--- trunk/OOPSE/libmdtools/NPTi.cpp	2003/07/09 02:15:29	578
+++ trunk/OOPSE/libmdtools/NPTi.cpp	2003/11/06 22:01:37	855
@@ -1,4 +1,4 @@
-#include <cmath>
+#include <math.h>
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -7,240 +7,170 @@
 #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.
 
-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;
+  GenericData* data;
+  DoubleArrayData * etaValue;
+  vector<double> etaArray;
+
   eta = 0.0;
-  have_tau_thermostat = 0;
-  have_tau_barostat = 0;
-  have_target_temp = 0;
-  have_target_pressure = 0;
+  oldEta = 0.0;
+
+  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;
+      }
+    }
+  }
 }
 
-void NPTi::moveA() {
-  
-  int i,j,k;
-  int atomIndex, aMatIndex;
-  DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
-  double rj[3];
-  double instaTemp, instaPress, instaVol;
-  double tt2, tb2;
-  double angle;
+template<typename T> NPTi<T>::~NPTi() {
+  //nothing for now
+}
 
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
+template<typename T> void NPTi<T>::resetIntegrator() {
+  eta = 0.0;
+  T::resetIntegrator();
+}
 
-  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) / (NkBT*tb2));
+template<typename T> void NPTi<T>::evolveEtaA() {
+  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
+		 (p_convert*NkBT*tb2));
+  oldEta = eta;
+}
 
-  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));
+template<typename T> void NPTi<T>::evolveEtaB() {
 
-    // position whole step    
+  prevEta = eta;
+  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
+		 (p_convert*NkBT*tb2));
+}
 
-    rj[0] = pos[atomIndex];
-    rj[1] = pos[atomIndex+1];
-    rj[2] = pos[atomIndex+2];
-    
-    info->wrapVector(rj);
+template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
+  int i;
 
-    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]);
-   
-    if( atoms[i]->isDirectional() ){
+  for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
+}
 
-      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 propagate a half step
+template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
+  int i;
 
-      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] );
-    }
-    
-  }
-  // Scale the box after all the positions have been moved:
+  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
+}
 
-  info->scaleBox(exp(dt*eta));
 
+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++)
+    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
+
+  for(j=0; j<3; j++)
+    sc[j] *= eta;
 }
 
-void NPTi::moveB( void ){
-  int i,j,k;
-  int atomIndex;
-  DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
-  double instaTemp, instaPress, instaVol;
-  double tt2, tb2;
-  
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
+template<typename T> void NPTi<T>::scaleSimBox( void ){
 
-  instaTemp = tStats->getTemperature();
-  instaPress = tStats->getPressure();
-  instaVol = tStats->getVolume();
+  double scaleFactor;
 
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
-  
-  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));
-    
-    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] );
-    }
-  }
-}
+  scaleFactor = exp(dt*eta);
 
-int NPTi::readyCheck() {
- 
-  // First check to see if we have a target temperature. 
-  // Not having one is fatal. 
-  
-  if (!have_target_temp) {
+  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
     sprintf( painCave.errMsg,
-             "NPTi error: You can't use the NPTi integrator\n"
-             "   without a targetTemp!\n"
+             "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();
-    return -1;
+  } else {
+    info->scaleBox(scaleFactor);
   }
 
-  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;
-  }    
+template<typename T> bool NPTi<T>::etaConverged() {
 
-  // We need NkBT a lot, so just set it here:
+  return ( fabs(prevEta - eta) <= etaTolerance );
+}
 
-  NkBT = (double)info->ndf * kB * targetTemp;
+template<typename T> double NPTi<T>::getConservedQuantity(void){
 
-  return 1;
+  double conservedQuantity;
+  double Energy;
+  double thermostat_kinetic;
+  double thermostat_potential;
+  double barostat_kinetic;
+  double barostat_potential;
+
+  Energy = tStats->getTotalE();
+
+  thermostat_kinetic = fkBT* tt2 * chi * chi /
+    (2.0 * eConvert);
+
+  thermostat_potential = fkBT* integralOfChidt / eConvert;
+
+
+  barostat_kinetic = 3.0 * NkBT * tb2 * 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;
 }
+
+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;
+
+}