[cig-commits] commit: Fix compiler warnings

Mercurial hg at geodynamics.org
Sun Oct 16 06:00:19 PDT 2011


changeset:   887:a3a5956268a8
user:        Walter Landry <wlandry at caltech.edu>
date:        Sun Oct 16 05:56:21 2011 -0700
files:       Rheology/src/ConstitutiveMatrixCartesian.cxx Rheology/src/Director.cxx Rheology/src/DruckerPrager.cxx Rheology/src/FaultingMoresiMuhlhaus2006.cxx Rheology/src/MohrCoulomb.cxx Rheology/src/Orthotropic.cxx Rheology/src/OrthotropicAligned.cxx Rheology/src/Pouliquen_etal.cxx Rheology/src/RheologyMaterial.cxx Rheology/src/VonMises.cxx Rheology/tests/ByerleeYieldingSuite.cxx Rheology/tests/ConstitutiveMatrixSuite.cxx Rheology/tests/DirectorSuite.cxx Rheology/tests/VonMisesYieldingSuite.cxx Utils/src/BaseRecoveryFeVar.cxx Utils/src/DivergenceForce.cxx Utils/src/MixedStabiliserTerm.cxx Utils/src/REP_Algorithm.cxx Utils/src/RecoveredFeVariable.cxx Utils/src/SPR_StrainRate.cxx Utils/src/SmoothVelGradField.cxx Utils/src/StressField.cxx Utils/src/TracerOutput.cxx plugins/Output/BoundaryLayers/BoundaryLayers.cxx plugins/Output/BuoyancyIntegrals/BuoyancyIntegrals.cxx
description:
Fix compiler warnings


diff -r 90a83768712b -r a3a5956268a8 Rheology/src/ConstitutiveMatrixCartesian.cxx
--- a/Rheology/src/ConstitutiveMatrixCartesian.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/ConstitutiveMatrixCartesian.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -60,7 +60,6 @@
 #include <assert.h>
 #include <string.h>
 #include <time.h>
-#include <limits>
 
 /* Textual name of this class - This is a global pointer which is used for times when you need to refer to class and not a particular instance of a class */
 const Type ConstitutiveMatrixCartesian_Type = "ConstitutiveMatrixCartesian";
@@ -304,12 +303,12 @@ void _ConstitutiveMatrixCartesian_Assemb
 
        OneToManyRef *ref;
        double **matrixData;
-       uint ii, jj, kk;
+       uint jj, kk;
 
        matrixData = Memory_Alloc_2DArray( double, self->columnSize, self->rowSize, (Name)self->name );
        memset(matrixData[0], 0, self->columnSize*self->rowSize*sizeof(double));
        ref = OneToManyMapper_GetMaterialRef(((IntegrationPointsSwarm*)swarm)->mapper, particle);
-       for(ii = 0; ii < ref->numParticles; ii++) {
+       for(int ii = 0; ii < ref->numParticles; ii++) {
          /* Assemble this material point. */
          ConstitutiveMatrix_AssembleMaterialPoint(
                                                   constitutiveMatrix, lElement_I,
@@ -326,30 +325,13 @@ void _ConstitutiveMatrixCartesian_Assemb
        Memory_Free(matrixData);
      }
      else if(nearestNeighbor) {
-       /* This does a search over all of the particles in the swarm in
-          the element to find the one that is closest to the gauss
-          point.  There may be more efficient ways of doing this, but
-          this works for now. */
        IntegrationPointsSwarm* NNswarm=
          ((NearestNeighborMapper*)((IntegrationPointsSwarm*)self->integrationSwarm)->mapper)->swarm;
        int NNcell_I            = CellLayout_MapElementIdToCellId( NNswarm->cellLayout, lElement_I );
-       int NNcellParticleCount = NNswarm->cellParticleCountTbl[ NNcell_I ];
-
-       Journal_Firewall( NNcellParticleCount != 0, Journal_Register( Error_Type, (Name)ConstitutiveMatrix_Type  ),
-         "In func %s: NNcellParticleCount is 0.\n", __func__ );
-
-       double min_dist(std::numeric_limits<double>::max());
-       int nearest_particle(-1);
-
-       for ( int NNcParticle_I = 0 ; NNcParticle_I < NNcellParticleCount ; NNcParticle_I++ ) {
-         IntegrationPoint* NNparticle = (IntegrationPoint*)Swarm_ParticleInCellAt( NNswarm, NNcell_I, NNcParticle_I );
-         double dist=StGermain_DistanceBetweenPoints(particle->xi,NNparticle->xi,dim);
-         if(dist<min_dist)
-           {
-             nearest_particle=NNcParticle_I;
-             min_dist=dist;
-           }
-       }
+       int nearest_particle=
+         NearestNeighbor_FindNeighbor(((IntegrationPointsSwarm*)self->integrationSwarm)->mapper,
+                                      lElement_I,NNcell_I,particle->xi,dim);
+                                      
        IntegrationPoint* NNparticle = (IntegrationPoint*)Swarm_ParticleInCellAt( NNswarm, NNcell_I, nearest_particle );
        ConstitutiveMatrix_Assemble(constitutiveMatrix, lElement_I,
                                    NNswarm->cellParticleTbl[NNcell_I][nearest_particle], NNparticle,
@@ -739,9 +721,7 @@ void ConstitutiveMatrixCartesian_SetupPa
 
    IntegrationPointsSwarm* swarm = (IntegrationPointsSwarm*)self->integrationSwarm;
    MaterialPointsSwarm **materialSwarms, *materialSwarm;
-   MaterialPoint particle;
    int materialSwarmCount;
-   double *cMatrix = NULL;
 
    if( beenHere ) return;
 
@@ -756,10 +736,10 @@ void ConstitutiveMatrixCartesian_SetupPa
    /* add extension to material swarm */
    self->storedConstHandle = ExtensionManager_Add( materialSwarm->particleExtensionMgr, (Name)self->type, self->rowSize * self->columnSize * sizeof(double)  );
 
-   cMatrix = (double*)ExtensionManager_Get( materialSwarm->particleExtensionMgr, &particle, self->storedConstHandle );
 
 #if 0
    /*This isn't needed so I've disabled it, 2Dec09, JG*/
+   double *cMatrix = (double*)ExtensionManager_Get( materialSwarm->particleExtensionMgr, &particle, self->storedConstHandle );
    if( self->dim == 2 ) {
       /* TODO: clean up this vector logic. The only reson there's an if is because
       *        * of the list of names the must be given as the final arguments to this function.  */
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/Director.cxx
--- a/Rheology/src/Director.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/Director.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -343,7 +343,6 @@ void _Director_Initialise( void* directo
 			  and check first is material is defined as random.*/
 			Material_Index	materialsCount = Materials_Register_GetCount( self->materialPointsSwarm->materials_Register);
 			XYZ*				materialDirectionVectors;
-			int				material_I;
 			Material*		material;
 			Bool*				randomInitialDirections;
 			int*				randomInitialDirectionSeeds;
@@ -356,7 +355,7 @@ void _Director_Initialise( void* directo
 			"randomInitialDirections");
 
 			/* Loop over materials and get material properties from dictionary */
-			for ( material_I = 0 ; material_I < materialsCount ; material_I++ ) {
+			for (uint material_I = 0 ; material_I < materialsCount ; material_I++ ) {
 				material = Materials_Register_GetByIndex( 
 						self->materialPointsSwarm->materials_Register, 
 						material_I );
@@ -386,7 +385,7 @@ void _Director_Initialise( void* directo
 			
 			/* If material is random, set the local srand, 
 			locate all random particles, and set their director */
-			for (material_I = 0; material_I < materialsCount; material_I++) {
+			for (uint material_I = 0; material_I < materialsCount; material_I++) {
 				if (randomInitialDirections[material_I] == True) {
 					Particle_Index	gParticle_I;
 					unsigned	approxGlobalParticleCount = particleLocalCount * self->materialPointsSwarm->nProc;
@@ -429,7 +428,7 @@ void _Director_Initialise( void* directo
 		    /* For each non-random particle, set the initial direction */
 			for ( lParticle_I = 0 ; lParticle_I < particleLocalCount ; lParticle_I++ ) {
 				/* Initialise the norm of each director */
-				material_I = MaterialPointsSwarm_GetMaterialIndexAt(
+				uint material_I = MaterialPointsSwarm_GetMaterialIndexAt(
 						self->materialPointsSwarm, 
 						lParticle_I );
 				if (randomInitialDirections[material_I] == False) {
@@ -474,7 +473,6 @@ Bool _Director_TimeDerivative( void* dir
 	MaterialPointsSwarm*     materialPointsSwarm = self->materialPointsSwarm;
 	TensorArray              velGrad;
 	double*                  normal;
-	Element_LocalIndex       lElement_I;
 	MaterialPoint*           materialPoint = (MaterialPoint*) Swarm_ParticleAt( materialPointsSwarm, lParticle_I );
 	Director_ParticleExt*    particleExt;
 	InterpolationResult      result;
@@ -491,8 +489,6 @@ Bool _Director_TimeDerivative( void* dir
 
 	normal     = particleExt->director;
 
-	lElement_I = materialPoint->owningCell;
-	
 	result = FieldVariable_InterpolateValueAt( self->velGradField, materialPoint->coord, velGrad );
 	/* if in debug mode, perform some tests */
 #ifdef DEBUG
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/DruckerPrager.cxx
--- a/Rheology/src/DruckerPrager.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/DruckerPrager.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -352,18 +352,11 @@ double _DruckerPrager_GetYieldCriterion(
 {
 	DruckerPrager*                    self             = (DruckerPrager*) druckerPrager;
         Dimension_Index                   dim = constitutiveMatrix->dim;
-	double                            cohesion;
-	double                            cohesionAfterSoftening;
-	double                            frictionCoefficient;
-	double                            frictionCoefficientAfterSoftening;
 	double                            minimumYieldStress;
-	double                            minimumViscosity;
-	double                            maxStrainRate;
 	double                            effectiveCohesion;
 	double                            effectiveFrictionCoefficient;
 	double                            frictionalStrength;
 	double                            pressure;
-	DruckerPrager_Particle*           particleExt;
         Cell_Index                        cell_I;
         Coord                             coord;
         Element_GlobalIndex	          element_gI = 0;
@@ -373,16 +366,8 @@ double _DruckerPrager_GetYieldCriterion(
         double                            factor;
 	
 	/* Get Parameters From Rheology */
-	cohesion                           = self->cohesion;
-	cohesionAfterSoftening             = self->cohesionAfterSoftening;
-	frictionCoefficient                = self->frictionCoefficient;
-	frictionCoefficientAfterSoftening  = self->frictionCoefficientAfterSoftening;
 	minimumYieldStress                 = self->minimumYieldStress;
-	minimumViscosity                   = self->minimumViscosity;
-	maxStrainRate                      = self->maxStrainRate;
 	
-	particleExt = (DruckerPrager_Particle*)ExtensionManager_Get( materialPointsSwarm->particleExtensionMgr, materialPoint, self->particleExtHandle );
-
         if( self->pressureField )
           FeVariable_InterpolateWithinElement( self->pressureField, lElement_I, xi, &pressure );
         else {
@@ -582,7 +567,6 @@ void _DruckerPrager_UpdateDrawParameters
 
 	double                           oneOverGlobalMaxStrainIncrement;
 	double                           postFailureWeakeningIncrement;
-   int ierr; /* mpi error code */
 
 	/* Note : this function defines some drawing parameters (brightness, opacity, diameter) as
 	 * functions of the strain weakening - this needs to be improved since most of the parameters
@@ -620,9 +604,9 @@ void _DruckerPrager_UpdateDrawParameters
 		}
 	}
 	
-	ierr = MPI_Allreduce( &localMaxStrainIncrement,  &globalMaxStrainIncrement,  1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD );
-	ierr = MPI_Allreduce( &localMeanStrainIncrement, &globalMeanStrainIncrement, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
-	ierr = MPI_Allreduce( &localFailed,              &globalFailed,              1, MPI_INT,    MPI_SUM, MPI_COMM_WORLD );
+	MPI_Allreduce( &localMaxStrainIncrement,  &globalMaxStrainIncrement,  1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD );
+	MPI_Allreduce( &localMeanStrainIncrement, &globalMeanStrainIncrement, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
+	MPI_Allreduce( &localFailed,              &globalFailed,              1, MPI_INT,    MPI_SUM, MPI_COMM_WORLD );
 	
 	if(globalFailed == 0) 
 		return;
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/FaultingMoresiMuhlhaus2006.cxx
--- a/Rheology/src/FaultingMoresiMuhlhaus2006.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/FaultingMoresiMuhlhaus2006.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -948,7 +948,6 @@ void _FaultingMoresiMuhlhaus2006_UpdateD
 	double                           averagedGlobalMaxStrainIncrement = 0.0;
 
 	double                           oneOverGlobalMaxSlipRate;
-	double                           oneOverGlobalMaxStrainIncrement;
 	double                           postFailureWeakeningIncrement;
 	
 	
@@ -1036,7 +1035,6 @@ void _FaultingMoresiMuhlhaus2006_UpdateD
 	
 	/* Let's simply assume that twice the mean is a good place to truncate these values */
 	oneOverGlobalMaxSlipRate = 1.0 / averagedGlobalMaxSlipRate;
-	oneOverGlobalMaxStrainIncrement = 1.0 / averagedGlobalMaxStrainIncrement;
 	
 	for ( lParticle_I = 0 ; lParticle_I < particleLocalCount ; lParticle_I++ ) { 
 		materialPoint = (GlobalParticle*) Swarm_ParticleAt( strainWeakening->swarm, lParticle_I );
@@ -1138,7 +1136,7 @@ void _FaultingMoresiMuhlhaus2006_UpdateD
 		opacity    = (slipRate/globalMaxSlipRate);
 		
 		if (opacity > 0.90)
-			opacity = 1.0;/* this condition is to make sure we have enough planes that will be clearly seen. */ /*
+                opacity = 1.0; // this condition is to make sure we have enough planes that will be clearly seen.
 
 		Variable_SetValueFloat( self->brightness->variable, lParticle_I, brightness );
 		Variable_SetValueFloat( self->opacity->variable,    lParticle_I, opacity );
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/MohrCoulomb.cxx
--- a/Rheology/src/MohrCoulomb.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/MohrCoulomb.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -383,7 +383,6 @@ void _MohrCoulomb_StoreCurrentParameters
 	Dimension_Index	dim = constitutiveMatrix->dim;
 	Eigenvector			evectors[3];
 	double				trace;
-	int					i;
 	
 	FeVariable_InterpolateWithinElement( self->pressureField, lElement_I, xi, &self->currentPressure );
 	if( !self->swarmStrainRate ) {
@@ -398,7 +397,7 @@ void _MohrCoulomb_StoreCurrentParameters
 	/* Subtract the trace (which should be zero anyway).  We can
 		use TensorMapST3D even for 2D, because it is the same for
 		the xx and yy components */
-	for(i=0;i<dim;++i)
+	for(uint i=0;i<dim;++i)
 		self->currentStrainRate[TensorMapST3D[i][i]]-=trace/dim;
 
 	ConstitutiveMatrix_CalculateStress( constitutiveMatrix, self->currentStrainRate, self->currentStress );
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/Orthotropic.cxx
--- a/Rheology/src/Orthotropic.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/Orthotropic.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -169,7 +169,6 @@ void _Orthotropic_ModifyConstitutiveMatr
 	Orthotropic*	                self = (Orthotropic*) rheology;
 	Dimension_Index                   dim  = swarm->dim;
 
-	int i,j;
 	double**   C  = constitutiveMatrix->matrixData;
 	double n1,n2,n3;
 	double m1,m2,m3;
@@ -187,8 +186,8 @@ void _Orthotropic_ModifyConstitutiveMatr
 	n1 = self->n[0];
 	n2 = self->n[1];
 
-	for(i=0;i<dim*(dim+1)/2;i++){
-	      for(j=0;j<dim*(dim+1)/2;j++){
+	for(uint i=0;i<dim*(dim+1)/2;i++){
+	      for(uint j=0;j<dim*(dim+1)/2;j++){
 		    C[i][j] = 0.0;
 	      }
 	}
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/OrthotropicAligned.cxx
--- a/Rheology/src/OrthotropicAligned.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/OrthotropicAligned.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -143,7 +143,6 @@ void _OrthotropicAligned_ModifyConstitut
         /*	double                          isotropicViscosity = ConstitutiveMatrix_GetIsotropicViscosity( constitutiveMatrix ); */
         /*	double                          deltaViscosity; */
         /*	XYZ                             normal; */
-	int i,j;
 	double**   D  = constitutiveMatrix->matrixData;
         /*	static int flag = 0; */
         /*	deltaViscosity = isotropicViscosity * (1.0 - self->viscosityRatio); */
@@ -151,11 +150,11 @@ void _OrthotropicAligned_ModifyConstitut
 
         /*	ConstitutiveMatrix_SetSecondViscosity( constitutiveMatrix, deltaViscosity, normal ); */
 	
-        /*	if(!flag){/* if not visited modify matrix else no need to update *\/ */
+        /*	if(!flag){ // if not visited modify matrix else no need to update */
         /* Snark dies if I only allow this to be called once.. */
 	/* ahh need to allow it to be called once for every particle */
-	   for(i=0;i<dim*(dim+1)/2;i++){
-	      for(j=0;j<dim*(dim+1)/2;j++){
+	   for(uint i=0;i<dim*(dim+1)/2;i++){
+	      for(uint j=0;j<dim*(dim+1)/2;j++){
 		 D[i][j] = 0.0;
 	      }
 	   }
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/Pouliquen_etal.cxx
--- a/Rheology/src/Pouliquen_etal.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/Pouliquen_etal.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -426,14 +426,14 @@ void _Pouliquen_etal_HasYielded(
 	double                    oneOnI;
 	Pouliquen_etal_Particle*         particleExt;
 	double                    mu;
-	double                    strainWeakeningRatio;
+	// double                    strainWeakeningRatio;
 	/*double                    mu_2_afterSoftening =	self->mu_2_afterSoftening;
 	double                    mu_s_afterSoftening =	self->mu_s_afterSoftening;*/
 	double                    effective_mu_s;
 	double                    effective_mu_2;
 	double                    pressure;
 
-	strainWeakeningRatio = StrainWeakening_CalcRatio( self->strainWeakening, materialPoint );
+	// strainWeakeningRatio = StrainWeakening_CalcRatio( self->strainWeakening, materialPoint );
 
 	particleExt = (Pouliquen_etal_Particle*)ExtensionManager_Get( materialPointsSwarm->particleExtensionMgr, materialPoint, self->particleExtHandle );
 
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/RheologyMaterial.cxx
--- a/Rheology/src/RheologyMaterial.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/RheologyMaterial.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -175,7 +175,7 @@ void _RheologyMaterial_Init(
          Rheology_Register_Add( self->rheology_Register, rheologyList[ rheology_I ] );
    }
 
-	/*	self->debug = Journal_Register( Debug_Type, (Name)self->type ); /* TODO make child of Underworld_Debug */
+	/*	self->debug = Journal_Register( Debug_Type, (Name)self->type ); // TODO make child of Underworld_Debug */
 }
 
 
diff -r 90a83768712b -r a3a5956268a8 Rheology/src/VonMises.cxx
--- a/Rheology/src/VonMises.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/src/VonMises.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -230,7 +230,6 @@ double _VonMises_GetYieldIndicator(
 {
 	VonMises*                         self             = (VonMises*) rheology;
 	SymmetricTensor                   strainRate;
-        int i;
         double stressTrace, strainRateTrace;
 	
 	/* Get Strain Rate */
@@ -252,7 +251,7 @@ double _VonMises_GetYieldIndicator(
         SymmetricTensor_GetTrace(strainRate, constitutiveMatrix->dim,
                                  &strainRateTrace);
 
-        for(i=0;i<constitutiveMatrix->dim;++i)
+        for(uint i=0;i<constitutiveMatrix->dim;++i)
           {
             strainRate[TensorMapST3D[i][i]]-=
               strainRateTrace/constitutiveMatrix->dim;
diff -r 90a83768712b -r a3a5956268a8 Rheology/tests/ByerleeYieldingSuite.cxx
--- a/Rheology/tests/ByerleeYieldingSuite.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/tests/ByerleeYieldingSuite.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -134,7 +134,6 @@ void ByerleeYieldingSuite_Check_Sync( Fi
 
 void ByerleeYieldingSuite_TestByerlee2D( ByerleeYieldingSuiteData* data ) {
 	UnderworldContext*		context;
-	Dictionary*					dictionary;
 	YieldRheology*          yieldRheology;
 	Stg_ComponentFactory*	cf;
 	char							expected_file[PCU_PATH_MAX];
@@ -147,8 +146,6 @@ void ByerleeYieldingSuite_TestByerlee2D(
 	Stream_Enable( context->info, False );
 	Stream_Enable( context->debug, False );
 	Stream_Enable( context->verbose, False );
-	dictionary = context->dictionary;
-
 	stgMainBuildAndInitialise( cf );
 
 	/* get pointer to the mesh */
diff -r 90a83768712b -r a3a5956268a8 Rheology/tests/ConstitutiveMatrixSuite.cxx
--- a/Rheology/tests/ConstitutiveMatrixSuite.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/tests/ConstitutiveMatrixSuite.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -84,7 +84,6 @@ void testConstitutiveMatrix( FiniteEleme
 
 
 void ConstitutiveMatrixSuite_CartesianMatrix2D( ConstitutiveMatrixSuiteData* data ) {
-	Dictionary*					dictionary;
 	UnderworldContext*		context;
 	Stg_ComponentFactory*	cf;
 	char							expected_file[PCU_PATH_MAX], output_file[PCU_PATH_MAX];
@@ -99,7 +98,6 @@ void ConstitutiveMatrixSuite_CartesianMa
 	cf = stgMainInitFromXML( xml_input, MPI_COMM_WORLD, NULL );
 	context = (UnderworldContext*)LiveComponentRegister_Get( cf->LCRegister, (Name)"context"  );
 	data->context = context;
-	dictionary = context->dictionary;
 
 	/* replace the Execute EP with the function to test the ConstitutiveMatrix */
 	ContextEP_ReplaceAll( context, AbstractContext_EP_Execute, testConstitutiveMatrix );
diff -r 90a83768712b -r a3a5956268a8 Rheology/tests/DirectorSuite.cxx
--- a/Rheology/tests/DirectorSuite.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/tests/DirectorSuite.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -56,7 +56,6 @@ void test( UnderworldContext* context ) 
 void test( UnderworldContext* context ) {
 	Director*			director = (Director*)LiveComponentRegister_Get( context->CF->LCRegister, (Name)"director" );
 	Particle_Index		lParticle_I;
-	GlobalParticle*	particle;
 	double				time = context->currentTime + context->dt;
 	Swarm*				swarm	= (Swarm* )LiveComponentRegister_Get( context->CF->LCRegister, (Name)"materialSwarm" );
 	XYZ					normal;
@@ -65,16 +64,14 @@ void test( UnderworldContext* context ) 
    double				angleDirector;
 	double				gError;
 	int					particleGlobalCount;
-   int ierr;
 
 	for ( lParticle_I = 0 ; lParticle_I < swarm->particleLocalCount ; lParticle_I++ ) {
-		particle = (GlobalParticle* )Swarm_ParticleAt( swarm, lParticle_I );
 		SwarmVariable_ValueAt( director->directorSwarmVariable, lParticle_I, normal );
       angleDirector = atan(-normal[1]/normal[0]);
 		error += fabs( angleDirector - angle );
 	}
-	ierr = MPI_Allreduce( &error, &gError, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
-	ierr = MPI_Allreduce( &swarm->particleLocalCount, &particleGlobalCount, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
+	MPI_Allreduce( &error, &gError, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
+	MPI_Allreduce( &swarm->particleLocalCount, &particleGlobalCount, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
 
 	//error /= (double) swarm->particleLocalCount;
 	//pcu_check_true( error < TOLERANCE );
@@ -86,7 +83,6 @@ void testRandom( UnderworldContext* cont
 	AlignmentSwarmVariable* alignment = (AlignmentSwarmVariable*) LiveComponentRegister_Get( context->CF->LCRegister, (Name)"alignment"  );
 	Director*               director;
 	Particle_Index          lParticle_I;
-	GlobalParticle*         particle;
 	Swarm*                  swarm;
 	XYZ                     normal;
 	int                     ii;
@@ -102,13 +98,11 @@ void testRandom( UnderworldContext* cont
 	int                     circleAngleUpperBound;
 	double						gCircleAngleAverage;
 	int                     gCircleAngleCounts[36] 	= {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
-   int ierr;
 
 	swarm = alignment->swarm;
 	director = alignment->director;
 
 	for ( lParticle_I = 0 ; lParticle_I < swarm->particleLocalCount ; lParticle_I++ ) {
-		particle = (GlobalParticle*)Swarm_ParticleAt( swarm, lParticle_I );
 		SwarmVariable_ValueAt( director->directorSwarmVariable, lParticle_I, normal );
 		/* Calculate dot product between normal and (0,1), then get an angle */
 
@@ -123,10 +117,10 @@ void testRandom( UnderworldContext* cont
 		}
 		circleAngleCounts[ (int)(circleAngle+0.5) / 10 ] += 1;
 	}
-	ierr = MPI_Allreduce( circleAngleCounts, gCircleAngleCounts, 36, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
+	MPI_Allreduce( circleAngleCounts, gCircleAngleCounts, 36, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
 
 	circleAngleAverage = (double)swarm->particleLocalCount / 36;
-	ierr = MPI_Allreduce( &circleAngleAverage, &gCircleAngleAverage, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
+	MPI_Allreduce( &circleAngleAverage, &gCircleAngleAverage, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
 
 	/*NB. This definition is determined based on a set no. of particlesPerCell. Currently this value is = 20 */
 	#define TheoreticalStandardDeviation 13.64
@@ -161,12 +155,10 @@ void testRandom( UnderworldContext* cont
 
 void testPerMaterial( UnderworldContext* context ) {
 	AlignmentSwarmVariable* alignment              = (AlignmentSwarmVariable*) LiveComponentRegister_Get( context->CF->LCRegister, (Name)"alignment" );
-	Materials_Register*     materials_Register     = context->materials_Register;
 	Director*               director;
 	Particle_Index          lParticle_I;
 	Swarm*                  swarm;
 	XYZ                     testVector;
-	Material_Index          materialsCount;
 	int                     material_I;
 	XYZ*                    matDirectionVectors;
 	double                  angle;
@@ -174,7 +166,6 @@ void testPerMaterial( UnderworldContext*
 	
 	swarm = alignment->swarm;
 	director = alignment->director;
-	materialsCount = Materials_Register_GetCount( materials_Register );
 	
 	/*  construct test for testDirectorPerMaterial.xml  */
 	/* assume a direction for each material and check that */
@@ -209,12 +200,10 @@ void testPerMaterial( UnderworldContext*
 
 void testPerMaterial2( UnderworldContext* context ) {
 	AlignmentSwarmVariable* alignment              = (AlignmentSwarmVariable*) LiveComponentRegister_Get( context->CF->LCRegister, (Name)"alignment" );
-	Materials_Register*     materials_Register     = context->materials_Register;
 	Director*               director;
 	Particle_Index          lParticle_I;
 	Swarm*                  swarm;
 	XYZ                     testVector;
-	Material_Index          materialsCount;
 	int                     material_I;
 	XYZ*                    matDirectionVectors;
 	double                  angle;
@@ -222,7 +211,6 @@ void testPerMaterial2( UnderworldContext
 	
 	swarm = alignment->swarm;
 	director = alignment->director;
-	materialsCount = Materials_Register_GetCount( materials_Register );
 	
 	matDirectionVectors = Memory_Alloc_Array(XYZ, DIR_TEST_NUM_MAT, "materialDirectionVectors");
 
diff -r 90a83768712b -r a3a5956268a8 Rheology/tests/VonMisesYieldingSuite.cxx
--- a/Rheology/tests/VonMisesYieldingSuite.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Rheology/tests/VonMisesYieldingSuite.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -129,7 +129,6 @@ void Underworld_testVonMisesYielding_Che
 
 void VonMisesYieldingSuite_VonMises2D( VonMisesYieldingSuiteData* data ) {
 	UnderworldContext* context;
-	Dictionary*					dictionary;
 	YieldRheology*          yieldRheology;
 	Stg_ComponentFactory*	cf;
 	char							expected_file[PCU_PATH_MAX];
@@ -139,7 +138,6 @@ void VonMisesYieldingSuite_VonMises2D( V
 	pcu_filename_input( "testVonMisesYieldCriterion.xml", xml_input );
 	cf = stgMainInitFromXML( xml_input, MPI_COMM_WORLD, NULL );
 	context = (UnderworldContext*)LiveComponentRegister_Get( cf->LCRegister, (Name)"context" );
-	dictionary = context->dictionary;
 
 	stgMainBuildAndInitialise( cf  );
 
diff -r 90a83768712b -r a3a5956268a8 Utils/src/BaseRecoveryFeVar.cxx
--- a/Utils/src/BaseRecoveryFeVar.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/BaseRecoveryFeVar.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -141,8 +141,8 @@ void _BaseRecoveryFeVar_Build( void* _se
 void _BaseRecoveryFeVar_Build( void* _self, void* data ) {
   BaseRecoveryFeVar* self = (BaseRecoveryFeVar*) _self;
 	Sync*	               sync;
-	int                  componentsCount = 0;
-	int                  variable_I, node_I;
+	uint                  componentsCount = 0;
+	uint                  variable_I;
 	int                  *nodeDomainCountPtr = NULL;
 	char                 **variableName, *tmpName;
 	Variable*            dataVariable;
@@ -194,7 +194,7 @@ void _BaseRecoveryFeVar_Build( void* _se
 			variable->arrayPtrPtr = &dataVariable->arrayPtr;
 
 			/* Assign variable to each node */
-			for( node_I = 0; node_I < *nodeDomainCountPtr; node_I++ ) {
+			for( int node_I = 0; node_I < *nodeDomainCountPtr; node_I++ ) {
 				DofLayout_AddDof_ByVarName( self->dofLayout, variableName[variable_I], node_I );
 			}
 			/* Free Name */
@@ -352,7 +352,6 @@ void _BaseRecoveryFeVar_GetValueInElemen
 void _BaseRecoveryFeVar_GetValueInElementWithCoeffInterpolation( void* feVariable, Element_Index lEl_I, double* xi, double* value ) {
 	BaseRecoveryFeVar* self = (BaseRecoveryFeVar*) feVariable;
 	FeMesh*              mesh = self->feMesh;
-	IArray*              inc  = self->inc;
 	double               globalCoord[3];
 	double               coeff[50]; 
 	int order, dof_I, dofThatExist;
@@ -382,7 +381,7 @@ double _BaseRecoveryFeVar_ApplyCoeff( Ba
 	return value;
 }
 
-void BaseUtils_Add2LmStruct( LmStruct* lmStruct, Index nodeID ) {
+void BaseUtils_Add2LmStruct( LmStruct* lmStruct, int nodeID ) {
 	int count_I;
 	for( count_I = 0 ; count_I < lmStruct->numberOfNodes ; count_I++ ) {
 		/* To prevent duplication in the list*/
@@ -409,22 +408,21 @@ void BaseUtils_PopulateBoundaryNodesInfo
  *  		if so, set onBoundary = true 
  * 
  */
-	Node_Index              dNodes_I, tmpNodeID, tmpNode_I;
-	Element_Index           nbrElementID, nbrElement_I;
-	int                     nEls, *els;
-	int                     nNodes, *nodes;
+	Node_Index              tmpNodeID, tmpNode_I;
+	Element_Index           nbrElementID;
+        int                     *els;
+	uint                    nNodes;
 	LmStruct                list;
 	Sync*                   sync;
-	int                     domainNodes;
-	int                     nLocalNodes;
+	uint                    nLocalNodes;
 	int                     nVerts;
-  const int               *verts;
+        const int               *verts;
 	IArray*			            inc[2];
 
 	sync = Mesh_GetSync( mesh, MT_VERTEX );
 	IGraph_GetBoundaryElements( mesh->topo, MT_VERTEX, &nVerts, &verts );
 	nLocalNodes = FeMesh_GetNodeLocalSize( mesh );
-	domainNodes = FeMesh_GetNodeDomainSize( mesh );
+	int domainNodes = FeMesh_GetNodeDomainSize( mesh );
 
 	assert( nVerts <= domainNodes );
 
@@ -434,14 +432,14 @@ void BaseUtils_PopulateBoundaryNodesInfo
    * numOfPatches2use = 0
    * patchNodes list = [-1,-1,-1,....,-1]
    * */
-	for( dNodes_I = 0 ; dNodes_I < domainNodes ; dNodes_I++ ) {
+	for( int dNodes_I = 0 ; dNodes_I < domainNodes ; dNodes_I++ ) {
 		bninfo[dNodes_I].onMeshBoundary = False;
 		bninfo[dNodes_I].numOfPatches2use = 0;
 		memset( bninfo[dNodes_I].patchNodes, -1, sizeof(int)*REP_MAXNODESPERPATCH );
 	}
 
 	/* First flag boundary nodes */
-	for( dNodes_I = 0 ; dNodes_I < nVerts ; dNodes_I++ )
+	for( int dNodes_I = 0 ; dNodes_I < nVerts ; dNodes_I++ )
 	       bninfo[verts[dNodes_I]].onMeshBoundary = True;
 
 	/* Update all other procs. */
@@ -462,7 +460,7 @@ void BaseUtils_PopulateBoundaryNodesInfo
 	 */
 	inc[0] = IArray_New();
 	inc[1] = IArray_New();
-	for( dNodes_I = 0 ; dNodes_I < FeMesh_GetNodeDomainSize( mesh ) ; dNodes_I++ ) {
+	for( uint dNodes_I = 0 ; dNodes_I < FeMesh_GetNodeDomainSize( mesh ) ; dNodes_I++ ) {
 		if( !bninfo[dNodes_I].onMeshBoundary ) 
 			continue;
 
@@ -470,15 +468,15 @@ void BaseUtils_PopulateBoundaryNodesInfo
 				
 		/* Go through all neighbour elements */
 		FeMesh_GetNodeElements( mesh, dNodes_I, inc[0] );
-		nEls = IArray_GetSize( inc[0] );
+		int nEls = IArray_GetSize( inc[0] );
 		els = IArray_GetPtr( inc[0] );
 
-		for( nbrElement_I = 0 ; nbrElement_I < nEls ; nbrElement_I++) {
+		for(int nbrElement_I = 0; nbrElement_I < nEls; nbrElement_I++) {
 			nbrElementID = els[nbrElement_I];
 			/* Go through nodes on elements and see if they're valid patchs */
 			FeMesh_GetElementNodes( mesh, nbrElementID, inc[1] );
 			nNodes = IArray_GetSize( inc[1] );
-			nodes = IArray_GetPtr( inc[1] );
+			int *nodes = IArray_GetPtr( inc[1] );
 
 			for( tmpNode_I = 0 ; tmpNode_I < nNodes ; tmpNode_I++ ) {
 				tmpNodeID = nodes[tmpNode_I];
diff -r 90a83768712b -r a3a5956268a8 Utils/src/DivergenceForce.cxx
--- a/Utils/src/DivergenceForce.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/DivergenceForce.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -158,7 +158,6 @@ void* _DivergenceForce_DefaultNew( Name 
 
 void _DivergenceForce_AssignFromXML( void* forceTerm, Stg_ComponentFactory* cf, void* data ) {
 	DivergenceForce*          self             = (DivergenceForce*)forceTerm;
-	Dictionary*		dict;
         Stg_Shape* domainShape=NULL;
         FeMesh* geometryMesh=NULL;
         StressBC_Entry force;
@@ -167,7 +166,6 @@ void _DivergenceForce_AssignFromXML( voi
 	/* Construct Parent */
 	_ForceTerm_AssignFromXML( self, cf, data );
 
-	dict = Dictionary_Entry_Value_AsDictionary( Dictionary_Get( cf->componentDict, self->name ) );
 	domainShape =  Stg_ComponentFactory_ConstructByKey(  cf,  self->name,  "DomainShape", Stg_Shape,  True, data  ) ;
         type = Stg_ComponentFactory_GetString( cf, self->name, "force_type", "");
 
@@ -290,6 +288,8 @@ void _DivergenceForce_AssembleElement( v
                elementNodes[eNode_I],0,self->context,&force);
             break;
           }
+
+        // This needs to be properly integrated.
         elForceVec[ eNode_I] += force*factor;
       }
   }
diff -r 90a83768712b -r a3a5956268a8 Utils/src/MixedStabiliserTerm.cxx
--- a/Utils/src/MixedStabiliserTerm.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/MixedStabiliserTerm.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -149,7 +149,6 @@ void _MixedStabiliserTerm_AssembleElemen
    ElementType* elementType;
    IntegrationPointsSwarm* swarm;
    IntegrationPoint* integrationPoint;
-   double geometric_factor;
    double** localElStiffMat;
    int ii, jj, kk;
    double sumVisc = 0.0, visc;
diff -r 90a83768712b -r a3a5956268a8 Utils/src/REP_Algorithm.cxx
--- a/Utils/src/REP_Algorithm.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/REP_Algorithm.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -459,7 +459,7 @@ void _REP_Algorithm_AssembleElement( REP
 	ElementType*            elementType;
 	IntegrationPoint*       particle;
  	double globalCoord[3], detJac;
-	int cell_I, cellParticleCount, nodesPerEl, cParticle_I;
+	int cell_I, cellParticleCount, cParticle_I;
 	/* Only need one */
 	int dim = self->repFieldList[0]->dim;
 	int field_I;
@@ -469,7 +469,6 @@ void _REP_Algorithm_AssembleElement( REP
 
 	/* Get the number of nodes per element */
 	FeMesh_GetElementNodes( mesh, lElement_I, self->incArray );
-	nodesPerEl = IArray_GetSize( self->incArray );
 
 	/* Get number of particles per element */
 	cell_I = CellLayout_MapElementIdToCellId( swarm->cellLayout, lElement_I );
diff -r 90a83768712b -r a3a5956268a8 Utils/src/RecoveredFeVariable.cxx
--- a/Utils/src/RecoveredFeVariable.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/RecoveredFeVariable.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -371,16 +371,15 @@ void _RecoveredFeVariable_AssembleAtPart
 		memcpy( pMatrix[dof_I], pVec, order*sizeof(double) );
 
 		if( self->recoverStrain ) {
-			Index ii;
 			if( !constitutiveMatrix ) {
         /* if no consitutive matrix make it up - assume viscosity = 1 */
-				for( ii = 0 ; ii < dofThatExist; ii++ ) { memset( tmpC[ii], 0, dofThatExist*sizeof(double)); }
+				for(int ii = 0 ; ii < dofThatExist; ii++ ) { memset( tmpC[ii], 0, dofThatExist*sizeof(double)); }
 				if (dim == 2) { tmpC[0][0] = tmpC[1][1] = tmpC[2][2] = 1; } 
         else { tmpC[0][0] = tmpC[1][1] = tmpC[2][2] = tmpC[3][3] = tmpC[4][4] = tmpC[5][5] = 1; }
 
 			} else {
 				/* copy constitutive matrix */
-				for(ii = 0 ; ii < dofThatExist ; ii++)
+				for(int ii = 0 ; ii < dofThatExist ; ii++)
 					memcpy( tmpC[ii], constitutiveMatrix->matrixData[ii], dofThatExist*sizeof(double) ); 
 			}
       if( dim == 2 ){
@@ -521,7 +520,7 @@ void _RecoveredFeVariable_CalcFi3D( Reco
 }
 
 void _RecoveredFeVariable_PutElIntoProc( RecoveredFeVariable* self, int lElement_I, double*** elHi_Mat, double** elFi_Mat ) {
-	int keyH, keyF, dof_I, row_I, order_I;
+	int keyF, dof_I, row_I, order_I;
 	int dim, dofThatExist, order, nodesPerEl, rowsInH;
 	double* ptrH = self->elementRep_H;
 	double* ptrF = self->elementRep_F;
@@ -533,7 +532,6 @@ void _RecoveredFeVariable_PutElIntoProc(
 	rowsInH = nodesPerEl * dim;
 	
 	for( dof_I = 0 ; dof_I < dofThatExist ; dof_I++ ) {  
-		keyH = (lElement_I*dofThatExist*rowsInH*order) + (dof_I*rowsInH*order);
 		keyF = (lElement_I*dofThatExist*rowsInH) + (dof_I*rowsInH);
 		for( row_I = 0 ; row_I < rowsInH ; row_I++ ) {
 			ptrF[ keyF + row_I ] =+ elFi_Mat[dof_I][row_I];
@@ -576,9 +574,8 @@ void RecoveredFeVariable_CommunicateHF( 
 }
 
 void RecoveredFeVariable_SetupWorkSpace( RecoveredFeVariable* self ) {
-	int dofThatExist, order, nodesPerEl, nodesInPatch, rowsInH;
+	int dofThatExist, order, nodesInPatch, rowsInH;
 
-	nodesPerEl = self->nodesPerEl;
 	dofThatExist = self->fieldComponentCount;
 	order = self->orderOfInterpolation;
 	nodesInPatch = self->nodesInPatch;
@@ -621,9 +618,8 @@ void RecoveredFeVariable_SolvePatch( Rec
 	double **el_H = self->tmpEl_H;
 	double *el_F = self->tmpEl_F;
 	double *ptrH, *ptrF;
-  double coeff[50];
+        double coeff[50];
 	IArray *inc;
-	double *coord;
 	int dim, dofThatExist, order, nodesPerEl, rowsInElH, rowsInPatchH, row, elID;
 	int dof_I, el_I, node_I, nodeID, indexOfEntry, order_I;
 	int *nodeList;
@@ -642,8 +638,6 @@ void RecoveredFeVariable_SolvePatch( Rec
 
 	/* use the inc on the FeVariable */
 	inc = self->inc;
-
-	coord = Mesh_GetVertex( self->feMesh , pNodeID );
 
 	for( dof_I = 0 ; dof_I < dofThatExist ; dof_I++ ) {
 			ZeroMatrix( self->patch_H[dof_I], rowsInPatchH, order );
diff -r 90a83768712b -r a3a5956268a8 Utils/src/SPR_StrainRate.cxx
--- a/Utils/src/SPR_StrainRate.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/SPR_StrainRate.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -227,7 +227,7 @@ void _SPR_StrainRate_AssemblePatch( SPR_
 	FeMesh*				feMesh = (FeMesh*)rawField->feMesh;
 	Index					dofThatExist = rawField->fieldComponentCount;
 	Index					nbrEl_I, nbrElementID, nbrElCount;
-	Index					count_i, count_j, dof_I;
+	Index					dof_I;
 	double				center[3] = {0.0,0.0,0.0};
 	int					orderOfInterpolation = self->orderOfInterpolation;
 	IArray*				inc = self->inc; 
@@ -263,13 +263,13 @@ void _SPR_StrainRate_AssemblePatch( SPR_
 
  	/* Construct A Matrix (Geometric based) and b Vectors (tensor based) */
 	for( nbrEl_I = 0 ; nbrEl_I < nbrElCount ; nbrEl_I++ ) {
-		for( count_i = 0 ; count_i < orderOfInterpolation ; count_i++ ) {
-			for( count_j = 0; count_j < orderOfInterpolation ; count_j++ ) {
+		for(int count_i = 0 ; count_i < orderOfInterpolation ; count_i++ ) {
+			for(int count_j = 0; count_j < orderOfInterpolation ; count_j++ ) {
 				AMatrix[count_i][count_j] += ( pVec[nbrEl_I][count_i] * pVec[nbrEl_I][count_j] );
 			}
 		}
 		for(dof_I = 0 ; dof_I < dofThatExist ; dof_I++ ) {
-			for( count_i = 0 ; count_i < orderOfInterpolation ; count_i++ ) {
+			for(int count_i = 0 ; count_i < orderOfInterpolation ; count_i++ ) {
 				bVector[dof_I][ count_i ] += (scp_eps[nbrEl_I][dof_I] * pVec[nbrEl_I][count_i]);
 			}
  		}
diff -r 90a83768712b -r a3a5956268a8 Utils/src/SmoothVelGradField.cxx
--- a/Utils/src/SmoothVelGradField.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/SmoothVelGradField.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -107,12 +107,10 @@ void* _SmoothVelGradField_Copy( const vo
 }
 
 void SmoothVelGradField_NonLinearUpdate( void* _sle, void* _ctx ) {
-   SystemLinearEquations* sle;
    DomainContext* ctx = (DomainContext*)_ctx;
    FieldVariable_Register* fieldVar_Register;
    SmoothVelGradField* preVar;
 
-	sle = (SystemLinearEquations*)_sle;
    fieldVar_Register = ctx->fieldVariable_Register;
    preVar = (SmoothVelGradField*)FieldVariable_Register_GetByName( fieldVar_Register, "VelocityGradientsField" );
    ParticleFeVariable_Update( preVar );
diff -r 90a83768712b -r a3a5956268a8 Utils/src/StressField.cxx
--- a/Utils/src/StressField.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/StressField.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -127,12 +127,10 @@ void* _StressField_DefaultNew( Name name
 }
 
 void StressField_NonLinearUpdate( void* _sle, void* _ctx ) {
-   SystemLinearEquations* sle;
    DomainContext* ctx = (DomainContext*)_ctx;
    FieldVariable_Register* fieldVar_Register;
    StressField* stressVar;
 
-	sle = (SystemLinearEquations*)_sle;
    fieldVar_Register = ctx->fieldVariable_Register;
    stressVar = (StressField*)FieldVariable_Register_GetByName( fieldVar_Register, "StressField" );
    ParticleFeVariable_Update( stressVar );
diff -r 90a83768712b -r a3a5956268a8 Utils/src/TracerOutput.cxx
--- a/Utils/src/TracerOutput.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/Utils/src/TracerOutput.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -188,23 +188,21 @@ void _TracerOutput_AssignFromXML( void* 
 }
 
 void _TracerOutput_Build( void* swarmOutput, void* data ) {
-  int i;
   TracerOutput*	self = (TracerOutput*) swarmOutput;
 
   if(self->pressureField)
     Stg_Component_Build( self->pressureField, data, False );
-  for(i=0;i<self->num_fields;++i)
+  for(uint i=0;i<self->num_fields;++i)
     Stg_Component_Build( self->fields[i], data, False );
 
   _SwarmOutput_Build( self, data );
 }
 void _TracerOutput_Initialise( void* swarmOutput, void* data ) {
-  int i;
   TracerOutput*	self = (TracerOutput*) swarmOutput;
 
   if(self->pressureField)
     Stg_Component_Initialise( self->pressureField, data, False );
-  for(i=0;i<self->num_fields;++i)
+  for(uint i=0;i<self->num_fields;++i)
     Stg_Component_Initialise( self->fields[i], data, False );
 	
   _SwarmOutput_Initialise( self, data );
@@ -215,12 +213,11 @@ void _TracerOutput_Execute( void* swarmO
   _SwarmOutput_Execute( self, data );
 }
 void _TracerOutput_Destroy( void* swarmOutput, void* data ) {
-  int i;
   TracerOutput*	self = (TracerOutput*)swarmOutput;
 
   if(self->pressureField)
     Stg_Component_Destroy( self->pressureField, data, False );
-  for(i=0;i<self->num_fields;++i)
+  for(uint i=0;i<self->num_fields;++i)
     Stg_Component_Destroy( self->fields[i], data, False );
 	
   _SwarmOutput_Destroy( self, data );
@@ -228,7 +225,6 @@ void _TracerOutput_Destroy( void* swarmO
 
 void _TracerOutput_PrintHeader( void* swarmOutput, Stream* stream,
                                 Particle_Index lParticle_I, void* context ){
-  int i;
   char name[32];
   TracerOutput*	self = (TracerOutput*)swarmOutput;
 	
@@ -236,7 +232,7 @@ void _TracerOutput_PrintHeader( void* sw
   _SwarmOutput_PrintHeader( self, stream, lParticle_I, context );
 	
   SwarmOutput_PrintString( self, stream, "Pressure" );
-  for(i=0;i<self->num_fields;++i)
+  for(uint i=0;i<self->num_fields;++i)
     {
       sprintf(name,"Field%d",i);
       SwarmOutput_PrintString( self, stream, name );
@@ -253,7 +249,6 @@ void _TracerOutput_PrintData( void* swar
   double* coord = particle->coord;
   HydrostaticTerm *hydrostaticTerm;
   double pressure, field;
-  int i;
 
   hydrostaticTerm =
     (HydrostaticTerm*)LiveComponentRegister_Get(fe_context->CF->LCRegister,
@@ -273,7 +268,7 @@ void _TracerOutput_PrintData( void* swar
       }
       SwarmOutput_PrintValue( self, stream, pressure );
     }
-  for(i=0;i<self->num_fields;++i)
+  for(uint i=0;i<self->num_fields;++i)
     {
       FieldVariable_InterpolateValueAt(self->fields[i],coord,&field);
       SwarmOutput_PrintValue( self, stream, field );
diff -r 90a83768712b -r a3a5956268a8 plugins/Output/BoundaryLayers/BoundaryLayers.cxx
--- a/plugins/Output/BoundaryLayers/BoundaryLayers.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/plugins/Output/BoundaryLayers/BoundaryLayers.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -183,7 +183,7 @@ double Underworld_BoundaryLayers_Interna
 	Element_LocalIndex  lElement_I;
 	Node_LocalIndex    	nodeAtElementBottom;
 	Node_LocalIndex    	nodeAtElementTop;
-	int                 elementNodeCount, *elementNodes;
+	int                 *elementNodes;
 	double              elementBottomHeight;
 	double              elementTopHeight;
 	double              detJac;
@@ -211,7 +211,6 @@ double Underworld_BoundaryLayers_Interna
 	for ( lElement_I = 0 ; lElement_I < FeMesh_GetElementLocalSize( mesh ) ; lElement_I++ ) {
 		elementType         = FeMesh_GetElementType( mesh, lElement_I );
 		FeMesh_GetElementNodes( mesh, lElement_I, incArray );
-		elementNodeCount = IArray_GetSize( incArray );
 		elementNodes = IArray_GetPtr( incArray );
 
 		nodeAtElementBottom = elementNodes[ 0 ] ;
diff -r 90a83768712b -r a3a5956268a8 plugins/Output/BuoyancyIntegrals/BuoyancyIntegrals.cxx
--- a/plugins/Output/BuoyancyIntegrals/BuoyancyIntegrals.cxx	Sat Oct 08 02:06:43 2011 -0700
+++ b/plugins/Output/BuoyancyIntegrals/BuoyancyIntegrals.cxx	Sun Oct 16 05:56:21 2011 -0700
@@ -273,7 +273,6 @@ void perform_integrals( UnderworldContex
 	Cell_Index cell_I;
 	double velocity[3], global_coord[3];
 	FeMesh* mesh;
-	Element_LocalIndex e;
 	
 	double i_T, i_v, i_y, i_vT; /* interpolated quantity */
 	double sum_T, sum_vT, sum_yT; /* integral sum */
@@ -342,7 +341,7 @@ void perform_integrals( UnderworldContex
 	n_elements = FeMesh_GetElementLocalSize( mesh  );
 	//	printf("n_elements = %d \n", n_elements );
 	
-	for( e=0; e<n_elements; e++ ) {
+	for(int e=0; e<n_elements; e++ ) {
 		cell_I = CellLayout_MapElementIdToCellId( gaussSwarm->cellLayout, e );
 		elementType = FeMesh_GetElementType( mesh, e );
 		
@@ -418,7 +417,6 @@ void eval_temperature( UnderworldContext
 {
 	Underworld_BuoyancyIntegrals_CTX *ctx;
 	double global_coord[3];
-	InterpolationResult result;
 	double T;
 	FeVariable* temperatureField;
 
@@ -439,7 +437,7 @@ void eval_temperature( UnderworldContext
 		global_coord[1] = y_b;
 	}
 
-	result = FieldVariable_InterpolateValueAt( temperatureField, global_coord, &T );
+	FieldVariable_InterpolateValueAt( temperatureField, global_coord, &T );
 	MPI_Allreduce ( &T, temp_b, 1, MPI_DOUBLE, MPI_MAX, context->communicator );
 
 }



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