Index: /issm/trunk/src/mex/Chaco/Chaco.cpp
===================================================================
--- /issm/trunk/src/mex/Chaco/Chaco.cpp	(revision 4640)
+++ /issm/trunk/src/mex/Chaco/Chaco.cpp	(revision 4640)
@@ -0,0 +1,146 @@
+/*\file Chaco.c
+ *\brief:  Chaco partitioner mex module
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+
+#include "./Chaco.h"
+
+void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){
+   
+	int i;
+	int nterms;
+
+	/*Inputs: */
+	int       nvtxs;		/* number of vertices in graph */
+    int      *start;		/* start of edge list for each vertex */
+    int      *adjacency;	/* edge list data */
+    int      *vwgts=NULL;	/* weights for all vertices */
+	int       nedges;
+    float    *ewgts=NULL;	/* weights for all edges */
+    float    *x=NULL;
+    float    *y=NULL;
+    float    *z=NULL;		/* coordinates for inertial method */
+    double    options[10]={1,1,0,0,1,1,50,0,.001,7654321}; /* architecture and partitioning options */
+    double*   in_options=NULL;
+    int      *nparts=NULL;	/* number of parts options */
+	int       npart;
+    double   *goal=NULL;	/* desired set sizes */
+
+	/*intermediary pointers: */
+	mwIndex *mwstart, *mwadjacency;
+	double  *doublepointer;
+
+	/*output: */
+    short    *assignment=NULL;	/* set number of each vtx (length nvtxs+1) */
+	double   *doubleassignment=NULL;	/*holds assignment, in double format, to return to matlab*/
+
+
+	#ifndef _HAVE_CHACO_ //only works if dakota library has been compiled in.
+	ISSMERROR(" Chaco not available! Cannot carry out Chaco partitioning!");
+	#endif
+
+
+	/*Boot module: */
+	MODULEBOOT();
+
+	/*checks on arguments on the matlab side: */
+	CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ChacoUsage);
+
+
+	/*Fetch adjacency matrix: */
+	nvtxs = mxGetN(A_IN);
+
+	mwstart = mxGetJc(A_IN);
+	start=(int*)xmalloc(nvtxs*sizeof(int));
+	for (i=0; i<nvtxs+1;i++)start[i]=(int)mwstart[i];
+
+	mwadjacency = mxGetIr(A_IN);
+	adjacency = (int*)xmalloc(mxGetNzmax(A_IN)*sizeof(int));
+	for (i=0; i<mxGetNzmax(A_IN); i++) adjacency[i]= (int)mwadjacency[i];
+
+	nedges = start[nvtxs];
+	if(!mxIsEmpty(EWGTS_IN)){
+		ewgts = (float *) xcalloc(nedges, sizeof(float));
+		doublepointer=mxGetPr(A_IN);
+		for (i = 0; i < nedges; i++)ewgts[i] = (float)doublepointer[i];
+	}
+	else ewgts=NULL;
+
+	/*Fetch rest of data: */
+	FetchData(&vwgts,&nterms,VWGTS_IN); 
+
+	FetchData(&x,&nterms,X_IN); 
+	FetchData(&y,&nterms,Y_IN); 
+	FetchData(&z,&nterms,Z_IN); 
+	
+	FetchData(&in_options,&nterms,OPTNS_IN); 
+	for (i=0;i<(nterms<10?nterms:10);i++) options[i]=in_options[i]; //copy in_options into default options
+	
+	FetchData(&npart,NPARTS_IN); 
+	nparts=(int*)xmalloc(sizeof(int)); nparts[0]=npart; //weird Chacox interface ain't it?
+
+	FetchData(&goal,&nterms,GOAL_IN); 
+	
+	/*Some debugging print: {{{*/
+	#ifdef _DEBUG_
+	printf("nvtxs: %i\n",nvtxs);
+	printf("options: [");
+	for(i=0;i<10;i++)printf("%g|",options[i]);
+	printf("]\n");
+	printf("start: \n");
+	for (i=0; i<nvtxs+1;i++)printf("%i ",start[i]);
+	printf("\n");
+	printf("adjacency: \n");
+	for (i=0; i<mxGetNzmax(A_IN);i++)printf("%i ",adjacency[i]);
+	printf("\n");
+	printf("nedges: %i %p\n",nedges,ewgts);
+	if(ewgts) for (i = 0; i < nedges; i++)printf("%g ",ewgts[i]);
+	printf("\n");
+	printf("vwgts:\n");
+	for (i = 0; i < nvtxs; i++)printf("%g ",vwgts[i]);
+	printf("\n");
+	printf("nparts: %i\n",nparts[0]);
+	printf("goal: %p\n",goal);
+	#endif
+	/*}}}*/
+	
+	/*Allocate output: */
+	assignment = (short *) xcalloc(nvtxs, sizeof(short));
+	
+    /*Call core: */
+	Chacox(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, assignment, options, nparts, goal);
+
+    /*Output data: */
+	doubleassignment=(double*)xmalloc(nvtxs*sizeof(double));
+	for (i=0;i<nvtxs;i++) doubleassignment[i]=(double)assignment[i];
+	WriteData(ASSGN_OUT,doubleassignment,nvtxs);
+
+	/*Free ressources:*/
+	xfree((void**)&assignment); 
+	xfree((void**)&goal);
+	xfree((void**)&nparts);
+	xfree((void**)&z);
+	xfree((void**)&y);
+	xfree((void**)&x);
+	xfree((void**)&ewgts);
+	xfree((void**)&vwgts);
+	xfree((void**)&adjacency);
+	xfree((void**)&start);
+
+	/*end module: */
+	MODULEEND();
+}
+
+void ChacoUsage( void )
+{
+	_printf_("\n");
+	_printf_("Usage: [assgn] = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal);\n");
+	_printf_("\n");
+}
+
Index: /issm/trunk/src/mex/Chaco/Chaco.h
===================================================================
--- /issm/trunk/src/mex/Chaco/Chaco.h	(revision 4640)
+++ /issm/trunk/src/mex/Chaco/Chaco.h	(revision 4640)
@@ -0,0 +1,42 @@
+/*!\file:  Chaco.h
+ * \brief header file for Chaco module.
+ */ 
+
+#ifndef _CHACO_H
+#define _CHACO_H
+
+/* local prototypes: */
+void ChacoUsage(void);
+
+#include <stdio.h>
+#include <string.h>    /*  strcasecmp  */
+#include <time.h>      /*  clock,time,difftime  */
+
+#include "../../c/modules/modules.h"
+#include "../../c/Container/Container.h"
+#include "../../c/shared/shared.h"
+    
+/* serial input macros: */
+#define A_IN (mxArray*)prhs[0]
+#define VWGTS_IN (mxArray*)prhs[1]
+#define EWGTS_IN (mxArray*)prhs[2]
+#define X_IN (mxArray*)prhs[3]
+#define Y_IN (mxArray*)prhs[4]
+#define Z_IN (mxArray*)prhs[5]
+#define OPTNS_IN (mxArray*)prhs[6]
+#define NPARTS_IN (mxArray*)prhs[7]
+#define GOAL_IN (mxArray*)prhs[8]
+
+/* serial output macros: */
+#define ASSGN_OUT (mxArray**)&plhs[0]
+
+/* serial arg counts: */
+#undef NLHS
+#define NLHS  1
+#undef NRHS
+#define NRHS  9
+
+#undef __FUNCT__ 
+#define __FUNCT__  "Chaco"
+
+#endif  /* _CHACO_H */
Index: /issm/trunk/src/mex/Makefile.am
===================================================================
--- /issm/trunk/src/mex/Makefile.am	(revision 4639)
+++ /issm/trunk/src/mex/Makefile.am	(revision 4640)
@@ -1,3 +1,3 @@
-INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@
+INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@
 EXEEXT=$(MEXEXT)
 
@@ -10,4 +10,5 @@
 				BamgConvertMesh\
 				BuildNodeSets\
+				Chaco\
 				ComputeBasalStress\
 				ComputePressure\
@@ -81,5 +82,5 @@
 
 
-LDADD =   $(TRIANGLELIB) ../c/libISSM.a $(PETSCLIB)   $(FLIBS)  $(PLAPACKLIB)  $(MUMPSLIB) $(SCALAPACKLIB)  $(BLACSLIB)  $(DAKOTALIB) $(METISLIB) $(BLASLAPACKLIB)  $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB)
+LDADD =   $(TRIANGLELIB) ../c/libISSM.a $(PETSCLIB)   $(FLIBS)  $(PLAPACKLIB)  $(MUMPSLIB) $(SCALAPACKLIB)  $(BLACSLIB)  $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(BLASLAPACKLIB)  $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB)
 
 AM_LDFLAGS = $(MEXLINK)
@@ -113,4 +114,7 @@
 					BamgConvertMesh/BamgConvertMesh.h
 
+Chaco_SOURCES = Chaco/Chaco.cpp\
+					Chaco/Chaco.h
+
 ComputeBasalStress_SOURCES = ComputeBasalStress/ComputeBasalStress.cpp\
 								  ComputeBasalStress/ComputeBasalStress.h