Index: /issm/trunk/src/mex/Bamg/Bamg.cpp
===================================================================
--- /issm/trunk/src/mex/Bamg/Bamg.cpp	(revision 3217)
+++ /issm/trunk/src/mex/Bamg/Bamg.cpp	(revision 3218)
@@ -9,9 +9,8 @@
 	int   noerr=1;
 	int   i;
-	int   nods=0; //to be removed
 	int   lines,cols;
 	BamgOpts bamgopts;
-	BamgMesh bamgmesh;
-	BamgGeom bamggeom;
+	BamgMesh bamgmesh_in,bamgmesh_out;
+	BamgGeom bamggeom_in,bamggeom_out;
 
 	/*Boot module: */
@@ -22,26 +21,26 @@
 
 	/*create bamg geometry input*/
-	BamgGeomInit(&bamggeom);
-	FetchData(&bamggeom.NumVertices,mxGetField(BAMGGEOMETRY,0,"NumVertices"));
-	FetchData(&bamggeom.Vertices,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"Vertices"));
-	FetchData(&bamggeom.NumEdges,mxGetField(BAMGGEOMETRY,0,"NumEdges"));
-	FetchData(&bamggeom.Edges,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"Edges"));
-	FetchData(&bamggeom.hVertices,&lines,&cols,mxGetField(BAMGGEOMETRY,0,"hVertices"));
-	FetchData(&bamggeom.NumCrackedEdges,mxGetField(BAMGGEOMETRY,0,"NumCrackedEdges"));
-	FetchData(&bamggeom.CrackedEdges,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"CrackedEdges"));
-	FetchData(&bamggeom.NumSubDomains,mxGetField(BAMGGEOMETRY,0,"NumSubDomains"));
-	FetchData(&bamggeom.SubDomains,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"SubDomains"));
-	if (bamggeom.hVertices && (cols!=1 || lines!=bamggeom.NumVertices)){throw ErrorException(__FUNCT__,exprintf("the size of 'hVertices' should be [%i %i]",bamggeom.NumVertices,1));}
+	BamgGeomInit(&bamggeom_in);
+	FetchData(&bamggeom_in.NumVertices,mxGetField(BAMGGEOMETRY,0,"NumVertices"));
+	FetchData(&bamggeom_in.Vertices,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"Vertices"));
+	FetchData(&bamggeom_in.NumEdges,mxGetField(BAMGGEOMETRY,0,"NumEdges"));
+	FetchData(&bamggeom_in.Edges,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"Edges"));
+	FetchData(&bamggeom_in.hVertices,&lines,&cols,mxGetField(BAMGGEOMETRY,0,"hVertices"));
+	FetchData(&bamggeom_in.NumCrackedEdges,mxGetField(BAMGGEOMETRY,0,"NumCrackedEdges"));
+	FetchData(&bamggeom_in.CrackedEdges,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"CrackedEdges"));
+	FetchData(&bamggeom_in.NumSubDomains,mxGetField(BAMGGEOMETRY,0,"NumSubDomains"));
+	FetchData(&bamggeom_in.SubDomains,NULL,NULL,mxGetField(BAMGGEOMETRY,0,"SubDomains"));
+	if (bamggeom_in.hVertices && (cols!=1 || lines!=bamggeom_in.NumVertices)){throw ErrorException(__FUNCT__,exprintf("the size of 'hVertices' should be [%i %i]",bamggeom_in.NumVertices,1));}
 
 	/*create bamg mesh input*/
-	BamgMeshInit(&bamgmesh);
-	FetchData(&bamgmesh.NumVertices,mxGetField(BAMGMESH,0,"NumVertices"));
-	FetchData(&bamgmesh.Vertices,NULL,NULL,mxGetField(BAMGMESH,0,"Vertices"));
-	FetchData(&bamgmesh.NumTriangles,mxGetField(BAMGMESH,0,"NumTriangles"));
-	FetchData(&bamgmesh.Triangles,NULL,NULL,mxGetField(BAMGMESH,0,"Triangles"));
-	FetchData(&bamgmesh.hVertices,&lines,&cols,mxGetField(BAMGMESH,0,"hVertices"));
-	FetchData(&bamgmesh.NumCrackedEdges,mxGetField(BAMGMESH,0,"NumCrackedEdges"));
-	FetchData(&bamgmesh.CrackedEdges,NULL,NULL,mxGetField(BAMGMESH,0,"CrackedEdges"));
-	if (bamgmesh.hVertices && (cols!=1 || lines!=bamgmesh.NumVertices)){throw ErrorException(__FUNCT__,exprintf("the size of 'hVertices' should be [%i %i]",bamgmesh.NumVertices,1));}
+	BamgMeshInit(&bamgmesh_in);
+	FetchData(&bamgmesh_in.NumVertices,mxGetField(BAMGMESH,0,"NumVertices"));
+	FetchData(&bamgmesh_in.Vertices,NULL,NULL,mxGetField(BAMGMESH,0,"Vertices"));
+	FetchData(&bamgmesh_in.NumTriangles,mxGetField(BAMGMESH,0,"NumTriangles"));
+	FetchData(&bamgmesh_in.Triangles,NULL,NULL,mxGetField(BAMGMESH,0,"Triangles"));
+	FetchData(&bamgmesh_in.hVertices,&lines,&cols,mxGetField(BAMGMESH,0,"hVertices"));
+	FetchData(&bamgmesh_in.NumCrackedEdges,mxGetField(BAMGMESH,0,"NumCrackedEdges"));
+	FetchData(&bamgmesh_in.CrackedEdges,NULL,NULL,mxGetField(BAMGMESH,0,"CrackedEdges"));
+	if (bamgmesh_in.hVertices && (cols!=1 || lines!=bamgmesh_in.NumVertices)){throw ErrorException(__FUNCT__,exprintf("the size of 'hVertices' should be [%i %i]",bamgmesh_in.NumVertices,1));}
 
 	/*create bamg options input*/
@@ -68,7 +67,7 @@
 	FetchData(&bamgopts.MaximalAngleOfCorner,mxGetField(BAMGOPTIONS,0,"MaximalAngleOfCorner"));
 	FetchData(&bamgopts.metric,&lines,&cols,mxGetField(BAMGOPTIONS,0,"metric"));
-	if (bamgopts.metric && (cols!=3 || lines!=bamgmesh.NumVertices)){throw ErrorException(__FUNCT__,exprintf("the size of 'metric' should be [%i %i]",bamgmesh.NumVertices,3));}
+	if (bamgopts.metric && (cols!=3 || lines!=bamgmesh_in.NumVertices)){throw ErrorException(__FUNCT__,exprintf("the size of 'metric' should be [%i %i]",bamgmesh_in.NumVertices,3));}
 	FetchData(&bamgopts.field,&lines,&bamgopts.numfields,mxGetField(BAMGOPTIONS,0,"field"));
-	if (bamgopts.field && lines!=bamgmesh.NumVertices){throw ErrorException(__FUNCT__,exprintf("the size of 'field' should be [%i %i]",bamgmesh.NumVertices,bamgopts.numfields));}
+	if (bamgopts.field && lines!=bamgmesh_in.NumVertices){throw ErrorException(__FUNCT__,exprintf("the size of 'field' should be [%i %i]",bamgmesh_in.NumVertices,bamgopts.numfields));}
 	FetchData(&bamgopts.err,NULL,&cols,mxGetField(BAMGOPTIONS,0,"err"));
 	if (bamgopts.numfields!=0 && cols!=bamgopts.numfields){throw ErrorException(__FUNCT__,exprintf("the size of 'err' should be the same as 'field'"));}
@@ -76,13 +75,12 @@
 
 	/*!Generate internal degree of freedom numbers: */
-	nods=bamgmesh.NumVertices;
-	Bamgx(&bamgmesh,&bamggeom,&bamgopts);
+	Bamgx(&bamgmesh_out,&bamggeom_out,&bamgmesh_in,&bamggeom_in,&bamgopts);
 
 	/*write output datasets: */
-	WriteData(TRIANGLESOUT,bamgmesh.Triangles,bamgmesh.NumTriangles,4);
-	WriteData(VERTICESOUT,bamgmesh.Vertices,bamgmesh.NumVertices,3);
-	WriteData(SEGMENTSOUT,bamgmesh.Segments,bamgmesh.NumSegments,3);
-	WriteData(SEGMENTSMARKERSOUT,bamgmesh.SegmentsMarkers,bamgmesh.NumSegments,1);
-	WriteData(METRICOUT,bamgopts.metric,nods,3);
+	WriteData(TRIANGLESOUT,bamgmesh_out.Triangles,bamgmesh_out.NumTriangles,4);
+	WriteData(VERTICESOUT,bamgmesh_out.Vertices,bamgmesh_out.NumVertices,3);
+	WriteData(SEGMENTSOUT,bamgmesh_out.Segments,bamgmesh_out.NumSegments,3);
+	WriteData(SEGMENTSMARKERSOUT,bamgmesh_out.SegmentsMarkers,bamgmesh_out.NumSegments,1);
+	WriteData(METRICOUT,bamgopts.metric,bamgmesh_in.NumVertices,3);
 
 	/*Free ressources: */