--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/10/30 18:59:20	845
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/11/21 19:31:05	872
@@ -20,6 +20,9 @@ inline double roundMe( double x ){
   return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
 }
 	  
+inline double min( double a, double b ){
+  return (a < b ) ? a : b;
+}
 
 SimInfo* currentInfo;
 
@@ -37,20 +40,18 @@ SimInfo::SimInfo(){
   thermalTime = 0.0;
   currentTime = 0.0;
   rCut = 0.0;
-  origRcut = -1.0;
   ecr = 0.0;
-  origEcr = -1.0;
   est = 0.0;
-  oldEcr = 0.0;
-  oldRcut = 0.0;
 
-  haveOrigRcut = 0;
-  haveOrigEcr = 0;
+  haveRcut = 0;
+  haveEcr = 0;
   boxIsInit = 0;
   
   resetTime = 1e99;
-  
 
+  orthoTolerance = 1E-6;
+  useInitXSstate = true;
+
   usePBC = 0;
   useLJ = 0; 
   useSticky = 0;
@@ -102,7 +103,6 @@ void SimInfo::setBoxM( double theBox[3][3] ){
                          // [ 2 5 8 ]
   double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
 
-  
   if( !boxIsInit ) boxIsInit = 1;
 
   for(i=0; i < 3; i++) 
@@ -146,6 +146,7 @@ void SimInfo::calcHmatInv( void ) {
 
 void SimInfo::calcHmatInv( void ) {
   
+  int oldOrtho;
   int i,j;
   double smallDiag;
   double tol;
@@ -153,28 +154,44 @@ 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]) {
@@ -512,17 +529,9 @@ void SimInfo::refreshSim(){
   this->ndfTrans = this->getNDFtranslational();
 }
 
-
-void SimInfo::setRcut( double theRcut ){
-
-  rCut = theRcut;
-  checkCutOffs();
-}
-
 void SimInfo::setDefaultRcut( double theRcut ){
 
-  haveOrigRcut = 1;
-  origRcut = theRcut;
+  haveRcut = 1;
   rCut = theRcut;
 
   ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
@@ -530,30 +539,16 @@ void SimInfo::setDefaultRcut( double theRcut ){
   notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
 }
 
-void SimInfo::setEcr( double theEcr ){
-
-  ecr = theEcr;
-  checkCutOffs();
-}
-
 void SimInfo::setDefaultEcr( double theEcr ){
 
-  haveOrigEcr = 1;
-  origEcr = theEcr;
+  haveEcr = 1;
+  ecr = theEcr;
   
   ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
 
-  ecr = theEcr;
-
   notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
 }
 
-void SimInfo::setEcr( double theEcr, double theEst ){
-
-  est = theEst;
-  setEcr( theEcr );
-}
-
 void SimInfo::setDefaultEcr( double theEcr, double theEst ){
 
   est = theEst;
@@ -562,77 +557,30 @@ void SimInfo::checkCutOffs( void ){
 
 
 void SimInfo::checkCutOffs( void ){
-
-  int cutChanged = 0;
   
   if( boxIsInit ){
     
     //we need to check cutOffs against the box
-
-    //detect the change of rCut
-    if(( maxCutoff > rCut )&&(usePBC)){
-      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 at time %lf\n",
-                    rCut, currentTime );
-          painCave.isFatal = 0;
-          simError();
-      }
-    }
-    else if ((rCut > maxCutoff)&&(usePBC)) {
+    
+    if( rCut > maxCutoff ){
       sprintf( painCave.errMsg,
-               "New Box size is setting the long range cutoff radius "
-               "to %lf at time %lf\n",
-               maxCutoff, currentTime );
-      painCave.isFatal = 0;
+	       "Box size is too small for the long range cutoff radius, "
+	       "%lf, at time %lf\n",
+	       rCut, currentTime );
+      painCave.isFatal = 1;
       simError();
-      rCut = maxCutoff;
     }
-
-
-    //detect the change of ecr
-    if( maxCutoff > ecr ){
-      if( ecr < origEcr ){
-        ecr = origEcr;
-        if (ecr > maxCutoff) ecr = maxCutoff;
-  
-          sprintf( painCave.errMsg,
-                    "New Box size is setting the electrostaticCutoffRadius "
-                    "to %lf at time %lf\n",
-                    ecr, currentTime );
-            painCave.isFatal = 0;
-            simError();
+    
+    if( haveEcr ){
+      if( ecr > maxCutoff ){
+	sprintf( painCave.errMsg,
+		 "Box size is too small for the electrostatic cutoff radius, "
+		 "%lf, at time %lf\n",
+		 ecr, currentTime );
+	painCave.isFatal = 1;
+	simError();
       }
     }
-    else if( ecr > maxCutoff){
-      sprintf( painCave.errMsg,
-               "New Box size is setting the electrostaticCutoffRadius "
-               "to %lf at time %lf\n",
-               maxCutoff, currentTime  );
-      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;
-    
   } else {
     // initialize this stuff before using it, OK?
     sprintf( painCave.errMsg,