PetscErrorCode MyFormMatrix(DMMG fdmmg,Mat A,Mat B)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatShift(A,1.0);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatShift_SMF(Mat Y, PetscReal a)
{
PetscErrorCode ierr;
MatSubMatFreeCtx ctx;
PetscFunctionBegin;
ierr = MatShellGetContext(Y,(void **)&ctx);CHKERRQ(ierr);
ierr = MatShift(ctx->A,a);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
const PetscScalar xvals[] = {11,13},yvals[] = {17,19};
const PetscInt inds[] = {0,1};
PetscScalar avals[] = {2,3,5,7};
Mat S1,S2;
Vec X,Y;
User user;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,2,2,2,NULL,&user->A);CHKERRQ(ierr);
ierr = MatSetUp(user->A);CHKERRQ(ierr);
ierr = MatSetValues(user->A,2,inds,2,inds,avals,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_WORLD,2,&X);CHKERRQ(ierr);
ierr = VecSetValues(X,2,inds,xvals,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(X);CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);CHKERRQ(ierr);
ierr = VecDuplicate(X,&Y);CHKERRQ(ierr);
ierr = VecSetValues(Y,2,inds,yvals,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(Y);CHKERRQ(ierr);
ierr = VecAssemblyEnd(Y);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,2,2,2,2,user,&S1);CHKERRQ(ierr);
ierr = MatSetUp(S1);CHKERRQ(ierr);
ierr = MatShellSetOperation(S1,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S1,MATOP_COPY,(void (*)(void))MatCopy_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S1,MATOP_DESTROY,(void (*)(void))MatDestroy_User);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,2,2,2,2,NULL,&S2);CHKERRQ(ierr);
ierr = MatSetUp(S2);CHKERRQ(ierr);
ierr = MatShellSetOperation(S2,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S2,MATOP_COPY,(void (*)(void))MatCopy_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S2,MATOP_DESTROY,(void (*)(void))MatDestroy_User);CHKERRQ(ierr);
ierr = MatScale(S1,31);CHKERRQ(ierr);
ierr = MatShift(S1,37);CHKERRQ(ierr);
ierr = MatDiagonalScale(S1,X,Y);CHKERRQ(ierr);
ierr = MatCopy(S1,S2,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatMult(S1,X,Y);CHKERRQ(ierr);
ierr = VecView(Y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatMult(S2,X,Y);CHKERRQ(ierr);
ierr = VecView(Y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&S1);CHKERRQ(ierr);
ierr = MatDestroy(&S2);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&Y);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
static PetscErrorCode TestMatrix(Mat A,Vec X,Vec Y,Vec Z)
{
PetscErrorCode ierr;
Vec W1,W2;
Mat E;
const char *mattypename;
PetscViewer viewer = PETSC_VIEWER_STDOUT_WORLD;
PetscFunctionBegin;
ierr = VecDuplicate(X,&W1);
CHKERRQ(ierr);
ierr = VecDuplicate(X,&W2);
CHKERRQ(ierr);
ierr = MatScale(A,31);
CHKERRQ(ierr);
ierr = MatShift(A,37);
CHKERRQ(ierr);
ierr = MatDiagonalScale(A,X,Y);
CHKERRQ(ierr);
ierr = MatScale(A,41);
CHKERRQ(ierr);
ierr = MatDiagonalScale(A,Y,Z);
CHKERRQ(ierr);
ierr = MatComputeExplicitOperator(A,&E);
CHKERRQ(ierr);
ierr = PetscObjectGetType((PetscObject)A,&mattypename);
CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Matrix of type: %s\n",mattypename);
CHKERRQ(ierr);
ierr = MatView(E,viewer);
CHKERRQ(ierr);
ierr = MatMult(A,Z,W1);
CHKERRQ(ierr);
ierr = MatMultTranspose(A,W1,W2);
CHKERRQ(ierr);
ierr = VecView(W2,viewer);
CHKERRQ(ierr);
ierr = MatGetDiagonal(A,W2);
CHKERRQ(ierr);
ierr = VecView(W2,viewer);
CHKERRQ(ierr);
ierr = MatDestroy(&E);
CHKERRQ(ierr);
ierr = VecDestroy(&W1);
CHKERRQ(ierr);
ierr = VecDestroy(&W2);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode TSPrecond_Sundials(realtype tn,N_Vector y,N_Vector fy,
booleantype jok,booleantype *jcurPtr,
realtype _gamma,void *P_data,
N_Vector vtemp1,N_Vector vtemp2,N_Vector vtemp3)
{
TS ts = (TS) P_data;
TS_Sundials *cvode = (TS_Sundials*)ts->data;
PC pc = cvode->pc;
PetscErrorCode ierr;
Mat Jac = ts->B;
Vec yy = cvode->w1;
PetscScalar one = 1.0,gm;
MatStructure str = DIFFERENT_NONZERO_PATTERN;
PetscScalar *y_data;
PetscFunctionBegin;
/* This allows us to construct preconditioners in-place if we like */
ierr = MatSetUnfactored(Jac);CHKERRQ(ierr);
/* jok - TRUE means reuse current Jacobian else recompute Jacobian */
if (jok) {
ierr = MatCopy(cvode->pmat,Jac,str);CHKERRQ(ierr);
*jcurPtr = FALSE;
} else {
/* make PETSc vector yy point to SUNDIALS vector y */
y_data = (PetscScalar *) N_VGetArrayPointer(y);
ierr = VecPlaceArray(yy,y_data); CHKERRQ(ierr);
/* compute the Jacobian */
ierr = TSComputeRHSJacobian(ts,ts->ptime,yy,&Jac,&Jac,&str);CHKERRQ(ierr);
ierr = VecResetArray(yy); CHKERRQ(ierr);
/* copy the Jacobian matrix */
if (!cvode->pmat) {
ierr = MatDuplicate(Jac,MAT_COPY_VALUES,&cvode->pmat);CHKERRQ(ierr);
ierr = PetscLogObjectParent(ts,cvode->pmat);CHKERRQ(ierr);
} else {
ierr = MatCopy(Jac,cvode->pmat,str);CHKERRQ(ierr);
}
*jcurPtr = TRUE;
}
/* construct I-gamma*Jac */
gm = -_gamma;
ierr = MatScale(Jac,gm);CHKERRQ(ierr);
ierr = MatShift(Jac,one);CHKERRQ(ierr);
ierr = PCSetOperators(pc,Jac,Jac,str);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char *argv[])
{
PetscErrorCode ierr;
Mat A,S = NULL,Sexplicit = NULL;
IS is0,is1;
ierr = PetscInitialize(&argc,&argv,0,help);if (ierr) return ierr;
/* Test the Schur complement one way */
ierr = Create(PETSC_COMM_WORLD,&A,&is0,&is1);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(is0,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(is1,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatGetSchurComplement(A,is0,is0,is1,is1,MAT_INITIAL_MATRIX,&S,MAT_SCHUR_COMPLEMENT_AINV_DIAG,MAT_IGNORE_MATRIX,NULL);CHKERRQ(ierr);
ierr = MatComputeExplicitOperator(S,&Sexplicit);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nExplicit Schur complement of (0,0) in (1,1)\n");CHKERRQ(ierr);
ierr = MatView(Sexplicit,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = Destroy(&A,&is0,&is1);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = MatDestroy(&Sexplicit);CHKERRQ(ierr);
/* And the other */
ierr = Create(PETSC_COMM_WORLD,&A,&is0,&is1);CHKERRQ(ierr);
ierr = MatGetSchurComplement(A,is1,is1,is0,is0,MAT_INITIAL_MATRIX,&S,MAT_SCHUR_COMPLEMENT_AINV_DIAG,MAT_IGNORE_MATRIX,NULL);CHKERRQ(ierr);
ierr = MatComputeExplicitOperator(S,&Sexplicit);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nExplicit Schur complement of (1,1) in (0,0)\n");CHKERRQ(ierr);
ierr = MatView(Sexplicit,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = Destroy(&A,&is0,&is1);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = MatDestroy(&Sexplicit);CHKERRQ(ierr);
/* This time just the preconditioning matrix. */
ierr = Create(PETSC_COMM_WORLD,&A,&is0,&is1);CHKERRQ(ierr);
ierr = MatGetSchurComplement(A,is0,is0,is1,is1,MAT_IGNORE_MATRIX,NULL,MAT_SCHUR_COMPLEMENT_AINV_DIAG,MAT_INITIAL_MATRIX,&S);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nPreconditioning Schur complement of (0,0) in (1,1)\n");CHKERRQ(ierr);
ierr = MatView(S,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Modify and refresh */
ierr = MatShift(A,1.);CHKERRQ(ierr);
ierr = MatGetSchurComplement(A,is0,is0,is1,is1,MAT_IGNORE_MATRIX,NULL,MAT_SCHUR_COMPLEMENT_AINV_DIAG,MAT_REUSE_MATRIX,&S);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nAfter update\n");CHKERRQ(ierr);
ierr = MatView(S,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = Destroy(&A,&is0,&is1);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
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);
ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr);
ierr = MatShift(A,X);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr);
ierr = MatLoad(A,viewer);CHKERRQ(ierr);
/* Free memory */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void PETSC_STDCALL matshift_(Mat Y,PetscScalar *a, int *__ierr ){
*__ierr = MatShift(
(Mat)PetscToPointer((Y) ),*a);
}
int main(int argc,char **args)
{
Mat A,B;
Vec xx,s1,s2,yy;
PetscErrorCode ierr;
PetscInt m=45,rows[2],cols[2],bs=1,i,row,col,*idx,M;
PetscScalar rval,vals1[4],vals2[4];
PetscRandom rdm;
IS is1,is2;
PetscReal s1norm,s2norm,rnorm,tol = 1.e-4;
PetscTruth flg;
MatFactorInfo info;
PetscInitialize(&argc,&args,(char *)0,help);
/* Test MatSetValues() and MatGetValues() */
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_block_size",&bs,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_size",&m,PETSC_NULL);CHKERRQ(ierr);
M = m*bs;
ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,bs,M,M,1,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,M,M,15,PETSC_NULL,&B);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,M,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&yy);CHKERRQ(ierr);
/* For each row add atleast 15 elements */
for (row=0; row<M; row++) {
for (i=0; i<25*bs; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
col = (PetscInt)(PetscRealPart(rval)*M);
ierr = MatSetValues(A,1,&row,1,&col,&rval,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&row,1,&col,&rval,INSERT_VALUES);CHKERRQ(ierr);
}
}
/* Now set blocks of values */
for (i=0; i<20*bs; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[0] = (PetscInt)(PetscRealPart(rval)*M);
vals1[0] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[1] = (PetscInt)(PetscRealPart(rval)*M);
vals1[1] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[0] = (PetscInt)(PetscRealPart(rval)*M);
vals1[2] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[1] = (PetscInt)(PetscRealPart(rval)*M);
vals1[3] = rval;
ierr = MatSetValues(A,2,rows,2,cols,vals1,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,2,rows,2,cols,vals1,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatNorm() */
ierr = MatNorm(A,NORM_FROBENIUS,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_FROBENIUS,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_FROBENIUS()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_INFINITY,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_INFINITY,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_INFINITY()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_1,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_1,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_NORM_1()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
/* MatShift() */
rval = 10*s1norm;
ierr = MatShift(A,rval);CHKERRQ(ierr);
ierr = MatShift(B,rval);CHKERRQ(ierr);
/* Test MatTranspose() */
ierr = MatTranspose(A,MAT_REUSE_MATRIX,&A);CHKERRQ(ierr);
ierr = MatTranspose(B,MAT_REUSE_MATRIX,&B);CHKERRQ(ierr);
/* Now do MatGetValues() */
for (i=0; i<30; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[0] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[1] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[0] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[1] = (PetscInt)(PetscRealPart(rval)*M);
ierr = MatGetValues(A,2,rows,2,cols,vals1);CHKERRQ(ierr);
ierr = MatGetValues(B,2,rows,2,cols,vals2);CHKERRQ(ierr);
ierr = PetscMemcmp(vals1,vals2,4*sizeof(PetscScalar),&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetValues bs = %D\n",bs);CHKERRQ(ierr);
}
}
/* Test MatMult(), MatMultAdd() */
for (i=0; i<40; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSet(s2,0.0);CHKERRQ(ierr);
ierr = MatMult(A,xx,s1);CHKERRQ(ierr);
ierr = MatMultAdd(A,xx,s2,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatMult not equal to MatMultAdd Norm1=%e Norm2=%e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatMult() */
ierr = MatMultEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult()\n");CHKERRQ(ierr);
}
/* Test MatMultAdd() */
ierr = MatMultAddEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultAdd()\n");CHKERRQ(ierr);
}
/* Test MatMultTranspose() */
ierr = MatMultTransposeEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultTranspose()\n");CHKERRQ(ierr);
}
/* Test MatMultTransposeAdd() */
ierr = MatMultTransposeAddEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultTransposeAdd()\n");CHKERRQ(ierr);
}
/* Do LUFactor() on both the matrices */
ierr = PetscMalloc(M*sizeof(PetscInt),&idx);CHKERRQ(ierr);
for (i=0; i<M; i++) idx[i] = i;
ierr = ISCreateGeneral(PETSC_COMM_SELF,M,idx,&is1);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,M,idx,&is2);CHKERRQ(ierr);
ierr = PetscFree(idx);CHKERRQ(ierr);
ierr = ISSetPermutation(is1);CHKERRQ(ierr);
ierr = ISSetPermutation(is2);CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&info);CHKERRQ(ierr);
info.fill = 2.0;
info.dtcol = 0.0;
info.zeropivot = 1.e-14;
info.pivotinblocks = 1.0;
ierr = MatLUFactor(B,is1,is2,&info);CHKERRQ(ierr);
ierr = MatLUFactor(A,is1,is2,&info);CHKERRQ(ierr);
/* Test MatSolveAdd() */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(yy,rdm);CHKERRQ(ierr);
ierr = MatSolveAdd(B,xx,yy,s2);CHKERRQ(ierr);
ierr = MatSolveAdd(A,xx,yy,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveAdd - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolveAdd() when x = A'b +x */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(s1,rdm);CHKERRQ(ierr);
ierr = VecCopy(s2,s1);CHKERRQ(ierr);
ierr = MatSolveAdd(B,xx,s2,s2);CHKERRQ(ierr);
ierr = MatSolveAdd(A,xx,s1,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveAdd(same) - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolve() */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatSolve(B,xx,s2);CHKERRQ(ierr);
ierr = MatSolve(A,xx,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolve - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolveTranspose() */
if (bs < 8) {
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatSolveTranspose(B,xx,s2);CHKERRQ(ierr);
ierr = MatSolveTranspose(A,xx,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveTranspose - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
}
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = MatDestroy(B);CHKERRQ(ierr);
ierr = VecDestroy(xx);CHKERRQ(ierr);
ierr = VecDestroy(s1);CHKERRQ(ierr);
ierr = VecDestroy(s2);CHKERRQ(ierr);
ierr = VecDestroy(yy);CHKERRQ(ierr);
ierr = ISDestroy(is1);CHKERRQ(ierr);
ierr = ISDestroy(is2);CHKERRQ(ierr);
ierr = PetscRandomDestroy(rdm);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
PetscErrorCode EPSSetUp_LAPACK(EPS eps)
{
PetscErrorCode ierr,ierra,ierrb;
PetscBool isshift,denseok=PETSC_FALSE;
Mat A,B,OP,Adense,Bdense;
PetscScalar shift,*Ap,*Bp;
PetscInt i,ld,nmat;
KSP ksp;
PC pc;
Vec v;
PetscFunctionBegin;
eps->ncv = eps->n;
if (eps->mpd) { ierr = PetscInfo(eps,"Warning: parameter mpd ignored\n");CHKERRQ(ierr); }
if (!eps->which) { ierr = EPSSetWhichEigenpairs_Default(eps);CHKERRQ(ierr); }
if (eps->balance!=EPS_BALANCE_NONE) { ierr = PetscInfo(eps,"Warning: balancing ignored\n");CHKERRQ(ierr); }
if (eps->extraction) { ierr = PetscInfo(eps,"Warning: extraction type ignored\n");CHKERRQ(ierr); }
ierr = EPSAllocateSolution(eps,0);CHKERRQ(ierr);
/* attempt to get dense representations of A and B separately */
ierr = PetscObjectTypeCompare((PetscObject)eps->st,STSHIFT,&isshift);CHKERRQ(ierr);
if (isshift) {
ierr = STGetNumMatrices(eps->st,&nmat);CHKERRQ(ierr);
ierr = STGetOperators(eps->st,0,&A);CHKERRQ(ierr);
if (nmat>1) { ierr = STGetOperators(eps->st,1,&B);CHKERRQ(ierr); }
PetscPushErrorHandler(PetscIgnoreErrorHandler,NULL);
ierra = SlepcMatConvertSeqDense(A,&Adense);CHKERRQ(ierr);
if (eps->isgeneralized) {
ierrb = SlepcMatConvertSeqDense(B,&Bdense);CHKERRQ(ierr);
} else {
ierrb = 0;
}
PetscPopErrorHandler();
denseok = (ierra == 0 && ierrb == 0)? PETSC_TRUE: PETSC_FALSE;
} else Adense = NULL;
/* setup DS */
if (denseok) {
if (eps->isgeneralized) {
if (eps->ishermitian) {
if (eps->ispositive) {
ierr = DSSetType(eps->ds,DSGHEP);CHKERRQ(ierr);
} else {
ierr = DSSetType(eps->ds,DSGNHEP);CHKERRQ(ierr); /* TODO: should be DSGHIEP */
}
} else {
ierr = DSSetType(eps->ds,DSGNHEP);CHKERRQ(ierr);
}
} else {
if (eps->ishermitian) {
ierr = DSSetType(eps->ds,DSHEP);CHKERRQ(ierr);
} else {
ierr = DSSetType(eps->ds,DSNHEP);CHKERRQ(ierr);
}
}
} else {
ierr = DSSetType(eps->ds,DSNHEP);CHKERRQ(ierr);
}
ierr = DSAllocate(eps->ds,eps->ncv);CHKERRQ(ierr);
ierr = DSGetLeadingDimension(eps->ds,&ld);CHKERRQ(ierr);
ierr = DSSetDimensions(eps->ds,eps->ncv,0,0,0);CHKERRQ(ierr);
if (denseok) {
ierr = STGetShift(eps->st,&shift);CHKERRQ(ierr);
if (shift != 0.0) {
ierr = MatShift(Adense,shift);CHKERRQ(ierr);
}
/* use dummy pc and ksp to avoid problems when B is not positive definite */
ierr = STGetKSP(eps->st,&ksp);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
} else {
ierr = PetscInfo(eps,"Using slow explicit operator\n");CHKERRQ(ierr);
ierr = STComputeExplicitOperator(eps->st,&OP);CHKERRQ(ierr);
ierr = MatDestroy(&Adense);CHKERRQ(ierr);
ierr = SlepcMatConvertSeqDense(OP,&Adense);CHKERRQ(ierr);
}
/* fill DS matrices */
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,ld,NULL,&v);CHKERRQ(ierr);
ierr = DSGetArray(eps->ds,DS_MAT_A,&Ap);CHKERRQ(ierr);
for (i=0;i<ld;i++) {
ierr = VecPlaceArray(v,Ap+i*ld);CHKERRQ(ierr);
ierr = MatGetColumnVector(Adense,v,i);CHKERRQ(ierr);
ierr = VecResetArray(v);CHKERRQ(ierr);
}
ierr = DSRestoreArray(eps->ds,DS_MAT_A,&Ap);CHKERRQ(ierr);
if (denseok && eps->isgeneralized) {
ierr = DSGetArray(eps->ds,DS_MAT_B,&Bp);CHKERRQ(ierr);
for (i=0;i<ld;i++) {
ierr = VecPlaceArray(v,Bp+i*ld);CHKERRQ(ierr);
ierr = MatGetColumnVector(Bdense,v,i);CHKERRQ(ierr);
ierr = VecResetArray(v);CHKERRQ(ierr);
}
ierr = DSRestoreArray(eps->ds,DS_MAT_B,&Bp);CHKERRQ(ierr);
}
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = MatDestroy(&Adense);CHKERRQ(ierr);
if (!denseok) { ierr = MatDestroy(&OP);CHKERRQ(ierr); }
if (denseok && eps->isgeneralized) { ierr = MatDestroy(&Bdense);CHKERRQ(ierr); }
PetscFunctionReturn(0);
}
PetscErrorCode cHamiltonianMatrix::hamiltonianRescaling(){
// ierr = MatCreateVecs(Hpolaron,NULL,&xr);CHKERRQ(ierr);
// ierr = MatCreateVecs(Hpolaron,NULL,&xi);CHKERRQ(ierr);
ierr = EPSCreate(PETSC_COMM_WORLD,&eps);CHKERRQ(ierr);
ierr = EPSSetOperators(eps,Hpolaron,NULL);CHKERRQ(ierr);
ierr = EPSSetProblemType(eps,EPS_HEP);CHKERRQ(ierr);
// PetscBool her;
// ierr = EPSIsHermitian(eps, &her); CHKERRQ(ierr); if (rank==0) {cout << endl;cout << "is hermitian? (has to be) " << her << endl;}
// PetscBool pos;
// ierr = EPSIsPositive(eps, &pos); CHKERRQ(ierr); if (rank==0) {cout << "is positive? (not really)" << pos << endl;cout << endl;}
// ierr = EPSSetType(eps,EPSPOWER);CHKERRQ(ierr);
ierr = EPSSetWhichEigenpairs(eps,EPS_LARGEST_REAL);CHKERRQ(ierr);
// ierr = EPSSetFromOptions(eps);CHKERRQ(ierr);
ierr = EPSSolve(eps);CHKERRQ(ierr);
// ierr = EPSGetIterationNumber(eps,&its);CHKERRQ(ierr);
// ierr = PetscPrintf(PETSC_COMM_WORLD," Number of iterations of the method: %D\n",its);CHKERRQ(ierr);
// ierr = EPSGetType(eps,&type);CHKERRQ(ierr);
// ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);CHKERRQ(ierr);
// ierr = EPSGetDimensions(eps,&nev,NULL,NULL);CHKERRQ(ierr);
// ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %D\n",nev);CHKERRQ(ierr);
// ierr = EPSGetTolerances(eps,&tol,&maxit);CHKERRQ(ierr);
// ierr = PetscPrintf(PETSC_COMM_WORLD," Stopping condition: tol=%.4g, maxit=%D\n",(double)tol,maxit);CHKERRQ(ierr);
// ------- maximum and minimum of energy spectrum ----------
ierr = EPSGetEigenpair(eps,0,&HpolaronMax,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = EPSSetWhichEigenpairs(eps,EPS_SMALLEST_REAL);CHKERRQ(ierr);
ierr = EPSSolve(eps);CHKERRQ(ierr);
ierr = EPSGetEigenpair(eps,0,&HpolaronMin,NULL,NULL,NULL);CHKERRQ(ierr);
double epsilon_cut_off = 0.01;
a_scaling = PetscRealPart(HpolaronMax-HpolaronMin)/(2.0-epsilon_cut_off);
b_scaling = PetscRealPart(HpolaronMax+HpolaronMin)/2.0;
if (rank==0) {
cout << "HpolaronMax is " << HpolaronMax << endl;
cout << "HpolaronMin is " << HpolaronMin << endl;
cout << "a_scaling is " << a_scaling << endl;
cout << "b_scaling is " << b_scaling << endl;
}
/*
% --------- rescaled Hamiltonian -------------
*/
ierr = MatShift(Hpolaron,-b_scaling);CHKERRQ(ierr);
ierr = MatScale(Hpolaron,1.0/a_scaling);
// ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_DENSE );CHKERRQ(ierr);
// // ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_MATLAB );CHKERRQ(ierr);
// ierr = MatView(Hpolaron, PETSC_VIEWER_STDOUT_WORLD );CHKERRQ(ierr);
// ierr = EPSSetOperators(eps,Hpolaron,NULL);CHKERRQ(ierr);
// ierr = EPSSetProblemType(eps,EPS_HEP);CHKERRQ(ierr);
// ierr = EPSSolve(eps);CHKERRQ(ierr);
// ierr = EPSGetConverged(eps,&nconv);CHKERRQ(ierr);
// ierr = PetscPrintf(PETSC_COMM_WORLD," Number of converged eigenpairs: %D\n\n",nconv);CHKERRQ(ierr);
// ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
// ierr = EPSReasonView(eps,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
// ierr = EPSErrorView(eps,EPS_ERROR_RELATIVE,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
// ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
if (rank==0) cout << "Characteristic Coherance Time: t_c=" << 1.0/(2.0*a_scaling/dim/L) << endl;
/*
%---------------------------------------------------
% -------- End of Cosntruction of Hamiltonian ------
%=============================================================
*/
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt its,n,Nx=PETSC_DECIDE,Ny=PETSC_DECIDE,nlocal,i;
PetscMPIInt size;
PC pc;
PetscInt mx,my;
Mat A;
GridCtx fine_ctx;
KSP ksp;
PetscBool flg;
PetscInitialize(&argc,&argv,NULL,help);
/* set up discretization matrix for fine grid */
/* ML requires input of fine-grid matrix. It determines nlevels. */
fine_ctx.mx = 9; fine_ctx.my = 9;
ierr = PetscOptionsGetInt(NULL,"-mx",&mx,&flg);CHKERRQ(ierr);
if (flg) fine_ctx.mx = mx;
ierr = PetscOptionsGetInt(NULL,"-my",&my,&flg);CHKERRQ(ierr);
if (flg) fine_ctx.my = my;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Fine grid size %D by %D\n",fine_ctx.mx,fine_ctx.my);CHKERRQ(ierr);
n = fine_ctx.mx*fine_ctx.my;
MPI_Comm_size(PETSC_COMM_WORLD,&size);
ierr = PetscOptionsGetInt(NULL,"-Nx",&Nx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-Ny",&Ny,NULL);CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,fine_ctx.mx,
fine_ctx.my,Nx,Ny,1,1,NULL,NULL,&fine_ctx.da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(fine_ctx.da,&fine_ctx.x);CHKERRQ(ierr);
ierr = VecDuplicate(fine_ctx.x,&fine_ctx.b);CHKERRQ(ierr);
ierr = VecGetLocalSize(fine_ctx.x,&nlocal);CHKERRQ(ierr);
ierr = DMCreateLocalVector(fine_ctx.da,&fine_ctx.localX);CHKERRQ(ierr);
ierr = VecDuplicate(fine_ctx.localX,&fine_ctx.localF);CHKERRQ(ierr);
ierr = MatCreateAIJ(PETSC_COMM_WORLD,nlocal,nlocal,n,n,5,NULL,3,NULL,&A);CHKERRQ(ierr);
ierr = FormJacobian_Grid(&fine_ctx,&A);CHKERRQ(ierr);
/* create linear solver */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCML);CHKERRQ(ierr);
/* set options, then solve system */
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); /* calls PCSetFromOptions_MG/ML */
for (i=0; i<3; i++) {
if (i<2) { /* test DIFFERENT_NONZERO_PATTERN */
/* set values for rhs vector */
ierr = VecSet(fine_ctx.b,i+1.0);CHKERRQ(ierr);
/* modify A */
ierr = MatShift(A,1.0);CHKERRQ(ierr);
ierr = MatScale(A,2.0);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
} else { /* test SAME_NONZERO_PATTERN */
ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
}
ierr = KSPSolve(ksp,fine_ctx.b,fine_ctx.x);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of iterations = %D\n",its);CHKERRQ(ierr);
}
/* free data structures */
ierr = VecDestroy(&fine_ctx.x);CHKERRQ(ierr);
ierr = VecDestroy(&fine_ctx.b);CHKERRQ(ierr);
ierr = DMDestroy(&fine_ctx.da);CHKERRQ(ierr);
ierr = VecDestroy(&fine_ctx.localX);CHKERRQ(ierr);
ierr = VecDestroy(&fine_ctx.localF);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
User user;
Mat A,S;
PetscScalar *data,diag = 1.3;
PetscReal tol = PETSC_SMALL;
PetscInt i,j,m = PETSC_DECIDE,n = PETSC_DECIDE,M = 17,N = 15,s1,s2;
PetscInt test, ntest = 2;
PetscMPIInt rank,size;
PetscBool nc = PETSC_FALSE, cong;
PetscBool ronl = PETSC_TRUE;
PetscBool randomize = PETSC_FALSE;
PetscBool keep = PETSC_FALSE;
PetscBool testzerorows = PETSC_TRUE, testdiagscale = PETSC_TRUE, testgetdiag = PETSC_TRUE;
PetscBool testshift = PETSC_TRUE, testscale = PETSC_TRUE, testdup = PETSC_TRUE, testreset = PETSC_TRUE;
PetscErrorCode ierr;
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);
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-ml",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-nl",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-square_nc",&nc,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-rows_only",&ronl,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-randomize",&randomize,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_zerorows",&testzerorows,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_diagscale",&testdiagscale,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_getdiag",&testgetdiag,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_shift",&testshift,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_scale",&testscale,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_dup",&testdup,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_reset",&testreset,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-loop",&ntest,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,NULL,"-tol",&tol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,NULL,"-diag",&diag,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-keep",&keep,NULL);CHKERRQ(ierr);
/* This tests square matrices with different row/col layout */
if (nc && size > 1) {
M = PetscMax(PetscMax(N,M),1);
N = M;
m = n = 0;
if (rank == 0) { m = M-1; n = 1; }
else if (rank == 1) { m = 1; n = N-1; }
}
ierr = MatCreateDense(PETSC_COMM_WORLD,m,n,M,N,NULL,&A);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
ierr = MatHasCongruentLayouts(A,&cong);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&s1,NULL);CHKERRQ(ierr);
s2 = 1;
while (s2 < M) s2 *= 10;
ierr = MatDenseGetArray(A,&data);CHKERRQ(ierr);
for (j = 0; j < N; j++) {
for (i = 0; i < m; i++) {
data[j*m + i] = s2*j + i + s1 + 1;
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatConvert(A,MATAIJ,MAT_INPLACE_MATRIX,&A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,keep);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)A,"initial");CHKERRQ(ierr);
ierr = MatViewFromOptions(A,NULL,"-view_mat");CHKERRQ(ierr);
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,m,n,M,N,user,&S);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT_TRANSPOSE,(void (*)(void))MatMultTranspose_User);CHKERRQ(ierr);
if (cong) {
ierr = MatShellSetOperation(S,MATOP_GET_DIAGONAL,(void (*)(void))MatGetDiagonal_User);CHKERRQ(ierr);
}
ierr = MatDuplicate(A,MAT_COPY_VALUES,&user->B);CHKERRQ(ierr);
/* Square and rows only scaling */
ronl = cong ? ronl : PETSC_TRUE;
for (test = 0; test < ntest; test++) {
PetscReal err;
if (testzerorows) {
Mat ST,B,C,BT,BTT;
IS zr;
Vec x = NULL, b1 = NULL, b2 = NULL;
PetscInt *idxs = NULL, nr = 0;
if (rank == (test%size)) {
nr = 1;
ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr);
if (test%2) {
idxs[0] = (2*M - 1 - test/2)%M;
} else {
idxs[0] = (test/2)%M;
}
idxs[0] = PetscMax(idxs[0],0);
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)zr,"ZR");CHKERRQ(ierr);
ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr);
ierr = MatCreateVecs(A,&x,&b1);CHKERRQ(ierr);
if (randomize) {
ierr = VecSetRandom(x,NULL);CHKERRQ(ierr);
ierr = VecSetRandom(b1,NULL);CHKERRQ(ierr);
} else {
ierr = VecSet(x,11.4);CHKERRQ(ierr);
ierr = VecSet(b1,-14.2);CHKERRQ(ierr);
}
ierr = VecDuplicate(b1,&b2);CHKERRQ(ierr);
ierr = VecCopy(b1,b2);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)b1,"A_B1");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)b2,"A_B2");CHKERRQ(ierr);
if (size > 1 && !cong) { /* MATMPIAIJ ZeroRows and ZeroRowsColumns are buggy in this case */
ierr = VecDestroy(&b1);CHKERRQ(ierr);
}
if (ronl) {
ierr = MatZeroRowsIS(A,zr,diag,x,b1);CHKERRQ(ierr);
ierr = MatZeroRowsIS(S,zr,diag,x,b2);CHKERRQ(ierr);
} else {
ierr = MatZeroRowsColumnsIS(A,zr,diag,x,b1);CHKERRQ(ierr);
ierr = MatZeroRowsColumnsIS(S,zr,diag,x,b2);CHKERRQ(ierr);
ierr = ISDestroy(&zr);CHKERRQ(ierr);
/* Mix zerorows and zerorowscols */
nr = 0;
idxs = NULL;
if (!rank) {
nr = 1;
ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr);
if (test%2) {
idxs[0] = (3*M - 2 - test/2)%M;
} else {
idxs[0] = (test/2+1)%M;
}
idxs[0] = PetscMax(idxs[0],0);
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)zr,"ZR2");CHKERRQ(ierr);
ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr);
ierr = MatZeroRowsIS(A,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr);
ierr = MatZeroRowsIS(S,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr);
}
ierr = ISDestroy(&zr);CHKERRQ(ierr);
if (b1) {
Vec b;
ierr = VecViewFromOptions(b1,NULL,"-view_b");CHKERRQ(ierr);
ierr = VecViewFromOptions(b2,NULL,"-view_b");CHKERRQ(ierr);
ierr = VecDuplicate(b1,&b);CHKERRQ(ierr);
ierr = VecCopy(b1,b);CHKERRQ(ierr);
ierr = VecAXPY(b,-1.0,b2);CHKERRQ(ierr);
ierr = VecNorm(b,NORM_INFINITY,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error b %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = VecDestroy(&b);CHKERRQ(ierr);
}
ierr = VecDestroy(&b1);CHKERRQ(ierr);
ierr = VecDestroy(&b2);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = MatConvert(S,MATDENSE,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
ierr = MatCreateTranspose(S,&ST);CHKERRQ(ierr);
ierr = MatComputeOperator(ST,MATDENSE,&BT);CHKERRQ(ierr);
ierr = MatTranspose(BT,MAT_INITIAL_MATRIX,&BTT);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)B,"S");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)BTT,"STT");CHKERRQ(ierr);
ierr = MatConvert(A,MATDENSE,MAT_INITIAL_MATRIX,&C);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)C,"A");CHKERRQ(ierr);
ierr = MatViewFromOptions(C,NULL,"-view_mat");CHKERRQ(ierr);
ierr = MatViewFromOptions(B,NULL,"-view_mat");CHKERRQ(ierr);
ierr = MatViewFromOptions(BTT,NULL,"-view_mat");CHKERRQ(ierr);
ierr = MatAXPY(C,-1.0,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = MatConvert(A,MATDENSE,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr);
ierr = MatAXPY(C,-1.0,BTT,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult transpose %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = MatDestroy(&ST);CHKERRQ(ierr);
ierr = MatDestroy(&BTT);CHKERRQ(ierr);
ierr = MatDestroy(&BT);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
}
if (testdiagscale) { /* MatDiagonalScale() */
Vec vr,vl;
ierr = MatCreateVecs(A,&vr,&vl);CHKERRQ(ierr);
if (randomize) {
ierr = VecSetRandom(vr,NULL);CHKERRQ(ierr);
ierr = VecSetRandom(vl,NULL);CHKERRQ(ierr);
} else {
ierr = VecSet(vr,test%2 ? 0.15 : 1.0/0.15);CHKERRQ(ierr);
ierr = VecSet(vl,test%2 ? -1.2 : 1.0/-1.2);CHKERRQ(ierr);
}
ierr = MatDiagonalScale(A,vl,vr);CHKERRQ(ierr);
ierr = MatDiagonalScale(S,vl,vr);CHKERRQ(ierr);
ierr = VecDestroy(&vr);CHKERRQ(ierr);
ierr = VecDestroy(&vl);CHKERRQ(ierr);
}
if (testscale) { /* MatScale() */
ierr = MatScale(A,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr);
ierr = MatScale(S,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr);
}
if (testshift && cong) { /* MatShift() : MATSHELL shift is broken when row/cols layout are not congruent and left/right scaling have been applied */
ierr = MatShift(A,test%2 ? -77.5 : 77.5);CHKERRQ(ierr);
ierr = MatShift(S,test%2 ? -77.5 : 77.5);CHKERRQ(ierr);
}
if (testgetdiag && cong) { /* MatGetDiagonal() */
Vec dA,dS;
ierr = MatCreateVecs(A,&dA,NULL);CHKERRQ(ierr);
ierr = MatCreateVecs(S,&dS,NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,dA);CHKERRQ(ierr);
ierr = MatGetDiagonal(S,dS);CHKERRQ(ierr);
ierr = VecAXPY(dA,-1.0,dS);CHKERRQ(ierr);
ierr = VecNorm(dA,NORM_INFINITY,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error diag %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = VecDestroy(&dA);CHKERRQ(ierr);
ierr = VecDestroy(&dS);CHKERRQ(ierr);
}
if (testdup && !test) {
Mat A2, S2;
ierr = MatDuplicate(A,MAT_COPY_VALUES,&A2);CHKERRQ(ierr);
ierr = MatDuplicate(S,MAT_COPY_VALUES,&S2);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
A = A2;
S = S2;
}
if (testreset && (ntest == 1 || test == ntest-2)) {
/* reset MATSHELL */
ierr = MatAssemblyBegin(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* reset A */
ierr = MatCopy(user->B,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
}
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&user->B);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
Mat C,C1,F;
Vec u,x,b;
PetscErrorCode ierr;
PetscMPIInt rank,nproc;
PetscInt i,M = 10,m,n,nfact,nsolve;
PetscScalar *array,rval;
PetscReal norm,tol=1.e-12;
IS perm,iperm;
MatFactorInfo info;
PetscRandom rand;
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, &nproc);CHKERRQ(ierr);
/* Create matrix and vectors */
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,M,M);CHKERRQ(ierr);
ierr = MatSetType(C,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatGetLocalSize(C,&m,&n);CHKERRQ(ierr);
if (m != n) SETERRQ2(PETSC_ERR_ARG_WRONG,"Matrix local size m %d must equal n %d",m,n);
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 */
/* Assembly */
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatGetArray(C,&array);CHKERRQ(ierr);
for (i=0; i<m*M; i++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[i] = rval;
}
ierr = MatRestoreArray(C,&array);CHKERRQ(ierr);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*if (!rank) {printf("main, C: \n");}
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
/* Test MatDuplicate() */
ierr = MatDuplicate(C,MAT_COPY_VALUES,&C1);CHKERRQ(ierr);
ierr = MatEqual(C,C1,&flg);CHKERRQ(ierr);
if (!flg){
SETERRQ(PETSC_ERR_ARG_WRONG,"Duplicate C1 != C");
}
/* Test LU Factorization */
ierr = MatGetOrdering(C1,MATORDERING_NATURAL,&perm,&iperm);CHKERRQ(ierr);
if (nproc == 1){
ierr = MatGetFactor(C1,MAT_SOLVER_PETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
} else {
ierr = MatGetFactor(C1,MAT_SOLVER_PLAPACK,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
}
ierr = MatLUFactorSymbolic(F,C1,perm,iperm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++){
if (!rank) printf(" LU nfact %d\n",nfact);
ierr = MatLUFactorNumeric(F,C1,&info);CHKERRQ(ierr);
/* Test MatSolve() */
for (nsolve = 0; nsolve < 5; 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(C,x,b);CHKERRQ(ierr);
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){
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, LU nfact %d\n",norm,nfact);CHKERRQ(ierr);
}
}
}
}
ierr = MatDestroy(C1);CHKERRQ(ierr);
ierr = MatDestroy(F);CHKERRQ(ierr);
/* Test Cholesky Factorization */
ierr = MatTranspose(C,MAT_INITIAL_MATRIX,&C1);CHKERRQ(ierr); /* C1 = C^T */
ierr = MatAXPY(C,1.0,C1,SAME_NONZERO_PATTERN);CHKERRQ(ierr); /* make C symmetric: C <- C + C^T */
ierr = MatShift(C,M);CHKERRQ(ierr); /* make C positive definite */
ierr = MatDestroy(C1);CHKERRQ(ierr);
ierr = MatSetOption(C,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatSetOption(C,MAT_SYMMETRY_ETERNAL,PETSC_TRUE);CHKERRQ(ierr);
if (nproc == 1){
ierr = MatGetFactor(C,MAT_SOLVER_PETSC,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
} else {
ierr = MatGetFactor(C,MAT_SOLVER_PLAPACK,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
}
ierr = MatCholeskyFactorSymbolic(F,C,perm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++){
if (!rank) printf(" Cholesky nfact %d\n",nfact);
ierr = MatCholeskyFactorNumeric(F,C,&info);CHKERRQ(ierr);
/* Test MatSolve() */
for (nsolve = 0; nsolve < 5; 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(C,x,b);CHKERRQ(ierr);
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){
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, Cholesky nfact %d\n",norm,nfact);CHKERRQ(ierr);
}
}
}
}
ierr = MatDestroy(F);CHKERRQ(ierr);
/* Free data structures */
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 = MatDestroy(C);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat C,F,Cpetsc,Csymm;
Vec u,x,b,bpla;
PetscErrorCode ierr;
PetscMPIInt rank,nproc;
PetscInt i,j,k,M = 10,m,nfact,nsolve,Istart,Iend,*im,*in,start,end;
PetscScalar *array,rval;
PetscReal norm,tol=1.e-12;
IS perm,iperm;
MatFactorInfo info;
PetscRandom rand;
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);
/* Test non-symmetric operations */
/*-------------------------------*/
/* Create a Plapack dense matrix C */
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,M,M);CHKERRQ(ierr);
ierr = MatSetType(C,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
/* Create vectors */
ierr = MatGetOwnershipRange(C,&start,&end);CHKERRQ(ierr);
m = end - start;
/* printf("[%d] C - local size m: %d\n",rank,m); */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&bpla);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */
/* Create a petsc dense matrix Cpetsc */
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&Cpetsc);CHKERRQ(ierr);
ierr = MatSetSizes(Cpetsc,m,m,M,M);CHKERRQ(ierr);
ierr = MatSetType(Cpetsc,MATDENSE);CHKERRQ(ierr);
ierr = MatMPIDenseSetPreallocation(Cpetsc,PETSC_NULL);CHKERRQ(ierr);
ierr = MatSetFromOptions(Cpetsc);CHKERRQ(ierr);
ierr = MatSetUp(Cpetsc);CHKERRQ(ierr);
ierr = MatSetOption(Cpetsc,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(C,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
/* Assembly */
/* PLAPACK doesn't support INSERT_VALUES mode, zero all entries before calling MatSetValues() */
ierr = MatZeroEntries(C);CHKERRQ(ierr);
ierr = MatZeroEntries(Cpetsc);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(C,&Istart,&Iend);CHKERRQ(ierr);
/* printf(" [%d] C m: %d, Istart/end: %d %d\n",rank,m,Istart,Iend); */
ierr = PetscMalloc((m*M+1)*sizeof(PetscScalar),&array);CHKERRQ(ierr);
ierr = PetscMalloc2(m,PetscInt,&im,M,PetscInt,&in);CHKERRQ(ierr);
k = 0;
for (j=0; j<M; j++){ /* column oriented! */
in[j] = j;
for (i=0; i<m; i++){
im[i] = i+Istart;
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[k++] = rval;
}
}
ierr = MatSetValues(Cpetsc,m,im,M,in,array,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,m,im,M,in,array,ADD_VALUES);CHKERRQ(ierr);
ierr = PetscFree(array);CHKERRQ(ierr);
ierr = PetscFree2(im,in);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
if (!rank) {printf("main, Cpetsc: \n");}
ierr = MatView(Cpetsc,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
*/
ierr = MatGetOrdering(C,MATORDERINGNATURAL,&perm,&iperm);CHKERRQ(ierr);
/* Test nonsymmetric MatMult() */
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 = MatMult(Cpetsc,x,b);CHKERRQ(ierr);
ierr = MatMult(C,x,bpla);CHKERRQ(ierr);
ierr = VecAXPY(bpla,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(bpla,NORM_2,&norm);CHKERRQ(ierr);
if (norm > 1.e-12 && !rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Nonsymmetric MatMult_Plapack error: |b_pla - b|= %g\n",norm);CHKERRQ(ierr);
}
/* Test LU Factorization */
if (nproc == 1){
ierr = MatGetFactor(C,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
} else {
ierr = MatGetFactor(C,MATSOLVERPLAPACK,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
}
ierr = MatLUFactorSymbolic(F,C,perm,iperm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++){
if (!rank) printf(" LU nfact %d\n",nfact);
if (nfact>0){ /* change matrix value for testing repeated MatLUFactorNumeric() */
if (!rank){
i = j = 0;
rval = nfact;
ierr = MatSetValues(Cpetsc,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
} else { /* PLAPACK seems requiring all processors call MatSetValues(), so we add 0.0 on processesses with rank>0! */
i = j = 0;
rval = 0.0;
ierr = MatSetValues(Cpetsc,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
ierr = MatLUFactorNumeric(F,C,&info);CHKERRQ(ierr);
/* Test MatSolve() */
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;
/* array[i] = rank + 1; */
}
ierr = VecRestoreArray(x,&array);CHKERRQ(ierr);
ierr = VecCopy(x,u);CHKERRQ(ierr);
ierr = MatMult(C,x,b);CHKERRQ(ierr);
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){
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, LU nfact %d\n",norm,nfact);CHKERRQ(ierr);
}
}
}
}
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* Test non-symmetric operations */
/*-------------------------------*/
/* Create a symmetric Plapack dense matrix Csymm */
ierr = MatCreate(PETSC_COMM_WORLD,&Csymm);CHKERRQ(ierr);
ierr = MatSetSizes(Csymm,PETSC_DECIDE,PETSC_DECIDE,M,M);CHKERRQ(ierr);
ierr = MatSetType(Csymm,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(Csymm);CHKERRQ(ierr);
ierr = MatSetUp(Csymm);CHKERRQ(ierr);
ierr = MatSetOption(Csymm,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(Csymm,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatSetOption(Csymm,MAT_SYMMETRY_ETERNAL,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatZeroEntries(Csymm);CHKERRQ(ierr);
ierr = MatZeroEntries(Cpetsc);CHKERRQ(ierr);
for (i=Istart; i<Iend; i++){
for (j=0; j<=i; j++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
ierr = MatSetValues(Cpetsc,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(Csymm,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
if (j<i){
/* Although PLAPACK only requires lower triangular entries, we must add all the entries.
MatSetValues_Plapack() will ignore the upper triangular entries AFTER an index map! */
ierr = MatSetValues(Cpetsc,1,&j,1,&i,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(Csymm,1,&j,1,&i,&rval,ADD_VALUES);CHKERRQ(ierr);
}
}
}
ierr = MatAssemblyBegin(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Csymm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Csymm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test symmetric MatMult() */
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 = MatMult(Cpetsc,x,b);CHKERRQ(ierr);
ierr = MatMult(Csymm,x,bpla);CHKERRQ(ierr);
ierr = VecAXPY(bpla,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(bpla,NORM_2,&norm);CHKERRQ(ierr);
if (norm > 1.e-12 && !rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Symmetric MatMult_Plapack error: |b_pla - b|= %g\n",norm);CHKERRQ(ierr);
}
/* Test Cholesky Factorization */
ierr = MatShift(Csymm,M);CHKERRQ(ierr); /* make Csymm positive definite */
if (nproc == 1){
ierr = MatGetFactor(Csymm,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
} else {
ierr = MatGetFactor(Csymm,MATSOLVERPLAPACK,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
}
ierr = MatCholeskyFactorSymbolic(F,Csymm,perm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++){
if (!rank) printf(" Cholesky nfact %d\n",nfact);
ierr = MatCholeskyFactorNumeric(F,Csymm,&info);CHKERRQ(ierr);
/* Test MatSolve() */
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(Csymm,x,b);CHKERRQ(ierr);
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){
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, Cholesky nfact %d\n",norm,nfact);CHKERRQ(ierr);
}
}
}
}
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* Free data structures */
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = ISDestroy(&iperm);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&bpla);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = MatDestroy(&Cpetsc);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&Csymm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode GetH(MPI_Comm comm, Mat *Hout, int mx, int my, int mz, double s, double nR, int dim, KSP *kspHout, PC *pcHout)
{
PetscErrorCode ierr;
Mat H;
int i,ns,ne;
int N=mx*my*mz;
MatCreate(comm, &H);
MatSetType(H,MATMPIAIJ);
MatSetSizes(H,PETSC_DECIDE, PETSC_DECIDE, N, N);
MatMPIAIJSetPreallocation(H, 3, PETSC_NULL, 3, PETSC_NULL);
if (dim==1){
double value[3];
int col[3];
ierr = MatGetOwnershipRange(H, &ns, &ne); CHKERRQ(ierr);
for (i = ns; i < ne; ++i) {
if (i==0){
col[0]= 0, value[0]= s*nR*nR*(-2.0)+1;
col[1]= 1, value[1]= s*nR*nR*2.0;
col[2]= 2, value[2]= 0;}
else if (i==N-1){
col[0]= N-3, value[0]= 0;
col[1]= N-2, value[1]= s*nR*nR*2.0;
col[2]= N-1, value[2]= s*nR*nR*(-2.0)+1;}
else{
col[0]= i-1, value[0]= s*nR*nR;
col[1]= i, value[1]= s*nR*nR*(-2.0)+1;
col[2]= i+1, value[2]= s*nR*nR;}
ierr = MatSetValues(H,1,&i,3,col,value,INSERT_VALUES); CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(H, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(H, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
}
if (dim==2) {
PetscPrintf(comm,"2D Helmholtz filter is not implemented yet!\n");
MatShift(H,1.0);}
if (dim==3) {
PetscPrintf(comm,"3D Helmholtz filter is not implemented yet!\n");
MatShift(H,1.0);}
ierr = PetscObjectSetName((PetscObject) H,"Hop"); CHKERRQ(ierr);
KSP ksp;
PC pc;
ierr = KSPCreate(comm,&ksp);CHKERRQ(ierr);
ierr = KSPSetType(ksp, KSPGMRES);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCLU);CHKERRQ(ierr);
ierr = PCFactorSetMatSolverPackage(pc,MATSOLVERMUMPS);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,1e-14,PETSC_DEFAULT,PETSC_DEFAULT,maxit);CHKERRQ(ierr);
ierr = PCSetFromOptions(pc);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
*Hout=H;
*kspHout=ksp;
*pcHout=pc;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
BV X;
Mat M;
Vec v,t,*C;
PetscInt i,j,n=20,k=8,nc=2;
PetscViewer view;
PetscBool verbose;
PetscReal norm;
PetscScalar alpha;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-k",&k,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-nc",&nc,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-verbose",&verbose);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Test BV orthogonalization with %D columns + %D constraints, of length %D.\n",k,nc,n);CHKERRQ(ierr);
/* Create template vector */
ierr = VecCreate(PETSC_COMM_WORLD,&t);CHKERRQ(ierr);
ierr = VecSetSizes(t,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(t);CHKERRQ(ierr);
/* Create BV object X */
ierr = BVCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)X,"X");CHKERRQ(ierr);
ierr = BVSetSizesFromVec(X,t,k);CHKERRQ(ierr);
ierr = BVSetFromOptions(X);CHKERRQ(ierr);
/* Generate constraints and attach them to X */
if (nc>0) {
ierr = VecDuplicateVecs(t,nc,&C);CHKERRQ(ierr);
for (j=0;j<nc;j++) {
for (i=0;i<=j;i++) {
ierr = VecSetValue(C[j],i,1.0,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(C[j]);CHKERRQ(ierr);
ierr = VecAssemblyEnd(C[j]);CHKERRQ(ierr);
}
ierr = BVInsertConstraints(X,&nc,C);CHKERRQ(ierr);
ierr = VecDestroyVecs(nc,&C);CHKERRQ(ierr);
}
/* Set up viewer */
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&view);CHKERRQ(ierr);
if (verbose) {
ierr = PetscViewerPushFormat(view,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
}
/* Fill X entries */
for (j=0;j<k;j++) {
ierr = BVGetColumn(X,j,&v);CHKERRQ(ierr);
ierr = VecZeroEntries(v);CHKERRQ(ierr);
for (i=0;i<=n/2;i++) {
if (i+j<n) {
alpha = (3.0*i+j-2)/(2*(i+j+1));
ierr = VecSetValue(v,i+j,alpha,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = VecAssemblyBegin(v);CHKERRQ(ierr);
ierr = VecAssemblyEnd(v);CHKERRQ(ierr);
ierr = BVRestoreColumn(X,j,&v);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Test BVOrthogonalizeColumn */
for (j=0;j<k;j++) {
ierr = BVOrthogonalizeColumn(X,j,NULL,&norm,NULL);CHKERRQ(ierr);
alpha = 1.0/norm;
ierr = BVScaleColumn(X,j,alpha);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Check orthogonality */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,k,k,NULL,&M);CHKERRQ(ierr);
ierr = BVDot(X,X,M);CHKERRQ(ierr);
ierr = MatShift(M,-1.0);CHKERRQ(ierr);
ierr = MatNorm(M,NORM_1,&norm);CHKERRQ(ierr);
if (norm<100*PETSC_MACHINE_EPSILON) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality < 100*eps\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality: %g\n",(double)norm);CHKERRQ(ierr);
}
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = BVDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&t);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
Vec t,v;
Mat B,M;
BV X;
PetscInt i,j,n=10,k=5,Istart,Iend,col[3];
PetscScalar value[3],alpha;
PetscReal nrm;
PetscViewer view;
PetscBool verbose,FirstBlock=PETSC_FALSE,LastBlock=PETSC_FALSE;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-k",&k,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-verbose",&verbose);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Test BV with non-standard inner product (n=%D, k=%D).\n",n,k);CHKERRQ(ierr);
/* Create inner product matrix */
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)B,"B");CHKERRQ(ierr);
ierr = MatGetOwnershipRange(B,&Istart,&Iend);CHKERRQ(ierr);
if (Istart==0) FirstBlock=PETSC_TRUE;
if (Iend==n) LastBlock=PETSC_TRUE;
value[0]=-1.0; value[1]=2.0; value[2]=-1.0;
for (i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++) {
col[0]=i-1; col[1]=i; col[2]=i+1;
ierr = MatSetValues(B,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (LastBlock) {
i=n-1; col[0]=n-2; col[1]=n-1;
ierr = MatSetValues(B,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (FirstBlock) {
i=0; col[0]=0; col[1]=1; value[0]=2.0; value[1]=-1.0;
ierr = MatSetValues(B,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetVecs(B,&t,NULL);CHKERRQ(ierr);
/* Create BV object X */
ierr = BVCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)X,"X");CHKERRQ(ierr);
ierr = BVSetSizesFromVec(X,t,k);CHKERRQ(ierr);
ierr = BVSetFromOptions(X);CHKERRQ(ierr);
ierr = BVSetMatrix(X,B,PETSC_FALSE);CHKERRQ(ierr);
/* Set up viewer */
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&view);CHKERRQ(ierr);
if (verbose) {
ierr = PetscViewerPushFormat(view,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
}
/* Fill X entries */
for (j=0;j<k;j++) {
ierr = BVGetColumn(X,j,&v);CHKERRQ(ierr);
ierr = VecZeroEntries(v);CHKERRQ(ierr);
for (i=0;i<4;i++) {
if (i+j<n) {
ierr = VecSetValue(v,i+j,(PetscScalar)(3*i+j-2),INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = VecAssemblyBegin(v);CHKERRQ(ierr);
ierr = VecAssemblyEnd(v);CHKERRQ(ierr);
ierr = BVRestoreColumn(X,j,&v);CHKERRQ(ierr);
}
if (verbose) {
ierr = MatView(B,view);CHKERRQ(ierr);
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Test BVNormColumn */
ierr = BVNormColumn(X,0,NORM_2,&nrm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"B-Norm or X[0] = %g\n",(double)nrm);CHKERRQ(ierr);
/* Test BVOrthogonalizeColumn */
for (j=0;j<k;j++) {
ierr = BVOrthogonalizeColumn(X,j,NULL,&nrm,NULL);CHKERRQ(ierr);
alpha = 1.0/nrm;
ierr = BVScaleColumn(X,j,alpha);CHKERRQ(ierr);
}
if (verbose) {
ierr = BVView(X,view);CHKERRQ(ierr);
}
/* Check orthogonality */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,k,k,NULL,&M);CHKERRQ(ierr);
ierr = BVDot(X,X,M);CHKERRQ(ierr);
ierr = MatShift(M,-1.0);CHKERRQ(ierr);
ierr = MatNorm(M,NORM_1,&nrm);CHKERRQ(ierr);
if (nrm<100*PETSC_MACHINE_EPSILON) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality < 100*eps\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Level of orthogonality: %g\n",(double)nrm);CHKERRQ(ierr);
}
ierr = BVDestroy(&X);CHKERRQ(ierr);
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = VecDestroy(&t);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
PetscErrorCode PCBDDCNullSpaceAssembleCorrection(PC pc, PetscBool isdir, IS local_dofs)
{
PC_BDDC *pcbddc = (PC_BDDC*)pc->data;
PC_IS *pcis = (PC_IS*)pc->data;
Mat_IS* matis = (Mat_IS*)pc->pmat->data;
KSP local_ksp;
PC newpc;
NullSpaceCorrection_ctx shell_ctx;
Mat local_mat,local_pmat,small_mat,inv_small_mat;
Vec work1,work2;
const Vec *nullvecs;
VecScatter scatter_ctx;
IS is_aux;
MatFactorInfo matinfo;
PetscScalar *basis_mat,*Kbasis_mat,*array,*array_mat;
PetscScalar one = 1.0,zero = 0.0, m_one = -1.0;
PetscInt basis_dofs,basis_size,nnsp_size,i,k;
PetscBool nnsp_has_cnst;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Infer the local solver */
ierr = ISGetSize(local_dofs,&basis_dofs);CHKERRQ(ierr);
if (isdir) {
/* Dirichlet solver */
local_ksp = pcbddc->ksp_D;
} else {
/* Neumann solver */
local_ksp = pcbddc->ksp_R;
}
ierr = KSPGetOperators(local_ksp,&local_mat,&local_pmat);CHKERRQ(ierr);
/* Get null space vecs */
ierr = MatNullSpaceGetVecs(pcbddc->NullSpace,&nnsp_has_cnst,&nnsp_size,&nullvecs);CHKERRQ(ierr);
basis_size = nnsp_size;
if (nnsp_has_cnst) {
basis_size++;
}
if (basis_dofs) {
/* Create shell ctx */
ierr = PetscNew(&shell_ctx);CHKERRQ(ierr);
/* Create work vectors in shell context */
ierr = VecCreate(PETSC_COMM_SELF,&shell_ctx->work_small_1);CHKERRQ(ierr);
ierr = VecSetSizes(shell_ctx->work_small_1,basis_size,basis_size);CHKERRQ(ierr);
ierr = VecSetType(shell_ctx->work_small_1,VECSEQ);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_small_1,&shell_ctx->work_small_2);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&shell_ctx->work_full_1);CHKERRQ(ierr);
ierr = VecSetSizes(shell_ctx->work_full_1,basis_dofs,basis_dofs);CHKERRQ(ierr);
ierr = VecSetType(shell_ctx->work_full_1,VECSEQ);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&shell_ctx->work_full_2);CHKERRQ(ierr);
/* Allocate workspace */
ierr = MatCreateSeqDense(PETSC_COMM_SELF,basis_dofs,basis_size,NULL,&shell_ctx->basis_mat );CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF,basis_dofs,basis_size,NULL,&shell_ctx->Kbasis_mat);CHKERRQ(ierr);
ierr = MatDenseGetArray(shell_ctx->basis_mat,&basis_mat);CHKERRQ(ierr);
ierr = MatDenseGetArray(shell_ctx->Kbasis_mat,&Kbasis_mat);CHKERRQ(ierr);
/* Restrict local null space on selected dofs (Dirichlet or Neumann)
and compute matrices N and K*N */
ierr = VecDuplicate(shell_ctx->work_full_1,&work1);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work2);CHKERRQ(ierr);
ierr = VecScatterCreate(pcis->vec1_N,local_dofs,work1,(IS)0,&scatter_ctx);CHKERRQ(ierr);
}
for (k=0;k<nnsp_size;k++) {
ierr = VecScatterBegin(matis->rctx,nullvecs[k],pcis->vec1_N,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(matis->rctx,nullvecs[k],pcis->vec1_N,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
if (basis_dofs) {
ierr = VecPlaceArray(work1,(const PetscScalar*)&basis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = VecScatterBegin(scatter_ctx,pcis->vec1_N,work1,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(scatter_ctx,pcis->vec1_N,work1,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecPlaceArray(work2,(const PetscScalar*)&Kbasis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
ierr = VecResetArray(work1);CHKERRQ(ierr);
ierr = VecResetArray(work2);CHKERRQ(ierr);
}
}
if (basis_dofs) {
if (nnsp_has_cnst) {
ierr = VecPlaceArray(work1,(const PetscScalar*)&basis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = VecSet(work1,one);CHKERRQ(ierr);
ierr = VecPlaceArray(work2,(const PetscScalar*)&Kbasis_mat[k*basis_dofs]);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
ierr = VecResetArray(work1);CHKERRQ(ierr);
ierr = VecResetArray(work2);CHKERRQ(ierr);
}
ierr = VecDestroy(&work1);CHKERRQ(ierr);
ierr = VecDestroy(&work2);CHKERRQ(ierr);
ierr = VecScatterDestroy(&scatter_ctx);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(shell_ctx->basis_mat,&basis_mat);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(shell_ctx->Kbasis_mat,&Kbasis_mat);CHKERRQ(ierr);
/* Assemble another Mat object in shell context */
ierr = MatTransposeMatMult(shell_ctx->basis_mat,shell_ctx->Kbasis_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&small_mat);CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&matinfo);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,basis_size,0,1,&is_aux);CHKERRQ(ierr);
ierr = MatLUFactor(small_mat,is_aux,is_aux,&matinfo);CHKERRQ(ierr);
ierr = ISDestroy(&is_aux);CHKERRQ(ierr);
ierr = PetscMalloc1(basis_size*basis_size,&array_mat);CHKERRQ(ierr);
for (k=0;k<basis_size;k++) {
ierr = VecSet(shell_ctx->work_small_1,zero);CHKERRQ(ierr);
ierr = VecSetValue(shell_ctx->work_small_1,k,one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(shell_ctx->work_small_1);CHKERRQ(ierr);
ierr = VecAssemblyEnd(shell_ctx->work_small_1);CHKERRQ(ierr);
ierr = MatSolve(small_mat,shell_ctx->work_small_1,shell_ctx->work_small_2);CHKERRQ(ierr);
ierr = VecGetArrayRead(shell_ctx->work_small_2,(const PetscScalar**)&array);CHKERRQ(ierr);
for (i=0;i<basis_size;i++) {
array_mat[i*basis_size+k]=array[i];
}
ierr = VecRestoreArrayRead(shell_ctx->work_small_2,(const PetscScalar**)&array);CHKERRQ(ierr);
}
ierr = MatCreateSeqDense(PETSC_COMM_SELF,basis_size,basis_size,array_mat,&inv_small_mat);CHKERRQ(ierr);
ierr = MatMatMult(shell_ctx->basis_mat,inv_small_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&shell_ctx->Lbasis_mat);CHKERRQ(ierr);
ierr = PetscFree(array_mat);CHKERRQ(ierr);
ierr = MatDestroy(&inv_small_mat);CHKERRQ(ierr);
ierr = MatDestroy(&small_mat);CHKERRQ(ierr);
ierr = MatScale(shell_ctx->Kbasis_mat,m_one);CHKERRQ(ierr);
/* Rebuild local PC */
ierr = KSPGetPC(local_ksp,&shell_ctx->local_pc);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)shell_ctx->local_pc);CHKERRQ(ierr);
ierr = PCCreate(PETSC_COMM_SELF,&newpc);CHKERRQ(ierr);
ierr = PCSetOperators(newpc,local_mat,local_mat);CHKERRQ(ierr);
ierr = PCSetType(newpc,PCSHELL);CHKERRQ(ierr);
ierr = PCShellSetContext(newpc,shell_ctx);CHKERRQ(ierr);
ierr = PCShellSetApply(newpc,PCBDDCApplyNullSpaceCorrectionPC);CHKERRQ(ierr);
ierr = PCShellSetDestroy(newpc,PCBDDCDestroyNullSpaceCorrectionPC);CHKERRQ(ierr);
ierr = PCSetUp(newpc);CHKERRQ(ierr);
ierr = KSPSetPC(local_ksp,newpc);CHKERRQ(ierr);
ierr = PCDestroy(&newpc);CHKERRQ(ierr);
ierr = KSPSetUp(local_ksp);CHKERRQ(ierr);
}
/* test */
if (pcbddc->dbg_flag && basis_dofs) {
KSP check_ksp;
PC check_pc;
Mat test_mat;
Vec work3;
PetscReal test_err,lambda_min,lambda_max;
PetscBool setsym,issym=PETSC_FALSE;
PetscInt tabs;
ierr = PetscViewerASCIIGetTab(pcbddc->dbg_viewer,&tabs);CHKERRQ(ierr);
ierr = KSPGetPC(local_ksp,&check_pc);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work1);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work2);CHKERRQ(ierr);
ierr = VecDuplicate(shell_ctx->work_full_1,&work3);CHKERRQ(ierr);
ierr = VecSetRandom(shell_ctx->work_small_1,NULL);CHKERRQ(ierr);
ierr = MatMult(shell_ctx->basis_mat,shell_ctx->work_small_1,work1);CHKERRQ(ierr);
ierr = VecCopy(work1,work2);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work3);CHKERRQ(ierr);
ierr = PCApply(check_pc,work3,work1);CHKERRQ(ierr);
ierr = VecAXPY(work1,m_one,work2);CHKERRQ(ierr);
ierr = VecNorm(work1,NORM_INFINITY,&test_err);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Subdomain %04d error for nullspace correction for ",PetscGlobalRank);CHKERRQ(ierr);
ierr = PetscViewerASCIIUseTabs(pcbddc->dbg_viewer,PETSC_FALSE);CHKERRQ(ierr);
if (isdir) {
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Dirichlet ");CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Neumann ");CHKERRQ(ierr);
}
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"solver is :%1.14e\n",test_err);CHKERRQ(ierr);
ierr = PetscViewerASCIISetTab(pcbddc->dbg_viewer,tabs);CHKERRQ(ierr);
ierr = PetscViewerASCIIUseTabs(pcbddc->dbg_viewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatTransposeMatMult(shell_ctx->Lbasis_mat,shell_ctx->Kbasis_mat,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&test_mat);CHKERRQ(ierr);
ierr = MatShift(test_mat,one);CHKERRQ(ierr);
ierr = MatNorm(test_mat,NORM_INFINITY,&test_err);CHKERRQ(ierr);
ierr = MatDestroy(&test_mat);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Subdomain %04d error for nullspace matrices is :%1.14e\n",PetscGlobalRank,test_err);CHKERRQ(ierr);
/* Create ksp object suitable for extreme eigenvalues' estimation */
ierr = KSPCreate(PETSC_COMM_SELF,&check_ksp);CHKERRQ(ierr);
ierr = KSPSetErrorIfNotConverged(check_ksp,pc->erroriffailure);CHKERRQ(ierr);
ierr = KSPSetOperators(check_ksp,local_mat,local_mat);CHKERRQ(ierr);
ierr = KSPSetTolerances(check_ksp,1.e-8,1.e-8,PETSC_DEFAULT,basis_dofs);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(check_ksp,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatIsSymmetricKnown(pc->pmat,&setsym,&issym);CHKERRQ(ierr);
if (issym) {
ierr = KSPSetType(check_ksp,KSPCG);CHKERRQ(ierr);
}
ierr = KSPSetPC(check_ksp,check_pc);CHKERRQ(ierr);
ierr = KSPSetUp(check_ksp);CHKERRQ(ierr);
ierr = VecSetRandom(work1,NULL);CHKERRQ(ierr);
ierr = MatMult(local_mat,work1,work2);CHKERRQ(ierr);
ierr = KSPSolve(check_ksp,work2,work2);CHKERRQ(ierr);
ierr = VecAXPY(work2,m_one,work1);CHKERRQ(ierr);
ierr = VecNorm(work2,NORM_INFINITY,&test_err);CHKERRQ(ierr);
ierr = KSPComputeExtremeSingularValues(check_ksp,&lambda_max,&lambda_min);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(check_ksp,&k);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(pcbddc->dbg_viewer,"Subdomain %04d error for adapted KSP %1.14e (it %d, eigs %1.6e %1.6e)\n",PetscGlobalRank,test_err,k,lambda_min,lambda_max);CHKERRQ(ierr);
ierr = KSPDestroy(&check_ksp);CHKERRQ(ierr);
ierr = VecDestroy(&work1);CHKERRQ(ierr);
ierr = VecDestroy(&work2);CHKERRQ(ierr);
ierr = VecDestroy(&work3);CHKERRQ(ierr);
}
/* all processes shoud call this, even the void ones */
if (pcbddc->dbg_flag) {
ierr = PetscViewerFlush(pcbddc->dbg_viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(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;
}
/*
Computes coefficients for the transformed polynomial,
and stores the result in argument S.
alpha - value of the parameter of the transformed polynomial
beta - value of the previous shift (only used in inplace mode)
k - number of A matrices involved in the computation
coeffs - coefficients of the expansion
initial - true if this is the first time (only relevant for shell mode)
*/
PetscErrorCode STMatMAXPY_Private(ST st,PetscScalar alpha,PetscScalar beta,PetscInt k,PetscScalar *coeffs,PetscBool initial,Mat *S)
{
PetscErrorCode ierr;
PetscInt *matIdx=NULL,nmat,i,ini=-1;
PetscScalar t=1.0,ta,gamma;
PetscBool nz=PETSC_FALSE;
PetscFunctionBegin;
nmat = st->nmat-k;
switch (st->shift_matrix) {
case ST_MATMODE_INPLACE:
if (st->nmat>2) SETERRQ(PetscObjectComm((PetscObject)st),PETSC_ERR_SUP,"ST_MATMODE_INPLACE not supported for polynomial eigenproblems");
if (initial) {
ierr = PetscObjectReference((PetscObject)st->A[0]);CHKERRQ(ierr);
*S = st->A[0];
gamma = alpha;
} else gamma = alpha-beta;
if (gamma != 0.0) {
if (st->nmat>1) {
ierr = MatAXPY(*S,gamma,st->A[1],st->str);CHKERRQ(ierr);
} else {
ierr = MatShift(*S,gamma);CHKERRQ(ierr);
}
}
break;
case ST_MATMODE_SHELL:
if (initial) {
if (st->nmat>2) {
ierr = PetscMalloc(nmat*sizeof(PetscInt),&matIdx);CHKERRQ(ierr);
for (i=0;i<nmat;i++) matIdx[i] = k+i;
}
ierr = STMatShellCreate(st,alpha,nmat,matIdx,coeffs,S);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)st,(PetscObject)*S);CHKERRQ(ierr);
if (st->nmat>2) { ierr = PetscFree(matIdx);CHKERRQ(ierr); }
} else {
ierr = STMatShellShift(*S,alpha);CHKERRQ(ierr);
}
break;
case ST_MATMODE_COPY:
if (coeffs) {
for (i=0;i<nmat && ini==-1;i++) {
if (coeffs[i]!=0.0) ini = i;
else t *= alpha;
}
if (coeffs[ini] != 1.0) nz = PETSC_TRUE;
for (i=ini+1;i<nmat&&!nz;i++) if (coeffs[i]!=0.0) nz = PETSC_TRUE;
} else { nz = PETSC_TRUE; ini = 0; }
if ((alpha == 0.0 || !nz) && t==1.0) {
ierr = MatDestroy(S);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)st->A[k+ini]);CHKERRQ(ierr);
*S = st->A[k+ini];
} else {
if (*S && *S!=st->A[k+ini]) {
ierr = MatCopy(st->A[k+ini],*S,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
} else {
ierr = MatDestroy(S);CHKERRQ(ierr);
ierr = MatDuplicate(st->A[k+ini],MAT_COPY_VALUES,S);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)st,(PetscObject)*S);CHKERRQ(ierr);
}
if (coeffs && coeffs[ini]!=1.0) {
ierr = MatScale(*S,coeffs[ini]);CHKERRQ(ierr);
}
for (i=ini+k+1;i<PetscMax(2,st->nmat);i++) {
t *= alpha;
ta = t;
if (coeffs) ta *= coeffs[i-k];
if (ta!=0.0) {
if (st->nmat>1) {
ierr = MatAXPY(*S,ta,st->A[i],st->str);CHKERRQ(ierr);
} else {
ierr = MatShift(*S,ta);CHKERRQ(ierr);
}
}
}
}
}
ierr = STMatSetHermitian(st,*S);CHKERRQ(ierr);
PetscFunctionReturn(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;
}
