--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/09/22 23:07:57	781
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/11/06 22:01:37	855
@@ -1,6 +1,6 @@
-#include <cstdlib>
-#include <cstring>
-#include <cmath>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
 
 #include <iostream>
 using namespace std;
@@ -49,8 +49,10 @@ SimInfo::SimInfo(){
   boxIsInit = 0;
   
   resetTime = 1e99;
-  
 
+  orthoTolerance = 1E-6;
+  useInitXSstate = true;
+
   usePBC = 0;
   useLJ = 0; 
   useSticky = 0;
@@ -94,8 +96,7 @@ void SimInfo::setBoxM( double theBox[3][3] ){
 
 void SimInfo::setBoxM( double theBox[3][3] ){
   
-  int i, j, status;
-  double smallestBoxL, maxCutoff;
+  int i, j;
   double FortranHmat[9]; // to preserve compatibility with Fortran the
                          // ordering in the array is as follows:
                          // [ 0 3 6 ]
@@ -147,6 +148,7 @@ void SimInfo::calcHmatInv( void ) {
 
 void SimInfo::calcHmatInv( void ) {
   
+  int oldOrtho;
   int i,j;
   double smallDiag;
   double tol;
@@ -154,27 +156,43 @@ 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();
+    }
   }
 }
 
@@ -302,7 +320,6 @@ void SimInfo::calcBoxL( void ){
 void SimInfo::calcBoxL( void ){
 
   double dx, dy, dz, dsq;
-  int i;
 
   // boxVol = Determinant of Hmat
 
@@ -372,7 +389,7 @@ void SimInfo::wrapVector( double thePos[3] ){
 
 void SimInfo::wrapVector( double thePos[3] ){
 
-  int i, j, k;
+  int i;
   double scaled[3];
 
   if( !orthoRhombic ){
@@ -410,7 +427,7 @@ int SimInfo::getNDF(){
 
 
 int SimInfo::getNDF(){
-  int ndf_local, ndf;
+  int ndf_local;
   
   ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
 
@@ -426,7 +443,7 @@ int SimInfo::getNDFraw() {
 }
 
 int SimInfo::getNDFraw() {
-  int ndfRaw_local, ndfRaw;
+  int ndfRaw_local;
 
   // Raw degrees of freedom that we have to set
   ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
@@ -441,7 +458,7 @@ int SimInfo::getNDFtranslational() {
 }
 
 int SimInfo::getNDFtranslational() {
-  int ndfTrans_local, ndfTrans;
+  int ndfTrans_local;
 
   ndfTrans_local = 3 * n_atoms - n_constraints;
 
@@ -517,33 +534,52 @@ void SimInfo::setRcut( double theRcut ){
 
 void SimInfo::setRcut( double theRcut ){
 
-  if( !haveOrigRcut ){
-    haveOrigRcut = 1;
-    origRcut = theRcut;
-  }
-
   rCut = theRcut;
   checkCutOffs();
 }
 
-void SimInfo::setEcr( double theEcr ){
+void SimInfo::setDefaultRcut( double theRcut ){
 
-  if( !haveOrigEcr ){
-    haveOrigEcr = 1;
-    origEcr = theEcr;
-  }
+  haveOrigRcut = 1;
+  origRcut = theRcut;
+  rCut = theRcut;
 
+  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
+
+  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+}
+
+void SimInfo::setEcr( double theEcr ){
+
   ecr = theEcr;
   checkCutOffs();
 }
 
+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 );
+}
+
 void SimInfo::setEcr( double theEcr, double theEst ){
 
   est = theEst;
   setEcr( theEcr );
 }
 
+void SimInfo::setDefaultEcr( double theEcr, double theEst ){
 
+  est = theEst;
+  setDefaultEcr( theEcr );
+}
+
+
 void SimInfo::checkCutOffs( void ){
 
   int cutChanged = 0;
@@ -610,7 +646,6 @@ void SimInfo::checkCutOffs( void ){
     ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
     
     if( cutChanged ){
-      
       notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
     }