--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/09/25 19:27:15	787
+++ branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp	2003/11/06 18:20:47	852
@@ -1,6 +1,6 @@
-#include <cstdlib>
-#include <cstring>
-#include <cmath>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
 
 #include <iostream>
 using namespace std;
@@ -61,6 +61,8 @@ SimInfo::SimInfo(){
 
   myConfiguration = new SimState();
 
+  properties = new GenericData();
+
   wrapMeSimInfo( this );
 }
 
@@ -68,12 +70,7 @@ SimInfo::~SimInfo(){
 SimInfo::~SimInfo(){
 
   delete myConfiguration;
-
-  map<string, GenericData*>::iterator i;
-  
-  for(i = properties.begin(); i != properties.end(); i++)
-    delete (*i).second;
-    
+  delete properties;    
 }
 
 void SimInfo::setBox(double newBox[3]) {
@@ -145,7 +142,8 @@ void SimInfo::calcHmatInv( void ) {
 }
 
 void SimInfo::calcHmatInv( void ) {
-  
+
+  int oldOrtho;
   int i,j;
   double smallDiag;
   double tol;
@@ -155,13 +153,16 @@ void SimInfo::calcHmatInv( void ) {
 
   // Check the inverse to make sure it is sane:
 
-  matMul3( Hmat, HmatInv, sanity );
+  // 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];
+  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 * 1E-6;
 
   orthoRhombic = 1;
@@ -170,9 +171,25 @@ void SimInfo::calcHmatInv( void ) {
     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 ortho tolerance in SimInfo.\n" );
+      simError();
+    }
+    else {
+      sprintf( painCave.errMsg,
+	       "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
+	       "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
+      simError();
     }
   }
 }
@@ -408,7 +425,7 @@ int SimInfo::getNDF(){
 
 
 int SimInfo::getNDF(){
-  int ndf_local, ndf;
+  int ndf_local;
   
   ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
 
@@ -424,7 +441,7 @@ 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;
@@ -439,7 +456,7 @@ int SimInfo::getNDFtranslational() {
 }
 
 int SimInfo::getNDFtranslational() {
-  int ndfTrans_local, ndfTrans;
+  int ndfTrans_local;
 
   ndfTrans_local = 3 * n_atoms - n_constraints;
 
@@ -514,34 +531,53 @@ 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;
@@ -608,7 +644,6 @@ void SimInfo::checkCutOffs( void ){
     ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
     
     if( cutChanged ){
-      
       notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
     }
     
@@ -625,53 +660,11 @@ void SimInfo::checkCutOffs( void ){
   
 }
 
-void SimInfo::addProperty(GenericData* prop){
+GenericData* SimInfo::getProperty(char* propName){
 
-  map<string, GenericData*>::iterator result;
-  result = properties.find(prop->getID());
-  
-  //we can't simply use  properties[prop->getID()] = prop,
-  //it will cause memory leak if we already contain a propery which has the same name of prop
-  
-  if(result != properties.end()){
-    
-    delete (*result).second;
-    (*result).second = prop;
-      
-  }
-  else{
-
-    properties[prop->getID()] = prop;
-
-  }
-    
+  return properties->find( propName );
 }
 
-GenericData* SimInfo::getProperty(const string& propName){
- 
-  map<string, GenericData*>::iterator result;
-  
-  //string lowerCaseName = ();
-  
-  result = properties.find(propName);
-  
-  if(result != properties.end()) 
-    return (*result).second;  
-  else   
-    return NULL;  
-}
-
-vector<GenericData*> SimInfo::getProperties(){
-
-  vector<GenericData*> result;
-  map<string, GenericData*>::iterator i;
-  
-  for(i = properties.begin(); i != properties.end(); i++)
-    result.push_back((*i).second);
-    
-  return result;
-}
-
 double SimInfo::matTrace3(double m[3][3]){
   double trace;
   trace = m[0][0] + m[1][1] + m[2][2];