--- trunk/OOPSE/libmdtools/NPTf.cpp	2003/07/09 01:41:11	577
+++ trunk/OOPSE/libmdtools/NPTf.cpp	2003/11/06 22:01:37	855
@@ -1,3 +1,4 @@
+#include <math.h>
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -6,285 +7,301 @@
 #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
+// Basic non-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.
 
-NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
-  Integrator( theInfo, the_ff )
+template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
+  T( theInfo, the_ff )
 {
-  int i;
-  chi = 0.0;
-  for(i = 0; i < 9; i++) eta[i] = 0.0;
-  have_tau_thermostat = 0;
-  have_tau_barostat = 0;
-  have_target_temp = 0;
-  have_target_pressure = 0;
-}
+  GenericData* data;
+  DoubleArrayData * etaValue;
+  vector<double> etaArray;
+  int i,j;
 
-void NPTf::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;
-  double press[9];
-  const double p_convert = 1.63882576e8;
+  for(i = 0; i < 3; i++){
+    for (j = 0; j < 3; j++){
 
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
+      eta[i][j] = 0.0;
+      oldEta[i][j] = 0.0;
+    }
+  }
 
-  instaTemp = tStats->getTemperature();
-  tStats->getPressureTensor(press);
 
-  for (i=0; i < 9; i++) press[i] *= p_convert;
+  if( theInfo->useInitXSstate ){
+    // retrieve eta array from simInfo if it exists
+    data = info->getProperty(ETAVALUE_ID);
+    if(data){
+      etaValue = dynamic_cast<DoubleArrayData*>(data);
+      
+      if(etaValue){
+	etaArray = etaValue->getData();
+	
+	for(i = 0; i < 3; i++){
+	  for (j = 0; j < 3; j++){
+	    eta[i][j] = etaArray[3*i+j];
+	    oldEta[i][j] = eta[i][j];
+	  }
+	}
+      }
+    }
+  }
 
-  instaVol = tStats->getVolume();
-   
-  // first evolve chi a half step
-  
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  
-  eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2);
-  eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2);
-  eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2);
-  eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2);
-  eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2);
-  eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2);
-  eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2);
-  eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2);
-  eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2);
-  
-  for( i=0; i<nAtoms; i++ ){
-    atomIndex = i * 3;
-    aMatIndex = i * 9;
-    
-    // velocity half step
-    
-    vx = vel[atomIndex];
-    vy = vel[atomIndex+1];
-    vz = vel[atomIndex+2];
-    
-    scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz;
-    scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz;
-    scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz;
-    
-    vx += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - scx);
-    vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy);
-    vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz);
+}
 
-    vel[atomIndex] = vx;
-    vel[atomIndex+1] = vy;
-    vel[atomIndex+2] = vz;
+template<typename T> NPTf<T>::~NPTf() {
 
-    // position whole step    
+  // empty for now
+}
 
-    rj[0] = pos[atomIndex];
-    rj[1] = pos[atomIndex+1];
-    rj[2] = pos[atomIndex+2];
+template<typename T> void NPTf<T>::resetIntegrator() {
 
-    info->wrapVector(rj);
+  int i, j;
 
-    scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2];
-    scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2];
-    scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2];
+  for(i = 0; i < 3; i++)
+    for (j = 0; j < 3; j++)
+      eta[i][j] = 0.0;
 
-    pos[atomIndex] += dt * (vel[atomIndex] + scx);
-    pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy);
-    pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz);
-   
-    if( atoms[i]->isDirectional() ){
+  T::resetIntegrator();
+}
 
-      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 NPTf<T>::evolveEtaA() {
 
-      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] );
+  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);
     }
-    
   }
 
-  // Scale the box after all the positions have been moved:
-  
+  for(i = 0; i < 3; i++)
+    for (j = 0; j < 3; j++)
+      oldEta[i][j] = eta[i][j];
+}
 
+template<typename T> void NPTf<T>::evolveEtaB() {
 
-  // Use a taylor expansion for eta products
-   
-  info->getBoxM(hm);
-  
+  int i,j;
 
+  for(i = 0; i < 3; i++)
+    for (j = 0; j < 3; j++)
+      prevEta[i][j] = eta[i][j];
 
+  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);
+      }
+    }
+  }
+}
 
+template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
+  int i,j;
+  double vScale[3][3];
 
+  for (i = 0; i < 3; i++ ) {
+    for (j = 0; j < 3; j++ ) {
+      vScale[i][j] = eta[i][j];
 
-   info->scaleBox(exp(dt*eta));
+      if (i == j) {
+        vScale[i][j] += chi;
+      }
+    }
+  }
 
-
+  info->matVecMul3( vScale, vel, sc );
 }
 
-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;
-
-  instaTemp = tStats->getTemperature();
-  instaPress = tStats->getPressure();
-  instaVol = tStats->getVolume();
+template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
+  int i,j;
+  double myVel[3];
+  double vScale[3][3];
 
-  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] );
+  for (i = 0; i < 3; i++ ) {
+    for (j = 0; j < 3; j++ ) {
+      vScale[i][j] = eta[i][j];
+
+      if (i == j) {
+        vScale[i][j] += chi;
+      }
     }
   }
+
+  for (j = 0; j < 3; j++)
+    myVel[j] = oldVel[3*index + j];
+
+  info->matVecMul3( vScale, myVel, sc );
 }
 
-int NPTi::readyCheck() {
- 
-  // 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;
+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[index*3+j] + pos[j]) / 2.0 - COM[j];
+
+  info->matVecMul3( eta, rj, sc );
+}
+
+template<typename T> void NPTf<T>::scaleSimBox( void ){
+
+  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)
+  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
+
+  bigScale = 1.0;
+  smallScale = 1.0;
+  offDiagMax = 0.0;
+
+  for(i=0; i<3; i++){
+    for(j=0; j<3; j++){
+
+      // Calculate the matrix Product of the eta array (we only need
+      // the ij element right now):
+
+      eta2ij = 0.0;
+      for(k=0; k<3; k++){
+        eta2ij += eta[i][k] * eta[k][j];
+      }
+
+      scaleMat[i][j] = 0.0;
+      // identity matrix (see above):
+      if (i == j) scaleMat[i][j] = 1.0;
+      // Taylor expansion for the exponential truncated at second order:
+      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
+
+      if (i != j)
+        if (fabs(scaleMat[i][j]) > offDiagMax)
+          offDiagMax = fabs(scaleMat[i][j]);
+    }
+
+    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
+    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
   }
 
-  if (!have_target_pressure) {
+  if ((bigScale > 1.01) || (smallScale < 0.99)) {
     sprintf( painCave.errMsg,
-             "NPTi error: You can't use the NPTi integrator\n"
-             "   without a targetPressure!\n"
-             );
+             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
+             " Check your tauBarostat, as it is probably too small!\n\n"
+             " scaleMat = [%lf\t%lf\t%lf]\n"
+             "            [%lf\t%lf\t%lf]\n"
+             "            [%lf\t%lf\t%lf]\n",
+             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
+             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
+             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
     painCave.isFatal = 1;
     simError();
-    return -1;
-  }
-  
-  // We must set tauThermostat.
-   
-  if (!have_tau_thermostat) {
+  } else if (offDiagMax > 0.01) {
     sprintf( painCave.errMsg,
-             "NPTi error: If you use the NPTi\n"
-             "   integrator, you must set tauThermostat.\n");
+             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
+             " Check your tauBarostat, as it is probably too small!\n\n"
+             " scaleMat = [%lf\t%lf\t%lf]\n"
+             "            [%lf\t%lf\t%lf]\n"
+             "            [%lf\t%lf\t%lf]\n",
+             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
+             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
+             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
     painCave.isFatal = 1;
     simError();
-    return -1;
-  }    
+  } else {
+    info->getBoxM(hm);
+    info->matMul3(hm, scaleMat, hmnew);
+    info->setBoxM(hmnew);
+  }
+}
 
-  // 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 NPTf<T>::etaConverged() {
+  int i;
+  double diffEta, sumEta;
 
-  // We need NkBT a lot, so just set it here:
+  sumEta = 0;
+  for(i = 0; i < 3; i++)
+    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
 
-  NkBT = (double)info->ndf * kB * targetTemp;
+  diffEta = sqrt( sumEta / 3.0 );
 
-  return 1;
+  return ( diffEta <= etaTolerance );
 }
+
+template<typename T> double NPTf<T>::getConservedQuantity(void){
+
+  double conservedQuantity;
+  double totalEnergy;
+  double thermostat_kinetic;
+  double thermostat_potential;
+  double barostat_kinetic;
+  double barostat_potential;
+  double trEta;
+  double a[3][3], b[3][3];
+
+  totalEnergy = tStats->getTotalE();
+
+  thermostat_kinetic = fkBT * tt2 * chi * chi /
+    (2.0 * eConvert);
+
+  thermostat_potential = fkBT* integralOfChidt / eConvert;
+
+  info->transposeMat3(eta, a);
+  info->matMul3(a, eta, b);
+  trEta = info->matTrace3(b);
+
+  barostat_kinetic = NkBT * tb2 * trEta /
+    (2.0 * eConvert);
+
+  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
+    eConvert;
+
+  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
+    barostat_kinetic + barostat_potential;
+
+  return conservedQuantity;
+
+}
+
+template<typename T> string NPTf<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;
+
+  for(int i = 0; i < 3; i++){
+    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
+    parameters += buffer;
+  }
+
+  return parameters;
+
+}