--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/10/29 20:41:39	843
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/11/06 22:01:37	855
@@ -49,8 +49,10 @@ SimInfo::SimInfo(){
   boxIsInit = 0;
   
   resetTime = 1e99;
-  
 
+  orthoTolerance = 1E-6;
+  useInitXSstate = true;
+
   usePBC = 0;
   useLJ = 0; 
   useSticky = 0;
@@ -146,6 +148,7 @@ void SimInfo::calcHmatInv( void ) {
 
 void SimInfo::calcHmatInv( void ) {
   
+  int oldOrtho;
   int i,j;
   double smallDiag;
   double tol;
@@ -153,28 +156,44 @@ void SimInfo::calcHmatInv( void ) {
 
   invertMat3( Hmat, HmatInv );
 
-  // Check the inverse to make sure it is sane:
-
-  matMul3( Hmat, HmatInv, sanity );
-    
   // check to see if Hmat is orthorhombic
   
-  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;
+  oldOrtho = orthoRhombic;
 
+  smallDiag = fabs(Hmat[0][0]);
+  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
+  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
+  tol = smallDiag * orthoTolerance;
+
   orthoRhombic = 1;
   
   for (i = 0; i < 3; i++ ) {
     for (j = 0 ; j < 3; j++) {
       if (i != j) {
         if (orthoRhombic) {
-          if (Hmat[i][j] >= tol) orthoRhombic = 0;
+          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
         }        
       }
     }
   }
+
+  if( oldOrtho != orthoRhombic ){
+    
+    if( orthoRhombic ){
+      sprintf( painCave.errMsg,
+	       "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
+	       "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
+	       orthoTolerance);
+      simError();
+    }
+    else {
+      sprintf( painCave.errMsg,
+	       "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
+	       "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
+	       orthoTolerance);
+      simError();
+    }
+  }
 }
 
 double SimInfo::matDet3(double a[3][3]) {
@@ -524,6 +543,8 @@ void SimInfo::setDefaultRcut( double theRcut ){
   haveOrigRcut = 1;
   origRcut = theRcut;
   rCut = theRcut;
+
+  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
 
   notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
 }
@@ -539,7 +560,10 @@ void SimInfo::setDefaultEcr( double theEcr ){
   haveOrigEcr = 1;
   origEcr = theEcr;
   
+  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
+
   ecr = theEcr;
+
   notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
 }
 
@@ -622,7 +646,6 @@ void SimInfo::checkCutOffs( void ){
     ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
     
     if( cutChanged ){
-      
       notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
     }