Index: ../trunk-jpl/src/c/toolkits/plapack/patches/CyclicalFactorization.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/plapack/patches/CyclicalFactorization.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/plapack/patches/CyclicalFactorization.cpp	(revision 13784)
@@ -38,11 +38,10 @@
 
 int PrimeDecomp(int** pdecomp,int* pdecomp_size,int input){
 
-	int* decomp=NULL;
 	int prime_factor;
 	int i;
 
-	decomp=xNew<int>(input);
+	int* decomp=xNew<int>(input);
 	*decomp=input;
 	for (i=0;i<input;i++){
 		SmallestPrimeFactor(&prime_factor,*(decomp+i));
Index: ../trunk-jpl/src/c/toolkits/plapack/patches/PlapackInvertMatrix.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/plapack/patches/PlapackInvertMatrix.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/plapack/patches/PlapackInvertMatrix.cpp	(revision 13784)
@@ -23,7 +23,7 @@
 	/*input*/
 	int mA,nA;
 	int local_mA,local_nA;
-	int lower_row,upper_row,range;
+	int lower_row,upper_row;
 	MatType type;
 
 	/*Plapack: */
@@ -35,7 +35,6 @@
 	int ierror;
 	int nb,nb_alg;
 	int nprows,npcols;
-	int initialized=0;
 
 	/*Petsc to Plapack: */
 	double    *arrayA=NULL;
@@ -95,7 +94,6 @@
 	any matrix type.*/
 	MatGetOwnershipRange(*A,&lower_row,&upper_row);
 	upper_row--; 
-	range=upper_row-lower_row+1;
 	arrayA = xNew<double>(nA);
 	idxnA  = xNew<int>(nA);
 	for (i=0;i<nA;i++){
Index: ../trunk-jpl/src/c/toolkits/plapack/patches/PlapackToPetsc.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/plapack/patches/PlapackToPetsc.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/plapack/patches/PlapackToPetsc.cpp	(revision 13784)
@@ -9,7 +9,7 @@
 
 	int i;
 
-	int lower_row,upper_row,range;
+	int lower_row,upper_row;
 	int* row_nodes=NULL;
 	int* col_nodes=NULL;
 	int* idxm=NULL;
@@ -33,7 +33,6 @@
 
 	MatGetOwnershipRange(*A,&lower_row,&upper_row);
 	upper_row--;
-	range=upper_row-lower_row+1;
 
 	/*Build the Plapack row and column indices corresponding to the local_buffer stored in a. 
 	  We need those indices to directly plug local_buffer into the Petsc matrix A. We do not 
Index: ../trunk-jpl/src/c/toolkits/plapack/plapackincludes.h
===================================================================
--- ../trunk-jpl/src/c/toolkits/plapack/plapackincludes.h	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/plapack/plapackincludes.h	(revision 13784)
@@ -11,14 +11,14 @@
 #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
 #endif
 
-#include "PLA.h"
+#include <PLA.h>
 
 /* missing Plapack prototypes: */
 int PLA_General_invert( int method, PLA_Obj A );
 
 /*our own patches: */
 #ifdef _HAVE_PETSC_
-#include "patches/petscpatches.h"
+#include "./patches/petscpatches.h"
 #endif
 
 #endif
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/KSPFree.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/KSPFree.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/KSPFree.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 void KSPFree(KSP* pksp){
 
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/MatMultPatch.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/MatMultPatch.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/MatMultPatch.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 #include "../../../shared/shared.h"
 
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/VecFree.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/VecFree.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/VecFree.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 void VecFree(Vec* pvec){
 
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 #include "./petscpatches.h"
 
@@ -28,7 +28,6 @@
 	#endif
 	char* first=NULL;
 	char* second=NULL;
-	char* final=NULL;
 	size_t len;
 	int first_token=1;
 
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp	(revision 13784)
@@ -10,26 +10,24 @@
 #include <string>
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 #include "../../../shared/shared.h"
 
 void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){
 
-	int     i;
 	int     rows;
-	int    *idxm   = NULL;
 	double *vector = NULL;
 
 	/*Get size of vector: */
 	if(petsc_vector){
 		VecGetSize(petsc_vector,&rows);
 		if(rows){
-			idxm=xNew<int>(rows);
+			int* idxm=xNew<int>(rows);
 			vector=xNew<double>(rows);
-			for(i=0;i<rows;i++)idxm[i]=i;
+			for(int i=0;i<rows;i++)idxm[i]=i;
 			VecGetValues(petsc_vector,rows,idxm,vector);
 			xDelete<int>(idxm);
 		}
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/MatFree.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/MatFree.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/MatFree.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscmat.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscmat.h>
+#include <petscksp.h>
 
 void MatFree(Mat* pmat){
 
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp	(revision 13784)
@@ -11,9 +11,9 @@
 #include <string>
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 /*Petsc includes: */
 #include "../../../shared/shared.h"
@@ -21,19 +21,15 @@
 void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat petsc_matrix){
 
 	/*output: */
+	int     i;
 	double* matrix=NULL;
 	int     rows,cols;
 
-	/*intermediary: */
-	int     i;
-	int*    idxm=NULL;
-	int*    idxn=NULL;
-
 	/*Some needed information: */
 	MatGetSize(petsc_matrix,&rows,&cols);
 
-	idxm=xNew<int>(rows);
-	idxn=xNew<int>(cols);
+	int* idxm=xNew<int>(rows);
+	int* idxn=xNew<int>(cols);
 
 	for(i=0;i<rows;i++)idxm[i]=i;
 	for(i=0;i<cols;i++)idxn[i]=i;
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/VecDuplicatePatch.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/VecDuplicatePatch.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/VecDuplicatePatch.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 void VecDuplicatePatch(Vec* output, Vec input){
 
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 #include "./petscpatches.h"
 
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp	(revision 13784)
@@ -25,18 +25,14 @@
 	/*output: */
 	int lower_row,upper_row;
 
-	/*intermediary :*/
-	int i;
-	int* allranges=NULL;
-
 	/*Gather all range values into allranges, for all nodes*/
-	allranges=xNew<int>(num_procs);
+	int* allranges=xNew<int>(num_procs);
 	MPI_Allgather(&range,1,MPI_INT,allranges,1,MPI_INT,comm);
 
 	/*From all ranges, get lower row and upper row*/
 	lower_row=0;
 	upper_row=lower_row+allranges[0];
-	for (i=1;i<=my_rank;i++){
+	for(int i=1;i<=my_rank;i++){
 		lower_row=lower_row+allranges[i-1];
 		upper_row=upper_row+allranges[i];
 	}
Index: ../trunk-jpl/src/c/toolkits/petsc/patches/VecMerge.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/patches/VecMerge.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/patches/VecMerge.cpp	(revision 13784)
@@ -9,9 +9,9 @@
 #endif
 
 /*Petsc includes: */
-#include "petscmat.h"
-#include "petscvec.h"
-#include "petscksp.h"
+#include <petscmat.h>
+#include <petscvec.h>
+#include <petscksp.h>
 
 #include "./petscpatches.h"
 
@@ -20,8 +20,6 @@
 
 void VecMerge(Vec A, Vec B, double* row_partition_vector,int row_partition_size){
 
-	int i;
-
 	/*Petsc matrix*/
 	int lower_row,upper_row,range;
 	int* idxm=NULL;
@@ -33,7 +31,7 @@
 	VecGetSize(B,&MB);
 
 	/*If the dimension of the partitioning vector is not the same as that of vector B, we have a problem: */
-	if ( (row_partition_size !=MB) ){
+	if ((row_partition_size !=MB) ){
 		_error_("Dimensions of partitioning vector incompatible with dimensions of input vector\n");
 	}
 
@@ -46,13 +44,13 @@
 		/*This node owns rows of vector B, get them*/
 		idxm=xNew<int>(range);
 		values=xNew<double>(range);
-		for (i=0;i<range;i++){
-			*(idxm+i)=lower_row+i;
+		for(int i=0;i<range;i++){
+			idxm[i]=lower_row+i;
 		}
 		VecGetValues(B,range,idxm,values);
 		/*Now, modify idxm using the partition vector, and plug values into A*/
-		for (i=0;i<range;i++){
-			*(idxm+i)=(int)*(row_partition_vector+lower_row+i)-1; //-1 because partition vector comes from Matlab, where indices start at 1.
+		for(int i=0;i<range;i++){
+			idxm[i]=int(row_partition_vector[lower_row+i])-1; //-1 because partition vector comes from Matlab, where indices start at 1.
 		}
 		VecSetValues(A,range,idxm,values,INSERT_VALUES);
 	}
Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp	(revision 13784)
@@ -132,9 +132,7 @@
 /*FUNCTION PetscMat::Duplicate{{{*/
 PetscMat* PetscMat::Duplicate(void){
 
-	PetscMat* output=NULL;
-
-	output=new PetscMat();
+	PetscMat* output=new PetscMat();
 	_assert_(this->matrix);
 	MatDuplicate(this->matrix,MAT_COPY_VALUES,&output->matrix);
 
Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.cpp
===================================================================
--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.cpp	(revision 13784)
@@ -128,11 +128,10 @@
 /*FUNCTION PetscVec::Duplicate{{{*/
 PetscVec* PetscVec::Duplicate(void){
 
-	PetscVec* output=NULL;
 	_assert_(this->vector);
 	Vec vec_output=NULL;
 	VecDuplicate(this->vector,&vec_output);
-	output=new PetscVec(vec_output);
+	PetscVec* output=new PetscVec(vec_output);
 	VecFree(&vec_output);
 
 	return output;
Index: ../trunk-jpl/src/c/classes/FemModel.cpp
===================================================================
--- ../trunk-jpl/src/c/classes/FemModel.cpp	(revision 13783)
+++ ../trunk-jpl/src/c/classes/FemModel.cpp	(revision 13784)
@@ -332,7 +332,6 @@
 		results->AddObject(new GenericExternalResult<IssmDouble>(results->Size()+1, ProfilingCurrentMemEnum, solution_memory, 1, 0));
 		results->AddObject(new GenericExternalResult<IssmDouble>(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops, 1, 0));
 	}
-
 }
 /*}}}*/
 
@@ -856,7 +855,7 @@
 void FemModel::DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses){/*{{{*/
 
 
-	int        i,j,k;
+	int        i,j;
 	int        my_rank;
 	bool       process_units = true;