int main(int argc,char **args)
{
Mat A,C,Bdense,Cdense;
PetscErrorCode ierr;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscBool flg,viewmats=PETSC_FALSE;
PetscMPIInt rank,size;
PetscReal fill=1.0;
PetscInt m,n,i,j,BN=10,rstart,rend,*rows,*cols;
PetscScalar *Barray,*Carray,rval,*array;
Vec x,y;
PetscRandom rand;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Print (for testing only) */
ierr = PetscOptionsHasName(NULL, "-view_mats", &viewmats);CHKERRQ(ierr);
if (viewmats) {
if (!rank) printf("A_aij:\n");
ierr = MatView(A,0);CHKERRQ(ierr);
}
/* Test MatTransposeMatMult_aij_aij() */
ierr = MatTransposeMatMult(A,A,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr);
if (viewmats) {
if (!rank) printf("\nC = A_aij^T * A_aij:\n");
ierr = MatView(C,0);CHKERRQ(ierr);
}
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
/* create a dense matrix Bdense */
ierr = MatCreate(PETSC_COMM_WORLD,&Bdense);CHKERRQ(ierr);
ierr = MatSetSizes(Bdense,m,PETSC_DECIDE,PETSC_DECIDE,BN);CHKERRQ(ierr);
ierr = MatSetType(Bdense,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(Bdense);CHKERRQ(ierr);
ierr = MatSetUp(Bdense);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Bdense,&rstart,&rend);CHKERRQ(ierr);
//printf("[%d] rstart/end %d %d; local size %d %d\n",rank,rstart,rend,m,n);
ierr = PetscMalloc3(m,PetscInt,&rows,BN,PetscInt,&cols,m*BN,PetscScalar,&array);CHKERRQ(ierr);
for (i=0; i<m; i++) rows[i] = rstart + i;
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
for (j=0; j<BN; j++) {
cols[j] = j;
for (i=0; i<m; i++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[m*j+i] = rval;
}
}
ierr = MatSetValues(Bdense,m,rows,BN,cols,array,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Bdense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Bdense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFree3(rows,cols,array);CHKERRQ(ierr);
if (viewmats) {
if (!rank) printf("\nBdense:\n");
ierr = MatView(Bdense,0);CHKERRQ(ierr);
}
/* Test MatTransposeMatMult_aij_dense() */
ierr = MatTransposeMatMult(A,Bdense,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr);
ierr = MatTransposeMatMult(A,Bdense,MAT_REUSE_MATRIX,fill,&C);CHKERRQ(ierr);
if (viewmats) {
if (!rank) printf("\nC=A^T*Bdense:\n");
ierr = MatView(C,0);CHKERRQ(ierr);
}
/* Check accuracy */
ierr = MatCreate(PETSC_COMM_WORLD,&Cdense);CHKERRQ(ierr);
ierr = MatSetSizes(Cdense,n,PETSC_DECIDE,PETSC_DECIDE,BN);CHKERRQ(ierr);
ierr = MatSetType(Cdense,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(Cdense);CHKERRQ(ierr);
ierr = MatSetUp(Cdense);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Cdense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cdense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size == 1) {
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,m,NULL,&x);CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,n,NULL,&y);CHKERRQ(ierr);
} else {
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,m,PETSC_DECIDE,NULL,&x);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&y);CHKERRQ(ierr);
}
/* Cdense[:,j] = A^T * Bdense[:,j] */
ierr = MatDenseGetArray(Bdense,&Barray);CHKERRQ(ierr);
ierr = MatDenseGetArray(Cdense,&Carray);CHKERRQ(ierr);
for (j=0; j<BN; j++) {
ierr = VecPlaceArray(x,Barray);CHKERRQ(ierr);
ierr = VecPlaceArray(y,Carray);CHKERRQ(ierr);
ierr = MatMultTranspose(A,x,y);CHKERRQ(ierr);
ierr = VecResetArray(x);CHKERRQ(ierr);
ierr = VecResetArray(y);CHKERRQ(ierr);
Barray += m;
Carray += n;
}
ierr = MatDenseRestoreArray(Bdense,&Barray);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(Cdense,&Carray);CHKERRQ(ierr);
if (viewmats) {
if (!rank) printf("\nCdense:\n");
ierr = MatView(Cdense,0);CHKERRQ(ierr);
}
ierr = MatEqual(C,Cdense,&flg);CHKERRQ(ierr);
if (!flg) {
if (!rank) printf(" C != Cdense\n");
}
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&Bdense);CHKERRQ(ierr);
ierr = MatDestroy(&Cdense);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
static char help[] = "MatLoad test for loading matrices that are created by DMCreateMatrix() and\n\
stored in binary via MatView_MPI_DA.MatView_MPI_DA stores the matrix\n\
in natural ordering. Hence MatLoad() has to read the matrix first in\n\
natural ordering and then permute it back to the application ordering.This\n\
example is used for testing the subroutine MatLoad_MPI_DA\n\n";
#include <petscdm.h>
#include <petscdmda.h>
int main(int argc,char **argv)
{
PetscInt X = 10,Y = 8,Z=8;
PetscErrorCode ierr;
DM da;
PetscViewer viewer;
Mat A;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(NULL,NULL,"-X",&X,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-Y",&Y,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-Z",&Z,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,X,Y,Z,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr);
int main(int argc,char **args)
{
KSP subksp;
Mat A,subA;
Vec x,b,u,subb,subx,subu;
PetscViewer fd;
char file[PETSC_MAX_PATH_LEN];
PetscBool flg;
PetscErrorCode ierr;
PetscInt i,m,n,its;
PetscReal norm;
PetscMPIInt rank,size;
MPI_Comm comm,subcomm;
PetscSubcomm psubcomm;
PetscInt nsubcomm=1,id;
PetscScalar *barray,*xarray,*uarray,*array,one=1.0;
PetscInt type=1;
PetscInitialize(&argc,&args,(char*)0,help);
/* Load the matrix */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/* Load the matrix; then destroy the viewer.*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
/* Create rhs vector b */
ierr = MatGetLocalSize(A,&m,NULL);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecSetSizes(b,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
ierr = VecSet(b,one);CHKERRQ(ierr);
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
ierr = VecDuplicate(b,&u);CHKERRQ(ierr);
ierr = VecSet(x,0.0);CHKERRQ(ierr);
/* Test MatGetMultiProcBlock() */
ierr = PetscOptionsGetInt(NULL,"-nsubcomm",&nsubcomm,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-subcomm_type",&type,NULL);CHKERRQ(ierr);
ierr = PetscSubcommCreate(comm,&psubcomm);CHKERRQ(ierr);
ierr = PetscSubcommSetNumber(psubcomm,nsubcomm);CHKERRQ(ierr);
if (type == PETSC_SUBCOMM_GENERAL) { /* user provides color, subrank and duprank */
PetscMPIInt color,subrank,duprank,subsize;
duprank = size-1 - rank;
subsize = size/nsubcomm;
if (subsize*nsubcomm != size) SETERRQ2(comm,PETSC_ERR_SUP,"This example requires nsubcomm %D divides nproc %D",nsubcomm,size);
color = duprank/subsize;
subrank = duprank - color*subsize;
ierr = PetscSubcommSetTypeGeneral(psubcomm,color,subrank,duprank);CHKERRQ(ierr);
} else if (type == PETSC_SUBCOMM_CONTIGUOUS) {
ierr = PetscSubcommSetType(psubcomm,PETSC_SUBCOMM_CONTIGUOUS);CHKERRQ(ierr);
} else if (type == PETSC_SUBCOMM_INTERLACED) {
ierr = PetscSubcommSetType(psubcomm,PETSC_SUBCOMM_INTERLACED);CHKERRQ(ierr);
} else SETERRQ1(psubcomm->parent,PETSC_ERR_SUP,"PetscSubcommType %D is not supported yet",type);
subcomm = psubcomm->comm;
ierr = PetscOptionsHasName(NULL, "-subcomm_view", &flg);CHKERRQ(ierr);
if (flg) {
PetscMPIInt subsize,subrank,duprank;
ierr = MPI_Comm_size((MPI_Comm)subcomm,&subsize);CHKERRQ(ierr);
ierr = MPI_Comm_rank((MPI_Comm)subcomm,&subrank);CHKERRQ(ierr);
ierr = MPI_Comm_rank((MPI_Comm)psubcomm->dupparent,&duprank);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(comm,"[%D], color %D, sub-size %D, sub-rank %D, duprank %D\n",rank,psubcomm->color,subsize,subrank,duprank);
ierr = PetscSynchronizedFlush(comm);CHKERRQ(ierr);
}
/* Create subA */
ierr = MatGetMultiProcBlock(A,subcomm,MAT_INITIAL_MATRIX,&subA);CHKERRQ(ierr);
/* Create sub vectors without arrays. Place b's and x's local arrays into subb and subx */
ierr = MatGetLocalSize(subA,&m,&n);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(subcomm,1,m,PETSC_DECIDE,NULL,&subb);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(subcomm,1,n,PETSC_DECIDE,NULL,&subx);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(subcomm,1,n,PETSC_DECIDE,NULL,&subu);CHKERRQ(ierr);
ierr = VecGetArray(b,&barray);CHKERRQ(ierr);
ierr = VecGetArray(x,&xarray);CHKERRQ(ierr);
ierr = VecGetArray(u,&uarray);CHKERRQ(ierr);
ierr = VecPlaceArray(subb,barray);CHKERRQ(ierr);
ierr = VecPlaceArray(subx,xarray);CHKERRQ(ierr);
ierr = VecPlaceArray(subu,uarray);CHKERRQ(ierr);
/* Create linear solvers associated with subA */
ierr = KSPCreate(subcomm,&subksp);CHKERRQ(ierr);
ierr = KSPSetOperators(subksp,subA,subA,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPSetFromOptions(subksp);CHKERRQ(ierr);
/* Solve sub systems */
ierr = KSPSolve(subksp,subb,subx);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(subksp,&its);CHKERRQ(ierr);
/* check residual */
ierr = MatMult(subA,subx,subu);CHKERRQ(ierr);
ierr = VecAXPY(subu,-1.0,subb);CHKERRQ(ierr);
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
if (norm > 1.e-4 && !rank) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%D] Number of iterations = %3D\n",rank,its);CHKERRQ(ierr);
printf("Error: Residual norm of each block |subb - subA*subx |= %G\n",norm);
}
ierr = VecResetArray(subb);CHKERRQ(ierr);
ierr = VecResetArray(subx);CHKERRQ(ierr);
ierr = VecResetArray(subu);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-subvec_view",&id,&flg);CHKERRQ(ierr);
if (flg && rank == id) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%D] subb:\n", rank);
ierr = VecGetArray(subb,&array);CHKERRQ(ierr);
for (i=0; i<m; i++) printf("%G\n",PetscRealPart(array[i]));
ierr = VecRestoreArray(subb,&array);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"[%D] subx:\n", rank);
ierr = VecGetArray(subx,&array);CHKERRQ(ierr);
for (i=0; i<m; i++) printf("%G\n",PetscRealPart(array[i]));
ierr = VecRestoreArray(subx,&array);CHKERRQ(ierr);
}
ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr);
ierr = VecRestoreArray(b,&barray);CHKERRQ(ierr);
ierr = VecRestoreArray(u,&uarray);CHKERRQ(ierr);
ierr = MatDestroy(&subA);CHKERRQ(ierr);
ierr = VecDestroy(&subb);CHKERRQ(ierr);
ierr = VecDestroy(&subx);CHKERRQ(ierr);
ierr = VecDestroy(&subu);CHKERRQ(ierr);
ierr = KSPDestroy(&subksp);CHKERRQ(ierr);
ierr = PetscSubcommDestroy(&psubcomm);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A;
PetscInt i,j,m = 3,n = 2,rstart,rend;
PetscErrorCode ierr;
PetscScalar v,*array;
PetscViewer view;
PetscInitialize(&argc,&args,(char*)0,help);
/*
Create a parallel dense matrix shared by all processors
*/
ierr = MatCreateDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,m,n,NULL,&A);CHKERRQ(ierr);
/*
Set values into the matrix
*/
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = 9.0/(i+j+1); ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
Print the matrix to the screen
*/
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Print the local portion of the matrix to the screen
*/
ierr = MatDenseGetArray(A,&array);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
for (j=0; j<n; j++) {
PetscSynchronizedPrintf(PETSC_COMM_WORLD,"%6.4e ",(double)PetscRealPart(array[j*(rend-rstart)+i-rstart]));
}
PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\n");
}
PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
ierr = MatDenseRestoreArray(A,&array);CHKERRQ(ierr);
/*
Store the binary matrix to a file
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, "matrix.dat", FILE_MODE_WRITE, &view);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view,PETSC_VIEWER_NATIVE);CHKERRQ(ierr);
ierr = MatView(A,view);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
/*
Now reload the matrix and view it
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_READ,&view);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATMPIDENSE);CHKERRQ(ierr);
ierr = MatLoad(A,view);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A,B,Y; /*input : the three imput matrix */
Mat P; /* P=QR factorization*/
PetscViewer fd1,fd2;
char file[4][PETSC_MAX_PATH_LEN];
//Mat C; /*C=B*Y*/
PetscInt m,n; /*size of matrix C;*/
Mat E,X; /*lhs and rhs of the linear equations;*/
Vec b,x; /*column vector of rhs;*/
KSP ksp; /* linear solver context */
PetscErrorCode ierr;
PetscInt i,its; /*iteration numbers of KSP*/
PetscBool flg;
m=10;
n=4;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscOptionsGetString(NULL,"-fa",file[0],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix A!\n");}
ierr = PetscOptionsGetString(NULL,"-fb",file[1],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix B!\n");}
ierr = PetscOptionsGetString(NULL,"-fy",file[2],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix Y!\n");}
ierr = PetscOptionsGetString(NULL,"-fp",file[3],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix P!\n");}
/*Load the matrices*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[0],FILE_MODE_READ,&fd1);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[1],FILE_MODE_READ,&fd2);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatLoad(A,fd1);CHKERRQ(ierr);
ierr = MatLoad(B,fd2);CHKERRQ(ierr);
readmm(file[2], &Y);
readmm(file[3], &P);
ierr = PetscPrintf(PETSC_COMM_SELF,"Read file completes.\n");CHKERRQ(ierr);
#if(cxDEBUG==1)
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
Mat Q1;
ierr = MatCreate(PETSC_COMM_WORLD, &Q1); CHKERRQ(ierr);
ierr = MatSetFromOptions(Q1); CHKERRQ(ierr);
ierr = MatMatMult(B,Y,MAT_INITIAL_MATRIX,PETSC_DEFAULT, &Q1);CHKERRQ(ierr);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"Cao this is BY.\n");CHKERRQ(ierr);
ierr = MatView(Q1,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
getQ1(&Q1);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nTHIS IS Q1.\n");CHKERRQ(ierr);
ierr = MatView(Q1,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
Mat SBP;
ierr = MatMatTransposeMult(Q1,Q1,MAT_INITIAL_MATRIX, PETSC_DEFAULT ,&SBP);
ierr = MatAssemblyBegin(SBP,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(SBP,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatShift(SBP,-1);
ierr = MatScale(SBP,-1);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nTHIS IS SBP = Q1*Q1'.\n");CHKERRQ(ierr);
ierr = MatView(SBP,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBelows is act_P.\n");CHKERRQ(ierr);
ierr = MatView(P ,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
ierr = MatMatMult(A,Y,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&E);CHKERRQ(ierr);
ierr = MatMatMult(SBP,E,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&E);CHKERRQ(ierr);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBelows is PAY.\n");CHKERRQ(ierr);
ierr = MatView(E,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
ierr = MatAssemblyBegin(E,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(E,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
//ierr = MatGetSize(E,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = MatSetSizes(X,PETSC_DECIDE,PETSC_DECIDE,m,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(X);CHKERRQ(ierr);
ierr = MatSetUp(X); CHKERRQ(ierr);
ierr = MatZeroEntries(X);CHKERRQ(ierr);
ierr = MatAssemblyBegin(X,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(X,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
// PetscInt ix[m];
// for(i=0;i<m;i++){
// ix[i] = i;
// }
VecCreate(PETSC_COMM_WORLD,&b);
VecSetSizes(b,PETSC_DECIDE,m);
VecSetFromOptions(b);
VecCreate(PETSC_COMM_WORLD,&x);
VecSetSizes(x,PETSC_DECIDE,m);
VecSetFromOptions(x);
//#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBEFORE CG Check A\n");CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBEFORE CG Check SBP\n");CHKERRQ(ierr);
ierr = MatView(SBP,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBEFORE CG Check E\n");CHKERRQ(ierr);
ierr = MatView(E,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
//#endif
for(i=0;i<n;i++){
MatGetColumnVector(E,b,i);
PetscPrintf(PETSC_COMM_WORLD,"the rhs\n");
VecView(b,PETSC_VIEWER_STDOUT_WORLD);
KSPCreate(PETSC_COMM_WORLD,&ksp);
KSPSetOperators(ksp,A,SBP);
KSPSetNormType(ksp,KSP_NORM_UNPRECONDITIONED);
KSPSetCheckNormIteration(ksp,-1);
KSPSetTolerances(ksp,1.0e-06,PETSC_DEFAULT,PETSC_DEFAULT,400);
KSPSetInitialGuessNonzero(ksp,PETSC_FALSE);
KSPSetFromOptions(ksp);
KSPSolve(ksp,b,x);
KSPGetIterationNumber(ksp,&its);
PetscPrintf(PETSC_COMM_WORLD,"%d-th equation,iteration=%D\n",i,its);
VecView(x,PETSC_VIEWER_STDOUT_WORLD);
}
return 0;
}
Example: mpiexec -n <np> ./ex130 -f <matrix binary file> -mat_solver_type 1 -mat_superlu_equil \n\n";
#include <petscmat.h>
int main(int argc,char **args)
{
Mat A,F;
Vec u,x,b;
PetscErrorCode ierr;
PetscMPIInt rank,size;
PetscInt m,n,nfact,ipack=0;
PetscReal norm,tol=1.e-12,Anorm;
IS perm,iperm;
MatFactorInfo info;
PetscBool flg,testMatSolve=PETSC_TRUE;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecLoad(b,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
if (m != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "This example is not intended for rectangular matrices (%d, %d)", m, n);
ierr = MatNorm(A,NORM_INFINITY,&Anorm);CHKERRQ(ierr);
/* Create vectors */
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */
/* Test LU Factorization */
ierr = MatGetOrdering(A,MATORDERINGNATURAL,&perm,&iperm);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mat_solver_type",&ipack,NULL);CHKERRQ(ierr);
switch (ipack) {
case 1:
#if defined(PETSC_HAVE_SUPERLU)
if (!rank) printf(" SUPERLU LU:\n");
ierr = MatGetFactor(A,MATSOLVERSUPERLU,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
break;
#endif
case 2:
#if defined(PETSC_HAVE_MUMPS)
if (!rank) printf(" MUMPS LU:\n");
ierr = MatGetFactor(A,MATSOLVERMUMPS,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
{
/* test mumps options */
PetscInt icntl_7 = 5;
ierr = MatMumpsSetIcntl(F,7,icntl_7);CHKERRQ(ierr);
}
break;
#endif
default:
if (!rank) printf(" PETSC LU:\n");
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
}
info.fill = 5.0;
ierr = MatLUFactorSymbolic(F,A,perm,iperm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 1; nfact++) {
if (!rank) printf(" %d-the LU numfactorization \n",nfact);
ierr = MatLUFactorNumeric(F,A,&info);CHKERRQ(ierr);
/* Test MatSolve() */
if (testMatSolve) {
ierr = MatSolve(F,b,x);CHKERRQ(ierr);
/* Check the residual */
ierr = MatMult(A,x,u);CHKERRQ(ierr);
ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(u,NORM_INFINITY,&norm);CHKERRQ(ierr);
if (norm > tol) {
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatSolve: rel residual %g/%g = %g, LU numfact %d\n",norm,Anorm,norm/Anorm,nfact);CHKERRQ(ierr);
}
}
}
}
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = ISDestroy(&iperm);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void readMat(Mat_dh *Aout, char *ft, char *fn, HYPRE_Int ignore)
{
START_FUNC_DH
bool makeStructurallySymmetric;
bool fixDiags;
*Aout = NULL;
makeStructurallySymmetric =
Parser_dhHasSwitch(parser_dh, "-makeSymmetric");
fixDiags =
Parser_dhHasSwitch(parser_dh, "-fixDiags");
if (fn == NULL) {
SET_V_ERROR("passed NULL filename; can't open for reading!");
}
if (!strcmp(ft, "csr"))
{
Mat_dhReadCSR(Aout, fn); CHECK_V_ERROR;
}
else if (!strcmp(ft, "trip"))
{
Mat_dhReadTriples(Aout, ignore, fn); CHECK_V_ERROR;
}
else if (!strcmp(ft, "ebin"))
{
Mat_dhReadBIN(Aout, fn); CHECK_V_ERROR;
}
#ifdef PETSC_MODE
else if (!strcmp(ft, "petsc")) {
Viewer_DH viewer;
Mat Apetsc;
HYPRE_Int ierr;
ierr = ViewerBinaryOpen_DH(comm_dh, fn, BINARY_RDONLY_DH, &viewer);
if (ierr) { SET_V_ERROR("ViewerBinaryOpen failed! [PETSc lib]"); }
ierr = MatLoad(viewer, MATSEQAIJ, &Apetsc);
if (ierr) { SET_V_ERROR("MatLoad failed! [PETSc lib]"); }
ierr = ViewerDestroy_DH(viewer);
if (ierr) { SET_V_ERROR("ViewerDestroy failed! [PETSc lib]"); }
ierr = convertPetscToEuclidMat(Apetsc, Aout);
if (ierr) { SET_V_ERROR("convertPetscToEuclidMat failed!"); }
ierr = MatDestroy(Apetsc);
if (ierr) { SET_V_ERROR("MatDestroy failed! [PETSc lib]"); }
}
#else
else if (!strcmp(ft, "petsc")) {
hypre_sprintf(msgBuf_dh, "must recompile Euclid using petsc mode!");
SET_V_ERROR(msgBuf_dh);
}
#endif
else
{
hypre_sprintf(msgBuf_dh, "unknown filetype: -ftin %s", ft);
SET_V_ERROR(msgBuf_dh);
}
if (makeStructurallySymmetric) {
hypre_printf("\npadding with zeros to make structurally symmetric\n");
Mat_dhMakeStructurallySymmetric(*Aout); CHECK_V_ERROR;
}
if ( (*Aout)->m == 0) {
SET_V_ERROR("row count = 0; something's wrong!");
}
if (fixDiags) {
fix_diags_private(*Aout); CHECK_V_ERROR;
}
END_FUNC_DH
}
int main(int argc, char **args)
{
Mat A, L;
AppCtx ctx;
PetscViewer viewer;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &args, (char *) 0, help);CHKERRQ(ierr);
ierr = ProcessOptions(&ctx);CHKERRQ(ierr);
/* Load matrix */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, ctx.matFilename, FILE_MODE_READ, &viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatLoad(A, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
/* Make graph Laplacian from matrix */
ierr = MatLaplacian(A, 1.0e-12, &L);CHKERRQ(ierr);
/* Check Laplacian */
PetscReal norm;
Vec x, y;
ierr = MatGetVecs(L, &x, NULL);CHKERRQ(ierr);
ierr = VecDuplicate(x, &y);CHKERRQ(ierr);
ierr = VecSet(x, 1.0);CHKERRQ(ierr);
ierr = MatMult(L, x, y);CHKERRQ(ierr);
ierr = VecNorm(y, NORM_INFINITY, &norm);CHKERRQ(ierr);
if (norm > 1.0e-10) SETERRQ(PetscObjectComm((PetscObject) y), PETSC_ERR_PLIB, "Invalid graph Laplacian");
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
/* Compute Fiedler vector, and perhaps more vectors */
Mat LD;
PetscScalar *a, *realpart, *imagpart, *eigvec, *work, sdummy;
PetscBLASInt bn, bN, lwork, lierr, idummy;
PetscInt n, i;
ierr = MatConvert(L, MATDENSE, MAT_INITIAL_MATRIX, &LD);CHKERRQ(ierr);
ierr = MatGetLocalSize(LD, &n, NULL);CHKERRQ(ierr);
ierr = MatDenseGetArray(LD, &a);CHKERRQ(ierr);
ierr = PetscBLASIntCast(n, &bn);CHKERRQ(ierr);
ierr = PetscBLASIntCast(n, &bN);CHKERRQ(ierr);
ierr = PetscBLASIntCast(5*n,&lwork);CHKERRQ(ierr);
ierr = PetscBLASIntCast(1,&idummy);CHKERRQ(ierr);
ierr = PetscMalloc4(n,PetscScalar,&realpart,n,PetscScalar,&imagpart,n*n,PetscScalar,&eigvec,lwork,PetscScalar,&work);CHKERRQ(ierr);
ierr = PetscFPTrapPush(PETSC_FP_TRAP_OFF);CHKERRQ(ierr);
PetscStackCall("LAPACKgeev", LAPACKgeev_("N","V",&bn,a,&bN,realpart,imagpart,&sdummy,&idummy,eigvec,&bN,work,&lwork,&lierr));
if (lierr) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in LAPACK routine %d", (int) lierr);
ierr = PetscFPTrapPop();CHKERRQ(ierr);
PetscReal *r, *c;
PetscInt *perm;
ierr = PetscMalloc3(n,PetscInt,&perm,n,PetscReal,&r,n,PetscReal,&c);CHKERRQ(ierr);
for (i = 0; i < n; ++i) perm[i] = i;
ierr = PetscSortRealWithPermutation(n,realpart,perm);CHKERRQ(ierr);
for (i = 0; i < n; ++i) {
r[i] = realpart[perm[i]];
c[i] = imagpart[perm[i]];
}
for (i = 0; i < n; ++i) {
realpart[i] = r[i];
imagpart[i] = c[i];
}
/* Output spectrum */
if (ctx.showSpectrum) {
ierr = PetscPrintf(PETSC_COMM_SELF, "Spectrum\n");CHKERRQ(ierr);
for (i = 0; i < n; ++i) {ierr = PetscPrintf(PETSC_COMM_SELF, "%d: Real %g Imag %g\n", i, realpart[i], imagpart[i]);CHKERRQ(ierr);}
}
/* Check lowest eigenvalue and eigenvector */
PetscInt evInd = perm[0];
if ((realpart[0] > 1.0e-12) || (imagpart[0] > 1.0e-12)) SETERRQ(PetscObjectComm((PetscObject) L), PETSC_ERR_PLIB, "Graph Laplacian must have lowest eigenvalue 0");
for (i = 0; i < n; ++i) {
if (fabs(eigvec[evInd*n+i] - eigvec[evInd*n+0]) > 1.0e-10) SETERRQ3(PetscObjectComm((PetscObject) L), PETSC_ERR_PLIB, "Graph Laplacian must have constant lowest eigenvector ev_%d %g != ev_0 %g", i, eigvec[evInd*n+i], eigvec[evInd*n+0]);
}
/* Output Fiedler vector */
evInd = perm[1];
if (ctx.showFiedler) {
ierr = PetscPrintf(PETSC_COMM_SELF, "Fiedler vector, Re{ev} %g\n", realpart[1]);CHKERRQ(ierr);
for (i = 0; i < n; ++i) {ierr = PetscPrintf(PETSC_COMM_SELF, "%d: %g\n", i, eigvec[evInd*n+i]);CHKERRQ(ierr);}
}
/* Construct Fiedler partition */
IS fIS, fIS2;
PetscInt *fperm, *fperm2, pos, neg, posSize = 0;
ierr = PetscMalloc(n * sizeof(PetscInt), &fperm);CHKERRQ(ierr);
for (i = 0; i < n; ++i) {
if (eigvec[evInd*n+i] > 0.0) ++posSize;
}
ierr = PetscMalloc(n * sizeof(PetscInt), &fperm2);CHKERRQ(ierr);
for (i = 0; i < n; ++i) fperm[i] = i;
ierr = PetscSortRealWithPermutation(n, &eigvec[evInd*n], fperm);CHKERRQ(ierr);
for (i = 0; i < n; ++i) fperm2[n-1-i] = fperm[i];
for (i = 0, pos = 0, neg = posSize; i < n; ++i) {
if (eigvec[evInd*n+i] > 0.0) fperm[pos++] = i;
else fperm[neg++] = i;
}
ierr = ISCreateGeneral(PetscObjectComm((PetscObject) L), n, fperm, PETSC_OWN_POINTER, &fIS);CHKERRQ(ierr);
ierr = ISSetPermutation(fIS);CHKERRQ(ierr);
ierr = ISCreateGeneral(PetscObjectComm((PetscObject) L), n, fperm2, PETSC_OWN_POINTER, &fIS2);CHKERRQ(ierr);
ierr = ISSetPermutation(fIS2);CHKERRQ(ierr);
ierr = PetscFree3(perm,r,c);CHKERRQ(ierr);
ierr = PetscFree4(realpart,imagpart,eigvec,work);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(LD, &a);CHKERRQ(ierr);
ierr = MatDestroy(&LD);CHKERRQ(ierr);
ierr = MatDestroy(&L);CHKERRQ(ierr);
/* Permute matrix */
Mat AR, AR2;
ierr = MatPermute(A, fIS, fIS, &AR);CHKERRQ(ierr);
ierr = MatView(A, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = MatView(AR, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = ISDestroy(&fIS);CHKERRQ(ierr);
ierr = MatPermute(A, fIS2, fIS2, &AR2);CHKERRQ(ierr);
ierr = MatView(AR2, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = ISDestroy(&fIS2);CHKERRQ(ierr);
ierr = MatDestroy(&AR);CHKERRQ(ierr);
AR = AR2;
/* Extract blocks and reorder */
Mat AP, AN, APR, ANR;
IS ispos, isneg, rpermpos, cpermpos, rpermneg, cpermneg;
PetscInt bw, bwr;
ierr = ISCreateStride(PETSC_COMM_SELF, posSize, 0, 1, &ispos);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF, n - posSize, posSize, 1, &isneg);CHKERRQ(ierr);
ierr = MatGetSubMatrix(AR, ispos, ispos, MAT_INITIAL_MATRIX, &AP);CHKERRQ(ierr);
ierr = MatGetSubMatrix(AR, isneg, isneg, MAT_INITIAL_MATRIX, &AN);CHKERRQ(ierr);
ierr = ISDestroy(&ispos);CHKERRQ(ierr);
ierr = ISDestroy(&isneg);CHKERRQ(ierr);
ierr = MatGetOrdering(AP, ctx.matOrdtype, &rpermpos, &cpermpos);CHKERRQ(ierr);
ierr = MatGetOrdering(AN, ctx.matOrdtype, &rpermneg, &cpermneg);CHKERRQ(ierr);
ierr = MatPermute(AP, rpermpos, cpermpos, &APR);CHKERRQ(ierr);
ierr = MatComputeBandwidth(AP, 0.0, &bw);CHKERRQ(ierr);
ierr = MatComputeBandwidth(APR, 0.0, &bwr);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Reduced positive bandwidth from %d to %d\n", bw, bwr);CHKERRQ(ierr);
ierr = MatPermute(AN, rpermneg, cpermneg, &ANR);CHKERRQ(ierr);
ierr = MatComputeBandwidth(AN, 0.0, &bw);CHKERRQ(ierr);
ierr = MatComputeBandwidth(ANR, 0.0, &bwr);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Reduced negative bandwidth from %d to %d\n", bw, bwr);CHKERRQ(ierr);
ierr = MatView(AP, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = MatView(APR, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = MatView(AN, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = MatView(ANR, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
/* Reorder original matrix */
Mat ARR;
IS rperm, cperm;
PetscInt *idx;
const PetscInt *cidx;
ierr = PetscMalloc(n * sizeof(PetscInt), &idx);CHKERRQ(ierr);
ierr = ISGetIndices(rpermpos, &cidx);CHKERRQ(ierr);
for (i = 0; i < posSize; ++i) idx[i] = cidx[i];
ierr = ISRestoreIndices(rpermpos, &cidx);CHKERRQ(ierr);
ierr = ISGetIndices(rpermneg, &cidx);CHKERRQ(ierr);
for (i = posSize; i < n; ++i) idx[i] = cidx[i-posSize] + posSize;
ierr = ISRestoreIndices(rpermneg, &cidx);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF, n, idx, PETSC_OWN_POINTER, &rperm);CHKERRQ(ierr);
ierr = ISSetPermutation(rperm);CHKERRQ(ierr);
ierr = PetscMalloc(n * sizeof(PetscInt), &idx);CHKERRQ(ierr);
ierr = ISGetIndices(cpermpos, &cidx);CHKERRQ(ierr);
for (i = 0; i < posSize; ++i) idx[i] = cidx[i];
ierr = ISRestoreIndices(cpermpos, &cidx);CHKERRQ(ierr);
ierr = ISGetIndices(cpermneg, &cidx);CHKERRQ(ierr);
for (i = posSize; i < n; ++i) idx[i] = cidx[i-posSize] + posSize;
ierr = ISRestoreIndices(cpermneg, &cidx);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF, n, idx, PETSC_OWN_POINTER, &cperm);CHKERRQ(ierr);
ierr = ISSetPermutation(cperm);CHKERRQ(ierr);
ierr = MatPermute(AR, rperm, cperm, &ARR);CHKERRQ(ierr);
ierr = MatView(ARR, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = ISDestroy(&rperm);CHKERRQ(ierr);
ierr = ISDestroy(&cperm);CHKERRQ(ierr);
ierr = ISDestroy(&rpermpos);CHKERRQ(ierr);
ierr = ISDestroy(&cpermpos);CHKERRQ(ierr);
ierr = ISDestroy(&rpermneg);CHKERRQ(ierr);
ierr = ISDestroy(&cpermneg);CHKERRQ(ierr);
ierr = MatDestroy(&AP);CHKERRQ(ierr);
ierr = MatDestroy(&AN);CHKERRQ(ierr);
ierr = MatDestroy(&APR);CHKERRQ(ierr);
ierr = MatDestroy(&ANR);CHKERRQ(ierr);
/* Compare bands */
Mat B, BR;
ierr = MatCreateSubMatrixBanded(A, 50, 0.95, &B);CHKERRQ(ierr);
ierr = MatCreateSubMatrixBanded(ARR, 50, 0.95, &BR);CHKERRQ(ierr);
ierr = MatView(B, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = MatView(BR, PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&BR);CHKERRQ(ierr);
/* Cleanup */
ierr = MatDestroy(&ARR);CHKERRQ(ierr);
ierr = MatDestroy(&AR);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A; /* linear system matrix */
PetscErrorCode ierr;
PetscMPIInt rank=0;
PetscBool flg;
PetscViewer fd; /* viewer */
PetscViewer log;
char file[PETSC_MAX_PATH_LEN];
char logfile[PETSC_MAX_PATH_LEN];
char lockfile[PETSC_MAX_PATH_LEN], tmpstr[PETSC_MAX_PATH_LEN], dirname[PETSC_MAX_PATH_LEN], matrix[PETSC_MAX_PATH_LEN];
char hash[20];
PetscLogDouble solveTime,endTime,startTime;
PetscInt its;
PetscReal norm;
KSP ksp; // Linear solver context
Vec b,x,u; // RHS, solution, vector for norm calculation
PetscScalar one = 1.0;
PetscInt m, n, i;
FILE *lock;
/*
if (rank == 0) {
printf("Command line arguments:\n");
for (i=0; i < argc; i++)
printf("%d: %s\n", i, args[i]);
}
// Save args
int argcount = argc;
char **argv = (char**) malloc (argc*sizeof(char*));
for (i=0; i < argc; i++) {
argv[i] = (char*) malloc(strlen(args[i]) + 1);
strcpy(argv[i],args[i]);
}
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
*/
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-hash",hash,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) {
strcpy(hash,"nohash");
}
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) {
PetscPrintf(PETSC_COMM_WORLD,"Must indicate matrix file with the -f option");
}
/* Create lock file */
if (rank == 0) {
for (i = strlen(file); i> 0; i--) if (file[i] == '.') break;
strncpy(tmpstr, file, i-1);
for (i = strlen(tmpstr); i> 0; i--) if (file[i] == '/') break;
strncpy(dirname, tmpstr, i);
dirname[i] = '\0';
sprintf(lockfile,"%s/../timing/.%s.%s", dirname, basename(tmpstr), hash);
sprintf(logfile,"%s/../timing/%s.%s.log", dirname, basename(tmpstr), hash);
lock = fopen(lockfile, "w");
fprintf(lock, "%s\n", file);
fclose(lock);
}
/* Read file */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
// Create matrix
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATMPIAIJ); CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
// Load matrix from file
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetSize(A, &m, &n); CHKERRQ(ierr);
// Assemble matrix
//ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
//ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
// Create RHS vector
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecSetSizes(b,PETSC_DECIDE,n); CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
ierr = VecSet(b,one); CHKERRQ(ierr);
//ierr = VecLoad(b,fd);CHKERRQ(ierr);
// Create vectors x and u
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
ierr = VecDuplicate(b,&u);CHKERRQ(ierr);
// Create KSP
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp); CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp,PETSC_FALSE);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp); CHKERRQ(ierr);
// Setup KSP
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
ierr = KSPSetUpOnBlocks(ksp);CHKERRQ(ierr);
// Get start time
ierr = PetscTime(&startTime);CHKERRQ(ierr);
// Get KSP and PC type
KSPType kt;
ierr = KSPGetType(ksp,&kt);
PC pc;
ierr = KSPGetPC(ksp,&pc);
PCType pt;
ierr = PCGetType(pc,&pt);
// Print method info
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD, logfile, &log); CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(log, "Hash: %s\n", hash);
ierr = PetscViewerASCIIPrintf(log, "%s | %s",kt,pt);CHKERRQ(ierr);
// Make sure the program doesn't crash
// while trying to solve the system
PetscPushErrorHandler(PetscIgnoreErrorHandler,NULL);
ierr = KSPSolve(ksp,b,x);
PetscPopErrorHandler();
// Check if anything went wrong
if(ierr == 0 || ierr == -1){
// If no error occurred or stopped by MyKSPMonitor,
// compute normal and stuff
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
ierr = MatMult(A,x,u);CHKERRQ(ierr);
ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscTime(&endTime);CHKERRQ(ierr);
// Compute solve time
solveTime = endTime - startTime;
// Check if KSP converged
KSPConvergedReason reason;
KSPGetConvergedReason(ksp,&reason);
// Print convergence code, solve time, preconditioned norm, iterations
ierr = PetscViewerASCIIPrintf(log, " | %D | %e | %g | %D\n",reason,solveTime,norm,its);CHKERRQ(ierr);
ierr = KSPView(ksp,log);
ierr = PCView(pc,log);
ierr = PetscLogView(log);
}
else{
// Disaster happened, bail out
if (rank == 0) remove(lockfile);
PetscFinalize();
return 0;
}
// Again, destroy KSP and vector
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
if (rank == 0) remove(lockfile);
PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
TS ts;
SNES snes_alg;
PetscErrorCode ierr;
PetscMPIInt size;
Userctx user;
PetscViewer Xview,Ybusview;
Vec X;
Mat J;
PetscInt i;
ierr = PetscInitialize(&argc,&argv,"petscoptions",help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
user.neqs_gen = 9*ngen; /* # eqs. for generator subsystem */
user.neqs_net = 2*nbus; /* # eqs. for network subsystem */
user.neqs_pgrid = user.neqs_gen + user.neqs_net;
/* Create indices for differential and algebraic equations */
PetscInt *idx2;
ierr = PetscMalloc1(7*ngen,&idx2);CHKERRQ(ierr);
for (i=0; i<ngen; i++) {
idx2[7*i] = 9*i; idx2[7*i+1] = 9*i+1; idx2[7*i+2] = 9*i+2; idx2[7*i+3] = 9*i+3;
idx2[7*i+4] = 9*i+6; idx2[7*i+5] = 9*i+7; idx2[7*i+6] = 9*i+8;
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,7*ngen,idx2,PETSC_COPY_VALUES,&user.is_diff);CHKERRQ(ierr);
ierr = ISComplement(user.is_diff,0,user.neqs_pgrid,&user.is_alg);CHKERRQ(ierr);
ierr = PetscFree(idx2);CHKERRQ(ierr);
/* Read initial voltage vector and Ybus */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"X.bin",FILE_MODE_READ,&Xview);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Ybus.bin",FILE_MODE_READ,&Ybusview);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&user.V0);CHKERRQ(ierr);
ierr = VecSetSizes(user.V0,PETSC_DECIDE,user.neqs_net);CHKERRQ(ierr);
ierr = VecLoad(user.V0,Xview);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&user.Ybus);CHKERRQ(ierr);
ierr = MatSetSizes(user.Ybus,PETSC_DECIDE,PETSC_DECIDE,user.neqs_net,user.neqs_net);CHKERRQ(ierr);
ierr = MatSetType(user.Ybus,MATBAIJ);CHKERRQ(ierr);
/* ierr = MatSetBlockSize(user.Ybus,2);CHKERRQ(ierr); */
ierr = MatLoad(user.Ybus,Ybusview);CHKERRQ(ierr);
/* Set run time options */
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Transient stability fault options","");CHKERRQ(ierr);
{
user.tfaulton = 1.0;
user.tfaultoff = 1.2;
user.Rfault = 0.0001;
user.faultbus = 8;
ierr = PetscOptionsReal("-tfaulton","","",user.tfaulton,&user.tfaulton,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tfaultoff","","",user.tfaultoff,&user.tfaultoff,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-faultbus","","",user.faultbus,&user.faultbus,NULL);CHKERRQ(ierr);
user.t0 = 0.0;
user.tmax = 5.0;
ierr = PetscOptionsReal("-t0","","",user.t0,&user.t0,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tmax","","",user.tmax,&user.tmax,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Xview);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Ybusview);CHKERRQ(ierr);
/* Create DMs for generator and network subsystems */
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,user.neqs_gen,1,1,NULL,&user.dmgen);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmgen,"dmgen_");CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,user.neqs_net,1,1,NULL,&user.dmnet);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmnet,"dmnet_");CHKERRQ(ierr);
/* Create a composite DM packer and add the two DMs */
ierr = DMCompositeCreate(PETSC_COMM_WORLD,&user.dmpgrid);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmpgrid,"pgrid_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(user.dmpgrid,user.dmgen);CHKERRQ(ierr);
ierr = DMCompositeAddDM(user.dmpgrid,user.dmnet);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.dmpgrid,&X);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,user.neqs_pgrid,user.neqs_pgrid);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = PreallocateJacobian(J,&user);CHKERRQ(ierr);
/* Create matrix to save solutions at each time step */
user.stepnum = 0;
ierr = MatCreateSeqDense(PETSC_COMM_SELF,user.neqs_pgrid+1,1002,NULL,&user.Sol);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetEquationType(ts,TS_EQ_DAE_IMPLICIT_INDEX1);CHKERRQ(ierr);
ierr = TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&user);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,(TSIJacobian)IJacobian,&user);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SetInitialGuess(X,&user);CHKERRQ(ierr);
/* Just to set up the Jacobian structure */
Vec Xdot;
MatStructure flg;
ierr = VecDuplicate(X,&Xdot);CHKERRQ(ierr);
ierr = IJacobian(ts,0.0,X,Xdot,0.0,J,J,&flg,&user);CHKERRQ(ierr);
ierr = VecDestroy(&Xdot);CHKERRQ(ierr);
/* Save initial solution */
PetscScalar *x,*mat;
PetscInt idx=user.stepnum*(user.neqs_pgrid+1);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
mat[idx] = 0.0;
ierr = PetscMemcpy(mat+idx+1,x,user.neqs_pgrid*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
user.stepnum++;
ierr = TSSetDuration(ts,1000,user.tfaulton);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,0.01);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,SaveSolution);CHKERRQ(ierr);
user.alg_flg = PETSC_FALSE;
/* Prefault period */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Create the nonlinear solver for solving the algebraic system */
/* Note that although the algebraic system needs to be solved only for
Idq and V, we reuse the entire system including xgen. The xgen
variables are held constant by setting their residuals to 0 and
putting a 1 on the Jacobian diagonal for xgen rows
*/
Vec F_alg;
ierr = VecDuplicate(X,&F_alg);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes_alg);CHKERRQ(ierr);
ierr = SNESSetFunction(snes_alg,F_alg,AlgFunction,&user);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes_alg,J,J,AlgJacobian,&user);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(snes_alg,"alg_");CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes_alg);CHKERRQ(ierr);
/* Apply disturbance - resistive fault at user.faultbus */
/* This is done by adding shunt conductance to the diagonal location
in the Ybus matrix */
PetscInt row_loc,col_loc;
PetscScalar val;
row_loc = 2*user.faultbus; col_loc = 2*user.faultbus+1; /* Location for G */
val = 1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*user.faultbus+1; col_loc = 2*user.faultbus; /* Location for G */
val = 1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Save fault-on solution */
idx = user.stepnum*(user.neqs_pgrid+1);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
mat[idx] = user.tfaulton;
ierr = PetscMemcpy(mat+idx+1,x,user.neqs_pgrid*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
user.stepnum++;
/* Disturbance period */
ierr = TSSetDuration(ts,1000,user.tfaultoff);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.tfaulton,.01);CHKERRQ(ierr);
user.alg_flg = PETSC_FALSE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Remove the fault */
row_loc = 2*user.faultbus; col_loc = 2*user.faultbus+1;
val = -1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*user.faultbus+1; col_loc = 2*user.faultbus;
val = -1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Save tfault off solution */
idx = user.stepnum*(user.neqs_pgrid+1);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
mat[idx] = user.tfaultoff;
ierr = PetscMemcpy(mat+idx+1,x,user.neqs_pgrid*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
user.stepnum++;
/* Post-disturbance period */
ierr = TSSetDuration(ts,1000,user.tmax);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.tfaultoff,.01);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Sol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Sol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
Mat A;
PetscScalar *amat;
ierr = MatCreateSeqDense(PETSC_COMM_SELF,user.neqs_pgrid+1,user.stepnum,NULL,&A);CHKERRQ(ierr);
ierr = MatDenseGetArray(user.Sol,&mat);CHKERRQ(ierr);
ierr = MatDenseGetArray(A,&amat);CHKERRQ(ierr);
ierr = PetscMemcpy(amat,mat,(user.stepnum*(user.neqs_pgrid+1))*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(A,&amat);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(user.Sol,&mat);CHKERRQ(ierr);
PetscViewer viewer;
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"out.bin",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = SNESDestroy(&snes_alg);CHKERRQ(ierr);
ierr = VecDestroy(&F_alg);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatDestroy(&user.Ybus);CHKERRQ(ierr);
ierr = MatDestroy(&user.Sol);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&user.V0);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmgen);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmnet);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmpgrid);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_diff);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_alg);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return(0);
}
int main(int argc,char **args)
{
Mat A,Asp;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscInt m,n,rstart,rend;
PetscBool flg;
PetscInt row,ncols,j,nrows,nnzA=0,nnzAsp=0;
const PetscInt *cols;
const PetscScalar *vals;
PetscReal norm,percent,val,dtol=1.e-16;
PetscMPIInt rank;
MatInfo matinfo;
PetscInt Dnnz,Onnz;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* Determine files from which we read the linear systems. */
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file. */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/* Load the matrix; then destroy the viewer. */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(A,"a_");CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatGetInfo(A,MAT_LOCAL,&matinfo);CHKERRQ(ierr);
//printf("matinfo.nz_used %g\n",matinfo.nz_used);
/* Get a sparse matrix Asp by dumping zero entries of A */
ierr = MatCreate(PETSC_COMM_WORLD,&Asp);CHKERRQ(ierr);
ierr = MatSetSizes(Asp,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(Asp,"asp_");CHKERRQ(ierr);
ierr = MatSetFromOptions(Asp);CHKERRQ(ierr);
Dnnz = (PetscInt)matinfo.nz_used/m + 1;
Onnz = Dnnz/2;
printf("Dnnz %d %d\n",Dnnz,Onnz);
ierr = MatSeqAIJSetPreallocation(Asp,Dnnz,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(Asp,Dnnz,PETSC_NULL,Onnz,PETSC_NULL);CHKERRQ(ierr);
/* Check zero rows */
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
nrows = 0;
for (row=rstart; row<rend; row++){
ierr = MatGetRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr);
nnzA += ncols;
norm = 0.0;
for (j=0; j<ncols; j++){
val = PetscAbsScalar(vals[j]);
if (norm < val) norm = norm;
if (val > dtol){
ierr = MatSetValues(Asp,1,&row,1,&cols[j],&vals[j],INSERT_VALUES);CHKERRQ(ierr);
nnzAsp++;
}
}
if (!norm) nrows++;
ierr = MatRestoreRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
percent=(PetscReal)nnzA*100/(m*n);
ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix A local size %d,%d; nnzA %d, %g percent; No. of zero rows: %d\n",rank,m,n,nnzA,percent,nrows);
percent=(PetscReal)nnzAsp*100/(m*n);
ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix Asp nnzAsp %d, %g percent\n",rank,nnzAsp,percent);
/* investigate matcoloring for Asp */
PetscBool Asp_coloring = PETSC_FALSE;
ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_color",&Asp_coloring);CHKERRQ(ierr);
if (Asp_coloring){
ISColoring iscoloring;
MatFDColoring matfdcoloring;
ierr = PetscPrintf(PETSC_COMM_WORLD," Create coloring of Asp...\n");
ierr = MatGetColoring(Asp,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(Asp,iscoloring,&matfdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
//ierr = MatFDColoringView(matfdcoloring,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);
}
/* Write Asp in binary for study - see ~petsc/src/mat/examples/tests/ex124.c */
PetscBool Asp_write = PETSC_FALSE;
ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_write",&Asp_write);CHKERRQ(ierr);
if (Asp_write){
PetscViewer viewer;
ierr = PetscPrintf(PETSC_COMM_SELF,"Write Asp into file Asp.dat ...\n");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Asp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(Asp,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&Asp);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
#include "private/fortranimpl.h"
#include "petscmat.h"
#if defined(PETSC_HAVE_FORTRAN_CAPS)
#define matload_ MATLOAD
#elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE)
#define matload_ matload
#endif
EXTERN_C_BEGIN
void PETSC_STDCALL matload_(PetscViewer *viewer,CHAR outtype PETSC_MIXED_LEN(len),Mat *newmat,PetscErrorCode *ierr PETSC_END_LEN(len))
{
char *t;
PetscViewer v;
FIXCHAR(outtype,len,t);
PetscPatchDefaultViewers_Fortran(viewer,v);
*ierr = MatLoad(v,t,newmat);
FREECHAR(outtype,t);
}
EXTERN_C_END
int main(int argc,char **args)
{
Mat A,RHS,C,F,X;
Vec u,x,b;
PetscErrorCode ierr;
PetscMPIInt rank,nproc;
PetscInt i,m,n,nfact,nsolve,nrhs,ipack=0;
PetscScalar *array,rval;
PetscReal norm,tol=1.e-12;
IS perm,iperm;
MatFactorInfo info;
PetscRandom rand;
PetscBool flg,testMatSolve=PETSC_TRUE,testMatMatSolve=PETSC_TRUE;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &nproc);CHKERRQ(ierr);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
if (m != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "This example is not intended for rectangular matrices (%d, %d)", m, n);
/* Create dense matrix C and X; C holds true solution with identical colums */
nrhs = 2;
ierr = PetscOptionsGetInt(NULL,"-nrhs",&nrhs,NULL);CHKERRQ(ierr);
if (!rank) printf("ex125: nrhs %d\n",nrhs);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,m,PETSC_DECIDE,PETSC_DECIDE,nrhs);CHKERRQ(ierr);
ierr = MatSetType(C,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatSetRandom(C,rand);CHKERRQ(ierr);
ierr = MatDuplicate(C,MAT_DO_NOT_COPY_VALUES,&X);CHKERRQ(ierr);
/* Create vectors */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */
/* Test LU Factorization */
ierr = MatGetOrdering(A,MATORDERINGND,&perm,&iperm);CHKERRQ(ierr);
/*ierr = ISView(perm,PETSC_VIEWER_STDOUT_WORLD);*/
/*ierr = ISView(perm,PETSC_VIEWER_STDOUT_SELF);*/
ierr = PetscOptionsGetInt(NULL,"-mat_solver_package",&ipack,NULL);CHKERRQ(ierr);
switch (ipack) {
case 0:
#if defined(PETSC_HAVE_SUPERLU)
if (!rank) printf(" SUPERLU LU:\n");
ierr = MatGetFactor(A,MATSOLVERSUPERLU,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
break;
#endif
case 1:
#if defined(PETSC_HAVE_SUPERLU_DIST)
if (!rank) printf(" SUPERLU_DIST LU:\n");
ierr = MatGetFactor(A,MATSOLVERSUPERLU_DIST,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
break;
#endif
case 2:
#if defined(PETSC_HAVE_MUMPS)
if (!rank) printf(" MUMPS LU:\n");
ierr = MatGetFactor(A,MATSOLVERMUMPS,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
{
/* test mumps options */
PetscInt icntl_7 = 5;
ierr = MatMumpsSetIcntl(F,7,icntl_7);CHKERRQ(ierr);
}
break;
#endif
default:
if (!rank) printf(" PETSC LU:\n");
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
}
info.fill = 5.0;
ierr = MatLUFactorSymbolic(F,A,perm,iperm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++) {
if (!rank) printf(" %d-the LU numfactorization \n",nfact);
ierr = MatLUFactorNumeric(F,A,&info);CHKERRQ(ierr);
/* Test MatMatSolve() */
/*
if ((ipack == 0 || ipack == 2) && testMatMatSolve) {
printf(" MatMatSolve() is not implemented for this package. Skip the testing.\n");
testMatMatSolve = PETSC_FALSE;
}
*/
if (testMatMatSolve) {
if (!nfact) {
ierr = MatMatMult(A,C,MAT_INITIAL_MATRIX,2.0,&RHS);CHKERRQ(ierr);
} else {
ierr = MatMatMult(A,C,MAT_REUSE_MATRIX,2.0,&RHS);CHKERRQ(ierr);
}
for (nsolve = 0; nsolve < 2; nsolve++) {
if (!rank) printf(" %d-the MatMatSolve \n",nsolve);
ierr = MatMatSolve(F,RHS,X);CHKERRQ(ierr);
/* Check the error */
ierr = MatAXPY(X,-1.0,C,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(X,NORM_FROBENIUS,&norm);CHKERRQ(ierr);
if (norm > tol) {
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"1st MatMatSolve: Norm of error %g, nsolve %d\n",norm,nsolve);CHKERRQ(ierr);
}
}
}
}
/* Test MatSolve() */
if (testMatSolve) {
for (nsolve = 0; nsolve < 2; nsolve++) {
ierr = VecGetArray(x,&array);CHKERRQ(ierr);
for (i=0; i<m; i++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[i] = rval;
}
ierr = VecRestoreArray(x,&array);CHKERRQ(ierr);
ierr = VecCopy(x,u);CHKERRQ(ierr);
ierr = MatMult(A,x,b);CHKERRQ(ierr);
if (!rank) printf(" %d-the MatSolve \n",nsolve);
ierr = MatSolve(F,b,x);CHKERRQ(ierr);
/* Check the error */
ierr = VecAXPY(u,-1.0,x);CHKERRQ(ierr); /* u <- (-1.0)x + u */
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = MatMult(A,x,u);CHKERRQ(ierr); /* u = A*x */
PetscReal resi;
ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr); /* u <- (-1.0)b + u */
ierr = VecNorm(u,NORM_2,&resi);CHKERRQ(ierr);
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatSolve: Norm of error %g, resi %g, LU numfact %d\n",norm,resi,nfact);CHKERRQ(ierr);
}
}
}
}
}
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&X);CHKERRQ(ierr);
if (testMatMatSolve) {
ierr = MatDestroy(&RHS);CHKERRQ(ierr);
}
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = ISDestroy(&iperm);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode InitializeData(const PetscScalar* P, void *ctx0, double noise, PetscScalar data_dt)
{
TS ts;
SNES snes_alg;
PetscErrorCode ierr;
Userctx *ctx = (Userctx*)ctx0;
Vec X;
Mat J;
Vec F_alg;
Vec Xdot;
PetscInt i,j,m,n;
PetscReal *mat;
//PetscReal temp;
PetscViewer obsView;
PetscFunctionBegin;
H[0] = P[0];
H[1] = P[1];
H[2] = P[2];
printf("InitializeData: x=[%.14f, %.14f, %.14f], obs_noise=%5.3f Nt = %4.2f, Nobs=%4.2f\n", H[0], H[1], H[2], noise, ((ctx->tfinal-ctx->t0)/ctx->dt)+1, ((ctx->tfinal-ctx->trestore)/ctx->data_dt)+1);
if(ctx->t0 > ctx->tdisturb) {
printf("t0 cannot be greater than tdisturb\n");
PetscFunctionReturn(-1);
}
if( (ctx->tdisturb >= ctx->trestore-1.0e-8) || (ctx->tdisturb >= ctx->tfinal-1.0e-8) ) {
printf("tdisturb should be less than trestore and tfinal\n");
PetscFunctionReturn(-1);
}
//use the reference PD0 from t0 to t_disturb to ensure steady state
for(i=0; i<3; i++) PD0[i] = PD0_ref[i];
ctx->stepnum = 0;
ierr = DMCreateGlobalVector(ctx->dmpgrid,&X);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,ctx->neqs_pgrid,ctx->neqs_pgrid);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = PreallocateJacobian(J,ctx);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,ctx);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,(TSIJacobian)IJacobian,ctx);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,ctx);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SetInitialGuess(X,ctx);CHKERRQ(ierr);
ierr = VecDuplicate(X,&F_alg);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes_alg);CHKERRQ(ierr);
ierr = SNESSetFunction(snes_alg,F_alg,AlgFunction,ctx);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes_alg,J,J,AlgJacobian,ctx);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(snes_alg,"alg_");CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes_alg);CHKERRQ(ierr);
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
ierr = SetSolution(ctx, ctx->t0, X); CHKERRQ(ierr);
ierr = SetObservation(ctx, ctx->t0, X); CHKERRQ(ierr);
/* Just to set up the Jacobian structure */
ierr = VecDuplicate(X,&Xdot);CHKERRQ(ierr);
ierr = IJacobian(ts,ctx->t0,X,Xdot,0.0,J,J,ctx);CHKERRQ(ierr);
ierr = VecDestroy(&Xdot);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve from on [t0,tdisturb] (steady state)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetDuration(ts,1000000,ctx->tdisturb);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ctx->t0,ctx->dt);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,SaveObservation);CHKERRQ(ierr);
/* Solve (from t0 to tdisturb) */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* set X at tdisturb as IC for the optimization/estimation */
/*ierr = VecDuplicate(X, &ctx->X0_disturb);CHKERRQ(ierr);*/
/*ierr = VecCopy(X, ctx->X0_disturb);CHKERRQ(ierr);*/
/* Continue integrating the DAE only if observations file is not specified */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve from on [tdisturb, trestore] (disturbance part of the transient)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* Induce a load perturbation at t=tdisturb */
for(i=0; i<3; i++) PD0[i] = PD0_disturb[i];
printf("Generate data - initiated a bump in load: new PD0[0]=%g\n", PD0[0]);
printf("Running with: tfinal=%.12f dt=%.12f data_dt=%.12f data_noise=%.12f prior_noise=%.12f load_disturb=%.12f\n",
ctx->tfinal, ctx->dt, ctx->data_dt,
ctx->data_noise, ctx->prior_noise, PD0[0]);
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
ierr = TSSetDuration(ts,100000,fmin(ctx->trestore,ctx->tfinal));CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ctx->tdisturb,ctx->dt);CHKERRQ(ierr);
/* Solve (from tdisturb to trestore) */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* set X at trestore as IC for the optimization/estimation */
ierr = VecDuplicate(X, &ctx->X0_disturb);CHKERRQ(ierr);
ierr = VecCopy(X, ctx->X0_disturb);CHKERRQ(ierr);
if(0==strlen(ctx->loadObsFile)) {
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve from on [trestore, tfinal] (post-disturbance transient)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
if(ctx->tfinal>=ctx->trestore+1.0e-8) {
//restore load at trestore
for(i=0; i<3; i++) PD0[i] = PD0_ref[i];
printf("In generate data: Restore load to PD0[0]=%g\n", PD0[0]);
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
ierr = TSSetDuration(ts,100000,ctx->tfinal);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ctx->trestore,ctx->dt);CHKERRQ(ierr);
/* Solve (from trestore to tfinal) */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
} else {
printf("Ignoring trestore since tfinal is less than it.\n");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Generate noise at level 'noise' percent
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatGetSize(ctx->obs, &m, &n);CHKERRQ(ierr);
/* allocate std dev for data */
ierr = PetscMalloc(m*sizeof(PetscReal),&ctx->data_stddev);CHKERRQ(ierr);
ierr = MatDenseGetArray(ctx->obs,&mat);CHKERRQ(ierr);
for(i=0;i<m;i++)
ctx->data_stddev[i] = ctx->data_noise;
/* for(i=0; i<m; i++) {
temp = 0.0;
for(j=0; j<n; j++) {
temp += mat[i*n+j]*mat[i*n+j];
}
ctx->data_stddev[i] = ctx->data_noise*sqrt(temp);
}
*/
for(i=0; i<m; i++) {
for(j=0; j<n; j++) {
mat[i*n+j] += ctx->data_stddev[i]*nrand();
}
}
ierr = MatDenseRestoreArray(ctx->obs,&mat);CHKERRQ(ierr);
} else {
/* observations are in an external file */
printf("Loading observations from %s.\n", ctx->loadObsFile);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,ctx->loadObsFile,FILE_MODE_READ, &obsView);CHKERRQ(ierr);
ierr = MatLoad(ctx->obs, obsView);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&obsView);CHKERRQ(ierr);
ierr = MatGetSize(ctx->obs, &m, &n);CHKERRQ(ierr);
ierr = PetscMalloc(m*sizeof(PetscReal),&ctx->data_stddev);CHKERRQ(ierr);
for(i=0;i<m;i++)
ctx->data_stddev[i] = ctx->data_noise;
}
ierr = SNESDestroy(&snes_alg);CHKERRQ(ierr);
ierr = VecDestroy(&F_alg);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat A,RHS,C,F,X,S;
Vec u,x,b;
Vec xschur,bschur,uschur;
IS is_schur;
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt isolver=0,size_schur,m,n,nfact,nsolve,nrhs;
PetscReal norm,tol=PETSC_SQRT_MACHINE_EPSILON;
PetscRandom rand;
PetscBool data_provided,herm,symm,use_lu;
PetscReal sratio = 5.1/12.;
PetscViewer fd; /* viewer */
char solver[256];
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor test");
/* Determine which type of solver we want to test for */
herm = PETSC_FALSE;
symm = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-symmetric_solve",&symm,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-hermitian_solve",&herm,NULL);CHKERRQ(ierr);
if (herm) symm = PETSC_TRUE;
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&data_provided);CHKERRQ(ierr);
if (!data_provided) { /* get matrices from PETSc distribution */
sprintf(file,PETSC_DIR);
ierr = PetscStrcat(file,"/share/petsc/datafiles/matrices/");CHKERRQ(ierr);
if (symm) {
#if defined (PETSC_USE_COMPLEX)
ierr = PetscStrcat(file,"hpd-complex-");CHKERRQ(ierr);
#else
ierr = PetscStrcat(file,"spd-real-");CHKERRQ(ierr);
#endif
} else {
#if defined (PETSC_USE_COMPLEX)
ierr = PetscStrcat(file,"nh-complex-");CHKERRQ(ierr);
#else
ierr = PetscStrcat(file,"ns-real-");CHKERRQ(ierr);
#endif
}
#if defined(PETSC_USE_64BIT_INDICES)
ierr = PetscStrcat(file,"int64-");CHKERRQ(ierr);
#else
ierr = PetscStrcat(file,"int32-");CHKERRQ(ierr);
#endif
#if defined (PETSC_USE_REAL_SINGLE)
ierr = PetscStrcat(file,"float32");CHKERRQ(ierr);
#else
ierr = PetscStrcat(file,"float64");CHKERRQ(ierr);
#endif
}
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
if (m != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "This example is not intended for rectangular matrices (%d, %d)", m, n);
/* Create dense matrix C and X; C holds true solution with identical colums */
nrhs = 2;
ierr = PetscOptionsGetInt(NULL,NULL,"-nrhs",&nrhs,NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,m,PETSC_DECIDE,PETSC_DECIDE,nrhs);CHKERRQ(ierr);
ierr = MatSetType(C,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatSetRandom(C,rand);CHKERRQ(ierr);
ierr = MatDuplicate(C,MAT_DO_NOT_COPY_VALUES,&X);CHKERRQ(ierr);
/* Create vectors */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */
ierr = PetscOptionsGetInt(NULL,NULL,"-solver",&isolver,NULL);CHKERRQ(ierr);
switch (isolver) {
#if defined(PETSC_HAVE_MUMPS)
case 0:
ierr = PetscStrcpy(solver,MATSOLVERMUMPS);CHKERRQ(ierr);
break;
#endif
#if defined(PETSC_HAVE_MKL_PARDISO)
case 1:
ierr = PetscStrcpy(solver,MATSOLVERMKL_PARDISO);CHKERRQ(ierr);
break;
#endif
default:
ierr = PetscStrcpy(solver,MATSOLVERPETSC);CHKERRQ(ierr);
break;
}
#if defined (PETSC_USE_COMPLEX)
if (isolver == 0 && symm && !data_provided) { /* MUMPS (5.0.0) does not have support for hermitian matrices, so make them symmetric */
PetscScalar im = PetscSqrtScalar((PetscScalar)-1.);
PetscScalar val = -1.0;
val = val + im;
ierr = MatSetValue(A,1,0,val,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
#endif
ierr = PetscOptionsGetReal(NULL,NULL,"-schur_ratio",&sratio,NULL);CHKERRQ(ierr);
if (sratio < 0. || sratio > 1.) {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "Invalid ratio for schur degrees of freedom %f", sratio);
}
size_schur = (PetscInt)(sratio*m);
ierr = PetscPrintf(PETSC_COMM_SELF,"Solving with %s: nrhs %d, sym %d, herm %d, size schur %d, size mat %d\n",solver,nrhs,symm,herm,size_schur,m);CHKERRQ(ierr);
/* Test LU/Cholesky Factorization */
use_lu = PETSC_FALSE;
if (!symm) use_lu = PETSC_TRUE;
#if defined (PETSC_USE_COMPLEX)
if (isolver == 1) use_lu = PETSC_TRUE;
#endif
if (herm && !use_lu) { /* test also conversion routines inside the solver packages */
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatConvert(A,MATSEQSBAIJ,MAT_INPLACE_MATRIX,&A);CHKERRQ(ierr);
}
if (use_lu) {
ierr = MatGetFactor(A,solver,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
} else {
if (herm) {
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_SPD,PETSC_TRUE);CHKERRQ(ierr);
} else {
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_SPD,PETSC_FALSE);CHKERRQ(ierr);
}
ierr = MatGetFactor(A,solver,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
}
ierr = ISCreateStride(PETSC_COMM_SELF,size_schur,m-size_schur,1,&is_schur);CHKERRQ(ierr);
ierr = MatFactorSetSchurIS(F,is_schur);CHKERRQ(ierr);
ierr = ISDestroy(&is_schur);CHKERRQ(ierr);
if (use_lu) {
ierr = MatLUFactorSymbolic(F,A,NULL,NULL,NULL);CHKERRQ(ierr);
} else {
ierr = MatCholeskyFactorSymbolic(F,A,NULL,NULL);CHKERRQ(ierr);
}
for (nfact = 0; nfact < 3; nfact++) {
Mat AD;
if (!nfact) {
ierr = VecSetRandom(x,rand);CHKERRQ(ierr);
if (symm && herm) {
ierr = VecAbs(x);CHKERRQ(ierr);
}
ierr = MatDiagonalSet(A,x,ADD_VALUES);CHKERRQ(ierr);
}
if (use_lu) {
ierr = MatLUFactorNumeric(F,A,NULL);CHKERRQ(ierr);
} else {
ierr = MatCholeskyFactorNumeric(F,A,NULL);CHKERRQ(ierr);
}
ierr = MatFactorCreateSchurComplement(F,&S);CHKERRQ(ierr);
ierr = MatCreateVecs(S,&xschur,&bschur);CHKERRQ(ierr);
ierr = VecDuplicate(xschur,&uschur);CHKERRQ(ierr);
if (nfact == 1) {
ierr = MatFactorInvertSchurComplement(F);CHKERRQ(ierr);
}
for (nsolve = 0; nsolve < 2; nsolve++) {
ierr = VecSetRandom(x,rand);CHKERRQ(ierr);
ierr = VecCopy(x,u);CHKERRQ(ierr);
if (nsolve) {
ierr = MatMult(A,x,b);CHKERRQ(ierr);
ierr = MatSolve(F,b,x);CHKERRQ(ierr);
} else {
ierr = MatMultTranspose(A,x,b);CHKERRQ(ierr);
ierr = MatSolveTranspose(F,b,x);CHKERRQ(ierr);
}
/* Check the error */
ierr = VecAXPY(u,-1.0,x);CHKERRQ(ierr); /* u <- (-1.0)x + u */
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
PetscReal resi;
if (nsolve) {
ierr = MatMult(A,x,u);CHKERRQ(ierr); /* u = A*x */
} else {
ierr = MatMultTranspose(A,x,u);CHKERRQ(ierr); /* u = A*x */
}
ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr); /* u <- (-1.0)b + u */
ierr = VecNorm(u,NORM_2,&resi);CHKERRQ(ierr);
if (nsolve) {
ierr = PetscPrintf(PETSC_COMM_SELF,"(f %d, s %d) MatSolve error: Norm of error %g, residual %f\n",nfact,nsolve,norm,resi);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_SELF,"(f %d, s %d) MatSolveTranspose error: Norm of error %g, residual %f\n",nfact,nsolve,norm,resi);CHKERRQ(ierr);
}
}
ierr = VecSetRandom(xschur,rand);CHKERRQ(ierr);
ierr = VecCopy(xschur,uschur);CHKERRQ(ierr);
if (nsolve) {
ierr = MatMult(S,xschur,bschur);CHKERRQ(ierr);
ierr = MatFactorSolveSchurComplement(F,bschur,xschur);CHKERRQ(ierr);
} else {
ierr = MatMultTranspose(S,xschur,bschur);CHKERRQ(ierr);
ierr = MatFactorSolveSchurComplementTranspose(F,bschur,xschur);CHKERRQ(ierr);
}
/* Check the error */
ierr = VecAXPY(uschur,-1.0,xschur);CHKERRQ(ierr); /* u <- (-1.0)x + u */
ierr = VecNorm(uschur,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
PetscReal resi;
if (nsolve) {
ierr = MatMult(S,xschur,uschur);CHKERRQ(ierr); /* u = A*x */
} else {
ierr = MatMultTranspose(S,xschur,uschur);CHKERRQ(ierr); /* u = A*x */
}
ierr = VecAXPY(uschur,-1.0,bschur);CHKERRQ(ierr); /* u <- (-1.0)b + u */
ierr = VecNorm(uschur,NORM_2,&resi);CHKERRQ(ierr);
if (nsolve) {
ierr = PetscPrintf(PETSC_COMM_SELF,"(f %d, s %d) MatFactorSolveSchurComplement error: Norm of error %g, residual %f\n",nfact,nsolve,norm,resi);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_SELF,"(f %d, s %d) MatFactorSolveSchurComplementTranspose error: Norm of error %g, residual %f\n",nfact,nsolve,norm,resi);CHKERRQ(ierr);
}
}
}
ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&AD);
if (!nfact) {
ierr = MatMatMult(AD,C,MAT_INITIAL_MATRIX,2.0,&RHS);CHKERRQ(ierr);
} else {
ierr = MatMatMult(AD,C,MAT_REUSE_MATRIX,2.0,&RHS);CHKERRQ(ierr);
}
ierr = MatDestroy(&AD);CHKERRQ(ierr);
for (nsolve = 0; nsolve < 2; nsolve++) {
ierr = MatMatSolve(F,RHS,X);CHKERRQ(ierr);
/* Check the error */
ierr = MatAXPY(X,-1.0,C,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(X,NORM_FROBENIUS,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"(f %D, s %D) MatMatSolve: Norm of error %g\n",nfact,nsolve,norm);CHKERRQ(ierr);
}
}
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = VecDestroy(&xschur);CHKERRQ(ierr);
ierr = VecDestroy(&bschur);CHKERRQ(ierr);
ierr = VecDestroy(&uschur);CHKERRQ(ierr);
}
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&X);CHKERRQ(ierr);
ierr = MatDestroy(&RHS);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main( int argc, char **argv )
{
Mat M, C, K; /* problem matrices */
QEP qep; /* quadratic eigenproblem solver context */
const QEPType type;
PetscReal error, tol, re, im;
PetscScalar kr, ki;
PetscErrorCode ierr;
PetscInt nev, maxit, i, its, nconv;
char filename[256];
PetscViewer viewer;
PetscBool flg;
SlepcInitialize(&argc,&argv,(char*)0,help);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Load the matrices that define the quadratic eigenproblem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nQuadratic eigenproblem stored in file.\n\n");CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
ierr = PetscPrintf(PETSC_COMM_WORLD," Reading COMPLEX matrices from binary files...\n");CHKERRQ(ierr);
#else
ierr = PetscPrintf(PETSC_COMM_WORLD," Reading REAL matrices from binary files...\n");CHKERRQ(ierr);
#endif
ierr = PetscOptionsGetString(PETSC_NULL,"-M",filename,256,&flg);CHKERRQ(ierr);
if (!flg) {
SETERRQ(PETSC_COMM_WORLD,1,"Must indicate a file name for matrix M with the -M option.");
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&M);CHKERRQ(ierr);
ierr = MatSetFromOptions(M);CHKERRQ(ierr);
ierr = MatLoad(M,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-C",filename,256,&flg);CHKERRQ(ierr);
if (!flg) {
SETERRQ(PETSC_COMM_WORLD,1,"Must indicate a file name for matrix C with the -C option.");
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatLoad(C,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-K",filename,256,&flg);CHKERRQ(ierr);
if (!flg) {
SETERRQ(PETSC_COMM_WORLD,1,"Must indicate a file name for matrix K with the -K option.");
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&K);CHKERRQ(ierr);
ierr = MatSetFromOptions(K);CHKERRQ(ierr);
ierr = MatLoad(K,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create eigensolver context
*/
ierr = QEPCreate(PETSC_COMM_WORLD,&qep);CHKERRQ(ierr);
/*
Set matrices
*/
ierr = QEPSetOperators(qep,M,C,K);CHKERRQ(ierr);
/*
Set solver parameters at runtime
*/
ierr = QEPSetFromOptions(qep);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the eigensystem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = QEPSolve(qep);CHKERRQ(ierr);
ierr = QEPGetIterationNumber(qep, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of iterations of the method: %d\n",its);CHKERRQ(ierr);
/*
Optional: Get some information from the solver and display it
*/
ierr = QEPGetType(qep,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);CHKERRQ(ierr);
ierr = QEPGetDimensions(qep,&nev,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %d\n",nev);CHKERRQ(ierr);
ierr = QEPGetTolerances(qep,&tol,&maxit);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Stopping condition: tol=%.4g, maxit=%d\n",tol,maxit);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Get number of converged approximate eigenpairs
*/
ierr = QEPGetConverged(qep,&nconv);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of converged approximate eigenpairs: %d\n\n",nconv);
CHKERRQ(ierr);
if (nconv>0) {
/*
Display eigenvalues and relative errors
*/
ierr = PetscPrintf(PETSC_COMM_WORLD,
" k ||(k^2M+Ck+K)x||/||kx||\n"
" ----------------- -------------------------\n" );CHKERRQ(ierr);
for( i=0; i<nconv; i++ ) {
/*
Get converged eigenpairs: i-th eigenvalue is stored in kr (real part) and
ki (imaginary part)
*/
ierr = QEPGetEigenpair(qep,i,&kr,&ki,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
/*
Compute the relative error associated to each eigenpair
*/
ierr = QEPComputeRelativeError(qep,i,&error);CHKERRQ(ierr);
#ifdef PETSC_USE_COMPLEX
re = PetscRealPart(kr);
im = PetscImaginaryPart(kr);
#else
re = kr;
im = ki;
#endif
if (im!=0.0) {
ierr = PetscPrintf(PETSC_COMM_WORLD," %9f%+9f j %12g\n",re,im,error);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD," %12f %12g\n",re,error);CHKERRQ(ierr);
}
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n" );CHKERRQ(ierr);
}
/*
Free work space
*/
ierr = QEPDestroy(qep);CHKERRQ(ierr);
ierr = MatDestroy(M);CHKERRQ(ierr);
ierr = MatDestroy(C);CHKERRQ(ierr);
ierr = MatDestroy(K);CHKERRQ(ierr);
ierr = SlepcFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat U,V; /* matrix */
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscBool flg;
Vec x,y,work1,work2;
PetscInt i,N,n,M,m;
PetscScalar *xx;
PetscInitialize(&argc,&args,(char *)0,help);
/*
Determine file from which we read the matrix
*/
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/*
Load the matrix; then destroy the viewer.
Note both U and V are stored as tall skinny matrices
*/
ierr = MatCreate(PETSC_COMM_WORLD,&U);CHKERRQ(ierr);
ierr = MatSetType(U,MATMPIDENSE);CHKERRQ(ierr);
ierr = MatLoad(U,fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&V);CHKERRQ(ierr);
ierr = MatSetType(V,MATMPIDENSE);CHKERRQ(ierr);
ierr = MatLoad(V,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetLocalSize(U,&N,&n);CHKERRQ(ierr);
ierr = MatGetLocalSize(V,&M,&m);CHKERRQ(ierr);
if (N != M) SETERRQ2(PETSC_COMM_SELF,1,"U and V matrices must have same number of local rows %D %D",N,M);
if (n != m) SETERRQ2(PETSC_COMM_SELF,1,"U and V matrices must have same number of local columns %D %D",n,m);
ierr = VecCreateMPI(PETSC_COMM_WORLD,N,PETSC_DETERMINE,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = MatGetSize(U,0,&n);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&work1);CHKERRQ(ierr);
ierr = VecDuplicate(work1,&work2);CHKERRQ(ierr);
/* put some initial values into x for testing */
ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
for (i=0; i<N; i++) xx[i] = i;
ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
ierr = LowRankUpdate(U,V,x,y,work1,work2,n);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = MatDestroy(&U);CHKERRQ(ierr);
ierr = MatDestroy(&V);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&work1);CHKERRQ(ierr);
ierr = VecDestroy(&work2);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat C;
PetscScalar v;
PetscInt i,j,Ii,J,Istart,Iend,N,m = 4,n = 4;
PetscMPIInt rank,size;
PetscErrorCode ierr;
PetscViewer viewer;
#if defined (PETSC_USE_LOG)
PetscLogEvent MATRIX_GENERATE,MATRIX_READ;
#endif
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
N = m*n;
/* PART 1: Generate matrix, then write it in binary format */
ierr = PetscLogEventRegister("Generate Matrix",0,&MATRIX_GENERATE);CHKERRQ(ierr);
ierr = PetscLogEventBegin(MATRIX_GENERATE,0,0,0,0);CHKERRQ(ierr);
/* Generate matrix */
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(C,&Istart,&Iend);CHKERRQ(ierr);
for (Ii=Istart; Ii<Iend; Ii++) {
v = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"writing matrix in binary to matrix.dat ...\n");CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(C,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscLogEventEnd(MATRIX_GENERATE,0,0,0,0);CHKERRQ(ierr);
/* PART 2: Read in matrix in binary format */
/* All processors wait until test matrix has been dumped */
ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = PetscLogEventRegister("Read Matrix",0,&MATRIX_READ);CHKERRQ(ierr);
ierr = PetscLogEventBegin(MATRIX_READ,0,0,0,0);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"reading matrix in binary from matrix.dat ...\n");CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatLoad(C,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscLogEventEnd(MATRIX_READ,0,0,0,0);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main( int argc, char **argv )
{
int ierr,i,j;
char infilename[PETSC_MAX_PATH_LEN]="", temporary[PETSC_MAX_PATH_LEN]="", path[PETSC_MAX_PATH_LEN]="";
PetscViewer viewer;
PetscBool isTail=PETSC_FALSE,isRight=PETSC_FALSE;
Mat mat;
PetscInt idxn[DIM], idxm[DIM], m, n, windowX=0, windowY=0;
PetscScalar values[DIM*DIM];
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetString(PETSC_NULL,"-file",infilename,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(PETSC_NULL, "-tail", &isTail, NULL);
ierr = PetscOptionsGetBool(PETSC_NULL, "-right", &isRight, NULL);
ierr = PetscGetWorkingDirectory(path,PETSC_MAX_PATH_LEN);
// concat filename
strcat(temporary, path); strcat(temporary, "/"); strcat(temporary, infilename); strcpy(infilename, temporary);
if ( strcmp(infilename, "") == 0 ){
SETERRQ(PETSC_COMM_WORLD,1,"Specifiy the filename!\nExample call: ./inspectBinary -file matrix.dat");
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,infilename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&mat);CHKERRQ(ierr);
ierr = MatSetFromOptions(mat);CHKERRQ(ierr);
ierr = MatLoad(mat,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
MatGetSize(mat,&m,&n);
if ( isTail == PETSC_TRUE ){
windowY = m - DIM;
}
if ( isRight == PETSC_TRUE ){
windowX = n - DIM;
}
for ( i = 0 ; i < DIM ; ++i ){
idxm[i] = i + windowY; idxn[i] = i + windowX;
}
MatGetValues(mat,DIM,idxm,DIM,idxn,values);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Dimension: %d rows x %d columns:\n", m, n);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"row index idxm:");CHKERRQ(ierr);
for ( i = 0 ; i < DIM ; ++i ){
ierr = PetscPrintf(PETSC_COMM_WORLD,"%d, ", idxm[i]);CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\ncol index idxn:");CHKERRQ(ierr);
for ( i = 0 ; i < DIM ; ++i ){
ierr = PetscPrintf(PETSC_COMM_WORLD,"%d, ", idxn[i]);CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n\n\n");CHKERRQ(ierr);
for ( i = 0 ; i < DIM ; ++i ){
for ( j = 0 ; j < DIM ; ++j ){
ierr = PetscPrintf(PETSC_COMM_WORLD,"(%2.10e/ %2.10e) ", PetscRealPart(values[i*DIM + j]), PetscImaginaryPart(values[i*DIM + j]) );CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
}
ierr = SlepcFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat A,B,MA;
PetscViewer fd;
char file[PETSC_MAX_PATH_LEN];
PetscInt m,n,M,N,dof=1;
PetscMPIInt rank,size;
PetscErrorCode ierr;
PetscTruth flg;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
SETERRQ(1,"This example does not work with complex numbers");
#else
/* Load aij matrix A */
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN-1,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_ERR_USER,"Must indicate binary file with the -f option");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatLoad(fd,MATAIJ,&A);CHKERRQ(ierr);
ierr = PetscViewerDestroy(fd);CHKERRQ(ierr);
/* Get dof, then create maij matrix MA */
ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr);
ierr = MatCreateMAIJ(A,dof,&MA);CHKERRQ(ierr);
ierr = MatGetLocalSize(MA,&m,&n);CHKERRQ(ierr);
ierr = MatGetSize(MA,&M,&N);CHKERRQ(ierr);
if (size == 1){
ierr = MatConvert(MA,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
} else {
ierr = MatConvert(MA,MATMPIAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
}
/* Test MatMult() */
ierr = MatMultEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg){
SETERRQ(PETSC_ERR_CONV_FAILED,"Error: MatMul() for MAIJ matrix");
}
/* Test MatMultAdd() */
ierr = MatMultAddEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg){
SETERRQ(PETSC_ERR_CONV_FAILED,"Error: MatMulAdd() for MAIJ matrix");
}
/* Test MatMultTranspose() */
ierr = MatMultTransposeEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg){
SETERRQ(PETSC_ERR_CONV_FAILED,"Error: MatMulAdd() for MAIJ matrix");
}
/* Test MatMultTransposeAdd() */
ierr = MatMultTransposeAddEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg){
SETERRQ(PETSC_ERR_CONV_FAILED,"Error: MatMulTransposeAdd() for MAIJ matrix");
}
ierr = MatDestroy(MA);CHKERRQ(ierr);
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = MatDestroy(B);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
#endif
return 0;
}
int main(int argc,char **args)
{
Vec x, b; /* approx solution, RHS, exact solution */
Mat A; /* linear system matrix */
KSP ksp; /* linear solver context */
PetscViewer fd,viewer;
PetscErrorCode ierr;
PetscInt its;
PetscMPIInt size;
char file[2][PETSC_MAX_PATH_LEN]; /* input file name */
PetscBool flg;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor example only!");
/*
Determine files from which we read the linear system (matrix and right-hand-side vector).
*/
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file[0],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) {
SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the matrix and right-hand-side vector that define
the linear system, Ax = b.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[0],FILE_MODE_READ,&fd);CHKERRQ(ierr);
/*
Load the matrix and vector; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
ierr = VecLoad(b,fd);CHKERRQ(ierr);
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the linear solver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create linear solver context
*/
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
/*
Set operators. Here the matrix that defines the linear system
also serves as the preconditioning matrix.
*/
ierr = KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
/*
Set runtime options, e.g.,
-ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
These options will override those specified above as long as
KSPSetFromOptions() is called _after_ any other customization
routines.
*/
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the linear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Solve linear system
*/
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Check solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Check the error
*/
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Iterations %D\n",its);CHKERRQ(ierr);
//VecView(x,PETSC_VIEWER_STDOUT_WORLD);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"solution.petsc",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
/*
Always call PetscFinalize() before exiting a program. This routine
- finalizes the PETSc libraries as well as MPI
- provides summary and diagnostic information if certain runtime
options are chosen (e.g., -log_summary).
*/
ierr = PetscFinalize();
return 0;
}
-ov <overlap> : >=0 amount of overlap between domains\n\n";
#include <petscmat.h>
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscInt nd = 2,ov=1,i,start,m,n,end,lsize;
PetscMPIInt rank;
PetscBool flg;
Mat A,B;
char file[PETSC_MAX_PATH_LEN];
PetscViewer fd;
IS *is1,*is2;
PetscRandom r;
PetscScalar rand;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
#if defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,1,"This example does not work with complex numbers");
#else
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must use -f filename to indicate a file containing a PETSc binary matrix");
ierr = PetscOptionsGetInt(NULL,NULL,"-nd",&nd,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-ov",&ov,NULL);CHKERRQ(ierr);
/* Read matrix and RHS */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Read the matrix again as a sequential matrix */
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr);
ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatLoad(B,fd);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Create the IS corresponding to subdomains */
ierr = PetscMalloc1(nd,&is1);CHKERRQ(ierr);
ierr = PetscMalloc1(nd,&is2);CHKERRQ(ierr);
/* Create the random Index Sets */
ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
for (i=0; i<nd; i++) {
ierr = PetscRandomGetValue(r,&rand);CHKERRQ(ierr);
start = (PetscInt)(rand*m);
ierr = PetscRandomGetValue(r,&rand);CHKERRQ(ierr);
end = (PetscInt)(rand*m);
lsize = end - start;
if (start > end) { start = end; lsize = -lsize;}
ierr = ISCreateStride(PETSC_COMM_SELF,lsize,start,1,is1+i);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,lsize,start,1,is2+i);CHKERRQ(ierr);
}
ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
ierr = MatIncreaseOverlap(B,nd,is2,ov);CHKERRQ(ierr);
/* Now see if the serial and parallel case have the same answers */
for (i=0; i<nd; ++i) {
ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"proc:[%d], i=%D, flg =%d\n",rank,i,(int)flg);CHKERRQ(ierr);
}
/* Free allocated memory */
for (i=0; i<nd; ++i) {
ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
}
ierr = PetscFree(is1);CHKERRQ(ierr);
ierr = PetscFree(is2);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
#endif
ierr = PetscFinalize();
return ierr;
}
/*
FormFunction - Evaluates the function and corresponding gradient.
Input Parameters:
tao - the Tao context
X - the input vector
ptr - optional user-defined context, as set by TaoSetObjectiveAndGradientRoutine()
Output Parameters:
f - the newly evaluated function
*/
PetscErrorCode FormFunction(Tao tao,Vec P,PetscReal *f,void *ctx0)
{
TS ts;
SNES snes_alg;
PetscErrorCode ierr;
Userctx *ctx = (Userctx*)ctx0;
Vec X;
Mat J;
/* sensitivity context */
PetscScalar *x_ptr;
PetscViewer Xview,Ybusview;
Vec F_alg;
Vec Xdot;
PetscInt row_loc,col_loc;
PetscScalar val;
ierr = VecGetArray(P,&x_ptr);CHKERRQ(ierr);
PG[0] = x_ptr[0];
PG[1] = x_ptr[1];
PG[2] = x_ptr[2];
ierr = VecRestoreArray(P,&x_ptr);CHKERRQ(ierr);
ctx->stepnum = 0;
ierr = VecZeroEntries(ctx->vec_q);CHKERRQ(ierr);
/* Read initial voltage vector and Ybus */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"X.bin",FILE_MODE_READ,&Xview);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Ybus.bin",FILE_MODE_READ,&Ybusview);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&ctx->V0);CHKERRQ(ierr);
ierr = VecSetSizes(ctx->V0,PETSC_DECIDE,ctx->neqs_net);CHKERRQ(ierr);
ierr = VecLoad(ctx->V0,Xview);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&ctx->Ybus);CHKERRQ(ierr);
ierr = MatSetSizes(ctx->Ybus,PETSC_DECIDE,PETSC_DECIDE,ctx->neqs_net,ctx->neqs_net);CHKERRQ(ierr);
ierr = MatSetType(ctx->Ybus,MATBAIJ);CHKERRQ(ierr);
/* ierr = MatSetBlockSize(ctx->Ybus,2);CHKERRQ(ierr); */
ierr = MatLoad(ctx->Ybus,Ybusview);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Xview);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Ybusview);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(ctx->dmpgrid,&X);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,ctx->neqs_pgrid,ctx->neqs_pgrid);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = PreallocateJacobian(J,ctx);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,ctx);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,(TSIJacobian)IJacobian,ctx);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,ctx);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,MonitorUpdateQ,ctx,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SetInitialGuess(X,ctx);CHKERRQ(ierr);
ierr = VecDuplicate(X,&F_alg);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes_alg);CHKERRQ(ierr);
ierr = SNESSetFunction(snes_alg,F_alg,AlgFunction,ctx);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes_alg,J,J,AlgJacobian,ctx);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(snes_alg,"alg_");CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes_alg);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Just to set up the Jacobian structure */
ierr = VecDuplicate(X,&Xdot);CHKERRQ(ierr);
ierr = IJacobian(ts,0.0,X,Xdot,0.0,J,J,ctx);CHKERRQ(ierr);
ierr = VecDestroy(&Xdot);CHKERRQ(ierr);
ctx->stepnum++;
ierr = TSSetDuration(ts,1000,ctx->tfaulton);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,0.01);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* ierr = TSSetPostStep(ts,SaveSolution);CHKERRQ(ierr); */
ctx->alg_flg = PETSC_FALSE;
/* Prefault period */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Create the nonlinear solver for solving the algebraic system */
/* Note that although the algebraic system needs to be solved only for
Idq and V, we reuse the entire system including xgen. The xgen
variables are held constant by setting their residuals to 0 and
putting a 1 on the Jacobian diagonal for xgen rows
*/
ierr = MatZeroEntries(J);CHKERRQ(ierr);
/* Apply disturbance - resistive fault at ctx->faultbus */
/* This is done by adding shunt conductance to the diagonal location
in the Ybus matrix */
row_loc = 2*ctx->faultbus; col_loc = 2*ctx->faultbus+1; /* Location for G */
val = 1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*ctx->faultbus+1; col_loc = 2*ctx->faultbus; /* Location for G */
val = 1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
ctx->stepnum++;
/* Disturbance period */
ierr = TSSetDuration(ts,1000,ctx->tfaultoff);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ctx->tfaulton,.01);CHKERRQ(ierr);
ctx->alg_flg = PETSC_FALSE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Remove the fault */
row_loc = 2*ctx->faultbus; col_loc = 2*ctx->faultbus+1;
val = -1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*ctx->faultbus+1; col_loc = 2*ctx->faultbus;
val = -1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
ctx->stepnum++;
/* Post-disturbance period */
ierr = TSSetDuration(ts,1000,ctx->tmax);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ctx->tfaultoff,.01);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
ierr = VecGetArray(ctx->vec_q,&x_ptr);CHKERRQ(ierr);
*f = x_ptr[0];
ierr = VecRestoreArray(ctx->vec_q,&x_ptr);CHKERRQ(ierr);
ierr = MatDestroy(&ctx->Ybus);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->V0);CHKERRQ(ierr);
ierr = SNESDestroy(&snes_alg);CHKERRQ(ierr);
ierr = VecDestroy(&F_alg);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
MatType mtype = MATMPIAIJ; /* matrix format */
Mat A,B; /* matrix */
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscBool flg,viewMats,viewIS,viewVecs;
PetscInt ierr,*nlocal,m,n;
PetscMPIInt rank,size;
MatPartitioning part;
IS is,isn;
Vec xin, xout;
VecScatter scat;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL, "-view_mats", &viewMats);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL, "-view_is", &viewIS);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL, "-view_vecs", &viewVecs);CHKERRQ(ierr);
/*
Determine file from which we read the matrix
*/
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/*
Load the matrix and vector; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,mtype);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&xin);CHKERRQ(ierr);
ierr = VecLoad(xin,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
if (viewMats) {
if (!rank) printf("Original matrix:\n");
ierr = MatView(A,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
}
if (viewVecs) {
if (!rank) printf("Original vector:\n");
ierr = VecView(xin,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Partition the graph of the matrix */
ierr = MatPartitioningCreate(PETSC_COMM_WORLD,&part);CHKERRQ(ierr);
ierr = MatPartitioningSetAdjacency(part,A);CHKERRQ(ierr);
ierr = MatPartitioningSetFromOptions(part);CHKERRQ(ierr);
/* get new processor owner number of each vertex */
ierr = MatPartitioningApply(part,&is);CHKERRQ(ierr);
if (viewIS) {
if (!rank) printf("IS1 - new processor ownership:\n");
ierr = ISView(is,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* get new global number of each old global number */
ierr = ISPartitioningToNumbering(is,&isn);CHKERRQ(ierr);
if (viewIS) {
if (!rank) printf("IS2 - new global numbering:\n");
ierr = ISView(isn,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* get number of new vertices for each processor */
ierr = PetscMalloc(size*sizeof(PetscInt),&nlocal);CHKERRQ(ierr);
ierr = ISPartitioningCount(is,size,nlocal);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
/* get old global number of each new global number */
ierr = ISInvertPermutation(isn,nlocal[rank],&is);CHKERRQ(ierr);
ierr = PetscFree(nlocal);CHKERRQ(ierr);
ierr = ISDestroy(&isn);CHKERRQ(ierr);
ierr = MatPartitioningDestroy(&part);CHKERRQ(ierr);
if (viewIS) {
if (!rank) printf("IS3=inv(IS2) - old global number of each new global number:\n");
ierr = ISView(is,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* move the matrix rows to the new processes they have been assigned to by the permutation */
ierr = ISSort(is);CHKERRQ(ierr);
ierr = MatGetSubMatrix(A,is,is,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
/* move the vector rows to the new processes they have been assigned to */
ierr = MatGetLocalSize(B,&m,&n);CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD,m,PETSC_DECIDE,&xout);CHKERRQ(ierr);
ierr = VecScatterCreate(xin,is,xout,NULL,&scat);CHKERRQ(ierr);
ierr = VecScatterBegin(scat,xin,xout,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(scat,xin,xout,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(&scat);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
if (viewMats) {
if (!rank) printf("Partitioned matrix:\n");
ierr = MatView(B,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
}
if (viewVecs) {
if (!rank) printf("Mapped vector:\n");
ierr = VecView(xout,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
{
PetscInt rstart,i,*nzd,*nzo,nzl,nzmax = 0,*ncols,nrow,j;
Mat J;
const PetscInt *cols;
const PetscScalar *vals;
PetscScalar *nvals;
ierr = MatGetOwnershipRange(B,&rstart,NULL);CHKERRQ(ierr);
ierr = PetscMalloc(2*m*sizeof(PetscInt),&nzd);CHKERRQ(ierr);
ierr = PetscMemzero(nzd,2*m*sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMalloc(2*m*sizeof(PetscInt),&nzo);CHKERRQ(ierr);
ierr = PetscMemzero(nzo,2*m*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0; i<m; i++) {
ierr = MatGetRow(B,i+rstart,&nzl,&cols,NULL);CHKERRQ(ierr);
for (j=0; j<nzl; j++) {
if (cols[j] >= rstart && cols[j] < rstart+n) {
nzd[2*i] += 2;
nzd[2*i+1] += 2;
} else {
nzo[2*i] += 2;
nzo[2*i+1] += 2;
}
}
nzmax = PetscMax(nzmax,nzd[2*i]+nzo[2*i]);
ierr = MatRestoreRow(B,i+rstart,&nzl,&cols,NULL);CHKERRQ(ierr);
}
ierr = MatCreateAIJ(PETSC_COMM_WORLD,2*m,2*m,PETSC_DECIDE,PETSC_DECIDE,0,nzd,0,nzo,&J);CHKERRQ(ierr);
ierr = PetscInfo(0,"Created empty Jacobian matrix\n");CHKERRQ(ierr);
ierr = PetscFree(nzd);CHKERRQ(ierr);
ierr = PetscFree(nzo);CHKERRQ(ierr);
ierr = PetscMalloc2(nzmax,PetscInt,&ncols,nzmax,PetscScalar,&nvals);CHKERRQ(ierr);
ierr = PetscMemzero(nvals,nzmax*sizeof(PetscScalar));CHKERRQ(ierr);
for (i=0; i<m; i++) {
ierr = MatGetRow(B,i+rstart,&nzl,&cols,&vals);CHKERRQ(ierr);
for (j=0; j<nzl; j++) {
ncols[2*j] = 2*cols[j];
ncols[2*j+1] = 2*cols[j]+1;
}
nrow = 2*(i+rstart);
ierr = MatSetValues(J,1,&nrow,2*nzl,ncols,nvals,INSERT_VALUES);CHKERRQ(ierr);
nrow = 2*(i+rstart) + 1;
ierr = MatSetValues(J,1,&nrow,2*nzl,ncols,nvals,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatRestoreRow(B,i+rstart,&nzl,&cols,&vals);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (viewMats) {
if (!rank) printf("Jacobian matrix structure:\n");
ierr = MatView(J,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = PetscFree2(ncols,nvals);CHKERRQ(ierr);
}
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = VecDestroy(&xin);CHKERRQ(ierr);
ierr = VecDestroy(&xout);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A,B,F;
PetscErrorCode ierr;
KSP ksp;
PC pc;
PetscInt N, n=10, m, Istart, Iend, II, J, i,j;
PetscInt nneg, nzero, npos;
PetscScalar v,sigma;
PetscBool flag,loadA=PETSC_FALSE,loadB=PETSC_FALSE;
char file[2][PETSC_MAX_PATH_LEN];
PetscViewer viewer;
PetscMPIInt rank;
PetscInitialize(&argc,&args,(char *)0,help);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the matrices that define the eigensystem, Ax=kBx
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscOptionsGetString(PETSC_NULL,"-fA",file[0],PETSC_MAX_PATH_LEN,&loadA);CHKERRQ(ierr);
if (loadA) {
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[0],FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATSBAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-fB",file[1],PETSC_MAX_PATH_LEN,&loadB);CHKERRQ(ierr);
if (loadB){
/* load B to get A = A + sigma*B */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[1],FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetType(B,MATSBAIJ);CHKERRQ(ierr);
ierr = MatLoad(B,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
}
if (!loadA) { /* Matrix A is copied from slepc-3.0.0-p6/src/examples/ex13.c. */
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,&flag);CHKERRQ(ierr);
if( flag==PETSC_FALSE ) m=n;
N = n*m;
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetType(A,MATSBAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
for( II=Istart; II<Iend; II++ ) {
v = -1.0; i = II/n; j = II-i*n;
if(i>0) { J=II-n; MatSetValues(A,1,&II,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr); }
if(i<m-1) { J=II+n; MatSetValues(A,1,&II,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr); }
if(j>0) { J=II-1; MatSetValues(A,1,&II,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr); }
if(j<n-1) { J=II+1; MatSetValues(A,1,&II,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr); }
v=4.0; MatSetValues(A,1,&II,1,&II,&v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
/* ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
if (!loadB) {
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(B,MATSBAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
ierr = MatSetOption(B,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
for( II=Istart; II<Iend; II++ ) {
/* v=4.0; MatSetValues(B,1,&II,1,&II,&v,INSERT_VALUES);CHKERRQ(ierr); */
v=1.0; MatSetValues(B,1,&II,1,&II,&v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
/* ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
/* Set a shift: A = A - sigma*B */
ierr = PetscOptionsGetScalar(PETSC_NULL,"-sigma",&sigma,&flag);CHKERRQ(ierr);
if (flag){
sigma = -1.0 * sigma;
ierr = MatAXPY(A,sigma,B,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); /* A <- A - sigma*B */
/* ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
}
/* Test MatGetInertia() */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCCHOLESKY);CHKERRQ(ierr);
ierr = PCSetFromOptions(pc);CHKERRQ(ierr);
ierr = PCSetUp(pc);CHKERRQ(ierr);
ierr = PCFactorGetMatrix(pc,&F);CHKERRQ(ierr);
ierr = MatGetInertia(F,&nneg,&nzero,&npos);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF," MatInertia: nneg: %D, nzero: %D, npos: %D\n",nneg,nzero,npos);CHKERRQ(ierr);
}
/* Destroy */
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A[3],B; /* matrix */
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscBool flg;
Vec x,y,z,work;
PetscReal rnorm;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
/*
Determine files from which we read the two linear systems
(matrix and right-hand-side vector).
*/
ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/*
Load the matrix; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A[0]);CHKERRQ(ierr);
ierr = MatLoad(A[0],fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatDuplicate(A[0],MAT_COPY_VALUES,&A[1]);CHKERRQ(ierr);
ierr = MatDuplicate(A[0],MAT_COPY_VALUES,&A[2]);CHKERRQ(ierr);
ierr = MatShift(A[1],1.0);CHKERRQ(ierr);
ierr = MatShift(A[1],2.0);CHKERRQ(ierr);
ierr = MatCreateVecs(A[0],&x,&y);CHKERRQ(ierr);
ierr = VecDuplicate(y,&work);CHKERRQ(ierr);
ierr = VecDuplicate(y,&z);CHKERRQ(ierr);
ierr = VecSet(x,1.0);CHKERRQ(ierr);
ierr = MatMult(A[0],x,z);CHKERRQ(ierr);
ierr = MatMultAdd(A[1],x,z,z);CHKERRQ(ierr);
ierr = MatMultAdd(A[2],x,z,z);CHKERRQ(ierr);
ierr = MatCreateComposite(PETSC_COMM_WORLD,3,A,&B);CHKERRQ(ierr);
ierr = MatMult(B,x,y);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = VecAXPY(y,-1.0,z);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&rnorm);CHKERRQ(ierr);
if (rnorm > 1.e-10) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error with composite add %g\n",(double)rnorm);CHKERRQ(ierr);
}
ierr = MatCreateComposite(PETSC_COMM_WORLD,3,A,&B);CHKERRQ(ierr);
ierr = MatCompositeMerge(B);CHKERRQ(ierr);
ierr = MatMult(B,x,y);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = VecAXPY(y,-1.0,z);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&rnorm);CHKERRQ(ierr);
if (rnorm > 1.e-10) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error with composite add after merge %g\n",(double)rnorm);CHKERRQ(ierr);
}
ierr = VecSet(x,1.0);CHKERRQ(ierr);
ierr = MatMult(A[0],x,z);CHKERRQ(ierr);
ierr = MatMult(A[1],z,work);CHKERRQ(ierr);
ierr = MatMult(A[2],work,z);CHKERRQ(ierr);
ierr = MatCreateComposite(PETSC_COMM_WORLD,3,A,&B);CHKERRQ(ierr);
ierr = MatCompositeSetType(B,MAT_COMPOSITE_MULTIPLICATIVE);CHKERRQ(ierr);
ierr = MatMult(B,x,y);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = VecAXPY(y,-1.0,z);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&rnorm);CHKERRQ(ierr);
if (rnorm > 1.e-10) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error with composite multiplicative %g\n",(double)rnorm);CHKERRQ(ierr);
}
ierr = MatCreateComposite(PETSC_COMM_WORLD,3,A,&B);CHKERRQ(ierr);
ierr = MatCompositeSetType(B,MAT_COMPOSITE_MULTIPLICATIVE);CHKERRQ(ierr);
ierr = MatCompositeMerge(B);CHKERRQ(ierr);
ierr = MatMult(B,x,y);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = VecAXPY(y,-1.0,z);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&rnorm);CHKERRQ(ierr);
if (rnorm > 1.e-10) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error with composite multiplicative after merge %g\n",(double)rnorm);CHKERRQ(ierr);
}
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&work);CHKERRQ(ierr);
ierr = VecDestroy(&z);CHKERRQ(ierr);
ierr = MatDestroy(&A[0]);CHKERRQ(ierr);
ierr = MatDestroy(&A[1]);CHKERRQ(ierr);
ierr = MatDestroy(&A[2]);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
Mat A,F;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscBool flg;
Vec x,y,w;
MatFactorInfo iluinfo;
IS perm;
PetscInt m;
PetscReal norm;
PetscInitialize(&argc,&args,(char*)0,help);
/*
Determine file from which we read the matrix
*/
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/*
Load the matrix; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQBAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecLoad(x,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = VecDuplicate(x,&w);CHKERRQ(ierr);
ierr = MatGetFactor(A,"petsc",MAT_FACTOR_ILU,&F);CHKERRQ(ierr);
iluinfo.fill = 1.0;
ierr = MatGetSize(A,&m,0);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_WORLD,m,0,1,&perm);CHKERRQ(ierr);
ierr = MatLUFactorSymbolic(F,A,perm,perm,&iluinfo);CHKERRQ(ierr);
ierr = MatLUFactorNumeric(F,A,&iluinfo);CHKERRQ(ierr);
ierr = MatSolveTranspose(F,x,y);CHKERRQ(ierr);
F->ops->solvetranspose = MatSolveTranspose_SeqBAIJ_N;
ierr = MatSolveTranspose(F,x,w);CHKERRQ(ierr);
/* VecView(w,0);VecView(y,0); */
ierr = VecAXPY(w,-1.0,y);CHKERRQ(ierr);
ierr = VecNorm(w,NORM_2,&norm);CHKERRQ(ierr);
if (norm) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Norm of difference is nonzero %g\n",norm);CHKERRQ(ierr);
}
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&w);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
TS ts;
SNES snes_alg;
PetscErrorCode ierr;
PetscMPIInt size;
Userctx user;
PetscViewer Xview,Ybusview;
Vec X;
Mat J;
PetscInt i;
/* sensitivity context */
PetscScalar *y_ptr;
Vec lambda[1];
PetscInt *idx2;
Vec Xdot;
Vec F_alg;
PetscInt row_loc,col_loc;
PetscScalar val;
ierr = PetscInitialize(&argc,&argv,"petscoptions",help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
user.neqs_gen = 9*ngen; /* # eqs. for generator subsystem */
user.neqs_net = 2*nbus; /* # eqs. for network subsystem */
user.neqs_pgrid = user.neqs_gen + user.neqs_net;
/* Create indices for differential and algebraic equations */
ierr = PetscMalloc1(7*ngen,&idx2);CHKERRQ(ierr);
for (i=0; i<ngen; i++) {
idx2[7*i] = 9*i; idx2[7*i+1] = 9*i+1; idx2[7*i+2] = 9*i+2; idx2[7*i+3] = 9*i+3;
idx2[7*i+4] = 9*i+6; idx2[7*i+5] = 9*i+7; idx2[7*i+6] = 9*i+8;
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,7*ngen,idx2,PETSC_COPY_VALUES,&user.is_diff);CHKERRQ(ierr);
ierr = ISComplement(user.is_diff,0,user.neqs_pgrid,&user.is_alg);CHKERRQ(ierr);
ierr = PetscFree(idx2);CHKERRQ(ierr);
/* Read initial voltage vector and Ybus */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"X.bin",FILE_MODE_READ,&Xview);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Ybus.bin",FILE_MODE_READ,&Ybusview);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&user.V0);CHKERRQ(ierr);
ierr = VecSetSizes(user.V0,PETSC_DECIDE,user.neqs_net);CHKERRQ(ierr);
ierr = VecLoad(user.V0,Xview);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&user.Ybus);CHKERRQ(ierr);
ierr = MatSetSizes(user.Ybus,PETSC_DECIDE,PETSC_DECIDE,user.neqs_net,user.neqs_net);CHKERRQ(ierr);
ierr = MatSetType(user.Ybus,MATBAIJ);CHKERRQ(ierr);
/* ierr = MatSetBlockSize(user.Ybus,2);CHKERRQ(ierr); */
ierr = MatLoad(user.Ybus,Ybusview);CHKERRQ(ierr);
/* Set run time options */
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Transient stability fault options","");CHKERRQ(ierr);
{
user.tfaulton = 1.0;
user.tfaultoff = 1.2;
user.Rfault = 0.0001;
user.faultbus = 8;
ierr = PetscOptionsReal("-tfaulton","","",user.tfaulton,&user.tfaulton,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tfaultoff","","",user.tfaultoff,&user.tfaultoff,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-faultbus","","",user.faultbus,&user.faultbus,NULL);CHKERRQ(ierr);
user.t0 = 0.0;
user.tmax = 5.0;
ierr = PetscOptionsReal("-t0","","",user.t0,&user.t0,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tmax","","",user.tmax,&user.tmax,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Xview);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Ybusview);CHKERRQ(ierr);
/* Create DMs for generator and network subsystems */
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,user.neqs_gen,1,1,NULL,&user.dmgen);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmgen,"dmgen_");CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,user.neqs_net,1,1,NULL,&user.dmnet);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmnet,"dmnet_");CHKERRQ(ierr);
/* Create a composite DM packer and add the two DMs */
ierr = DMCompositeCreate(PETSC_COMM_WORLD,&user.dmpgrid);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(user.dmpgrid,"pgrid_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(user.dmpgrid,user.dmgen);CHKERRQ(ierr);
ierr = DMCompositeAddDM(user.dmpgrid,user.dmnet);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.dmpgrid,&X);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,user.neqs_pgrid,user.neqs_pgrid);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = PreallocateJacobian(J,&user);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&user);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,(TSIJacobian)IJacobian,&user);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SetInitialGuess(X,&user);CHKERRQ(ierr);
/* Just to set up the Jacobian structure */
ierr = VecDuplicate(X,&Xdot);CHKERRQ(ierr);
ierr = IJacobian(ts,0.0,X,Xdot,0.0,J,J,&user);CHKERRQ(ierr);
ierr = VecDestroy(&Xdot);CHKERRQ(ierr);
/*
Save trajectory of solution so that TSAdjointSolve() may be used
*/
ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr);
ierr = TSSetDuration(ts,1000,user.tfaulton);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,0.01);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
user.alg_flg = PETSC_FALSE;
/* Prefault period */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Create the nonlinear solver for solving the algebraic system */
/* Note that although the algebraic system needs to be solved only for
Idq and V, we reuse the entire system including xgen. The xgen
variables are held constant by setting their residuals to 0 and
putting a 1 on the Jacobian diagonal for xgen rows
*/
ierr = VecDuplicate(X,&F_alg);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes_alg);CHKERRQ(ierr);
ierr = SNESSetFunction(snes_alg,F_alg,AlgFunction,&user);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes_alg,J,J,AlgJacobian,&user);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(snes_alg,"alg_");CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes_alg);CHKERRQ(ierr);
/* Apply disturbance - resistive fault at user.faultbus */
/* This is done by adding shunt conductance to the diagonal location
in the Ybus matrix */
row_loc = 2*user.faultbus; col_loc = 2*user.faultbus+1; /* Location for G */
val = 1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*user.faultbus+1; col_loc = 2*user.faultbus; /* Location for G */
val = 1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Disturbance period */
ierr = TSSetDuration(ts,1000,user.tfaultoff);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.tfaulton,.01);CHKERRQ(ierr);
user.alg_flg = PETSC_FALSE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Remove the fault */
row_loc = 2*user.faultbus; col_loc = 2*user.faultbus+1;
val = -1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*user.faultbus+1; col_loc = 2*user.faultbus;
val = -1/user.Rfault;
ierr = MatSetValues(user.Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user.Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Post-disturbance period */
ierr = TSSetDuration(ts,1000,user.tmax);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.tfaultoff,.01);CHKERRQ(ierr);
user.alg_flg = PETSC_TRUE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Adjoint model starts here
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetPostStep(ts,NULL);CHKERRQ(ierr);
ierr = MatCreateVecs(J,&lambda[0],NULL);CHKERRQ(ierr);
/* Set initial conditions for the adjoint integration */
ierr = VecZeroEntries(lambda[0]);CHKERRQ(ierr);
ierr = VecGetArray(lambda[0],&y_ptr);CHKERRQ(ierr);
y_ptr[0] = 1.0;
ierr = VecRestoreArray(lambda[0],&y_ptr);CHKERRQ(ierr);
ierr = TSSetCostGradients(ts,1,lambda,NULL);CHKERRQ(ierr);
ierr = TSAdjointSolve(ts);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n sensitivity wrt initial conditions: \n");CHKERRQ(ierr);
ierr = VecView(lambda[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&lambda[0]);CHKERRQ(ierr);
ierr = SNESDestroy(&snes_alg);CHKERRQ(ierr);
ierr = VecDestroy(&F_alg);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatDestroy(&user.Ybus);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&user.V0);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmgen);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmnet);CHKERRQ(ierr);
ierr = DMDestroy(&user.dmpgrid);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_diff);CHKERRQ(ierr);
ierr = ISDestroy(&user.is_alg);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
Mat A,B;
PetscErrorCode ierr;
char file[PETSC_MAX_PATH_LEN];
PetscBool flg;
PetscViewer fd;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);
CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);
CHKERRQ(ierr);
/*
Load the matrix; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);
CHKERRQ(ierr);
ierr = MatSetFromOptions(A);
CHKERRQ(ierr);
ierr = MatLoad(A,fd);
CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);
CHKERRQ(ierr);
/*
Open another binary file. Note that we use FILE_MODE_WRITE to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fileoutput",FILE_MODE_WRITE,&fd);
CHKERRQ(ierr);
ierr = PetscViewerBinarySetFlowControl(fd,3);
CHKERRQ(ierr);
/*
Save the matrix and vector; then destroy the viewer.
*/
ierr = MatView(A,fd);
CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);
CHKERRQ(ierr);
/* load the new matrix */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fileoutput",FILE_MODE_READ,&fd);
CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);
CHKERRQ(ierr);
ierr = MatSetFromOptions(B);
CHKERRQ(ierr);
ierr = MatLoad(B,fd);
CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);
CHKERRQ(ierr);
ierr = MatEqual(A,B,&flg);
CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrices are equal\n");
CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrices are not equal\n");
CHKERRQ(ierr);
}
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = MatDestroy(&B);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
void PETSC_STDCALL matload_(Mat *mat,PetscViewer *vin,PetscErrorCode *ierr)
{
PetscViewer v;
PetscPatchDefaultViewers_Fortran(vin,v);
*ierr = MatLoad(*mat,v);
}