/*@
MatColoringSetFromOptions - Sets MatColoring options from user parameters
Collective on MatColoring
Input Parameters:
. mc - MatColoring context
Options Database Keys:
+ -mat_coloring_type - the type of coloring algorithm used
. -mat_coloring_maxcolors - the maximum number of relevant colors, all nodes not in a color are in maxcolors+1
. -mat_coloring_distance - compute a distance 1,2,... coloring.
. -mat_coloring_view - print information about the coloring and the produced index sets
Level: beginner
.keywords: Coloring, Matrix
.seealso: MatColoring, MatColoringApply()
@*/
PetscErrorCode MatColoringSetFromOptions(MatColoring mc)
{
PetscBool flg;
MatColoringType deft = MATCOLORINGSL;
char type[256];
PetscErrorCode ierr;
PetscInt dist,maxcolors;
PetscFunctionBegin;
PetscValidHeaderSpecific(mc,MAT_COLORING_CLASSID,1);
ierr = MatColoringGetDistance(mc,&dist);CHKERRQ(ierr);
ierr = MatColoringGetMaxColors(mc,&maxcolors);CHKERRQ(ierr);
if (!MatColoringRegisterAllCalled) {ierr = MatColoringRegisterAll();CHKERRQ(ierr);}
ierr = PetscObjectOptionsBegin((PetscObject)mc);CHKERRQ(ierr);
if (((PetscObject)mc)->type_name) deft = ((PetscObject)mc)->type_name;
ierr = PetscOptionsFList("-mat_coloring_type","The coloring method used","MatColoringSetType",MatColoringList,deft,type,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatColoringSetType(mc,type);CHKERRQ(ierr);
} else if (!((PetscObject)mc)->type_name) {
ierr = MatColoringSetType(mc,deft);CHKERRQ(ierr);
}
ierr = PetscOptionsInt("-mat_coloring_distance","Distance of the coloring","MatColoringSetDistance",dist,&dist,&flg);CHKERRQ(ierr);
if (flg) {ierr = MatColoringSetDistance(mc,dist);CHKERRQ(ierr);}
ierr = PetscOptionsInt("-mat_coloring_maxcolors","Maximum colors returned at the end. 1 returns an independent set","MatColoringSetMaxColors",maxcolors,&maxcolors,&flg);CHKERRQ(ierr);
if (flg) {ierr = MatColoringSetMaxColors(mc,maxcolors);CHKERRQ(ierr);}
if (mc->ops->setfromoptions) {
ierr = (*mc->ops->setfromoptions)(mc);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-mat_coloring_valid","Check that a valid coloring has been produced","",mc->valid,&mc->valid,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnum("-mat_coloring_weight_type","Sets the type of vertex weighting used","MatColoringSetWeightType",MatColoringWeightTypes,(PetscEnum)mc->weight_type,(PetscEnum*)&mc->weight_type,NULL);CHKERRQ(ierr);
ierr = PetscObjectProcessOptionsHandlers((PetscObject)mc);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode MatColoringApply_Power(MatColoring mc,ISColoring *iscoloring)
{
PetscErrorCode ierr;
Mat m = mc->mat,mp,ms;
MatColoring imc;
PetscInt i;
const char *optionsprefix;
PetscFunctionBegin;
/* square the matrix repeatedly if necessary */
if (mc->dist == 1) {
mp = m;
} else {
ierr = MatMatMult(m,m,MAT_INITIAL_MATRIX,2.0,&mp);CHKERRQ(ierr);
for (i=2;i<mc->dist;i++) {
ms = mp;
ierr = MatMatMult(m,ms,MAT_INITIAL_MATRIX,2.0,&mp);CHKERRQ(ierr);
ierr = MatDestroy(&ms);CHKERRQ(ierr);
}
}
ierr = MatColoringCreate(mp,&imc);CHKERRQ(ierr);
ierr = PetscObjectGetOptionsPrefix((PetscObject)mc,&optionsprefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)imc,optionsprefix);CHKERRQ(ierr);
ierr = PetscObjectAppendOptionsPrefix((PetscObject)imc,"power_");CHKERRQ(ierr);
ierr = MatColoringSetType(imc,MATCOLORINGGREEDY);CHKERRQ(ierr);
ierr = MatColoringSetDistance(imc,1);CHKERRQ(ierr);
ierr = MatColoringSetWeightType(imc,mc->weight_type);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(imc);CHKERRQ(ierr);
ierr = MatColoringApply(imc,iscoloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&imc);CHKERRQ(ierr);
if (mp != m) {ierr = MatDestroy(&mp);CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
PetscErrorCode SNESComputeJacobianDefaultColor(SNES snes,Vec x1,Mat J,Mat B,void *ctx)
{
MatFDColoring color = (MatFDColoring)ctx;
PetscErrorCode ierr;
DM dm;
MatColoring mc;
ISColoring iscoloring;
PetscBool hascolor;
PetscBool solvec,matcolor = PETSC_FALSE;
PetscFunctionBegin;
if (color) PetscValidHeaderSpecific(color,MAT_FDCOLORING_CLASSID,6);
if (!color) {ierr = PetscObjectQuery((PetscObject)B,"SNESMatFDColoring",(PetscObject*)&color);CHKERRQ(ierr);}
if (!color) {
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMHasColoring(dm,&hascolor);CHKERRQ(ierr);
matcolor = PETSC_FALSE;
ierr = PetscOptionsGetBool(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-snes_fd_color_use_mat",&matcolor,NULL);CHKERRQ(ierr);
if (hascolor && !matcolor) {
ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
} else {
ierr = MatColoringCreate(B,&mc);CHKERRQ(ierr);
ierr = MatColoringSetDistance(mc,2);CHKERRQ(ierr);
ierr = MatColoringSetType(mc,MATCOLORINGSL);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
ierr = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
}
ierr = PetscObjectCompose((PetscObject)B,"SNESMatFDColoring",(PetscObject)color);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)color);CHKERRQ(ierr);
}
/* F is only usable if there is no RHS on the SNES and the full solution corresponds to x1 */
ierr = VecEqual(x1,snes->vec_sol,&solvec);CHKERRQ(ierr);
if (!snes->vec_rhs && solvec) {
Vec F;
ierr = SNESGetFunction(snes,&F,NULL,NULL);CHKERRQ(ierr);
ierr = MatFDColoringSetF(color,F);CHKERRQ(ierr);
}
ierr = MatFDColoringApply(B,color,x1,snes);CHKERRQ(ierr);
if (J != B) {
ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
Mat A,R,C,C_dense,C_sparse,Rt_dense,P,PtAP;
PetscInt row,col,m,n;
PetscErrorCode ierr;
MatScalar one =1.0,val;
MatColoring mc;
MatTransposeColoring matcoloring = 0;
ISColoring iscoloring;
PetscBool equal;
PetscMPIInt size;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!");
/* Create seqaij A */
ierr = MatCreate(PETSC_COMM_SELF,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,4,4,4,4);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
row = 0; col=0; val=1.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr);
row = 1; col=3; val=2.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr);
row = 2; col=2; val=3.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr);
row = 3; col=0; val=4.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(A,"A_");CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr);
/* Create seqaij R */
ierr = MatCreate(PETSC_COMM_SELF,&R);CHKERRQ(ierr);
ierr = MatSetSizes(R,2,4,2,4);CHKERRQ(ierr);
ierr = MatSetType(R,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(R);CHKERRQ(ierr);
ierr = MatSetUp(R);CHKERRQ(ierr);
row = 0; col=0; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr);
row = 0; col=1; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr);
row = 1; col=1; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr);
row = 1; col=2; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr);
row = 1; col=3; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(R,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(R,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(R,"R_");CHKERRQ(ierr);
ierr = MatView(R,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr);
/* C = A*R^T */
ierr = MatMatTransposeMult(A,R,MAT_INITIAL_MATRIX,2.0,&C);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(C,"ARt_");CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr);
/* Create MatTransposeColoring from symbolic C=A*R^T */
ierr = MatColoringCreate(C,&mc);CHKERRQ(ierr);
ierr = MatColoringSetDistance(mc,2);CHKERRQ(ierr);
/* ierr = MatColoringSetType(mc,MATCOLORINGSL);CHKERRQ(ierr); */
ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
ierr = MatTransposeColoringCreate(C,iscoloring,&matcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
/* Create Rt_dense */
ierr = MatCreate(PETSC_COMM_WORLD,&Rt_dense);CHKERRQ(ierr);
ierr = MatSetSizes(Rt_dense,4,matcoloring->ncolors,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(Rt_dense,MATDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(Rt_dense,NULL);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Rt_dense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Rt_dense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetLocalSize(Rt_dense,&m,&n);CHKERRQ(ierr);
printf("Rt_dense: %d,%d\n",(int)m,(int)n);
/* Get Rt_dense by Apply MatTransposeColoring to R */
ierr = MatTransColoringApplySpToDen(matcoloring,R,Rt_dense);CHKERRQ(ierr);
/* C_dense = A*Rt_dense */
ierr = MatMatMult(A,Rt_dense,MAT_INITIAL_MATRIX,2.0,&C_dense);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(C_dense,"ARt_dense_");CHKERRQ(ierr);
/*ierr = MatView(C_dense,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
/*ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr); */
/* Recover C from C_dense */
ierr = MatDuplicate(C,MAT_DO_NOT_COPY_VALUES,&C_sparse);CHKERRQ(ierr);
ierr = MatTransColoringApplyDenToSp(matcoloring,C_dense,C_sparse);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(C_sparse,"ARt_color_");CHKERRQ(ierr);
ierr = MatView(C_sparse,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr);
ierr = MatDestroy(&C_dense);CHKERRQ(ierr);
ierr = MatDestroy(&C_sparse);CHKERRQ(ierr);
ierr = MatDestroy(&Rt_dense);CHKERRQ(ierr);
ierr = MatTransposeColoringDestroy(&matcoloring);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
/* Test PtAP = P^T*A*P, P = R^T */
ierr = MatTranspose(R,MAT_INITIAL_MATRIX,&P);CHKERRQ(ierr);
ierr = MatPtAP(A,P,MAT_INITIAL_MATRIX,2.0,&PtAP);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(PtAP,"PtAP_");CHKERRQ(ierr);
ierr = MatView(PtAP,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&P);CHKERRQ(ierr);
/* Test C = RARt */
ierr = MatRARt(A,R,MAT_INITIAL_MATRIX,2.0,&C);CHKERRQ(ierr);
ierr = MatRARt(A,R,MAT_REUSE_MATRIX,2.0,&C);CHKERRQ(ierr);
ierr = MatEqual(C,PtAP,&equal);CHKERRQ(ierr);
if (!equal) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: PtAP != RARt");CHKERRQ(ierr);
}
/* Free spaces */
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&R);CHKERRQ(ierr);
ierr = MatDestroy(&PtAP);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode MatRARtSymbolic_SeqAIJ_SeqAIJ_colorrart(Mat A,Mat R,PetscReal fill,Mat *C)
{
PetscErrorCode ierr;
Mat P;
PetscInt *rti,*rtj;
Mat_RARt *rart;
MatColoring coloring;
MatTransposeColoring matcoloring;
ISColoring iscoloring;
Mat Rt_dense,RARt_dense;
Mat_SeqAIJ *c;
PetscFunctionBegin;
/* create symbolic P=Rt */
ierr = MatGetSymbolicTranspose_SeqAIJ(R,&rti,&rtj);CHKERRQ(ierr);
ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,R->cmap->n,R->rmap->n,rti,rtj,NULL,&P);CHKERRQ(ierr);
/* get symbolic C=Pt*A*P */
ierr = MatPtAPSymbolic_SeqAIJ_SeqAIJ_SparseAxpy(A,P,fill,C);CHKERRQ(ierr);
ierr = MatSetBlockSizes(*C,PetscAbs(R->rmap->bs),PetscAbs(R->rmap->bs));CHKERRQ(ierr);
(*C)->ops->rartnumeric = MatRARtNumeric_SeqAIJ_SeqAIJ_colorrart;
/* create a supporting struct */
ierr = PetscNew(&rart);CHKERRQ(ierr);
c = (Mat_SeqAIJ*)(*C)->data;
c->rart = rart;
/* ------ Use coloring ---------- */
/* inode causes memory problem, don't know why */
if (c->inode.use) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MAT_USE_INODES is not supported. Use '-mat_no_inode'");
/* Create MatTransposeColoring from symbolic C=R*A*R^T */
ierr = MatColoringCreate(*C,&coloring);CHKERRQ(ierr);
ierr = MatColoringSetDistance(coloring,2);CHKERRQ(ierr);
ierr = MatColoringSetType(coloring,MATCOLORINGSL);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(coloring);CHKERRQ(ierr);
ierr = MatColoringApply(coloring,&iscoloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&coloring);CHKERRQ(ierr);
ierr = MatTransposeColoringCreate(*C,iscoloring,&matcoloring);CHKERRQ(ierr);
rart->matcoloring = matcoloring;
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
/* Create Rt_dense */
ierr = MatCreate(PETSC_COMM_SELF,&Rt_dense);CHKERRQ(ierr);
ierr = MatSetSizes(Rt_dense,A->cmap->n,matcoloring->ncolors,A->cmap->n,matcoloring->ncolors);CHKERRQ(ierr);
ierr = MatSetType(Rt_dense,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(Rt_dense,NULL);CHKERRQ(ierr);
Rt_dense->assembled = PETSC_TRUE;
rart->Rt = Rt_dense;
/* Create RARt_dense = R*A*Rt_dense */
ierr = MatCreate(PETSC_COMM_SELF,&RARt_dense);CHKERRQ(ierr);
ierr = MatSetSizes(RARt_dense,(*C)->rmap->n,matcoloring->ncolors,(*C)->rmap->n,matcoloring->ncolors);CHKERRQ(ierr);
ierr = MatSetType(RARt_dense,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(RARt_dense,NULL);CHKERRQ(ierr);
rart->RARt = RARt_dense;
/* Allocate work array to store columns of A*R^T used in MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqDense() */
ierr = PetscMalloc1(A->rmap->n*4,&rart->work);CHKERRQ(ierr);
rart->destroy = (*C)->ops->destroy;
(*C)->ops->destroy = MatDestroy_SeqAIJ_RARt;
/* clean up */
ierr = MatRestoreSymbolicTranspose_SeqAIJ(R,&rti,&rtj);CHKERRQ(ierr);
ierr = MatDestroy(&P);CHKERRQ(ierr);
#if defined(PETSC_USE_INFO)
{
PetscReal density= (PetscReal)(c->nz)/(RARt_dense->rmap->n*RARt_dense->cmap->n);
ierr = PetscInfo(*C,"C=R*(A*Rt) via coloring C - use sparse-dense inner products\n");CHKERRQ(ierr);
ierr = PetscInfo6(*C,"RARt_den %D %D; Rt %D %D (RARt->nz %D)/(m*ncolors)=%g\n",RARt_dense->rmap->n,RARt_dense->cmap->n,R->cmap->n,R->rmap->n,c->nz,density);CHKERRQ(ierr);
}
#endif
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode SNESComputeNGSDefaultSecant(SNES snes,Vec X,Vec B,void *ctx)
{
PetscErrorCode ierr;
SNES_NGS *gs = (SNES_NGS*)snes->data;
PetscInt i,j,k,ncolors;
DM dm;
PetscBool flg;
ISColoring coloring = gs->coloring;
MatColoring mc;
Vec W,G,F;
PetscScalar h=gs->h;
IS *coloris;
PetscScalar f,g,x,w,d;
PetscReal dxt,xt,ft,ft1=0;
const PetscInt *idx;
PetscInt size,s;
PetscReal atol,rtol,stol;
PetscInt its;
PetscErrorCode (*func)(SNES,Vec,Vec,void*);
void *fctx;
PetscBool mat = gs->secant_mat,equal,isdone,alldone;
PetscScalar *xa,*fa,*wa,*ga;
PetscFunctionBegin;
if (snes->nwork < 3) {
ierr = SNESSetWorkVecs(snes,3);CHKERRQ(ierr);
}
W = snes->work[0];
G = snes->work[1];
F = snes->work[2];
ierr = VecGetOwnershipRange(X,&s,NULL);CHKERRQ(ierr);
ierr = SNESNGSGetTolerances(snes,&atol,&rtol,&stol,&its);CHKERRQ(ierr);
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = SNESGetFunction(snes,NULL,&func,&fctx);CHKERRQ(ierr);
if (!coloring) {
/* create the coloring */
ierr = DMHasColoring(dm,&flg);CHKERRQ(ierr);
if (flg && !mat) {
ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&coloring);CHKERRQ(ierr);
} else {
if (!snes->jacobian) {ierr = SNESSetUpMatrices(snes);CHKERRQ(ierr);}
ierr = MatColoringCreate(snes->jacobian,&mc);CHKERRQ(ierr);
ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
ierr = MatColoringApply(mc,&coloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
}
gs->coloring = coloring;
}
ierr = ISColoringGetIS(coloring,&ncolors,&coloris);CHKERRQ(ierr);
ierr = VecEqual(X,snes->vec_sol,&equal);CHKERRQ(ierr);
if (equal && snes->normschedule == SNES_NORM_ALWAYS) {
/* assume that the function is already computed */
ierr = VecCopy(snes->vec_func,F);CHKERRQ(ierr);
} else {
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);}
}
ierr = VecGetArray(X,&xa);CHKERRQ(ierr);
ierr = VecGetArray(F,&fa);CHKERRQ(ierr);
ierr = VecGetArray(G,&ga);CHKERRQ(ierr);
ierr = VecGetArray(W,&wa);CHKERRQ(ierr);
for (i=0;i<ncolors;i++) {
ierr = ISGetIndices(coloris[i],&idx);CHKERRQ(ierr);
ierr = ISGetLocalSize(coloris[i],&size);CHKERRQ(ierr);
ierr = VecCopy(X,W);CHKERRQ(ierr);
for (j=0;j<size;j++) {
wa[idx[j]-s] += h;
}
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,W,G,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(G,-1.0,B);CHKERRQ(ierr);}
for (k=0;k<its;k++) {
dxt = 0.;
xt = 0.;
ft = 0.;
for (j=0;j<size;j++) {
f = fa[idx[j]-s];
x = xa[idx[j]-s];
g = ga[idx[j]-s];
w = wa[idx[j]-s];
if (PetscAbsScalar(g-f) > atol) {
/* This is equivalent to d = x - (h*f) / PetscRealPart(g-f) */
d = (x*g-w*f) / PetscRealPart(g-f);
} else {
d = x;
}
dxt += PetscRealPart(PetscSqr(d-x));
xt += PetscRealPart(PetscSqr(x));
ft += PetscRealPart(PetscSqr(f));
xa[idx[j]-s] = d;
}
if (k == 0) ft1 = PetscSqrtReal(ft);
if (k<its-1) {
isdone = PETSC_FALSE;
if (stol*PetscSqrtReal(xt) > PetscSqrtReal(dxt)) isdone = PETSC_TRUE;
if (PetscSqrtReal(ft) < atol) isdone = PETSC_TRUE;
if (rtol*ft1 > PetscSqrtReal(ft)) isdone = PETSC_TRUE;
ierr = MPIU_Allreduce(&isdone,&alldone,1,MPIU_BOOL,MPI_BAND,PetscObjectComm((PetscObject)snes));CHKERRQ(ierr);
if (alldone) break;
}
if (i < ncolors-1 || k < its-1) {
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);}
}
if (k<its-1) {
ierr = VecSwap(X,W);CHKERRQ(ierr);
ierr = VecSwap(F,G);CHKERRQ(ierr);
}
}
}
ierr = VecRestoreArray(X,&xa);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&fa);CHKERRQ(ierr);
ierr = VecRestoreArray(G,&ga);CHKERRQ(ierr);
ierr = VecRestoreArray(W,&wa);CHKERRQ(ierr);
ierr = ISColoringRestoreIS(coloring,&coloris);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
