1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsclandau.h> /*I "petsclandau.h" I*/ 3 #include <petscts.h> 4 #include <petscdmforest.h> 5 6 /* Landau collision operator */ 7 #define PETSC_THREAD_SYNC 8 #define PETSC_DEVICE_FUNC_DECL static 9 #include "land_tensors.h" 10 11 /* vector padding not supported */ 12 #define LANDAU_VL 1 13 14 int LandauGetIPDataSize(const LandauIPData *const d) { 15 return d->nip_*(1 + d->dim_ + d->ns_); /* assumes Nq == Nd */ 16 } 17 18 static PetscErrorCode LandauPointDataCreate(LandauIPData *IPData, PetscInt dim, PetscInt nip, PetscInt Ns) 19 { 20 PetscErrorCode ierr; 21 PetscInt sz, nip_pad = nip ; /* LANDAU_VL*(nip/LANDAU_VL + !!(nip%LANDAU_VL)); */ 22 LandauIPReal *pdata; 23 PetscFunctionBegin; 24 IPData->dim_ = dim; 25 IPData->nip_ = nip_pad; 26 IPData->ns_ = Ns; 27 sz = LandauGetIPDataSize(IPData); 28 ierr = PetscMalloc(sizeof(LandauIPReal)*sz,&pdata);CHKERRQ(ierr); 29 /* pack data */ 30 IPData->w = pdata + 0; /* w */ 31 IPData->x = pdata + 1*nip_pad; 32 IPData->y = pdata + 2*nip_pad; 33 IPData->z = pdata + 3*nip_pad; 34 IPData->coefs= pdata + (dim+1)*nip_pad; 35 PetscFunctionReturn(0); 36 } 37 static PetscErrorCode LandauGPUDataDestroy(void *ptr) 38 { 39 P4estVertexMaps *maps = (P4estVertexMaps *)ptr; 40 PetscErrorCode ierr; 41 PetscFunctionBegin; 42 if (maps->deviceType != LANDAU_CPU) { 43 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 44 if (maps->deviceType == LANDAU_KOKKOS) { 45 ierr = LandauKokkosDestroyMatMaps(maps);CHKERRQ(ierr); // imples Kokkos does 46 } // else could be CUDA 47 #elif defined(PETSC_HAVE_CUDA) 48 if (maps->deviceType == LANDAU_CUDA){ 49 ierr = LandauCUDADestroyMatMaps(maps);CHKERRQ(ierr); 50 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps->deviceType %D ?????",maps->deviceType); 51 #endif 52 } 53 ierr = PetscFree(maps->c_maps);CHKERRQ(ierr); 54 ierr = PetscFree(maps->gIdx);CHKERRQ(ierr); 55 ierr = PetscFree(maps);CHKERRQ(ierr); 56 PetscFunctionReturn(0); 57 } 58 static PetscErrorCode LandauPointDataDestroy(LandauIPData *IPData) 59 { 60 PetscErrorCode ierr; 61 PetscFunctionBegin; 62 ierr = PetscFree(IPData->w);CHKERRQ(ierr); 63 PetscFunctionReturn(0); 64 } 65 /* ------------------------------------------------------------------- */ 66 /* 67 LandauFormJacobian_Internal - Evaluates Jacobian matrix. 68 69 Input Parameters: 70 . globX - input vector 71 . actx - optional user-defined context 72 . dim - dimension 73 74 Output Parameters: 75 . J0acP - Jacobian matrix filled, not created 76 */ 77 static PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, PetscReal shift, void *a_ctx) 78 { 79 LandauCtx *ctx = (LandauCtx*)a_ctx; 80 PetscErrorCode ierr; 81 PetscInt cStart, cEnd, elemMatSize; 82 DM plex = NULL; 83 PetscDS prob; 84 PetscSection section,globsection; 85 PetscInt numCells,totDim,ej,Nq,*Nbf,*Ncf,Nb,Ncx,Nf,d,f,fieldA,qj; 86 PetscQuadrature quad; 87 PetscTabulation *Tf; 88 PetscReal nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES]; 89 const PetscReal *quadWeights; 90 PetscReal *invJ,*invJ_a=NULL,*mass_w=NULL; 91 PetscReal invMass[LANDAU_MAX_SPECIES],Eq_m[LANDAU_MAX_SPECIES],m_0=ctx->m_0; /* normalize mass -- not needed! */ 92 PetscLogDouble flops; 93 Vec locX; 94 LandauIPData IPData; 95 PetscContainer container; 96 P4estVertexMaps *maps=NULL; 97 98 PetscFunctionBegin; 99 PetscValidHeaderSpecific(a_X,VEC_CLASSID,1); 100 PetscValidHeaderSpecific(JacP,MAT_CLASSID,2); 101 PetscValidPointer(ctx,4); 102 103 /* check for matrix container for GPU assembly */ 104 ierr = PetscLogEventBegin(ctx->events[10],0,0,0,0);CHKERRQ(ierr); 105 ierr = PetscObjectQuery((PetscObject) JacP, "assembly_maps", (PetscObject *) &container);CHKERRQ(ierr); 106 if (container /* && ctx->deviceType != LANDAU_CPU */) { 107 if (!ctx->gpu_assembly) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"GPU matrix container but no GPU assembly"); 108 ierr = PetscContainerGetPointer(container, (void **) &maps);CHKERRQ(ierr); 109 if (!maps) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"empty GPU matrix container"); 110 } 111 ierr = DMConvert(ctx->dmv, DMPLEX, &plex);CHKERRQ(ierr); 112 ierr = DMCreateLocalVector(plex, &locX);CHKERRQ(ierr); 113 ierr = VecZeroEntries(locX);CHKERRQ(ierr); /* zero BCs so don't set */ 114 ierr = DMGlobalToLocalBegin(plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 115 ierr = DMGlobalToLocalEnd (plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 116 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 117 ierr = DMGetLocalSection(plex, §ion);CHKERRQ(ierr); 118 ierr = DMGetGlobalSection(plex, &globsection);CHKERRQ(ierr); 119 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 120 ierr = PetscDSGetTabulation(prob, &Tf);CHKERRQ(ierr); // Bf, &Df 121 ierr = PetscDSGetDimensions(prob, &Nbf);CHKERRQ(ierr); Nb = Nbf[0]; /* number of vertices*S */ 122 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); if (Nf!=ctx->num_species) SETERRQ1(ctx->comm, PETSC_ERR_PLIB, "Nf %D != S",Nf); 123 ierr = PetscDSGetComponents(prob, &Ncf);CHKERRQ(ierr); Ncx = Ncf[0]; if (Ncx!=1) SETERRQ1(ctx->comm, PETSC_ERR_PLIB, "Nc %D != 1",Ncx); 124 if (shift==0.0) { 125 for (fieldA=0;fieldA<Nf;fieldA++) { 126 invMass[fieldA] = m_0/ctx->masses[fieldA]; 127 Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */ 128 if (dim==2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */ 129 nu_alpha[fieldA] = PetscSqr(ctx->charges[fieldA]/m_0)*m_0/ctx->masses[fieldA]; 130 nu_beta[fieldA] = PetscSqr(ctx->charges[fieldA]/ctx->epsilon0)*ctx->lnLam / (8*PETSC_PI) * ctx->t_0*ctx->n_0/PetscPowReal(ctx->v_0,3); 131 } 132 } 133 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 134 numCells = cEnd - cStart; 135 ierr = PetscFEGetQuadrature(ctx->fe[0], &quad);CHKERRQ(ierr); 136 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights);CHKERRQ(ierr); 137 if (Nb!=Nq) SETERRQ4(ctx->comm, PETSC_ERR_PLIB, "Nb!=Nq %D %D over integration or simplices? Tf[0]->Nb=%D dim=%D",Nb,Nq,Tf[0]->Nb,dim); 138 if (Nq >LANDAU_MAX_NQ) SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"Order too high. Nq = %D > LANDAU_MAX_NQ (%D)",Nq,LANDAU_MAX_NQ); 139 if (LANDAU_DIM != dim) SETERRQ2(ctx->comm, PETSC_ERR_PLIB, "dim %D != LANDAU_DIM %d",dim,LANDAU_DIM); 140 if (shift==0.0) { 141 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 142 flops = (PetscLogDouble)numCells*(PetscLogDouble)Nq*(PetscLogDouble)(5*dim*dim*Nf*Nf + 165); 143 } else { 144 flops = (PetscLogDouble)numCells*(PetscLogDouble)Nq*(PetscLogDouble)(5*dim*dim*Nf*Nf); 145 } 146 elemMatSize = totDim*totDim; 147 ierr = PetscLogEventEnd(ctx->events[10],0,0,0,0);CHKERRQ(ierr); 148 { 149 static int cc = 0; 150 /* collect f data */ 151 if (ctx->verbose > 1 || (ctx->verbose > 0 && cc++ == 0)) { 152 PetscInt N,Nloc; 153 ierr = MatGetSize(JacP,&N,NULL);CHKERRQ(ierr); 154 ierr = VecGetSize(locX,&Nloc);CHKERRQ(ierr); 155 ierr = PetscPrintf(ctx->comm,"[%D]%s: %D IPs, %D cells, totDim=%D, Nb=%D, Nq=%D, elemMatSize=%D, dim=%D, Tab: Nb=%D Nf=%D Np=%D cdim=%D N=%D N+hang=%D, shift=%g\n", 156 0,"FormLandau",Nq*numCells,numCells, totDim, Nb, Nq, elemMatSize, dim, Tf[0]->Nb, Nf, Tf[0]->Np, Tf[0]->cdim, N, Nloc, shift);CHKERRQ(ierr); 157 } 158 if (shift==0.0) { 159 ierr = LandauPointDataCreate(&IPData, dim, Nq*numCells, Nf);CHKERRQ(ierr); 160 ierr = PetscMalloc1(numCells*Nq*dim*dim,&invJ_a);CHKERRQ(ierr); 161 ierr = PetscLogEventBegin(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 162 } else { // mass 163 ierr = PetscMalloc1(numCells*Nq,&mass_w);CHKERRQ(ierr); 164 IPData.w = NULL; 165 ierr = PetscLogEventBegin(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 166 } 167 /* cache geometry and x, f and df/dx at IPs */ 168 for (ej = 0 ; ej < numCells; ++ej) { 169 PetscReal vj[LANDAU_MAX_NQ*LANDAU_DIM],detJj[LANDAU_MAX_NQ], Jdummy[LANDAU_MAX_NQ*LANDAU_DIM*LANDAU_DIM]; 170 PetscScalar *coef = NULL; 171 invJ = invJ_a ? invJ_a + ej * Nq*dim*dim : NULL; 172 ierr = DMPlexComputeCellGeometryFEM(plex, cStart+ej, quad, vj, Jdummy, invJ, detJj);CHKERRQ(ierr); 173 if (shift!=0.0) { // mass 174 for (qj = 0; qj < Nq; ++qj) { 175 PetscInt gidx = (ej*Nq + qj); 176 mass_w[gidx] = detJj[qj] * quadWeights[qj]; 177 if (dim==2) mass_w[gidx] *= 2.*PETSC_PI*vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */ 178 } 179 } else { 180 ierr = DMPlexVecGetClosure(plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 181 ierr = PetscMemcpy(&IPData.coefs[ej*Nb*Nf],coef,Nb*Nf*sizeof(PetscScalar));CHKERRQ(ierr); /* change if LandauIPReal != PetscScalar */ 182 /* create point data for cell i for Landau tensor: x, f(x), grad f(x) */ 183 for (qj = 0; qj < Nq; ++qj) { 184 PetscInt gidx = (ej*Nq + qj); 185 IPData.x[gidx] = vj[qj * dim + 0]; /* coordinate */ 186 IPData.y[gidx] = vj[qj * dim + 1]; 187 if (dim==3) IPData.z[gidx] = vj[qj * dim + 2]; 188 IPData.w[gidx] = detJj[qj] * quadWeights[qj]; 189 if (dim==2) IPData.w[gidx] *= IPData.x[gidx]; /* cylindrical coordinate, w/o 2pi */ 190 } /* q */ 191 ierr = DMPlexVecRestoreClosure(plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 192 } 193 } /* ej */ 194 if (shift==0.0) { 195 ierr = PetscLogEventEnd(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 196 } else { // mass 197 ierr = PetscLogEventEnd(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 198 } 199 } 200 ierr = DMRestoreLocalVector(plex, &locX);CHKERRQ(ierr); 201 202 /* do it */ 203 if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) { 204 if (ctx->deviceType == LANDAU_CUDA) { 205 #if defined(PETSC_HAVE_CUDA) 206 ierr = LandauCUDAJacobian(plex,Nq,nu_alpha,nu_beta,invMass,Eq_m,&IPData,invJ_a,mass_w,shift,ctx->events,JacP);CHKERRQ(ierr); 207 #else 208 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 209 #endif 210 } else if (ctx->deviceType == LANDAU_KOKKOS) { 211 #if defined(PETSC_HAVE_KOKKOS) 212 ierr = LandauKokkosJacobian(plex,Nq,nu_alpha,nu_beta,invMass,Eq_m,&IPData,invJ_a,ctx->subThreadBlockSize,mass_w,shift,ctx->events,JacP);CHKERRQ(ierr); 213 #else 214 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 215 #endif 216 } 217 } else { /* CPU version */ 218 PetscInt ei, qi; 219 PetscScalar *elemMat; 220 PetscReal *ff, *dudx, *dudy, *dudz; 221 const PetscReal * const BB = Tf[0]->T[0], * const DD = Tf[0]->T[1]; 222 if (shift!=0.0) { // mass 223 ierr = PetscMalloc1(elemMatSize, &elemMat);CHKERRQ(ierr); 224 } else { 225 ierr = PetscLogEventBegin(ctx->events[8],0,0,0,0);CHKERRQ(ierr); 226 ierr = PetscMalloc5(elemMatSize, &elemMat, IPData.nip_*Nf, &ff,IPData.nip_*Nf, &dudx, IPData.nip_*Nf, &dudy, dim==3 ? IPData.nip_*Nf : 0, &dudz);CHKERRQ(ierr); 227 /* compute f and df */ 228 for (ei = cStart, invJ = invJ_a; ei < cEnd; ++ei, invJ += Nq*dim*dim) { 229 LandauIPReal *coef = &IPData.coefs[ei*Nb*Nf]; 230 PetscScalar u_x[LANDAU_MAX_SPECIES][LANDAU_DIM]; 231 /* get f and df */ 232 for (qi = 0; qi < Nq; ++qi) { 233 const PetscReal *Bq = &BB[qi*Nb]; 234 const PetscReal *Dq = &DD[qi*Nb*dim]; 235 const PetscInt gidx = ei*Nq + qi; 236 /* get f & df */ 237 for (f = 0; f < Nf; ++f) { 238 PetscInt b, e; 239 PetscScalar refSpaceDer[LANDAU_DIM]; 240 ff[gidx + f*IPData.nip_] = 0.0; 241 for (d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0; 242 for (b = 0; b < Nb; ++b) { 243 const PetscInt cidx = b; 244 ff[gidx + f*IPData.nip_] += Bq[cidx]*coef[f*Nb+cidx]; 245 for (d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx*dim+d]*coef[f*Nb+cidx]; 246 } 247 for (d = 0; d < dim; ++d) { 248 for (e = 0, u_x[f][d] = 0.0; e < dim; ++e) { 249 u_x[f][d] += invJ[qi * dim * dim + e*dim+d]*refSpaceDer[e]; 250 } 251 } 252 } 253 for (f=0;f<Nf;f++) { 254 dudx[gidx + f*IPData.nip_] = PetscRealPart(u_x[f][0]); 255 dudy[gidx + f*IPData.nip_] = PetscRealPart(u_x[f][1]); 256 #if LANDAU_DIM==3 257 dudz[gidx + f*IPData.nip_] = PetscRealPart(u_x[f][2]); 258 #endif 259 } 260 } 261 } 262 ierr = PetscLogEventEnd(ctx->events[8],0,0,0,0);CHKERRQ(ierr); 263 } 264 for (ej = cStart; ej < cEnd; ++ej) { 265 ierr = PetscLogEventBegin(ctx->events[3],0,0,0,0);CHKERRQ(ierr); 266 ierr = PetscMemzero(elemMat, totDim *totDim * sizeof(PetscScalar));CHKERRQ(ierr); 267 ierr = PetscLogEventEnd(ctx->events[3],0,0,0,0);CHKERRQ(ierr); 268 ierr = PetscLogEventBegin(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 269 ierr = PetscLogFlops((PetscLogDouble)Nq*flops);CHKERRQ(ierr); 270 invJ = invJ_a ? invJ_a + ej * Nq*dim*dim : NULL; 271 for (qj = 0; qj < Nq; ++qj) { 272 const PetscReal * const BB = Tf[0]->T[0], * const DD = Tf[0]->T[1]; 273 PetscReal g0[LANDAU_MAX_SPECIES], g2[LANDAU_MAX_SPECIES][LANDAU_DIM], g3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM]; 274 PetscInt d,d2,dp,d3,ipidx,fieldA; 275 const PetscInt jpidx = Nq*(ej-cStart) + qj; 276 if (shift==0.0) { 277 const PetscReal * const invJj = &invJ[qj*dim*dim]; 278 PetscReal gg2[LANDAU_MAX_SPECIES][LANDAU_DIM],gg3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM], gg2_temp[LANDAU_DIM], gg3_temp[LANDAU_DIM][LANDAU_DIM]; 279 const PetscReal vj[3] = {IPData.x[jpidx], IPData.y[jpidx], IPData.z ? IPData.z[jpidx] : 0}, wj = IPData.w[jpidx]; 280 281 // create g2 & g3 282 for (d=0;d<dim;d++) { // clear accumulation data D & K 283 gg2_temp[d] = 0; 284 for (d2=0;d2<dim;d2++) gg3_temp[d][d2] = 0; 285 } 286 for (ipidx = 0; ipidx < IPData.nip_; ipidx++) { 287 const PetscReal wi = IPData.w[ipidx], x = IPData.x[ipidx], y = IPData.y[ipidx]; 288 PetscReal temp1[3] = {0, 0, 0}, temp2 = 0; 289 #if LANDAU_DIM==2 290 PetscReal Ud[2][2], Uk[2][2]; 291 LandauTensor2D(vj, x, y, Ud, Uk, (ipidx==jpidx) ? 0. : 1.); 292 #else 293 PetscReal U[3][3], z = IPData.z[ipidx]; 294 LandauTensor3D(vj, x, y, z, U, (ipidx==jpidx) ? 0. : 1.); 295 #endif 296 for (fieldA = 0; fieldA < Nf; ++fieldA) { 297 temp1[0] += dudx[ipidx + fieldA*IPData.nip_]*nu_beta[fieldA]*invMass[fieldA]; 298 temp1[1] += dudy[ipidx + fieldA*IPData.nip_]*nu_beta[fieldA]*invMass[fieldA]; 299 #if LANDAU_DIM==3 300 temp1[2] += dudz[ipidx + fieldA*IPData.nip_]*nu_beta[fieldA]*invMass[fieldA]; 301 #endif 302 temp2 += ff[ipidx + fieldA*IPData.nip_]*nu_beta[fieldA]; 303 } 304 temp1[0] *= wi; 305 temp1[1] *= wi; 306 #if LANDAU_DIM==3 307 temp1[2] *= wi; 308 #endif 309 temp2 *= wi; 310 #if LANDAU_DIM==2 311 for (d2 = 0; d2 < 2; d2++) { 312 for (d3 = 0; d3 < 2; ++d3) { 313 /* K = U * grad(f): g2=e: i,A */ 314 gg2_temp[d2] += Uk[d2][d3]*temp1[d3]; 315 /* D = -U * (I \kron (fx)): g3=f: i,j,A */ 316 gg3_temp[d2][d3] += Ud[d2][d3]*temp2; 317 } 318 } 319 #else 320 for (d2 = 0; d2 < 3; ++d2) { 321 for (d3 = 0; d3 < 3; ++d3) { 322 /* K = U * grad(f): g2 = e: i,A */ 323 gg2_temp[d2] += U[d2][d3]*temp1[d3]; 324 /* D = -U * (I \kron (fx)): g3 = f: i,j,A */ 325 gg3_temp[d2][d3] += U[d2][d3]*temp2; 326 } 327 } 328 #endif 329 } /* IPs */ 330 //if (ej==0) printf("\t:%d.%d) temp gg3=%e %e %e %e\n",ej,qj,gg3_temp[0][0],gg3_temp[1][0],gg3_temp[0][1],gg3_temp[1][1]); 331 // add alpha and put in gg2/3 332 for (fieldA = 0; fieldA < Nf; ++fieldA) { 333 for (d2 = 0; d2 < dim; d2++) { 334 gg2[fieldA][d2] = gg2_temp[d2]*nu_alpha[fieldA]; 335 for (d3 = 0; d3 < dim; d3++) { 336 gg3[fieldA][d2][d3] = -gg3_temp[d2][d3]*nu_alpha[fieldA]*invMass[fieldA]; 337 } 338 } 339 } 340 /* add electric field term once per IP */ 341 for (fieldA = 0; fieldA < Nf; ++fieldA) { 342 gg2[fieldA][dim-1] += Eq_m[fieldA]; 343 } 344 /* Jacobian transform - g2, g3 */ 345 for (fieldA = 0; fieldA < Nf; ++fieldA) { 346 for (d = 0; d < dim; ++d) { 347 g2[fieldA][d] = 0.0; 348 for (d2 = 0; d2 < dim; ++d2) { 349 g2[fieldA][d] += invJj[d*dim+d2]*gg2[fieldA][d2]; 350 g3[fieldA][d][d2] = 0.0; 351 for (d3 = 0; d3 < dim; ++d3) { 352 for (dp = 0; dp < dim; ++dp) { 353 g3[fieldA][d][d2] += invJj[d*dim + d3]*gg3[fieldA][d3][dp]*invJj[d2*dim + dp]; 354 } 355 } 356 g3[fieldA][d][d2] *= wj; 357 } 358 g2[fieldA][d] *= wj; 359 } 360 } 361 } else { // mass 362 /* Jacobian transform - g0 */ 363 for (fieldA = 0; fieldA < Nf; ++fieldA) { 364 g0[fieldA] = mass_w[jpidx] * shift; // move this to below and remove g0 365 } 366 } 367 /* FE matrix construction */ 368 { 369 PetscInt fieldA,d,f,d2,g; 370 const PetscReal *BJq = &BB[qj*Nb], *DIq = &DD[qj*Nb*dim]; 371 /* assemble - on the diagonal (I,I) */ 372 for (fieldA = 0; fieldA < Nf ; fieldA++) { 373 for (f = 0; f < Nb ; f++) { 374 const PetscInt i = fieldA*Nb + f; /* Element matrix row */ 375 for (g = 0; g < Nb; ++g) { 376 const PetscInt j = fieldA*Nb + g; /* Element matrix column */ 377 const PetscInt fOff = i*totDim + j; 378 if (shift==0.0) { 379 for (d = 0; d < dim; ++d) { 380 elemMat[fOff] += DIq[f*dim+d]*g2[fieldA][d]*BJq[g]; 381 for (d2 = 0; d2 < dim; ++d2) { 382 elemMat[fOff] += DIq[f*dim + d]*g3[fieldA][d][d2]*DIq[g*dim + d2]; 383 } 384 } 385 } else { // mass 386 elemMat[fOff] += BJq[f]*g0[fieldA]*BJq[g]; 387 } 388 } 389 } 390 } 391 } 392 } /* qj loop */ 393 ierr = PetscLogEventEnd(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 394 /* assemble matrix */ 395 ierr = PetscLogEventBegin(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 396 if (!maps) { 397 ierr = DMPlexMatSetClosure(plex, section, globsection, JacP, ej, elemMat, ADD_VALUES);CHKERRQ(ierr); 398 } else { // GPU like assembly for debugging 399 PetscInt fieldA,idx,q,f,g,d,nr,nc,rows0[LANDAU_MAX_Q_FACE],cols0[LANDAU_MAX_Q_FACE],rows[LANDAU_MAX_Q_FACE],cols[LANDAU_MAX_Q_FACE]; 400 PetscScalar vals[LANDAU_MAX_Q_FACE*LANDAU_MAX_Q_FACE],row_scale[LANDAU_MAX_Q_FACE],col_scale[LANDAU_MAX_Q_FACE]; 401 for (g=0;g<LANDAU_MAX_Q_FACE;g++) { col_scale[g]=0.; cols0[g]=0.; } 402 /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */ 403 for (fieldA = 0; fieldA < Nf ; fieldA++) { 404 LandauIdx *const Idxs = &maps->gIdx[ej-cStart][fieldA][0]; 405 for (f = 0; f < Nb ; f++) { 406 idx = Idxs[f]; 407 if (idx >= 0) { 408 nr = 1; 409 rows0[0] = idx; 410 row_scale[0] = 1.; 411 } else { 412 idx = -idx - 1; 413 nr = maps->num_face; 414 for (q = 0; q < maps->num_face; q++) { 415 rows0[q] = maps->c_maps[idx][q].gid; 416 row_scale[q] = maps->c_maps[idx][q].scale; 417 } 418 } 419 for (g = 0; g < Nb; ++g) { 420 idx = Idxs[g]; 421 if (idx >= 0) { 422 nc = 1; 423 cols0[0] = idx; 424 col_scale[0] = 1.; 425 } else { 426 idx = -idx - 1; 427 nc = maps->num_face; 428 for (q = 0; q < maps->num_face; q++) { 429 cols0[q] = maps->c_maps[idx][q].gid; 430 col_scale[q] = maps->c_maps[idx][q].scale; 431 } 432 } 433 const PetscInt i = fieldA*Nb + f; /* Element matrix row */ 434 const PetscInt j = fieldA*Nb + g; /* Element matrix column */ 435 const PetscScalar Aij = elemMat[i*totDim + j]; 436 for (q = 0; q < nr; q++) rows[q] = rows0[q]; 437 for (q = 0; q < nc; q++) cols[q] = cols0[q]; 438 for (q = 0; q < nr; q++) { 439 for (d = 0; d < nc; d++) { 440 vals[q*nc + d] = row_scale[q]*col_scale[d]*Aij; 441 } 442 } 443 ierr = MatSetValues(JacP,nr,rows,nc,cols,vals,ADD_VALUES);CHKERRQ(ierr); 444 } 445 } 446 } 447 } 448 if (ej==-3) { 449 PetscErrorCode ierr2; 450 ierr2 = PetscPrintf(ctx->comm,"CPU Element matrix\n");CHKERRQ(ierr2); 451 for (d = 0; d < totDim; ++d){ 452 for (f = 0; f < totDim; ++f) {ierr2 = PetscPrintf(ctx->comm," %12.5e", PetscRealPart(elemMat[d*totDim + f]));CHKERRQ(ierr2);} 453 ierr2 = PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr2); 454 } 455 exit(12); 456 } 457 ierr = PetscLogEventEnd(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 458 } /* ej cells loop, not cuda */ 459 if (shift!=0.0) { // mass 460 ierr = PetscFree(elemMat);CHKERRQ(ierr); 461 } else { 462 ierr = PetscFree5(elemMat, ff, dudx, dudy, dudz);CHKERRQ(ierr); 463 } 464 } /* CPU version */ 465 /* assemble matrix or vector */ 466 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 467 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 468 #define MAP_BF_SIZE (128*LANDAU_DIM*LANDAU_MAX_Q_FACE*LANDAU_MAX_SPECIES) 469 if (ctx->gpu_assembly && !container) { 470 PetscScalar elemMatrix[LANDAU_MAX_NQ*LANDAU_MAX_NQ*LANDAU_MAX_SPECIES*LANDAU_MAX_SPECIES], *elMat; 471 pointInterpolationP4est pointMaps[MAP_BF_SIZE][LANDAU_MAX_Q_FACE]; 472 PetscInt q,eidx,fieldA; 473 MatType type; 474 ierr = PetscInfo1(JacP, "Make GPU maps %D\n",1);CHKERRQ(ierr); 475 ierr = MatGetType(JacP,&type);CHKERRQ(ierr); 476 ierr = PetscLogEventBegin(ctx->events[2],0,0,0,0);CHKERRQ(ierr); 477 ierr = PetscMalloc(sizeof(P4estVertexMaps), &maps);CHKERRQ(ierr); 478 ierr = PetscContainerCreate(PETSC_COMM_SELF, &container);CHKERRQ(ierr); 479 ierr = PetscContainerSetPointer(container, (void *)maps);CHKERRQ(ierr); 480 ierr = PetscContainerSetUserDestroy(container, LandauGPUDataDestroy);CHKERRQ(ierr); 481 ierr = PetscObjectCompose((PetscObject) JacP, "assembly_maps", (PetscObject) container);CHKERRQ(ierr); 482 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 483 // make maps 484 maps->data = NULL; 485 maps->num_elements = numCells; 486 maps->num_face = (PetscInt)(pow(Nq,1./((double)dim))+.001); // Q 487 maps->num_face = (PetscInt)(pow(maps->num_face,(double)(dim-1))+.001); // Q^2 488 maps->num_reduced = 0; 489 maps->deviceType = ctx->deviceType; 490 // count reduced and get 491 ierr = PetscMalloc(maps->num_elements * sizeof *maps->gIdx, &maps->gIdx);CHKERRQ(ierr); 492 for (fieldA=0;fieldA<Nf;fieldA++) { 493 for (ej = cStart, eidx = 0 ; ej < cEnd; ++ej, ++eidx) { 494 for (q = 0; q < Nb; ++q) { 495 PetscInt numindices,*indices; 496 PetscScalar *valuesOrig = elMat = elemMatrix; 497 ierr = PetscMemzero(elMat, totDim*totDim*sizeof(PetscScalar));CHKERRQ(ierr); 498 elMat[ (fieldA*Nb + q)*totDim + fieldA*Nb + q] = 1; 499 ierr = DMPlexGetClosureIndices(plex, section, globsection, ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 500 for (f = 0 ; f < numindices ; ++f) { // look for a non-zero on the diagonal 501 if (PetscAbs(PetscRealPart(elMat[f*numindices + f])) > PETSC_MACHINE_EPSILON) { 502 // found it 503 if (PetscAbs(PetscRealPart(elMat[f*numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { 504 maps->gIdx[eidx][fieldA][q] = (LandauIdx)indices[f]; // normal vertex 1.0 505 } else { //found a constraint 506 int jj = 0; 507 PetscReal sum = 0; 508 const PetscInt ff = f; 509 maps->gIdx[eidx][fieldA][q] = -maps->num_reduced - 1; // gid = -(idx+1): idx = -gid - 1 510 do { // constraints are continous in Plex - exploit that here 511 int ii; 512 for (ii = 0, pointMaps[maps->num_reduced][jj].scale = 0; ii < maps->num_face; ii++) { // DMPlex puts them all together 513 if (ff + ii < numindices) { 514 pointMaps[maps->num_reduced][jj].scale += PetscRealPart(elMat[f*numindices + ff + ii]); 515 } 516 } 517 sum += pointMaps[maps->num_reduced][jj].scale; 518 if (pointMaps[maps->num_reduced][jj].scale == 0) pointMaps[maps->num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps -- all contiguous??? 519 else pointMaps[maps->num_reduced][jj].gid = indices[f]; 520 } while (++jj < maps->num_face && ++f < numindices); // jj is incremented if we hit the end 521 while (jj++ < maps->num_face) { 522 pointMaps[maps->num_reduced][jj].scale = 0; 523 pointMaps[maps->num_reduced][jj].gid = -1; 524 } 525 if (PetscAbs(sum-1.0)>PETSC_MACHINE_EPSILON*2.0) { // debug 526 int d,f; 527 PetscReal tmp = 0; 528 PetscPrintf(PETSC_COMM_SELF,"\t\t%D.%D.%D) ERROR total I = %22.16e (LANDAU_MAX_Q_FACE=%d, #face=%D)\n",eidx,q,fieldA,tmp,LANDAU_MAX_Q_FACE,maps->num_face); 529 for (d = 0, tmp = 0; d < numindices; ++d){ 530 if (tmp!=0 && PetscAbs(tmp-1.0)>2*PETSC_MACHINE_EPSILON) ierr = PetscPrintf(PETSC_COMM_WORLD,"%3D) %3D: ",d,indices[d]);CHKERRQ(ierr); 531 for (f = 0; f < numindices; ++f) { 532 tmp += PetscRealPart(elMat[d*numindices + f]); 533 } 534 if (tmp!=0) ierr = PetscPrintf(ctx->comm," | %22.16e\n",tmp);CHKERRQ(ierr); 535 } 536 } 537 maps->num_reduced++; 538 if (maps->num_reduced>=MAP_BF_SIZE) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps->num_reduced %d > %d",maps->num_reduced,MAP_BF_SIZE); 539 } 540 break; 541 } 542 } 543 // cleanup 544 ierr = DMPlexRestoreClosureIndices(plex, section, globsection, ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 545 if (elMat != valuesOrig) {ierr = DMRestoreWorkArray(plex, numindices*numindices, MPIU_SCALAR, &elMat);} 546 } 547 } 548 } 549 // allocate and copy point datamaps->gIdx[eidx][field][q] -- for CPU version of this code, for debugging 550 ierr = PetscMalloc(maps->num_reduced * sizeof *maps->c_maps, &maps->c_maps);CHKERRQ(ierr); 551 for (ej = 0; ej < maps->num_reduced; ++ej) { 552 for (q = 0; q < maps->num_face; ++q) { 553 maps->c_maps[ej][q].scale = pointMaps[ej][q].scale; 554 maps->c_maps[ej][q].gid = pointMaps[ej][q].gid; 555 } 556 } 557 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 558 if (ctx->deviceType == LANDAU_KOKKOS) { 559 ierr = LandauKokkosCreateMatMaps(maps, pointMaps,Nf,Nq);CHKERRQ(ierr); // imples Kokkos does 560 } // else could be CUDA 561 #endif 562 #if defined(PETSC_HAVE_CUDA) 563 if (ctx->deviceType == LANDAU_CUDA){ 564 ierr = LandauCUDACreateMatMaps(maps, pointMaps,Nf,Nq);CHKERRQ(ierr); 565 } 566 #endif 567 ierr = PetscLogEventEnd(ctx->events[2],0,0,0,0);CHKERRQ(ierr); 568 } 569 /* clean up */ 570 ierr = DMDestroy(&plex);CHKERRQ(ierr); 571 if (shift==0.0) { 572 ierr = LandauPointDataDestroy(&IPData);CHKERRQ(ierr); 573 ierr = PetscFree(invJ_a);CHKERRQ(ierr); 574 } else { 575 ierr = PetscFree(mass_w);CHKERRQ(ierr); 576 } 577 PetscFunctionReturn(0); 578 } 579 580 #if defined(LANDAU_ADD_BCS) 581 static void zero_bc(PetscInt dim, PetscInt Nf, PetscInt NfAux, 582 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 583 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 584 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar uexact[]) 585 { 586 uexact[0] = 0; 587 } 588 #endif 589 590 #define MATVEC2(__a,__x,__p) {int i,j; for (i=0.; i<2; i++) {__p[i] = 0; for (j=0.; j<2; j++) __p[i] += __a[i][j]*__x[j]; }} 591 static void CircleInflate(PetscReal r1, PetscReal r2, PetscReal r0, PetscInt num_sections, PetscReal x, PetscReal y, 592 PetscReal *outX, PetscReal *outY) 593 { 594 PetscReal rr = PetscSqrtReal(x*x + y*y), outfact, efact; 595 if (rr < r1 + PETSC_SQRT_MACHINE_EPSILON) { 596 *outX = x; *outY = y; 597 } else { 598 const PetscReal xy[2] = {x,y}, sinphi=y/rr, cosphi=x/rr; 599 PetscReal cth,sth,xyprime[2],Rth[2][2],rotcos,newrr; 600 if (num_sections==2) { 601 rotcos = 0.70710678118654; 602 outfact = 1.5; efact = 2.5; 603 /* rotate normalized vector into [-pi/4,pi/4) */ 604 if (sinphi >= 0.) { /* top cell, -pi/2 */ 605 cth = 0.707106781186548; sth = -0.707106781186548; 606 } else { /* bottom cell -pi/8 */ 607 cth = 0.707106781186548; sth = .707106781186548; 608 } 609 } else if (num_sections==3) { 610 rotcos = 0.86602540378443; 611 outfact = 1.5; efact = 2.5; 612 /* rotate normalized vector into [-pi/6,pi/6) */ 613 if (sinphi >= 0.5) { /* top cell, -pi/3 */ 614 cth = 0.5; sth = -0.866025403784439; 615 } else if (sinphi >= -.5) { /* mid cell 0 */ 616 cth = 1.; sth = .0; 617 } else { /* bottom cell +pi/3 */ 618 cth = 0.5; sth = 0.866025403784439; 619 } 620 } else if (num_sections==4) { 621 rotcos = 0.9238795325112; 622 outfact = 1.5; efact = 3; 623 /* rotate normalized vector into [-pi/8,pi/8) */ 624 if (sinphi >= 0.707106781186548) { /* top cell, -3pi/8 */ 625 cth = 0.38268343236509; sth = -0.923879532511287; 626 } else if (sinphi >= 0.) { /* mid top cell -pi/8 */ 627 cth = 0.923879532511287; sth = -.38268343236509; 628 } else if (sinphi >= -0.707106781186548) { /* mid bottom cell + pi/8 */ 629 cth = 0.923879532511287; sth = 0.38268343236509; 630 } else { /* bottom cell + 3pi/8 */ 631 cth = 0.38268343236509; sth = .923879532511287; 632 } 633 } else { 634 cth = 0.; sth = 0.; rotcos = 0; efact = 0; 635 } 636 Rth[0][0] = cth; Rth[0][1] =-sth; 637 Rth[1][0] = sth; Rth[1][1] = cth; 638 MATVEC2(Rth,xy,xyprime); 639 if (num_sections==2) { 640 newrr = xyprime[0]/rotcos; 641 } else { 642 PetscReal newcosphi=xyprime[0]/rr, rin = r1, rout = rr - rin; 643 PetscReal routmax = r0*rotcos/newcosphi - rin, nroutmax = r0 - rin, routfrac = rout/routmax; 644 newrr = rin + routfrac*nroutmax; 645 } 646 *outX = cosphi*newrr; *outY = sinphi*newrr; 647 /* grade */ 648 PetscReal fact,tt,rs,re, rr = PetscSqrtReal(PetscSqr(*outX) + PetscSqr(*outY)); 649 if (rr > r2) { rs = r2; re = r0; fact = outfact;} /* outer zone */ 650 else { rs = r1; re = r2; fact = efact;} /* electron zone */ 651 tt = (rs + PetscPowReal((rr - rs)/(re - rs),fact) * (re-rs)) / rr; 652 *outX *= tt; 653 *outY *= tt; 654 } 655 } 656 657 static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx) 658 { 659 LandauCtx *ctx = (LandauCtx*)a_ctx; 660 PetscReal r = abc[0], z = abc[1]; 661 if (ctx->inflate) { 662 PetscReal absR, absZ; 663 absR = PetscAbs(r); 664 absZ = PetscAbs(z); 665 CircleInflate(ctx->i_radius,ctx->e_radius,ctx->radius,ctx->num_sections,absR,absZ,&absR,&absZ); 666 r = (r > 0) ? absR : -absR; 667 z = (z > 0) ? absZ : -absZ; 668 } 669 xyz[0] = r; 670 xyz[1] = z; 671 if (dim==3) xyz[2] = abc[2]; 672 673 PetscFunctionReturn(0); 674 } 675 676 static PetscErrorCode ErrorIndicator_Simple(PetscInt dim, PetscReal volume, PetscReal x[], PetscInt Nc, const PetscInt Nf[], const PetscScalar u[], const PetscScalar u_x[], PetscReal *error, void *actx) 677 { 678 PetscReal err = 0.0; 679 PetscInt f = *(PetscInt*)actx, j; 680 PetscFunctionBegin; 681 for (j = 0; j < dim; ++j) { 682 err += PetscSqr(PetscRealPart(u_x[f*dim+j])); 683 } 684 err = PetscRealPart(u[f]); /* just use rho */ 685 *error = volume * err; /* * (ctx->axisymmetric ? 2.*PETSC_PI * r : 1); */ 686 PetscFunctionReturn(0); 687 } 688 689 static PetscErrorCode LandauDMCreateVMesh(MPI_Comm comm, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM *dm) 690 { 691 PetscErrorCode ierr; 692 PetscReal radius = ctx->radius; 693 size_t len; 694 char fname[128] = ""; /* we can add a file if we want */ 695 696 PetscFunctionBegin; 697 /* create DM */ 698 ierr = PetscStrlen(fname, &len);CHKERRQ(ierr); 699 if (len) { 700 PetscInt dim2; 701 ierr = DMPlexCreateFromFile(comm, fname, ctx->interpolate, dm);CHKERRQ(ierr); 702 ierr = DMGetDimension(*dm, &dim2);CHKERRQ(ierr); 703 if (LANDAU_DIM != dim2) SETERRQ2(comm, PETSC_ERR_PLIB, "dim %D != LANDAU_DIM %d",dim2,LANDAU_DIM); 704 } else { /* p4est, quads */ 705 /* Create plex mesh of Landau domain */ 706 if (!ctx->sphere) { 707 PetscInt cells[] = {2,2,2}; 708 PetscReal lo[] = {-radius,-radius,-radius}, hi[] = {radius,radius,radius}; 709 DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim==2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 710 if (dim==2) { lo[0] = 0; cells[0] = 1; } 711 ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, cells, lo, hi, periodicity, PETSC_TRUE, dm);CHKERRQ(ierr); 712 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); /* needed for periodic */ 713 if (dim==3) {ierr = PetscObjectSetName((PetscObject) *dm, "cube");CHKERRQ(ierr);} 714 else {ierr = PetscObjectSetName((PetscObject) *dm, "half-plane");CHKERRQ(ierr);} 715 } else if (dim==2) { 716 PetscInt numCells,cells[16][4],i,j; 717 PetscInt numVerts; 718 PetscReal inner_radius1 = ctx->i_radius, inner_radius2 = ctx->e_radius; 719 PetscReal *flatCoords = NULL; 720 PetscInt *flatCells = NULL, *pcell; 721 if (ctx->num_sections==2) { 722 #if 1 723 numCells = 5; 724 numVerts = 10; 725 int cells2[][4] = { {0,1,4,3}, 726 {1,2,5,4}, 727 {3,4,7,6}, 728 {4,5,8,7}, 729 {6,7,8,9} }; 730 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 731 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 732 { 733 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 734 for (j = 0; j < numVerts-1; j++) { 735 PetscReal z, r, theta = -PETSC_PI/2 + (j%3) * PETSC_PI/2; 736 PetscReal rad = (j >= 6) ? inner_radius1 : (j >= 3) ? inner_radius2 : ctx->radius; 737 z = rad * PetscSinReal(theta); 738 coords[j][1] = z; 739 r = rad * PetscCosReal(theta); 740 coords[j][0] = r; 741 } 742 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 743 } 744 #else 745 numCells = 4; 746 numVerts = 8; 747 static int cells2[][4] = {{0,1,2,3}, 748 {4,5,1,0}, 749 {5,6,2,1}, 750 {6,7,3,2}}; 751 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 752 ierr = loc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 753 { 754 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 755 PetscInt j; 756 for (j = 0; j < 8; j++) { 757 PetscReal z, r; 758 PetscReal theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3.; 759 PetscReal rad = ctx->radius * ((j < 4) ? 0.5 : 1.0); 760 z = rad * PetscSinReal(theta); 761 coords[j][1] = z; 762 r = rad * PetscCosReal(theta); 763 coords[j][0] = r; 764 } 765 } 766 #endif 767 } else if (ctx->num_sections==3) { 768 numCells = 7; 769 numVerts = 12; 770 int cells2[][4] = { {0,1,5,4}, 771 {1,2,6,5}, 772 {2,3,7,6}, 773 {4,5,9,8}, 774 {5,6,10,9}, 775 {6,7,11,10}, 776 {8,9,10,11} }; 777 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 778 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 779 { 780 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 781 for (j = 0; j < numVerts; j++) { 782 PetscReal z, r, theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3; 783 PetscReal rad = (j >= 8) ? inner_radius1 : (j >= 4) ? inner_radius2 : ctx->radius; 784 z = rad * PetscSinReal(theta); 785 coords[j][1] = z; 786 r = rad * PetscCosReal(theta); 787 coords[j][0] = r; 788 } 789 } 790 } else if (ctx->num_sections==4) { 791 numCells = 10; 792 numVerts = 16; 793 int cells2[][4] = { {0,1,6,5}, 794 {1,2,7,6}, 795 {2,3,8,7}, 796 {3,4,9,8}, 797 {5,6,11,10}, 798 {6,7,12,11}, 799 {7,8,13,12}, 800 {8,9,14,13}, 801 {10,11,12,15}, 802 {12,13,14,15}}; 803 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 804 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 805 { 806 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 807 for (j = 0; j < numVerts-1; j++) { 808 PetscReal z, r, theta = -PETSC_PI/2 + (j%5) * PETSC_PI/4; 809 PetscReal rad = (j >= 10) ? inner_radius1 : (j >= 5) ? inner_radius2 : ctx->radius; 810 z = rad * PetscSinReal(theta); 811 coords[j][1] = z; 812 r = rad * PetscCosReal(theta); 813 coords[j][0] = r; 814 } 815 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 816 } 817 } else { 818 numCells = 0; 819 numVerts = 0; 820 } 821 for (j = 0, pcell = flatCells; j < numCells; j++, pcell += 4) { 822 pcell[0] = cells[j][0]; pcell[1] = cells[j][1]; 823 pcell[2] = cells[j][2]; pcell[3] = cells[j][3]; 824 } 825 ierr = DMPlexCreateFromCellListPetsc(comm,2,numCells,numVerts,4,ctx->interpolate,flatCells,2,flatCoords,dm);CHKERRQ(ierr); 826 ierr = PetscFree2(flatCoords,flatCells);CHKERRQ(ierr); 827 ierr = PetscObjectSetName((PetscObject) *dm, "semi-circle");CHKERRQ(ierr); 828 } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Velocity space meshes does not support cubed sphere"); 829 } 830 ierr = PetscObjectSetOptionsPrefix((PetscObject)*dm,prefix);CHKERRQ(ierr); 831 832 ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); /* Plex refine */ 833 834 { /* p4est? */ 835 char convType[256]; 836 PetscBool flg; 837 ierr = PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); 838 ierr = PetscOptionsFList("-dm_landau_type","Convert DMPlex to another format (should not be Plex!)","plexland.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); 839 ierr = PetscOptionsEnd(); 840 if (flg) { 841 DM dmforest; 842 ierr = DMConvert(*dm,convType,&dmforest);CHKERRQ(ierr); 843 if (dmforest) { 844 PetscBool isForest; 845 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 846 ierr = PetscObjectSetOptionsPrefix((PetscObject)dmforest,prefix);CHKERRQ(ierr); 847 ierr = DMIsForest(dmforest,&isForest);CHKERRQ(ierr); 848 if (isForest) { 849 if (ctx->sphere && ctx->inflate) { 850 ierr = DMForestSetBaseCoordinateMapping(dmforest,GeometryDMLandau,ctx);CHKERRQ(ierr); 851 } 852 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 853 ierr = DMDestroy(dm);CHKERRQ(ierr); 854 *dm = dmforest; 855 ctx->errorIndicator = ErrorIndicator_Simple; /* flag for Forest */ 856 } else SETERRQ(ctx->comm, PETSC_ERR_USER, "Converted to non Forest?"); 857 } else SETERRQ(ctx->comm, PETSC_ERR_USER, "Convert failed?"); 858 } 859 } 860 ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); 861 PetscFunctionReturn(0); 862 } 863 864 static PetscErrorCode SetupDS(DM dm, PetscInt dim, LandauCtx *ctx) 865 { 866 PetscErrorCode ierr; 867 PetscInt ii; 868 PetscFunctionBegin; 869 for (ii=0;ii<ctx->num_species;ii++) { 870 char buf[256]; 871 if (ii==0) ierr = PetscSNPrintf(buf, 256, "e"); 872 else {ierr = PetscSNPrintf(buf, 256, "i%D", ii);CHKERRQ(ierr);} 873 /* Setup Discretization - FEM */ 874 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &ctx->fe[ii]);CHKERRQ(ierr); 875 ierr = PetscObjectSetName((PetscObject) ctx->fe[ii], buf);CHKERRQ(ierr); 876 ierr = DMSetField(dm, ii, NULL, (PetscObject) ctx->fe[ii]);CHKERRQ(ierr); 877 } 878 ierr = DMCreateDS(dm);CHKERRQ(ierr); 879 if (1) { 880 PetscInt ii; 881 PetscSection section; 882 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 883 for (ii=0;ii<ctx->num_species;ii++){ 884 char buf[256]; 885 if (ii==0) ierr = PetscSNPrintf(buf, 256, "se"); 886 else ierr = PetscSNPrintf(buf, 256, "si%D", ii); 887 ierr = PetscSectionSetComponentName(section, ii, 0, buf);CHKERRQ(ierr); 888 } 889 } 890 PetscFunctionReturn(0); 891 } 892 893 /* Define a Maxwellian function for testing out the operator. */ 894 895 /* Using cartesian velocity space coordinates, the particle */ 896 /* density, [1/m^3], is defined according to */ 897 898 /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */ 899 900 /* Using some constant, c, we normalize the velocity vector into a */ 901 /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */ 902 903 /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */ 904 905 /* Defining $\theta=2T/mc^2$, we thus find that the probability density */ 906 /* for finding the particle within the interval in a box dx^3 around x is */ 907 908 /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */ 909 910 typedef struct { 911 LandauCtx *ctx; 912 PetscReal kT_m; 913 PetscReal n; 914 PetscReal shift; 915 } MaxwellianCtx; 916 917 static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx) 918 { 919 MaxwellianCtx *mctx = (MaxwellianCtx*)actx; 920 LandauCtx *ctx = mctx->ctx; 921 PetscInt i; 922 PetscReal v2 = 0, theta = 2*mctx->kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 923 PetscFunctionBegin; 924 /* compute the exponents, v^2 */ 925 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 926 /* evaluate the Maxwellian */ 927 u[0] = mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 928 if (mctx->shift!=0.) { 929 v2 = 0; 930 for (i = 0; i < dim-1; ++i) v2 += x[i]*x[i]; 931 v2 += (x[dim-1]-mctx->shift)*(x[dim-1]-mctx->shift); 932 /* evaluate the shifted Maxwellian */ 933 u[0] += mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 934 } 935 PetscFunctionReturn(0); 936 } 937 938 /*@ 939 LandauAddMaxwellians - Add a Maxwellian distribution to a state 940 941 Collective on X 942 943 Input Parameters: 944 . dm - The mesh 945 + time - Current time 946 - temps - Temperatures of each species 947 . ns - Number density of each species 948 + actx - Landau context 949 950 Output Parameter: 951 . X - The state 952 953 Level: beginner 954 955 .keywords: mesh 956 .seealso: LandauCreateVelocitySpace() 957 @*/ 958 PetscErrorCode LandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], void *actx) 959 { 960 LandauCtx *ctx = (LandauCtx*)actx; 961 PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar [], void *); 962 PetscErrorCode ierr,ii; 963 PetscInt dim; 964 MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES]; 965 966 PetscFunctionBegin; 967 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 968 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 969 for (ii=0;ii<ctx->num_species;ii++) { 970 mctxs[ii] = &data[ii]; 971 data[ii].ctx = ctx; 972 data[ii].kT_m = ctx->k*temps[ii]/ctx->masses[ii]; /* kT/m */ 973 data[ii].n = ns[ii]; 974 initu[ii] = maxwellian; 975 data[ii].shift = 0; 976 } 977 data[0].shift = ctx->electronShift; 978 /* need to make ADD_ALL_VALUES work - TODO */ 979 ierr = DMProjectFunction(dm, time, initu, (void**)mctxs, INSERT_ALL_VALUES, X);CHKERRQ(ierr); 980 PetscFunctionReturn(0); 981 } 982 983 /* 984 LandauSetInitialCondition - Addes Maxwellians with context 985 986 Collective on X 987 988 Input Parameters: 989 . dm - The mesh 990 + actx - Landau context with T and n 991 992 Output Parameter: 993 . X - The state 994 995 Level: beginner 996 997 .keywords: mesh 998 .seealso: LandauCreateVelocitySpace(), LandauAddMaxwellians() 999 */ 1000 static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, void *actx) 1001 { 1002 LandauCtx *ctx = (LandauCtx*)actx; 1003 PetscErrorCode ierr; 1004 PetscFunctionBegin; 1005 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 1006 ierr = VecZeroEntries(X);CHKERRQ(ierr); 1007 ierr = LandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, ctx);CHKERRQ(ierr); 1008 PetscFunctionReturn(0); 1009 } 1010 1011 static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscReal refineTol[], PetscReal coarsenTol[], PetscInt type, LandauCtx *ctx, DM *newDM) 1012 { 1013 DM dm, plex, adaptedDM = NULL; 1014 PetscDS prob; 1015 PetscBool isForest; 1016 PetscQuadrature quad; 1017 PetscInt Nq, *Nb, cStart, cEnd, c, dim, qj, k; 1018 DMLabel adaptLabel = NULL; 1019 PetscErrorCode ierr; 1020 1021 PetscFunctionBegin; 1022 ierr = VecGetDM(sol, &dm);CHKERRQ(ierr); 1023 ierr = DMCreateDS(dm);CHKERRQ(ierr); 1024 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1025 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1026 ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr); 1027 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1028 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1029 ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr); 1030 ierr = PetscFEGetQuadrature(fem, &quad);CHKERRQ(ierr); 1031 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1032 if (Nq >LANDAU_MAX_NQ) SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"Order too high. Nq = %D > LANDAU_MAX_NQ (%D)",Nq,LANDAU_MAX_NQ); 1033 ierr = PetscDSGetDimensions(prob, &Nb);CHKERRQ(ierr); 1034 if (type==4) { 1035 for (c = cStart; c < cEnd; c++) { 1036 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 1037 } 1038 ierr = PetscInfo1(sol, "Phase:%s: Uniform refinement\n","adaptToleranceFEM");CHKERRQ(ierr); 1039 } else if (type==2) { 1040 PetscInt rCellIdx[8], eCellIdx[64], iCellIdx[64], eMaxIdx = -1, iMaxIdx = -1, nr = 0, nrmax = (dim==3) ? 8 : 2; 1041 PetscReal minRad = PETSC_INFINITY, r, eMinRad = PETSC_INFINITY, iMinRad = PETSC_INFINITY; 1042 for (c = 0; c < 64; c++) { eCellIdx[c] = iCellIdx[c] = -1; } 1043 for (c = cStart; c < cEnd; c++) { 1044 PetscReal tt, v0[LANDAU_MAX_NQ*3], detJ[LANDAU_MAX_NQ]; 1045 ierr = DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ);CHKERRQ(ierr); 1046 for (qj = 0; qj < Nq; ++qj) { 1047 tt = PetscSqr(v0[dim*qj+0]) + PetscSqr(v0[dim*qj+1]) + PetscSqr(((dim==3) ? v0[dim*qj+2] : 0)); 1048 r = PetscSqrtReal(tt); 1049 if (r < minRad - PETSC_SQRT_MACHINE_EPSILON*10.) { 1050 minRad = r; 1051 nr = 0; 1052 rCellIdx[nr++]= c; 1053 ierr = PetscInfo4(sol, "\t\tPhase: adaptToleranceFEM Found first inner r=%e, cell %D, qp %D/%D\n", r, c, qj+1, Nq);CHKERRQ(ierr); 1054 } else if ((r-minRad) < PETSC_SQRT_MACHINE_EPSILON*100. && nr < nrmax) { 1055 for (k=0;k<nr;k++) if (c == rCellIdx[k]) break; 1056 if (k==nr) { 1057 rCellIdx[nr++]= c; 1058 ierr = PetscInfo5(sol, "\t\t\tPhase: adaptToleranceFEM Found another inner r=%e, cell %D, qp %D/%D, d=%e\n", r, c, qj+1, Nq, r-minRad);CHKERRQ(ierr); 1059 } 1060 } 1061 if (ctx->sphere) { 1062 if ((tt=r-ctx->e_radius) > 0) { 1063 PetscInfo2(sol, "\t\t\t %D cell r=%g\n",c,tt); 1064 if (tt < eMinRad - PETSC_SQRT_MACHINE_EPSILON*100.) { 1065 eMinRad = tt; 1066 eMaxIdx = 0; 1067 eCellIdx[eMaxIdx++] = c; 1068 } else if (eMaxIdx > 0 && (tt-eMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != eCellIdx[eMaxIdx-1]) { 1069 eCellIdx[eMaxIdx++] = c; 1070 } 1071 } 1072 if ((tt=r-ctx->i_radius) > 0) { 1073 if (tt < iMinRad - 1.e-5) { 1074 iMinRad = tt; 1075 iMaxIdx = 0; 1076 iCellIdx[iMaxIdx++] = c; 1077 } else if (iMaxIdx > 0 && (tt-iMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != iCellIdx[iMaxIdx-1]) { 1078 iCellIdx[iMaxIdx++] = c; 1079 } 1080 } 1081 } 1082 } 1083 } 1084 for (k=0;k<nr;k++) { 1085 ierr = DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE);CHKERRQ(ierr); 1086 } 1087 if (ctx->sphere) { 1088 for (c = 0; c < eMaxIdx; c++) { 1089 ierr = DMLabelSetValue(adaptLabel, eCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 1090 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere e cell %D r=%g\n","adaptToleranceFEM",eCellIdx[c],eMinRad); 1091 } 1092 for (c = 0; c < iMaxIdx; c++) { 1093 ierr = DMLabelSetValue(adaptLabel, iCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 1094 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere i cell %D r=%g\n","adaptToleranceFEM",iCellIdx[c],iMinRad); 1095 } 1096 } 1097 ierr = PetscInfo4(sol, "Phase:%s: Adaptive refine origin cells %D,%D r=%g\n","adaptToleranceFEM",rCellIdx[0],rCellIdx[1],minRad); 1098 } else if (type==0 || type==1 || type==3) { /* refine along r=0 axis */ 1099 PetscScalar *coef = NULL; 1100 Vec coords; 1101 PetscInt csize,Nv,d,nz; 1102 DM cdm; 1103 PetscSection cs; 1104 ierr = DMGetCoordinatesLocal(dm, &coords);CHKERRQ(ierr); 1105 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1106 ierr = DMGetLocalSection(cdm, &cs);CHKERRQ(ierr); 1107 for (c = cStart; c < cEnd; c++) { 1108 PetscInt doit = 0, outside = 0; 1109 ierr = DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 1110 Nv = csize/dim; 1111 for (nz = d = 0; d < Nv; d++) { 1112 PetscReal z = PetscRealPart(coef[d*dim + (dim-1)]), x = PetscSqr(PetscRealPart(coef[d*dim + 0])) + ((dim==3) ? PetscSqr(PetscRealPart(coef[d*dim + 1])) : 0); 1113 x = PetscSqrtReal(x); 1114 if (x < PETSC_MACHINE_EPSILON*10. && PetscAbs(z)<PETSC_MACHINE_EPSILON*10.) doit = 1; /* refine origin */ 1115 else if (type==0 && (z < -PETSC_MACHINE_EPSILON*10. || z > ctx->re_radius+PETSC_MACHINE_EPSILON*10.)) outside++; /* first pass don't refine bottom */ 1116 else if (type==1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) outside++; /* don't refine outside electron refine radius */ 1117 else if (type==3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) outside++; /* don't refine outside ion refine radius */ 1118 if (x < PETSC_MACHINE_EPSILON*10.) nz++; 1119 } 1120 ierr = DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 1121 if (doit || (outside<Nv && nz)) { 1122 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 1123 } 1124 } 1125 ierr = PetscInfo1(sol, "Phase:%s: RE refinement\n","adaptToleranceFEM"); 1126 } 1127 /* ierr = VecDestroy(&locX);CHKERRQ(ierr); */ 1128 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1129 ierr = DMAdaptLabel(dm, adaptLabel, &adaptedDM);CHKERRQ(ierr); 1130 ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); 1131 *newDM = adaptedDM; 1132 if (adaptedDM) { 1133 if (isForest) { 1134 ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr); 1135 } 1136 ierr = DMConvert(adaptedDM, DMPLEX, &plex);CHKERRQ(ierr); 1137 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1138 ierr = PetscInfo2(sol, "\tPhase: adaptToleranceFEM: %D cells, %d total quadrature points\n",cEnd-cStart,Nq*(cEnd-cStart));CHKERRQ(ierr); 1139 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1140 } 1141 PetscFunctionReturn(0); 1142 } 1143 1144 static PetscErrorCode adapt(DM *dm, LandauCtx *ctx, Vec *uu) 1145 { 1146 PetscErrorCode ierr; 1147 PetscInt type, limits[5] = {ctx->numRERefine,ctx->nZRefine1,ctx->maxRefIts,ctx->nZRefine2,ctx->postAMRRefine}; 1148 PetscInt adaptIter; 1149 1150 PetscFunctionBegin; 1151 for (type=0;type<5;type++) { 1152 for (adaptIter = 0; adaptIter<limits[type];adaptIter++) { 1153 DM dmNew = NULL; 1154 ierr = adaptToleranceFEM(ctx->fe[0], *uu, ctx->refineTol, ctx->coarsenTol, type, ctx, &dmNew);CHKERRQ(ierr); 1155 if (!dmNew) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"should not happen"); 1156 else { 1157 ierr = DMDestroy(dm);CHKERRQ(ierr); 1158 ierr = VecDestroy(uu);CHKERRQ(ierr); 1159 ierr = DMCreateGlobalVector(dmNew,uu);CHKERRQ(ierr); 1160 ierr = PetscObjectSetName((PetscObject) *uu, "u");CHKERRQ(ierr); 1161 ierr = LandauSetInitialCondition(dmNew, *uu, ctx);CHKERRQ(ierr); 1162 *dm = dmNew; 1163 } 1164 } 1165 } 1166 PetscFunctionReturn(0); 1167 } 1168 1169 static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[]) 1170 { 1171 PetscErrorCode ierr; 1172 PetscBool flg, sph_flg; 1173 PetscInt ii,nt,nm,nc; 1174 DM dummy; 1175 1176 PetscFunctionBegin; 1177 ierr = DMCreate(ctx->comm,&dummy);CHKERRQ(ierr); 1178 /* get options - initialize context */ 1179 ctx->normJ = 0; 1180 ctx->verbose = 1; 1181 ctx->interpolate = PETSC_TRUE; 1182 ctx->gpu_assembly = PETSC_TRUE; 1183 ctx->sphere = PETSC_FALSE; 1184 ctx->inflate = PETSC_FALSE; 1185 ctx->electronShift = 0; 1186 ctx->errorIndicator = NULL; 1187 ctx->radius = 5.; /* electron thermal radius (velocity) */ 1188 ctx->re_radius = 0.; 1189 ctx->vperp0_radius1 = 0; 1190 ctx->vperp0_radius2 = 0; 1191 ctx->e_radius = .1; 1192 ctx->i_radius = .01; 1193 ctx->maxRefIts = 5; 1194 ctx->postAMRRefine = 0; 1195 ctx->nZRefine1 = 0; 1196 ctx->nZRefine2 = 0; 1197 ctx->numRERefine = 0; 1198 ctx->aux_bool = PETSC_FALSE; 1199 ctx->num_sections = 3; /* 2, 3 or 4 */ 1200 /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */ 1201 ctx->charges[0] = -1; /* electron charge (MKS) */ 1202 ctx->masses[0] = 1/1835.5; /* temporary value in proton mass */ 1203 ctx->n[0] = 1; 1204 ctx->thermal_temps[0] = 1; 1205 /* constants, etc. */ 1206 ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */ 1207 ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */ 1208 ctx->lnLam = 10; /* cross section ratio large - small angle collisions */ 1209 ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */ 1210 ctx->Ez = 0; 1211 ctx->v_0 = 1; /* in electron thermal velocity */ 1212 ctx->subThreadBlockSize = 1; /* for device and maybe OMP */ 1213 ctx->numConcurrency = 1; /* for device */ 1214 ierr = PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");CHKERRQ(ierr); 1215 { 1216 char opstring[256]; 1217 #if defined(PETSC_HAVE_KOKKOS) 1218 ctx->deviceType = LANDAU_KOKKOS; 1219 ierr = PetscStrcpy(opstring,"kokkos");CHKERRQ(ierr); 1220 #if defined(PETSC_HAVE_CUDA) 1221 ctx->subThreadBlockSize = 8; 1222 #endif 1223 #elif defined(PETSC_HAVE_CUDA) 1224 ctx->deviceType = LANDAU_CUDA; 1225 ierr = PetscStrcpy(opstring,"cuda");CHKERRQ(ierr); 1226 #else 1227 ctx->deviceType = LANDAU_CPU; 1228 ierr = PetscStrcpy(opstring,"cpu");CHKERRQ(ierr); 1229 ctx->subThreadBlockSize = 0; 1230 #endif 1231 ierr = PetscOptionsString("-dm_landau_device_type","Use kernels on 'cpu', 'cuda', or 'kokkos'","plexland.c",opstring,opstring,256,NULL);CHKERRQ(ierr); 1232 ierr = PetscStrcmp("cpu",opstring,&flg);CHKERRQ(ierr); 1233 if (flg) { 1234 ctx->deviceType = LANDAU_CPU; 1235 ctx->subThreadBlockSize = 0; 1236 } else { 1237 ierr = PetscStrcmp("cuda",opstring,&flg);CHKERRQ(ierr); 1238 if (flg) { 1239 ctx->deviceType = LANDAU_CUDA; 1240 ctx->subThreadBlockSize = 0; 1241 } else { 1242 ierr = PetscStrcmp("kokkos",opstring,&flg);CHKERRQ(ierr); 1243 if (flg) ctx->deviceType = LANDAU_KOKKOS; 1244 else SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-dm_landau_device_type %s",opstring); 1245 } 1246 } 1247 } 1248 ierr = PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL);CHKERRQ(ierr); 1249 ierr = PetscOptionsReal("-dm_landau_electron_shift","Shift in thermal velocity of electrons","none",ctx->electronShift,&ctx->electronShift, NULL);CHKERRQ(ierr); 1250 ierr = PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, &sph_flg);CHKERRQ(ierr); 1251 ierr = PetscOptionsBool("-dm_landau_inflate", "With sphere, inflate for curved edges (no AMR)", "plexland.c", ctx->inflate, &ctx->inflate, NULL);CHKERRQ(ierr); 1252 ierr = PetscOptionsInt("-dm_landau_amr_re_levels", "Number of levels to refine along v_perp=0, z>0", "plexland.c", ctx->numRERefine, &ctx->numRERefine, NULL);CHKERRQ(ierr); 1253 ierr = PetscOptionsInt("-dm_landau_amr_z_refine1", "Number of levels to refine along v_perp=0", "plexland.c", ctx->nZRefine1, &ctx->nZRefine1, NULL);CHKERRQ(ierr); 1254 ierr = PetscOptionsInt("-dm_landau_amr_z_refine2", "Number of levels to refine along v_perp=0", "plexland.c", ctx->nZRefine2, &ctx->nZRefine2, NULL);CHKERRQ(ierr); 1255 ierr = PetscOptionsInt("-dm_landau_amr_levels_max", "Number of AMR levels of refinement around origin after r=0 refinements", "plexland.c", ctx->maxRefIts, &ctx->maxRefIts, NULL);CHKERRQ(ierr); 1256 ierr = PetscOptionsInt("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &ctx->postAMRRefine, NULL);CHKERRQ(ierr); 1257 ierr = PetscOptionsInt("-dm_landau_verbose", "", "plexland.c", ctx->verbose, &ctx->verbose, NULL);CHKERRQ(ierr); 1258 ierr = PetscOptionsReal("-dm_landau_re_radius","velocity range to refine on positive (z>0) r=0 axis for runaways","plexland.c",ctx->re_radius,&ctx->re_radius, &flg);CHKERRQ(ierr); 1259 ierr = PetscOptionsReal("-dm_landau_z_radius1","velocity range to refine r=0 axis (for electrons)","plexland.c",ctx->vperp0_radius1,&ctx->vperp0_radius1, &flg);CHKERRQ(ierr); 1260 ierr = PetscOptionsReal("-dm_landau_z_radius2","velocity range to refine r=0 axis (for ions) after origin AMR","plexland.c",ctx->vperp0_radius2,&ctx->vperp0_radius2, &flg);CHKERRQ(ierr); 1261 ierr = PetscOptionsReal("-dm_landau_Ez","Initial parallel electric field in unites of Conner-Hastie criticle field","plexland.c",ctx->Ez,&ctx->Ez, NULL);CHKERRQ(ierr); 1262 ierr = PetscOptionsReal("-dm_landau_n_0","Normalization constant for number density","plexland.c",ctx->n_0,&ctx->n_0, NULL);CHKERRQ(ierr); 1263 ierr = PetscOptionsReal("-dm_landau_ln_lambda","Cross section parameter","plexland.c",ctx->lnLam,&ctx->lnLam, NULL);CHKERRQ(ierr); 1264 ierr = PetscOptionsInt("-dm_landau_num_sections", "Number of tangential section in (2D) grid, 2, 3, of 4", "plexland.c", ctx->num_sections, &ctx->num_sections, NULL);CHKERRQ(ierr); 1265 ierr = PetscOptionsInt("-dm_landau_num_thread_teams", "The number of other concurrent runs to make room for", "plexland.c", ctx->numConcurrency, &ctx->numConcurrency, NULL);CHKERRQ(ierr); 1266 1267 /* get num species with tempurature*/ 1268 { 1269 PetscReal arr[100]; 1270 nt = 100; 1271 ierr = PetscOptionsRealArray("-dm_landau_thermal_temps", "Temperature of each species [e,i_0,i_1,...] in keV", "plexland.c", arr, &nt, &flg);CHKERRQ(ierr); 1272 if (flg && nt > LANDAU_MAX_SPECIES) SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"-thermal_temps ,t1,t2,.. number of species %D > MAX %D",nt,LANDAU_MAX_SPECIES); 1273 } 1274 nt = LANDAU_MAX_SPECIES; 1275 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) { 1276 ctx->thermal_temps[ii] = 1.; 1277 ctx->charges[ii] = 1; 1278 ctx->masses[ii] = 1; 1279 ctx->n[ii] = (ii==1) ? 1 : 0; 1280 } 1281 ierr = PetscOptionsRealArray("-dm_landau_thermal_temps", "Temperature of each species [e,i_0,i_1,...] in keV (must be set to set number of species)", "plexland.c", ctx->thermal_temps, &nt, &flg);CHKERRQ(ierr); 1282 if (flg) { 1283 PetscInfo1(dummy, "num_species set to number of thermal temps provided (%D)\n",nt); 1284 ctx->num_species = nt; 1285 } else SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species"); 1286 for (ii=0;ii<ctx->num_species;ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */ 1287 nm = LANDAU_MAX_SPECIES-1; 1288 ierr = PetscOptionsRealArray("-dm_landau_ion_masses", "Mass of each species in units of proton mass [i_0=2,i_1=40...]", "plexland.c", &ctx->masses[1], &nm, &flg);CHKERRQ(ierr); 1289 if (flg && nm != ctx->num_species-1) { 1290 SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"num ion masses %D != num species %D",nm,ctx->num_species-1); 1291 } 1292 nm = LANDAU_MAX_SPECIES; 1293 ierr = PetscOptionsRealArray("-dm_landau_n", "Normalized (by -n_0) number density of each species", "plexland.c", ctx->n, &nm, &flg);CHKERRQ(ierr); 1294 if (flg && nm != ctx->num_species) SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"wrong num n: %D != num species %D",nm,ctx->num_species); 1295 ctx->n_0 *= ctx->n[0]; /* normalized number density */ 1296 for (ii=1;ii<ctx->num_species;ii++) ctx->n[ii] = ctx->n[ii]/ctx->n[0]; 1297 ctx->n[0] = 1; 1298 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */ 1299 ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */ 1300 ctx->m_0 = ctx->masses[0]; /* arbitrary reference mass, electrons */ 1301 ierr = PetscOptionsReal("-dm_landau_v_0","Velocity to normalize with in units of initial electrons thermal velocity (not recommended to change default)","plexland.c",ctx->v_0,&ctx->v_0, NULL);CHKERRQ(ierr); 1302 ctx->v_0 *= PetscSqrtReal(ctx->k*ctx->thermal_temps[0]/(ctx->masses[0])); /* electron mean velocity in 1D (need 3D form in computing T from FE integral) */ 1303 nc = LANDAU_MAX_SPECIES-1; 1304 ierr = PetscOptionsRealArray("-dm_landau_ion_charges", "Charge of each species in units of proton charge [i_0=2,i_1=18,...]", "plexland.c", &ctx->charges[1], &nc, &flg);CHKERRQ(ierr); 1305 if (flg && nc != ctx->num_species-1) SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"num charges %D != num species %D",nc,ctx->num_species-1); 1306 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */ 1307 ctx->t_0 = 8*PETSC_PI*PetscSqr(ctx->epsilon0*ctx->m_0/PetscSqr(ctx->charges[0]))/ctx->lnLam/ctx->n_0*PetscPowReal(ctx->v_0,3); /* note, this t_0 makes nu[0,0]=1 */ 1308 /* geometry */ 1309 for (ii=0;ii<ctx->num_species;ii++) ctx->refineTol[ii] = PETSC_MAX_REAL; 1310 for (ii=0;ii<ctx->num_species;ii++) ctx->coarsenTol[ii] = 0.; 1311 ii = LANDAU_MAX_SPECIES; 1312 ierr = PetscOptionsRealArray("-dm_landau_refine_tol","tolerance for refining cells in AMR","plexland.c",ctx->refineTol, &ii, &flg);CHKERRQ(ierr); 1313 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #refine_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 1314 ii = LANDAU_MAX_SPECIES; 1315 ierr = PetscOptionsRealArray("-dm_landau_coarsen_tol","tolerance for coarsening cells in AMR","plexland.c",ctx->coarsenTol, &ii, &flg);CHKERRQ(ierr); 1316 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #coarsen_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 1317 ierr = PetscOptionsReal("-dm_landau_domain_radius","Phase space size in units of electron thermal velocity","plexland.c",ctx->radius,&ctx->radius, &flg);CHKERRQ(ierr); 1318 if (flg && ctx->radius <= 0) { /* negative is ratio of c */ 1319 if (ctx->radius == 0) ctx->radius = 0.75; 1320 else ctx->radius = -ctx->radius; 1321 ctx->radius = ctx->radius*299792458.0/ctx->v_0; 1322 ierr = PetscInfo1(dummy, "Change domain radius to %e\n",ctx->radius);CHKERRQ(ierr); 1323 } 1324 ierr = PetscOptionsReal("-dm_landau_i_radius","Ion thermal velocity, used for circular meshes","plexland.c",ctx->i_radius,&ctx->i_radius, &flg);CHKERRQ(ierr); 1325 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an ion radius but did not set sphere, user error really */ 1326 if (!flg) { 1327 ctx->i_radius = 1.5*PetscSqrtReal(8*ctx->k*ctx->thermal_temps[1]/ctx->masses[1]/PETSC_PI)/ctx->v_0; /* normalized radius with thermal velocity of first ion */ 1328 } 1329 ierr = PetscOptionsReal("-dm_landau_e_radius","Electron thermal velocity, used for circular meshes","plexland.c",ctx->e_radius,&ctx->e_radius, &flg);CHKERRQ(ierr); 1330 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an e radius but did not set sphere, user error really */ 1331 if (!flg) { 1332 ctx->e_radius = 1.5*PetscSqrtReal(8*ctx->k*ctx->thermal_temps[0]/ctx->masses[0]/PETSC_PI)/ctx->v_0; /* normalized radius with thermal velocity of electrons */ 1333 } 1334 if (ctx->sphere && (ctx->e_radius <= ctx->i_radius || ctx->radius <= ctx->e_radius)) SETERRQ3(ctx->comm,PETSC_ERR_ARG_WRONG,"bad radii: %g < %g < %g",ctx->i_radius,ctx->e_radius,ctx->radius); 1335 ierr = PetscOptionsInt("-dm_landau_sub_thread_block_size", "Number of threads in Kokkos integration point subblock", "plexland.c", ctx->subThreadBlockSize, &ctx->subThreadBlockSize, NULL);CHKERRQ(ierr); 1336 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1337 for (ii=ctx->num_species;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0; 1338 if (ctx->verbose > 0) { 1339 ierr = PetscPrintf(ctx->comm, "masses: e=%10.3e; ions in proton mass units: %10.3e %10.3e ...\n",ctx->masses[0],ctx->masses[1]/1.6720e-27,ctx->num_species>2 ? ctx->masses[2]/1.6720e-27 : 0);CHKERRQ(ierr); 1340 ierr = PetscPrintf(ctx->comm, "charges: e=%10.3e; charges in elementary units: %10.3e %10.3e\n", ctx->charges[0],-ctx->charges[1]/ctx->charges[0],ctx->num_species>2 ? -ctx->charges[2]/ctx->charges[0] : 0);CHKERRQ(ierr); 1341 ierr = PetscPrintf(ctx->comm, "thermal T (K): e=%10.3e i=%10.3e imp=%10.3e. v_0=%10.3e n_0=%10.3e t_0=%10.3e domain=%10.3e\n",ctx->thermal_temps[0],ctx->thermal_temps[1],ctx->num_species>2 ? ctx->thermal_temps[2] : 0,ctx->v_0,ctx->n_0,ctx->t_0,ctx->radius);CHKERRQ(ierr); 1342 } 1343 ierr = DMDestroy(&dummy);CHKERRQ(ierr); 1344 { 1345 PetscMPIInt rank; 1346 ierr = MPI_Comm_rank(ctx->comm, &rank);CHKERRMPI(ierr); 1347 /* PetscLogStage setup_stage; */ 1348 ierr = PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0]);CHKERRQ(ierr); /* 0 */ 1349 ierr = PetscLogEventRegister(" Initialize", DM_CLASSID, &ctx->events[10]);CHKERRQ(ierr); /* 10 */ 1350 ierr = PetscLogEventRegister(" IP Data-jac", DM_CLASSID, &ctx->events[7]);CHKERRQ(ierr); /* 7 */ 1351 ierr = PetscLogEventRegister(" Kernal-init", DM_CLASSID, &ctx->events[3]);CHKERRQ(ierr); /* 3 */ 1352 ierr = PetscLogEventRegister(" GPU Kernel", DM_CLASSID, &ctx->events[4]);CHKERRQ(ierr); /* 4 */ 1353 ierr = PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5]);CHKERRQ(ierr); /* 5 */ 1354 ierr = PetscLogEventRegister(" Jac-assemble", DM_CLASSID, &ctx->events[6]);CHKERRQ(ierr); /* 6 */ 1355 ierr = PetscLogEventRegister(" Jac-f-df", DM_CLASSID, &ctx->events[8]);CHKERRQ(ierr); /* 8 */ 1356 ierr = PetscLogEventRegister(" Jac asmbl setup", DM_CLASSID, &ctx->events[2]);CHKERRQ(ierr); /* 2 */ 1357 ierr = PetscLogEventRegister("Mass Operator", DM_CLASSID, &ctx->events[9]);CHKERRQ(ierr); /* 9 */ 1358 ierr = PetscLogEventRegister(" IP Data-mass", DM_CLASSID, &ctx->events[1]);CHKERRQ(ierr); /* 1 */ 1359 1360 if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */ 1361 ierr = PetscOptionsClearValue(NULL,"-snes_converged_reason");CHKERRQ(ierr); 1362 ierr = PetscOptionsClearValue(NULL,"-ksp_converged_reason");CHKERRQ(ierr); 1363 ierr = PetscOptionsClearValue(NULL,"-snes_monitor");CHKERRQ(ierr); 1364 ierr = PetscOptionsClearValue(NULL,"-ksp_monitor");CHKERRQ(ierr); 1365 ierr = PetscOptionsClearValue(NULL,"-ts_monitor");CHKERRQ(ierr); 1366 ierr = PetscOptionsClearValue(NULL,"-ts_adapt_monitor");CHKERRQ(ierr); 1367 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1368 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_vec_view");CHKERRQ(ierr); 1369 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1370 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_vec_view");CHKERRQ(ierr); 1371 ierr = PetscOptionsClearValue(NULL,"-info");CHKERRQ(ierr); 1372 } 1373 } 1374 PetscFunctionReturn(0); 1375 } 1376 1377 /*@C 1378 LandauCreateVelocitySpace - Create a DMPlex velocity space mesh 1379 1380 Collective on comm 1381 1382 Input Parameters: 1383 + comm - The MPI communicator 1384 . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver) 1385 - prefix - prefix for options 1386 1387 Output Parameter: 1388 . dm - The DM object representing the mesh 1389 + X - A vector (user destroys) 1390 - J - Optional matrix (object destroys) 1391 1392 Level: beginner 1393 1394 .keywords: mesh 1395 .seealso: DMPlexCreate(), LandauDestroyVelocitySpace() 1396 @*/ 1397 PetscErrorCode LandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *dm) 1398 { 1399 PetscErrorCode ierr; 1400 LandauCtx *ctx; 1401 PetscBool prealloc_only,flg; 1402 1403 PetscFunctionBegin; 1404 if (dim!=2 && dim!=3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported"); 1405 ctx = (LandauCtx*)malloc(sizeof(LandauCtx)); 1406 ctx->comm = comm; /* used for diagnostics and global errors */ 1407 /* process options */ 1408 ierr = ProcessOptions(ctx,prefix);CHKERRQ(ierr); 1409 /* Create Mesh */ 1410 ierr = LandauDMCreateVMesh(PETSC_COMM_SELF, dim, prefix, ctx, dm);CHKERRQ(ierr); 1411 prealloc_only = (*dm)->prealloc_only; 1412 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1413 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1414 /* create FEM */ 1415 ierr = SetupDS(*dm,dim,ctx);CHKERRQ(ierr); 1416 /* set initial state */ 1417 ierr = DMCreateGlobalVector(*dm,X);CHKERRQ(ierr); 1418 ierr = PetscObjectSetName((PetscObject) *X, "u");CHKERRQ(ierr); 1419 /* initial static refinement, no solve */ 1420 ierr = LandauSetInitialCondition(*dm, *X, ctx);CHKERRQ(ierr); 1421 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_pre_vec_view");CHKERRQ(ierr); 1422 /* forest refinement */ 1423 if (ctx->errorIndicator) { 1424 /* AMR */ 1425 ierr = adapt(dm,ctx,X);CHKERRQ(ierr); 1426 if ((*dm)->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"(*dm)->prealloc_only != prealloc_only"); 1427 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1428 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_amr_vec_view");CHKERRQ(ierr); 1429 } 1430 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1431 ctx->dmv = *dm; 1432 if (ctx->dmv->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"ctx->dmv->prealloc_only != prealloc_only"); 1433 ierr = DMCreateMatrix(ctx->dmv, &ctx->J);CHKERRQ(ierr); 1434 ierr = MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1435 ierr = MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE);CHKERRQ(ierr); 1436 if (J) *J = ctx->J; 1437 /* check for types that we need */ 1438 #if defined(PETSC_HAVE_KOKKOS) 1439 if (ctx->deviceType == LANDAU_CPU) { 1440 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJKOKKOS,MATMPIAIJKOKKOS,MATAIJKOKKOS,"");CHKERRQ(ierr); 1441 //if (flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"with device=cpu must not use '-dm_mat_type aijkokkos -dm_vec_type kokkos' for GPU assembly and Kokkos"); 1442 } 1443 #elif defined(PETSC_HAVE_CUDA) 1444 if (ctx->deviceType == LANDAU_CPU) { 1445 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJCUSPARSE,MATMPIAIJCUSPARSE,MATAIJCUSPARSE,"");CHKERRQ(ierr); 1446 //if (flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"with device=cpu must not use '-dm_mat_type aijcusparse -dm_vec_type cuda' for GPU assembly and Cuda"); 1447 } 1448 #endif 1449 if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */ 1450 if (ctx->deviceType == LANDAU_CUDA) { 1451 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJCUSPARSE,MATMPIAIJCUSPARSE,MATAIJCUSPARSE,"");CHKERRQ(ierr); 1452 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must use '-dm_mat_type aijcusparse -dm_vec_type cuda' for GPU assembly and Cuda"); 1453 } else if (ctx->deviceType == LANDAU_KOKKOS) { 1454 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJKOKKOS,MATMPIAIJKOKKOS,MATAIJKOKKOS,"");CHKERRQ(ierr); 1455 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 1456 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must use '-dm_mat_type aijkokkos -dm_vec_type kokkos' for GPU assembly and Kokkos"); 1457 #else 1458 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must configure with '--download-kokkos-kernels=1' for GPU assembly and Kokkos"); 1459 #endif 1460 } 1461 } 1462 PetscFunctionReturn(0); 1463 } 1464 1465 /*@ 1466 LandauDestroyVelocitySpace - Destroy a DMPlex velocity space mesh 1467 1468 Collective on dm 1469 1470 Input/Output Parameters: 1471 . dm - the dm to destroy 1472 1473 Level: beginner 1474 1475 .keywords: mesh 1476 .seealso: LandauCreateVelocitySpace() 1477 @*/ 1478 PetscErrorCode LandauDestroyVelocitySpace(DM *dm) 1479 { 1480 PetscErrorCode ierr,ii; 1481 LandauCtx *ctx; 1482 PetscContainer container = NULL; 1483 PetscFunctionBegin; 1484 ierr = DMGetApplicationContext(*dm, &ctx);CHKERRQ(ierr); 1485 ierr = PetscObjectQuery((PetscObject)ctx->J,"coloring", (PetscObject*)&container);CHKERRQ(ierr); 1486 if (container) { 1487 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 1488 } 1489 ierr = MatDestroy(&ctx->M);CHKERRQ(ierr); 1490 ierr = MatDestroy(&ctx->J);CHKERRQ(ierr); 1491 for (ii=0;ii<ctx->num_species;ii++) { 1492 ierr = PetscFEDestroy(&ctx->fe[ii]);CHKERRQ(ierr); 1493 } 1494 free(ctx); 1495 ierr = DMDestroy(dm);CHKERRQ(ierr); 1496 PetscFunctionReturn(0); 1497 } 1498 1499 /* < v, ru > */ 1500 static void f0_s_den(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1501 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1502 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1503 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1504 { 1505 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1506 f0[0] = u[ii]; 1507 } 1508 1509 /* < v, ru > */ 1510 static void f0_s_mom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1511 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1512 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1513 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1514 { 1515 PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]); 1516 f0[0] = x[jj]*u[ii]; /* x momentum */ 1517 } 1518 1519 static void f0_s_v2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1520 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1521 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1522 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1523 { 1524 PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]); 1525 double tmp1 = 0.; 1526 for (i = 0; i < dim; ++i) tmp1 += x[i]*x[i]; 1527 f0[0] = tmp1*u[ii]; 1528 } 1529 1530 /* < v, ru > */ 1531 static void f0_s_rden(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1532 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1533 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1534 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1535 { 1536 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1537 f0[0] = 2.*PETSC_PI*x[0]*u[ii]; 1538 } 1539 1540 /* < v, ru > */ 1541 static void f0_s_rmom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1542 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1543 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1544 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1545 { 1546 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1547 f0[0] = 2.*PETSC_PI*x[0]*x[1]*u[ii]; 1548 } 1549 1550 static void f0_s_rv2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1551 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1552 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1553 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1554 { 1555 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1556 f0[0] = 2.*PETSC_PI*x[0]*(x[0]*x[0] + x[1]*x[1])*u[ii]; 1557 } 1558 1559 /*@ 1560 LandauPrintNorms - collects moments and prints them 1561 1562 Collective on dm 1563 1564 Input Parameters: 1565 + X - the state 1566 - stepi - current step to print 1567 1568 Level: beginner 1569 1570 .keywords: mesh 1571 .seealso: LandauCreateVelocitySpace() 1572 @*/ 1573 PetscErrorCode LandauPrintNorms(Vec X, PetscInt stepi) 1574 { 1575 PetscErrorCode ierr; 1576 LandauCtx *ctx; 1577 PetscDS prob; 1578 DM plex,dm; 1579 PetscInt cStart, cEnd, dim, ii; 1580 PetscScalar xmomentumtot=0, ymomentumtot=0, zmomentumtot=0, energytot=0, densitytot=0, tt[LANDAU_MAX_SPECIES]; 1581 PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES]; 1582 1583 PetscFunctionBegin; 1584 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 1585 if (!dm) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no DM"); 1586 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1587 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1588 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1589 ierr = DMConvert(ctx->dmv, DMPLEX, &plex);CHKERRQ(ierr); 1590 ierr = DMCreateDS(plex);CHKERRQ(ierr); 1591 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 1592 /* print momentum and energy */ 1593 for (ii=0;ii<ctx->num_species;ii++) { 1594 PetscScalar user[2] = { (PetscScalar)ii, (PetscScalar)ctx->charges[ii]}; 1595 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 1596 if (dim==2) { /* 2/3X + 3V (cylindrical coordinates) */ 1597 ierr = PetscDSSetObjective(prob, 0, &f0_s_rden);CHKERRQ(ierr); 1598 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1599 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1600 ierr = PetscDSSetObjective(prob, 0, &f0_s_rmom);CHKERRQ(ierr); 1601 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1602 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1603 ierr = PetscDSSetObjective(prob, 0, &f0_s_rv2);CHKERRQ(ierr); 1604 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1605 energy[ii] = tt[0]*0.5*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1606 zmomentumtot += zmomentum[ii]; 1607 energytot += energy[ii]; 1608 densitytot += density[ii]; 1609 ierr = PetscPrintf(ctx->comm, "%3D) species-%D: charge density= %20.13e z-momentum= %20.13e energy= %20.13e",stepi,ii,PetscRealPart(density[ii]),PetscRealPart(zmomentum[ii]),PetscRealPart(energy[ii]));CHKERRQ(ierr); 1610 } else { /* 2/3X + 3V */ 1611 ierr = PetscDSSetObjective(prob, 0, &f0_s_den);CHKERRQ(ierr); 1612 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1613 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1614 ierr = PetscDSSetObjective(prob, 0, &f0_s_mom);CHKERRQ(ierr); 1615 user[1] = 0; 1616 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1617 xmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1618 user[1] = 1; 1619 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1620 ymomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1621 user[1] = 2; 1622 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1623 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1624 ierr = PetscDSSetObjective(prob, 0, &f0_s_v2);CHKERRQ(ierr); 1625 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1626 energy[ii] = 0.5*tt[0]*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1627 ierr = PetscPrintf(ctx->comm, "%3D) species %D: density=%20.13e, x-momentum=%20.13e, y-momentum=%20.13e, z-momentum=%20.13e, energy=%21.13e", 1628 stepi,ii,PetscRealPart(density[ii]),PetscRealPart(xmomentum[ii]),PetscRealPart(ymomentum[ii]),PetscRealPart(zmomentum[ii]),PetscRealPart(energy[ii]));CHKERRQ(ierr); 1629 xmomentumtot += xmomentum[ii]; 1630 ymomentumtot += ymomentum[ii]; 1631 zmomentumtot += zmomentum[ii]; 1632 energytot += energy[ii]; 1633 densitytot += density[ii]; 1634 } 1635 if (ctx->num_species>1) PetscPrintf(ctx->comm, "\n"); 1636 } 1637 /* totals */ 1638 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1639 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1640 if (ctx->num_species>1) { 1641 if (dim==2) { 1642 ierr = PetscPrintf(ctx->comm, "\t%3D) Total: charge density=%21.13e, momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %D cells)", 1643 stepi,(double)PetscRealPart(densitytot),(double)PetscRealPart(zmomentumtot),(double)PetscRealPart(energytot),(double)(ctx->masses[1]/ctx->masses[0]),cEnd-cStart);CHKERRQ(ierr); 1644 } else { 1645 ierr = PetscPrintf(ctx->comm, "\t%3D) Total: charge density=%21.13e, x-momentum=%21.13e, y-momentum=%21.13e, z-momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %D cells)", 1646 stepi,(double)PetscRealPart(densitytot),(double)PetscRealPart(xmomentumtot),(double)PetscRealPart(ymomentumtot),(double)PetscRealPart(zmomentumtot),(double)PetscRealPart(energytot),(double)(ctx->masses[1]/ctx->masses[0]),cEnd-cStart);CHKERRQ(ierr); 1647 } 1648 } else { 1649 ierr = PetscPrintf(ctx->comm, " -- %D cells",cEnd-cStart);CHKERRQ(ierr); 1650 } 1651 if (ctx->verbose > 1) {ierr = PetscPrintf(ctx->comm,", %D sub (vector) threads\n",ctx->subThreadBlockSize);CHKERRQ(ierr);} 1652 else {ierr = PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr);} 1653 PetscFunctionReturn(0); 1654 } 1655 1656 static PetscErrorCode destroy_coloring (void *is) 1657 { 1658 ISColoring tmp = (ISColoring)is; 1659 return ISColoringDestroy(&tmp); 1660 } 1661 1662 /*@ 1663 LandauCreateColoring - create a coloring and add to matrix (Landau context used just for 'print' flag, should be in DMPlex) 1664 1665 Collective on JacP 1666 1667 Input Parameters: 1668 + JacP - matrix to add coloring to 1669 - plex - The DM 1670 1671 Output Parameter: 1672 . container - Container with coloring 1673 1674 Level: beginner 1675 1676 .keywords: mesh 1677 .seealso: LandauCreateVelocitySpace() 1678 @*/ 1679 PetscErrorCode LandauCreateColoring(Mat JacP, DM plex, PetscContainer *container) 1680 { 1681 PetscErrorCode ierr; 1682 PetscInt dim,cell,i,ej,nc,Nv,totDim,numGCells,cStart,cEnd; 1683 ISColoring iscoloring = NULL; 1684 Mat G,Q; 1685 PetscScalar ones[128]; 1686 MatColoring mc; 1687 IS *is; 1688 PetscInt csize,colour,j,k; 1689 const PetscInt *indices; 1690 PetscInt numComp[1]; 1691 PetscInt numDof[4]; 1692 PetscFE fe; 1693 DM colordm; 1694 PetscSection csection, section, globalSection; 1695 PetscDS prob; 1696 LandauCtx *ctx; 1697 1698 PetscFunctionBegin; 1699 ierr = DMGetApplicationContext(plex, &ctx);CHKERRQ(ierr); 1700 ierr = DMGetLocalSection(plex, §ion);CHKERRQ(ierr); 1701 ierr = DMGetGlobalSection(plex, &globalSection);CHKERRQ(ierr); 1702 ierr = DMGetDimension(plex, &dim);CHKERRQ(ierr); 1703 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 1704 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1705 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1706 numGCells = cEnd - cStart; 1707 /* create cell centered DM */ 1708 ierr = DMClone(plex, &colordm);CHKERRQ(ierr); 1709 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) plex), dim, 1, PETSC_FALSE, "color_", PETSC_DECIDE, &fe);CHKERRQ(ierr); 1710 ierr = PetscObjectSetName((PetscObject) fe, "color");CHKERRQ(ierr); 1711 ierr = DMSetField(colordm, 0, NULL, (PetscObject)fe);CHKERRQ(ierr); 1712 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 1713 for (i = 0; i < (dim+1); ++i) numDof[i] = 0; 1714 numDof[dim] = 1; 1715 numComp[0] = 1; 1716 ierr = DMPlexCreateSection(colordm, NULL, numComp, numDof, 0, NULL, NULL, NULL, NULL, &csection);CHKERRQ(ierr); 1717 ierr = PetscSectionSetFieldName(csection, 0, "color");CHKERRQ(ierr); 1718 ierr = DMSetLocalSection(colordm, csection);CHKERRQ(ierr); 1719 ierr = DMViewFromOptions(colordm,NULL,"-color_dm_view");CHKERRQ(ierr); 1720 /* get vertex to element map Q and colroing graph G */ 1721 ierr = MatGetSize(JacP,NULL,&Nv);CHKERRQ(ierr); 1722 ierr = MatCreateAIJ(PETSC_COMM_SELF,PETSC_DECIDE,PETSC_DECIDE,numGCells,Nv,totDim,NULL,0,NULL,&Q);CHKERRQ(ierr); 1723 for (i=0;i<128;i++) ones[i] = 1.0; 1724 for (cell = cStart, ej = 0 ; cell < cEnd; ++cell, ++ej) { 1725 PetscInt numindices,*indices; 1726 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1727 if (numindices>128) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many indices. %D > %D",numindices,128); 1728 ierr = MatSetValues(Q,1,&ej,numindices,indices,ones,ADD_VALUES);CHKERRQ(ierr); 1729 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1730 } 1731 ierr = MatAssemblyBegin(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1732 ierr = MatAssemblyEnd(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1733 ierr = MatMatTransposeMult(Q,Q,MAT_INITIAL_MATRIX,4.0,&G);CHKERRQ(ierr); 1734 ierr = PetscObjectSetName((PetscObject) Q, "Q");CHKERRQ(ierr); 1735 ierr = PetscObjectSetName((PetscObject) G, "coloring graph");CHKERRQ(ierr); 1736 ierr = MatViewFromOptions(G,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1737 ierr = MatViewFromOptions(Q,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1738 ierr = MatDestroy(&Q);CHKERRQ(ierr); 1739 /* coloring */ 1740 ierr = MatColoringCreate(G,&mc);CHKERRQ(ierr); 1741 ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr); 1742 ierr = MatColoringSetType(mc,MATCOLORINGJP);CHKERRQ(ierr); 1743 ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr); 1744 ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr); 1745 ierr = MatColoringDestroy(&mc);CHKERRQ(ierr); 1746 /* view */ 1747 ierr = ISColoringViewFromOptions(iscoloring,NULL,"-coloring_is_view");CHKERRQ(ierr); 1748 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1749 if (ctx && ctx->verbose > 2) { 1750 PetscViewer viewer; 1751 Vec color_vec, eidx_vec; 1752 ierr = DMGetGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1753 ierr = DMGetGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1754 for (colour=0; colour<nc; colour++) { 1755 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1756 ierr = ISGetIndices(is[colour],&indices);CHKERRQ(ierr); 1757 for (j=0; j<csize; j++) { 1758 PetscScalar v = (PetscScalar)colour; 1759 k = indices[j]; 1760 ierr = VecSetValues(color_vec,1,&k,&v,INSERT_VALUES); 1761 v = (PetscScalar)k; 1762 ierr = VecSetValues(eidx_vec,1,&k,&v,INSERT_VALUES); 1763 } 1764 ierr = ISRestoreIndices(is[colour],&indices);CHKERRQ(ierr); 1765 } 1766 /* view */ 1767 ierr = PetscViewerVTKOpen(ctx->comm, "color.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1768 ierr = PetscObjectSetName((PetscObject) color_vec, "color");CHKERRQ(ierr); 1769 ierr = VecView(color_vec, viewer);CHKERRQ(ierr); 1770 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1771 ierr = PetscViewerVTKOpen(ctx->comm, "eidx.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1772 ierr = PetscObjectSetName((PetscObject) eidx_vec, "element-idx");CHKERRQ(ierr); 1773 ierr = VecView(eidx_vec, viewer);CHKERRQ(ierr); 1774 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1775 ierr = DMRestoreGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1776 ierr = DMRestoreGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1777 } 1778 ierr = PetscSectionDestroy(&csection);CHKERRQ(ierr); 1779 ierr = DMDestroy(&colordm);CHKERRQ(ierr); 1780 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1781 ierr = MatDestroy(&G);CHKERRQ(ierr); 1782 /* stash coloring */ 1783 ierr = PetscContainerCreate(PETSC_COMM_SELF, container);CHKERRQ(ierr); 1784 ierr = PetscContainerSetPointer(*container,(void*)iscoloring);CHKERRQ(ierr); 1785 ierr = PetscContainerSetUserDestroy(*container, destroy_coloring);CHKERRQ(ierr); 1786 ierr = PetscObjectCompose((PetscObject)JacP,"coloring",(PetscObject)*container);CHKERRQ(ierr); 1787 if (ctx && ctx->verbose > 0) { 1788 ierr = PetscPrintf(ctx->comm, "Made coloring with %D colors\n", nc);CHKERRQ(ierr); 1789 } 1790 PetscFunctionReturn(0); 1791 } 1792 1793 PetscErrorCode LandauAssembleOpenMP(PetscInt cStart, PetscInt cEnd, PetscInt totDim, DM plex, PetscSection section, PetscSection globalSection, Mat JacP, PetscScalar elemMats[], PetscContainer container) 1794 { 1795 PetscErrorCode ierr; 1796 IS *is; 1797 PetscInt nc,colour,j; 1798 const PetscInt *clr_idxs; 1799 ISColoring iscoloring; 1800 PetscFunctionBegin; 1801 ierr = PetscContainerGetPointer(container,(void**)&iscoloring);CHKERRQ(ierr); 1802 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1803 for (colour=0; colour<nc; colour++) { 1804 PetscInt *idx_arr[1024]; /* need to make dynamic for general use */ 1805 PetscScalar *new_el_mats[1024]; 1806 PetscInt idx_size[1024],csize; 1807 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1808 if (csize>1024) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many elements in color. %D > %D",csize,1024); 1809 ierr = ISGetIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1810 /* get indices and mats */ 1811 for (j=0; j<csize; j++) { 1812 PetscInt cell = cStart + clr_idxs[j]; 1813 PetscInt numindices,*indices; 1814 PetscScalar *elMat = &elemMats[clr_idxs[j]*totDim*totDim]; 1815 PetscScalar *valuesOrig = elMat; 1816 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1817 idx_size[j] = numindices; 1818 ierr = PetscMalloc2(numindices,&idx_arr[j],numindices*numindices,&new_el_mats[j]);CHKERRQ(ierr); 1819 ierr = PetscMemcpy(idx_arr[j],indices,numindices*sizeof(PetscInt));CHKERRQ(ierr); 1820 ierr = PetscMemcpy(new_el_mats[j],elMat,numindices*numindices*sizeof(PetscScalar));CHKERRQ(ierr); 1821 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1822 if (elMat != valuesOrig) {ierr = DMRestoreWorkArray(plex, numindices*numindices, MPIU_SCALAR, &elMat);} 1823 } 1824 /* assemble matrix - pragmas break CI ? */ 1825 //#pragma omp parallel default(JacP,idx_size,idx_arr,new_el_mats,colour,clr_idxs) private(j) 1826 //#pragma omp parallel for private(j) 1827 for (j=0; j<csize; j++) { 1828 PetscInt numindices = idx_size[j], *indices = idx_arr[j]; 1829 PetscScalar *elMat = new_el_mats[j]; 1830 MatSetValues(JacP,numindices,indices,numindices,indices,elMat,ADD_VALUES); 1831 } 1832 /* free */ 1833 ierr = ISRestoreIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1834 for (j=0; j<csize; j++) { 1835 ierr = PetscFree2(idx_arr[j],new_el_mats[j]);CHKERRQ(ierr); 1836 } 1837 } 1838 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1839 PetscFunctionReturn(0); 1840 } 1841 1842 /* < v, u > */ 1843 static void g0_1(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1844 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1845 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1846 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1847 { 1848 g0[0] = 1.; 1849 } 1850 1851 /* < v, u > */ 1852 static void g0_r(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1853 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1854 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1855 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1856 { 1857 g0[0] = 2.*PETSC_PI*x[0]; 1858 } 1859 1860 /*@ 1861 LandauCreateMassMatrix - Create mass matrix for Landau 1862 1863 Collective on dm 1864 1865 Input Parameters: 1866 . dm - the DM object 1867 1868 Output Parameters: 1869 . Amat - The mass matrix (optional), mass matrix is added to the DM context 1870 1871 Level: beginner 1872 1873 .keywords: mesh 1874 .seealso: LandauCreateVelocitySpace() 1875 @*/ 1876 PetscErrorCode LandauCreateMassMatrix(DM dm, Mat *Amat) 1877 { 1878 DM massDM; 1879 PetscDS prob; 1880 PetscInt ii,dim,N1=1,N2; 1881 PetscErrorCode ierr; 1882 LandauCtx *ctx; 1883 Mat M; 1884 1885 PetscFunctionBegin; 1886 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1887 if (Amat) PetscValidPointer(Amat,3); 1888 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1889 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1890 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1891 ierr = DMClone(dm, &massDM);CHKERRQ(ierr); 1892 ierr = DMCopyFields(dm, massDM);CHKERRQ(ierr); 1893 ierr = DMCreateDS(massDM);CHKERRQ(ierr); 1894 ierr = DMGetDS(massDM, &prob);CHKERRQ(ierr); 1895 for (ii=0;ii<ctx->num_species;ii++) { 1896 if (dim==3) {ierr = PetscDSSetJacobian(prob, ii, ii, g0_1, NULL, NULL, NULL);CHKERRQ(ierr);} 1897 else {ierr = PetscDSSetJacobian(prob, ii, ii, g0_r, NULL, NULL, NULL);CHKERRQ(ierr);} 1898 } 1899 ierr = DMViewFromOptions(massDM,NULL,"-dm_landau_mass_dm_view");CHKERRQ(ierr); 1900 ierr = DMCreateMatrix(massDM, &M);CHKERRQ(ierr); 1901 ierr = MatSetOption(M, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1902 { 1903 Vec locX; 1904 DM plex; 1905 ierr = DMConvert(massDM, DMPLEX, &plex);CHKERRQ(ierr); 1906 ierr = DMGetLocalVector(massDM, &locX);CHKERRQ(ierr); 1907 /* Mass matrix is independent of the input, so no need to fill locX */ 1908 if (plex->prealloc_only != dm->prealloc_only) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "plex->prealloc_only = massDM->prealloc_only %D, =%D",plex->prealloc_only,massDM->prealloc_only); 1909 ierr = DMPlexSNESComputeJacobianFEM(plex, locX, M, M, ctx);CHKERRQ(ierr); 1910 ierr = DMRestoreLocalVector(massDM, &locX);CHKERRQ(ierr); 1911 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1912 } 1913 ierr = DMDestroy(&massDM);CHKERRQ(ierr); 1914 ierr = MatGetSize(ctx->J, &N1, NULL);CHKERRQ(ierr); 1915 ierr = MatGetSize(M, &N2, NULL);CHKERRQ(ierr); 1916 if (N1 != N2) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %D, |Mass|=%D",N1,N2); 1917 ierr = PetscObjectSetName((PetscObject)M, "mass");CHKERRQ(ierr); 1918 ierr = MatViewFromOptions(M,NULL,"-dm_landau_mass_mat_view");CHKERRQ(ierr); 1919 ctx->M = M; /* this could be a noop, a = a */ 1920 if (Amat) *Amat = M; 1921 PetscFunctionReturn(0); 1922 } 1923 1924 /*@ 1925 LandauIFunction - TS residual calculation 1926 1927 Collective on ts 1928 1929 Input Parameters: 1930 + TS - The time stepping context 1931 . time_dummy - current time (not used) 1932 - X - Current state 1933 + X_t - Time derivative of current state 1934 . actx - Landau context 1935 1936 Output Parameter: 1937 . F - The residual 1938 1939 Level: beginner 1940 1941 .keywords: mesh 1942 .seealso: LandauCreateVelocitySpace(), LandauIJacobian() 1943 @*/ 1944 PetscErrorCode LandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx) 1945 { 1946 PetscErrorCode ierr; 1947 LandauCtx *ctx=(LandauCtx*)actx; 1948 PetscInt dim; 1949 DM dm; 1950 1951 PetscFunctionBegin; 1952 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 1953 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1954 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1955 ierr = PetscLogEventBegin(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 1956 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 1957 ierr = PetscInfo3(ts, "Create Landau Jacobian t=%g X'=%p %s\n",time_dummy,X_t,ctx->aux_bool ? " -- seems to be in line search" : "");CHKERRQ(ierr); 1958 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,0.0,(void*)ctx);CHKERRQ(ierr); 1959 ctx->aux_bool = PETSC_TRUE; 1960 ierr = MatViewFromOptions(ctx->J,NULL,"-landau_jacobian_mat_view");CHKERRQ(ierr); 1961 /* mat vec for op */ 1962 ierr = MatMult(ctx->J,X,F);CHKERRQ(ierr);CHKERRQ(ierr); /* C*f */ 1963 /* add time term */ 1964 if (X_t) { 1965 ierr = MatMultAdd(ctx->M,X_t,F,F);CHKERRQ(ierr); 1966 } 1967 ierr = PetscLogEventEnd(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 1968 PetscFunctionReturn(0); 1969 } 1970 static PetscErrorCode MatrixNfDestroy(void *ptr) 1971 { 1972 PetscInt *nf = (PetscInt *)ptr; 1973 PetscErrorCode ierr; 1974 PetscFunctionBegin; 1975 ierr = PetscFree(nf);CHKERRQ(ierr); 1976 PetscFunctionReturn(0); 1977 } 1978 /*@ 1979 LandauIJacobian - TS Jacobian construction 1980 1981 Collective on ts 1982 1983 Input Parameters: 1984 + TS - The time stepping context 1985 . time_dummy - current time (not used) 1986 - X - Current state 1987 + U_tdummy - Time derivative of current state (not used) 1988 . shift - shift for du/dt term 1989 - actx - Landau context 1990 1991 Output Parameter: 1992 . Amat - Jacobian 1993 + Pmat - same as Amat 1994 1995 Level: beginner 1996 1997 .keywords: mesh 1998 .seealso: LandauCreateVelocitySpace(), LandauIFunction() 1999 @*/ 2000 PetscErrorCode LandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx) 2001 { 2002 PetscErrorCode ierr; 2003 LandauCtx *ctx=(LandauCtx*)actx; 2004 PetscInt dim; 2005 DM dm; 2006 PetscContainer container; 2007 PetscFunctionBegin; 2008 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 2009 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 2010 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2011 if (Amat!=Pmat || Amat!=ctx->J) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J"); 2012 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 2013 /* get collision Jacobian into A */ 2014 ierr = PetscLogEventBegin(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 2015 ierr = PetscInfo2(ts, "Adding mass to Jacobian t=%g, shift=%g\n",(double)time_dummy,(double)shift);CHKERRQ(ierr); 2016 if (shift==0.0) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "zero shift"); 2017 if (!ctx->aux_bool) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "wrong state"); 2018 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,shift,(void*)ctx);CHKERRQ(ierr); 2019 ctx->aux_bool = PETSC_FALSE; 2020 ierr = MatViewFromOptions(Pmat,NULL,"-landau_mat_view");CHKERRQ(ierr); 2021 ierr = PetscLogEventEnd(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 2022 /* set number species in Jacobian */ 2023 ierr = PetscObjectQuery((PetscObject) ctx->J, "Nf", (PetscObject *) &container);CHKERRQ(ierr); 2024 if (!container) { 2025 PetscInt *pNf; 2026 ierr = PetscContainerCreate(PETSC_COMM_SELF, &container);CHKERRQ(ierr); 2027 ierr = PetscMalloc(sizeof(PetscInt), &pNf);CHKERRQ(ierr); 2028 *pNf = ctx->num_species + 1000*ctx->numConcurrency; 2029 ierr = PetscContainerSetPointer(container, (void *)pNf);CHKERRQ(ierr); 2030 ierr = PetscContainerSetUserDestroy(container, MatrixNfDestroy);CHKERRQ(ierr); 2031 ierr = PetscObjectCompose((PetscObject)ctx->J, "Nf", (PetscObject) container);CHKERRQ(ierr); 2032 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 2033 } 2034 2035 PetscFunctionReturn(0); 2036 } 2037