--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/07/15 18:52:16	616
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/07/22 16:41:08	644
@@ -398,9 +398,9 @@ void SimSetup::initFromBass( void ){
     have_extra =1;
 
     n_cells = (int)temp3 - 1;
-    cellx = info->boxLx / temp3;
-    celly = info->boxLy / temp3;
-    cellz = info->boxLz / temp3;
+    cellx = info->boxL[0] / temp3;
+    celly = info->boxL[1] / temp3;
+    cellz = info->boxL[2] / temp3;
     n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
     temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
     n_per_extra = (int)ceil( temp1 );
@@ -415,9 +415,9 @@ void SimSetup::initFromBass( void ){
   }
   else{
     n_cells = (int)temp3;
-    cellx = info->boxLx / temp3;
-    celly = info->boxLy / temp3;
-    cellz = info->boxLz / temp3;
+    cellx = info->boxL[0] / temp3;
+    celly = info->boxL[1] / temp3;
+    cellz = info->boxL[2] / temp3;
   }
 
   current_mol = 0;
@@ -762,6 +762,7 @@ void SimSetup::finalInfoCheck( void ){
   MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
 #endif //is_mpi
 
+  double theEcr, theEst;
 
   if (globals->getUseRF() ) {
     info->useReactionField = 1;
@@ -774,12 +775,12 @@ void SimSetup::finalInfoCheck( void ){
       painCave.isFatal = 0;
       simError();
       double smallest;
-      smallest = info->boxLx;
-      if (info->boxLy <= smallest) smallest = info->boxLy;
-      if (info->boxLz <= smallest) smallest = info->boxLz;
-      info->ecr = 0.5 * smallest;
+      smallest = info->boxL[0];
+      if (info->boxL[1] <= smallest) smallest = info->boxL[1];
+      if (info->boxL[2] <= smallest) smallest = info->boxL[2];
+      theEcr = 0.5 * smallest;
     } else {
-      info->ecr        = globals->getECR();
+      theEcr = globals->getECR();
     }
 
     if( !globals->haveEST() ){
@@ -789,10 +790,12 @@ void SimSetup::finalInfoCheck( void ){
                );
       painCave.isFatal = 0;
       simError();
-      info->est = 0.05 * info->ecr;
+      theEst = 0.05 * theEcr;
     } else {
-      info->est        = globals->getEST();
+      theEst= globals->getEST();
     }
+
+    info->setEcr( theEcr, theEst );
     
     if(!globals->haveDielectric() ){
       sprintf( painCave.errMsg,
@@ -808,33 +811,35 @@ void SimSetup::finalInfoCheck( void ){
     if (usesDipoles) {
       
       if( !globals->haveECR() ){
-        sprintf( painCave.errMsg,
-                 "SimSetup Warning: using default value of 1/2 the smallest "
-                 "box length for the electrostaticCutoffRadius.\n"
-                 "I hope you have a very fast processor!\n");
-        painCave.isFatal = 0;
-        simError();
-        double smallest;
-        smallest = info->boxLx;
-        if (info->boxLy <= smallest) smallest = info->boxLy;
-        if (info->boxLz <= smallest) smallest = info->boxLz;
-        info->ecr = 0.5 * smallest;
+	sprintf( painCave.errMsg,
+		 "SimSetup Warning: using default value of 1/2 the smallest "
+		 "box length for the electrostaticCutoffRadius.\n"
+		 "I hope you have a very fast processor!\n");
+	painCave.isFatal = 0;
+	simError();
+	double smallest;
+	smallest = info->boxL[0];
+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
+	theEcr = 0.5 * smallest;
       } else {
-        info->ecr        = globals->getECR();
+	theEcr = globals->getECR();
       }
       
       if( !globals->haveEST() ){
-        sprintf( painCave.errMsg,
-                 "SimSetup Warning: using default value of 5%% of the "
-                 "electrostaticCutoffRadius for the "
-                 "electrostaticSkinThickness\n"
-                 );
-        painCave.isFatal = 0;
-        simError();
-        info->est = 0.05 * info->ecr;
-      } else {
-        info->est        = globals->getEST();
+	sprintf( painCave.errMsg,
+		 "SimSetup Warning: using default value of 0.05 * the "
+		 "electrostaticCutoffRadius for the "
+		 "electrostaticSkinThickness\n"
+		 );
+	painCave.isFatal = 0;
+	simError();
+	theEst = 0.05 * theEcr;
+      } else {
+	theEst= globals->getEST();
       }
+
+      info->setEcr( theEcr, theEst );
     }
   }  
 
@@ -857,7 +862,7 @@ void SimSetup::initSystemCoords( void ){
 #ifdef IS_MPI
      }else fileInit = new InitializeFromFile( NULL );
 #endif
-   fileInit->read_xyz( info ); // default velocities on
+   fileInit->readInit( info ); // default velocities on
 
    delete fileInit;
  }