--- trunk/OOPSE/libmdtools/NPTf.cpp	2003/07/14 22:38:13	600
+++ 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"
@@ -6,320 +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 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 )
 {
+  GenericData* data;
+  DoubleArrayData * etaValue;
+  vector<double> etaArray;
+  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;
+    }
+  }
+
+
+  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];
+	  }
+	}
+      }
+    }
+  }
+
+}
+
+template<typename T> NPTf<T>::~NPTf() {
+
+  // empty for now
+}
+
+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++) 
+  for(i = 0; i < 3; i++)
+    for (j = 0; j < 3; j++)
       eta[i][j] = 0.0;
 
-  have_tau_thermostat = 0;
-  have_tau_barostat = 0;
-  have_target_temp = 0;
-  have_target_pressure = 0;
+  T::resetIntegrator();
 }
 
-void NPTf::moveA() {
-  
-  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 NPTf<T>::evolveEtaA() {
 
-  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];
+  int i, j;
 
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
+  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);
+    }
+  }
 
-  instaTemp = tStats->getTemperature();
-  tStats->getPressureTensor(press);
-  instaVol = tStats->getVolume();
-   
-  // first evolve chi a half step
-  
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
+  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() {
+
+  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++ ) {
-      if (i == j) {
-        
-        eta[i][j] += dt2 * instaVol * 
-          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
-        
-        vScale[i][j] = eta[i][j] + chi;
-        
-      } else {
-        
-        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
+      vScale[i][j] = eta[i][j];
 
-        vScale[i][j] = eta[i][j];
-        
+      if (i == j) {
+        vScale[i][j] += chi;
       }
     }
   }
 
-  for( i=0; i<nAtoms; i++ ){
+  info->matVecMul3( vScale, vel, sc );
+}
 
-    atoms[i]->getVel( vel );
-    atoms[i]->getPos( pos );
-    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();
-    
-    // velocity half step
-        
-    info->matVecMul3( vScale, vel, sc );
-    
-    for (j = 0; j < 3; j++) {
-      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
-      rj[j] = pos[j];
+  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;
+      }
     }
+  }
 
-    atoms[i]->setVel( vel );
+  for (j = 0; j < 3; j++)
+    myVel[j] = oldVel[3*index + j];
 
-    // position whole step    
+  info->matVecMul3( vScale, myVel, sc );
+}
 
-    info->wrapVector(rj);
+template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
+					       int index, double sc[3]){
+  int j;
+  double rj[3];
 
-    info->matVecMul3( eta, rj, sc );
+  for(j=0; j<3; j++)
+    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
 
-    for (j = 0; j < 3; j++ ) 
-      pos[j] += dt * (vel[j] + sc[j]);
-   
-    if( atoms[i]->isDirectional() ){
+  info->matVecMul3( eta, rj, sc );
+}
 
-      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
+template<typename T> void NPTf<T>::scaleSimBox( void ){
 
-      dAtom->getJ( ji );
+  int i,j,k;
+  double scaleMat[3][3];
+  double eta2ij;
+  double bigScale, smallScale, offDiagMax;
+  double hm[3][3], hmnew[3][3];
 
-      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:
-  
+
   // 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];
   }
-  
-  info->getBoxM(hm);
-  info->matMul3(hm, scaleMat, hmnew);
-  info->setBoxM(hmnew);
-  
+
+  if ((bigScale > 1.01) || (smallScale < 0.99)) {
+    sprintf( painCave.errMsg,
+             "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();
+  } else if (offDiagMax > 0.01) {
+    sprintf( painCave.errMsg,
+             "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();
+  } else {
+    info->getBoxM(hm);
+    info->matMul3(hm, scaleMat, hmnew);
+    info->setBoxM(hmnew);
+  }
 }
 
-void NPTf::moveB( void ){
+template<typename T> bool NPTf<T>::etaConverged() {
+  int i;
+  double diffEta, sumEta;
 
-  int i, j;
-  DirectionalAtom* dAtom;
-  double Tb[3], ji[3];
-  double vel[3], frc[3];
-  double mass;
+  sumEta = 0;
+  for(i = 0; i < 3; i++)
+    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
 
-  double instaTemp, instaPress, instaVol;
-  double tt2, tb2;
-  double sc[3];
-  double press[3][3], vScale[3][3];
-  
-  tt2 = tauThermostat * tauThermostat;
-  tb2 = tauBarostat * tauBarostat;
+  diffEta = sqrt( sumEta / 3.0 );
 
-  instaTemp = tStats->getTemperature();
-  tStats->getPressureTensor(press);
-  instaVol = tStats->getVolume();
-   
-  // first evolve chi a half step
-  
-  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  
-  for (i = 0; i < 3; i++ ) {
-    for (j = 0; j < 3; j++ ) {
-      if (i == j) {
+  return ( diffEta <= etaTolerance );
+}
 
-        eta[i][j] += dt2 * instaVol * 
-          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
+template<typename T> double NPTf<T>::getConservedQuantity(void){
 
-        vScale[i][j] = eta[i][j] + chi;
-        
-      } else {
-        
-        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
+  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];
 
-        vScale[i][j] = eta[i][j];
-        
-      }
-    }
-  }
+  totalEnergy = tStats->getTotalE();
 
-  for( i=0; i<nAtoms; i++ ){
+  thermostat_kinetic = fkBT * tt2 * chi * chi /
+    (2.0 * eConvert);
 
-    atoms[i]->getVel( vel );
-    atoms[i]->getFrc( frc );
+  thermostat_potential = fkBT* integralOfChidt / eConvert;
 
-    mass = atoms[i]->getMass();
-    
-    // velocity half step
-        
-    info->matVecMul3( vScale, vel, sc );
-    
-    for (j = 0; j < 3; j++) {
-      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
-    }
+  info->transposeMat3(eta, a);
+  info->matMul3(a, eta, b);
+  trEta = info->matTrace3(b);
 
-    atoms[i]->setVel( vel );
-    
-    if( atoms[i]->isDirectional() ){
+  barostat_kinetic = NkBT * tb2 * trEta /
+    (2.0 * eConvert);
 
-      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);
-      
-      dAtom->setJ( ji );
+  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
+    eConvert;
 
-    }                    
-  }
-}
+  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
+    barostat_kinetic + barostat_potential;
 
-int NPTf::readyCheck() {
- 
-  // 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;
-  }
+  return conservedQuantity;
 
-  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;
-  }    
+template<typename T> string NPTf<T>::getAdditionalParameters(void){
+  string parameters;
+  const int BUFFERSIZE = 2000; // size of the read buffer
+  char buffer[BUFFERSIZE];
 
-  // We need NkBT a lot, so just set it here:
+  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
+  parameters += buffer;
 
-  NkBT = (double)info->ndf * kB * targetTemp;
+  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 1;
+  return parameters;
+
 }