PetscErrorCode MatColoringCreateLargestFirstWeights(MatColoring mc,PetscReal *weights)
{
PetscErrorCode ierr;
PetscInt i,s,e,n,ncols;
PetscRandom rand;
PetscReal r;
PetscInt *degrees;
Mat G = mc->mat;
PetscFunctionBegin;
/* each weight should be the degree plus a random perturbation */
ierr = PetscRandomCreate(PetscObjectComm((PetscObject)mc),&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(G,&s,&e);CHKERRQ(ierr);
n=e-s;
ierr = PetscMalloc1(n,°rees);CHKERRQ(ierr);
ierr = MatColoringGetDegrees(G,mc->dist,degrees);CHKERRQ(ierr);
for (i=s;i<e;i++) {
ierr = MatGetRow(G,i,&ncols,NULL,NULL);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(rand,&r);CHKERRQ(ierr);
weights[i-s] = ncols + PetscAbsReal(r);
ierr = MatRestoreRow(G,i,&ncols,NULL,NULL);CHKERRQ(ierr);
}
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFree(degrees);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode TestSetup(DMLabel label, AppCtx *user)
{
PetscRandom r;
PetscInt n = (PetscInt) (user->fill*(user->pEnd - user->pStart)), i;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);/* -random_type <> */
ierr = PetscRandomSetInterval(r, user->pStart, user->pEnd);CHKERRQ(ierr);
ierr = PetscRandomSetSeed(r, 123456789L);CHKERRQ(ierr);
ierr = PetscRandomSeed(r);CHKERRQ(ierr);
user->size = 0;
for(i = 0; i < n; ++i) {
PetscReal p;
PetscInt val;
ierr = PetscRandomGetValueReal(r, &p);CHKERRQ(ierr);
ierr = DMLabelGetValue(label, (PetscInt) p, &val);CHKERRQ(ierr);
if (val < 0) {
++user->size;
ierr = DMLabelSetValue(label, (PetscInt) p, i % user->numStrata);CHKERRQ(ierr);
}
}
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
ierr = DMLabelCreateIndex(label, user->pStart, user->pEnd);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF, "Created label with chart [%D, %D) and set %D values\n", user->pStart, user->pEnd, user->size);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscInt i,n = 1000,*values;
int event;
PetscRandom rand;
PetscReal value;
PetscErrorCode ierr;
PetscBool values_view=PETSC_FALSE;
PetscMPIInt rank;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,0,"-values_view",&values_view,NULL);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = PetscMalloc1(n,&values);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValueReal(rand,&value);CHKERRQ(ierr);
values[i] = (PetscInt)(n*value + 2.0);
}
ierr = PetscSortInt(n,values);CHKERRQ(ierr);
ierr = PetscLogEventRegister("Sort",0,&event);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValueReal(rand,&value);CHKERRQ(ierr);
values[i] = (PetscInt)(n*value + 2.0);
}
ierr = PetscSortInt(n,values);CHKERRQ(ierr);
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
for (i=1; i<n; i++) {
if (values[i] < values[i-1]) SETERRQ(PETSC_COMM_SELF,1,"Values not sorted");
if (values_view && !rank) {ierr = PetscPrintf(PETSC_COMM_SELF,"%D %D\n",i,values[i]);CHKERRQ(ierr);}
}
ierr = PetscFree(values);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode MatColoringCreateRandomWeights(MatColoring mc,PetscReal *weights)
{
PetscErrorCode ierr;
PetscInt i,s,e;
PetscRandom rand;
PetscReal r;
Mat G = mc->mat;
PetscFunctionBegin;
/* each weight should be the degree plus a random perturbation */
ierr = PetscRandomCreate(PetscObjectComm((PetscObject)mc),&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(G,&s,&e);CHKERRQ(ierr);
for (i=s;i<e;i++) {
ierr = PetscRandomGetValueReal(rand,&r);CHKERRQ(ierr);
weights[i-s] = PetscAbsReal(r);
}
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int Argc,char **Args)
{
PetscBool flg;
PetscInt n = -6;
PetscScalar rho = 1.0;
PetscReal h;
PetscReal beta = 1.0;
DM da;
PetscRandom rctx;
PetscMPIInt comm_size;
Mat H,HtH;
PetscInt x, y, xs, ys, xm, ym;
PetscReal r1, r2;
PetscScalar uxy1, uxy2;
MatStencil sxy, sxy_m;
PetscScalar val, valconj;
Vec b, Htb,xvec;
KSP kspmg;
PC pcmg;
PetscErrorCode ierr;
PetscInt ix[1] = {0};
PetscScalar vals[1] = {1.0};
PetscInitialize(&Argc,&Args,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-size",&n,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-beta",&beta,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-rho",&rho,&flg);CHKERRQ(ierr);
/* Set the fudge parameters, we scale the whole thing by 1/(2*h) later */
h = 1.;
rho *= 1./(2.*h);
/* Geometry info */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC, DMDA_STENCIL_STAR, n, n,
PETSC_DECIDE, PETSC_DECIDE, 2 /* this is the # of dof's */,
1, NULL, NULL, &da);CHKERRQ(ierr);
/* Random numbers */
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
/* Single or multi processor ? */
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&comm_size);CHKERRQ(ierr);
/* construct matrix */
ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(da, &H);CHKERRQ(ierr);
/* get local corners for this processor */
ierr = DMDAGetCorners(da,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
/* Assemble the matrix */
for (x=xs; x<xs+xm; x++) {
for (y=ys; y<ys+ym; y++) {
/* each lattice point sets only the *forward* pointing parameters (right, down),
i.e. Nabla_1^+ and Nabla_2^+.
In this way we can use only local random number creation. That means
we also have to set the corresponding backward pointing entries. */
/* Compute some normally distributed random numbers via Box-Muller */
ierr = PetscRandomGetValueReal(rctx, &r1);CHKERRQ(ierr);
r1 = 1.-r1; /* to change from [0,1) to (0,1], which we need for the log */
ierr = PetscRandomGetValueReal(rctx, &r2);CHKERRQ(ierr);
PetscReal R = PetscSqrtReal(-2.*PetscLogReal(r1));
PetscReal c = PetscCosReal(2.*PETSC_PI*r2);
PetscReal s = PetscSinReal(2.*PETSC_PI*r2);
/* use those to set the field */
uxy1 = PetscExpScalar(((PetscScalar) (R*c/beta))*PETSC_i);
uxy2 = PetscExpScalar(((PetscScalar) (R*s/beta))*PETSC_i);
sxy.i = x; sxy.j = y; /* the point where we are */
/* center action */
sxy.c = 0; /* spin 0, 0 */
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy, &rho, ADD_VALUES);CHKERRQ(ierr);
sxy.c = 1; /* spin 1, 1 */
val = -rho;
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
sxy_m.i = x+1; sxy_m.j = y; /* right action */
sxy.c = 0; sxy_m.c = 0; /* spin 0, 0 */
val = -uxy1; valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
sxy.c = 0; sxy_m.c = 1; /* spin 0, 1 */
val = -uxy1; valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
sxy.c = 1; sxy_m.c = 0; /* spin 1, 0 */
val = uxy1; valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
sxy.c = 1; sxy_m.c = 1; /* spin 1, 1 */
val = uxy1; valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
sxy_m.i = x; sxy_m.j = y+1; /* down action */
sxy.c = 0; sxy_m.c = 0; /* spin 0, 0 */
val = -uxy2; valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
sxy.c = 0; sxy_m.c = 1; /* spin 0, 1 */
val = -PETSC_i*uxy2; valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
sxy.c = 1; sxy_m.c = 0; /* spin 1, 0 */
val = -PETSC_i*uxy2; valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
sxy.c = 1; sxy_m.c = 1; /* spin 1, 1 */
val = PetscConj(uxy2); valconj = PetscConj(val);
ierr = MatSetValuesStencil(H, 1, &sxy_m, 1, &sxy, &val, ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesStencil(H, 1, &sxy, 1, &sxy_m, &valconj, ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(H, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(H, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* scale H */
ierr = MatScale(H, 1./(2.*h));CHKERRQ(ierr);
/* it looks like H is Hermetian */
/* construct normal equations */
ierr = MatMatMult(H, H, MAT_INITIAL_MATRIX, 1., &HtH);CHKERRQ(ierr);
/* permutation matrix to check whether H and HtH are identical to the ones in the paper */
/* Mat perm; */
/* ierr = DMCreateMatrix(da, &perm);CHKERRQ(ierr); */
/* PetscInt row, col; */
/* PetscScalar one = 1.0; */
/* for (PetscInt i=0; i<n; i++) { */
/* for (PetscInt j=0; j<n; j++) { */
/* row = (i*n+j)*2; col = i*n+j; */
/* ierr = MatSetValues(perm, 1, &row, 1, &col, &one, INSERT_VALUES);CHKERRQ(ierr); */
/* row = (i*n+j)*2+1; col = i*n+j + n*n; */
/* ierr = MatSetValues(perm, 1, &row, 1, &col, &one, INSERT_VALUES);CHKERRQ(ierr); */
/* } */
/* } */
/* ierr = MatAssemblyBegin(perm, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); */
/* ierr = MatAssemblyEnd(perm, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); */
/* Mat Hperm; */
/* ierr = MatPtAP(H, perm, MAT_INITIAL_MATRIX, 1.0, &Hperm);CHKERRQ(ierr); */
/* ierr = PetscPrintf(PETSC_COMM_WORLD, "Matrix H after construction\n");CHKERRQ(ierr); */
/* ierr = MatView(Hperm, PETSC_VIEWER_STDOUT_(PETSC_COMM_WORLD));CHKERRQ(ierr); */
/* Mat HtHperm; */
/* ierr = MatPtAP(HtH, perm, MAT_INITIAL_MATRIX, 1.0, &HtHperm);CHKERRQ(ierr); */
/* ierr = PetscPrintf(PETSC_COMM_WORLD, "Matrix HtH:\n");CHKERRQ(ierr); */
/* ierr = MatView(HtHperm, PETSC_VIEWER_STDOUT_(PETSC_COMM_WORLD));CHKERRQ(ierr); */
/* right hand side */
ierr = DMCreateGlobalVector(da, &b);CHKERRQ(ierr);
ierr = VecSet(b,0.0);CHKERRQ(ierr);
ierr = VecSetValues(b, 1, ix, vals, INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
/* ierr = VecSetRandom(b, rctx);CHKERRQ(ierr); */
ierr = VecDuplicate(b, &Htb);CHKERRQ(ierr);
ierr = MatMultTranspose(H, b, Htb);CHKERRQ(ierr);
/* construct solver */
ierr = KSPCreate(PETSC_COMM_WORLD,&kspmg);CHKERRQ(ierr);
ierr = KSPSetType(kspmg, KSPCG);CHKERRQ(ierr);
ierr = KSPGetPC(kspmg,&pcmg);CHKERRQ(ierr);
ierr = PCSetType(pcmg,PCASA);CHKERRQ(ierr);
/* maybe user wants to override some of the choices */
ierr = KSPSetFromOptions(kspmg);CHKERRQ(ierr);
ierr = KSPSetOperators(kspmg, HtH, HtH, DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = DMDASetRefinementFactor(da, 3, 3, 3);CHKERRQ(ierr);
ierr = PCSetDM(pcmg,da);CHKERRQ(ierr);
ierr = PCASASetTolerances(pcmg, 1.e-6, 1.e-10,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRQ(ierr);
ierr = VecDuplicate(b, &xvec);CHKERRQ(ierr);
ierr = VecSet(xvec, 0.0);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the linear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = KSPSolve(kspmg, Htb, xvec);CHKERRQ(ierr);
/* ierr = VecView(xvec, PETSC_VIEWER_STDOUT_(PETSC_COMM_WORLD));CHKERRQ(ierr); */
ierr = KSPDestroy(&kspmg);CHKERRQ(ierr);
ierr = VecDestroy(&xvec);CHKERRQ(ierr);
/* seems to be destroyed by KSPDestroy */
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&Htb);CHKERRQ(ierr);
ierr = MatDestroy(&HtH);CHKERRQ(ierr);
ierr = MatDestroy(&H);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode TestTriangle(MPI_Comm comm, PetscBool interpolate, PetscBool transform)
{
DM dm;
PetscRandom r, ang, ang2;
PetscInt dim, t;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Create reference triangle */
dim = 2;
ierr = DMCreate(comm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) dm, "triangle");CHKERRQ(ierr);
ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
ierr = DMPlexSetDimension(dm, dim);CHKERRQ(ierr);
{
PetscInt numPoints[2] = {3, 1};
PetscInt coneSize[4] = {3, 0, 0, 0};
PetscInt cones[3] = {1, 2, 3};
PetscInt coneOrientations[3] = {0, 0, 0};
PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0};
ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
if (interpolate) {
DM idm;
ierr = DMPlexInterpolate(dm, &idm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) idm, "triangle");CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(dm, idm);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = idm;
}
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
}
/* Check reference geometry: determinant is scaled by reference volume (2.0) */
{
PetscReal v0Ex[2] = {-1.0, -1.0};
PetscReal JEx[4] = {1.0, 0.0, 0.0, 1.0};
PetscReal invJEx[4] = {1.0, 0.0, 0.0, 1.0};
PetscReal detJEx = 1.0;
PetscReal centroidEx[2] = {-0.333333333333, -0.333333333333};
PetscReal normalEx[2] = {0.0, 0.0};
PetscReal volEx = 2.0;
ierr = CheckFEMGeometry(dm, 0, dim, v0Ex, JEx, invJEx, detJEx);CHKERRQ(ierr);
if (interpolate) {ierr = CheckFVMGeometry(dm, 0, dim, centroidEx, normalEx, volEx);CHKERRQ(ierr);}
}
/* Check random triangles: rotate, scale, then translate */
if (transform) {
ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(r, 0.0, 10.0);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF, &ang);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(ang);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(ang, 0.0, 2*PETSC_PI);CHKERRQ(ierr);
for (t = 0; t < 100; ++t) {
PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}, trans[2];
PetscReal v0Ex[2] = {-1.0, -1.0};
PetscReal JEx[4] = {1.0, 0.0, 0.0, 1.0}, R[4], rot[2], rotM[4];
PetscReal invJEx[4] = {1.0, 0.0, 0.0, 1.0};
PetscReal detJEx = 1.0, scale, phi;
PetscReal centroidEx[2] = {-0.333333333333, -0.333333333333};
PetscReal normalEx[2] = {0.0, 0.0};
PetscReal volEx = 2.0;
PetscInt d, e, f, p;
ierr = PetscRandomGetValueReal(r, &scale);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(ang, &phi);CHKERRQ(ierr);
R[0] = cos(phi); R[1] = -sin(phi);
R[2] = sin(phi); R[3] = cos(phi);
for (p = 0; p < 3; ++p) {
for (d = 0; d < dim; ++d) {
for (e = 0, rot[d] = 0.0; e < dim; ++e) {
rot[d] += R[d*dim+e] * vertexCoords[p*dim+e];
}
}
for (d = 0; d < dim; ++d) vertexCoords[p*dim+d] = rot[d];
}
for (d = 0; d < dim; ++d) {
for (e = 0, rot[d] = 0.0; e < dim; ++e) {
rot[d] += R[d*dim+e] * centroidEx[e];
}
}
for (d = 0; d < dim; ++d) centroidEx[d] = rot[d];
for (d = 0; d < dim; ++d) {
for (e = 0; e < dim; ++e) {
for (f = 0, rotM[d*dim+e] = 0.0; f < dim; ++f) {
rotM[d*dim+e] += R[d*dim+f] * JEx[f*dim+e];
}
}
}
for (d = 0; d < dim; ++d) {
for (e = 0; e < dim; ++e) {
JEx[d*dim+e] = rotM[d*dim+e];
}
}
for (d = 0; d < dim; ++d) {
for (e = 0; e < dim; ++e) {
for (f = 0, rotM[d*dim+e] = 0.0; f < dim; ++f) {
rotM[d*dim+e] += invJEx[d*dim+f] * R[e*dim+f];
}
}
}
for (d = 0; d < dim; ++d) {
for (e = 0; e < dim; ++e) {
invJEx[d*dim+e] = rotM[d*dim+e];
}
}
for (d = 0; d < dim; ++d) {
ierr = PetscRandomGetValueReal(r, &trans[d]);CHKERRQ(ierr);
for (p = 0; p < 3; ++p) {
vertexCoords[p*dim+d] *= scale;
vertexCoords[p*dim+d] += trans[d];
}
v0Ex[d] = vertexCoords[d];
for (e = 0; e < dim; ++e) {
JEx[d*dim+e] *= scale;
invJEx[d*dim+e] /= scale;
}
detJEx *= scale;
centroidEx[d] *= scale;
centroidEx[d] += trans[d];
volEx *= scale;
}
ierr = ChangeCoordinates(dm, dim, vertexCoords);CHKERRQ(ierr);
ierr = CheckFEMGeometry(dm, 0, dim, v0Ex, JEx, invJEx, detJEx);CHKERRQ(ierr);
if (interpolate) {ierr = CheckFVMGeometry(dm, 0, dim, centroidEx, normalEx, volEx);CHKERRQ(ierr);}
}
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&ang);CHKERRQ(ierr);
}
/* Move to 3D: Check reference geometry: determinant is scaled by reference volume (2.0) */
dim = 3;
{
PetscScalar vertexCoords[9] = {-1.0, -1.0, 0.0, 1.0, -1.0, 0.0, -1.0, 1.0, 0.0};
PetscReal v0Ex[3] = {-1.0, -1.0, 0.0};
PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0};
PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0};
PetscReal detJEx = 1.0;
PetscReal centroidEx[3] = {-0.333333333333, -0.333333333333, 0.0};
PetscReal normalEx[3] = {0.0, 0.0, 1.0};
PetscReal volEx = 2.0;
ierr = ChangeCoordinates(dm, dim, vertexCoords);CHKERRQ(ierr);
ierr = CheckFEMGeometry(dm, 0, dim, v0Ex, JEx, invJEx, detJEx);CHKERRQ(ierr);
if (interpolate) {ierr = CheckFVMGeometry(dm, 0, dim, centroidEx, normalEx, volEx);CHKERRQ(ierr);}
}
/* Rotated reference element */
{
PetscScalar vertexCoords[9] = {0.0, -1.0, -1.0, 0.0, 1.0, -1.0, 0.0, -1.0, 1.0};
PetscReal v0Ex[3] = {0.0, -1.0, -1.0};
PetscReal JEx[9] = {0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0};
PetscReal invJEx[9] = {0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0};
PetscReal detJEx = 1.0;
PetscReal centroidEx[3] = {0.0, -0.333333333333, -0.333333333333};
PetscReal normalEx[3] = {1.0, 0.0, 0.0};
PetscReal volEx = 2.0;
ierr = ChangeCoordinates(dm, dim, vertexCoords);CHKERRQ(ierr);
ierr = CheckFEMGeometry(dm, 0, dim, v0Ex, JEx, invJEx, detJEx);CHKERRQ(ierr);
if (interpolate) {ierr = CheckFVMGeometry(dm, 0, dim, centroidEx, normalEx, volEx);CHKERRQ(ierr);}
}
/* Check random triangles: scale, translate, then rotate */
if (transform) {
ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(r, 0.0, 10.0);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF, &ang);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(ang);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(ang, 0.0, 2*PETSC_PI);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF, &ang2);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(ang2);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(ang2, 0.0, PETSC_PI);CHKERRQ(ierr);
for (t = 0; t < 100; ++t) {
PetscScalar vertexCoords[9] = {-1.0, -1.0, 0.0, 1.0, -1.0, 0.0, -1.0, 1.0, 0.0}, trans[3];
PetscReal v0Ex[3] = {-1.0, -1.0, 0.0};
PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}, R[9], rot[3], rotM[9];
PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0};
PetscReal detJEx = 1.0, scale, phi, theta, psi = 0.0;
PetscReal centroidEx[3] = {-0.333333333333, -0.333333333333, 0.0};
PetscReal normalEx[3] = {0.0, 0.0, 1.0};
PetscReal volEx = 2.0;
PetscInt d, e, f, p;
ierr = PetscRandomGetValueReal(r, &scale);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(ang, &phi);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(ang2, &theta);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) {
ierr = PetscRandomGetValueReal(r, &trans[d]);CHKERRQ(ierr);
for (p = 0; p < 3; ++p) {
vertexCoords[p*dim+d] *= scale;
vertexCoords[p*dim+d] += trans[d];
}
centroidEx[d] *= scale;
centroidEx[d] += trans[d];
for (e = 0; e < dim-1; ++e) {
JEx[d*dim+e] *= scale;
invJEx[d*dim+e] /= scale;
}
if (d < dim-1) {
detJEx *= scale;
volEx *= scale;
}
}
R[0] = cos(theta)*cos(psi); R[1] = sin(phi)*sin(theta)*cos(psi) - cos(phi)*sin(psi); R[2] = sin(phi)*sin(psi) + cos(phi)*sin(theta)*cos(psi);
R[3] = cos(theta)*sin(psi); R[4] = cos(phi)*cos(psi) + sin(phi)*sin(theta)*sin(psi); R[5] = cos(phi)*sin(theta)*sin(psi) - sin(phi)*cos(psi);
R[6] = -sin(theta); R[7] = sin(phi)*cos(theta); R[8] = cos(phi)*cos(theta);
for (p = 0; p < 3; ++p) {
for (d = 0; d < dim; ++d) {
for (e = 0, rot[d] = 0.0; e < dim; ++e) {
rot[d] += R[d*dim+e] * vertexCoords[p*dim+e];
}
}
for (d = 0; d < dim; ++d) vertexCoords[p*dim+d] = rot[d];
}
for (d = 0; d < dim; ++d) {
for (e = 0, rot[d] = 0.0; e < dim; ++e) {
rot[d] += R[d*dim+e] * centroidEx[e];
}
}
for (d = 0; d < dim; ++d) centroidEx[d] = rot[d];
for (d = 0; d < dim; ++d) {
for (e = 0, rot[d] = 0.0; e < dim; ++e) {
rot[d] += R[d*dim+e] * normalEx[e];
}
}
for (d = 0; d < dim; ++d) normalEx[d] = rot[d];
for (d = 0; d < dim; ++d) {
v0Ex[d] = vertexCoords[d];
for (e = 0; e < dim; ++e) {
for (f = 0, rotM[d*dim+e] = 0.0; f < dim; ++f) {
rotM[d*dim+e] += R[d*dim+f] * JEx[f*dim+e];
}
}
}
for (d = 0; d < dim; ++d) {
for (e = 0; e < dim; ++e) {
JEx[d*dim+e] = rotM[d*dim+e];
}
}
for (d = 0; d < dim; ++d) {
for (e = 0; e < dim; ++e) {
for (f = 0, rotM[d*dim+e] = 0.0; f < dim; ++f) {
rotM[d*dim+e] += invJEx[d*dim+f] * R[e*dim+f];
}
}
}
for (d = 0; d < dim; ++d) {
for (e = 0; e < dim; ++e) {
invJEx[d*dim+e] = rotM[d*dim+e];
}
}
ierr = ChangeCoordinates(dm, dim, vertexCoords);CHKERRQ(ierr);
ierr = CheckFEMGeometry(dm, 0, dim, v0Ex, JEx, invJEx, detJEx);CHKERRQ(ierr);
if (interpolate) {ierr = CheckFVMGeometry(dm, 0, dim, centroidEx, normalEx, volEx);CHKERRQ(ierr);}
}
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&ang);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&ang2);CHKERRQ(ierr);
}
/* Cleanup */
ierr = DMDestroy(&dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode random_network(PetscInt nvertex,PetscInt *pnbranch,Node **pnode,Branch **pbranch,PetscInt **pedgelist,PetscInt seed)
{
PetscErrorCode ierr;
PetscInt i, j, nedges = 0;
PetscInt *edgelist;
PetscInt nbat, ncurr, fr, to;
PetscReal *x, *y, value, xmax = 10.0; /* generate points in square */
PetscReal maxdist = 0.0, dist, alpha, beta, prob;
PetscRandom rnd;
Branch *branch;
Node *node;
Edge *head = NULL, *nnew= NULL, *aux= NULL;
PetscFunctionBeginUser;
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rnd);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rnd);CHKERRQ(ierr);
ierr = PetscRandomSetSeed(rnd, seed);CHKERRQ(ierr);
ierr = PetscRandomSeed(rnd);CHKERRQ(ierr);
/* These parameters might be modified for experimentation */
nbat = (PetscInt)(0.1*nvertex);
ncurr = (PetscInt)(0.1*nvertex);
alpha = 0.6;
beta = 0.2;
ierr = PetscMalloc2(nvertex,&x,nvertex,&y);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(rnd,0.0,xmax);CHKERRQ(ierr);
for (i=0; i<nvertex; i++) {
ierr = PetscRandomGetValueReal(rnd,&x[i]);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(rnd,&y[i]);CHKERRQ(ierr);
}
/* find maximum distance */
for (i=0; i<nvertex; i++) {
for (j=0; j<nvertex; j++) {
dist = findDistance(x[i],x[j],y[i],y[j]);
if (dist >= maxdist) maxdist = dist;
}
}
ierr = PetscRandomSetInterval(rnd,0.0,1.0);CHKERRQ(ierr);
for (i=0; i<nvertex; i++) {
for (j=0; j<nvertex; j++) {
if (j != i) {
dist = findDistance(x[i],x[j],y[i],y[j]);
prob = beta*PetscExpScalar(-dist/(maxdist*alpha));
ierr = PetscRandomGetValueReal(rnd,&value);CHKERRQ(ierr);
if (value <= prob) {
ierr = PetscMalloc1(1,&nnew);CHKERRQ(ierr);
if (head == NULL) {
head = nnew;
head->next = NULL;
head->n = nedges;
head->i = i;
head->j = j;
} else {
aux = head;
head = nnew;
head->n = nedges;
head->next = aux;
head->i = i;
head->j = j;
}
nedges += 1;
}
}
}
}
ierr = PetscMalloc1(2*nedges,&edgelist);CHKERRQ(ierr);
for (aux = head; aux; aux = aux->next) {
edgelist[(aux->n)*2] = aux->i;
edgelist[(aux->n)*2 + 1] = aux->j;
}
aux = head;
while (aux != NULL) {
nnew = aux;
aux = aux->next;
ierr = PetscFree(nnew);CHKERRQ(ierr);
}
ierr = PetscCalloc2(nvertex,&node,nedges,&branch);CHKERRQ(ierr);
for (i = 0; i < nvertex; i++) {
node[i].id = i;
node[i].inj = 0;
node[i].gr = PETSC_FALSE;
}
for (i = 0; i < nedges; i++) {
branch[i].id = i;
branch[i].r = 1.0;
branch[i].bat = 0;
}
/* Chose random node as ground voltage */
ierr = PetscRandomSetInterval(rnd,0.0,nvertex);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(rnd,&value);CHKERRQ(ierr);
node[(int)value].gr = PETSC_TRUE;
/* Create random current and battery injectionsa */
for (i=0; i<ncurr; i++) {
ierr = PetscRandomSetInterval(rnd,0.0,nvertex);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(rnd,&value);CHKERRQ(ierr);
fr = edgelist[(int)value*2];
to = edgelist[(int)value*2 + 1];
node[fr].inj += 1.0;
node[to].inj -= 1.0;
}
for (i=0; i<nbat; i++) {
ierr = PetscRandomSetInterval(rnd,0.0,nedges);CHKERRQ(ierr);
ierr = PetscRandomGetValueReal(rnd,&value);CHKERRQ(ierr);
branch[(int)value].bat += 1.0;
}
ierr = PetscFree2(x,y);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rnd);CHKERRQ(ierr);
/* assign pointers */
*pnbranch = nedges;
*pedgelist = edgelist;
*pbranch = branch;
*pnode = node;
PetscFunctionReturn(ierr);
}
int main(int argc,char **argv)
{
Mat A1,A2; /* problem matrices */
EPS eps; /* eigenproblem solver context */
PetscScalar value[3];
PetscReal tol=1000*PETSC_MACHINE_EPSILON,v;
Vec d;
PetscInt n=30,i,Istart,Iend,col[3];
PetscBool FirstBlock=PETSC_FALSE,LastBlock=PETSC_FALSE;
PetscRandom myrand;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nTridiagonal with random diagonal, n=%D\n\n",n);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix tridiag([-1 0 -1])
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A1);CHKERRQ(ierr);
ierr = MatSetSizes(A1,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A1);CHKERRQ(ierr);
ierr = MatSetUp(A1);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A1,&Istart,&Iend);CHKERRQ(ierr);
if (Istart==0) FirstBlock=PETSC_TRUE;
if (Iend==n) LastBlock=PETSC_TRUE;
value[0]=-1.0; value[1]=0.0; 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(A1,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (LastBlock) {
i=n-1; col[0]=n-2; col[1]=n-1;
ierr = MatSetValues(A1,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (FirstBlock) {
i=0; col[0]=0; col[1]=1; value[0]=0.0; value[1]=-1.0;
ierr = MatSetValues(A1,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create two matrices by filling the diagonal with rand values
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatDuplicate(A1,MAT_COPY_VALUES,&A2);CHKERRQ(ierr);
ierr = MatGetVecs(A1,NULL,&d);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&myrand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(myrand);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(myrand,0.0,1.0);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValueReal(myrand,&v);CHKERRQ(ierr);
ierr = VecSetValue(d,i,v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(d);CHKERRQ(ierr);
ierr = VecAssemblyEnd(d);CHKERRQ(ierr);
ierr = MatDiagonalSet(A1,d,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValueReal(myrand,&v);CHKERRQ(ierr);
ierr = VecSetValue(d,i,v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(d);CHKERRQ(ierr);
ierr = VecAssemblyEnd(d);CHKERRQ(ierr);
ierr = MatDiagonalSet(A2,d,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecDestroy(&d);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&myrand);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSCreate(PETSC_COMM_WORLD,&eps);CHKERRQ(ierr);
ierr = EPSSetProblemType(eps,EPS_HEP);CHKERRQ(ierr);
ierr = EPSSetTolerances(eps,tol,PETSC_DEFAULT);CHKERRQ(ierr);
ierr = EPSSetOperators(eps,A1,NULL);CHKERRQ(ierr);
ierr = EPSSetFromOptions(eps);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve first eigenproblem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSSolve(eps);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," - - - First matrix - - -\n");CHKERRQ(ierr);
ierr = EPSPrintSolution(eps,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve second eigenproblem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSSetOperators(eps,A2,NULL);CHKERRQ(ierr);
ierr = EPSSolve(eps);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," - - - Second matrix - - -\n");CHKERRQ(ierr);
ierr = EPSPrintSolution(eps,NULL);CHKERRQ(ierr);
ierr = EPSDestroy(&eps);CHKERRQ(ierr);
ierr = MatDestroy(&A1);CHKERRQ(ierr);
ierr = MatDestroy(&A2);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
PetscErrorCode MatColoringCreateSmallestLastWeights(MatColoring mc,PetscReal *weights)
{
PetscInt *degrees,*degb,*llprev,*llnext;
PetscInt j,i,s,e,n,nin,ln,lm,degree,maxdegree=0,bidx,idx,dist,distance=mc->dist;
Mat lG,*lGs;
IS ris;
PetscErrorCode ierr;
PetscInt *seen;
const PetscInt *gidx;
PetscInt *idxbuf;
PetscInt *distbuf;
PetscInt ncols,nxt,prv,cur;
const PetscInt *cols;
PetscBool isSEQAIJ;
Mat_SeqAIJ *aij;
PetscInt *Gi,*Gj,*rperm;
Mat G = mc->mat;
PetscReal *lweights,r;
PetscRandom rand;
PetscFunctionBegin;
ierr = MatGetOwnershipRange(G,&s,&e);CHKERRQ(ierr);
n=e-s;
ierr = ISCreateStride(PetscObjectComm((PetscObject)G),n,s,1,&ris);CHKERRQ(ierr);
ierr = MatIncreaseOverlap(G,1,&ris,distance+1);CHKERRQ(ierr);
ierr = ISSort(ris);CHKERRQ(ierr);
ierr = MatGetSubMatrices(G,1,&ris,&ris,MAT_INITIAL_MATRIX,&lGs);CHKERRQ(ierr);
lG = lGs[0];
ierr = PetscObjectTypeCompare((PetscObject)lG,MATSEQAIJ,&isSEQAIJ);CHKERRQ(ierr);
if (!isSEQAIJ) SETERRQ(PetscObjectComm((PetscObject)G),PETSC_ERR_ARG_WRONGSTATE,"Requires an MPI/SEQAIJ Matrix");
ierr = MatGetSize(lG,&ln,&lm);CHKERRQ(ierr);
aij = (Mat_SeqAIJ*)lG->data;
Gi = aij->i;
Gj = aij->j;
ierr = PetscMalloc3(lm,&seen,lm,&idxbuf,lm,&distbuf);CHKERRQ(ierr);
ierr = PetscMalloc1(lm,°rees);CHKERRQ(ierr);
ierr = PetscMalloc1(lm,&lweights);CHKERRQ(ierr);
for (i=0;i<ln;i++) {
seen[i]=-1;
lweights[i] = 1.;
}
ierr = ISGetIndices(ris,&gidx);CHKERRQ(ierr);
for (i=0;i<ln;i++) {
bidx=-1;
ncols = Gi[i+1]-Gi[i];
cols = &(Gj[Gi[i]]);
degree = 0;
/* place the distance-one neighbors on the queue */
for (j=0;j<ncols;j++) {
bidx++;
seen[cols[j]] = i;
distbuf[bidx] = 1;
idxbuf[bidx] = cols[j];
}
while (bidx >= 0) {
/* pop */
idx = idxbuf[bidx];
dist = distbuf[bidx];
bidx--;
degree++;
if (dist < distance) {
ncols = Gi[idx+1]-Gi[idx];
cols = &(Gj[Gi[idx]]);
for (j=0;j<ncols;j++) {
if (seen[cols[j]] != i) {
bidx++;
seen[cols[j]] = i;
idxbuf[bidx] = cols[j];
distbuf[bidx] = dist+1;
}
}
}
}
degrees[i] = degree;
if (degree > maxdegree) maxdegree = degree;
}
/* bucket by degree by some random permutation */
ierr = PetscRandomCreate(PetscObjectComm((PetscObject)mc),&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = PetscMalloc1(ln,&rperm);CHKERRQ(ierr);
for (i=0;i<ln;i++) {
ierr = PetscRandomGetValueReal(rand,&r);CHKERRQ(ierr);
lweights[i] = r;
rperm[i]=i;
}
ierr = PetscSortRealWithPermutation(lm,lweights,rperm);CHKERRQ(ierr);
ierr = PetscMalloc1(maxdegree+1,°b);CHKERRQ(ierr);
ierr = PetscMalloc2(ln,&llnext,ln,&llprev);CHKERRQ(ierr);
for (i=0;i<maxdegree+1;i++) {
degb[i] = -1;
}
for (i=0;i<ln;i++) {
llnext[i] = -1;
llprev[i] = -1;
seen[i] = -1;
}
for (i=0;i<ln;i++) {
idx = rperm[i];
llnext[idx] = degb[degrees[idx]];
if (degb[degrees[idx]] > 0) llprev[degb[degrees[idx]]] = idx;
degb[degrees[idx]] = idx;
}
ierr = PetscFree(rperm);CHKERRQ(ierr);
/* remove the lowest degree one */
i=0;
nin=0;
while (i != maxdegree+1) {
for (i=1;i<maxdegree+1; i++) {
if (degb[i] > 0) {
cur = degb[i];
nin++;
degrees[cur] = 0;
degb[i] = llnext[cur];
bidx=-1;
ncols = Gi[cur+1]-Gi[cur];
cols = &(Gj[Gi[cur]]);
/* place the distance-one neighbors on the queue */
for (j=0;j<ncols;j++) {
if (cols[j] != cur) {
bidx++;
seen[cols[j]] = i;
distbuf[bidx] = 1;
idxbuf[bidx] = cols[j];
}
}
while (bidx >= 0) {
/* pop */
idx = idxbuf[bidx];
dist = distbuf[bidx];
bidx--;
nxt=llnext[idx];
prv=llprev[idx];
if (degrees[idx] > 0) {
/* change up the degree of the neighbors still in the graph */
if (lweights[idx] <= lweights[cur]) lweights[idx] = lweights[cur]+1;
if (nxt > 0) {
llprev[nxt] = prv;
}
if (prv > 0) {
llnext[prv] = nxt;
} else {
degb[degrees[idx]] = nxt;
}
degrees[idx]--;
llnext[idx] = degb[degrees[idx]];
llprev[idx] = -1;
if (degb[degrees[idx]] >= 0) {
llprev[degb[degrees[idx]]] = idx;
}
degb[degrees[idx]] = idx;
if (dist < distance) {
ncols = Gi[idx+1]-Gi[idx];
cols = &(Gj[Gi[idx]]);
for (j=0;j<ncols;j++) {
if (seen[cols[j]] != i) {
bidx++;
seen[cols[j]] = i;
idxbuf[bidx] = cols[j];
distbuf[bidx] = dist+1;
}
}
}
}
}
break;
}
}
}
for (i=0;i<lm;i++) {
if (gidx[i] >= s && gidx[i] < e) {
weights[gidx[i]-s] = lweights[i];
}
}
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFree(degb);CHKERRQ(ierr);
ierr = PetscFree2(llnext,llprev);CHKERRQ(ierr);
ierr = PetscFree(degrees);CHKERRQ(ierr);
ierr = PetscFree(lweights);CHKERRQ(ierr);
ierr = ISRestoreIndices(ris,&gidx);CHKERRQ(ierr);
ierr = ISDestroy(&ris);CHKERRQ(ierr);
ierr = PetscFree3(seen,idxbuf,distbuf);CHKERRQ(ierr);
ierr = MatDestroyMatrices(1,&lGs);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent)
{
PetscErrorCode ierr;
PetscInt Istart,Iend,nloc,kk,Ii,ncols;
IS perm;
GAMGNode *gnodes;
PetscInt *permute;
Mat Gmat = *a_Gmat;
MPI_Comm comm;
MatCoarsen crs;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)a_pc,&comm);CHKERRQ(ierr);
ierr = PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr);
nloc = (Iend-Istart);
/* create random permutation with sort for geo-mg */
ierr = PetscMalloc1(nloc, &gnodes);CHKERRQ(ierr);
ierr = PetscMalloc1(nloc, &permute);CHKERRQ(ierr);
for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */
ierr = MatGetRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr);
{
PetscInt lid = Ii - Istart;
gnodes[lid].lid = lid;
gnodes[lid].degree = ncols;
}
ierr = MatRestoreRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr);
}
if (PETSC_TRUE) {
PetscRandom rand;
PetscBool *bIndexSet;
PetscReal rr;
PetscInt iSwapIndex;
ierr = PetscRandomCreate(comm,&rand);CHKERRQ(ierr);
ierr = PetscCalloc1(nloc, &bIndexSet);CHKERRQ(ierr);
for (Ii = 0; Ii < nloc; Ii++) {
ierr = PetscRandomGetValueReal(rand,&rr);CHKERRQ(ierr);
iSwapIndex = (PetscInt) (rr*nloc);
if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) {
GAMGNode iTemp = gnodes[iSwapIndex];
gnodes[iSwapIndex] = gnodes[Ii];
gnodes[Ii] = iTemp;
bIndexSet[Ii] = PETSC_TRUE;
bIndexSet[iSwapIndex] = PETSC_TRUE;
}
}
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFree(bIndexSet);CHKERRQ(ierr);
}
/* only sort locals */
qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare);
/* create IS of permutation */
for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */
ierr = ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr);
ierr = PetscFree(gnodes);CHKERRQ(ierr);
/* get MIS aggs */
ierr = MatCoarsenCreate(comm, &crs);CHKERRQ(ierr);
ierr = MatCoarsenSetType(crs, MATCOARSENMIS);CHKERRQ(ierr);
ierr = MatCoarsenSetGreedyOrdering(crs, perm);CHKERRQ(ierr);
ierr = MatCoarsenSetAdjacency(crs, Gmat);CHKERRQ(ierr);
ierr = MatCoarsenSetStrictAggs(crs, PETSC_FALSE);CHKERRQ(ierr);
ierr = MatCoarsenApply(crs);CHKERRQ(ierr);
ierr = MatCoarsenGetData(crs, a_llist_parent);CHKERRQ(ierr);
ierr = MatCoarsenDestroy(&crs);CHKERRQ(ierr);
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
