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 static PetscErrorCode LandauGPUMapsDestroy(void *ptr) 15 { 16 P4estVertexMaps *maps = (P4estVertexMaps *)ptr; 17 PetscErrorCode ierr; 18 PetscFunctionBegin; 19 if (maps->deviceType != LANDAU_CPU) { 20 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 21 if (maps->deviceType == LANDAU_KOKKOS) { 22 ierr = LandauKokkosDestroyMatMaps(maps);CHKERRQ(ierr); // imples Kokkos does 23 } // else could be CUDA 24 #elif defined(PETSC_HAVE_CUDA) 25 if (maps->deviceType == LANDAU_CUDA){ 26 ierr = LandauCUDADestroyMatMaps(maps);CHKERRQ(ierr); 27 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps->deviceType %D ?????",maps->deviceType); 28 #endif 29 } 30 ierr = PetscFree(maps->c_maps);CHKERRQ(ierr); 31 ierr = PetscFree(maps->gIdx);CHKERRQ(ierr); 32 ierr = PetscFree(maps);CHKERRQ(ierr); 33 PetscFunctionReturn(0); 34 } 35 36 /* ------------------------------------------------------------------- */ 37 /* 38 LandauFormJacobian_Internal - Evaluates Jacobian matrix. 39 40 Input Parameters: 41 . globX - input vector 42 . actx - optional user-defined context 43 . dim - dimension 44 45 Output Parameters: 46 . J0acP - Jacobian matrix filled, not created 47 */ 48 static PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, PetscReal shift, void *a_ctx) 49 { 50 LandauCtx *ctx = (LandauCtx*)a_ctx; 51 PetscErrorCode ierr; 52 PetscInt cStart, cEnd, elemMatSize; 53 DM plex = NULL; 54 PetscDS prob; 55 PetscSection section,globsection; 56 PetscInt numCells,totDim,ej,Nq,*Nbf,*Ncf,Nb,Ncx,Nf,d,f,fieldA,qj,N; 57 PetscQuadrature quad; 58 const PetscReal *quadWeights; 59 PetscTabulation *Tf; // used for CPU and print info 60 PetscReal Eq_m[LANDAU_MAX_SPECIES], m_0=ctx->m_0; /* normalize mass -- not needed! */ 61 PetscScalar *IPf=NULL; 62 const PetscScalar *xarray=NULL; 63 PetscLogDouble flops; 64 PetscContainer container; 65 P4estVertexMaps *maps=NULL; 66 67 PetscFunctionBegin; 68 PetscValidHeaderSpecific(a_X,VEC_CLASSID,1); 69 PetscValidHeaderSpecific(JacP,MAT_CLASSID,2); 70 PetscValidPointer(ctx,5); 71 /* static PetscLogStage stage0 = 0; */ 72 /* if (!stage0) { */ 73 /* ierr = PetscLogStageRegister("Preamble", &stage0);CHKERRQ(ierr); */ 74 /* } */ 75 /* ierr = PetscLogStagePush(stage0);CHKERRQ(ierr); */ 76 /* check for matrix container for GPU assembly */ 77 ierr = PetscLogEventBegin(ctx->events[10],0,0,0,0);CHKERRQ(ierr); 78 ierr = PetscObjectQuery((PetscObject) JacP, "assembly_maps", (PetscObject *) &container);CHKERRQ(ierr); 79 if (container /* && ctx->deviceType != LANDAU_CPU */) { 80 if (!ctx->gpu_assembly) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"GPU matrix container but no GPU assembly"); 81 ierr = PetscContainerGetPointer(container, (void **) &maps);CHKERRQ(ierr); 82 if (!maps) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"empty GPU matrix container"); 83 } 84 ierr = DMConvert(ctx->dmv, DMPLEX, &plex);CHKERRQ(ierr); 85 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 86 ierr = DMGetLocalSection(plex, §ion);CHKERRQ(ierr); 87 ierr = DMGetGlobalSection(plex, &globsection);CHKERRQ(ierr); 88 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 89 ierr = PetscDSGetTabulation(prob, &Tf);CHKERRQ(ierr); // Bf, &Df 90 ierr = PetscDSGetDimensions(prob, &Nbf);CHKERRQ(ierr); Nb = Nbf[0]; /* number of vertices*S */ 91 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); if (Nf!=ctx->num_species) SETERRQ1(ctx->comm, PETSC_ERR_PLIB, "Nf %D != S",Nf); 92 ierr = PetscDSGetComponents(prob, &Ncf);CHKERRQ(ierr); Ncx = Ncf[0]; if (Ncx!=1) SETERRQ1(ctx->comm, PETSC_ERR_PLIB, "Nc %D != 1",Ncx); 93 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 94 numCells = cEnd - cStart; 95 ierr = PetscFEGetQuadrature(ctx->fe[0], &quad);CHKERRQ(ierr); 96 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights);CHKERRQ(ierr); 97 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); 98 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); 99 if (LANDAU_DIM != dim) SETERRQ2(ctx->comm, PETSC_ERR_PLIB, "dim %D != LANDAU_DIM %d",dim,LANDAU_DIM); 100 if (!ctx->SData_d) { 101 ierr = PetscNew(&ctx->SData_d);CHKERRQ(ierr); 102 } 103 elemMatSize = totDim*totDim; // used for CPU and print info 104 ierr = PetscLogEventEnd(ctx->events[10],0,0,0,0);CHKERRQ(ierr); 105 //ierr = PetscLogStagePop();CHKERRQ(ierr); 106 ierr = VecGetSize(a_X,&N);CHKERRQ(ierr); 107 if (!ctx->init) { /* create static point data, Jacobian called first */ 108 PetscReal *invJ,*ww,*xx,*yy,*zz=NULL,*mass_w,*invJ_a; 109 const PetscInt nip = Nq*numCells; 110 111 ierr = PetscLogEventBegin(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 112 ctx->init = PETSC_TRUE; 113 ierr = PetscInfo(plex, "Initialize static data\n");CHKERRQ(ierr); 114 /* collect f data, first time is for Jacobian, but make mass now */ 115 if (ctx->verbose > 1 || ctx->verbose > 0) { 116 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 shift=%g\n", 117 0,"FormLandau",Nq*numCells,numCells, totDim, Nb, Nq, elemMatSize, dim, Tf[0]->Nb, Nf, Tf[0]->Np, Tf[0]->cdim, N, shift);CHKERRQ(ierr); 118 } 119 ierr = PetscMalloc5(nip,&mass_w,nip,&ww,nip,&xx,nip,&yy,nip*dim*dim,&invJ_a);CHKERRQ(ierr); 120 if (dim==3) { 121 ierr = PetscMalloc1(nip,&zz);CHKERRQ(ierr); 122 } 123 for (ej = 0 ; ej < numCells; ++ej) { 124 PetscReal vj[LANDAU_MAX_NQ*LANDAU_DIM],detJj[LANDAU_MAX_NQ], Jdummy[LANDAU_MAX_NQ*LANDAU_DIM*LANDAU_DIM]; 125 invJ = invJ_a ? invJ_a + ej * Nq*dim*dim : NULL; 126 ierr = DMPlexComputeCellGeometryFEM(plex, cStart+ej, quad, vj, Jdummy, invJ, detJj);CHKERRQ(ierr); 127 /* create dynamic point data */ 128 for (qj = 0; qj < Nq; ++qj) { 129 PetscInt gidx = (ej*Nq + qj); 130 mass_w[gidx] = detJj[qj] * quadWeights[qj]; 131 if (dim==2) mass_w[gidx] *= 2.*PETSC_PI*vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */ 132 xx[gidx] = vj[qj * dim + 0]; /* coordinate */ 133 yy[gidx] = vj[qj * dim + 1]; 134 if (dim==3) zz[gidx] = vj[qj * dim + 2]; 135 ww[gidx] = detJj[qj] * quadWeights[qj]; 136 if (dim==2) ww[gidx] *= xx[gidx]; /* cylindrical coordinate, w/o 2pi */ 137 } /* q */ 138 } /* ej */ 139 /* cache static data */ 140 if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) { 141 #if defined(PETSC_HAVE_CUDA) || defined(PETSC_HAVE_KOKKOS) 142 PetscReal invMass[LANDAU_MAX_SPECIES],nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES]; 143 for (fieldA=0;fieldA<Nf;fieldA++) { 144 invMass[fieldA] = m_0/ctx->masses[fieldA]; 145 nu_alpha[fieldA] = PetscSqr(ctx->charges[fieldA]/m_0)*m_0/ctx->masses[fieldA]; 146 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); 147 } 148 if (ctx->deviceType == LANDAU_CUDA) { 149 #if defined(PETSC_HAVE_CUDA) 150 ierr = LandauCUDAStaticDataSet(plex,Nq,nu_alpha,nu_beta,invMass,invJ_a,mass_w,xx,yy,zz,ww,ctx->SData_d);CHKERRQ(ierr); 151 #else 152 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 153 #endif 154 } else if (ctx->deviceType == LANDAU_KOKKOS) { 155 #if defined(PETSC_HAVE_KOKKOS) 156 ierr = LandauKokkosStaticDataSet(plex,Nq,nu_alpha,nu_beta,invMass,invJ_a,mass_w,xx,yy,zz,ww,ctx->SData_d);CHKERRQ(ierr); 157 #else 158 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 159 #endif 160 } 161 #endif 162 /* free */ 163 ierr = PetscFree5(mass_w,ww,xx,yy,invJ_a);CHKERRQ(ierr); 164 if (dim==3) { 165 ierr = PetscFree(zz);CHKERRQ(ierr); 166 } 167 } else { /* CPU version, just copy in, only use part */ 168 ctx->SData_d->w = (void*)ww; 169 ctx->SData_d->x = (void*)xx; 170 ctx->SData_d->y = (void*)yy; 171 ctx->SData_d->z = (void*)zz; 172 ctx->SData_d->invJ = (void*)invJ_a; 173 ctx->SData_d->mass_w = (void*)mass_w; 174 } 175 ierr = PetscLogEventEnd(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 176 } 177 if (shift==0) { /* create dynamic point data */ 178 ierr = PetscLogEventBegin(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 179 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 180 flops = (PetscLogDouble)numCells*(PetscLogDouble)Nq*(PetscLogDouble)(5*dim*dim*Nf*Nf + 165); 181 for (fieldA=0;fieldA<Nf;fieldA++) { 182 Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */ 183 if (dim==2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */ 184 } 185 if (!ctx->gpu_assembly || !container) { 186 Vec locX; 187 ierr = DMGetLocalVector(plex, &locX);CHKERRQ(ierr); 188 ierr = VecZeroEntries(locX);CHKERRQ(ierr); /* zero BCs so don't set */ 189 ierr = DMGlobalToLocalBegin(plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 190 ierr = DMGlobalToLocalEnd (plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 191 ierr = PetscMalloc1(Nq*numCells*Nf,&IPf);CHKERRQ(ierr); 192 for (ej = 0 ; ej < numCells; ++ej) { 193 PetscScalar *coef = NULL; 194 ierr = DMPlexVecGetClosure(plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 195 ierr = PetscMemcpy(&IPf[ej*Nb*Nf],coef,Nb*Nf*sizeof(PetscScalar));CHKERRQ(ierr); /* change if LandauIPReal != PetscScalar */ 196 ierr = DMPlexVecRestoreClosure(plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 197 } /* ej */ 198 ierr = DMRestoreLocalVector(plex, &locX);CHKERRQ(ierr); 199 } else { 200 ierr = VecGetArrayRead(a_X,&xarray);CHKERRQ(ierr); 201 } 202 ierr = PetscLogEventEnd(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 203 } else { 204 flops = (PetscLogDouble)numCells*(PetscLogDouble)Nq*(PetscLogDouble)(5*dim*dim*Nf*Nf); 205 } 206 /* do it */ 207 if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) { 208 /* static PetscLogStage stage0 = 0; */ 209 /* if (!stage0) { */ 210 /* ierr = PetscLogStageRegister("Landau", &stage0);CHKERRQ(ierr); */ 211 /* } */ 212 /* ierr = PetscLogStagePush(stage0);CHKERRQ(ierr); */ 213 if (ctx->deviceType == LANDAU_CUDA) { 214 #if defined(PETSC_HAVE_CUDA) 215 ierr = LandauCUDAJacobian(plex,Nq,Eq_m,IPf,N,xarray,ctx->SData_d,ctx->subThreadBlockSize,shift,ctx->events,JacP);CHKERRQ(ierr); 216 #else 217 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 218 #endif 219 } else if (ctx->deviceType == LANDAU_KOKKOS) { 220 #if defined(PETSC_HAVE_KOKKOS) 221 ierr = LandauKokkosJacobian(plex,Nq,Eq_m,IPf,ctx->SData_d,ctx->subThreadBlockSize,shift,ctx->events,JacP);CHKERRQ(ierr); 222 #else 223 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 224 #endif 225 } 226 //ierr = PetscLogStagePop();CHKERRQ(ierr); 227 } else { /* CPU version */ 228 PetscInt ei, qi; 229 PetscScalar *elemMat,coef_buff[LANDAU_MAX_SPECIES*LANDAU_MAX_NQ]; 230 PetscReal *ff, *dudx, *dudy, *dudz, *invJ, *invJ_a = (PetscReal*)ctx->SData_d->invJ, *xx = (PetscReal*)ctx->SData_d->x, *yy = (PetscReal*)ctx->SData_d->y, *zz = (PetscReal*)ctx->SData_d->z, *ww = (PetscReal*)ctx->SData_d->w, *mass_w = (PetscReal*)ctx->SData_d->mass_w; 231 const PetscInt nip = Nq*numCells; 232 const PetscReal *const BB = Tf[0]->T[0], * const DD = Tf[0]->T[1]; 233 PetscReal Eq_m[LANDAU_MAX_SPECIES], invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES]; 234 if (shift!=0.0) { // mass 235 ierr = PetscMalloc1(elemMatSize, &elemMat);CHKERRQ(ierr); 236 } else { /* compute f and df and init data for Jacobian */ 237 ierr = PetscLogEventBegin(ctx->events[8],0,0,0,0);CHKERRQ(ierr); 238 for (fieldA=0;fieldA<Nf;fieldA++) { 239 invMass[fieldA] = m_0/ctx->masses[fieldA]; 240 Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */ 241 if (dim==2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */ 242 nu_alpha[fieldA] = PetscSqr(ctx->charges[fieldA]/m_0)*m_0/ctx->masses[fieldA]; 243 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); 244 } 245 ierr = PetscMalloc5(elemMatSize, &elemMat, nip*Nf, &ff, nip*Nf, &dudx, nip*Nf, &dudy, dim==3 ? nip*Nf : 0, &dudz);CHKERRQ(ierr); 246 for (ei = cStart, invJ = invJ_a; ei < cEnd; ++ei, invJ += Nq*dim*dim) { 247 PetscScalar *coef; 248 PetscInt b,f,idx,q; 249 PetscReal u_x[LANDAU_MAX_SPECIES][LANDAU_DIM]; 250 if (IPf) { 251 coef = &IPf[ei*Nb*Nf]; // this is const 252 /* for (f = 0; f < Nf; ++f) { */ 253 /* for (b = 0; b < Nb; ++b) { */ 254 /* PetscPrintf(ctx->comm,"%f ",coef[f*Nb+b]);CHKERRQ(ierr); */ 255 /* } */ 256 /* PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr); */ 257 /* } */ 258 /* PetscPrintf(ctx->comm,"*\n");CHKERRQ(ierr); */ 259 } else { 260 if (!maps) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"!maps"); 261 coef = coef_buff; 262 for (f = 0; f < Nf; ++f) { 263 LandauIdx *const Idxs = &maps->gIdx[ei-cStart][f][0]; 264 for (b = 0; b < Nb; ++b) { 265 idx = Idxs[b]; 266 if (idx >= 0) { 267 coef[f*Nb+b] = xarray[idx]; 268 } else { 269 idx = -idx - 1; 270 coef[f*Nb+b] = 0; 271 for (q = 0; q < maps->num_face; q++) { 272 PetscInt id = maps->c_maps[idx][q].gid; 273 PetscScalar scale = maps->c_maps[idx][q].scale; 274 coef[f*Nb+b] += scale*xarray[id]; 275 } 276 } 277 //PetscPrintf(ctx->comm,"%f ",coef[f*Nb+b]);CHKERRQ(ierr); 278 } 279 //PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr); 280 } 281 //PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr); 282 } 283 /* get f and df */ 284 for (qi = 0; qi < Nq; ++qi) { 285 const PetscReal *Bq = &BB[qi*Nb]; 286 const PetscReal *Dq = &DD[qi*Nb*dim]; 287 const PetscInt gidx = ei*Nq + qi; 288 /* get f & df */ 289 for (f = 0; f < Nf; ++f) { 290 PetscInt b, e; 291 PetscReal refSpaceDer[LANDAU_DIM]; 292 ff[gidx + f*nip] = 0.0; 293 for (d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0; 294 for (b = 0; b < Nb; ++b) { 295 const PetscInt cidx = b; 296 ff[gidx + f*nip] += Bq[cidx]*PetscRealPart(coef[f*Nb+cidx]); 297 for (d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx*dim+d]*PetscRealPart(coef[f*Nb+cidx]); 298 } 299 for (d = 0; d < dim; ++d) { 300 for (e = 0, u_x[f][d] = 0.0; e < dim; ++e) { 301 u_x[f][d] += invJ[qi * dim * dim + e*dim+d]*refSpaceDer[e]; 302 } 303 } 304 } 305 for (f=0;f<Nf;f++) { 306 dudx[gidx + f*nip] = u_x[f][0]; 307 dudy[gidx + f*nip] = u_x[f][1]; 308 #if LANDAU_DIM==3 309 dudz[gidx + f*nip] = u_x[f][2]; 310 #endif 311 } 312 } 313 } 314 ierr = PetscLogEventEnd(ctx->events[8],0,0,0,0);CHKERRQ(ierr); 315 } 316 for (ej = cStart, invJ = invJ_a; ej < cEnd; ++ej, invJ += Nq*dim*dim) { 317 ierr = PetscMemzero(elemMat, totDim *totDim * sizeof(PetscScalar));CHKERRQ(ierr); 318 ierr = PetscLogEventBegin(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 319 ierr = PetscLogFlops((PetscLogDouble)Nq*flops);CHKERRQ(ierr); 320 //printf("\t:%d.%d) Invj[0] = %e (%d)\n",ej,qj,invJ[0],(int)(invJ-invJ_a)); 321 for (qj = 0; qj < Nq; ++qj) { 322 const PetscReal * const BB = Tf[0]->T[0], * const DD = Tf[0]->T[1]; 323 PetscReal g0[LANDAU_MAX_SPECIES], g2[LANDAU_MAX_SPECIES][LANDAU_DIM], g3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM]; 324 PetscInt d,d2,dp,d3,ipidx,fieldA; 325 const PetscInt jpidx = Nq*(ej-cStart) + qj; 326 if (shift==0.0) { 327 const PetscReal * const invJj = &invJ[qj*dim*dim]; 328 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]; 329 const PetscReal vj[3] = {xx[jpidx], yy[jpidx], zz ? zz[jpidx] : 0}, wj = ww[jpidx]; 330 331 // create g2 & g3 332 for (d=0;d<dim;d++) { // clear accumulation data D & K 333 gg2_temp[d] = 0; 334 for (d2=0;d2<dim;d2++) gg3_temp[d][d2] = 0; 335 } 336 for (ipidx = 0; ipidx < nip; ipidx++) { 337 const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx]; 338 PetscReal temp1[3] = {0, 0, 0}, temp2 = 0; 339 #if LANDAU_DIM==2 340 PetscReal Ud[2][2], Uk[2][2]; 341 LandauTensor2D(vj, x, y, Ud, Uk, (ipidx==jpidx) ? 0. : 1.); 342 #else 343 PetscReal U[3][3], z = zz[ipidx]; 344 LandauTensor3D(vj, x, y, z, U, (ipidx==jpidx) ? 0. : 1.); 345 #endif 346 for (fieldA = 0; fieldA < Nf; ++fieldA) { 347 temp1[0] += dudx[ipidx + fieldA*nip]*nu_beta[fieldA]*invMass[fieldA]; 348 temp1[1] += dudy[ipidx + fieldA*nip]*nu_beta[fieldA]*invMass[fieldA]; 349 #if LANDAU_DIM==3 350 temp1[2] += dudz[ipidx + fieldA*nip]*nu_beta[fieldA]*invMass[fieldA]; 351 #endif 352 temp2 += ff[ipidx + fieldA*nip]*nu_beta[fieldA]; 353 } 354 temp1[0] *= wi; 355 temp1[1] *= wi; 356 #if LANDAU_DIM==3 357 temp1[2] *= wi; 358 #endif 359 temp2 *= wi; 360 #if LANDAU_DIM==2 361 for (d2 = 0; d2 < 2; d2++) { 362 for (d3 = 0; d3 < 2; ++d3) { 363 /* K = U * grad(f): g2=e: i,A */ 364 gg2_temp[d2] += Uk[d2][d3]*temp1[d3]; 365 /* D = -U * (I \kron (fx)): g3=f: i,j,A */ 366 gg3_temp[d2][d3] += Ud[d2][d3]*temp2; 367 } 368 } 369 #else 370 for (d2 = 0; d2 < 3; ++d2) { 371 for (d3 = 0; d3 < 3; ++d3) { 372 /* K = U * grad(f): g2 = e: i,A */ 373 gg2_temp[d2] += U[d2][d3]*temp1[d3]; 374 /* D = -U * (I \kron (fx)): g3 = f: i,j,A */ 375 gg3_temp[d2][d3] += U[d2][d3]*temp2; 376 } 377 } 378 #endif 379 } /* IPs */ 380 //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]); 381 // add alpha and put in gg2/3 382 for (fieldA = 0; fieldA < Nf; ++fieldA) { 383 for (d2 = 0; d2 < dim; d2++) { 384 gg2[fieldA][d2] = gg2_temp[d2]*nu_alpha[fieldA]; 385 for (d3 = 0; d3 < dim; d3++) { 386 gg3[fieldA][d2][d3] = -gg3_temp[d2][d3]*nu_alpha[fieldA]*invMass[fieldA]; 387 } 388 } 389 } 390 /* add electric field term once per IP */ 391 for (fieldA = 0; fieldA < Nf; ++fieldA) { 392 gg2[fieldA][dim-1] += Eq_m[fieldA]; 393 //printf("\t:%d.%d.%d) gg2 = %e %e\n",ej,qj,fieldA,gg2[fieldA][dim-1],Eq_m[fieldA]); 394 } 395 /* Jacobian transform - g2, g3 */ 396 for (fieldA = 0; fieldA < Nf; ++fieldA) { 397 for (d = 0; d < dim; ++d) { 398 g2[fieldA][d] = 0.0; 399 for (d2 = 0; d2 < dim; ++d2) { 400 //printf("\t:%d.%d.%d.%d.%d) gg2 = %e += %e (%d) %e\n",ej,qj,fieldA,d,d2,g2[fieldA][d],invJj[d*dim+d2],(int)(&invJj[d*dim+d2]-invJ_a),gg2[fieldA][d2]); 401 g2[fieldA][d] += invJj[d*dim+d2]*gg2[fieldA][d2]; 402 g3[fieldA][d][d2] = 0.0; 403 for (d3 = 0; d3 < dim; ++d3) { 404 for (dp = 0; dp < dim; ++dp) { 405 g3[fieldA][d][d2] += invJj[d*dim + d3]*gg3[fieldA][d3][dp]*invJj[d2*dim + dp]; 406 } 407 } 408 g3[fieldA][d][d2] *= wj; 409 } 410 //printf("\t:%d.%d.%d.%d) g2 = %e %e\n",ej,qj,fieldA,d,g2[fieldA][d],wj); 411 g2[fieldA][d] *= wj; 412 } 413 } 414 } else { // mass 415 /* Jacobian transform - g0 */ 416 for (fieldA = 0; fieldA < Nf; ++fieldA) { 417 g0[fieldA] = mass_w[jpidx] * shift; // move this to below and remove g0 418 } 419 } 420 /* FE matrix construction */ 421 { 422 PetscInt fieldA,d,f,d2,g; 423 const PetscReal *BJq = &BB[qj*Nb], *DIq = &DD[qj*Nb*dim]; 424 /* assemble - on the diagonal (I,I) */ 425 for (fieldA = 0; fieldA < Nf ; fieldA++) { 426 for (f = 0; f < Nb ; f++) { 427 const PetscInt i = fieldA*Nb + f; /* Element matrix row */ 428 for (g = 0; g < Nb; ++g) { 429 const PetscInt j = fieldA*Nb + g; /* Element matrix column */ 430 const PetscInt fOff = i*totDim + j; 431 if (shift==0.0) { 432 for (d = 0; d < dim; ++d) { 433 elemMat[fOff] += DIq[f*dim+d]*g2[fieldA][d]*BJq[g]; 434 //printf("\t:%d.%d.%d.%d.%d.%d) elemMat=%e += %e %e %e\n",ej,qj,fieldA,f,g,d,elemMat[fOff],DIq[f*dim+d],g2[fieldA][d],BJq[g]); 435 for (d2 = 0; d2 < dim; ++d2) { 436 elemMat[fOff] += DIq[f*dim + d]*g3[fieldA][d][d2]*DIq[g*dim + d2]; 437 } 438 } 439 } else { // mass 440 elemMat[fOff] += BJq[f]*g0[fieldA]*BJq[g]; 441 } 442 } 443 } 444 } 445 } 446 } /* qj loop */ 447 ierr = PetscLogEventEnd(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 448 /* assemble matrix */ 449 ierr = PetscLogEventBegin(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 450 if (!maps) { 451 ierr = DMPlexMatSetClosure(plex, section, globsection, JacP, ej, elemMat, ADD_VALUES);CHKERRQ(ierr); 452 } else { // GPU like assembly for debugging 453 PetscInt fieldA,idx,q,f,g,d,nr,nc,rows0[LANDAU_MAX_Q_FACE],cols0[LANDAU_MAX_Q_FACE]={0},rows[LANDAU_MAX_Q_FACE],cols[LANDAU_MAX_Q_FACE]; 454 PetscScalar vals[LANDAU_MAX_Q_FACE*LANDAU_MAX_Q_FACE],row_scale[LANDAU_MAX_Q_FACE],col_scale[LANDAU_MAX_Q_FACE]={0}; 455 //for (q = 0; q <LANDAU_MAX_Q_FACE; q++) cols0[q] = 0; 456 //for (q = 0; q < LANDAU_MAX_Q_FACE; q++) col_scale[q] = 0.0; // suppress warnings 457 /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */ 458 for (fieldA = 0; fieldA < Nf ; fieldA++) { 459 LandauIdx *const Idxs = &maps->gIdx[ej-cStart][fieldA][0]; 460 for (f = 0; f < Nb ; f++) { 461 idx = Idxs[f]; 462 if (idx >= 0) { 463 nr = 1; 464 rows0[0] = idx; 465 row_scale[0] = 1.; 466 } else { 467 idx = -idx - 1; 468 nr = maps->num_face; 469 for (q = 0; q < maps->num_face; q++) { 470 rows0[q] = maps->c_maps[idx][q].gid; 471 row_scale[q] = maps->c_maps[idx][q].scale; 472 } 473 } 474 for (g = 0; g < Nb; ++g) { 475 idx = Idxs[g]; 476 if (idx >= 0) { 477 nc = 1; 478 cols0[0] = idx; 479 col_scale[0] = 1.; 480 } else { 481 idx = -idx - 1; 482 nc = maps->num_face; 483 for (q = 0; q < maps->num_face; q++) { 484 cols0[q] = maps->c_maps[idx][q].gid; 485 col_scale[q] = maps->c_maps[idx][q].scale; 486 } 487 } 488 const PetscInt i = fieldA*Nb + f; /* Element matrix row */ 489 const PetscInt j = fieldA*Nb + g; /* Element matrix column */ 490 const PetscScalar Aij = elemMat[i*totDim + j]; 491 for (q = 0; q < nr; q++) rows[q] = rows0[q]; 492 for (q = 0; q < nc; q++) cols[q] = cols0[q]; 493 for (q = 0; q < nr; q++) { 494 for (d = 0; d < nc; d++) { 495 vals[q*nc + d] = row_scale[q]*col_scale[d]*Aij; 496 } 497 } 498 ierr = MatSetValues(JacP,nr,rows,nc,cols,vals,ADD_VALUES);CHKERRQ(ierr); 499 } 500 } 501 } 502 } 503 if (ej==-1) { 504 PetscErrorCode ierr2; 505 ierr2 = PetscPrintf(ctx->comm,"CPU Element matrix\n");CHKERRQ(ierr2); 506 for (d = 0; d < totDim; ++d){ 507 for (f = 0; f < totDim; ++f) {ierr2 = PetscPrintf(ctx->comm," %12.5e", PetscRealPart(elemMat[d*totDim + f]));CHKERRQ(ierr2);} 508 ierr2 = PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr2); 509 } 510 exit(12); 511 } 512 ierr = PetscLogEventEnd(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 513 } /* ej cells loop, not cuda */ 514 if (shift!=0.0) { // mass 515 ierr = PetscFree(elemMat);CHKERRQ(ierr); 516 } else { 517 ierr = PetscFree5(elemMat, ff, dudx, dudy, dudz);CHKERRQ(ierr); 518 } 519 } /* CPU version */ 520 521 /* assemble matrix or vector */ 522 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 523 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 524 #define MAP_BF_SIZE (128*LANDAU_DIM*LANDAU_MAX_Q_FACE*LANDAU_MAX_SPECIES) 525 if (ctx->gpu_assembly && !container) { 526 PetscScalar elemMatrix[LANDAU_MAX_NQ*LANDAU_MAX_NQ*LANDAU_MAX_SPECIES*LANDAU_MAX_SPECIES], *elMat; 527 pointInterpolationP4est pointMaps[MAP_BF_SIZE][LANDAU_MAX_Q_FACE]; 528 PetscInt q,eidx,fieldA; 529 MatType type; 530 ierr = PetscInfo1(plex, "Make GPU maps %D\n",1);CHKERRQ(ierr); 531 ierr = MatGetType(JacP,&type);CHKERRQ(ierr); 532 ierr = PetscLogEventBegin(ctx->events[2],0,0,0,0);CHKERRQ(ierr); 533 ierr = PetscMalloc(sizeof(P4estVertexMaps), &maps);CHKERRQ(ierr); 534 ierr = PetscContainerCreate(PETSC_COMM_SELF, &container);CHKERRQ(ierr); 535 ierr = PetscContainerSetPointer(container, (void *)maps);CHKERRQ(ierr); 536 ierr = PetscContainerSetUserDestroy(container, LandauGPUMapsDestroy);CHKERRQ(ierr); 537 ierr = PetscObjectCompose((PetscObject) JacP, "assembly_maps", (PetscObject) container);CHKERRQ(ierr); 538 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 539 // make maps 540 maps->data = NULL; 541 maps->num_elements = numCells; 542 maps->num_face = (PetscInt)(pow(Nq,1./((double)dim))+.001); // Q 543 maps->num_face = (PetscInt)(pow(maps->num_face,(double)(dim-1))+.001); // Q^2 544 maps->num_reduced = 0; 545 maps->deviceType = ctx->deviceType; 546 547 // count reduced and get 548 ierr = PetscMalloc(maps->num_elements * sizeof *maps->gIdx, &maps->gIdx);CHKERRQ(ierr); 549 for (fieldA=0;fieldA<Nf;fieldA++) { 550 for (ej = cStart, eidx = 0 ; ej < cEnd; ++ej, ++eidx) { 551 for (q = 0; q < Nb; ++q) { 552 PetscInt numindices,*indices; 553 PetscScalar *valuesOrig = elMat = elemMatrix; 554 ierr = PetscMemzero(elMat, totDim*totDim*sizeof(PetscScalar));CHKERRQ(ierr); 555 elMat[ (fieldA*Nb + q)*totDim + fieldA*Nb + q] = 1; 556 ierr = DMPlexGetClosureIndices(plex, section, globsection, ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 557 for (f = 0 ; f < numindices ; ++f) { // look for a non-zero on the diagonal 558 if (PetscAbs(PetscRealPart(elMat[f*numindices + f])) > PETSC_MACHINE_EPSILON) { 559 // found it 560 if (PetscAbs(PetscRealPart(elMat[f*numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { 561 maps->gIdx[eidx][fieldA][q] = (LandauIdx)indices[f]; // normal vertex 1.0 562 } else { //found a constraint 563 int jj = 0; 564 PetscReal sum = 0; 565 const PetscInt ff = f; 566 maps->gIdx[eidx][fieldA][q] = -maps->num_reduced - 1; // gid = -(idx+1): idx = -gid - 1 567 do { // constraints are continous in Plex - exploit that here 568 int ii; 569 for (ii = 0, pointMaps[maps->num_reduced][jj].scale = 0; ii < maps->num_face; ii++) { // DMPlex puts them all together 570 if (ff + ii < numindices) { 571 pointMaps[maps->num_reduced][jj].scale += PetscRealPart(elMat[f*numindices + ff + ii]); 572 } 573 } 574 sum += pointMaps[maps->num_reduced][jj].scale; 575 if (pointMaps[maps->num_reduced][jj].scale == 0) pointMaps[maps->num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps -- all contiguous??? 576 else pointMaps[maps->num_reduced][jj].gid = indices[f]; 577 } while (++jj < maps->num_face && ++f < numindices); // jj is incremented if we hit the end 578 while (jj++ < maps->num_face) { 579 pointMaps[maps->num_reduced][jj].scale = 0; 580 pointMaps[maps->num_reduced][jj].gid = -1; 581 } 582 if (PetscAbs(sum-1.0) > 10*PETSC_MACHINE_EPSILON) { // debug 583 int d,f; 584 PetscReal tmp = 0; 585 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,sum,LANDAU_MAX_Q_FACE,maps->num_face); 586 for (d = 0, tmp = 0; d < numindices; ++d){ 587 if (tmp!=0 && PetscAbs(tmp-1.0) > 10*PETSC_MACHINE_EPSILON) ierr = PetscPrintf(PETSC_COMM_WORLD,"%3D) %3D: ",d,indices[d]);CHKERRQ(ierr); 588 for (f = 0; f < numindices; ++f) { 589 tmp += PetscRealPart(elMat[d*numindices + f]); 590 } 591 if (tmp!=0) ierr = PetscPrintf(ctx->comm," | %22.16e\n",tmp);CHKERRQ(ierr); 592 } 593 } 594 maps->num_reduced++; 595 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); 596 } 597 break; 598 } 599 } 600 // cleanup 601 ierr = DMPlexRestoreClosureIndices(plex, section, globsection, ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 602 if (elMat != valuesOrig) {ierr = DMRestoreWorkArray(plex, numindices*numindices, MPIU_SCALAR, &elMat);} 603 } 604 } 605 } 606 // allocate and copy point datamaps->gIdx[eidx][field][q] -- for CPU version of this code, for debugging 607 ierr = PetscMalloc(maps->num_reduced * sizeof *maps->c_maps, &maps->c_maps);CHKERRQ(ierr); 608 for (ej = 0; ej < maps->num_reduced; ++ej) { 609 for (q = 0; q < maps->num_face; ++q) { 610 maps->c_maps[ej][q].scale = pointMaps[ej][q].scale; 611 maps->c_maps[ej][q].gid = pointMaps[ej][q].gid; 612 } 613 } 614 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 615 if (ctx->deviceType == LANDAU_KOKKOS) { 616 ierr = LandauKokkosCreateMatMaps(maps, pointMaps,Nf,Nq);CHKERRQ(ierr); // imples Kokkos does 617 } // else could be CUDA 618 #endif 619 #if defined(PETSC_HAVE_CUDA) 620 if (ctx->deviceType == LANDAU_CUDA){ 621 ierr = LandauCUDACreateMatMaps(maps, pointMaps,Nf,Nq);CHKERRQ(ierr); 622 } 623 #endif 624 625 ierr = PetscLogEventEnd(ctx->events[2],0,0,0,0);CHKERRQ(ierr); 626 } 627 /* clean up */ 628 ierr = DMDestroy(&plex);CHKERRQ(ierr); 629 if (IPf) { 630 ierr = PetscFree(IPf);CHKERRQ(ierr); 631 } 632 if (xarray) { 633 ierr = VecRestoreArrayRead(a_X,&xarray);CHKERRQ(ierr); 634 } 635 636 PetscFunctionReturn(0); 637 } 638 639 #if defined(LANDAU_ADD_BCS) 640 static void zero_bc(PetscInt dim, PetscInt Nf, PetscInt NfAux, 641 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 642 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 643 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar uexact[]) 644 { 645 uexact[0] = 0; 646 } 647 #endif 648 649 #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]; }} 650 static void CircleInflate(PetscReal r1, PetscReal r2, PetscReal r0, PetscInt num_sections, PetscReal x, PetscReal y, 651 PetscReal *outX, PetscReal *outY) 652 { 653 PetscReal rr = PetscSqrtReal(x*x + y*y), outfact, efact; 654 if (rr < r1 + PETSC_SQRT_MACHINE_EPSILON) { 655 *outX = x; *outY = y; 656 } else { 657 const PetscReal xy[2] = {x,y}, sinphi=y/rr, cosphi=x/rr; 658 PetscReal cth,sth,xyprime[2],Rth[2][2],rotcos,newrr; 659 if (num_sections==2) { 660 rotcos = 0.70710678118654; 661 outfact = 1.5; efact = 2.5; 662 /* rotate normalized vector into [-pi/4,pi/4) */ 663 if (sinphi >= 0.) { /* top cell, -pi/2 */ 664 cth = 0.707106781186548; sth = -0.707106781186548; 665 } else { /* bottom cell -pi/8 */ 666 cth = 0.707106781186548; sth = .707106781186548; 667 } 668 } else if (num_sections==3) { 669 rotcos = 0.86602540378443; 670 outfact = 1.5; efact = 2.5; 671 /* rotate normalized vector into [-pi/6,pi/6) */ 672 if (sinphi >= 0.5) { /* top cell, -pi/3 */ 673 cth = 0.5; sth = -0.866025403784439; 674 } else if (sinphi >= -.5) { /* mid cell 0 */ 675 cth = 1.; sth = .0; 676 } else { /* bottom cell +pi/3 */ 677 cth = 0.5; sth = 0.866025403784439; 678 } 679 } else if (num_sections==4) { 680 rotcos = 0.9238795325112; 681 outfact = 1.5; efact = 3; 682 /* rotate normalized vector into [-pi/8,pi/8) */ 683 if (sinphi >= 0.707106781186548) { /* top cell, -3pi/8 */ 684 cth = 0.38268343236509; sth = -0.923879532511287; 685 } else if (sinphi >= 0.) { /* mid top cell -pi/8 */ 686 cth = 0.923879532511287; sth = -.38268343236509; 687 } else if (sinphi >= -0.707106781186548) { /* mid bottom cell + pi/8 */ 688 cth = 0.923879532511287; sth = 0.38268343236509; 689 } else { /* bottom cell + 3pi/8 */ 690 cth = 0.38268343236509; sth = .923879532511287; 691 } 692 } else { 693 cth = 0.; sth = 0.; rotcos = 0; efact = 0; 694 } 695 Rth[0][0] = cth; Rth[0][1] =-sth; 696 Rth[1][0] = sth; Rth[1][1] = cth; 697 MATVEC2(Rth,xy,xyprime); 698 if (num_sections==2) { 699 newrr = xyprime[0]/rotcos; 700 } else { 701 PetscReal newcosphi=xyprime[0]/rr, rin = r1, rout = rr - rin; 702 PetscReal routmax = r0*rotcos/newcosphi - rin, nroutmax = r0 - rin, routfrac = rout/routmax; 703 newrr = rin + routfrac*nroutmax; 704 } 705 *outX = cosphi*newrr; *outY = sinphi*newrr; 706 /* grade */ 707 PetscReal fact,tt,rs,re, rr = PetscSqrtReal(PetscSqr(*outX) + PetscSqr(*outY)); 708 if (rr > r2) { rs = r2; re = r0; fact = outfact;} /* outer zone */ 709 else { rs = r1; re = r2; fact = efact;} /* electron zone */ 710 tt = (rs + PetscPowReal((rr - rs)/(re - rs),fact) * (re-rs)) / rr; 711 *outX *= tt; 712 *outY *= tt; 713 } 714 } 715 716 static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx) 717 { 718 LandauCtx *ctx = (LandauCtx*)a_ctx; 719 PetscReal r = abc[0], z = abc[1]; 720 if (ctx->inflate) { 721 PetscReal absR, absZ; 722 absR = PetscAbs(r); 723 absZ = PetscAbs(z); 724 CircleInflate(ctx->i_radius,ctx->e_radius,ctx->radius,ctx->num_sections,absR,absZ,&absR,&absZ); 725 r = (r > 0) ? absR : -absR; 726 z = (z > 0) ? absZ : -absZ; 727 } 728 xyz[0] = r; 729 xyz[1] = z; 730 if (dim==3) xyz[2] = abc[2]; 731 732 PetscFunctionReturn(0); 733 } 734 735 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) 736 { 737 PetscReal err = 0.0; 738 PetscInt f = *(PetscInt*)actx, j; 739 PetscFunctionBegin; 740 for (j = 0; j < dim; ++j) { 741 err += PetscSqr(PetscRealPart(u_x[f*dim+j])); 742 } 743 err = PetscRealPart(u[f]); /* just use rho */ 744 *error = volume * err; /* * (ctx->axisymmetric ? 2.*PETSC_PI * r : 1); */ 745 PetscFunctionReturn(0); 746 } 747 748 static PetscErrorCode LandauDMCreateVMesh(MPI_Comm comm, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM *dm) 749 { 750 PetscErrorCode ierr; 751 PetscReal radius = ctx->radius; 752 size_t len; 753 char fname[128] = ""; /* we can add a file if we want */ 754 755 PetscFunctionBegin; 756 /* create DM */ 757 ierr = PetscStrlen(fname, &len);CHKERRQ(ierr); 758 if (len) { 759 PetscInt dim2; 760 ierr = DMPlexCreateFromFile(comm, fname, ctx->interpolate, dm);CHKERRQ(ierr); 761 ierr = DMGetDimension(*dm, &dim2);CHKERRQ(ierr); 762 if (LANDAU_DIM != dim2) SETERRQ2(comm, PETSC_ERR_PLIB, "dim %D != LANDAU_DIM %d",dim2,LANDAU_DIM); 763 } else { /* p4est, quads */ 764 /* Create plex mesh of Landau domain */ 765 if (!ctx->sphere) { 766 PetscInt cells[] = {2,2,2}; 767 PetscReal lo[] = {-radius,-radius,-radius}, hi[] = {radius,radius,radius}; 768 DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim==2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 769 if (dim==2) { lo[0] = 0; cells[0] = 1; } 770 ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, cells, lo, hi, periodicity, PETSC_TRUE, dm);CHKERRQ(ierr); 771 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); /* needed for periodic */ 772 if (dim==3) {ierr = PetscObjectSetName((PetscObject) *dm, "cube");CHKERRQ(ierr);} 773 else {ierr = PetscObjectSetName((PetscObject) *dm, "half-plane");CHKERRQ(ierr);} 774 } else if (dim==2) { 775 PetscInt numCells,cells[16][4],i,j; 776 PetscInt numVerts; 777 PetscReal inner_radius1 = ctx->i_radius, inner_radius2 = ctx->e_radius; 778 PetscReal *flatCoords = NULL; 779 PetscInt *flatCells = NULL, *pcell; 780 if (ctx->num_sections==2) { 781 #if 1 782 numCells = 5; 783 numVerts = 10; 784 int cells2[][4] = { {0,1,4,3}, 785 {1,2,5,4}, 786 {3,4,7,6}, 787 {4,5,8,7}, 788 {6,7,8,9} }; 789 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 790 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 791 { 792 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 793 for (j = 0; j < numVerts-1; j++) { 794 PetscReal z, r, theta = -PETSC_PI/2 + (j%3) * PETSC_PI/2; 795 PetscReal rad = (j >= 6) ? inner_radius1 : (j >= 3) ? inner_radius2 : ctx->radius; 796 z = rad * PetscSinReal(theta); 797 coords[j][1] = z; 798 r = rad * PetscCosReal(theta); 799 coords[j][0] = r; 800 } 801 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 802 } 803 #else 804 numCells = 4; 805 numVerts = 8; 806 static int cells2[][4] = {{0,1,2,3}, 807 {4,5,1,0}, 808 {5,6,2,1}, 809 {6,7,3,2}}; 810 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 811 ierr = loc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 812 { 813 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 814 PetscInt j; 815 for (j = 0; j < 8; j++) { 816 PetscReal z, r; 817 PetscReal theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3.; 818 PetscReal rad = ctx->radius * ((j < 4) ? 0.5 : 1.0); 819 z = rad * PetscSinReal(theta); 820 coords[j][1] = z; 821 r = rad * PetscCosReal(theta); 822 coords[j][0] = r; 823 } 824 } 825 #endif 826 } else if (ctx->num_sections==3) { 827 numCells = 7; 828 numVerts = 12; 829 int cells2[][4] = { {0,1,5,4}, 830 {1,2,6,5}, 831 {2,3,7,6}, 832 {4,5,9,8}, 833 {5,6,10,9}, 834 {6,7,11,10}, 835 {8,9,10,11} }; 836 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 837 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 838 { 839 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 840 for (j = 0; j < numVerts; j++) { 841 PetscReal z, r, theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3; 842 PetscReal rad = (j >= 8) ? inner_radius1 : (j >= 4) ? inner_radius2 : ctx->radius; 843 z = rad * PetscSinReal(theta); 844 coords[j][1] = z; 845 r = rad * PetscCosReal(theta); 846 coords[j][0] = r; 847 } 848 } 849 } else if (ctx->num_sections==4) { 850 numCells = 10; 851 numVerts = 16; 852 int cells2[][4] = { {0,1,6,5}, 853 {1,2,7,6}, 854 {2,3,8,7}, 855 {3,4,9,8}, 856 {5,6,11,10}, 857 {6,7,12,11}, 858 {7,8,13,12}, 859 {8,9,14,13}, 860 {10,11,12,15}, 861 {12,13,14,15}}; 862 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 863 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 864 { 865 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 866 for (j = 0; j < numVerts-1; j++) { 867 PetscReal z, r, theta = -PETSC_PI/2 + (j%5) * PETSC_PI/4; 868 PetscReal rad = (j >= 10) ? inner_radius1 : (j >= 5) ? inner_radius2 : ctx->radius; 869 z = rad * PetscSinReal(theta); 870 coords[j][1] = z; 871 r = rad * PetscCosReal(theta); 872 coords[j][0] = r; 873 } 874 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 875 } 876 } else { 877 numCells = 0; 878 numVerts = 0; 879 } 880 for (j = 0, pcell = flatCells; j < numCells; j++, pcell += 4) { 881 pcell[0] = cells[j][0]; pcell[1] = cells[j][1]; 882 pcell[2] = cells[j][2]; pcell[3] = cells[j][3]; 883 } 884 ierr = DMPlexCreateFromCellListPetsc(comm,2,numCells,numVerts,4,ctx->interpolate,flatCells,2,flatCoords,dm);CHKERRQ(ierr); 885 ierr = PetscFree2(flatCoords,flatCells);CHKERRQ(ierr); 886 ierr = PetscObjectSetName((PetscObject) *dm, "semi-circle");CHKERRQ(ierr); 887 } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Velocity space meshes does not support cubed sphere"); 888 } 889 ierr = PetscObjectSetOptionsPrefix((PetscObject)*dm,prefix);CHKERRQ(ierr); 890 891 ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); /* Plex refine */ 892 893 { /* p4est? */ 894 char convType[256]; 895 PetscBool flg; 896 ierr = PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); 897 ierr = PetscOptionsFList("-dm_landau_type","Convert DMPlex to another format (should not be Plex!)","plexland.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); 898 ierr = PetscOptionsEnd(); 899 if (flg) { 900 DM dmforest; 901 ierr = DMConvert(*dm,convType,&dmforest);CHKERRQ(ierr); 902 if (dmforest) { 903 PetscBool isForest; 904 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 905 ierr = PetscObjectSetOptionsPrefix((PetscObject)dmforest,prefix);CHKERRQ(ierr); 906 ierr = DMIsForest(dmforest,&isForest);CHKERRQ(ierr); 907 if (isForest) { 908 if (ctx->sphere && ctx->inflate) { 909 ierr = DMForestSetBaseCoordinateMapping(dmforest,GeometryDMLandau,ctx);CHKERRQ(ierr); 910 } 911 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 912 ierr = DMDestroy(dm);CHKERRQ(ierr); 913 *dm = dmforest; 914 ctx->errorIndicator = ErrorIndicator_Simple; /* flag for Forest */ 915 } else SETERRQ(ctx->comm, PETSC_ERR_USER, "Converted to non Forest?"); 916 } else SETERRQ(ctx->comm, PETSC_ERR_USER, "Convert failed?"); 917 } 918 } 919 ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); 920 PetscFunctionReturn(0); 921 } 922 923 static PetscErrorCode SetupDS(DM dm, PetscInt dim, LandauCtx *ctx) 924 { 925 PetscErrorCode ierr; 926 PetscInt ii; 927 PetscFunctionBegin; 928 for (ii=0;ii<ctx->num_species;ii++) { 929 char buf[256]; 930 if (ii==0) ierr = PetscSNPrintf(buf, 256, "e"); 931 else {ierr = PetscSNPrintf(buf, 256, "i%D", ii);CHKERRQ(ierr);} 932 /* Setup Discretization - FEM */ 933 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &ctx->fe[ii]);CHKERRQ(ierr); 934 ierr = PetscObjectSetName((PetscObject) ctx->fe[ii], buf);CHKERRQ(ierr); 935 ierr = DMSetField(dm, ii, NULL, (PetscObject) ctx->fe[ii]);CHKERRQ(ierr); 936 } 937 ierr = DMCreateDS(dm);CHKERRQ(ierr); 938 if (1) { 939 PetscInt ii; 940 PetscSection section; 941 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 942 for (ii=0;ii<ctx->num_species;ii++){ 943 char buf[256]; 944 if (ii==0) ierr = PetscSNPrintf(buf, 256, "se"); 945 else ierr = PetscSNPrintf(buf, 256, "si%D", ii); 946 ierr = PetscSectionSetComponentName(section, ii, 0, buf);CHKERRQ(ierr); 947 } 948 } 949 PetscFunctionReturn(0); 950 } 951 952 /* Define a Maxwellian function for testing out the operator. */ 953 954 /* Using cartesian velocity space coordinates, the particle */ 955 /* density, [1/m^3], is defined according to */ 956 957 /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */ 958 959 /* Using some constant, c, we normalize the velocity vector into a */ 960 /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */ 961 962 /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */ 963 964 /* Defining $\theta=2T/mc^2$, we thus find that the probability density */ 965 /* for finding the particle within the interval in a box dx^3 around x is */ 966 967 /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */ 968 969 typedef struct { 970 LandauCtx *ctx; 971 PetscReal kT_m; 972 PetscReal n; 973 PetscReal shift; 974 } MaxwellianCtx; 975 976 static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx) 977 { 978 MaxwellianCtx *mctx = (MaxwellianCtx*)actx; 979 LandauCtx *ctx = mctx->ctx; 980 PetscInt i; 981 PetscReal v2 = 0, theta = 2*mctx->kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 982 PetscFunctionBegin; 983 /* compute the exponents, v^2 */ 984 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 985 /* evaluate the Maxwellian */ 986 u[0] = mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 987 if (mctx->shift!=0.) { 988 v2 = 0; 989 for (i = 0; i < dim-1; ++i) v2 += x[i]*x[i]; 990 v2 += (x[dim-1]-mctx->shift)*(x[dim-1]-mctx->shift); 991 /* evaluate the shifted Maxwellian */ 992 u[0] += mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 993 } 994 PetscFunctionReturn(0); 995 } 996 997 /*@ 998 LandauAddMaxwellians - Add a Maxwellian distribution to a state 999 1000 Collective on X 1001 1002 Input Parameters: 1003 . dm - The mesh 1004 + time - Current time 1005 - temps - Temperatures of each species 1006 . ns - Number density of each species 1007 + actx - Landau context 1008 1009 Output Parameter: 1010 . X - The state 1011 1012 Level: beginner 1013 1014 .keywords: mesh 1015 .seealso: LandauCreateVelocitySpace() 1016 @*/ 1017 PetscErrorCode LandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], void *actx) 1018 { 1019 LandauCtx *ctx = (LandauCtx*)actx; 1020 PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar [], void *); 1021 PetscErrorCode ierr,ii; 1022 PetscInt dim; 1023 MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES]; 1024 1025 PetscFunctionBegin; 1026 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1027 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 1028 for (ii=0;ii<ctx->num_species;ii++) { 1029 mctxs[ii] = &data[ii]; 1030 data[ii].ctx = ctx; 1031 data[ii].kT_m = ctx->k*temps[ii]/ctx->masses[ii]; /* kT/m */ 1032 data[ii].n = ns[ii]; 1033 initu[ii] = maxwellian; 1034 data[ii].shift = 0; 1035 } 1036 data[0].shift = ctx->electronShift; 1037 /* need to make ADD_ALL_VALUES work - TODO */ 1038 ierr = DMProjectFunction(dm, time, initu, (void**)mctxs, INSERT_ALL_VALUES, X);CHKERRQ(ierr); 1039 PetscFunctionReturn(0); 1040 } 1041 1042 /* 1043 LandauSetInitialCondition - Addes Maxwellians with context 1044 1045 Collective on X 1046 1047 Input Parameters: 1048 . dm - The mesh 1049 + actx - Landau context with T and n 1050 1051 Output Parameter: 1052 . X - The state 1053 1054 Level: beginner 1055 1056 .keywords: mesh 1057 .seealso: LandauCreateVelocitySpace(), LandauAddMaxwellians() 1058 */ 1059 static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, void *actx) 1060 { 1061 LandauCtx *ctx = (LandauCtx*)actx; 1062 PetscErrorCode ierr; 1063 PetscFunctionBegin; 1064 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 1065 ierr = VecZeroEntries(X);CHKERRQ(ierr); 1066 ierr = LandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, ctx);CHKERRQ(ierr); 1067 PetscFunctionReturn(0); 1068 } 1069 1070 static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscReal refineTol[], PetscReal coarsenTol[], PetscInt type, LandauCtx *ctx, DM *newDM) 1071 { 1072 DM dm, plex, adaptedDM = NULL; 1073 PetscDS prob; 1074 PetscBool isForest; 1075 PetscQuadrature quad; 1076 PetscInt Nq, *Nb, cStart, cEnd, c, dim, qj, k; 1077 DMLabel adaptLabel = NULL; 1078 PetscErrorCode ierr; 1079 1080 PetscFunctionBegin; 1081 ierr = VecGetDM(sol, &dm);CHKERRQ(ierr); 1082 ierr = DMCreateDS(dm);CHKERRQ(ierr); 1083 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1084 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1085 ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr); 1086 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1087 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1088 ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr); 1089 ierr = PetscFEGetQuadrature(fem, &quad);CHKERRQ(ierr); 1090 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1091 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); 1092 ierr = PetscDSGetDimensions(prob, &Nb);CHKERRQ(ierr); 1093 if (type==4) { 1094 for (c = cStart; c < cEnd; c++) { 1095 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 1096 } 1097 ierr = PetscInfo1(sol, "Phase:%s: Uniform refinement\n","adaptToleranceFEM");CHKERRQ(ierr); 1098 } else if (type==2) { 1099 PetscInt rCellIdx[8], eCellIdx[64], iCellIdx[64], eMaxIdx = -1, iMaxIdx = -1, nr = 0, nrmax = (dim==3) ? 8 : 2; 1100 PetscReal minRad = PETSC_INFINITY, r, eMinRad = PETSC_INFINITY, iMinRad = PETSC_INFINITY; 1101 for (c = 0; c < 64; c++) { eCellIdx[c] = iCellIdx[c] = -1; } 1102 for (c = cStart; c < cEnd; c++) { 1103 PetscReal tt, v0[LANDAU_MAX_NQ*3], detJ[LANDAU_MAX_NQ]; 1104 ierr = DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ);CHKERRQ(ierr); 1105 for (qj = 0; qj < Nq; ++qj) { 1106 tt = PetscSqr(v0[dim*qj+0]) + PetscSqr(v0[dim*qj+1]) + PetscSqr(((dim==3) ? v0[dim*qj+2] : 0)); 1107 r = PetscSqrtReal(tt); 1108 if (r < minRad - PETSC_SQRT_MACHINE_EPSILON*10.) { 1109 minRad = r; 1110 nr = 0; 1111 rCellIdx[nr++]= c; 1112 ierr = PetscInfo4(sol, "\t\tPhase: adaptToleranceFEM Found first inner r=%e, cell %D, qp %D/%D\n", r, c, qj+1, Nq);CHKERRQ(ierr); 1113 } else if ((r-minRad) < PETSC_SQRT_MACHINE_EPSILON*100. && nr < nrmax) { 1114 for (k=0;k<nr;k++) if (c == rCellIdx[k]) break; 1115 if (k==nr) { 1116 rCellIdx[nr++]= c; 1117 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); 1118 } 1119 } 1120 if (ctx->sphere) { 1121 if ((tt=r-ctx->e_radius) > 0) { 1122 PetscInfo2(sol, "\t\t\t %D cell r=%g\n",c,tt); 1123 if (tt < eMinRad - PETSC_SQRT_MACHINE_EPSILON*100.) { 1124 eMinRad = tt; 1125 eMaxIdx = 0; 1126 eCellIdx[eMaxIdx++] = c; 1127 } else if (eMaxIdx > 0 && (tt-eMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != eCellIdx[eMaxIdx-1]) { 1128 eCellIdx[eMaxIdx++] = c; 1129 } 1130 } 1131 if ((tt=r-ctx->i_radius) > 0) { 1132 if (tt < iMinRad - 1.e-5) { 1133 iMinRad = tt; 1134 iMaxIdx = 0; 1135 iCellIdx[iMaxIdx++] = c; 1136 } else if (iMaxIdx > 0 && (tt-iMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != iCellIdx[iMaxIdx-1]) { 1137 iCellIdx[iMaxIdx++] = c; 1138 } 1139 } 1140 } 1141 } 1142 } 1143 for (k=0;k<nr;k++) { 1144 ierr = DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE);CHKERRQ(ierr); 1145 } 1146 if (ctx->sphere) { 1147 for (c = 0; c < eMaxIdx; c++) { 1148 ierr = DMLabelSetValue(adaptLabel, eCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 1149 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere e cell %D r=%g\n","adaptToleranceFEM",eCellIdx[c],eMinRad); 1150 } 1151 for (c = 0; c < iMaxIdx; c++) { 1152 ierr = DMLabelSetValue(adaptLabel, iCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 1153 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere i cell %D r=%g\n","adaptToleranceFEM",iCellIdx[c],iMinRad); 1154 } 1155 } 1156 ierr = PetscInfo4(sol, "Phase:%s: Adaptive refine origin cells %D,%D r=%g\n","adaptToleranceFEM",rCellIdx[0],rCellIdx[1],minRad); 1157 } else if (type==0 || type==1 || type==3) { /* refine along r=0 axis */ 1158 PetscScalar *coef = NULL; 1159 Vec coords; 1160 PetscInt csize,Nv,d,nz; 1161 DM cdm; 1162 PetscSection cs; 1163 ierr = DMGetCoordinatesLocal(dm, &coords);CHKERRQ(ierr); 1164 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1165 ierr = DMGetLocalSection(cdm, &cs);CHKERRQ(ierr); 1166 for (c = cStart; c < cEnd; c++) { 1167 PetscInt doit = 0, outside = 0; 1168 ierr = DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 1169 Nv = csize/dim; 1170 for (nz = d = 0; d < Nv; d++) { 1171 PetscReal z = PetscRealPart(coef[d*dim + (dim-1)]), x = PetscSqr(PetscRealPart(coef[d*dim + 0])) + ((dim==3) ? PetscSqr(PetscRealPart(coef[d*dim + 1])) : 0); 1172 x = PetscSqrtReal(x); 1173 if (x < PETSC_MACHINE_EPSILON*10. && PetscAbs(z)<PETSC_MACHINE_EPSILON*10.) doit = 1; /* refine origin */ 1174 else if (type==0 && (z < -PETSC_MACHINE_EPSILON*10. || z > ctx->re_radius+PETSC_MACHINE_EPSILON*10.)) outside++; /* first pass don't refine bottom */ 1175 else if (type==1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) outside++; /* don't refine outside electron refine radius */ 1176 else if (type==3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) outside++; /* don't refine outside ion refine radius */ 1177 if (x < PETSC_MACHINE_EPSILON*10.) nz++; 1178 } 1179 ierr = DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 1180 if (doit || (outside<Nv && nz)) { 1181 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 1182 } 1183 } 1184 ierr = PetscInfo1(sol, "Phase:%s: RE refinement\n","adaptToleranceFEM"); 1185 } 1186 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1187 ierr = DMAdaptLabel(dm, adaptLabel, &adaptedDM);CHKERRQ(ierr); 1188 ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); 1189 *newDM = adaptedDM; 1190 if (adaptedDM) { 1191 if (isForest) { 1192 ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr); 1193 } 1194 ierr = DMConvert(adaptedDM, DMPLEX, &plex);CHKERRQ(ierr); 1195 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1196 ierr = PetscInfo2(sol, "\tPhase: adaptToleranceFEM: %D cells, %d total quadrature points\n",cEnd-cStart,Nq*(cEnd-cStart));CHKERRQ(ierr); 1197 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1198 } 1199 PetscFunctionReturn(0); 1200 } 1201 1202 static PetscErrorCode adapt(DM *dm, LandauCtx *ctx, Vec *uu) 1203 { 1204 PetscErrorCode ierr; 1205 PetscInt type, limits[5] = {ctx->numRERefine,ctx->nZRefine1,ctx->maxRefIts,ctx->nZRefine2,ctx->postAMRRefine}; 1206 PetscInt adaptIter; 1207 1208 PetscFunctionBegin; 1209 for (type=0;type<5;type++) { 1210 for (adaptIter = 0; adaptIter<limits[type];adaptIter++) { 1211 DM dmNew = NULL; 1212 ierr = adaptToleranceFEM(ctx->fe[0], *uu, ctx->refineTol, ctx->coarsenTol, type, ctx, &dmNew);CHKERRQ(ierr); 1213 if (!dmNew) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"should not happen"); 1214 else { 1215 ierr = DMDestroy(dm);CHKERRQ(ierr); 1216 ierr = VecDestroy(uu);CHKERRQ(ierr); 1217 ierr = DMCreateGlobalVector(dmNew,uu);CHKERRQ(ierr); 1218 ierr = PetscObjectSetName((PetscObject) *uu, "u");CHKERRQ(ierr); 1219 ierr = LandauSetInitialCondition(dmNew, *uu, ctx);CHKERRQ(ierr); 1220 *dm = dmNew; 1221 } 1222 } 1223 } 1224 PetscFunctionReturn(0); 1225 } 1226 1227 static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[]) 1228 { 1229 PetscErrorCode ierr; 1230 PetscBool flg, sph_flg; 1231 PetscInt ii,nt,nm,nc; 1232 DM dummy; 1233 1234 PetscFunctionBegin; 1235 ierr = DMCreate(ctx->comm,&dummy);CHKERRQ(ierr); 1236 /* get options - initialize context */ 1237 ctx->verbose = 1; 1238 ctx->interpolate = PETSC_TRUE; 1239 ctx->gpu_assembly = PETSC_TRUE; 1240 ctx->sphere = PETSC_FALSE; 1241 ctx->inflate = PETSC_FALSE; 1242 ctx->electronShift = 0; 1243 ctx->errorIndicator = NULL; 1244 ctx->radius = 5.; /* electron thermal radius (velocity) */ 1245 ctx->re_radius = 0.; 1246 ctx->vperp0_radius1 = 0; 1247 ctx->vperp0_radius2 = 0; 1248 ctx->e_radius = .1; 1249 ctx->i_radius = .01; 1250 ctx->maxRefIts = 5; 1251 ctx->postAMRRefine = 0; 1252 ctx->nZRefine1 = 0; 1253 ctx->nZRefine2 = 0; 1254 ctx->numRERefine = 0; 1255 ctx->aux_bool = PETSC_FALSE; 1256 ctx->num_sections = 3; /* 2, 3 or 4 */ 1257 /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */ 1258 ctx->charges[0] = -1; /* electron charge (MKS) */ 1259 ctx->masses[0] = 1/1835.5; /* temporary value in proton mass */ 1260 ctx->n[0] = 1; 1261 ctx->thermal_temps[0] = 1; 1262 /* constants, etc. */ 1263 ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */ 1264 ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */ 1265 ctx->lnLam = 10; /* cross section ratio large - small angle collisions */ 1266 ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */ 1267 ctx->Ez = 0; 1268 ctx->v_0 = 1; /* in electron thermal velocity */ 1269 ctx->subThreadBlockSize = 1; /* for device and maybe OMP */ 1270 ctx->numConcurrency = 1; /* for device */ 1271 ctx->SData_d = NULL; /* for device */ 1272 ctx->times[0] = 0; 1273 ctx->init = PETSC_FALSE; // doit first time 1274 ctx->use_matrix_mass = PETSC_FALSE; /* fast but slightly fragile */ 1275 ierr = PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");CHKERRQ(ierr); 1276 { 1277 char opstring[256]; 1278 #if defined(PETSC_HAVE_KOKKOS) 1279 ctx->deviceType = LANDAU_KOKKOS; 1280 ierr = PetscStrcpy(opstring,"kokkos");CHKERRQ(ierr); 1281 #if defined(PETSC_HAVE_CUDA) 1282 ctx->subThreadBlockSize = 16; 1283 #endif 1284 #elif defined(PETSC_HAVE_CUDA) 1285 ctx->deviceType = LANDAU_CUDA; 1286 ierr = PetscStrcpy(opstring,"cuda");CHKERRQ(ierr); 1287 #else 1288 ctx->deviceType = LANDAU_CPU; 1289 ierr = PetscStrcpy(opstring,"cpu");CHKERRQ(ierr); 1290 ctx->subThreadBlockSize = 0; 1291 #endif 1292 ierr = PetscOptionsString("-dm_landau_device_type","Use kernels on 'cpu', 'cuda', or 'kokkos'","plexland.c",opstring,opstring,256,NULL);CHKERRQ(ierr); 1293 ierr = PetscStrcmp("cpu",opstring,&flg);CHKERRQ(ierr); 1294 if (flg) { 1295 ctx->deviceType = LANDAU_CPU; 1296 ctx->subThreadBlockSize = 0; 1297 } else { 1298 ierr = PetscStrcmp("cuda",opstring,&flg);CHKERRQ(ierr); 1299 if (flg) { 1300 ctx->deviceType = LANDAU_CUDA; 1301 ctx->subThreadBlockSize = 0; 1302 } else { 1303 ierr = PetscStrcmp("kokkos",opstring,&flg);CHKERRQ(ierr); 1304 if (flg) ctx->deviceType = LANDAU_KOKKOS; 1305 else SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-dm_landau_device_type %s",opstring); 1306 } 1307 } 1308 } 1309 ierr = PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL);CHKERRQ(ierr); 1310 ierr = PetscOptionsReal("-dm_landau_electron_shift","Shift in thermal velocity of electrons","none",ctx->electronShift,&ctx->electronShift, NULL);CHKERRQ(ierr); 1311 ierr = PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, &sph_flg);CHKERRQ(ierr); 1312 ierr = PetscOptionsBool("-dm_landau_inflate", "With sphere, inflate for curved edges (no AMR)", "plexland.c", ctx->inflate, &ctx->inflate, NULL);CHKERRQ(ierr); 1313 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); 1314 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); 1315 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); 1316 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); 1317 ierr = PetscOptionsInt("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &ctx->postAMRRefine, NULL);CHKERRQ(ierr); 1318 ierr = PetscOptionsInt("-dm_landau_verbose", "", "plexland.c", ctx->verbose, &ctx->verbose, NULL);CHKERRQ(ierr); 1319 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); 1320 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); 1321 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); 1322 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); 1323 ierr = PetscOptionsReal("-dm_landau_n_0","Normalization constant for number density","plexland.c",ctx->n_0,&ctx->n_0, NULL);CHKERRQ(ierr); 1324 ierr = PetscOptionsReal("-dm_landau_ln_lambda","Cross section parameter","plexland.c",ctx->lnLam,&ctx->lnLam, NULL);CHKERRQ(ierr); 1325 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); 1326 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); 1327 ierr = PetscOptionsBool("-dm_landau_use_mataxpy_mass", "Use fast but slightly fragile MATAXPY to add mass term", "plexland.c", ctx->use_matrix_mass, &ctx->use_matrix_mass, NULL);CHKERRQ(ierr); 1328 1329 /* get num species with tempurature*/ 1330 { 1331 PetscReal arr[100]; 1332 nt = 100; 1333 ierr = PetscOptionsRealArray("-dm_landau_thermal_temps", "Temperature of each species [e,i_0,i_1,...] in keV", "plexland.c", arr, &nt, &flg);CHKERRQ(ierr); 1334 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); 1335 } 1336 nt = LANDAU_MAX_SPECIES; 1337 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) { 1338 ctx->thermal_temps[ii] = 1.; 1339 ctx->charges[ii] = 1; 1340 ctx->masses[ii] = 1; 1341 ctx->n[ii] = (ii==1) ? 1 : 0; 1342 } 1343 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); 1344 if (flg) { 1345 PetscInfo1(dummy, "num_species set to number of thermal temps provided (%D)\n",nt); 1346 ctx->num_species = nt; 1347 } else SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species"); 1348 for (ii=0;ii<ctx->num_species;ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */ 1349 nm = LANDAU_MAX_SPECIES-1; 1350 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); 1351 if (flg && nm != ctx->num_species-1) { 1352 SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"num ion masses %D != num species %D",nm,ctx->num_species-1); 1353 } 1354 nm = LANDAU_MAX_SPECIES; 1355 ierr = PetscOptionsRealArray("-dm_landau_n", "Normalized (by -n_0) number density of each species", "plexland.c", ctx->n, &nm, &flg);CHKERRQ(ierr); 1356 if (flg && nm != ctx->num_species) SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"wrong num n: %D != num species %D",nm,ctx->num_species); 1357 ctx->n_0 *= ctx->n[0]; /* normalized number density */ 1358 for (ii=1;ii<ctx->num_species;ii++) ctx->n[ii] = ctx->n[ii]/ctx->n[0]; 1359 ctx->n[0] = 1; 1360 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */ 1361 ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */ 1362 ctx->m_0 = ctx->masses[0]; /* arbitrary reference mass, electrons */ 1363 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); 1364 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) */ 1365 nc = LANDAU_MAX_SPECIES-1; 1366 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); 1367 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); 1368 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */ 1369 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 */ 1370 /* geometry */ 1371 for (ii=0;ii<ctx->num_species;ii++) ctx->refineTol[ii] = PETSC_MAX_REAL; 1372 for (ii=0;ii<ctx->num_species;ii++) ctx->coarsenTol[ii] = 0.; 1373 ii = LANDAU_MAX_SPECIES; 1374 ierr = PetscOptionsRealArray("-dm_landau_refine_tol","tolerance for refining cells in AMR","plexland.c",ctx->refineTol, &ii, &flg);CHKERRQ(ierr); 1375 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #refine_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 1376 ii = LANDAU_MAX_SPECIES; 1377 ierr = PetscOptionsRealArray("-dm_landau_coarsen_tol","tolerance for coarsening cells in AMR","plexland.c",ctx->coarsenTol, &ii, &flg);CHKERRQ(ierr); 1378 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #coarsen_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 1379 ierr = PetscOptionsReal("-dm_landau_domain_radius","Phase space size in units of electron thermal velocity","plexland.c",ctx->radius,&ctx->radius, &flg);CHKERRQ(ierr); 1380 if (flg && ctx->radius <= 0) { /* negative is ratio of c */ 1381 if (ctx->radius == 0) ctx->radius = 0.75; 1382 else ctx->radius = -ctx->radius; 1383 ctx->radius = ctx->radius*299792458.0/ctx->v_0; 1384 ierr = PetscInfo1(dummy, "Change domain radius to %e\n",ctx->radius);CHKERRQ(ierr); 1385 } 1386 ierr = PetscOptionsReal("-dm_landau_i_radius","Ion thermal velocity, used for circular meshes","plexland.c",ctx->i_radius,&ctx->i_radius, &flg);CHKERRQ(ierr); 1387 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an ion radius but did not set sphere, user error really */ 1388 if (!flg) { 1389 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 */ 1390 } 1391 ierr = PetscOptionsReal("-dm_landau_e_radius","Electron thermal velocity, used for circular meshes","plexland.c",ctx->e_radius,&ctx->e_radius, &flg);CHKERRQ(ierr); 1392 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an e radius but did not set sphere, user error really */ 1393 if (!flg) { 1394 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 */ 1395 } 1396 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); 1397 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); 1398 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1399 for (ii=ctx->num_species;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0; 1400 if (ctx->verbose > 0) { 1401 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); 1402 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); 1403 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); 1404 } 1405 ierr = DMDestroy(&dummy);CHKERRQ(ierr); 1406 { 1407 PetscMPIInt rank; 1408 ierr = MPI_Comm_rank(ctx->comm, &rank);CHKERRMPI(ierr); 1409 /* PetscLogStage setup_stage; */ 1410 ierr = PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11]);CHKERRQ(ierr); /* 11 */ 1411 ierr = PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0]);CHKERRQ(ierr); /* 0 */ 1412 ierr = PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9]);CHKERRQ(ierr); /* 9 */ 1413 ierr = PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10]);CHKERRQ(ierr); /* 10 */ 1414 ierr = PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7]);CHKERRQ(ierr); /* 7 */ 1415 ierr = PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1]);CHKERRQ(ierr); /* 1 */ 1416 ierr = PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3]);CHKERRQ(ierr); /* 3 */ 1417 ierr = PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8]);CHKERRQ(ierr); /* 8 */ 1418 ierr = PetscLogEventRegister(" Kernel (GPU)", DM_CLASSID, &ctx->events[4]);CHKERRQ(ierr); /* 4 */ 1419 ierr = PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5]);CHKERRQ(ierr); /* 5 */ 1420 ierr = PetscLogEventRegister(" Jac-assemble", DM_CLASSID, &ctx->events[6]);CHKERRQ(ierr); /* 6 */ 1421 ierr = PetscLogEventRegister(" Jac asmbl setup", DM_CLASSID, &ctx->events[2]);CHKERRQ(ierr); /* 2 */ 1422 ierr = PetscLogEventRegister(" Other", DM_CLASSID, &ctx->events[13]);CHKERRQ(ierr); /* 13 */ 1423 1424 if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */ 1425 ierr = PetscOptionsClearValue(NULL,"-snes_converged_reason");CHKERRQ(ierr); 1426 ierr = PetscOptionsClearValue(NULL,"-ksp_converged_reason");CHKERRQ(ierr); 1427 ierr = PetscOptionsClearValue(NULL,"-snes_monitor");CHKERRQ(ierr); 1428 ierr = PetscOptionsClearValue(NULL,"-ksp_monitor");CHKERRQ(ierr); 1429 ierr = PetscOptionsClearValue(NULL,"-ts_monitor");CHKERRQ(ierr); 1430 ierr = PetscOptionsClearValue(NULL,"-ts_adapt_monitor");CHKERRQ(ierr); 1431 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1432 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_vec_view");CHKERRQ(ierr); 1433 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1434 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_vec_view");CHKERRQ(ierr); 1435 ierr = PetscOptionsClearValue(NULL,"-info");CHKERRQ(ierr); 1436 } 1437 } 1438 PetscFunctionReturn(0); 1439 } 1440 1441 /*@C 1442 LandauCreateVelocitySpace - Create a DMPlex velocity space mesh 1443 1444 Collective on comm 1445 1446 Input Parameters: 1447 + comm - The MPI communicator 1448 . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver) 1449 - prefix - prefix for options 1450 1451 Output Parameter: 1452 . dm - The DM object representing the mesh 1453 + X - A vector (user destroys) 1454 - J - Optional matrix (object destroys) 1455 1456 Level: beginner 1457 1458 .keywords: mesh 1459 .seealso: DMPlexCreate(), LandauDestroyVelocitySpace() 1460 @*/ 1461 PetscErrorCode LandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *dm) 1462 { 1463 PetscErrorCode ierr; 1464 LandauCtx *ctx; 1465 PetscBool prealloc_only,flg; 1466 1467 PetscFunctionBegin; 1468 if (dim!=2 && dim!=3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported"); 1469 ierr = PetscNew(&ctx);CHKERRQ(ierr); 1470 ctx->comm = comm; /* used for diagnostics and global errors */ 1471 /* process options */ 1472 ierr = ProcessOptions(ctx,prefix);CHKERRQ(ierr); 1473 /* Create Mesh */ 1474 ierr = LandauDMCreateVMesh(PETSC_COMM_SELF, dim, prefix, ctx, dm);CHKERRQ(ierr); 1475 prealloc_only = (*dm)->prealloc_only; 1476 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1477 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1478 /* create FEM */ 1479 ierr = SetupDS(*dm,dim,ctx);CHKERRQ(ierr); 1480 /* set initial state */ 1481 ierr = DMCreateGlobalVector(*dm,X);CHKERRQ(ierr); 1482 ierr = PetscObjectSetName((PetscObject) *X, "u");CHKERRQ(ierr); 1483 /* initial static refinement, no solve */ 1484 ierr = LandauSetInitialCondition(*dm, *X, ctx);CHKERRQ(ierr); 1485 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_pre_vec_view");CHKERRQ(ierr); 1486 /* forest refinement */ 1487 if (ctx->errorIndicator) { 1488 /* AMR */ 1489 ierr = adapt(dm,ctx,X);CHKERRQ(ierr); 1490 if ((*dm)->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"(*dm)->prealloc_only != prealloc_only"); 1491 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1492 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_amr_vec_view");CHKERRQ(ierr); 1493 } 1494 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1495 ctx->dmv = *dm; 1496 if (ctx->dmv->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"ctx->dmv->prealloc_only != prealloc_only"); 1497 ierr = DMCreateMatrix(ctx->dmv, &ctx->J);CHKERRQ(ierr); 1498 ierr = MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1499 ierr = MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE);CHKERRQ(ierr); 1500 if (J) *J = ctx->J; 1501 /* check for types that we need */ 1502 #if defined(PETSC_HAVE_KOKKOS) 1503 if (ctx->deviceType == LANDAU_CPU) { 1504 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJKOKKOS,MATMPIAIJKOKKOS,MATAIJKOKKOS,"");CHKERRQ(ierr); 1505 //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"); 1506 } 1507 #elif defined(PETSC_HAVE_CUDA) 1508 if (ctx->deviceType == LANDAU_CPU) { 1509 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJCUSPARSE,MATMPIAIJCUSPARSE,MATAIJCUSPARSE,"");CHKERRQ(ierr); 1510 //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"); 1511 } 1512 #endif 1513 if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */ 1514 if (ctx->deviceType == LANDAU_CUDA) { 1515 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJCUSPARSE,MATMPIAIJCUSPARSE,MATAIJCUSPARSE,"");CHKERRQ(ierr); 1516 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must use '-dm_mat_type aijcusparse -dm_vec_type cuda' for GPU assembly and Cuda"); 1517 } else if (ctx->deviceType == LANDAU_KOKKOS) { 1518 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJKOKKOS,MATMPIAIJKOKKOS,MATAIJKOKKOS,"");CHKERRQ(ierr); 1519 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 1520 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must use '-dm_mat_type aijkokkos -dm_vec_type kokkos' for GPU assembly and Kokkos"); 1521 #else 1522 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must configure with '--download-kokkos-kernels=1' for GPU assembly and Kokkos"); 1523 #endif 1524 } 1525 } 1526 PetscFunctionReturn(0); 1527 } 1528 1529 /*@ 1530 LandauDestroyVelocitySpace - Destroy a DMPlex velocity space mesh 1531 1532 Collective on dm 1533 1534 Input/Output Parameters: 1535 . dm - the dm to destroy 1536 1537 Level: beginner 1538 1539 .keywords: mesh 1540 .seealso: LandauCreateVelocitySpace() 1541 @*/ 1542 PetscErrorCode LandauDestroyVelocitySpace(DM *dm) 1543 { 1544 PetscErrorCode ierr,ii; 1545 LandauCtx *ctx; 1546 PetscContainer container = NULL; 1547 PetscFunctionBegin; 1548 ierr = DMGetApplicationContext(*dm, &ctx);CHKERRQ(ierr); 1549 ierr = PetscObjectQuery((PetscObject)ctx->J,"coloring", (PetscObject*)&container);CHKERRQ(ierr); 1550 if (container) { 1551 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 1552 } 1553 ierr = MatDestroy(&ctx->M);CHKERRQ(ierr); 1554 ierr = MatDestroy(&ctx->J);CHKERRQ(ierr); 1555 for (ii=0;ii<ctx->num_species;ii++) { 1556 ierr = PetscFEDestroy(&ctx->fe[ii]);CHKERRQ(ierr); 1557 } 1558 if (ctx->deviceType == LANDAU_CUDA) { 1559 #if defined(PETSC_HAVE_CUDA) 1560 ierr = LandauCUDAStaticDataClear(ctx->SData_d);CHKERRQ(ierr); 1561 #else 1562 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 1563 #endif 1564 } else if (ctx->deviceType == LANDAU_KOKKOS) { 1565 #if defined(PETSC_HAVE_KOKKOS) 1566 ierr = LandauKokkosStaticDataClear(ctx->SData_d);CHKERRQ(ierr); 1567 #else 1568 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 1569 #endif 1570 } else { 1571 if (ctx->SData_d) { /* in a CPU run */ 1572 PetscReal *invJ = (PetscReal*)ctx->SData_d->invJ, *xx = (PetscReal*)ctx->SData_d->x, *yy = (PetscReal*)ctx->SData_d->y, *zz = (PetscReal*)ctx->SData_d->z, *ww = (PetscReal*)ctx->SData_d->w, *mass_w = (PetscReal*)ctx->SData_d->mass_w; 1573 ierr = PetscFree5(mass_w,ww,xx,yy,invJ);CHKERRQ(ierr); 1574 if (zz) { 1575 ierr = PetscFree(zz);CHKERRQ(ierr); 1576 } 1577 } 1578 } 1579 ierr = PetscFree(ctx->SData_d);CHKERRQ(ierr); 1580 if (ctx->times[0] > 0) { 1581 ierr = PetscPrintf(ctx->comm, "Landau Operator %d 1.0 %10.3e ....\n",10000,ctx->times[0]);CHKERRQ(ierr); 1582 } 1583 PetscFree(ctx); 1584 ierr = DMDestroy(dm);CHKERRQ(ierr); 1585 PetscFunctionReturn(0); 1586 } 1587 1588 /* < v, ru > */ 1589 static void f0_s_den(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1590 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1591 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1592 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1593 { 1594 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1595 f0[0] = u[ii]; 1596 } 1597 1598 /* < v, ru > */ 1599 static void f0_s_mom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1600 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1601 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1602 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1603 { 1604 PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]); 1605 f0[0] = x[jj]*u[ii]; /* x momentum */ 1606 } 1607 1608 static void f0_s_v2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1609 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1610 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1611 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1612 { 1613 PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]); 1614 double tmp1 = 0.; 1615 for (i = 0; i < dim; ++i) tmp1 += x[i]*x[i]; 1616 f0[0] = tmp1*u[ii]; 1617 } 1618 1619 /* < v, ru > */ 1620 static void f0_s_rden(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1621 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1622 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1623 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1624 { 1625 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1626 f0[0] = 2.*PETSC_PI*x[0]*u[ii]; 1627 } 1628 1629 /* < v, ru > */ 1630 static void f0_s_rmom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1631 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1632 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1633 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1634 { 1635 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1636 f0[0] = 2.*PETSC_PI*x[0]*x[1]*u[ii]; 1637 } 1638 1639 static void f0_s_rv2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1640 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1641 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1642 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1643 { 1644 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1645 f0[0] = 2.*PETSC_PI*x[0]*(x[0]*x[0] + x[1]*x[1])*u[ii]; 1646 } 1647 1648 /*@ 1649 LandauPrintNorms - collects moments and prints them 1650 1651 Collective on dm 1652 1653 Input Parameters: 1654 + X - the state 1655 - stepi - current step to print 1656 1657 Level: beginner 1658 1659 .keywords: mesh 1660 .seealso: LandauCreateVelocitySpace() 1661 @*/ 1662 PetscErrorCode LandauPrintNorms(Vec X, PetscInt stepi) 1663 { 1664 PetscErrorCode ierr; 1665 LandauCtx *ctx; 1666 PetscDS prob; 1667 DM plex,dm; 1668 PetscInt cStart, cEnd, dim, ii; 1669 PetscScalar xmomentumtot=0, ymomentumtot=0, zmomentumtot=0, energytot=0, densitytot=0, tt[LANDAU_MAX_SPECIES]; 1670 PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES]; 1671 1672 PetscFunctionBegin; 1673 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 1674 if (!dm) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no DM"); 1675 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1676 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1677 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1678 ierr = DMConvert(ctx->dmv, DMPLEX, &plex);CHKERRQ(ierr); 1679 ierr = DMCreateDS(plex);CHKERRQ(ierr); 1680 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 1681 /* print momentum and energy */ 1682 for (ii=0;ii<ctx->num_species;ii++) { 1683 PetscScalar user[2] = { (PetscScalar)ii, (PetscScalar)ctx->charges[ii]}; 1684 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 1685 if (dim==2) { /* 2/3X + 3V (cylindrical coordinates) */ 1686 ierr = PetscDSSetObjective(prob, 0, &f0_s_rden);CHKERRQ(ierr); 1687 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1688 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1689 ierr = PetscDSSetObjective(prob, 0, &f0_s_rmom);CHKERRQ(ierr); 1690 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1691 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1692 ierr = PetscDSSetObjective(prob, 0, &f0_s_rv2);CHKERRQ(ierr); 1693 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1694 energy[ii] = tt[0]*0.5*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1695 zmomentumtot += zmomentum[ii]; 1696 energytot += energy[ii]; 1697 densitytot += density[ii]; 1698 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); 1699 } else { /* 2/3X + 3V */ 1700 ierr = PetscDSSetObjective(prob, 0, &f0_s_den);CHKERRQ(ierr); 1701 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1702 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1703 ierr = PetscDSSetObjective(prob, 0, &f0_s_mom);CHKERRQ(ierr); 1704 user[1] = 0; 1705 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1706 xmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1707 user[1] = 1; 1708 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1709 ymomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1710 user[1] = 2; 1711 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1712 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1713 ierr = PetscDSSetObjective(prob, 0, &f0_s_v2);CHKERRQ(ierr); 1714 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1715 energy[ii] = 0.5*tt[0]*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1716 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", 1717 stepi,ii,PetscRealPart(density[ii]),PetscRealPart(xmomentum[ii]),PetscRealPart(ymomentum[ii]),PetscRealPart(zmomentum[ii]),PetscRealPart(energy[ii]));CHKERRQ(ierr); 1718 xmomentumtot += xmomentum[ii]; 1719 ymomentumtot += ymomentum[ii]; 1720 zmomentumtot += zmomentum[ii]; 1721 energytot += energy[ii]; 1722 densitytot += density[ii]; 1723 } 1724 if (ctx->num_species>1) PetscPrintf(ctx->comm, "\n"); 1725 } 1726 /* totals */ 1727 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1728 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1729 if (ctx->num_species>1) { 1730 if (dim==2) { 1731 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)", 1732 stepi,(double)PetscRealPart(densitytot),(double)PetscRealPart(zmomentumtot),(double)PetscRealPart(energytot),(double)(ctx->masses[1]/ctx->masses[0]),cEnd-cStart);CHKERRQ(ierr); 1733 } else { 1734 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)", 1735 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); 1736 } 1737 } else { 1738 ierr = PetscPrintf(ctx->comm, " -- %D cells",cEnd-cStart);CHKERRQ(ierr); 1739 } 1740 if (ctx->verbose > 1) {ierr = PetscPrintf(ctx->comm,", %D sub (vector) threads\n",ctx->subThreadBlockSize);CHKERRQ(ierr);} 1741 else {ierr = PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr);} 1742 PetscFunctionReturn(0); 1743 } 1744 1745 static PetscErrorCode destroy_coloring (void *is) 1746 { 1747 ISColoring tmp = (ISColoring)is; 1748 return ISColoringDestroy(&tmp); 1749 } 1750 1751 /*@ 1752 LandauCreateColoring - create a coloring and add to matrix (Landau context used just for 'print' flag, should be in DMPlex) 1753 1754 Collective on JacP 1755 1756 Input Parameters: 1757 + JacP - matrix to add coloring to 1758 - plex - The DM 1759 1760 Output Parameter: 1761 . container - Container with coloring 1762 1763 Level: beginner 1764 1765 .keywords: mesh 1766 .seealso: LandauCreateVelocitySpace() 1767 @*/ 1768 PetscErrorCode LandauCreateColoring(Mat JacP, DM plex, PetscContainer *container) 1769 { 1770 PetscErrorCode ierr; 1771 PetscInt dim,cell,i,ej,nc,Nv,totDim,numGCells,cStart,cEnd; 1772 ISColoring iscoloring = NULL; 1773 Mat G,Q; 1774 PetscScalar ones[128]; 1775 MatColoring mc; 1776 IS *is; 1777 PetscInt csize,colour,j,k; 1778 const PetscInt *indices; 1779 PetscInt numComp[1]; 1780 PetscInt numDof[4]; 1781 PetscFE fe; 1782 DM colordm; 1783 PetscSection csection, section, globalSection; 1784 PetscDS prob; 1785 LandauCtx *ctx; 1786 1787 PetscFunctionBegin; 1788 ierr = DMGetApplicationContext(plex, &ctx);CHKERRQ(ierr); 1789 ierr = DMGetLocalSection(plex, §ion);CHKERRQ(ierr); 1790 ierr = DMGetGlobalSection(plex, &globalSection);CHKERRQ(ierr); 1791 ierr = DMGetDimension(plex, &dim);CHKERRQ(ierr); 1792 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 1793 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1794 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1795 numGCells = cEnd - cStart; 1796 /* create cell centered DM */ 1797 ierr = DMClone(plex, &colordm);CHKERRQ(ierr); 1798 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) plex), dim, 1, PETSC_FALSE, "color_", PETSC_DECIDE, &fe);CHKERRQ(ierr); 1799 ierr = PetscObjectSetName((PetscObject) fe, "color");CHKERRQ(ierr); 1800 ierr = DMSetField(colordm, 0, NULL, (PetscObject)fe);CHKERRQ(ierr); 1801 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 1802 for (i = 0; i < (dim+1); ++i) numDof[i] = 0; 1803 numDof[dim] = 1; 1804 numComp[0] = 1; 1805 ierr = DMPlexCreateSection(colordm, NULL, numComp, numDof, 0, NULL, NULL, NULL, NULL, &csection);CHKERRQ(ierr); 1806 ierr = PetscSectionSetFieldName(csection, 0, "color");CHKERRQ(ierr); 1807 ierr = DMSetLocalSection(colordm, csection);CHKERRQ(ierr); 1808 ierr = DMViewFromOptions(colordm,NULL,"-color_dm_view");CHKERRQ(ierr); 1809 /* get vertex to element map Q and colroing graph G */ 1810 ierr = MatGetSize(JacP,NULL,&Nv);CHKERRQ(ierr); 1811 ierr = MatCreateAIJ(PETSC_COMM_SELF,PETSC_DECIDE,PETSC_DECIDE,numGCells,Nv,totDim,NULL,0,NULL,&Q);CHKERRQ(ierr); 1812 for (i=0;i<128;i++) ones[i] = 1.0; 1813 for (cell = cStart, ej = 0 ; cell < cEnd; ++cell, ++ej) { 1814 PetscInt numindices,*indices; 1815 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1816 if (numindices>128) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many indices. %D > %D",numindices,128); 1817 ierr = MatSetValues(Q,1,&ej,numindices,indices,ones,ADD_VALUES);CHKERRQ(ierr); 1818 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1819 } 1820 ierr = MatAssemblyBegin(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1821 ierr = MatAssemblyEnd(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1822 ierr = MatMatTransposeMult(Q,Q,MAT_INITIAL_MATRIX,4.0,&G);CHKERRQ(ierr); 1823 ierr = PetscObjectSetName((PetscObject) Q, "Q");CHKERRQ(ierr); 1824 ierr = PetscObjectSetName((PetscObject) G, "coloring graph");CHKERRQ(ierr); 1825 ierr = MatViewFromOptions(G,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1826 ierr = MatViewFromOptions(Q,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1827 ierr = MatDestroy(&Q);CHKERRQ(ierr); 1828 /* coloring */ 1829 ierr = MatColoringCreate(G,&mc);CHKERRQ(ierr); 1830 ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr); 1831 ierr = MatColoringSetType(mc,MATCOLORINGJP);CHKERRQ(ierr); 1832 ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr); 1833 ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr); 1834 ierr = MatColoringDestroy(&mc);CHKERRQ(ierr); 1835 /* view */ 1836 ierr = ISColoringViewFromOptions(iscoloring,NULL,"-coloring_is_view");CHKERRQ(ierr); 1837 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1838 if (ctx && ctx->verbose > 2) { 1839 PetscViewer viewer; 1840 Vec color_vec, eidx_vec; 1841 ierr = DMGetGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1842 ierr = DMGetGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1843 for (colour=0; colour<nc; colour++) { 1844 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1845 ierr = ISGetIndices(is[colour],&indices);CHKERRQ(ierr); 1846 for (j=0; j<csize; j++) { 1847 PetscScalar v = (PetscScalar)colour; 1848 k = indices[j]; 1849 ierr = VecSetValues(color_vec,1,&k,&v,INSERT_VALUES); 1850 v = (PetscScalar)k; 1851 ierr = VecSetValues(eidx_vec,1,&k,&v,INSERT_VALUES); 1852 } 1853 ierr = ISRestoreIndices(is[colour],&indices);CHKERRQ(ierr); 1854 } 1855 /* view */ 1856 ierr = PetscViewerVTKOpen(ctx->comm, "color.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1857 ierr = PetscObjectSetName((PetscObject) color_vec, "color");CHKERRQ(ierr); 1858 ierr = VecView(color_vec, viewer);CHKERRQ(ierr); 1859 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1860 ierr = PetscViewerVTKOpen(ctx->comm, "eidx.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1861 ierr = PetscObjectSetName((PetscObject) eidx_vec, "element-idx");CHKERRQ(ierr); 1862 ierr = VecView(eidx_vec, viewer);CHKERRQ(ierr); 1863 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1864 ierr = DMRestoreGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1865 ierr = DMRestoreGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1866 } 1867 ierr = PetscSectionDestroy(&csection);CHKERRQ(ierr); 1868 ierr = DMDestroy(&colordm);CHKERRQ(ierr); 1869 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1870 ierr = MatDestroy(&G);CHKERRQ(ierr); 1871 /* stash coloring */ 1872 ierr = PetscContainerCreate(PETSC_COMM_SELF, container);CHKERRQ(ierr); 1873 ierr = PetscContainerSetPointer(*container,(void*)iscoloring);CHKERRQ(ierr); 1874 ierr = PetscContainerSetUserDestroy(*container, destroy_coloring);CHKERRQ(ierr); 1875 ierr = PetscObjectCompose((PetscObject)JacP,"coloring",(PetscObject)*container);CHKERRQ(ierr); 1876 if (ctx && ctx->verbose > 0) { 1877 ierr = PetscPrintf(ctx->comm, "Made coloring with %D colors\n", nc);CHKERRQ(ierr); 1878 } 1879 PetscFunctionReturn(0); 1880 } 1881 1882 PetscErrorCode LandauAssembleOpenMP(PetscInt cStart, PetscInt cEnd, PetscInt totDim, DM plex, PetscSection section, PetscSection globalSection, Mat JacP, PetscScalar elemMats[], PetscContainer container) 1883 { 1884 PetscErrorCode ierr; 1885 IS *is; 1886 PetscInt nc,colour,j; 1887 const PetscInt *clr_idxs; 1888 ISColoring iscoloring; 1889 PetscFunctionBegin; 1890 ierr = PetscContainerGetPointer(container,(void**)&iscoloring);CHKERRQ(ierr); 1891 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1892 for (colour=0; colour<nc; colour++) { 1893 PetscInt *idx_arr[1024]; /* need to make dynamic for general use */ 1894 PetscScalar *new_el_mats[1024]; 1895 PetscInt idx_size[1024],csize; 1896 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1897 if (csize>1024) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many elements in color. %D > %D",csize,1024); 1898 ierr = ISGetIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1899 /* get indices and mats */ 1900 for (j=0; j<csize; j++) { 1901 PetscInt cell = cStart + clr_idxs[j]; 1902 PetscInt numindices,*indices; 1903 PetscScalar *elMat = &elemMats[clr_idxs[j]*totDim*totDim]; 1904 PetscScalar *valuesOrig = elMat; 1905 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1906 idx_size[j] = numindices; 1907 ierr = PetscMalloc2(numindices,&idx_arr[j],numindices*numindices,&new_el_mats[j]);CHKERRQ(ierr); 1908 ierr = PetscMemcpy(idx_arr[j],indices,numindices*sizeof(PetscInt));CHKERRQ(ierr); 1909 ierr = PetscMemcpy(new_el_mats[j],elMat,numindices*numindices*sizeof(PetscScalar));CHKERRQ(ierr); 1910 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1911 if (elMat != valuesOrig) {ierr = DMRestoreWorkArray(plex, numindices*numindices, MPIU_SCALAR, &elMat);} 1912 } 1913 /* assemble matrix */ 1914 for (j=0; j<csize; j++) { 1915 PetscInt numindices = idx_size[j], *indices = idx_arr[j]; 1916 PetscScalar *elMat = new_el_mats[j]; 1917 MatSetValues(JacP,numindices,indices,numindices,indices,elMat,ADD_VALUES); 1918 } 1919 /* free */ 1920 ierr = ISRestoreIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1921 for (j=0; j<csize; j++) { 1922 ierr = PetscFree2(idx_arr[j],new_el_mats[j]);CHKERRQ(ierr); 1923 } 1924 } 1925 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1926 PetscFunctionReturn(0); 1927 } 1928 1929 /* < v, u > */ 1930 static void g0_1(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1931 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1932 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1933 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1934 { 1935 g0[0] = 1.; 1936 } 1937 1938 /* < v, u > */ 1939 static void g0_r(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1940 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1941 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1942 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1943 { 1944 g0[0] = 2.*PETSC_PI*x[0]; 1945 } 1946 1947 /*@ 1948 LandauCreateMassMatrix - Create mass matrix for Landau 1949 1950 Collective on dm 1951 1952 Input Parameters: 1953 . dm - the DM object 1954 1955 Output Parameters: 1956 . Amat - The mass matrix (optional), mass matrix is added to the DM context 1957 1958 Level: beginner 1959 1960 .keywords: mesh 1961 .seealso: LandauCreateVelocitySpace() 1962 @*/ 1963 PetscErrorCode LandauCreateMassMatrix(DM dm, Mat *Amat) 1964 { 1965 DM massDM; 1966 PetscDS prob; 1967 PetscInt ii,dim,N1=1,N2; 1968 PetscErrorCode ierr; 1969 LandauCtx *ctx; 1970 Mat M; 1971 1972 PetscFunctionBegin; 1973 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1974 if (Amat) PetscValidPointer(Amat,2); 1975 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1976 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1977 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1978 ierr = DMClone(dm, &massDM);CHKERRQ(ierr); 1979 ierr = DMCopyFields(dm, massDM);CHKERRQ(ierr); 1980 ierr = DMCreateDS(massDM);CHKERRQ(ierr); 1981 ierr = DMGetDS(massDM, &prob);CHKERRQ(ierr); 1982 for (ii=0;ii<ctx->num_species;ii++) { 1983 if (dim==3) {ierr = PetscDSSetJacobian(prob, ii, ii, g0_1, NULL, NULL, NULL);CHKERRQ(ierr);} 1984 else {ierr = PetscDSSetJacobian(prob, ii, ii, g0_r, NULL, NULL, NULL);CHKERRQ(ierr);} 1985 } 1986 ierr = DMViewFromOptions(massDM,NULL,"-dm_landau_mass_dm_view");CHKERRQ(ierr); 1987 ierr = DMCreateMatrix(massDM, &M);CHKERRQ(ierr); 1988 ierr = MatSetOption(M, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1989 { 1990 Vec locX; 1991 DM plex; 1992 ierr = DMConvert(massDM, DMPLEX, &plex);CHKERRQ(ierr); 1993 ierr = DMGetLocalVector(massDM, &locX);CHKERRQ(ierr); 1994 /* Mass matrix is independent of the input, so no need to fill locX */ 1995 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); 1996 ierr = DMPlexSNESComputeJacobianFEM(plex, locX, M, M, ctx);CHKERRQ(ierr); 1997 ierr = DMRestoreLocalVector(massDM, &locX);CHKERRQ(ierr); 1998 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1999 } 2000 ierr = DMDestroy(&massDM);CHKERRQ(ierr); 2001 ierr = MatGetSize(ctx->J, &N1, NULL);CHKERRQ(ierr); 2002 ierr = MatGetSize(M, &N2, NULL);CHKERRQ(ierr); 2003 if (N1 != N2) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %D, |Mass|=%D",N1,N2); 2004 ierr = PetscObjectSetName((PetscObject)M, "mass");CHKERRQ(ierr); 2005 ierr = MatViewFromOptions(M,NULL,"-dm_landau_mass_mat_view");CHKERRQ(ierr); 2006 ctx->M = M; /* this could be a noop, a = a */ 2007 if (Amat) *Amat = M; 2008 PetscFunctionReturn(0); 2009 } 2010 2011 /*@ 2012 LandauIFunction - TS residual calculation 2013 2014 Collective on ts 2015 2016 Input Parameters: 2017 + TS - The time stepping context 2018 . time_dummy - current time (not used) 2019 - X - Current state 2020 + X_t - Time derivative of current state 2021 . actx - Landau context 2022 2023 Output Parameter: 2024 . F - The residual 2025 2026 Level: beginner 2027 2028 .keywords: mesh 2029 .seealso: LandauCreateVelocitySpace(), LandauIJacobian() 2030 @*/ 2031 PetscErrorCode LandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx) 2032 { 2033 PetscErrorCode ierr; 2034 LandauCtx *ctx=(LandauCtx*)actx; 2035 PetscInt dim; 2036 DM dm; 2037 #if defined(PETSC_HAVE_THREADSAFETY) 2038 double starttime, endtime; 2039 #endif 2040 2041 PetscFunctionBegin; 2042 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 2043 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 2044 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2045 //ierr = MPI_Barrier(MPI_COMM_WORLD);CHKERRMPI(ierr); 2046 ierr = PetscLogEventBegin(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2047 ierr = PetscLogEventBegin(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 2048 #if defined(PETSC_HAVE_THREADSAFETY) 2049 starttime = MPI_Wtime(); 2050 #endif 2051 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 2052 if (!ctx->aux_bool) { 2053 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); 2054 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,0.0,(void*)ctx);CHKERRQ(ierr); 2055 ctx->aux_bool = PETSC_TRUE; 2056 } else { 2057 ierr = PetscInfo(ts, "Skip forming Jacobian, has not changed (should check norm)\n");CHKERRQ(ierr); 2058 } 2059 ierr = MatViewFromOptions(ctx->J,NULL,"-landau_jacobian_mat_view");CHKERRQ(ierr); 2060 /* mat vec for op */ 2061 ierr = MatMult(ctx->J,X,F);CHKERRQ(ierr);CHKERRQ(ierr); /* C*f */ 2062 /* add time term */ 2063 if (X_t) { 2064 ierr = MatMultAdd(ctx->M,X_t,F,F);CHKERRQ(ierr); 2065 } 2066 #if defined(PETSC_HAVE_THREADSAFETY) 2067 endtime = MPI_Wtime(); 2068 ctx->times[0] += (endtime - starttime); 2069 #endif 2070 ierr = PetscLogEventEnd(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 2071 ierr = PetscLogEventEnd(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2072 PetscFunctionReturn(0); 2073 } 2074 static PetscErrorCode MatrixNfDestroy(void *ptr) 2075 { 2076 PetscInt *nf = (PetscInt *)ptr; 2077 PetscErrorCode ierr; 2078 PetscFunctionBegin; 2079 ierr = PetscFree(nf);CHKERRQ(ierr); 2080 PetscFunctionReturn(0); 2081 } 2082 /*@ 2083 LandauIJacobian - TS Jacobian construction 2084 2085 Collective on ts 2086 2087 Input Parameters: 2088 + TS - The time stepping context 2089 . time_dummy - current time (not used) 2090 - X - Current state 2091 + U_tdummy - Time derivative of current state (not used) 2092 . shift - shift for du/dt term 2093 - actx - Landau context 2094 2095 Output Parameter: 2096 . Amat - Jacobian 2097 + Pmat - same as Amat 2098 2099 Level: beginner 2100 2101 .keywords: mesh 2102 .seealso: LandauCreateVelocitySpace(), LandauIFunction() 2103 @*/ 2104 PetscErrorCode LandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx) 2105 { 2106 PetscErrorCode ierr; 2107 LandauCtx *ctx=(LandauCtx*)actx; 2108 PetscInt dim; 2109 DM dm; 2110 PetscContainer container; 2111 #if defined(PETSC_HAVE_THREADSAFETY) 2112 double starttime, endtime; 2113 #endif 2114 2115 PetscFunctionBegin; 2116 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 2117 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 2118 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2119 if (Amat!=Pmat || Amat!=ctx->J) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J"); 2120 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 2121 /* get collision Jacobian into A */ 2122 ierr = PetscLogEventBegin(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2123 ierr = PetscLogEventBegin(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 2124 #if defined(PETSC_HAVE_THREADSAFETY) 2125 starttime = MPI_Wtime(); 2126 #endif 2127 ierr = PetscInfo2(ts, "Adding just mass to Jacobian t=%g, shift=%g\n",(double)time_dummy,(double)shift);CHKERRQ(ierr); 2128 if (shift==0.0) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "zero shift"); 2129 if (!ctx->aux_bool) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "wrong state"); 2130 if (!ctx->use_matrix_mass) { 2131 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,shift,(void*)ctx);CHKERRQ(ierr); 2132 } else { /* add mass */ 2133 ierr = MatAXPY(Pmat,shift,ctx->M,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 2134 } 2135 ctx->aux_bool = PETSC_FALSE; 2136 ierr = MatViewFromOptions(Pmat,NULL,"-landau_mat_view");CHKERRQ(ierr); 2137 /* set number species in Jacobian */ 2138 ierr = PetscObjectQuery((PetscObject) ctx->J, "Nf", (PetscObject *) &container);CHKERRQ(ierr); 2139 if (!container) { 2140 PetscInt *pNf; 2141 ierr = PetscContainerCreate(PETSC_COMM_SELF, &container);CHKERRQ(ierr); 2142 ierr = PetscMalloc(sizeof(PetscInt), &pNf);CHKERRQ(ierr); 2143 *pNf = ctx->num_species + 1000*ctx->numConcurrency; 2144 ierr = PetscContainerSetPointer(container, (void *)pNf);CHKERRQ(ierr); 2145 ierr = PetscContainerSetUserDestroy(container, MatrixNfDestroy);CHKERRQ(ierr); 2146 ierr = PetscObjectCompose((PetscObject)ctx->J, "Nf", (PetscObject) container);CHKERRQ(ierr); 2147 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 2148 } 2149 #if defined(PETSC_HAVE_THREADSAFETY) 2150 endtime = MPI_Wtime(); 2151 ctx->times[0] += (endtime - starttime); 2152 #endif 2153 ierr = PetscLogEventEnd(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 2154 ierr = PetscLogEventEnd(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2155 PetscFunctionReturn(0); 2156 } 2157