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 PetscDS prob; 54 PetscSection section,globsection; 55 PetscInt numCells,totDim,ej,Nq,*Nbf,*Ncf,Nb,Ncx,Nf,d,f,fieldA,qj,N; 56 PetscQuadrature quad; 57 const PetscReal *quadWeights; 58 PetscTabulation *Tf; // used for CPU and print info 59 PetscReal Eq_m[LANDAU_MAX_SPECIES], m_0=ctx->m_0; /* normalize mass -- not needed! */ 60 PetscScalar *IPf=NULL; 61 const PetscScalar *xdata=NULL; 62 PetscLogDouble flops; 63 PetscContainer container; 64 P4estVertexMaps *maps=NULL; 65 66 PetscFunctionBegin; 67 PetscValidHeaderSpecific(a_X,VEC_CLASSID,1); 68 PetscValidHeaderSpecific(JacP,MAT_CLASSID,2); 69 PetscValidPointer(ctx,5); 70 /* static PetscLogStage stage0 = 0; */ 71 /* if (!stage0) { */ 72 /* ierr = PetscLogStageRegister("Preamble", &stage0);CHKERRQ(ierr); */ 73 /* } */ 74 /* ierr = PetscLogStagePush(stage0);CHKERRQ(ierr); */ 75 /* check for matrix container for GPU assembly */ 76 ierr = PetscLogEventBegin(ctx->events[10],0,0,0,0);CHKERRQ(ierr); 77 ierr = PetscObjectQuery((PetscObject) JacP, "assembly_maps", (PetscObject *) &container);CHKERRQ(ierr); 78 if (container /* && ctx->deviceType != LANDAU_CPU */) { 79 if (!ctx->gpu_assembly) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"GPU matrix container but no GPU assembly"); 80 ierr = PetscContainerGetPointer(container, (void **) &maps);CHKERRQ(ierr); 81 if (!maps) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"empty GPU matrix container"); 82 } 83 if (ctx->plex == NULL) { 84 ierr = DMConvert(ctx->dmv, DMPLEX, &ctx->plex);CHKERRQ(ierr); 85 } 86 ierr = DMPlexGetHeightStratum(ctx->plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 87 ierr = DMGetLocalSection(ctx->plex, §ion);CHKERRQ(ierr); 88 ierr = DMGetGlobalSection(ctx->plex, &globsection);CHKERRQ(ierr); 89 ierr = DMGetDS(ctx->plex, &prob);CHKERRQ(ierr); 90 ierr = PetscDSGetTabulation(prob, &Tf);CHKERRQ(ierr); // Bf, &Df 91 ierr = PetscDSGetDimensions(prob, &Nbf);CHKERRQ(ierr); Nb = Nbf[0]; /* number of vertices*S */ 92 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); if (Nf!=ctx->num_species) SETERRQ1(ctx->comm, PETSC_ERR_PLIB, "Nf %D != S",Nf); 93 ierr = PetscDSGetComponents(prob, &Ncf);CHKERRQ(ierr); Ncx = Ncf[0]; if (Ncx!=1) SETERRQ1(ctx->comm, PETSC_ERR_PLIB, "Nc %D != 1",Ncx); 94 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 95 numCells = cEnd - cStart; 96 ierr = PetscFEGetQuadrature(ctx->fe[0], &quad);CHKERRQ(ierr); 97 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights);CHKERRQ(ierr); 98 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); 99 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); 100 if (LANDAU_DIM != dim) SETERRQ2(ctx->comm, PETSC_ERR_PLIB, "dim %D != LANDAU_DIM %d",dim,LANDAU_DIM); 101 if (!ctx->SData_d) { 102 ierr = PetscNew(&ctx->SData_d);CHKERRQ(ierr); 103 } 104 elemMatSize = totDim*totDim; // used for CPU and print info 105 ierr = PetscLogEventEnd(ctx->events[10],0,0,0,0);CHKERRQ(ierr); 106 //ierr = PetscLogStagePop();CHKERRQ(ierr); 107 ierr = VecGetSize(a_X,&N);CHKERRQ(ierr); 108 if (!ctx->init) { /* create static point data, Jacobian called first */ 109 PetscReal *invJ,*ww,*xx,*yy,*zz=NULL,*mass_w,*invJ_a; 110 const PetscInt nip = Nq*numCells; 111 112 ierr = PetscLogEventBegin(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 113 ctx->init = PETSC_TRUE; 114 ierr = PetscInfo(ctx->plex, "Initialize static data\n");CHKERRQ(ierr); 115 /* collect f data, first time is for Jacobian, but make mass now */ 116 if (ctx->verbose > 1 || ctx->verbose > 0) { 117 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", 118 0,"FormLandau",Nq*numCells,numCells, totDim, Nb, Nq, elemMatSize, dim, Tf[0]->Nb, Nf, Tf[0]->Np, Tf[0]->cdim, N, shift);CHKERRQ(ierr); 119 } 120 ierr = PetscMalloc5(nip,&mass_w,nip,&ww,nip,&xx,nip,&yy,nip*dim*dim,&invJ_a);CHKERRQ(ierr); 121 if (dim==3) { 122 ierr = PetscMalloc1(nip,&zz);CHKERRQ(ierr); 123 } 124 for (ej = 0 ; ej < numCells; ++ej) { 125 PetscReal vj[LANDAU_MAX_NQ*LANDAU_DIM],detJj[LANDAU_MAX_NQ], Jdummy[LANDAU_MAX_NQ*LANDAU_DIM*LANDAU_DIM]; 126 invJ = invJ_a ? invJ_a + ej * Nq*dim*dim : NULL; 127 ierr = DMPlexComputeCellGeometryFEM(ctx->plex, cStart+ej, quad, vj, Jdummy, invJ, detJj);CHKERRQ(ierr); 128 /* create dynamic point data */ 129 for (qj = 0; qj < Nq; ++qj) { 130 PetscInt gidx = (ej*Nq + qj); 131 mass_w[gidx] = detJj[qj] * quadWeights[qj]; 132 if (dim==2) mass_w[gidx] *= 2.*PETSC_PI*vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */ 133 xx[gidx] = vj[qj * dim + 0]; /* coordinate */ 134 yy[gidx] = vj[qj * dim + 1]; 135 if (dim==3) zz[gidx] = vj[qj * dim + 2]; 136 ww[gidx] = detJj[qj] * quadWeights[qj]; 137 if (dim==2) ww[gidx] *= xx[gidx]; /* cylindrical coordinate, w/o 2pi */ 138 } /* q */ 139 } /* ej */ 140 /* cache static data */ 141 if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) { 142 #if defined(PETSC_HAVE_CUDA) || defined(PETSC_HAVE_KOKKOS) 143 PetscReal invMass[LANDAU_MAX_SPECIES],nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES]; 144 for (fieldA=0;fieldA<Nf;fieldA++) { 145 invMass[fieldA] = m_0/ctx->masses[fieldA]; 146 nu_alpha[fieldA] = PetscSqr(ctx->charges[fieldA]/m_0)*m_0/ctx->masses[fieldA]; 147 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); 148 } 149 if (ctx->deviceType == LANDAU_CUDA) { 150 #if defined(PETSC_HAVE_CUDA) 151 ierr = LandauCUDAStaticDataSet(ctx->plex,Nq,nu_alpha,nu_beta,invMass,invJ_a,mass_w,xx,yy,zz,ww,ctx->SData_d);CHKERRQ(ierr); 152 #else 153 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 154 #endif 155 } else if (ctx->deviceType == LANDAU_KOKKOS) { 156 #if defined(PETSC_HAVE_KOKKOS) 157 ierr = LandauKokkosStaticDataSet(ctx->plex,Nq,nu_alpha,nu_beta,invMass,invJ_a,mass_w,xx,yy,zz,ww,ctx->SData_d);CHKERRQ(ierr); 158 #else 159 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 160 #endif 161 } 162 #endif 163 /* free */ 164 ierr = PetscFree5(mass_w,ww,xx,yy,invJ_a);CHKERRQ(ierr); 165 if (dim==3) { 166 ierr = PetscFree(zz);CHKERRQ(ierr); 167 } 168 } else { /* CPU version, just copy in, only use part */ 169 ctx->SData_d->w = (void*)ww; 170 ctx->SData_d->x = (void*)xx; 171 ctx->SData_d->y = (void*)yy; 172 ctx->SData_d->z = (void*)zz; 173 ctx->SData_d->invJ = (void*)invJ_a; 174 ctx->SData_d->mass_w = (void*)mass_w; 175 } 176 ierr = PetscLogEventEnd(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 177 } 178 if (shift==0) { /* create dynamic point data */ 179 ierr = PetscLogEventBegin(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 180 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 181 flops = (PetscLogDouble)numCells*(PetscLogDouble)Nq*(PetscLogDouble)(5*dim*dim*Nf*Nf + 165); 182 for (fieldA=0;fieldA<Nf;fieldA++) { 183 Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */ 184 if (dim==2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */ 185 } 186 if (!ctx->gpu_assembly || !container) { 187 Vec locX; 188 ierr = DMGetLocalVector(ctx->plex, &locX);CHKERRQ(ierr); 189 ierr = VecZeroEntries(locX);CHKERRQ(ierr); /* zero BCs so don't set */ 190 ierr = DMGlobalToLocalBegin(ctx->plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 191 ierr = DMGlobalToLocalEnd (ctx->plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 192 ierr = PetscMalloc1(Nq*numCells*Nf,&IPf);CHKERRQ(ierr); 193 for (ej = 0 ; ej < numCells; ++ej) { 194 PetscScalar *coef = NULL; 195 ierr = DMPlexVecGetClosure(ctx->plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 196 ierr = PetscMemcpy(&IPf[ej*Nb*Nf],coef,Nb*Nf*sizeof(PetscScalar));CHKERRQ(ierr); /* change if LandauIPReal != PetscScalar */ 197 ierr = DMPlexVecRestoreClosure(ctx->plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 198 } /* ej */ 199 ierr = DMRestoreLocalVector(ctx->plex, &locX);CHKERRQ(ierr); 200 } else { 201 PetscMemType mtype; 202 ierr = VecGetArrayReadAndMemType(a_X,&xdata,&mtype);CHKERRQ(ierr); 203 } 204 ierr = PetscLogEventEnd(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 205 } else { 206 flops = (PetscLogDouble)numCells*(PetscLogDouble)Nq*(PetscLogDouble)(5*dim*dim*Nf*Nf); 207 } 208 /* do it */ 209 if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) { 210 /* static PetscLogStage stage0 = 0; */ 211 /* if (!stage0) { */ 212 /* ierr = PetscLogStageRegister("Landau", &stage0);CHKERRQ(ierr); */ 213 /* } */ 214 /* ierr = PetscLogStagePush(stage0);CHKERRQ(ierr); */ 215 if (ctx->deviceType == LANDAU_CUDA) { 216 #if defined(PETSC_HAVE_CUDA) 217 ierr = LandauCUDAJacobian(ctx->plex,Nq,Eq_m,IPf,N,xdata,ctx->SData_d,ctx->subThreadBlockSize,shift,ctx->events,JacP);CHKERRQ(ierr); 218 #else 219 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 220 #endif 221 } else if (ctx->deviceType == LANDAU_KOKKOS) { 222 #if defined(PETSC_HAVE_KOKKOS) 223 ierr = LandauKokkosJacobian(ctx->plex,Nq,Eq_m,IPf,N,xdata,ctx->SData_d,ctx->subThreadBlockSize,shift,ctx->events,JacP);CHKERRQ(ierr); 224 #else 225 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 226 #endif 227 } 228 //ierr = PetscLogStagePop();CHKERRQ(ierr); 229 } else { /* CPU version */ 230 PetscInt ei, qi; 231 PetscScalar *elemMat,coef_buff[LANDAU_MAX_SPECIES*LANDAU_MAX_NQ]; 232 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; 233 const PetscInt nip = Nq*numCells; 234 const PetscReal *const BB = Tf[0]->T[0], * const DD = Tf[0]->T[1]; 235 PetscReal Eq_m[LANDAU_MAX_SPECIES], invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES]; 236 if (shift!=0.0) { // mass 237 ierr = PetscMalloc1(elemMatSize, &elemMat);CHKERRQ(ierr); 238 } else { /* compute f and df and init data for Jacobian */ 239 ierr = PetscLogEventBegin(ctx->events[8],0,0,0,0);CHKERRQ(ierr); 240 for (fieldA=0;fieldA<Nf;fieldA++) { 241 invMass[fieldA] = m_0/ctx->masses[fieldA]; 242 Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */ 243 if (dim==2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */ 244 nu_alpha[fieldA] = PetscSqr(ctx->charges[fieldA]/m_0)*m_0/ctx->masses[fieldA]; 245 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); 246 } 247 ierr = PetscMalloc5(elemMatSize, &elemMat, nip*Nf, &ff, nip*Nf, &dudx, nip*Nf, &dudy, dim==3 ? nip*Nf : 0, &dudz);CHKERRQ(ierr); 248 for (ei = cStart, invJ = invJ_a; ei < cEnd; ++ei, invJ += Nq*dim*dim) { 249 PetscScalar *coef; 250 PetscInt b,f,idx,q; 251 PetscReal u_x[LANDAU_MAX_SPECIES][LANDAU_DIM]; 252 if (IPf) { 253 coef = &IPf[ei*Nb*Nf]; // this is const 254 /* for (f = 0; f < Nf; ++f) { */ 255 /* for (b = 0; b < Nb; ++b) { */ 256 /* PetscPrintf(ctx->comm,"%f ",coef[f*Nb+b]);CHKERRQ(ierr); */ 257 /* } */ 258 /* PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr); */ 259 /* } */ 260 /* PetscPrintf(ctx->comm,"*\n");CHKERRQ(ierr); */ 261 } else { 262 if (!maps) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"!maps"); 263 coef = coef_buff; 264 for (f = 0; f < Nf; ++f) { 265 LandauIdx *const Idxs = &maps->gIdx[ei-cStart][f][0]; 266 for (b = 0; b < Nb; ++b) { 267 idx = Idxs[b]; 268 if (idx >= 0) { 269 coef[f*Nb+b] = xdata[idx]; 270 } else { 271 idx = -idx - 1; 272 coef[f*Nb+b] = 0; 273 for (q = 0; q < maps->num_face; q++) { 274 PetscInt id = maps->c_maps[idx][q].gid; 275 PetscScalar scale = maps->c_maps[idx][q].scale; 276 coef[f*Nb+b] += scale*xdata[id]; 277 } 278 } 279 //PetscPrintf(ctx->comm,"%f ",coef[f*Nb+b]);CHKERRQ(ierr); 280 } 281 //PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr); 282 } 283 //PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr); 284 } 285 /* get f and df */ 286 for (qi = 0; qi < Nq; ++qi) { 287 const PetscReal *Bq = &BB[qi*Nb]; 288 const PetscReal *Dq = &DD[qi*Nb*dim]; 289 const PetscInt gidx = ei*Nq + qi; 290 /* get f & df */ 291 for (f = 0; f < Nf; ++f) { 292 PetscInt b, e; 293 PetscReal refSpaceDer[LANDAU_DIM]; 294 ff[gidx + f*nip] = 0.0; 295 for (d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0; 296 for (b = 0; b < Nb; ++b) { 297 const PetscInt cidx = b; 298 ff[gidx + f*nip] += Bq[cidx]*PetscRealPart(coef[f*Nb+cidx]); 299 for (d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx*dim+d]*PetscRealPart(coef[f*Nb+cidx]); 300 } 301 for (d = 0; d < dim; ++d) { 302 for (e = 0, u_x[f][d] = 0.0; e < dim; ++e) { 303 u_x[f][d] += invJ[qi * dim * dim + e*dim+d]*refSpaceDer[e]; 304 } 305 } 306 } 307 for (f=0;f<Nf;f++) { 308 dudx[gidx + f*nip] = u_x[f][0]; 309 dudy[gidx + f*nip] = u_x[f][1]; 310 #if LANDAU_DIM==3 311 dudz[gidx + f*nip] = u_x[f][2]; 312 #endif 313 } 314 } 315 } 316 ierr = PetscLogEventEnd(ctx->events[8],0,0,0,0);CHKERRQ(ierr); 317 } 318 for (ej = cStart, invJ = invJ_a; ej < cEnd; ++ej, invJ += Nq*dim*dim) { 319 ierr = PetscMemzero(elemMat, totDim *totDim * sizeof(PetscScalar));CHKERRQ(ierr); 320 ierr = PetscLogEventBegin(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 321 ierr = PetscLogFlops((PetscLogDouble)Nq*flops);CHKERRQ(ierr); 322 //printf("\t:%d.%d) Invj[0] = %e (%d)\n",ej,qj,invJ[0],(int)(invJ-invJ_a)); 323 for (qj = 0; qj < Nq; ++qj) { 324 const PetscReal * const BB = Tf[0]->T[0], * const DD = Tf[0]->T[1]; 325 PetscReal g0[LANDAU_MAX_SPECIES], g2[LANDAU_MAX_SPECIES][LANDAU_DIM], g3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM]; 326 PetscInt d,d2,dp,d3,ipidx,fieldA; 327 const PetscInt jpidx = Nq*(ej-cStart) + qj; 328 if (shift==0.0) { 329 const PetscReal * const invJj = &invJ[qj*dim*dim]; 330 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]; 331 const PetscReal vj[3] = {xx[jpidx], yy[jpidx], zz ? zz[jpidx] : 0}, wj = ww[jpidx]; 332 333 // create g2 & g3 334 for (d=0;d<dim;d++) { // clear accumulation data D & K 335 gg2_temp[d] = 0; 336 for (d2=0;d2<dim;d2++) gg3_temp[d][d2] = 0; 337 } 338 for (ipidx = 0; ipidx < nip; ipidx++) { 339 const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx]; 340 PetscReal temp1[3] = {0, 0, 0}, temp2 = 0; 341 #if LANDAU_DIM==2 342 PetscReal Ud[2][2], Uk[2][2]; 343 LandauTensor2D(vj, x, y, Ud, Uk, (ipidx==jpidx) ? 0. : 1.); 344 #else 345 PetscReal U[3][3], z = zz[ipidx]; 346 LandauTensor3D(vj, x, y, z, U, (ipidx==jpidx) ? 0. : 1.); 347 #endif 348 for (fieldA = 0; fieldA < Nf; ++fieldA) { 349 temp1[0] += dudx[ipidx + fieldA*nip]*nu_beta[fieldA]*invMass[fieldA]; 350 temp1[1] += dudy[ipidx + fieldA*nip]*nu_beta[fieldA]*invMass[fieldA]; 351 #if LANDAU_DIM==3 352 temp1[2] += dudz[ipidx + fieldA*nip]*nu_beta[fieldA]*invMass[fieldA]; 353 #endif 354 temp2 += ff[ipidx + fieldA*nip]*nu_beta[fieldA]; 355 } 356 temp1[0] *= wi; 357 temp1[1] *= wi; 358 #if LANDAU_DIM==3 359 temp1[2] *= wi; 360 #endif 361 temp2 *= wi; 362 #if LANDAU_DIM==2 363 for (d2 = 0; d2 < 2; d2++) { 364 for (d3 = 0; d3 < 2; ++d3) { 365 /* K = U * grad(f): g2=e: i,A */ 366 gg2_temp[d2] += Uk[d2][d3]*temp1[d3]; 367 /* D = -U * (I \kron (fx)): g3=f: i,j,A */ 368 gg3_temp[d2][d3] += Ud[d2][d3]*temp2; 369 } 370 } 371 #else 372 for (d2 = 0; d2 < 3; ++d2) { 373 for (d3 = 0; d3 < 3; ++d3) { 374 /* K = U * grad(f): g2 = e: i,A */ 375 gg2_temp[d2] += U[d2][d3]*temp1[d3]; 376 /* D = -U * (I \kron (fx)): g3 = f: i,j,A */ 377 gg3_temp[d2][d3] += U[d2][d3]*temp2; 378 } 379 } 380 #endif 381 } /* IPs */ 382 //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]); 383 // add alpha and put in gg2/3 384 for (fieldA = 0; fieldA < Nf; ++fieldA) { 385 for (d2 = 0; d2 < dim; d2++) { 386 gg2[fieldA][d2] = gg2_temp[d2]*nu_alpha[fieldA]; 387 for (d3 = 0; d3 < dim; d3++) { 388 gg3[fieldA][d2][d3] = -gg3_temp[d2][d3]*nu_alpha[fieldA]*invMass[fieldA]; 389 } 390 } 391 } 392 /* add electric field term once per IP */ 393 for (fieldA = 0; fieldA < Nf; ++fieldA) { 394 gg2[fieldA][dim-1] += Eq_m[fieldA]; 395 //printf("\t:%d.%d.%d) gg2 = %e %e\n",ej,qj,fieldA,gg2[fieldA][dim-1],Eq_m[fieldA]); 396 } 397 /* Jacobian transform - g2, g3 */ 398 for (fieldA = 0; fieldA < Nf; ++fieldA) { 399 for (d = 0; d < dim; ++d) { 400 g2[fieldA][d] = 0.0; 401 for (d2 = 0; d2 < dim; ++d2) { 402 //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]); 403 g2[fieldA][d] += invJj[d*dim+d2]*gg2[fieldA][d2]; 404 g3[fieldA][d][d2] = 0.0; 405 for (d3 = 0; d3 < dim; ++d3) { 406 for (dp = 0; dp < dim; ++dp) { 407 g3[fieldA][d][d2] += invJj[d*dim + d3]*gg3[fieldA][d3][dp]*invJj[d2*dim + dp]; 408 } 409 } 410 g3[fieldA][d][d2] *= wj; 411 } 412 //printf("\t:%d.%d.%d.%d) g2 = %e %e\n",ej,qj,fieldA,d,g2[fieldA][d],wj); 413 g2[fieldA][d] *= wj; 414 } 415 } 416 } else { // mass 417 /* Jacobian transform - g0 */ 418 for (fieldA = 0; fieldA < Nf; ++fieldA) { 419 g0[fieldA] = mass_w[jpidx] * shift; // move this to below and remove g0 420 } 421 } 422 /* FE matrix construction */ 423 { 424 PetscInt fieldA,d,f,d2,g; 425 const PetscReal *BJq = &BB[qj*Nb], *DIq = &DD[qj*Nb*dim]; 426 /* assemble - on the diagonal (I,I) */ 427 for (fieldA = 0; fieldA < Nf ; fieldA++) { 428 for (f = 0; f < Nb ; f++) { 429 const PetscInt i = fieldA*Nb + f; /* Element matrix row */ 430 for (g = 0; g < Nb; ++g) { 431 const PetscInt j = fieldA*Nb + g; /* Element matrix column */ 432 const PetscInt fOff = i*totDim + j; 433 if (shift==0.0) { 434 for (d = 0; d < dim; ++d) { 435 elemMat[fOff] += DIq[f*dim+d]*g2[fieldA][d]*BJq[g]; 436 //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]); 437 for (d2 = 0; d2 < dim; ++d2) { 438 elemMat[fOff] += DIq[f*dim + d]*g3[fieldA][d][d2]*DIq[g*dim + d2]; 439 } 440 } 441 } else { // mass 442 elemMat[fOff] += BJq[f]*g0[fieldA]*BJq[g]; 443 } 444 } 445 } 446 } 447 } 448 } /* qj loop */ 449 ierr = PetscLogEventEnd(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 450 /* assemble matrix */ 451 ierr = PetscLogEventBegin(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 452 if (!maps) { 453 ierr = DMPlexMatSetClosure(ctx->plex, section, globsection, JacP, ej, elemMat, ADD_VALUES);CHKERRQ(ierr); 454 } else { // GPU like assembly for debugging 455 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]; 456 PetscScalar vals[LANDAU_MAX_Q_FACE*LANDAU_MAX_Q_FACE],row_scale[LANDAU_MAX_Q_FACE],col_scale[LANDAU_MAX_Q_FACE]={0}; 457 //for (q = 0; q <LANDAU_MAX_Q_FACE; q++) cols0[q] = 0; 458 //for (q = 0; q < LANDAU_MAX_Q_FACE; q++) col_scale[q] = 0.0; // suppress warnings 459 /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */ 460 for (fieldA = 0; fieldA < Nf ; fieldA++) { 461 LandauIdx *const Idxs = &maps->gIdx[ej-cStart][fieldA][0]; 462 for (f = 0; f < Nb ; f++) { 463 idx = Idxs[f]; 464 if (idx >= 0) { 465 nr = 1; 466 rows0[0] = idx; 467 row_scale[0] = 1.; 468 } else { 469 idx = -idx - 1; 470 nr = maps->num_face; 471 for (q = 0; q < maps->num_face; q++) { 472 rows0[q] = maps->c_maps[idx][q].gid; 473 row_scale[q] = maps->c_maps[idx][q].scale; 474 } 475 } 476 for (g = 0; g < Nb; ++g) { 477 idx = Idxs[g]; 478 if (idx >= 0) { 479 nc = 1; 480 cols0[0] = idx; 481 col_scale[0] = 1.; 482 } else { 483 idx = -idx - 1; 484 nc = maps->num_face; 485 for (q = 0; q < maps->num_face; q++) { 486 cols0[q] = maps->c_maps[idx][q].gid; 487 col_scale[q] = maps->c_maps[idx][q].scale; 488 } 489 } 490 const PetscInt i = fieldA*Nb + f; /* Element matrix row */ 491 const PetscInt j = fieldA*Nb + g; /* Element matrix column */ 492 const PetscScalar Aij = elemMat[i*totDim + j]; 493 for (q = 0; q < nr; q++) rows[q] = rows0[q]; 494 for (q = 0; q < nc; q++) cols[q] = cols0[q]; 495 for (q = 0; q < nr; q++) { 496 for (d = 0; d < nc; d++) { 497 vals[q*nc + d] = row_scale[q]*col_scale[d]*Aij; 498 } 499 } 500 ierr = MatSetValues(JacP,nr,rows,nc,cols,vals,ADD_VALUES);CHKERRQ(ierr); 501 } 502 } 503 } 504 } 505 if (ej==-1) { 506 PetscErrorCode ierr2; 507 ierr2 = PetscPrintf(ctx->comm,"CPU Element matrix\n");CHKERRQ(ierr2); 508 for (d = 0; d < totDim; ++d){ 509 for (f = 0; f < totDim; ++f) {ierr2 = PetscPrintf(ctx->comm," %12.5e", PetscRealPart(elemMat[d*totDim + f]));CHKERRQ(ierr2);} 510 ierr2 = PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr2); 511 } 512 exit(12); 513 } 514 ierr = PetscLogEventEnd(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 515 } /* ej cells loop, not cuda */ 516 if (shift!=0.0) { // mass 517 ierr = PetscFree(elemMat);CHKERRQ(ierr); 518 } else { 519 ierr = PetscFree5(elemMat, ff, dudx, dudy, dudz);CHKERRQ(ierr); 520 } 521 } /* CPU version */ 522 523 /* assemble matrix or vector */ 524 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 525 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 526 #define MAP_BF_SIZE (128*LANDAU_DIM*LANDAU_MAX_Q_FACE*LANDAU_MAX_SPECIES) 527 if (ctx->gpu_assembly && !container) { 528 PetscScalar elemMatrix[LANDAU_MAX_NQ*LANDAU_MAX_NQ*LANDAU_MAX_SPECIES*LANDAU_MAX_SPECIES], *elMat; 529 pointInterpolationP4est pointMaps[MAP_BF_SIZE][LANDAU_MAX_Q_FACE]; 530 PetscInt q,eidx,fieldA; 531 MatType type; 532 ierr = PetscInfo1(ctx->plex, "Make GPU maps %D\n",1);CHKERRQ(ierr); 533 ierr = MatGetType(JacP,&type);CHKERRQ(ierr); 534 ierr = PetscLogEventBegin(ctx->events[2],0,0,0,0);CHKERRQ(ierr); 535 ierr = PetscMalloc(sizeof(P4estVertexMaps), &maps);CHKERRQ(ierr); 536 ierr = PetscContainerCreate(PETSC_COMM_SELF, &container);CHKERRQ(ierr); 537 ierr = PetscContainerSetPointer(container, (void *)maps);CHKERRQ(ierr); 538 ierr = PetscContainerSetUserDestroy(container, LandauGPUMapsDestroy);CHKERRQ(ierr); 539 ierr = PetscObjectCompose((PetscObject) JacP, "assembly_maps", (PetscObject) container);CHKERRQ(ierr); 540 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 541 // make maps 542 maps->data = NULL; 543 maps->num_elements = numCells; 544 maps->num_face = (PetscInt)(pow(Nq,1./((double)dim))+.001); // Q 545 maps->num_face = (PetscInt)(pow(maps->num_face,(double)(dim-1))+.001); // Q^2 546 maps->num_reduced = 0; 547 maps->deviceType = ctx->deviceType; 548 549 // count reduced and get 550 ierr = PetscMalloc(maps->num_elements * sizeof *maps->gIdx, &maps->gIdx);CHKERRQ(ierr); 551 for (fieldA=0;fieldA<Nf;fieldA++) { 552 for (ej = cStart, eidx = 0 ; ej < cEnd; ++ej, ++eidx) { 553 for (q = 0; q < Nb; ++q) { 554 PetscInt numindices,*indices; 555 PetscScalar *valuesOrig = elMat = elemMatrix; 556 ierr = PetscMemzero(elMat, totDim*totDim*sizeof(PetscScalar));CHKERRQ(ierr); 557 elMat[ (fieldA*Nb + q)*totDim + fieldA*Nb + q] = 1; 558 ierr = DMPlexGetClosureIndices(ctx->plex, section, globsection, ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 559 for (f = 0 ; f < numindices ; ++f) { // look for a non-zero on the diagonal 560 if (PetscAbs(PetscRealPart(elMat[f*numindices + f])) > PETSC_MACHINE_EPSILON) { 561 // found it 562 if (PetscAbs(PetscRealPart(elMat[f*numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { 563 maps->gIdx[eidx][fieldA][q] = (LandauIdx)indices[f]; // normal vertex 1.0 564 } else { //found a constraint 565 int jj = 0; 566 PetscReal sum = 0; 567 const PetscInt ff = f; 568 maps->gIdx[eidx][fieldA][q] = -maps->num_reduced - 1; // gid = -(idx+1): idx = -gid - 1 569 do { // constraints are continous in Plex - exploit that here 570 int ii; 571 for (ii = 0, pointMaps[maps->num_reduced][jj].scale = 0; ii < maps->num_face; ii++) { // DMPlex puts them all together 572 if (ff + ii < numindices) { 573 pointMaps[maps->num_reduced][jj].scale += PetscRealPart(elMat[f*numindices + ff + ii]); 574 } 575 } 576 sum += pointMaps[maps->num_reduced][jj].scale; 577 if (pointMaps[maps->num_reduced][jj].scale == 0) pointMaps[maps->num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps -- all contiguous??? 578 else pointMaps[maps->num_reduced][jj].gid = indices[f]; 579 } while (++jj < maps->num_face && ++f < numindices); // jj is incremented if we hit the end 580 while (jj++ < maps->num_face) { 581 pointMaps[maps->num_reduced][jj].scale = 0; 582 pointMaps[maps->num_reduced][jj].gid = -1; 583 } 584 if (PetscAbs(sum-1.0) > 10*PETSC_MACHINE_EPSILON) { // debug 585 int d,f; 586 PetscReal tmp = 0; 587 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); 588 for (d = 0, tmp = 0; d < numindices; ++d){ 589 if (tmp!=0 && PetscAbs(tmp-1.0) > 10*PETSC_MACHINE_EPSILON) ierr = PetscPrintf(PETSC_COMM_WORLD,"%3D) %3D: ",d,indices[d]);CHKERRQ(ierr); 590 for (f = 0; f < numindices; ++f) { 591 tmp += PetscRealPart(elMat[d*numindices + f]); 592 } 593 if (tmp!=0) ierr = PetscPrintf(ctx->comm," | %22.16e\n",tmp);CHKERRQ(ierr); 594 } 595 } 596 maps->num_reduced++; 597 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); 598 } 599 break; 600 } 601 } 602 // cleanup 603 ierr = DMPlexRestoreClosureIndices(ctx->plex, section, globsection, ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 604 if (elMat != valuesOrig) {ierr = DMRestoreWorkArray(ctx->plex, numindices*numindices, MPIU_SCALAR, &elMat);} 605 } 606 } 607 } 608 // allocate and copy point datamaps->gIdx[eidx][field][q] -- for CPU version of this code, for debugging 609 ierr = PetscMalloc(maps->num_reduced * sizeof *maps->c_maps, &maps->c_maps);CHKERRQ(ierr); 610 for (ej = 0; ej < maps->num_reduced; ++ej) { 611 for (q = 0; q < maps->num_face; ++q) { 612 maps->c_maps[ej][q].scale = pointMaps[ej][q].scale; 613 maps->c_maps[ej][q].gid = pointMaps[ej][q].gid; 614 } 615 } 616 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 617 if (ctx->deviceType == LANDAU_KOKKOS) { 618 ierr = LandauKokkosCreateMatMaps(maps, pointMaps,Nf,Nq);CHKERRQ(ierr); // imples Kokkos does 619 } // else could be CUDA 620 #endif 621 #if defined(PETSC_HAVE_CUDA) 622 if (ctx->deviceType == LANDAU_CUDA){ 623 ierr = LandauCUDACreateMatMaps(maps, pointMaps,Nf,Nq);CHKERRQ(ierr); 624 } 625 #endif 626 627 ierr = PetscLogEventEnd(ctx->events[2],0,0,0,0);CHKERRQ(ierr); 628 } 629 /* clean up */ 630 if (IPf) { 631 ierr = PetscFree(IPf);CHKERRQ(ierr); 632 } 633 if (xdata) { 634 ierr = VecRestoreArrayReadAndMemType(a_X,&xdata);CHKERRQ(ierr); 635 } 636 637 PetscFunctionReturn(0); 638 } 639 640 #if defined(LANDAU_ADD_BCS) 641 static void zero_bc(PetscInt dim, PetscInt Nf, PetscInt NfAux, 642 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 643 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 644 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar uexact[]) 645 { 646 uexact[0] = 0; 647 } 648 #endif 649 650 #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]; }} 651 static void CircleInflate(PetscReal r1, PetscReal r2, PetscReal r0, PetscInt num_sections, PetscReal x, PetscReal y, 652 PetscReal *outX, PetscReal *outY) 653 { 654 PetscReal rr = PetscSqrtReal(x*x + y*y), outfact, efact; 655 if (rr < r1 + PETSC_SQRT_MACHINE_EPSILON) { 656 *outX = x; *outY = y; 657 } else { 658 const PetscReal xy[2] = {x,y}, sinphi=y/rr, cosphi=x/rr; 659 PetscReal cth,sth,xyprime[2],Rth[2][2],rotcos,newrr; 660 if (num_sections==2) { 661 rotcos = 0.70710678118654; 662 outfact = 1.5; efact = 2.5; 663 /* rotate normalized vector into [-pi/4,pi/4) */ 664 if (sinphi >= 0.) { /* top cell, -pi/2 */ 665 cth = 0.707106781186548; sth = -0.707106781186548; 666 } else { /* bottom cell -pi/8 */ 667 cth = 0.707106781186548; sth = .707106781186548; 668 } 669 } else if (num_sections==3) { 670 rotcos = 0.86602540378443; 671 outfact = 1.5; efact = 2.5; 672 /* rotate normalized vector into [-pi/6,pi/6) */ 673 if (sinphi >= 0.5) { /* top cell, -pi/3 */ 674 cth = 0.5; sth = -0.866025403784439; 675 } else if (sinphi >= -.5) { /* mid cell 0 */ 676 cth = 1.; sth = .0; 677 } else { /* bottom cell +pi/3 */ 678 cth = 0.5; sth = 0.866025403784439; 679 } 680 } else if (num_sections==4) { 681 rotcos = 0.9238795325112; 682 outfact = 1.5; efact = 3; 683 /* rotate normalized vector into [-pi/8,pi/8) */ 684 if (sinphi >= 0.707106781186548) { /* top cell, -3pi/8 */ 685 cth = 0.38268343236509; sth = -0.923879532511287; 686 } else if (sinphi >= 0.) { /* mid top cell -pi/8 */ 687 cth = 0.923879532511287; sth = -.38268343236509; 688 } else if (sinphi >= -0.707106781186548) { /* mid bottom cell + pi/8 */ 689 cth = 0.923879532511287; sth = 0.38268343236509; 690 } else { /* bottom cell + 3pi/8 */ 691 cth = 0.38268343236509; sth = .923879532511287; 692 } 693 } else { 694 cth = 0.; sth = 0.; rotcos = 0; efact = 0; 695 } 696 Rth[0][0] = cth; Rth[0][1] =-sth; 697 Rth[1][0] = sth; Rth[1][1] = cth; 698 MATVEC2(Rth,xy,xyprime); 699 if (num_sections==2) { 700 newrr = xyprime[0]/rotcos; 701 } else { 702 PetscReal newcosphi=xyprime[0]/rr, rin = r1, rout = rr - rin; 703 PetscReal routmax = r0*rotcos/newcosphi - rin, nroutmax = r0 - rin, routfrac = rout/routmax; 704 newrr = rin + routfrac*nroutmax; 705 } 706 *outX = cosphi*newrr; *outY = sinphi*newrr; 707 /* grade */ 708 PetscReal fact,tt,rs,re, rr = PetscSqrtReal(PetscSqr(*outX) + PetscSqr(*outY)); 709 if (rr > r2) { rs = r2; re = r0; fact = outfact;} /* outer zone */ 710 else { rs = r1; re = r2; fact = efact;} /* electron zone */ 711 tt = (rs + PetscPowReal((rr - rs)/(re - rs),fact) * (re-rs)) / rr; 712 *outX *= tt; 713 *outY *= tt; 714 } 715 } 716 717 static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx) 718 { 719 LandauCtx *ctx = (LandauCtx*)a_ctx; 720 PetscReal r = abc[0], z = abc[1]; 721 if (ctx->inflate) { 722 PetscReal absR, absZ; 723 absR = PetscAbs(r); 724 absZ = PetscAbs(z); 725 CircleInflate(ctx->i_radius,ctx->e_radius,ctx->radius,ctx->num_sections,absR,absZ,&absR,&absZ); 726 r = (r > 0) ? absR : -absR; 727 z = (z > 0) ? absZ : -absZ; 728 } 729 xyz[0] = r; 730 xyz[1] = z; 731 if (dim==3) xyz[2] = abc[2]; 732 733 PetscFunctionReturn(0); 734 } 735 736 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) 737 { 738 PetscReal err = 0.0; 739 PetscInt f = *(PetscInt*)actx, j; 740 PetscFunctionBegin; 741 for (j = 0; j < dim; ++j) { 742 err += PetscSqr(PetscRealPart(u_x[f*dim+j])); 743 } 744 err = PetscRealPart(u[f]); /* just use rho */ 745 *error = volume * err; /* * (ctx->axisymmetric ? 2.*PETSC_PI * r : 1); */ 746 PetscFunctionReturn(0); 747 } 748 749 static PetscErrorCode LandauDMCreateVMesh(MPI_Comm comm, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM *dm) 750 { 751 PetscErrorCode ierr; 752 PetscReal radius = ctx->radius; 753 size_t len; 754 char fname[128] = ""; /* we can add a file if we want */ 755 756 PetscFunctionBegin; 757 /* create DM */ 758 ierr = PetscStrlen(fname, &len);CHKERRQ(ierr); 759 if (len) { 760 PetscInt dim2; 761 ierr = DMPlexCreateFromFile(comm, fname, ctx->interpolate, dm);CHKERRQ(ierr); 762 ierr = DMGetDimension(*dm, &dim2);CHKERRQ(ierr); 763 if (LANDAU_DIM != dim2) SETERRQ2(comm, PETSC_ERR_PLIB, "dim %D != LANDAU_DIM %d",dim2,LANDAU_DIM); 764 } else { /* p4est, quads */ 765 /* Create plex mesh of Landau domain */ 766 if (!ctx->sphere) { 767 PetscInt cells[] = {2,2,2}; 768 PetscReal lo[] = {-radius,-radius,-radius}, hi[] = {radius,radius,radius}; 769 DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim==2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 770 if (dim==2) { lo[0] = 0; cells[0] = 1; } 771 ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, cells, lo, hi, periodicity, PETSC_TRUE, dm);CHKERRQ(ierr); 772 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); /* needed for periodic */ 773 if (dim==3) {ierr = PetscObjectSetName((PetscObject) *dm, "cube");CHKERRQ(ierr);} 774 else {ierr = PetscObjectSetName((PetscObject) *dm, "half-plane");CHKERRQ(ierr);} 775 } else if (dim==2) { 776 PetscInt numCells,cells[16][4],i,j; 777 PetscInt numVerts; 778 PetscReal inner_radius1 = ctx->i_radius, inner_radius2 = ctx->e_radius; 779 PetscReal *flatCoords = NULL; 780 PetscInt *flatCells = NULL, *pcell; 781 if (ctx->num_sections==2) { 782 #if 1 783 numCells = 5; 784 numVerts = 10; 785 int cells2[][4] = { {0,1,4,3}, 786 {1,2,5,4}, 787 {3,4,7,6}, 788 {4,5,8,7}, 789 {6,7,8,9} }; 790 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 791 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 792 { 793 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 794 for (j = 0; j < numVerts-1; j++) { 795 PetscReal z, r, theta = -PETSC_PI/2 + (j%3) * PETSC_PI/2; 796 PetscReal rad = (j >= 6) ? inner_radius1 : (j >= 3) ? inner_radius2 : ctx->radius; 797 z = rad * PetscSinReal(theta); 798 coords[j][1] = z; 799 r = rad * PetscCosReal(theta); 800 coords[j][0] = r; 801 } 802 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 803 } 804 #else 805 numCells = 4; 806 numVerts = 8; 807 static int cells2[][4] = {{0,1,2,3}, 808 {4,5,1,0}, 809 {5,6,2,1}, 810 {6,7,3,2}}; 811 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 812 ierr = loc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 813 { 814 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 815 PetscInt j; 816 for (j = 0; j < 8; j++) { 817 PetscReal z, r; 818 PetscReal theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3.; 819 PetscReal rad = ctx->radius * ((j < 4) ? 0.5 : 1.0); 820 z = rad * PetscSinReal(theta); 821 coords[j][1] = z; 822 r = rad * PetscCosReal(theta); 823 coords[j][0] = r; 824 } 825 } 826 #endif 827 } else if (ctx->num_sections==3) { 828 numCells = 7; 829 numVerts = 12; 830 int cells2[][4] = { {0,1,5,4}, 831 {1,2,6,5}, 832 {2,3,7,6}, 833 {4,5,9,8}, 834 {5,6,10,9}, 835 {6,7,11,10}, 836 {8,9,10,11} }; 837 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 838 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 839 { 840 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 841 for (j = 0; j < numVerts; j++) { 842 PetscReal z, r, theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3; 843 PetscReal rad = (j >= 8) ? inner_radius1 : (j >= 4) ? inner_radius2 : ctx->radius; 844 z = rad * PetscSinReal(theta); 845 coords[j][1] = z; 846 r = rad * PetscCosReal(theta); 847 coords[j][0] = r; 848 } 849 } 850 } else if (ctx->num_sections==4) { 851 numCells = 10; 852 numVerts = 16; 853 int cells2[][4] = { {0,1,6,5}, 854 {1,2,7,6}, 855 {2,3,8,7}, 856 {3,4,9,8}, 857 {5,6,11,10}, 858 {6,7,12,11}, 859 {7,8,13,12}, 860 {8,9,14,13}, 861 {10,11,12,15}, 862 {12,13,14,15}}; 863 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 864 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 865 { 866 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 867 for (j = 0; j < numVerts-1; j++) { 868 PetscReal z, r, theta = -PETSC_PI/2 + (j%5) * PETSC_PI/4; 869 PetscReal rad = (j >= 10) ? inner_radius1 : (j >= 5) ? inner_radius2 : ctx->radius; 870 z = rad * PetscSinReal(theta); 871 coords[j][1] = z; 872 r = rad * PetscCosReal(theta); 873 coords[j][0] = r; 874 } 875 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 876 } 877 } else { 878 numCells = 0; 879 numVerts = 0; 880 } 881 for (j = 0, pcell = flatCells; j < numCells; j++, pcell += 4) { 882 pcell[0] = cells[j][0]; pcell[1] = cells[j][1]; 883 pcell[2] = cells[j][2]; pcell[3] = cells[j][3]; 884 } 885 ierr = DMPlexCreateFromCellListPetsc(comm,2,numCells,numVerts,4,ctx->interpolate,flatCells,2,flatCoords,dm);CHKERRQ(ierr); 886 ierr = PetscFree2(flatCoords,flatCells);CHKERRQ(ierr); 887 ierr = PetscObjectSetName((PetscObject) *dm, "semi-circle");CHKERRQ(ierr); 888 } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Velocity space meshes does not support cubed sphere"); 889 } 890 ierr = PetscObjectSetOptionsPrefix((PetscObject)*dm,prefix);CHKERRQ(ierr); 891 892 ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); /* Plex refine */ 893 894 { /* p4est? */ 895 char convType[256]; 896 PetscBool flg; 897 ierr = PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); 898 ierr = PetscOptionsFList("-dm_landau_type","Convert DMPlex to another format (should not be Plex!)","plexland.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); 899 ierr = PetscOptionsEnd(); 900 if (flg) { 901 DM dmforest; 902 ierr = DMConvert(*dm,convType,&dmforest);CHKERRQ(ierr); 903 if (dmforest) { 904 PetscBool isForest; 905 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 906 ierr = PetscObjectSetOptionsPrefix((PetscObject)dmforest,prefix);CHKERRQ(ierr); 907 ierr = DMIsForest(dmforest,&isForest);CHKERRQ(ierr); 908 if (isForest) { 909 if (ctx->sphere && ctx->inflate) { 910 ierr = DMForestSetBaseCoordinateMapping(dmforest,GeometryDMLandau,ctx);CHKERRQ(ierr); 911 } 912 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 913 ierr = DMDestroy(dm);CHKERRQ(ierr); 914 *dm = dmforest; 915 ctx->errorIndicator = ErrorIndicator_Simple; /* flag for Forest */ 916 } else SETERRQ(ctx->comm, PETSC_ERR_USER, "Converted to non Forest?"); 917 } else SETERRQ(ctx->comm, PETSC_ERR_USER, "Convert failed?"); 918 } 919 } 920 ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); 921 PetscFunctionReturn(0); 922 } 923 924 static PetscErrorCode SetupDS(DM dm, PetscInt dim, LandauCtx *ctx) 925 { 926 PetscErrorCode ierr; 927 PetscInt ii; 928 PetscFunctionBegin; 929 for (ii=0;ii<ctx->num_species;ii++) { 930 char buf[256]; 931 if (ii==0) ierr = PetscSNPrintf(buf, 256, "e"); 932 else {ierr = PetscSNPrintf(buf, 256, "i%D", ii);CHKERRQ(ierr);} 933 /* Setup Discretization - FEM */ 934 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &ctx->fe[ii]);CHKERRQ(ierr); 935 ierr = PetscObjectSetName((PetscObject) ctx->fe[ii], buf);CHKERRQ(ierr); 936 ierr = DMSetField(dm, ii, NULL, (PetscObject) ctx->fe[ii]);CHKERRQ(ierr); 937 } 938 ierr = DMCreateDS(dm);CHKERRQ(ierr); 939 if (1) { 940 PetscInt ii; 941 PetscSection section; 942 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 943 for (ii=0;ii<ctx->num_species;ii++){ 944 char buf[256]; 945 if (ii==0) ierr = PetscSNPrintf(buf, 256, "se"); 946 else ierr = PetscSNPrintf(buf, 256, "si%D", ii); 947 ierr = PetscSectionSetComponentName(section, ii, 0, buf);CHKERRQ(ierr); 948 } 949 } 950 PetscFunctionReturn(0); 951 } 952 953 /* Define a Maxwellian function for testing out the operator. */ 954 955 /* Using cartesian velocity space coordinates, the particle */ 956 /* density, [1/m^3], is defined according to */ 957 958 /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */ 959 960 /* Using some constant, c, we normalize the velocity vector into a */ 961 /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */ 962 963 /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */ 964 965 /* Defining $\theta=2T/mc^2$, we thus find that the probability density */ 966 /* for finding the particle within the interval in a box dx^3 around x is */ 967 968 /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */ 969 970 typedef struct { 971 LandauCtx *ctx; 972 PetscReal kT_m; 973 PetscReal n; 974 PetscReal shift; 975 } MaxwellianCtx; 976 977 static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx) 978 { 979 MaxwellianCtx *mctx = (MaxwellianCtx*)actx; 980 LandauCtx *ctx = mctx->ctx; 981 PetscInt i; 982 PetscReal v2 = 0, theta = 2*mctx->kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 983 PetscFunctionBegin; 984 /* compute the exponents, v^2 */ 985 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 986 /* evaluate the Maxwellian */ 987 u[0] = mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 988 if (mctx->shift!=0.) { 989 v2 = 0; 990 for (i = 0; i < dim-1; ++i) v2 += x[i]*x[i]; 991 v2 += (x[dim-1]-mctx->shift)*(x[dim-1]-mctx->shift); 992 /* evaluate the shifted Maxwellian */ 993 u[0] += mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 994 } 995 PetscFunctionReturn(0); 996 } 997 998 /*@ 999 LandauAddMaxwellians - Add a Maxwellian distribution to a state 1000 1001 Collective on X 1002 1003 Input Parameters: 1004 . dm - The mesh 1005 + time - Current time 1006 - temps - Temperatures of each species 1007 . ns - Number density of each species 1008 + actx - Landau context 1009 1010 Output Parameter: 1011 . X - The state 1012 1013 Level: beginner 1014 1015 .keywords: mesh 1016 .seealso: LandauCreateVelocitySpace() 1017 @*/ 1018 PetscErrorCode LandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], void *actx) 1019 { 1020 LandauCtx *ctx = (LandauCtx*)actx; 1021 PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar [], void *); 1022 PetscErrorCode ierr,ii; 1023 PetscInt dim; 1024 MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES]; 1025 1026 PetscFunctionBegin; 1027 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1028 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 1029 for (ii=0;ii<ctx->num_species;ii++) { 1030 mctxs[ii] = &data[ii]; 1031 data[ii].ctx = ctx; 1032 data[ii].kT_m = ctx->k*temps[ii]/ctx->masses[ii]; /* kT/m */ 1033 data[ii].n = ns[ii]; 1034 initu[ii] = maxwellian; 1035 data[ii].shift = 0; 1036 } 1037 data[0].shift = ctx->electronShift; 1038 /* need to make ADD_ALL_VALUES work - TODO */ 1039 ierr = DMProjectFunction(dm, time, initu, (void**)mctxs, INSERT_ALL_VALUES, X);CHKERRQ(ierr); 1040 PetscFunctionReturn(0); 1041 } 1042 1043 /* 1044 LandauSetInitialCondition - Addes Maxwellians with context 1045 1046 Collective on X 1047 1048 Input Parameters: 1049 . dm - The mesh 1050 + actx - Landau context with T and n 1051 1052 Output Parameter: 1053 . X - The state 1054 1055 Level: beginner 1056 1057 .keywords: mesh 1058 .seealso: LandauCreateVelocitySpace(), LandauAddMaxwellians() 1059 */ 1060 static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, void *actx) 1061 { 1062 LandauCtx *ctx = (LandauCtx*)actx; 1063 PetscErrorCode ierr; 1064 PetscFunctionBegin; 1065 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 1066 ierr = VecZeroEntries(X);CHKERRQ(ierr); 1067 ierr = LandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, ctx);CHKERRQ(ierr); 1068 PetscFunctionReturn(0); 1069 } 1070 1071 static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscReal refineTol[], PetscReal coarsenTol[], PetscInt type, LandauCtx *ctx, DM *newDM) 1072 { 1073 DM dm, plex, adaptedDM = NULL; 1074 PetscDS prob; 1075 PetscBool isForest; 1076 PetscQuadrature quad; 1077 PetscInt Nq, *Nb, cStart, cEnd, c, dim, qj, k; 1078 DMLabel adaptLabel = NULL; 1079 PetscErrorCode ierr; 1080 1081 PetscFunctionBegin; 1082 ierr = VecGetDM(sol, &dm);CHKERRQ(ierr); 1083 ierr = DMCreateDS(dm);CHKERRQ(ierr); 1084 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1085 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1086 ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr); 1087 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1088 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1089 ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr); 1090 ierr = PetscFEGetQuadrature(fem, &quad);CHKERRQ(ierr); 1091 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1092 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); 1093 ierr = PetscDSGetDimensions(prob, &Nb);CHKERRQ(ierr); 1094 if (type==4) { 1095 for (c = cStart; c < cEnd; c++) { 1096 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 1097 } 1098 ierr = PetscInfo1(sol, "Phase:%s: Uniform refinement\n","adaptToleranceFEM");CHKERRQ(ierr); 1099 } else if (type==2) { 1100 PetscInt rCellIdx[8], eCellIdx[64], iCellIdx[64], eMaxIdx = -1, iMaxIdx = -1, nr = 0, nrmax = (dim==3) ? 8 : 2; 1101 PetscReal minRad = PETSC_INFINITY, r, eMinRad = PETSC_INFINITY, iMinRad = PETSC_INFINITY; 1102 for (c = 0; c < 64; c++) { eCellIdx[c] = iCellIdx[c] = -1; } 1103 for (c = cStart; c < cEnd; c++) { 1104 PetscReal tt, v0[LANDAU_MAX_NQ*3], detJ[LANDAU_MAX_NQ]; 1105 ierr = DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ);CHKERRQ(ierr); 1106 for (qj = 0; qj < Nq; ++qj) { 1107 tt = PetscSqr(v0[dim*qj+0]) + PetscSqr(v0[dim*qj+1]) + PetscSqr(((dim==3) ? v0[dim*qj+2] : 0)); 1108 r = PetscSqrtReal(tt); 1109 if (r < minRad - PETSC_SQRT_MACHINE_EPSILON*10.) { 1110 minRad = r; 1111 nr = 0; 1112 rCellIdx[nr++]= c; 1113 ierr = PetscInfo4(sol, "\t\tPhase: adaptToleranceFEM Found first inner r=%e, cell %D, qp %D/%D\n", r, c, qj+1, Nq);CHKERRQ(ierr); 1114 } else if ((r-minRad) < PETSC_SQRT_MACHINE_EPSILON*100. && nr < nrmax) { 1115 for (k=0;k<nr;k++) if (c == rCellIdx[k]) break; 1116 if (k==nr) { 1117 rCellIdx[nr++]= c; 1118 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); 1119 } 1120 } 1121 if (ctx->sphere) { 1122 if ((tt=r-ctx->e_radius) > 0) { 1123 PetscInfo2(sol, "\t\t\t %D cell r=%g\n",c,tt); 1124 if (tt < eMinRad - PETSC_SQRT_MACHINE_EPSILON*100.) { 1125 eMinRad = tt; 1126 eMaxIdx = 0; 1127 eCellIdx[eMaxIdx++] = c; 1128 } else if (eMaxIdx > 0 && (tt-eMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != eCellIdx[eMaxIdx-1]) { 1129 eCellIdx[eMaxIdx++] = c; 1130 } 1131 } 1132 if ((tt=r-ctx->i_radius) > 0) { 1133 if (tt < iMinRad - 1.e-5) { 1134 iMinRad = tt; 1135 iMaxIdx = 0; 1136 iCellIdx[iMaxIdx++] = c; 1137 } else if (iMaxIdx > 0 && (tt-iMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != iCellIdx[iMaxIdx-1]) { 1138 iCellIdx[iMaxIdx++] = c; 1139 } 1140 } 1141 } 1142 } 1143 } 1144 for (k=0;k<nr;k++) { 1145 ierr = DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE);CHKERRQ(ierr); 1146 } 1147 if (ctx->sphere) { 1148 for (c = 0; c < eMaxIdx; c++) { 1149 ierr = DMLabelSetValue(adaptLabel, eCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 1150 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere e cell %D r=%g\n","adaptToleranceFEM",eCellIdx[c],eMinRad); 1151 } 1152 for (c = 0; c < iMaxIdx; c++) { 1153 ierr = DMLabelSetValue(adaptLabel, iCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 1154 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere i cell %D r=%g\n","adaptToleranceFEM",iCellIdx[c],iMinRad); 1155 } 1156 } 1157 ierr = PetscInfo4(sol, "Phase:%s: Adaptive refine origin cells %D,%D r=%g\n","adaptToleranceFEM",rCellIdx[0],rCellIdx[1],minRad); 1158 } else if (type==0 || type==1 || type==3) { /* refine along r=0 axis */ 1159 PetscScalar *coef = NULL; 1160 Vec coords; 1161 PetscInt csize,Nv,d,nz; 1162 DM cdm; 1163 PetscSection cs; 1164 ierr = DMGetCoordinatesLocal(dm, &coords);CHKERRQ(ierr); 1165 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1166 ierr = DMGetLocalSection(cdm, &cs);CHKERRQ(ierr); 1167 for (c = cStart; c < cEnd; c++) { 1168 PetscInt doit = 0, outside = 0; 1169 ierr = DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 1170 Nv = csize/dim; 1171 for (nz = d = 0; d < Nv; d++) { 1172 PetscReal z = PetscRealPart(coef[d*dim + (dim-1)]), x = PetscSqr(PetscRealPart(coef[d*dim + 0])) + ((dim==3) ? PetscSqr(PetscRealPart(coef[d*dim + 1])) : 0); 1173 x = PetscSqrtReal(x); 1174 if (x < PETSC_MACHINE_EPSILON*10. && PetscAbs(z)<PETSC_MACHINE_EPSILON*10.) doit = 1; /* refine origin */ 1175 else if (type==0 && (z < -PETSC_MACHINE_EPSILON*10. || z > ctx->re_radius+PETSC_MACHINE_EPSILON*10.)) outside++; /* first pass don't refine bottom */ 1176 else if (type==1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) outside++; /* don't refine outside electron refine radius */ 1177 else if (type==3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) outside++; /* don't refine outside ion refine radius */ 1178 if (x < PETSC_MACHINE_EPSILON*10.) nz++; 1179 } 1180 ierr = DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 1181 if (doit || (outside<Nv && nz)) { 1182 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 1183 } 1184 } 1185 ierr = PetscInfo1(sol, "Phase:%s: RE refinement\n","adaptToleranceFEM"); 1186 } 1187 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1188 ierr = DMAdaptLabel(dm, adaptLabel, &adaptedDM);CHKERRQ(ierr); 1189 ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); 1190 *newDM = adaptedDM; 1191 if (adaptedDM) { 1192 if (isForest) { 1193 ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr); 1194 } 1195 ierr = DMConvert(adaptedDM, DMPLEX, &plex);CHKERRQ(ierr); 1196 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1197 ierr = PetscInfo2(sol, "\tPhase: adaptToleranceFEM: %D cells, %d total quadrature points\n",cEnd-cStart,Nq*(cEnd-cStart));CHKERRQ(ierr); 1198 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1199 } 1200 PetscFunctionReturn(0); 1201 } 1202 1203 static PetscErrorCode adapt(DM *dm, LandauCtx *ctx, Vec *uu) 1204 { 1205 PetscErrorCode ierr; 1206 PetscInt type, limits[5] = {ctx->numRERefine,ctx->nZRefine1,ctx->maxRefIts,ctx->nZRefine2,ctx->postAMRRefine}; 1207 PetscInt adaptIter; 1208 1209 PetscFunctionBegin; 1210 for (type=0;type<5;type++) { 1211 for (adaptIter = 0; adaptIter<limits[type];adaptIter++) { 1212 DM dmNew = NULL; 1213 ierr = adaptToleranceFEM(ctx->fe[0], *uu, ctx->refineTol, ctx->coarsenTol, type, ctx, &dmNew);CHKERRQ(ierr); 1214 if (!dmNew) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"should not happen"); 1215 else { 1216 ierr = DMDestroy(dm);CHKERRQ(ierr); 1217 ierr = VecDestroy(uu);CHKERRQ(ierr); 1218 ierr = DMCreateGlobalVector(dmNew,uu);CHKERRQ(ierr); 1219 ierr = PetscObjectSetName((PetscObject) *uu, "u");CHKERRQ(ierr); 1220 ierr = LandauSetInitialCondition(dmNew, *uu, ctx);CHKERRQ(ierr); 1221 *dm = dmNew; 1222 } 1223 } 1224 } 1225 PetscFunctionReturn(0); 1226 } 1227 1228 static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[]) 1229 { 1230 PetscErrorCode ierr; 1231 PetscBool flg, sph_flg; 1232 PetscInt ii,nt,nm,nc; 1233 DM dummy; 1234 1235 PetscFunctionBegin; 1236 ierr = DMCreate(ctx->comm,&dummy);CHKERRQ(ierr); 1237 /* get options - initialize context */ 1238 ctx->verbose = 1; 1239 ctx->interpolate = PETSC_TRUE; 1240 ctx->gpu_assembly = PETSC_TRUE; 1241 ctx->sphere = PETSC_FALSE; 1242 ctx->inflate = PETSC_FALSE; 1243 ctx->electronShift = 0; 1244 ctx->errorIndicator = NULL; 1245 ctx->radius = 5.; /* electron thermal radius (velocity) */ 1246 ctx->re_radius = 0.; 1247 ctx->vperp0_radius1 = 0; 1248 ctx->vperp0_radius2 = 0; 1249 ctx->e_radius = .1; 1250 ctx->i_radius = .01; 1251 ctx->maxRefIts = 5; 1252 ctx->postAMRRefine = 0; 1253 ctx->nZRefine1 = 0; 1254 ctx->nZRefine2 = 0; 1255 ctx->numRERefine = 0; 1256 ctx->aux_bool = PETSC_FALSE; 1257 ctx->num_sections = 3; /* 2, 3 or 4 */ 1258 /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */ 1259 ctx->charges[0] = -1; /* electron charge (MKS) */ 1260 ctx->masses[0] = 1/1835.5; /* temporary value in proton mass */ 1261 ctx->n[0] = 1; 1262 ctx->thermal_temps[0] = 1; 1263 /* constants, etc. */ 1264 ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */ 1265 ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */ 1266 ctx->lnLam = 10; /* cross section ratio large - small angle collisions */ 1267 ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */ 1268 ctx->Ez = 0; 1269 ctx->v_0 = 1; /* in electron thermal velocity */ 1270 ctx->subThreadBlockSize = 1; /* for device and maybe OMP */ 1271 ctx->numConcurrency = 1; /* for device */ 1272 ctx->SData_d = NULL; /* for device */ 1273 ctx->times[0] = 0; 1274 ctx->init = PETSC_FALSE; // doit first time 1275 ctx->use_matrix_mass = PETSC_FALSE; /* fast but slightly fragile */ 1276 ctx->plex = NULL; /* cache as expensive to Convert */ 1277 ierr = PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");CHKERRQ(ierr); 1278 { 1279 char opstring[256]; 1280 #if defined(PETSC_HAVE_KOKKOS) 1281 ctx->deviceType = LANDAU_KOKKOS; 1282 ierr = PetscStrcpy(opstring,"kokkos");CHKERRQ(ierr); 1283 #if defined(PETSC_HAVE_CUDA) 1284 ctx->subThreadBlockSize = 16; 1285 #endif 1286 #elif defined(PETSC_HAVE_CUDA) 1287 ctx->deviceType = LANDAU_CUDA; 1288 ierr = PetscStrcpy(opstring,"cuda");CHKERRQ(ierr); 1289 #else 1290 ctx->deviceType = LANDAU_CPU; 1291 ierr = PetscStrcpy(opstring,"cpu");CHKERRQ(ierr); 1292 ctx->subThreadBlockSize = 0; 1293 #endif 1294 ierr = PetscOptionsString("-dm_landau_device_type","Use kernels on 'cpu', 'cuda', or 'kokkos'","plexland.c",opstring,opstring,256,NULL);CHKERRQ(ierr); 1295 ierr = PetscStrcmp("cpu",opstring,&flg);CHKERRQ(ierr); 1296 if (flg) { 1297 ctx->deviceType = LANDAU_CPU; 1298 ctx->subThreadBlockSize = 0; 1299 } else { 1300 ierr = PetscStrcmp("cuda",opstring,&flg);CHKERRQ(ierr); 1301 if (flg) { 1302 ctx->deviceType = LANDAU_CUDA; 1303 ctx->subThreadBlockSize = 0; 1304 } else { 1305 ierr = PetscStrcmp("kokkos",opstring,&flg);CHKERRQ(ierr); 1306 if (flg) ctx->deviceType = LANDAU_KOKKOS; 1307 else SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-dm_landau_device_type %s",opstring); 1308 } 1309 } 1310 } 1311 ierr = PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL);CHKERRQ(ierr); 1312 ierr = PetscOptionsReal("-dm_landau_electron_shift","Shift in thermal velocity of electrons","none",ctx->electronShift,&ctx->electronShift, NULL);CHKERRQ(ierr); 1313 ierr = PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, &sph_flg);CHKERRQ(ierr); 1314 ierr = PetscOptionsBool("-dm_landau_inflate", "With sphere, inflate for curved edges (no AMR)", "plexland.c", ctx->inflate, &ctx->inflate, NULL);CHKERRQ(ierr); 1315 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); 1316 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); 1317 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); 1318 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); 1319 ierr = PetscOptionsInt("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &ctx->postAMRRefine, NULL);CHKERRQ(ierr); 1320 ierr = PetscOptionsInt("-dm_landau_verbose", "", "plexland.c", ctx->verbose, &ctx->verbose, NULL);CHKERRQ(ierr); 1321 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); 1322 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); 1323 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); 1324 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); 1325 ierr = PetscOptionsReal("-dm_landau_n_0","Normalization constant for number density","plexland.c",ctx->n_0,&ctx->n_0, NULL);CHKERRQ(ierr); 1326 ierr = PetscOptionsReal("-dm_landau_ln_lambda","Cross section parameter","plexland.c",ctx->lnLam,&ctx->lnLam, NULL);CHKERRQ(ierr); 1327 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); 1328 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); 1329 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); 1330 1331 /* get num species with tempurature*/ 1332 { 1333 PetscReal arr[100]; 1334 nt = 100; 1335 ierr = PetscOptionsRealArray("-dm_landau_thermal_temps", "Temperature of each species [e,i_0,i_1,...] in keV", "plexland.c", arr, &nt, &flg);CHKERRQ(ierr); 1336 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); 1337 } 1338 nt = LANDAU_MAX_SPECIES; 1339 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) { 1340 ctx->thermal_temps[ii] = 1.; 1341 ctx->charges[ii] = 1; 1342 ctx->masses[ii] = 1; 1343 ctx->n[ii] = (ii==1) ? 1 : 0; 1344 } 1345 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); 1346 if (flg) { 1347 PetscInfo1(dummy, "num_species set to number of thermal temps provided (%D)\n",nt); 1348 ctx->num_species = nt; 1349 } else SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species"); 1350 for (ii=0;ii<ctx->num_species;ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */ 1351 nm = LANDAU_MAX_SPECIES-1; 1352 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); 1353 if (flg && nm != ctx->num_species-1) { 1354 SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"num ion masses %D != num species %D",nm,ctx->num_species-1); 1355 } 1356 nm = LANDAU_MAX_SPECIES; 1357 ierr = PetscOptionsRealArray("-dm_landau_n", "Normalized (by -n_0) number density of each species", "plexland.c", ctx->n, &nm, &flg);CHKERRQ(ierr); 1358 if (flg && nm != ctx->num_species) SETERRQ2(ctx->comm,PETSC_ERR_ARG_WRONG,"wrong num n: %D != num species %D",nm,ctx->num_species); 1359 ctx->n_0 *= ctx->n[0]; /* normalized number density */ 1360 for (ii=1;ii<ctx->num_species;ii++) ctx->n[ii] = ctx->n[ii]/ctx->n[0]; 1361 ctx->n[0] = 1; 1362 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */ 1363 ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */ 1364 ctx->m_0 = ctx->masses[0]; /* arbitrary reference mass, electrons */ 1365 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); 1366 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) */ 1367 nc = LANDAU_MAX_SPECIES-1; 1368 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); 1369 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); 1370 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */ 1371 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 */ 1372 /* geometry */ 1373 for (ii=0;ii<ctx->num_species;ii++) ctx->refineTol[ii] = PETSC_MAX_REAL; 1374 for (ii=0;ii<ctx->num_species;ii++) ctx->coarsenTol[ii] = 0.; 1375 ii = LANDAU_MAX_SPECIES; 1376 ierr = PetscOptionsRealArray("-dm_landau_refine_tol","tolerance for refining cells in AMR","plexland.c",ctx->refineTol, &ii, &flg);CHKERRQ(ierr); 1377 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #refine_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 1378 ii = LANDAU_MAX_SPECIES; 1379 ierr = PetscOptionsRealArray("-dm_landau_coarsen_tol","tolerance for coarsening cells in AMR","plexland.c",ctx->coarsenTol, &ii, &flg);CHKERRQ(ierr); 1380 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #coarsen_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 1381 ierr = PetscOptionsReal("-dm_landau_domain_radius","Phase space size in units of electron thermal velocity","plexland.c",ctx->radius,&ctx->radius, &flg);CHKERRQ(ierr); 1382 if (flg && ctx->radius <= 0) { /* negative is ratio of c */ 1383 if (ctx->radius == 0) ctx->radius = 0.75; 1384 else ctx->radius = -ctx->radius; 1385 ctx->radius = ctx->radius*299792458.0/ctx->v_0; 1386 ierr = PetscInfo1(dummy, "Change domain radius to %e\n",ctx->radius);CHKERRQ(ierr); 1387 } 1388 ierr = PetscOptionsReal("-dm_landau_i_radius","Ion thermal velocity, used for circular meshes","plexland.c",ctx->i_radius,&ctx->i_radius, &flg);CHKERRQ(ierr); 1389 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an ion radius but did not set sphere, user error really */ 1390 if (!flg) { 1391 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 */ 1392 } 1393 ierr = PetscOptionsReal("-dm_landau_e_radius","Electron thermal velocity, used for circular meshes","plexland.c",ctx->e_radius,&ctx->e_radius, &flg);CHKERRQ(ierr); 1394 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an e radius but did not set sphere, user error really */ 1395 if (!flg) { 1396 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 */ 1397 } 1398 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); 1399 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); 1400 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1401 for (ii=ctx->num_species;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0; 1402 if (ctx->verbose > 0) { 1403 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); 1404 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); 1405 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); 1406 } 1407 ierr = DMDestroy(&dummy);CHKERRQ(ierr); 1408 { 1409 PetscMPIInt rank; 1410 ierr = MPI_Comm_rank(ctx->comm, &rank);CHKERRMPI(ierr); 1411 /* PetscLogStage setup_stage; */ 1412 ierr = PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11]);CHKERRQ(ierr); /* 11 */ 1413 ierr = PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0]);CHKERRQ(ierr); /* 0 */ 1414 ierr = PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9]);CHKERRQ(ierr); /* 9 */ 1415 ierr = PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10]);CHKERRQ(ierr); /* 10 */ 1416 ierr = PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7]);CHKERRQ(ierr); /* 7 */ 1417 ierr = PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1]);CHKERRQ(ierr); /* 1 */ 1418 ierr = PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3]);CHKERRQ(ierr); /* 3 */ 1419 ierr = PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8]);CHKERRQ(ierr); /* 8 */ 1420 ierr = PetscLogEventRegister(" Kernel (GPU)", DM_CLASSID, &ctx->events[4]);CHKERRQ(ierr); /* 4 */ 1421 ierr = PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5]);CHKERRQ(ierr); /* 5 */ 1422 ierr = PetscLogEventRegister(" Jac-assemble", DM_CLASSID, &ctx->events[6]);CHKERRQ(ierr); /* 6 */ 1423 ierr = PetscLogEventRegister(" Jac asmbl setup", DM_CLASSID, &ctx->events[2]);CHKERRQ(ierr); /* 2 */ 1424 ierr = PetscLogEventRegister(" Other", DM_CLASSID, &ctx->events[13]);CHKERRQ(ierr); /* 13 */ 1425 1426 if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */ 1427 ierr = PetscOptionsClearValue(NULL,"-snes_converged_reason");CHKERRQ(ierr); 1428 ierr = PetscOptionsClearValue(NULL,"-ksp_converged_reason");CHKERRQ(ierr); 1429 ierr = PetscOptionsClearValue(NULL,"-snes_monitor");CHKERRQ(ierr); 1430 ierr = PetscOptionsClearValue(NULL,"-ksp_monitor");CHKERRQ(ierr); 1431 ierr = PetscOptionsClearValue(NULL,"-ts_monitor");CHKERRQ(ierr); 1432 ierr = PetscOptionsClearValue(NULL,"-ts_adapt_monitor");CHKERRQ(ierr); 1433 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1434 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_vec_view");CHKERRQ(ierr); 1435 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1436 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_vec_view");CHKERRQ(ierr); 1437 ierr = PetscOptionsClearValue(NULL,"-info");CHKERRQ(ierr); 1438 } 1439 } 1440 PetscFunctionReturn(0); 1441 } 1442 1443 /*@C 1444 LandauCreateVelocitySpace - Create a DMPlex velocity space mesh 1445 1446 Collective on comm 1447 1448 Input Parameters: 1449 + comm - The MPI communicator 1450 . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver) 1451 - prefix - prefix for options 1452 1453 Output Parameter: 1454 . dm - The DM object representing the mesh 1455 + X - A vector (user destroys) 1456 - J - Optional matrix (object destroys) 1457 1458 Level: beginner 1459 1460 .keywords: mesh 1461 .seealso: DMPlexCreate(), LandauDestroyVelocitySpace() 1462 @*/ 1463 PetscErrorCode LandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *dm) 1464 { 1465 PetscErrorCode ierr; 1466 LandauCtx *ctx; 1467 PetscBool prealloc_only,flg; 1468 1469 PetscFunctionBegin; 1470 if (dim!=2 && dim!=3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported"); 1471 ierr = PetscNew(&ctx);CHKERRQ(ierr); 1472 ctx->comm = comm; /* used for diagnostics and global errors */ 1473 /* process options */ 1474 ierr = ProcessOptions(ctx,prefix);CHKERRQ(ierr); 1475 /* Create Mesh */ 1476 ierr = LandauDMCreateVMesh(PETSC_COMM_SELF, dim, prefix, ctx, dm);CHKERRQ(ierr); 1477 prealloc_only = (*dm)->prealloc_only; 1478 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1479 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1480 /* create FEM */ 1481 ierr = SetupDS(*dm,dim,ctx);CHKERRQ(ierr); 1482 /* set initial state */ 1483 ierr = DMCreateGlobalVector(*dm,X);CHKERRQ(ierr); 1484 ierr = PetscObjectSetName((PetscObject) *X, "u");CHKERRQ(ierr); 1485 /* initial static refinement, no solve */ 1486 ierr = LandauSetInitialCondition(*dm, *X, ctx);CHKERRQ(ierr); 1487 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_pre_vec_view");CHKERRQ(ierr); 1488 /* forest refinement */ 1489 if (ctx->errorIndicator) { 1490 /* AMR */ 1491 ierr = adapt(dm,ctx,X);CHKERRQ(ierr); 1492 if ((*dm)->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"(*dm)->prealloc_only != prealloc_only"); 1493 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1494 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_amr_vec_view");CHKERRQ(ierr); 1495 } 1496 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1497 ctx->dmv = *dm; 1498 if (ctx->dmv->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"ctx->dmv->prealloc_only != prealloc_only"); 1499 ierr = DMCreateMatrix(ctx->dmv, &ctx->J);CHKERRQ(ierr); 1500 ierr = MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1501 ierr = MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE);CHKERRQ(ierr); 1502 if (J) *J = ctx->J; 1503 /* check for types that we need */ 1504 #if defined(PETSC_HAVE_KOKKOS) 1505 if (ctx->deviceType == LANDAU_CPU) { 1506 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJKOKKOS,MATMPIAIJKOKKOS,MATAIJKOKKOS,"");CHKERRQ(ierr); 1507 //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"); 1508 } 1509 #elif defined(PETSC_HAVE_CUDA) 1510 if (ctx->deviceType == LANDAU_CPU) { 1511 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJCUSPARSE,MATMPIAIJCUSPARSE,MATAIJCUSPARSE,"");CHKERRQ(ierr); 1512 //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"); 1513 } 1514 #endif 1515 if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */ 1516 if (ctx->deviceType == LANDAU_CUDA) { 1517 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJCUSPARSE,MATMPIAIJCUSPARSE,MATAIJCUSPARSE,"");CHKERRQ(ierr); 1518 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must use '-dm_mat_type aijcusparse -dm_vec_type cuda' for GPU assembly and Cuda"); 1519 } else if (ctx->deviceType == LANDAU_KOKKOS) { 1520 ierr = PetscObjectTypeCompareAny((PetscObject)ctx->J,&flg,MATSEQAIJKOKKOS,MATMPIAIJKOKKOS,MATAIJKOKKOS,"");CHKERRQ(ierr); 1521 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 1522 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must use '-dm_mat_type aijkokkos -dm_vec_type kokkos' for GPU assembly and Kokkos"); 1523 #else 1524 if (!flg) SETERRQ(ctx->comm,PETSC_ERR_ARG_WRONG,"must configure with '--download-kokkos-kernels=1' for GPU assembly and Kokkos"); 1525 #endif 1526 } 1527 } 1528 PetscFunctionReturn(0); 1529 } 1530 1531 /*@ 1532 LandauDestroyVelocitySpace - Destroy a DMPlex velocity space mesh 1533 1534 Collective on dm 1535 1536 Input/Output Parameters: 1537 . dm - the dm to destroy 1538 1539 Level: beginner 1540 1541 .keywords: mesh 1542 .seealso: LandauCreateVelocitySpace() 1543 @*/ 1544 PetscErrorCode LandauDestroyVelocitySpace(DM *dm) 1545 { 1546 PetscErrorCode ierr,ii; 1547 LandauCtx *ctx; 1548 PetscContainer container = NULL; 1549 PetscFunctionBegin; 1550 ierr = DMGetApplicationContext(*dm, &ctx);CHKERRQ(ierr); 1551 ierr = PetscObjectQuery((PetscObject)ctx->J,"coloring", (PetscObject*)&container);CHKERRQ(ierr); 1552 if (container) { 1553 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 1554 } 1555 ierr = MatDestroy(&ctx->M);CHKERRQ(ierr); 1556 ierr = MatDestroy(&ctx->J);CHKERRQ(ierr); 1557 for (ii=0;ii<ctx->num_species;ii++) { 1558 ierr = PetscFEDestroy(&ctx->fe[ii]);CHKERRQ(ierr); 1559 } 1560 if (ctx->deviceType == LANDAU_CUDA) { 1561 #if defined(PETSC_HAVE_CUDA) 1562 ierr = LandauCUDAStaticDataClear(ctx->SData_d);CHKERRQ(ierr); 1563 #else 1564 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 1565 #endif 1566 } else if (ctx->deviceType == LANDAU_KOKKOS) { 1567 #if defined(PETSC_HAVE_KOKKOS) 1568 ierr = LandauKokkosStaticDataClear(ctx->SData_d);CHKERRQ(ierr); 1569 #else 1570 SETERRQ1(ctx->comm,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 1571 #endif 1572 } else { 1573 if (ctx->SData_d) { /* in a CPU run */ 1574 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; 1575 ierr = PetscFree5(mass_w,ww,xx,yy,invJ);CHKERRQ(ierr); 1576 if (zz) { 1577 ierr = PetscFree(zz);CHKERRQ(ierr); 1578 } 1579 } 1580 } 1581 ierr = PetscFree(ctx->SData_d);CHKERRQ(ierr); 1582 if (ctx->times[0] > 0) { 1583 ierr = PetscPrintf(ctx->comm, "Landau Operator %d 1.0 %10.3e ....\n",10000,ctx->times[0]);CHKERRQ(ierr); 1584 } 1585 if (ctx->plex != NULL) { 1586 ierr = DMDestroy(&ctx->plex);CHKERRQ(ierr); 1587 } 1588 PetscFree(ctx); 1589 ierr = DMDestroy(dm);CHKERRQ(ierr); 1590 PetscFunctionReturn(0); 1591 } 1592 1593 /* < v, ru > */ 1594 static void f0_s_den(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1595 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1596 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1597 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1598 { 1599 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1600 f0[0] = u[ii]; 1601 } 1602 1603 /* < v, ru > */ 1604 static void f0_s_mom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1605 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1606 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1607 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1608 { 1609 PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]); 1610 f0[0] = x[jj]*u[ii]; /* x momentum */ 1611 } 1612 1613 static void f0_s_v2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1614 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1615 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1616 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1617 { 1618 PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]); 1619 double tmp1 = 0.; 1620 for (i = 0; i < dim; ++i) tmp1 += x[i]*x[i]; 1621 f0[0] = tmp1*u[ii]; 1622 } 1623 1624 /* < v, ru > */ 1625 static void f0_s_rden(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1626 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1627 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1628 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1629 { 1630 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1631 f0[0] = 2.*PETSC_PI*x[0]*u[ii]; 1632 } 1633 1634 /* < v, ru > */ 1635 static void f0_s_rmom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1636 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1637 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1638 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1639 { 1640 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1641 f0[0] = 2.*PETSC_PI*x[0]*x[1]*u[ii]; 1642 } 1643 1644 static void f0_s_rv2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1645 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1646 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1647 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1648 { 1649 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1650 f0[0] = 2.*PETSC_PI*x[0]*(x[0]*x[0] + x[1]*x[1])*u[ii]; 1651 } 1652 1653 /*@ 1654 LandauPrintNorms - collects moments and prints them 1655 1656 Collective on dm 1657 1658 Input Parameters: 1659 + X - the state 1660 - stepi - current step to print 1661 1662 Level: beginner 1663 1664 .keywords: mesh 1665 .seealso: LandauCreateVelocitySpace() 1666 @*/ 1667 PetscErrorCode LandauPrintNorms(Vec X, PetscInt stepi) 1668 { 1669 PetscErrorCode ierr; 1670 LandauCtx *ctx; 1671 PetscDS prob; 1672 DM dm; 1673 PetscInt cStart, cEnd, dim, ii; 1674 PetscScalar xmomentumtot=0, ymomentumtot=0, zmomentumtot=0, energytot=0, densitytot=0, tt[LANDAU_MAX_SPECIES]; 1675 PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES]; 1676 1677 PetscFunctionBegin; 1678 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 1679 if (!dm) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no DM"); 1680 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1681 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1682 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1683 if (!ctx->plex) { 1684 ierr = DMConvert(ctx->dmv, DMPLEX, &ctx->plex);CHKERRQ(ierr); 1685 } 1686 ierr = DMCreateDS(ctx->plex);CHKERRQ(ierr); 1687 ierr = DMGetDS(ctx->plex, &prob);CHKERRQ(ierr); 1688 /* print momentum and energy */ 1689 for (ii=0;ii<ctx->num_species;ii++) { 1690 PetscScalar user[2] = { (PetscScalar)ii, (PetscScalar)ctx->charges[ii]}; 1691 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 1692 if (dim==2) { /* 2/3X + 3V (cylindrical coordinates) */ 1693 ierr = PetscDSSetObjective(prob, 0, &f0_s_rden);CHKERRQ(ierr); 1694 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1695 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1696 ierr = PetscDSSetObjective(prob, 0, &f0_s_rmom);CHKERRQ(ierr); 1697 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1698 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1699 ierr = PetscDSSetObjective(prob, 0, &f0_s_rv2);CHKERRQ(ierr); 1700 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1701 energy[ii] = tt[0]*0.5*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1702 zmomentumtot += zmomentum[ii]; 1703 energytot += energy[ii]; 1704 densitytot += density[ii]; 1705 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); 1706 } else { /* 2/3X + 3V */ 1707 ierr = PetscDSSetObjective(prob, 0, &f0_s_den);CHKERRQ(ierr); 1708 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1709 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1710 ierr = PetscDSSetObjective(prob, 0, &f0_s_mom);CHKERRQ(ierr); 1711 user[1] = 0; 1712 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1713 xmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1714 user[1] = 1; 1715 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1716 ymomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1717 user[1] = 2; 1718 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1719 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1720 ierr = PetscDSSetObjective(prob, 0, &f0_s_v2);CHKERRQ(ierr); 1721 ierr = DMPlexComputeIntegralFEM(ctx->plex,X,tt,ctx);CHKERRQ(ierr); 1722 energy[ii] = 0.5*tt[0]*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1723 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", 1724 stepi,ii,PetscRealPart(density[ii]),PetscRealPart(xmomentum[ii]),PetscRealPart(ymomentum[ii]),PetscRealPart(zmomentum[ii]),PetscRealPart(energy[ii]));CHKERRQ(ierr); 1725 xmomentumtot += xmomentum[ii]; 1726 ymomentumtot += ymomentum[ii]; 1727 zmomentumtot += zmomentum[ii]; 1728 energytot += energy[ii]; 1729 densitytot += density[ii]; 1730 } 1731 if (ctx->num_species>1) PetscPrintf(ctx->comm, "\n"); 1732 } 1733 /* totals */ 1734 ierr = DMPlexGetHeightStratum(ctx->plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1735 if (ctx->num_species>1) { 1736 if (dim==2) { 1737 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)", 1738 stepi,(double)PetscRealPart(densitytot),(double)PetscRealPart(zmomentumtot),(double)PetscRealPart(energytot),(double)(ctx->masses[1]/ctx->masses[0]),cEnd-cStart);CHKERRQ(ierr); 1739 } else { 1740 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)", 1741 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); 1742 } 1743 } else { 1744 ierr = PetscPrintf(ctx->comm, " -- %D cells",cEnd-cStart);CHKERRQ(ierr); 1745 } 1746 if (ctx->verbose > 1) {ierr = PetscPrintf(ctx->comm,", %D sub (vector) threads\n",ctx->subThreadBlockSize);CHKERRQ(ierr);} 1747 else {ierr = PetscPrintf(ctx->comm,"\n");CHKERRQ(ierr);} 1748 PetscFunctionReturn(0); 1749 } 1750 1751 static PetscErrorCode destroy_coloring (void *is) 1752 { 1753 ISColoring tmp = (ISColoring)is; 1754 return ISColoringDestroy(&tmp); 1755 } 1756 1757 /*@ 1758 LandauCreateColoring - create a coloring and add to matrix (Landau context used just for 'print' flag, should be in DMPlex) 1759 1760 Collective on JacP 1761 1762 Input Parameters: 1763 + JacP - matrix to add coloring to 1764 - plex - The DM 1765 1766 Output Parameter: 1767 . container - Container with coloring 1768 1769 Level: beginner 1770 1771 .keywords: mesh 1772 .seealso: LandauCreateVelocitySpace() 1773 @*/ 1774 PetscErrorCode LandauCreateColoring(Mat JacP, DM plex, PetscContainer *container) 1775 { 1776 PetscErrorCode ierr; 1777 PetscInt dim,cell,i,ej,nc,Nv,totDim,numGCells,cStart,cEnd; 1778 ISColoring iscoloring = NULL; 1779 Mat G,Q; 1780 PetscScalar ones[128]; 1781 MatColoring mc; 1782 IS *is; 1783 PetscInt csize,colour,j,k; 1784 const PetscInt *indices; 1785 PetscInt numComp[1]; 1786 PetscInt numDof[4]; 1787 PetscFE fe; 1788 DM colordm; 1789 PetscSection csection, section, globalSection; 1790 PetscDS prob; 1791 LandauCtx *ctx; 1792 1793 PetscFunctionBegin; 1794 ierr = DMGetApplicationContext(plex, &ctx);CHKERRQ(ierr); 1795 ierr = DMGetLocalSection(plex, §ion);CHKERRQ(ierr); 1796 ierr = DMGetGlobalSection(plex, &globalSection);CHKERRQ(ierr); 1797 ierr = DMGetDimension(plex, &dim);CHKERRQ(ierr); 1798 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 1799 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1800 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1801 numGCells = cEnd - cStart; 1802 /* create cell centered DM */ 1803 ierr = DMClone(plex, &colordm);CHKERRQ(ierr); 1804 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) plex), dim, 1, PETSC_FALSE, "color_", PETSC_DECIDE, &fe);CHKERRQ(ierr); 1805 ierr = PetscObjectSetName((PetscObject) fe, "color");CHKERRQ(ierr); 1806 ierr = DMSetField(colordm, 0, NULL, (PetscObject)fe);CHKERRQ(ierr); 1807 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 1808 for (i = 0; i < (dim+1); ++i) numDof[i] = 0; 1809 numDof[dim] = 1; 1810 numComp[0] = 1; 1811 ierr = DMPlexCreateSection(colordm, NULL, numComp, numDof, 0, NULL, NULL, NULL, NULL, &csection);CHKERRQ(ierr); 1812 ierr = PetscSectionSetFieldName(csection, 0, "color");CHKERRQ(ierr); 1813 ierr = DMSetLocalSection(colordm, csection);CHKERRQ(ierr); 1814 ierr = DMViewFromOptions(colordm,NULL,"-color_dm_view");CHKERRQ(ierr); 1815 /* get vertex to element map Q and colroing graph G */ 1816 ierr = MatGetSize(JacP,NULL,&Nv);CHKERRQ(ierr); 1817 ierr = MatCreateAIJ(PETSC_COMM_SELF,PETSC_DECIDE,PETSC_DECIDE,numGCells,Nv,totDim,NULL,0,NULL,&Q);CHKERRQ(ierr); 1818 for (i=0;i<128;i++) ones[i] = 1.0; 1819 for (cell = cStart, ej = 0 ; cell < cEnd; ++cell, ++ej) { 1820 PetscInt numindices,*indices; 1821 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1822 if (numindices>128) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many indices. %D > %D",numindices,128); 1823 ierr = MatSetValues(Q,1,&ej,numindices,indices,ones,ADD_VALUES);CHKERRQ(ierr); 1824 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1825 } 1826 ierr = MatAssemblyBegin(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1827 ierr = MatAssemblyEnd(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1828 ierr = MatMatTransposeMult(Q,Q,MAT_INITIAL_MATRIX,4.0,&G);CHKERRQ(ierr); 1829 ierr = PetscObjectSetName((PetscObject) Q, "Q");CHKERRQ(ierr); 1830 ierr = PetscObjectSetName((PetscObject) G, "coloring graph");CHKERRQ(ierr); 1831 ierr = MatViewFromOptions(G,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1832 ierr = MatViewFromOptions(Q,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1833 ierr = MatDestroy(&Q);CHKERRQ(ierr); 1834 /* coloring */ 1835 ierr = MatColoringCreate(G,&mc);CHKERRQ(ierr); 1836 ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr); 1837 ierr = MatColoringSetType(mc,MATCOLORINGJP);CHKERRQ(ierr); 1838 ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr); 1839 ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr); 1840 ierr = MatColoringDestroy(&mc);CHKERRQ(ierr); 1841 /* view */ 1842 ierr = ISColoringViewFromOptions(iscoloring,NULL,"-coloring_is_view");CHKERRQ(ierr); 1843 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1844 if (ctx && ctx->verbose > 2) { 1845 PetscViewer viewer; 1846 Vec color_vec, eidx_vec; 1847 ierr = DMGetGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1848 ierr = DMGetGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1849 for (colour=0; colour<nc; colour++) { 1850 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1851 ierr = ISGetIndices(is[colour],&indices);CHKERRQ(ierr); 1852 for (j=0; j<csize; j++) { 1853 PetscScalar v = (PetscScalar)colour; 1854 k = indices[j]; 1855 ierr = VecSetValues(color_vec,1,&k,&v,INSERT_VALUES); 1856 v = (PetscScalar)k; 1857 ierr = VecSetValues(eidx_vec,1,&k,&v,INSERT_VALUES); 1858 } 1859 ierr = ISRestoreIndices(is[colour],&indices);CHKERRQ(ierr); 1860 } 1861 /* view */ 1862 ierr = PetscViewerVTKOpen(ctx->comm, "color.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1863 ierr = PetscObjectSetName((PetscObject) color_vec, "color");CHKERRQ(ierr); 1864 ierr = VecView(color_vec, viewer);CHKERRQ(ierr); 1865 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1866 ierr = PetscViewerVTKOpen(ctx->comm, "eidx.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1867 ierr = PetscObjectSetName((PetscObject) eidx_vec, "element-idx");CHKERRQ(ierr); 1868 ierr = VecView(eidx_vec, viewer);CHKERRQ(ierr); 1869 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1870 ierr = DMRestoreGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1871 ierr = DMRestoreGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1872 } 1873 ierr = PetscSectionDestroy(&csection);CHKERRQ(ierr); 1874 ierr = DMDestroy(&colordm);CHKERRQ(ierr); 1875 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1876 ierr = MatDestroy(&G);CHKERRQ(ierr); 1877 /* stash coloring */ 1878 ierr = PetscContainerCreate(PETSC_COMM_SELF, container);CHKERRQ(ierr); 1879 ierr = PetscContainerSetPointer(*container,(void*)iscoloring);CHKERRQ(ierr); 1880 ierr = PetscContainerSetUserDestroy(*container, destroy_coloring);CHKERRQ(ierr); 1881 ierr = PetscObjectCompose((PetscObject)JacP,"coloring",(PetscObject)*container);CHKERRQ(ierr); 1882 if (ctx && ctx->verbose > 0) { 1883 ierr = PetscPrintf(ctx->comm, "Made coloring with %D colors\n", nc);CHKERRQ(ierr); 1884 } 1885 PetscFunctionReturn(0); 1886 } 1887 1888 PetscErrorCode LandauAssembleOpenMP(PetscInt cStart, PetscInt cEnd, PetscInt totDim, DM plex, PetscSection section, PetscSection globalSection, Mat JacP, PetscScalar elemMats[], PetscContainer container) 1889 { 1890 PetscErrorCode ierr; 1891 IS *is; 1892 PetscInt nc,colour,j; 1893 const PetscInt *clr_idxs; 1894 ISColoring iscoloring; 1895 PetscFunctionBegin; 1896 ierr = PetscContainerGetPointer(container,(void**)&iscoloring);CHKERRQ(ierr); 1897 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1898 for (colour=0; colour<nc; colour++) { 1899 PetscInt *idx_arr[1024]; /* need to make dynamic for general use */ 1900 PetscScalar *new_el_mats[1024]; 1901 PetscInt idx_size[1024],csize; 1902 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1903 if (csize>1024) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many elements in color. %D > %D",csize,1024); 1904 ierr = ISGetIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1905 /* get indices and mats */ 1906 for (j=0; j<csize; j++) { 1907 PetscInt cell = cStart + clr_idxs[j]; 1908 PetscInt numindices,*indices; 1909 PetscScalar *elMat = &elemMats[clr_idxs[j]*totDim*totDim]; 1910 PetscScalar *valuesOrig = elMat; 1911 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1912 idx_size[j] = numindices; 1913 ierr = PetscMalloc2(numindices,&idx_arr[j],numindices*numindices,&new_el_mats[j]);CHKERRQ(ierr); 1914 ierr = PetscMemcpy(idx_arr[j],indices,numindices*sizeof(PetscInt));CHKERRQ(ierr); 1915 ierr = PetscMemcpy(new_el_mats[j],elMat,numindices*numindices*sizeof(PetscScalar));CHKERRQ(ierr); 1916 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1917 if (elMat != valuesOrig) {ierr = DMRestoreWorkArray(plex, numindices*numindices, MPIU_SCALAR, &elMat);} 1918 } 1919 /* assemble matrix */ 1920 for (j=0; j<csize; j++) { 1921 PetscInt numindices = idx_size[j], *indices = idx_arr[j]; 1922 PetscScalar *elMat = new_el_mats[j]; 1923 MatSetValues(JacP,numindices,indices,numindices,indices,elMat,ADD_VALUES); 1924 } 1925 /* free */ 1926 ierr = ISRestoreIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1927 for (j=0; j<csize; j++) { 1928 ierr = PetscFree2(idx_arr[j],new_el_mats[j]);CHKERRQ(ierr); 1929 } 1930 } 1931 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1932 PetscFunctionReturn(0); 1933 } 1934 1935 /* < v, u > */ 1936 static void g0_1(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1937 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1938 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1939 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1940 { 1941 g0[0] = 1.; 1942 } 1943 1944 /* < v, u > */ 1945 static void g0_r(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1946 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1947 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1948 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1949 { 1950 g0[0] = 2.*PETSC_PI*x[0]; 1951 } 1952 1953 /*@ 1954 LandauCreateMassMatrix - Create mass matrix for Landau 1955 1956 Collective on dm 1957 1958 Input Parameters: 1959 . dm - the DM object 1960 1961 Output Parameters: 1962 . Amat - The mass matrix (optional), mass matrix is added to the DM context 1963 1964 Level: beginner 1965 1966 .keywords: mesh 1967 .seealso: LandauCreateVelocitySpace() 1968 @*/ 1969 PetscErrorCode LandauCreateMassMatrix(DM dm, Mat *Amat) 1970 { 1971 DM massDM; 1972 PetscDS prob; 1973 PetscInt ii,dim,N1=1,N2; 1974 PetscErrorCode ierr; 1975 LandauCtx *ctx; 1976 Mat M; 1977 1978 PetscFunctionBegin; 1979 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1980 if (Amat) PetscValidPointer(Amat,2); 1981 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1982 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1983 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1984 ierr = DMClone(dm, &massDM);CHKERRQ(ierr); 1985 ierr = DMCopyFields(dm, massDM);CHKERRQ(ierr); 1986 ierr = DMCreateDS(massDM);CHKERRQ(ierr); 1987 ierr = DMGetDS(massDM, &prob);CHKERRQ(ierr); 1988 for (ii=0;ii<ctx->num_species;ii++) { 1989 if (dim==3) {ierr = PetscDSSetJacobian(prob, ii, ii, g0_1, NULL, NULL, NULL);CHKERRQ(ierr);} 1990 else {ierr = PetscDSSetJacobian(prob, ii, ii, g0_r, NULL, NULL, NULL);CHKERRQ(ierr);} 1991 } 1992 ierr = DMViewFromOptions(massDM,NULL,"-dm_landau_mass_dm_view");CHKERRQ(ierr); 1993 ierr = DMCreateMatrix(massDM, &M);CHKERRQ(ierr); 1994 ierr = MatSetOption(M, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1995 { 1996 Vec locX; 1997 DM plex; 1998 ierr = DMConvert(massDM, DMPLEX, &plex);CHKERRQ(ierr); 1999 ierr = DMGetLocalVector(massDM, &locX);CHKERRQ(ierr); 2000 /* Mass matrix is independent of the input, so no need to fill locX */ 2001 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); 2002 ierr = DMPlexSNESComputeJacobianFEM(plex, locX, M, M, ctx);CHKERRQ(ierr); 2003 ierr = DMRestoreLocalVector(massDM, &locX);CHKERRQ(ierr); 2004 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2005 } 2006 ierr = DMDestroy(&massDM);CHKERRQ(ierr); 2007 ierr = MatGetSize(ctx->J, &N1, NULL);CHKERRQ(ierr); 2008 ierr = MatGetSize(M, &N2, NULL);CHKERRQ(ierr); 2009 if (N1 != N2) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %D, |Mass|=%D",N1,N2); 2010 ierr = PetscObjectSetName((PetscObject)M, "mass");CHKERRQ(ierr); 2011 ierr = MatViewFromOptions(M,NULL,"-dm_landau_mass_mat_view");CHKERRQ(ierr); 2012 ctx->M = M; /* this could be a noop, a = a */ 2013 if (Amat) *Amat = M; 2014 PetscFunctionReturn(0); 2015 } 2016 2017 /*@ 2018 LandauIFunction - TS residual calculation 2019 2020 Collective on ts 2021 2022 Input Parameters: 2023 + TS - The time stepping context 2024 . time_dummy - current time (not used) 2025 - X - Current state 2026 + X_t - Time derivative of current state 2027 . actx - Landau context 2028 2029 Output Parameter: 2030 . F - The residual 2031 2032 Level: beginner 2033 2034 .keywords: mesh 2035 .seealso: LandauCreateVelocitySpace(), LandauIJacobian() 2036 @*/ 2037 PetscErrorCode LandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx) 2038 { 2039 PetscErrorCode ierr; 2040 LandauCtx *ctx=(LandauCtx*)actx; 2041 PetscInt dim; 2042 DM dm; 2043 #if defined(PETSC_HAVE_THREADSAFETY) 2044 double starttime, endtime; 2045 #endif 2046 2047 PetscFunctionBegin; 2048 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 2049 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 2050 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2051 //ierr = MPI_Barrier(MPI_COMM_WORLD);CHKERRMPI(ierr); 2052 ierr = PetscLogEventBegin(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2053 ierr = PetscLogEventBegin(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 2054 #if defined(PETSC_HAVE_THREADSAFETY) 2055 starttime = MPI_Wtime(); 2056 #endif 2057 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 2058 if (!ctx->aux_bool) { 2059 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); 2060 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,0.0,(void*)ctx);CHKERRQ(ierr); 2061 ctx->aux_bool = PETSC_TRUE; 2062 } else { 2063 ierr = PetscInfo(ts, "Skip forming Jacobian, has not changed (should check norm)\n");CHKERRQ(ierr); 2064 } 2065 ierr = MatViewFromOptions(ctx->J,NULL,"-landau_jacobian_mat_view");CHKERRQ(ierr); 2066 /* mat vec for op */ 2067 ierr = MatMult(ctx->J,X,F);CHKERRQ(ierr);CHKERRQ(ierr); /* C*f */ 2068 /* add time term */ 2069 if (X_t) { 2070 ierr = MatMultAdd(ctx->M,X_t,F,F);CHKERRQ(ierr); 2071 } 2072 #if defined(PETSC_HAVE_THREADSAFETY) 2073 endtime = MPI_Wtime(); 2074 ctx->times[0] += (endtime - starttime); 2075 #endif 2076 ierr = PetscLogEventEnd(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 2077 ierr = PetscLogEventEnd(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2078 PetscFunctionReturn(0); 2079 } 2080 static PetscErrorCode MatrixNfDestroy(void *ptr) 2081 { 2082 PetscInt *nf = (PetscInt *)ptr; 2083 PetscErrorCode ierr; 2084 PetscFunctionBegin; 2085 ierr = PetscFree(nf);CHKERRQ(ierr); 2086 PetscFunctionReturn(0); 2087 } 2088 /*@ 2089 LandauIJacobian - TS Jacobian construction 2090 2091 Collective on ts 2092 2093 Input Parameters: 2094 + TS - The time stepping context 2095 . time_dummy - current time (not used) 2096 - X - Current state 2097 + U_tdummy - Time derivative of current state (not used) 2098 . shift - shift for du/dt term 2099 - actx - Landau context 2100 2101 Output Parameter: 2102 . Amat - Jacobian 2103 + Pmat - same as Amat 2104 2105 Level: beginner 2106 2107 .keywords: mesh 2108 .seealso: LandauCreateVelocitySpace(), LandauIFunction() 2109 @*/ 2110 PetscErrorCode LandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx) 2111 { 2112 PetscErrorCode ierr; 2113 LandauCtx *ctx=(LandauCtx*)actx; 2114 PetscInt dim; 2115 DM dm; 2116 PetscContainer container; 2117 #if defined(PETSC_HAVE_THREADSAFETY) 2118 double starttime, endtime; 2119 #endif 2120 2121 PetscFunctionBegin; 2122 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 2123 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 2124 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 2125 if (Amat!=Pmat || Amat!=ctx->J) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J"); 2126 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 2127 /* get collision Jacobian into A */ 2128 ierr = PetscLogEventBegin(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2129 ierr = PetscLogEventBegin(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 2130 #if defined(PETSC_HAVE_THREADSAFETY) 2131 starttime = MPI_Wtime(); 2132 #endif 2133 ierr = PetscInfo2(ts, "Adding just mass to Jacobian t=%g, shift=%g\n",(double)time_dummy,(double)shift);CHKERRQ(ierr); 2134 if (shift==0.0) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "zero shift"); 2135 if (!ctx->aux_bool) SETERRQ(ctx->comm, PETSC_ERR_PLIB, "wrong state"); 2136 if (!ctx->use_matrix_mass) { 2137 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,shift,(void*)ctx);CHKERRQ(ierr); 2138 } else { /* add mass */ 2139 ierr = MatAXPY(Pmat,shift,ctx->M,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 2140 } 2141 ctx->aux_bool = PETSC_FALSE; 2142 ierr = MatViewFromOptions(Pmat,NULL,"-landau_mat_view");CHKERRQ(ierr); 2143 /* set number species in Jacobian */ 2144 ierr = PetscObjectQuery((PetscObject) ctx->J, "Nf", (PetscObject *) &container);CHKERRQ(ierr); 2145 if (!container) { 2146 PetscInt *pNf; 2147 ierr = PetscContainerCreate(PETSC_COMM_SELF, &container);CHKERRQ(ierr); 2148 ierr = PetscMalloc(sizeof(PetscInt), &pNf);CHKERRQ(ierr); 2149 *pNf = ctx->num_species + 1000*ctx->numConcurrency; 2150 ierr = PetscContainerSetPointer(container, (void *)pNf);CHKERRQ(ierr); 2151 ierr = PetscContainerSetUserDestroy(container, MatrixNfDestroy);CHKERRQ(ierr); 2152 ierr = PetscObjectCompose((PetscObject)ctx->J, "Nf", (PetscObject) container);CHKERRQ(ierr); 2153 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 2154 } 2155 #if defined(PETSC_HAVE_THREADSAFETY) 2156 endtime = MPI_Wtime(); 2157 ctx->times[0] += (endtime - starttime); 2158 #endif 2159 ierr = PetscLogEventEnd(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 2160 ierr = PetscLogEventEnd(ctx->events[11],0,0,0,0);CHKERRQ(ierr); 2161 PetscFunctionReturn(0); 2162 } 2163