--- trunk/OOPSE/libmdtools/NPTi.cpp	2003/07/09 01:41:11	577
+++ trunk/OOPSE/libmdtools/NPTi.cpp	2003/07/31 15:35:07	658
@@ -1,3 +1,4 @@
+#include <cmath>
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "AbstractClasses.hpp"
@@ -19,8 +20,8 @@ NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
 // 
 //    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;
   eta = 0.0;
@@ -30,17 +31,18 @@ void NPTi::moveA() {
   have_target_pressure = 0;
 }
 
-void NPTi::moveA() {
+template<typename T> void NPTi<T>::moveA() {
   
-  int i,j,k;
-  int atomIndex, aMatIndex;
+  int i, j;
   DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
+  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;
-  double angle;
+  double tt2, tb2, scaleFactor;
 
   tt2 = tauThermostat * tauThermostat;
   tb2 = tauBarostat * tauBarostat;
@@ -49,95 +51,107 @@ void NPTi::moveA() {
   instaPress = tStats->getPressure();
   instaVol = tStats->getVolume();
    
-  // first evolve chi a half step
+   // first evolve chi a half step
   
   chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
+  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
+		 (p_convert*NkBT*tb2));
 
   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));
+    atoms[i]->getVel( vel );
+    atoms[i]->getPos( pos );
+    atoms[i]->getFrc( frc );
 
-    // position whole step    
+    mass = atoms[i]->getMass();
 
-    rj[0] = pos[atomIndex];
-    rj[1] = pos[atomIndex+1];
-    rj[2] = pos[atomIndex+2];
-    
+    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 );
+
     info->wrapVector(rj);
 
-    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]);
-   
+    for (j = 0; j < 3; j++) 
+      pos[j] += dt * (vel[j] + eta*rj[j]);
+
+    atoms[i]->setPos( pos );
+
     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->getTrq( Tb );
       dAtom->lab2Body( Tb );
       
       // get the angular momentum, and propagate a half step
 
-      ji[0] = dAtom->getJx();
-      ji[1] = dAtom->getJy();
-      ji[2] = dAtom->getJz();
+      dAtom->getJ( ji );
+
+      for (j=0; j < 3; j++) 
+        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
       
-      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
-      
+
+      dAtom->getA(A);
+      dAtom->getI(I);
+    
       // rotate about the x-axis      
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); 
-      
+      angle = dt2 * ji[0] / I[0][0];
+      this->rotate( 1, 2, angle, ji, A ); 
+
       // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[1] / I[1][1];
+      this->rotate( 2, 0, angle, ji, A );
       
       // rotate about the z-axis
-      angle = dt * ji[2] / dAtom->getIzz();
-      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
+      angle = dt * ji[2] / I[2][2];
+      this->rotate( 0, 1, angle, ji, A);
       
       // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[1] / I[1][1];
+      this->rotate( 2, 0, angle, ji, A );
       
        // rotate about the x-axis
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[0] / I[0][0];
+      this->rotate( 1, 2, angle, ji, A );
       
-      dAtom->setJx( ji[0] );
-      dAtom->setJy( ji[1] );
-      dAtom->setJz( ji[2] );
-    }
-    
+      dAtom->setJ( ji );
+      dAtom->setA( A  );    
+    }                
+
   }
+
   // Scale the box after all the positions have been moved:
+  
+  scaleFactor = exp(dt*eta);
 
-  info->scaleBox(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));      
+  }
 
 }
 
-void NPTi::moveB( void ){
-  int i,j,k;
-  int atomIndex;
+template<typename T> void NPTi<T>::moveB( void ){
+
+  int i, j;
   DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
+  double Tb[3], ji[3];
+  double vel[3], frc[3];
+  double mass;
+
   double instaTemp, instaPress, instaVol;
   double tt2, tb2;
   
@@ -149,48 +163,48 @@ void NPTi::moveB( void ){
   instaVol = tStats->getVolume();
 
   chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
+  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
+		 (p_convert*NkBT*tb2));
   
   for( i=0; i<nAtoms; i++ ){
-    atomIndex = i * 3;
-    
+
+    atoms[i]->getVel( vel );
+    atoms[i]->getFrc( frc );
+
+    mass = atoms[i]->getMass();
+
     // 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));
+    for (j=0; j < 3; j++) 
+      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
-      
-      Tb[0] = dAtom->getTx();
-      Tb[1] = dAtom->getTy();
-      Tb[2] = dAtom->getTz();
-      
+
+      // get and convert the torque to body frame      
+
+      dAtom->getTrq( Tb );
       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] );
+
+      // 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 );
     }
   }
 }
 
-int NPTi::readyCheck() {
+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.