--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/07/09 22:14:06	586
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/07/10 17:10:56	588
@@ -48,38 +48,52 @@ 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];
 
+  for(i=0; i < 3; i++) 
+    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
+  
   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";
+    << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
+    << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
+    << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
 
-  calcHmatI();
   calcBoxL();
+  calcHmatInv();
 
+  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(Hmat, HmatI, &orthoRhombic);
+  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
  
   smallestBoxL = boxLx;
   if (boxLy < smallestBoxL) smallestBoxL = boxLy;
@@ -127,128 +141,161 @@ void SimInfo::getBoxM (double theBox[9]) {
 }
  
 
-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";
 
-  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 ) {
+void SimInfo::calcHmatInv( void ) {
 
-  double C[3][3];
-  double detHmat;
-  int i, j, k;
   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]);
+  matMul3( Hmat, HmatInv, sanity );
 
-  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
-  
-  detHmat = 0.0;
-  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
-
-  
-  // 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++;
-    }
-  }
-
-  // sanity check
-
-  for(i=0; i<3; i++){
-    for(j=0; j<3; j++){
-      
-      sanity[i][j] = 0.0;
-      for(k=0; k<3; k++){
-	sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
-      }
-    }
-  }
-
   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";
     
-
   // check to see if Hmat is orthorhombic
   
-  smallDiag = Hmat[0];
-  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
-  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
+  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;
-  for(i=0; (i<9) && orthoRhombic; i++){
-    
-    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
-      orthoRhombic = (Hmat[i] <= tol);
+  
+  for (i = 0; i < 3; i++ ) {
+    for (j = 0 ; j < 3; j++) {
+      if (i != j) {
+        if (orthoRhombic) {
+          if (Hmat[i][j] >= tol) orthoRhombic = 0;
+        }        
+      }
     }
   }
-    
 }
 
+double SimInfo::matDet3(double a[3][3]) {
+  int i, j, k;
+  double determinant;
+
+  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;
+      
+      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
+    }
+  }
+}
+
+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;
+
+  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];
+  
+  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;
+}
+
+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::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 );
 
   // 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 );
 
   // 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 );
   
@@ -262,27 +309,23 @@ 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 +335,9 @@ 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];
   }
     
-    
 }