--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/07/09 22:14:06	586
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/07/21 16:23:57	642
@@ -33,8 +33,19 @@ SimInfo::SimInfo(){
   the_integrator = NULL;
   setTemp = 0;
   thermalTime = 0.0;
+  currentTime = 0.0;
   rCut = 0.0;
+  ecr = 0.0;
+  est = 0.0;
+  oldEcr = 0.0;
+  oldRcut = 0.0;
 
+  haveOrigRcut = 0;
+  haveOrigEcr = 0;
+  boxIsInit = 0;
+  
+  
+
   usePBC = 0;
   useLJ = 0; 
   useSticky = 0;
@@ -48,210 +59,240 @@ void SimInfo::setBox(double newBox[3]) {
 
 void SimInfo::setBox(double newBox[3]) {
   
-  int i;
-  double tempMat[9];
+  int i, j;
+  double tempMat[3][3];
 
-  for(i=0; i<9; i++) tempMat[i] = 0.0;;
+  for(i=0; i<3; i++) 
+    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
 
-  tempMat[0] = newBox[0];
-  tempMat[4] = newBox[1];
-  tempMat[8] = newBox[2];
+  tempMat[0][0] = newBox[0];
+  tempMat[1][1] = newBox[1];
+  tempMat[2][2] = newBox[2];
 
   setBoxM( tempMat );
 
 }
 
-void SimInfo::setBoxM( double theBox[9] ){
+void SimInfo::setBoxM( double theBox[3][3] ){
   
-  int i, status;
+  int i, j, status;
   double smallestBoxL, maxCutoff;
+  double FortranHmat[9]; // to preserve compatibility with Fortran the
+                         // ordering in the array is as follows:
+                         // [ 0 3 6 ]
+                         // [ 1 4 7 ]
+                         // [ 2 5 8 ]
+  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
 
-  for(i=0; i<9; i++) Hmat[i] = theBox[i];
+  
+  if( !boxIsInit ) boxIsInit = 1;
 
-  cerr 
-    << "setting Hmat ->\n"
-    << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n"
-    << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n"
-    << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n";
-
-  calcHmatI();
+  for(i=0; i < 3; i++) 
+    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
+  
   calcBoxL();
+  calcHmatInv();
 
-
-
-  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
- 
-  smallestBoxL = boxLx;
-  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
-  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
-
-  maxCutoff = smallestBoxL / 2.0;
-
-  if (rList > maxCutoff) {
-    sprintf( painCave.errMsg,
-             "New Box size is forcing neighborlist radius down to %lf\n",
-             maxCutoff );
-    painCave.isFatal = 0;
-    simError();
-
-    rList = maxCutoff;
-
-    sprintf( painCave.errMsg,
-             "New Box size is forcing cutoff radius down to %lf\n",
-             maxCutoff - 1.0 );
-    painCave.isFatal = 0;
-    simError();
-
-    rCut = rList - 1.0;
-
-    // list radius changed so we have to refresh the simulation structure.
-    refreshSim();
-  }
-
-  if (rCut > maxCutoff) {
-    sprintf( painCave.errMsg,
-             "New Box size is forcing cutoff radius down to %lf\n",
-             maxCutoff );
-    painCave.isFatal = 0;
-    simError();
-
-    status = 0;
-    LJ_new_rcut(&rCut, &status);
-    if (status != 0) {
-      sprintf( painCave.errMsg,
-               "Error in recomputing LJ shifts based on new rcut\n");
-      painCave.isFatal = 1;
-      simError();
+  for(i=0; i < 3; i++) {
+    for (j=0; j < 3; j++) {
+      FortranHmat[3*j + i] = Hmat[i][j];
+      FortranHmatInv[3*j + i] = HmatInv[i][j];
     }
   }
+
+  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
+ 
 }
  
 
-void SimInfo::getBoxM (double theBox[9]) {
+void SimInfo::getBoxM (double theBox[3][3]) {
 
-  int i;
-  for(i=0; i<9; i++) theBox[i] = Hmat[i];
+  int i, j;
+  for(i=0; i<3; i++) 
+    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
 }
 
 
 void SimInfo::scaleBox(double scale) {
-  double theBox[9];
-  int i;
+  double theBox[3][3];
+  int i, j;
 
-  cerr << "Scaling box by " << scale << "\n";
+  // cerr << "Scaling box by " << scale << "\n";
 
-  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
+  for(i=0; i<3; i++) 
+    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
 
   setBoxM(theBox);
 
 }
 
-void SimInfo::calcHmatI( void ) {
-
-  double C[3][3];
-  double detHmat;
-  int i, j, k;
+void SimInfo::calcHmatInv( void ) {
+  
+  int i,j;
   double smallDiag;
   double tol;
   double sanity[3][3];
 
-  // calculate the adjunct of Hmat;
+  invertMat3( Hmat, HmatInv );
 
-  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
-  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
-  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
+  // Check the inverse to make sure it is sane:
 
-  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
-  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
-  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
-
-  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
-  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
-  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
-
-  // calcutlate the determinant of Hmat
+  matMul3( Hmat, HmatInv, sanity );
+    
+  // check to see if Hmat is orthorhombic
   
-  detHmat = 0.0;
-  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
+  smallDiag = Hmat[0][0];
+  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
+  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
+  tol = smallDiag * 1E-6;
 
+  orthoRhombic = 1;
   
-  // H^-1 = C^T / det(H)
-  
-  i=0;
-  for(j=0; j<3; j++){
-    for(k=0; k<3; k++){
-
-      HmatI[i] = C[j][k] / detHmat;
-      i++;
+  for (i = 0; i < 3; i++ ) {
+    for (j = 0 ; j < 3; j++) {
+      if (i != j) {
+        if (orthoRhombic) {
+          if (Hmat[i][j] >= tol) orthoRhombic = 0;
+        }        
+      }
     }
   }
+}
 
-  // sanity check
+double SimInfo::matDet3(double a[3][3]) {
+  int i, j, k;
+  double determinant;
 
-  for(i=0; i<3; i++){
-    for(j=0; j<3; j++){
+  determinant = 0.0;
+
+  for(i = 0; i < 3; i++) {
+    j = (i+1)%3;
+    k = (i+2)%3;
+
+    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
+  }
+
+  return determinant;
+}
+
+void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
+  
+  int  i, j, k, l, m, n;
+  double determinant;
+
+  determinant = matDet3( a );
+
+  if (determinant == 0.0) {
+    sprintf( painCave.errMsg,
+             "Can't invert a matrix with a zero determinant!\n");
+    painCave.isFatal = 1;
+    simError();
+  }
+
+  for (i=0; i < 3; i++) {
+    j = (i+1)%3;
+    k = (i+2)%3;
+    for(l = 0; l < 3; l++) {
+      m = (l+1)%3;
+      n = (l+2)%3;
       
-      sanity[i][j] = 0.0;
-      for(k=0; k<3; k++){
-	sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
-      }
+      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
     }
   }
+}
 
-  cerr << "sanity => \n" 
-       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
-       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
-       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] 
-       << "\n";
-    
+void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
+  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
 
-  // check to see if Hmat is orthorhombic
+  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
+  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
+  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
   
-  smallDiag = Hmat[0];
-  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
-  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
-  tol = smallDiag * 1E-6;
+  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
+  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
+  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
+  
+  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
+  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
+  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
+  
+  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
+  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
+  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
+}
 
-  orthoRhombic = 1;
-  for(i=0; (i<9) && orthoRhombic; i++){
-    
-    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
-      orthoRhombic = (Hmat[i] <= tol);
+void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
+  double a0, a1, a2;
+
+  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
+
+  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
+  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
+  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
+}
+
+void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
+  double temp[3][3];
+  int i, j;
+
+  for (i = 0; i < 3; i++) {
+    for (j = 0; j < 3; j++) {
+      temp[j][i] = in[i][j];
     }
   }
-    
+  for (i = 0; i < 3; i++) {
+    for (j = 0; j < 3; j++) {
+      out[i][j] = temp[i][j];
+    }
+  }
 }
+  
+void SimInfo::printMat3(double A[3][3] ){
 
+  std::cerr 
+	    << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
+	    << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
+	    << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
+}
+
+void SimInfo::printMat9(double A[9] ){
+
+  std::cerr 
+	    << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
+	    << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
+	    << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
+}
+
 void SimInfo::calcBoxL( void ){
 
   double dx, dy, dz, dsq;
   int i;
 
-  // boxVol = h1 (dot) h2 (cross) h3
+  // boxVol = Determinant of Hmat
 
-  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
-         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
-         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
+  boxVol = matDet3( Hmat );
 
-
   // boxLx
   
-  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
+  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
   dsq = dx*dx + dy*dy + dz*dz;
-  boxLx = sqrt( dsq );
+  boxL[0] = sqrt( dsq );
+  maxCutoff = 0.5 * boxL[0];
 
   // boxLy
   
-  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
+  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
   dsq = dx*dx + dy*dy + dz*dz;
-  boxLy = sqrt( dsq );
+  boxL[1] = sqrt( dsq );
+  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
 
   // boxLz
   
-  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
+  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
   dsq = dx*dx + dy*dy + dz*dz;
-  boxLz = sqrt( dsq );
-  
+  boxL[2] = sqrt( dsq );
+  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
+
 }
 
 
@@ -262,27 +303,23 @@ void SimInfo::wrapVector( double thePos[3] ){
 
   if( !orthoRhombic ){
     // calc the scaled coordinates.
+  
+
+    matVecMul3(HmatInv, thePos, scaled);
     
     for(i=0; i<3; i++)
-      scaled[i] = 
-	thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
-    
-    // wrap the scaled coordinates
-    
-    for(i=0; i<3; i++)
       scaled[i] -= roundMe(scaled[i]);
     
     // calc the wrapped real coordinates from the wrapped scaled coordinates
     
-    for(i=0; i<3; i++)
-      thePos[i] = 
-	scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
+    matVecMul3(Hmat, scaled, thePos);
+
   }
   else{
     // calc the scaled coordinates.
     
     for(i=0; i<3; i++)
-      scaled[i] = thePos[i]*HmatI[i*4];
+      scaled[i] = thePos[i]*HmatInv[i][i];
     
     // wrap the scaled coordinates
     
@@ -292,10 +329,9 @@ void SimInfo::wrapVector( double thePos[3] ){
     // calc the wrapped real coordinates from the wrapped scaled coordinates
     
     for(i=0; i<3; i++)
-      thePos[i] = scaled[i]*Hmat[i*4];
+      thePos[i] = scaled[i]*Hmat[i][i];
   }
     
-    
 }
 
 
@@ -336,17 +372,10 @@ void SimInfo::refreshSim(){
   int isError;
   int n_global;
   int* excl;
-  
-  fInfo.rrf = 0.0;
-  fInfo.rt = 0.0;
+
   fInfo.dielect = 0.0;
 
-  fInfo.rlist = rList;
-  fInfo.rcut = rCut;
-
   if( useDipole ){
-    fInfo.rrf = ecr;
-    fInfo.rt = ecr - est;
     if( useReactionField )fInfo.dielect = dielectric;
   }
 
@@ -395,3 +424,108 @@ void SimInfo::refreshSim(){
 
 }
 
+
+void SimInfo::setRcut( double theRcut ){
+
+  if( !haveOrigRcut ){
+    haveOrigRcut = 1;
+    origRcut = theRcut;
+  }
+
+  rCut = theRcut;
+  checkCutOffs();
+}
+
+void SimInfo::setEcr( double theEcr ){
+
+  if( !haveOrigEcr ){
+    haveOrigEcr = 1;
+    origEcr = theEcr;
+  }
+
+  ecr = theEcr;
+  checkCutOffs();
+}
+
+void SimInfo::setEcr( double theEcr, double theEst ){
+
+  est = theEst;
+  setEcr( theEcr );
+}
+
+
+void SimInfo::checkCutOffs( void ){
+
+  int cutChanged = 0;
+
+  if( boxIsInit ){
+    
+    //we need to check cutOffs against the box
+    
+    if( maxCutoff > rCut ){
+      if( rCut < origRcut ){
+	rCut = origRcut;
+	if (rCut > maxCutoff) rCut = maxCutoff;
+	
+	sprintf( painCave.errMsg,
+		 "New Box size is setting the long range cutoff radius "
+		 "to %lf\n",
+		 rCut );
+	painCave.isFatal = 0;
+	simError();
+      }
+    }
+
+    if( maxCutoff > ecr ){
+      if( ecr < origEcr ){
+	rCut = origEcr;
+	if (ecr > maxCutoff) ecr = maxCutoff;
+	
+	sprintf( painCave.errMsg,
+		 "New Box size is setting the electrostaticCutoffRadius "
+		 "to %lf\n",
+		 ecr );
+	painCave.isFatal = 0;
+	simError();
+      }
+    }
+
+
+    if (rCut > maxCutoff) {
+      sprintf( painCave.errMsg,
+               "New Box size is setting the long range cutoff radius "
+	       "to %lf\n",
+               maxCutoff );
+      painCave.isFatal = 0;
+      simError();
+      rCut = maxCutoff;
+    }
+
+    if( ecr > maxCutoff){
+      sprintf( painCave.errMsg,
+               "New Box size is setting the electrostaticCutoffRadius "
+               "to %lf\n",
+               maxCutoff  );
+      painCave.isFatal = 0;
+      simError();      
+      ecr = maxCutoff;
+    }
+
+    
+  }
+   
+
+  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
+
+  // rlist is the 1.0 plus max( rcut, ecr )
+  
+  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
+
+  if( cutChanged ){
+    
+    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+  }
+
+  oldEcr = ecr;
+  oldRcut = rCut;
+}