--- trunk/OOPSE-4/src/integrators/NPTi.cpp	2004/10/21 16:22:01	1625
+++ trunk/OOPSE-4/src/integrators/NPTi.cpp	2005/01/12 22:41:40	1930
@@ -1,17 +1,53 @@
-#include <math.h>
-#include "primitives/Atom.hpp"
-#include "primitives/SRI.hpp"
-#include "primitives/AbstractClasses.hpp"
+ /*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * non-exclusive, royalty free, license to use, modify and
+ * redistribute this software in source and binary code form, provided
+ * that the following conditions are met:
+ *
+ * 1. Acknowledgement of the program authors must be made in any
+ *    publication of scientific results based in part on use of the
+ *    program.  An acceptable form of acknowledgement is citation of
+ *    the article in which the program was described (Matthew
+ *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
+ *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
+ *    Parallel Simulation Engine for Molecular Dynamics,"
+ *    J. Comput. Chem. 26, pp. 252-271 (2005))
+ *
+ * 2. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 3. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * arising out of the use of or inability to use software, even if the
+ * University of Notre Dame has been advised of the possibility of
+ * such damages.
+ */
+ 
+#include "NPTi.hpp"
 #include "brains/SimInfo.hpp"
-#include "UseTheForce/ForceFields.hpp"
 #include "brains/Thermo.hpp"
-#include "io/ReadWrite.hpp"
-#include "integrators/Integrator.hpp"
+#include "integrators/NPT.hpp"
+#include "primitives/Molecule.hpp"
+#include "utils/OOPSEConstant.hpp"
 #include "utils/simError.h"
 
-#ifdef IS_MPI
-#include "brains/mpiSimulation.hpp"
-#endif
+namespace oopse {
 
 // Basic isotropic thermostating and barostating via the Melchionna
 // modification of the Hoover algorithm:
@@ -23,157 +59,127 @@ template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo,
 //
 //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
 
-template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
-  T( theInfo, the_ff )
-{
-  GenericData* data;
-  DoubleVectorGenericData * etaValue;
-  vector<double> etaArray;
+NPTi::NPTi ( SimInfo *info) : NPT(info){
 
-  eta = 0.0;
-  oldEta = 0.0;
-
-  if( theInfo->useInitXSstate ){
-    // retrieve eta from simInfo if
-    data = info->getProperty(ETAVALUE_ID);
-    if(data){
-      etaValue = dynamic_cast<DoubleVectorGenericData*>(data);
-      
-      if(etaValue){
-	eta = (*etaValue)[0];
-	oldEta = eta;
-      }
-    }
-  }
 }
 
-template<typename T> NPTi<T>::~NPTi() {
-  //nothing for now
+void NPTi::evolveEtaA() {
+    eta += dt2 * ( instaVol * (instaPress - targetPressure) /
+         (OOPSEConstant::pressureConvert*NkBT*tb2));
+    oldEta = eta;
 }
 
-template<typename T> void NPTi<T>::resetIntegrator() {
-  eta = 0.0;
-  T::resetIntegrator();
-}
+void NPTi::evolveEtaB() {
 
-template<typename T> void NPTi<T>::evolveEtaA() {
-  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
-		 (p_convert*NkBT*tb2));
-  oldEta = eta;
+    prevEta = eta;
+    eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
+         (OOPSEConstant::pressureConvert*NkBT*tb2));
 }
 
-template<typename T> void NPTi<T>::evolveEtaB() {
-
-  prevEta = eta;
-  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
-		 (p_convert*NkBT*tb2));
+void NPTi::calcVelScale() {
+    vScale = chi + eta;
 }
 
-template<typename T> void NPTi<T>::calcVelScale(void) {
-  vScale = chi + eta;
+void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
+    sc = vel * vScale;
 }
 
-template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
-  int i;
-
-  for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
+void NPTi::getVelScaleB(Vector3d& sc, int index ){
+    sc = oldVel[index] * vScale;    
 }
 
-template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
-  int i;
 
-  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale;
+void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
+                           int index, Vector3d& sc){
+    /**@todo*/
+    sc  = (oldPos[index] + pos)/2.0 -COM;
+    sc *= eta;
 }
 
+void NPTi::scaleSimBox(){
 
-template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
-					       int index, double sc[3]){
-  int j;
+    double scaleFactor;
 
-  for(j=0; j<3; j++)
-    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
+    scaleFactor = exp(dt*eta);
 
-  for(j=0; j<3; j++)
-    sc[j] *= eta;
-}
-
-template<typename T> void NPTi<T>::scaleSimBox( void ){
-
-  double scaleFactor;
-
-  scaleFactor = exp(dt*eta);
-
-  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
-    sprintf( painCave.errMsg,
+    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(scaleFactor);
-  }
+        painCave.isFatal = 1;
+        simError();
+    } else {
+        Mat3x3d hmat = currentSnapshot_->getHmat();
+        hmat *= scaleFactor;
+        currentSnapshot_->setHmat(hmat);
+    }
 
 }
 
-template<typename T> bool NPTi<T>::etaConverged() {
+bool NPTi::etaConverged() {
 
-  return ( fabs(prevEta - eta) <= etaTolerance );
+    return ( fabs(prevEta - eta) <= etaTolerance );
 }
 
-template<typename T> double NPTi<T>::getConservedQuantity(void){
+double NPTi::calcConservedQuantity(){
 
-  double conservedQuantity;
-  double Energy;
-  double thermostat_kinetic;
-  double thermostat_potential;
-  double barostat_kinetic;
-  double barostat_potential;
+    chi= currentSnapshot_->getChi();
+    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
+    loadEta();
+    // We need NkBT a lot, so just set it here: This is the RAW number
+    // of integrableObjects, so no subtraction or addition of constraints or
+    // orientational degrees of freedom:
+    NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp;
 
-  Energy = tStats->getTotalE();
+    // fkBT is used because the thermostat operates on more degrees of freedom
+    // than the barostat (when there are particles with orientational degrees
+    // of freedom).  
+    fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp;    
+    
+    double conservedQuantity;
+    double Energy;
+    double thermostat_kinetic;
+    double thermostat_potential;
+    double barostat_kinetic;
+    double barostat_potential;
 
-  thermostat_kinetic = fkBT* tt2 * chi * chi /
-    (2.0 * eConvert);
+    Energy =thermo.getTotalE();
 
-  thermostat_potential = fkBT* integralOfChidt / eConvert;
+    thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);
 
+    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
 
-  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
-    (2.0 * eConvert);
 
-  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
-    eConvert;
+    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);
 
-  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
-    barostat_kinetic + barostat_potential;
+    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
+        OOPSEConstant::energyConvert;
 
-//   cout.width(8);
-//   cout.precision(8);
+    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
+        barostat_kinetic + barostat_potential;
+    
+    return conservedQuantity;
+}
 
-//   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
-//       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
-//       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
-  return conservedQuantity;
+void NPTi::loadEta() {
+    Mat3x3d etaMat = currentSnapshot_->getEta();
+    eta = etaMat(0,0);
+    //if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) {
+    //    sprintf( painCave.errMsg,
+    //             "NPTi error: the diagonal elements of  eta matrix are not the same or etaMat is not a diagonal matrix");
+    //    painCave.isFatal = 1;
+    //    simError();
+    //}
 }
 
-template<typename T> string NPTi<T>::getAdditionalParameters(void){
-  string parameters;
-  const int BUFFERSIZE = 2000; // size of the read buffer
-  char buffer[BUFFERSIZE];
+void NPTi::saveEta() {
+    Mat3x3d etaMat(0.0);
+    etaMat(0, 0) = eta;
+    etaMat(1, 1) = eta;
+    etaMat(2, 2) = eta;
+    currentSnapshot_->setEta(etaMat);
+}
 
-  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;
-
 }