--- trunk/OOPSE/utils/sysbuilder/sysBuild.cpp	2003/08/11 22:12:31	678
+++ trunk/OOPSE/utils/sysbuilder/sysBuild.cpp	2003/10/27 16:20:59	822
@@ -1,4 +1,3 @@
-
 #include <cstdlib>
 #include <cstdio>
 #include <cstring>
@@ -54,15 +53,8 @@ int main( int argc, char* argv[]){
   //  char* in_name;
   char* id;
 
-  int* hasErrors;
+  int hasErrors;
 
-
-  MakeStamps* the_stamps = NULL;
-  Globals* the_globals = NULL;
-  Component** the_components = NULL;
-  LinkedMolStamp* headStamp = NULL;
-  LinkedMolStamp* currStamp;
-
   // initialize all functions and variables
 
   initSimError();
@@ -74,33 +66,8 @@ int main( int argc, char* argv[]){
   headInc = NULL;
 
   bsInfo.includes = NULL;
-  bsInfo.componentsNmol = NULL;
-  bsInfo.compStamps = NULL;
-  bsInfo.havePressure = 0;
-  bsInfo.haveTauBarostat = 0;
-  bsInfo.haveTauThermostat = 0;
-  bsInfo.haveQmass = 0;
-
-  //Nanobuilder components.
-  bsInfo.latticeType = FCC_LATTICE_TYPE; // set lattice type to FCC.
-  bsInfo.hasVacancies = 0; //set vacancies to false.
-  bsInfo.buildCoreShell = 0;
-
-  bsInfo.latticeSpacing = 0.0;
-  bsInfo.coreRadius = 0.0;
-  bsInfo.particleRadius = 0.0;
-  bsInfo.shellRadius = 0.0;
-  bsInfo.vacancyRadius = 0.0;
-  bsInfo.vacancyFraction = 0.0;
-  bsInfo.soluteX = 0.0;
 
 
-
-  headStamp = new LinkedMolStamp();
-  the_stamps = new MakeStamps();
-  the_globals = new Globals();
-  set_interface_stamps( the_stamps, the_globals );
-
   // parse command line arguments
 
   if (cmdline_parser (argc, argv, &args_info) != 0)
@@ -109,13 +76,13 @@ int main( int argc, char* argv[]){
   // Handle command line arguments.
   sysType = grabCmdArgs();
 
-// Keep me
-if(in_name == NULL){
+  // Keep me
+  if(in_name == NULL){
     sprintf( painCave.errMsg,
 	     "No input bass file was specified.\n");
     painCave.isFatal = 0;
     simError();    
-    usage();
+    cmdline_parser_print_help();
   }
 
   if( sysType < 0 ){
@@ -123,7 +90,7 @@ if(in_name == NULL){
 	     "No system type was specified.\n");
     painCave.isFatal = 0;
     simError();    
-    usage();
+    cmdline_parser_print_help();
   }
   
   
@@ -138,7 +105,6 @@ if(in_name == NULL){
   bsInfo.outPrefix = out_prefix;
   bsInfo.includes = headInc;
   
-
   // open and parse the bass file.
 
   set_interface_stamps( the_stamps, the_globals );
@@ -288,11 +254,19 @@ if(in_name == NULL){
   }
 
   // get and set the boxSize
+  
+  bsInfo.haveBox = false;
 
+  std::cerr << "Box setting...";
+
+  std::cerr <<" haveBox= " << the_globals->haveBox() << "\n";
+
   if( the_globals->haveBox() ){
     bsInfo.boxX = the_globals->getBox();
     bsInfo.boxY = the_globals->getBox();
     bsInfo.boxZ = the_globals->getBox();
+    bsInfo.haveBox = true;
+    std::cerr<< "box=>yes\n";
   }
   else if( the_globals->haveDensity() ){
 
@@ -301,40 +275,22 @@ if(in_name == NULL){
     bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
     bsInfo.boxY = bsInfo.boxX;
     bsInfo.boxZ = bsInfo.boxY;
+    bsInfo.haveBox = true;
+
+    std::cerr<< "dens=>yes\n";
   }
   else{
-    if( !the_globals->haveBoxX() ){
-      sprintf( painCave.errMsg,
-	       "sysBuild error, no periodic BoxX size given.\n" );
-      painCave.isFatal = 1;
-      simError();
-    }
-    bsInfo.boxX = the_globals->getBoxX();
-
-    if( !the_globals->haveBoxY() ){
-      sprintf( painCave.errMsg,
-	       "sysBuild error, no periodic BoxY size given.\n" );
-      painCave.isFatal = 1;
-      simError();
-    }
-    bsInfo.boxY = the_globals->getBoxY();
-
-    if( !the_globals->haveBoxZ() ){
-      sprintf( painCave.errMsg,
-	       "SimSetup error, no periodic BoxZ size given.\n" );
-      painCave.isFatal = 1;
-      simError();
-    }
-    bsInfo.boxZ = the_globals->getBoxZ();
+    std::cerr<< "none.\n";
   }
   
 
-  //************************************************************
+  // ************************************************************
   // that should be all we need from bass. now to switch to the
   // appropriate system builder.
   // ***********************************************************
-
-
+  
+  nanoBuilder* buildNano;
+				
   switch( sysType ){
     
   case BILAYER:
@@ -343,10 +299,10 @@ if(in_name == NULL){
 
   case NANOPARTICLE:
 
-    //    nanoBuilder buildNano(hasErrors);
-
-    // buildNano.buildNanoParticle();
-
+    buildNano = new nanoBuilder(hasErrors);
+    
+    buildNano->buildNanoParticle();
+    
     break;
 
   default:
@@ -364,7 +320,7 @@ if(in_name == NULL){
   if( headStamp!= NULL )       delete headStamp;
   if( the_stamps != NULL )     delete the_stamps;
   if( the_globals != NULL )    delete the_globals;
-  if( the_components != NULL ) delete[] the_components;
+  //  if( the_components != NULL ) delete[] the_components;
   
   if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
   if( bsInfo.compStamps != NULL )     delete[] bsInfo.compStamps;
@@ -489,7 +445,8 @@ int grabCmdArgs(){
   }
 
   if (args_info.inputs_num) {  //Get input file name
-    in_name = args_info.inputs[1];
+    in_name = args_info.inputs[0];
+    cerr << in_name << "\n";
       }
   else {
 	sprintf( painCave.errMsg,