--- trunk/OOPSE/libmdtools/Atom.cpp	2003/07/14 21:48:43	599
+++ trunk/OOPSE/libmdtools/Atom.cpp	2003/08/07 21:47:18	670
@@ -2,30 +2,26 @@ using namespace std;
 
 using namespace std;
 
+#include "simError.h"
 #include "Atom.hpp"
 
-double* Atom::pos; // the position array
-double* Atom::vel; // the velocity array
-double* Atom::frc; // the forc array
-double* Atom::trq; // the torque vector  ( space fixed )
-double* Atom::Amat; // the rotation matrix
-double* Atom::mu;   // the array of dipole moments
-double* Atom::ul;   // the lab frame unit directional vector
-int Atom::nElements;
-
-Atom::Atom(int theIndex) {
+Atom::Atom(int theIndex, SimState* theConfig) {
+  
+  myConfig = theConfig;
+  hasCoords = false;
+  
   c_n_hyd = 0; 
   has_dipole = 0;
   is_VDW = 0;
   is_LJ = 0;
   
   index = theIndex;
-  offset = 3 * index;
+  offset = 0;
   offsetX = offset;
   offsetY = offset+1;
   offsetZ = offset+2;
   
-  Axx = index*9;
+  Axx = 0;
   Axy = Axx+1;
   Axz = Axx+2;
   
@@ -38,252 +34,292 @@ void Atom::createArrays (int the_nElements) {
   Azz = Axx+8;
 }
 
-void Atom::createArrays (int the_nElements) {
-  int i;
-  
-  nElements = the_nElements;
+void Atom::setIndex(int theIndex) {
+  index = theIndex; 
+}
 
-  pos = new double[nElements*3];
-  vel = new double[nElements*3];
-  frc = new double[nElements*3];
-  trq = new double[nElements*3];
-  Amat = new double[nElements*9];
-  mu = new double[nElements];
-  ul = new double[nElements*3];
-  
-  // init directional values to zero
-  
-  for( i=0; i<nElements; i++){
-    trq[i] = 0.0;
-    trq[i+1] = 0.0;
-    trq[i+2] = 0.0;
-    
-    Amat[i] = 1.0;
-    Amat[i+1] = 0.0;
-    Amat[i+2] = 0.0;
-    
-    Amat[i+3] = 0.0;
-    Amat[i+4] = 1.0;
-    Amat[i+5] = 0.0;
-    
-    Amat[i+6] = 0.0;
-    Amat[i+7] = 0.0;
-    Amat[i+8] = 1.0;
-    
-    mu[i] = 0.0;    
-    
-    ul[i] = 1.0;
-    ul[i+1] = 0.0;
-    ul[i+2] = 0.0;
+void Atom::setCoords(void){
+
+  if( myConfig->isAllocated() ){
+
+    myConfig->getAtomPointers( index,
+		     &pos, 
+		     &vel, 
+		     &frc, 
+		     &trq, 
+		     &Amat,
+		     &mu,  
+		     &ul );
   }
-}
+  else{
+    sprintf( painCave.errMsg,
+	     "Attempted to set Atom %d  coordinates with an unallocated "
+	     "SimState object.\n" );
+    painCave.isFatal = 1;
+    simError();
+  }
 
-void Atom::destroyArrays(void) {
-  delete[] pos;
-  delete[] vel;
-  delete[] frc;
-  delete[] trq;
-  delete[] Amat;
-  delete[] mu;
-}
+  hasCoords = true;
 
-void Atom::setIndex(int theIndex) {
-  index = theIndex; 
-  offset = index*3;
-  offsetX = offset;
-  offsetY = offset+1;
-  offsetZ = offset+2;
-  
-  Axx = index*9;
-  Axy = Axx+1;
-  Axz = Axx+2;
-  
-  Ayx = Axx+3;
-  Ayy = Axx+4;
-  Ayz = Axx+5;
-  
-  Azx = Axx+6;
-  Azy = Axx+7;
-  Azz = Axx+8;
 }
 
-void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, 
-                   double* Atrq, double* AAmat, double* Amu, 
-                   double* Aul) {
+// void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, 
+//                    double* Atrq, double* AAmat, double* Amu, 
+//                    double* Aul) {
 
-  int nNew = nElements+nAdded;
+//   int nNew = nElements+nAdded;
 
-  double* new_pos = new double[nNew*3];
-  double* new_vel = new double[nNew*3];
-  double* new_frc = new double[nNew*3];
-  double* new_trq = new double[nNew*3];
-  double* new_Amat = new double[nNew*9];
-  double* new_mu = new double[nNew];
-  double* new_ul = new double[nNew*3];
-  int i, j;
+//   double* new_pos = new double[nNew*3];
+//   double* new_vel = new double[nNew*3];
+//   double* new_frc = new double[nNew*3];
+//   double* new_trq = new double[nNew*3];
+//   double* new_Amat = new double[nNew*9];
+//   double* new_mu = new double[nNew];
+//   double* new_ul = new double[nNew*3];
+//   int i, j;
   
-  for (i = 0; i < 3*nElements; i++) {
-    new_pos[i] = pos[i];
-    new_vel[i] = vel[i];
-    new_frc[i] = frc[i];
-    new_trq[i] = trq[i];
-    new_ul[i] = ul[i];
-  }
+//   for (i = 0; i < 3*nElements; i++) {
+//     new_pos[i] = pos[i];
+//     new_vel[i] = vel[i];
+//     new_frc[i] = frc[i];
+//     new_trq[i] = trq[i];
+//     new_ul[i] = ul[i];
+//   }
 
-  for(i = 0; i < 3*nAdded; i++) {
-    j = i + 3*nElements;
-    new_pos[j] = Apos[i];
-    new_vel[j] = Avel[i];
-    new_frc[j] = Afrc[i];
-    new_trq[j] = Atrq[i];
-    new_ul[j] = Aul[i]; 
-  }
+//   for(i = 0; i < 3*nAdded; i++) {
+//     j = i + 3*nElements;
+//     new_pos[j] = Apos[i];
+//     new_vel[j] = Avel[i];
+//     new_frc[j] = Afrc[i];
+//     new_trq[j] = Atrq[i];
+//     new_ul[j] = Aul[i]; 
+//   }
 
-  for (i = 0; i < 9*nElements; i++) {
-    new_Amat[i] = Amat[i];
-  }
+//   for (i = 0; i < 9*nElements; i++) {
+//     new_Amat[i] = Amat[i];
+//   }
 
-  for(i = 0; i < 9*nAdded; i++) {
-    j = i + 9*nElements;
-    new_Amat[j] = AAmat[i];
-  }
+//   for(i = 0; i < 9*nAdded; i++) {
+//     j = i + 9*nElements;
+//     new_Amat[j] = AAmat[i];
+//   }
 
-  for (i = 0; i < nElements; i++) {
-    new_mu[i] = mu[i];
-  }
+//   for (i = 0; i < nElements; i++) {
+//     new_mu[i] = mu[i];
+//   }
 
-  for(i = 0; i < nAdded; i++) {
-    j = i + nElements;
-    new_mu[j] = Amu[i];
-  }
+//   for(i = 0; i < nAdded; i++) {
+//     j = i + nElements;
+//     new_mu[j] = Amu[i];
+//   }
 
-  delete[] pos;
-  delete[] vel;
-  delete[] frc;
-  delete[] trq;
-  delete[] Amat;
-  delete[] mu;
+//   delete[] pos;
+//   delete[] vel;
+//   delete[] frc;
+//   delete[] trq;
+//   delete[] Amat;
+//   delete[] mu;
 
-  pos = new_pos;
-  vel = new_vel;
-  frc = new_frc;
-  trq = new_trq;
-  ul = new_ul;
-  Amat = new_Amat;
-  mu = new_mu;
+//   pos = new_pos;
+//   vel = new_vel;
+//   frc = new_frc;
+//   trq = new_trq;
+//   ul = new_ul;
+//   Amat = new_Amat;
+//   mu = new_mu;
 
-  nElements = nNew;
-}
+//   nElements = nNew;
+// }
 
-void Atom::deleteAtom(int theIndex) {
-  deleteRange(theIndex, theIndex);
-}
+// void Atom::deleteAtom(int theIndex) {
+//   deleteRange(theIndex, theIndex);
+// }
 
-void Atom::deleteRange(int startIndex, int stopIndex) {
+// void Atom::deleteRange(int startIndex, int stopIndex) {
  
-  int nNew = nElements-(stopIndex-startIndex+1);
+//   int nNew = nElements-(stopIndex-startIndex+1);
 
-  double* new_pos = new double[nNew*3];
-  double* new_vel = new double[nNew*3];
-  double* new_frc = new double[nNew*3];
-  double* new_trq = new double[nNew*3];
-  double* new_Amat = new double[nNew*9];
-  double* new_mu = new double[nNew];
-  double* new_ul = new double[nNew*3];
-  int i, j;
+//   double* new_pos = new double[nNew*3];
+//   double* new_vel = new double[nNew*3];
+//   double* new_frc = new double[nNew*3];
+//   double* new_trq = new double[nNew*3];
+//   double* new_Amat = new double[nNew*9];
+//   double* new_mu = new double[nNew];
+//   double* new_ul = new double[nNew*3];
+//   int i, j;
   
-  for (i = 0; i < 3*startIndex; i++) {
-    new_pos[i] = pos[i];
-    new_vel[i] = vel[i];
-    new_frc[i] = frc[i];
-    new_trq[i] = trq[i];
-    new_ul[i] = ul[i];
-  }
+//   for (i = 0; i < 3*startIndex; i++) {
+//     new_pos[i] = pos[i];
+//     new_vel[i] = vel[i];
+//     new_frc[i] = frc[i];
+//     new_trq[i] = trq[i];
+//     new_ul[i] = ul[i];
+//   }
 
-  for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
-    j = i - 3*startIndex + 1;
-    new_pos[j] = pos[i];
-    new_vel[j] = vel[i];
-    new_frc[j] = frc[i];
-    new_trq[j] = trq[i];
-    new_ul[j] = ul[i]; 
-  }
+//   for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
+//     j = i - 3*startIndex + 1;
+//     new_pos[j] = pos[i];
+//     new_vel[j] = vel[i];
+//     new_frc[j] = frc[i];
+//     new_trq[j] = trq[i];
+//     new_ul[j] = ul[i]; 
+//   }
 
-  for (i = 0; i < 9*startIndex; i++) {
-    new_Amat[i] = Amat[i];
-  }
+//   for (i = 0; i < 9*startIndex; i++) {
+//     new_Amat[i] = Amat[i];
+//   }
 
-  for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
-    j = i - 9*startIndex + 1;
-    new_Amat[j] = Amat[i];
-  }
+//   for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
+//     j = i - 9*startIndex + 1;
+//     new_Amat[j] = Amat[i];
+//   }
 
-  for (i = 0; i < startIndex; i++) {
-    new_mu[i] = mu[i];
-  }
+//   for (i = 0; i < startIndex; i++) {
+//     new_mu[i] = mu[i];
+//   }
 
-  for(i = (stopIndex+1); i < nElements; i++) {
-    j = i - startIndex + 1;
-    new_mu[j] = mu[i];
-  }
+//   for(i = (stopIndex+1); i < nElements; i++) {
+//     j = i - startIndex + 1;
+//     new_mu[j] = mu[i];
+//   }
 
-  delete[] pos;
-  delete[] vel;
-  delete[] frc;
-  delete[] trq;
-  delete[] Amat;
-  delete[] mu;
+//   delete[] pos;
+//   delete[] vel;
+//   delete[] frc;
+//   delete[] trq;
+//   delete[] Amat;
+//   delete[] mu;
 
-  pos = new_pos;
-  vel = new_vel;
-  frc = new_frc;
-  trq = new_trq;
-  ul = new_ul;
-  Amat = new_Amat;
-  mu = new_mu;
+//   pos = new_pos;
+//   vel = new_vel;
+//   frc = new_frc;
+//   trq = new_trq;
+//   ul = new_ul;
+//   Amat = new_Amat;
+//   mu = new_mu;
 
-  nElements = nNew;
-}
+//   nElements = nNew;
+// }
 
 
 void Atom::getPos( double theP[3] ){
   
-  theP[0] = pos[offsetX];
-  theP[1] = pos[offsetY];
-  theP[2] = pos[offsetZ];
+  if( hasCoords ){
+    theP[0] = pos[offsetX];
+    theP[1] = pos[offsetY];
+    theP[2] = pos[offsetZ];
+  }
+  else{
+
+    sprintf( painCave.errMsg,
+	     "Attempt to get Pos for atom %d before coords set.\n",
+	     index );
+    painCave.isFatal = 1;
+    simError();
+  }
 }
 
 void Atom::setPos( double theP[3] ){
   
-  pos[offsetX] = theP[0];
-  pos[offsetY] = theP[1];
-  pos[offsetZ] = theP[2];
+  if( hasCoords ){
+    pos[offsetX] = theP[0];
+    pos[offsetY] = theP[1];
+    pos[offsetZ] = theP[2];
+  }
+  else{
+
+    sprintf( painCave.errMsg,
+	     "Attempt to set Pos for atom %d before coords set.\n",
+	     index );
+    painCave.isFatal = 1;
+    simError();
+  }
 }
 
 void Atom::getVel( double theV[3] ){
   
-  theV[0] = vel[offsetX];
-  theV[1] = vel[offsetY];
-  theV[2] = vel[offsetZ];
+  if( hasCoords ){
+    theV[0] = vel[offsetX];
+    theV[1] = vel[offsetY];
+    theV[2] = vel[offsetZ];
+  }
+  else{
+    
+    sprintf( painCave.errMsg,
+	     "Attempt to get vel for atom %d before coords set.\n",
+	     index );
+    painCave.isFatal = 1;
+    simError();
+  }
+
 }
 
 void Atom::setVel( double theV[3] ){
   
-  vel[offsetX] = theV[0];
-  vel[offsetY] = theV[1];
-  vel[offsetZ] = theV[2];
+  if( hasCoords ){
+    vel[offsetX] = theV[0];
+    vel[offsetY] = theV[1];
+    vel[offsetZ] = theV[2];
+  }
+  else{
+    
+    sprintf( painCave.errMsg,
+	     "Attempt to set vel for atom %d before coords set.\n",
+	     index );
+    painCave.isFatal = 1;
+    simError();
+  }
 }
 
 void Atom::getFrc( double theF[3] ){
   
-  theF[0] = frc[offsetX];
-  theF[1] = frc[offsetY];
-  theF[2] = frc[offsetZ];
+  if( hasCoords ){
+    theF[0] = frc[offsetX];
+    theF[1] = frc[offsetY];
+    theF[2] = frc[offsetZ];
+  }
+  else{
+    
+    sprintf( painCave.errMsg,
+	     "Attempt to get frc for atom %d before coords set.\n",
+	     index );
+    painCave.isFatal = 1;
+    simError();
+  }
 }
 
 void Atom::addFrc( double theF[3] ){
   
-  frc[offsetX] += theF[0];
-  frc[offsetY] += theF[1];
-  frc[offsetZ] += theF[2];
+  if( hasCoords ){
+    frc[offsetX] += theF[0];
+    frc[offsetY] += theF[1];
+    frc[offsetZ] += theF[2];
+  }
+  else{
+    
+    sprintf( painCave.errMsg,
+	     "Attempt to add frc for atom %d before coords set.\n",
+	     index );
+    painCave.isFatal = 1;
+    simError();
+  }
 }
+
+
+void GeneralAtom::zeroForces( void ){
+  
+  
+  if( hasCoords ){
+    frc[offsetX] = 0.0; 
+    frc[offsetY] = 0.0; 
+    frc[offsetZ] = 0.0;
+  }
+  else{
+    
+    sprintf( painCave.errMsg,
+	     "Attempt to zero frc for atom %d before coords set.\n",
+	     index );
+    painCave.isFatal = 1;
+    simError();
+  }
+}