--- trunk/OOPSE/utils/sysbuilder/latticeBilayer.cpp	2003/11/06 22:01:37	855
+++ trunk/OOPSE/utils/sysbuilder/latticeBilayer.cpp	2004/01/14 16:28:37	943
@@ -549,7 +549,7 @@ int main(int argC,char* argV[]){
   simInit->setSimInfo( mainInfo );
   simInit->suspendInit();
   simInit->parseFile( inName );
-   simInit->createSim();
+  simInit->createSim();
 
   delete simInit;
 
@@ -581,7 +581,7 @@ int buildLatticeBilayer(double aLat, 
   double *posX, *posY, *posZ;
   double pos[3], posA[3], posB[3];
 
-  const double waterFudge = 5.0;
+  const double waterFudge = 6.0;
 
   int i,j,k,l;
   int nAtoms, atomIndex, molIndex, molID;
@@ -597,7 +597,6 @@ int buildLatticeBilayer(double aLat, 
   int targetWaters;
   
   Atom** atoms;
-  SimInfo* simnfo;
   SimInfo* testInfo;
   coord testSite;
   SimState* theConfig;
@@ -612,15 +611,9 @@ int buildLatticeBilayer(double aLat, 
   int targetNlipids, targetNwaters;
   double targetWaterLipidRatio;
   double maxZ, minZ, zHeight;
-  double maxY, minY;
-  double maxX, minX;
    
   molStart = NULL;
 
-  // create the simInfo objects
-
-  simnfo = new SimInfo;
-
   // set the the lipidStamp
 
   foundLipid = 0;
@@ -694,11 +687,15 @@ int buildLatticeBilayer(double aLat, 
   }
   zHeight = maxZ - minZ;
     
-  nCells = (int) sqrt( (double)targetNlipids * bLat / (4.0 * aLat) );
+  std::cerr << "aLat = " << aLat << "; bLat = " << bLat << "\n";
+
+  nCells = (int)ceil( sqrt( (double)targetNlipids * bLat / (4.0 * aLat) ));
 
   nx = nCells;
   ny = (int) ((double)nCells  * aLat / bLat);
 
+  std::cerr << "nx = " << nx << "; ny = " << ny << "\n";
+
   boxX = nx * aLat;
   boxY = ny * bLat;  
 
@@ -789,35 +786,22 @@ int buildLatticeBilayer(double aLat, 
 
   atoms[0]->getPos( myPos );
 
-  maxX = myPos[0];
-  minX = myPos[0];
-
-  maxY = myPos[1];
-  minY = myPos[1];
-
   maxZ = myPos[2];
   minZ = myPos[2];
 
   for(i=0;i<nAtoms;i++){
     atoms[i]->getPos( myPos );
-    minX = (minX > myPos[0]) ? myPos[0] : minX;
-    maxX = (maxX < myPos[0]) ? myPos[0] : maxX;
 
-    minY = (minY > myPos[1]) ? myPos[1] : minY;
-    maxY = (maxY < myPos[1]) ? myPos[1] : maxY;
-
     minZ = (minZ > myPos[2]) ? myPos[2] : minZ;
     maxZ = (maxZ < myPos[2]) ? myPos[2] : maxZ;
   }
 
-  boxX = (maxX - minX)+2.0;
-  boxY = (maxY - minY)+2.0;
   boxZ = (maxZ - minZ)+2.0;
 
   double centerX, centerY, centerZ;
   
-  centerX = ((maxX - minX) / 2.0) + minX;
-  centerY = ((maxY - minY) / 2.0) + minY;
+  centerX = (boxX / 2.0);
+  centerY = (boxY / 2.0);
   centerZ = ((maxZ - minZ) / 2.0) + minZ;
 
   // set up water coordinates
@@ -904,11 +888,12 @@ int buildLatticeBilayer(double aLat, 
   
   // create the real Atom arrays 
 
-  theConfig = simnfo->getConfiguration();
+  delete[] (mainInfo->atoms);
+  theConfig = mainInfo->getConfiguration();
   theConfig->createArrays( nAtoms );
-  simnfo->atoms = new Atom*[nAtoms];
-  simnfo->n_atoms = nAtoms;
-  atoms = simnfo->atoms;
+  mainInfo->atoms = new Atom*[nAtoms];
+  mainInfo->n_atoms = nAtoms;
+  atoms = mainInfo->atoms;
 
   // wrap back to <0,0,0> as center
 
@@ -927,7 +912,6 @@ int buildLatticeBilayer(double aLat, 
   Hmat[2][2] = boxZ;
   
   mainInfo->setBoxM( Hmat );
-  simnfo->setBoxM( Hmat );
 
   for(j=0;j<nLipids;j++){
 
@@ -935,7 +919,7 @@ int buildLatticeBilayer(double aLat, 
     lipidSites[j].pos[1] -= centerY;
     lipidSites[j].pos[2] -= centerZ;
 
-    simnfo->wrapVector( lipidSites[j].pos );
+    mainInfo->wrapVector( lipidSites[j].pos );
   }
 
   for(j=0;j<nWaters;j++){
@@ -944,7 +928,7 @@ int buildLatticeBilayer(double aLat, 
     waterSites[j].pos[1] -= centerY;
     waterSites[j].pos[2] -= centerZ;
 
-    simnfo->wrapVector( waterSites[j].pos );
+    mainInfo->wrapVector( waterSites[j].pos );
   }
 
   // initialize lipid positions
@@ -966,12 +950,9 @@ int buildLatticeBilayer(double aLat, 
     molIndex++;
   }
 
-  strcpy( simnfo->sampleName, mainInfo->sampleName );
-  strcpy( simnfo->finalName, mainInfo->finalName );
-
   // set up the writer and write out
   
-  writer = new DumpWriter( simnfo );
+  writer = new DumpWriter( mainInfo );
   writer->writeFinal( 0.0 );
 
   std::cout << "\n"