::resetIntegrator();
+}
 
-  double rj[3];
-  double instaTemp, instaPress, instaVol;
-  double tt2, tb2, scaleFactor;
-  double COM[3];
+template<typename T> void NPTi<T>::evolveEtaA() {
+  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
+		 (p_convert*NkBT*tb2));
+  oldEta = eta;
+}
 
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
+template<typename T> void NPTi<T>::evolveEtaB() {
 
-  instaTemp = tStats->getTemperature();
-  instaPress = tStats->getPressure();
-  instaVol = tStats->getVolume();
-  
-  tStats->getCOM(COM);
-  
-  //evolve velocity half step
-  for( i=0; i<nAtoms; i++ ){
+  prevEta = eta;
+  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
+		 (p_convert*NkBT*tb2));
+}
 
-    atoms[i]->getVel( vel );
-    atoms[i]->getFrc( frc );
+template<typename T> void NPTi<T>::calcVelScale(void) {
+  vScale = chi + eta;
+}
 
-    mass = atoms[i]->getMass();
+template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
+  int i;
 
-    for (j=0; j < 3; j++) {
-      // velocity half step 
-      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
-    }
+  for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
+}
 
-    atoms[i]->setVel( vel );
-   
-    if( atoms[i]->isDirectional() ){
+template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
+  int i;
 
-      dAtom = (DirectionalAtom *)atoms[i];
+  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale;
+}
 
-      // 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 );
+template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
+					       int index, double sc[3]){
+  int j;
 
-      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
+  for(j=0; j<3; j++)
+    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
 
-      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 ); 
+  for(j=0; j<3; j++)
+    sc[j] *= eta;
+}
 
-      // 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  );    
-    }    
-  }
+template<typename T> void NPTi<T>::scaleSimBox( void ){
 
-  // advance chi half step
-  
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
+  double scaleFactor;
 
-  // 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);
 
   if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
@@ -195,243 +112,69 @@ template<typename T> void NPTi<T>::moveA() {
              );
     painCave.isFatal = 1;
     simError();
-  } else {         
-    info->scaleBox(scaleFactor);      
-  }  
-
-}
-
-template<typename T> void NPTi<T>::moveB( void ){
-  
-  //new version of NPTi
-  int i, j, k;
-  DirectionalAtom* dAtom;
-  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;
-
-  // 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];
-
-    }
+  } else {
+    info->scaleBox(scaleFactor);
   }
 
-  // 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);
-      
-      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 (nConstrained){
-      constrainB();
-    }    
-    
-    if (fabs(prevChi - chi) <= 
-	chiTolerance && fabs(prevEta -eta) <= etaTolerance) 
-      break;
-  }
-
-  //calculate integral of chidt
-  integralOfChidt += dt2*chi;
-
 }
 
-template<typename T> void NPTi<T>::resetIntegrator() {
-  chi = 0.0;
-  eta = 0.0;
-}
+template<typename T> bool NPTi<T>::etaConverged() {
 
-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. 
-  
-  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;
-  }
-
-  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;
-  }    
-
-  // 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;
-  }    
-
-  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();
-  } 
-
-  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;
+  return ( fabs(prevEta - eta) <= etaTolerance );
 }
 
 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 / 
+  thermostat_kinetic = fkBT* tt2 * chi * chi /
     (2.0 * eConvert);
 
   thermostat_potential = fkBT* integralOfChidt / eConvert;
 
 
-  barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta / 
+  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
     (2.0 * eConvert);
-  
-  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / 
+
+  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;
+//   cout.width(8);
+//   cout.precision(8);
 
-  return conservedQuantity; 
+//   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> string NPTi<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;
+
+  sprintf(buffer,"\t%G\t0\t0;", eta);
+  parameters += buffer;
+
+  sprintf(buffer,"\t0\t%G\t0;", eta);
+  parameters += buffer;
+
+  sprintf(buffer,"\t0\t0\t%G;", eta);
+  parameters += buffer;
+
+  return parameters;
+
+}