Index: sm/trunk-jpl/src/c/toolkits/issm/SeqMat.h
===================================================================
--- /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.h	(revision 14658)
+++ 	(revision )
@@ -1,239 +1,0 @@
-/*!\file:  SeqMat.h
- * \brief wrapper to SeqMat objects, which are just wrappers to a simple IssmDouble or IssmPDouble* buffer.
- */ 
-
-#ifndef _SEQMAT_H_
-#define _SEQMAT_H_
-
-/*Headers:*/
-/*{{{*/
-#ifdef HAVE_CONFIG_H
-	#include <config.h>
-#else
-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
-#endif
-
-#include "../../shared/Exceptions/exceptions.h"
-#include "../../shared/MemOps/xMemCpy.h"
-#include "../../shared/Alloc/alloc.h"
-#include "../../include/macros.h"
-#include "./SeqVec.h"
-#include <math.h>
-
-/*}}}*/
-
-/*We need to template this class, in case we want to create Matrices that hold IssmDouble* matrix or IssmPDouble* matrix. 
-  Such matrices would be useful for use without or with the matlab or python interface (which do not care for IssmDouble types, 
-  but only rely on IssmPDouble types)*/
-
-template <class doubletype> 
-class SeqMat{
-
-	public:
-
-		int M,N; 
-		doubletype* matrix;  /*here, doubletype is either IssmDouble or IssmPDouble*/
-
-		/*SeqMat constructors, destructors*/
-		/*FUNCTION SeqMat(){{{*/
-		SeqMat(){
-
-			this->M=0;
-			this->N=0;
-			this->matrix=NULL;
-		}
-		/*}}}*/
-		/*FUNCTION SeqMat(int M,int N){{{*/
-		SeqMat(int pM,int pN){
-
-			this->M=pM;
-			this->N=pN;
-			this->matrix=NULL;
-			if(M*N) this->matrix=xNewZeroInit<doubletype>(pM*pN);
-		}
-		/*}}}*/
-		/*FUNCTION SeqMat(int M,int N, doubletype sparsity){{{*/
-		SeqMat(int pM,int pN, doubletype sparsity){
-
-			this->M=pM;
-			this->N=pN;
-			this->matrix=NULL;
-			if(M*N) this->matrix=xNewZeroInit<doubletype>(pM*pN);
-		}
-		/*}}}*/
-		/*FUNCTION SeqMat(int m,int n,int M,int N,int* d_nnz,int* o_nnz){{{*/
-		SeqMat(int m,int n,int pM,int pN,int* d_nnz,int* o_nnz){
-
-			this->M=pM;
-			this->N=pN;
-			this->matrix=NULL;
-			if(pM*pN) this->matrix=xNewZeroInit<doubletype>(pM*pN);
-		}
-		/*}}}*/
-		/*FUNCTION SeqMat(doubletype* serial_mat,int M,int N,doubletype sparsity){{{*/
-		SeqMat(doubletype* serial_mat,int pM,int pN,doubletype sparsity){
-
-			this->M=pM;
-			this->N=pN;
-			this->matrix=NULL;
-			if(M*N){
-				this->matrix=xNewZeroInit<doubletype>(pM*pN);
-				xMemCpy<doubletype>(this->matrix,serial_mat,pM*pN);
-			}
-
-		}
-		/*}}}*/
-		/*FUNCTION SeqMat(int M,int N, int connectivity, int numberofdofspernode){{{*/
-		SeqMat(int pM,int pN, int connectivity,int numberofdofspernode){
-
-			this->M=pM;
-			this->N=pN;
-			this->matrix=NULL;
-			if(M*N) this->matrix=xNewZeroInit<doubletype>(pM*pN);
-		}
-		/*}}}*/
-		/*FUNCTION ~SeqMat(){{{*/
-		~SeqMat(){
-
-			xDelete<doubletype>(this->matrix);
-			M=0;
-			N=0;
-		}
-		/*}}}*/
-
-		/*SeqMat specific routines */
-		/*FUNCTION Echo{{{*/
-		void Echo(void){
-
-			int i,j;
-			_printLine_("SeqMat size " << this->M << "-" << this->N);
-			for(i=0;i<M;i++){
-				for(j=0;j<N;j++){
-					_printString_(this->matrix[N*i+j] << " ");
-				}
-				_printLine_("");
-			}
-		}
-		/*}}}*/
-		/*FUNCTION Assemble{{{*/
-		void Assemble(void){
-
-			/*do nothing*/
-
-		}
-		/*}}}*/
-		/*FUNCTION Norm{{{*/
-		doubletype Norm(NormMode mode){
-
-			doubletype norm;
-			doubletype absolute;
-			int i,j;
-
-			switch(mode){
-				case NORM_INF:
-					norm=0;
-					for(i=0;i<this->M;i++){
-						absolute=0;
-						for(j=0;j<this->N;j++){
-							absolute+=fabs(this->matrix[N*i+j]);
-						}
-						norm=max(norm,absolute);
-					}
-					return norm;
-					break; 
-				default:
-					_error_("unknown norm !");
-					break;
-			}
-		}
-		/*}}}*/
-		/*FUNCTION GetSize{{{*/
-		void GetSize(int* pM,int* pN){
-
-			*pM=this->M;
-			*pN=this->N;
-
-		}
-		/*}}}*/
-		/*FUNCTION GetLocalSize{{{*/
-		void GetLocalSize(int* pM,int* pN){
-
-			*pM=this->M;
-			*pN=this->N;
-
-		}
-		/*}}}*/
-		/*FUNCTION MatMult{{{*/
-		void MatMult(SeqVec<doubletype>* X,SeqVec<doubletype>* AX){
-
-			int i,j;
-			int XM,AXM;
-			doubletype dummy;
-
-			X->GetSize(&XM);
-			AX->GetSize(&AXM);
-
-			if(M!=AXM)_error_("A and AX should have the same number of rows!");
-			if(N!=XM)_error_("A and X should have the same number of columns!");
-
-			for(i=0;i<M;i++){
-				dummy=0;
-				for(j=0;j<N;j++){
-					dummy+= this->matrix[N*i+j]*X->vector[j];
-				}
-				AX->vector[i]=dummy;
-			}
-
-		}
-		/*}}}*/
-		/*FUNCTION Duplicate{{{*/
-		SeqMat* Duplicate(void){
-
-			doubletype dummy=0;
-
-			return new SeqMat(this->matrix,this->M,this->N,dummy);
-
-		}
-		/*}}}*/
-		/*FUNCTION ToSerial{{{*/
-		doubletype* ToSerial(void){
-
-			doubletype* buffer=NULL;
-
-			if(this->M*this->N){
-				buffer=xNew<doubletype>(this->M*this->N);
-				xMemCpy<doubletype>(buffer,this->matrix,this->M*this->N);
-			}
-			return buffer;
-
-		}
-		/*}}}*/
-		/*FUNCTION SetValues{{{*/
-		void SetValues(int m,int* idxm,int n,int* idxn,doubletype* values,InsMode mode){
-
-			int i,j;
-			switch(mode){
-				case ADD_VAL:
-					for(i=0;i<m;i++) for(j=0;j<n;j++) this->matrix[N*idxm[i]+idxn[j]]+=values[n*i+j];
-					break;
-				case INS_VAL:
-					for(i=0;i<m;i++) for(j=0;j<n;j++) this->matrix[N*idxm[i]+idxn[j]]=values[n*i+j];
-					break;
-				default:
-					_error_("unknown insert mode!");
-					break;
-			}
-
-		}
-		/*}}}*/
-		/*FUNCTION Convert{{{*/
-		void Convert(MatrixType type){
-
-			/*do nothing*/
-
-		}
-		/*}}}*/		
-
-};
-
-#endif //#ifndef _SEQMAT_H_
Index: sm/trunk-jpl/src/c/toolkits/issm/SeqVec.h
===================================================================
--- /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.h	(revision 14658)
+++ 	(revision )
@@ -1,267 +1,0 @@
-/*!\file:  SeqVec.h
- * \brief wrapper to our SeqVec object, which is just a wrapper to a IssmDouble* 
- */ 
-
-#ifndef _SEQVEC_H_
-#define _SEQVEC_H_
-
-/*Headers:*/
-/*{{{*/
-#ifdef HAVE_CONFIG_H
-	#include <config.h>
-#else
-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
-#endif
-
-#include "../../shared/Exceptions/exceptions.h"
-#include "../../shared/MemOps/xMemCpy.h"
-#include "../../shared/Alloc/alloc.h"
-#include <math.h>
-#include "../../include/macros.h"
-
-/*}}}*/
-
-/*We need to template this class, in case we want to create vectors that hold IssmDouble* matrix or IssmPDouble* matrix. 
-  Such vectors would be useful for use without or with the matlab or python interface (which do not care for IssmDouble types, 
-  but only rely on IssmPDouble types)*/
-
-template <class doubletype> 
-class SeqVec{
-
-	public:
-
-		doubletype* vector;
-		int M;
-
-		/*SeqVec constructors, destructors*/
-		/*FUNCTION SeqVec(){{{*/
-		SeqVec(){
-
-			this->M=0;
-			this->vector=NULL;
-		}
-		/*}}}*/
-		/*FUNCTION SeqVec(int M){{{*/
-		SeqVec(int pM){
-
-			this->M=pM;
-			this->vector=NULL;
-			if(this->M) this->vector=xNewZeroInit<doubletype>(pM);
-		}
-		/*}}}*/
-		/*FUNCTION SeqVec(int m,int M){{{*/
-		SeqVec(int pm,int pM){
-
-			this->M=pM;
-			this->vector=NULL;
-			if(this->M) this->vector=xNewZeroInit<doubletype>(pM);
-		}
-		/*}}}*/
-		/*FUNCTION SeqVec(int M,bool fromlocalsize){{{*/
-		SeqVec(int pM,bool fromlocalsize){
-
-			this->M=pM;
-			this->vector=NULL;
-			if(this->M) this->vector=xNewZeroInit<doubletype>(pM);
-		}
-		/*}}}*/
-		/*FUNCTION SeqVec(doubletype* serial_vec,int M){{{*/
-		SeqVec(doubletype* buffer,int pM){
-
-			this->M=pM;
-			this->vector=NULL;
-			if(this->M){
-				this->vector=xNew<doubletype>(pM);
-				xMemCpy<doubletype>(this->vector,buffer,pM);
-			}
-		}
-		/*}}}*/
-		/*FUNCTION ~SeqVec(){{{*/
-		~SeqVec(){
-			xDelete<doubletype>(this->vector);
-			M=0;
-		}
-		/*}}}*/
-
-		/*SeqVec specific routines*/
-		/*FUNCTION Echo{{{*/
-		void Echo(void){
-
-			int i;
-			_printLine_("SeqVec size " << this->M);
-			for(i=0;i<M;i++){
-				_printString_(vector[i] << "\n ");
-			}
-		}
-		/*}}}*/
-		/*FUNCTION Assemble{{{*/
-		void Assemble(void){
-
-			/*do nothing*/
-
-		}
-		/*}}}*/
-		/*FUNCTION SetValues{{{*/
-		void SetValues(int ssize, int* list, doubletype* values, InsMode mode){
-
-			int i;
-			switch(mode){
-				case ADD_VAL:
-					for(i=0;i<ssize;i++) this->vector[list[i]]+=values[i];
-					break;
-				case INS_VAL:
-					for(i=0;i<ssize;i++) this->vector[list[i]]=values[i];
-					break;
-				default:
-					_error_("unknown insert mode!");
-					break;
-			}
-
-		}
-		/*}}}*/
-		/*FUNCTION SetValue{{{*/
-		void SetValue(int dof, doubletype value, InsMode mode){
-
-			switch(mode){
-				case ADD_VAL:
-					this->vector[dof]+=value;
-					break;
-				case INS_VAL:
-					this->vector[dof]=value;
-					break;
-				default:
-					_error_("unknown insert mode!");
-					break;
-			}
-		}
-		/*}}}*/
-		/*FUNCTION GetValue{{{*/
-		void GetValue(doubletype* pvalue,int dof){
-
-			*pvalue=this->vector[dof];
-
-		}
-		/*}}}*/
-		/*FUNCTION GetSize{{{*/
-		void GetSize(int* pM){
-
-			*pM=this->M;
-
-		}
-		/*}}}*/
-		/*FUNCTION GetLocalSize{{{*/
-		void GetLocalSize(int* pM){
-
-			*pM=this->M;
-
-		}
-		/*}}}*/
-		/*FUNCTION Duplicate{{{*/
-		SeqVec* Duplicate(void){
-
-			return new SeqVec(this->vector,this->M);
-
-		}
-		/*}}}*/
-		/*FUNCTION Set{{{*/
-		void Set(doubletype value){
-
-			int i;
-			for(i=0;i<this->M;i++)this->vector[i]=value;
-
-		}
-		/*}}}*/
-		/*FUNCTION AXPY{{{*/
-		void AXPY(SeqVec* X, doubletype a){
-
-			int i;
-
-			/*y=a*x+y where this->vector is y*/
-			for(i=0;i<this->M;i++)this->vector[i]=a*X->vector[i]+this->vector[i];
-
-		}
-		/*}}}*/
-		/*FUNCTION AYPX{{{*/
-		void AYPX(SeqVec* X, doubletype a){
-
-			int i;
-
-			/*y=x+a*y where this->vector is y*/
-			for(i=0;i<this->M;i++)this->vector[i]=X->vector[i]+a*this->vector[i];
-
-		}
-		/*}}}*/
-		/*FUNCTION ToMPISerial{{{*/
-		doubletype* ToMPISerial(void){
-
-			doubletype* buffer=NULL;
-
-			if(this->M){
-				buffer=xNew<doubletype>(this->M);
-				xMemCpy<doubletype>(buffer,this->vector,this->M);
-			}
-			return buffer;
-
-		}
-		/*}}}*/
-		/*FUNCTION Copy{{{*/
-		void Copy(SeqVec* to){
-
-			int i;
-
-			to->M=this->M;
-			for(i=0;i<this->M;i++)to->vector[i]=this->vector[i];
-
-		}
-		/*}}}*/
-		/*FUNCTION Norm{{{*/
-		doubletype Norm(NormMode mode){
-
-			doubletype norm;
-			int i;
-
-			switch(mode){
-				case NORM_INF:
-					norm=0; for(i=0;i<this->M;i++)norm=max(norm,fabs(this->vector[i]));
-					return norm;
-					break;
-				case NORM_TWO:
-					norm=0; 
-					for(i=0;i<this->M;i++)norm+=pow(this->vector[i],2);
-					return sqrt(norm);
-					break;
-				default:
-					_error_("unknown norm !");
-					break;
-			}
-		}
-		/*}}}*/
-		/*FUNCTION Scale{{{*/
-		void Scale(doubletype scale_factor){
-
-			int i;
-			for(i=0;i<this->M;i++)this->vector[i]=scale_factor*this->vector[i];
-
-		}
-		/*}}}*/
-		/*FUNCTION Dot{{{*/
-		doubletype Dot(SeqVec* input){
-
-			int i;
-
-			doubletype dot=0;
-			for(i=0;i<this->M;i++)dot+=this->vector[i]*input->vector[i];
-			return dot;
-
-		}
-		/*}}}*/
-		/*FUNCTION PointwiseDivide{{{*/
-		void PointwiseDivide(SeqVec* x,SeqVec* y){
-
-			int i;
-			/*pointwise w=x/y where this->vector is w: */
-			for(i=0;i<this->M;i++)this->vector[i]=x->vector[i]/y->vector[i];
-		}
-		/*}}}*/
-};
-#endif //#ifndef _SEQVEC_H_