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_kernel.h" 10 11 #define LANDAU_VL 1 12 static PetscErrorCode LandauPointDataCreate(PetscReal **IPData, PetscInt dim, PetscInt nip, PetscInt Ns) 13 { 14 PetscErrorCode ierr, d, s, jj, nip_pad = LANDAU_VL*(nip/LANDAU_VL + !!(nip%LANDAU_VL)), pnt_sz = (dim + Ns*(1+dim)); 15 PetscReal *pdata; 16 PetscFunctionBegin; 17 ierr = PetscMalloc(nip_pad*pnt_sz*sizeof(PetscReal),IPData);CHKERRQ(ierr); 18 /* pad with zeros in case we vectorize into this */ 19 for (jj=nip, pdata = *IPData + nip*pnt_sz; jj < nip_pad; jj++, pdata += pnt_sz){ 20 LandauPointData *fplpt = (LandauPointData*)pdata; /* [dim + NS*(1+dim)] */ 21 for (d=0;d<dim;d++) fplpt->crd[d] = -1; 22 for (s=0;s<Ns;s++) { 23 fplpt->fdf[s].f = 0; 24 for (d=0;d<dim;d++) fplpt->fdf[s].df[d] = 0; 25 } 26 } 27 PetscFunctionReturn(0); 28 } 29 30 static PetscErrorCode LandauPointDataDestroy(PetscReal *IPData) 31 { 32 PetscErrorCode ierr; 33 PetscFunctionBegin; 34 ierr = PetscFree(IPData);CHKERRQ(ierr); 35 PetscFunctionReturn(0); 36 } 37 /* ------------------------------------------------------------------- */ 38 /* 39 LandauFormJacobian_Internal - Evaluates Jacobian matrix. 40 41 Input Parameters: 42 . globX - input vector 43 . actx - optional user-defined context 44 . dim - dimension 45 46 Output Parameters: 47 . J0acP - Jacobian matrix filled, not created 48 */ 49 PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, void *a_ctx) 50 { 51 LandauCtx *ctx = (LandauCtx*)a_ctx; 52 PetscErrorCode ierr; 53 PetscInt cStart, cEnd, elemMatSize; 54 DM plex = NULL; 55 PetscDS prob; 56 PetscSection section,globsection; 57 PetscScalar *elemMat; 58 PetscInt numCells,totDim,ej,Nq,*Nbf,*Ncf,Nb,Ncx,Nf,d,f,fieldA,Nip,nip_pad,ipdata_sz; 59 PetscQuadrature quad; 60 PetscTabulation *Tf; 61 PetscReal *wiGlob, nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES]; 62 const PetscReal *quadWeights; 63 PetscReal *IPData,*invJ,*invJ_a; 64 PetscReal invMass[LANDAU_MAX_SPECIES],Eq_m[LANDAU_MAX_SPECIES],m_0=ctx->m_0; /* normalize mass -- not needed! */ 65 PetscLogDouble flops; 66 Vec locX; 67 68 PetscFunctionBegin; 69 PetscValidHeaderSpecific(a_X,VEC_CLASSID,1); 70 PetscValidHeaderSpecific(JacP,MAT_CLASSID,2); 71 PetscValidPointer(ctx,4); 72 73 ierr = PetscLogEventBegin(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 74 ierr = DMConvert(ctx->dmv, DMPLEX, &plex);CHKERRQ(ierr); 75 ierr = DMCreateLocalVector(plex, &locX);CHKERRQ(ierr); 76 ierr = VecZeroEntries(locX);CHKERRQ(ierr); /* zero BCs so don't set */ 77 ierr = DMGlobalToLocalBegin(plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 78 ierr = DMGlobalToLocalEnd (plex, a_X, INSERT_VALUES, locX);CHKERRQ(ierr); 79 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 80 ierr = DMGetLocalSection(plex, §ion);CHKERRQ(ierr); 81 ierr = DMGetGlobalSection(plex, &globsection);CHKERRQ(ierr); 82 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 83 ierr = PetscDSGetTabulation(prob, &Tf);CHKERRQ(ierr); // Bf, &Df 84 ierr = PetscDSGetDimensions(prob, &Nbf);CHKERRQ(ierr); Nb = Nbf[0]; /* number of vertices*S */ 85 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); if (Nf!=ctx->num_species) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Nf %D != S",Nf); 86 ierr = PetscDSGetComponents(prob, &Ncf);CHKERRQ(ierr); Ncx = Ncf[0]; if (Ncx!=1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Nc %D != 1",Ncx); 87 for (fieldA=0;fieldA<Nf;fieldA++) { 88 invMass[fieldA] = m_0/ctx->masses[fieldA]; 89 Eq_m[fieldA] = -ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */ 90 if (dim==2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */ 91 nu_alpha[fieldA] = PetscSqr(ctx->charges[fieldA]/m_0)*m_0/ctx->masses[fieldA]; 92 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); 93 } 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(PETSC_COMM_SELF, 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(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Order too high. Nq = %D > LANDAU_MAX_NQ (%D)",Nq,LANDAU_MAX_NQ); 100 Nip = numCells*Nq; 101 nip_pad = LANDAU_VL*(Nip/LANDAU_VL + !!(Nip%LANDAU_VL)); 102 flops = (PetscLogDouble)numCells*(PetscLogDouble)Nq*(PetscLogDouble)(5*dim*dim*Nf*Nf + 165); 103 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 104 elemMatSize = totDim*totDim; 105 { 106 static int cc = 0; 107 PetscScalar uu[LANDAU_MAX_SPECIES],u_x[LANDAU_MAX_SPECIES*LANDAU_DIM]; 108 /* collect f data */ 109 if (ctx->verbose > 2 || (ctx->verbose > 0 && cc++ == 0)) { 110 PetscInt N,Nloc; 111 ierr = MatGetSize(JacP,&N,NULL);CHKERRQ(ierr); 112 ierr = VecGetSize(locX,&Nloc);CHKERRQ(ierr); 113 ierr = PetscPrintf(PETSC_COMM_WORLD,"[%D]%s: %D IPs, %D cells, %s elements, totDim=%D, Nb=%D, Nq=%D, elemMatSize=%D, dim=%D, Tab: Nb=%D Nf=%D Np=%D cdim=%D N=%D N_loc=%D\n", 114 0,"FormLandau",Nq*numCells,numCells,ctx->simplex ? "SIMPLEX" : "TENSOR", totDim, Nb, Nq, elemMatSize, dim, Tf[0]->Nb, Nf, Tf[0]->Np, Tf[0]->cdim, N, Nloc);CHKERRQ(ierr); 115 } 116 ierr = LandauPointDataCreate(&IPData, dim, Nq*numCells, Nf);CHKERRQ(ierr); 117 ipdata_sz = (dim + Nf*(1+dim)); 118 ierr = PetscMalloc3(elemMatSize,&elemMat,nip_pad,&wiGlob,nip_pad*dim*dim,&invJ_a);CHKERRQ(ierr); 119 /* cache geometry and x, f and df/dx at IPs */ 120 for (ej = 0, invJ = invJ_a ; ej < numCells; ++ej, invJ += Nq*dim*dim) { 121 PetscReal vj[LANDAU_MAX_NQ*LANDAU_DIM],detJj[LANDAU_MAX_NQ], Jdummy[LANDAU_MAX_NQ*LANDAU_DIM*LANDAU_DIM]; 122 PetscInt qj,f; 123 PetscScalar *coef = NULL; 124 ierr = DMPlexComputeCellGeometryFEM(plex, cStart+ej, quad, vj, Jdummy, invJ, detJj);CHKERRQ(ierr); 125 ierr = DMPlexVecGetClosure(plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 126 /* create point data for cell i for Landau tensor: x, f(x), grad f(x) */ 127 for (qj = 0; qj < Nq; ++qj) { 128 PetscInt gidx = (ej*Nq + qj); 129 LandauPointData *pnt_data = (LandauPointData*)(IPData + gidx*ipdata_sz); 130 PetscScalar refSpaceDer[LANDAU_DIM]; 131 PetscInt dOffset = 0, fOffset = 0; 132 for (d = 0; d < dim; ++d) pnt_data->crd[d] = vj[qj * dim + d]; /* coordinate */ 133 wiGlob[gidx] = detJj[qj] * quadWeights[qj]; 134 if (dim==2) wiGlob[gidx] *= pnt_data->crd[0]; /* cylindrical coordinate, w/o 2pi */ 135 /* get u & du (EvaluateFieldJets) */ 136 for (f = 0; f < Nf; ++f) { 137 const PetscReal *Bq = &Tf[f]->T[0][qj*Nb]; 138 const PetscReal *Dq = &Tf[f]->T[1][qj*Nb*dim]; 139 PetscInt b, e; 140 uu[fOffset] = 0.0; 141 for (d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0; 142 for (b = 0; b < Nb; ++b) { 143 const PetscInt cidx = b; 144 uu[fOffset] += Bq[cidx]*coef[dOffset+cidx]; 145 for (d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx*dim+d]*coef[dOffset+cidx]; 146 } 147 for (d = 0; d < dim; ++d) { 148 for (e = 0, u_x[fOffset*dim+d] = 0.0; e < dim; ++e) { // should add directly to point data here!!! 149 u_x[fOffset*dim+d] += invJ[qj * dim * dim + e*dim+d]*refSpaceDer[e]; 150 } 151 } 152 fOffset += 1; 153 dOffset += Nb; 154 } 155 /* copy to IPDataLocal */ 156 for (f=0;f<Nf;f++) { 157 pnt_data->fdf[f].f = PetscRealPart(uu[f]); 158 for (d = 0; d < dim; ++d) pnt_data->fdf[f].df[d] = PetscRealPart(u_x[f*dim+d]); 159 } 160 } /* q */ 161 ierr = DMPlexVecRestoreClosure(plex, section, locX, cStart+ej, NULL, &coef);CHKERRQ(ierr); 162 } /* e */ 163 } 164 ierr = DMRestoreLocalVector(plex, &locX);CHKERRQ(ierr); 165 ierr = PetscLogEventEnd(ctx->events[1],0,0,0,0);CHKERRQ(ierr); 166 167 /* outer element loop j is like a regular assembly loop */ 168 if (ctx->deviceType == LANDAU_CUDA) { 169 #if defined(PETSC_HAVE_CUDA) 170 ierr = LandauCUDAJacobian(plex,Nq,nu_alpha,nu_beta,invMass,Eq_m,IPData,wiGlob,invJ_a,ctx->subThreadBlockSize,ctx->events,ctx->quarter3DDomain,JacP);CHKERRQ(ierr); 171 #else 172 SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","cuda"); 173 #endif 174 } else if (ctx->deviceType == LANDAU_KOKKOS) { 175 #if defined(PETSC_HAVE_KOKKOS) 176 ierr = LandauKokkosJacobian(plex,Nq,nu_alpha,nu_beta,invMass,Eq_m,IPData,wiGlob,invJ_a,ctx->subThreadBlockSize,ctx->events,ctx->quarter3DDomain,JacP);CHKERRQ(ierr); 177 #else 178 SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"-landau_device_type %s not built","kokkos"); 179 #endif 180 } else { /* CPU version */ 181 for (ej = cStart, invJ = invJ_a; ej < cEnd; ++ej, invJ += Nq*dim*dim) { 182 PetscInt qj; 183 ierr = PetscLogEventBegin(ctx->events[3],0,0,0,0);CHKERRQ(ierr); 184 ierr = PetscMemzero(elemMat, totDim *totDim * sizeof(PetscScalar));CHKERRQ(ierr); 185 ierr = PetscLogEventEnd(ctx->events[3],0,0,0,0);CHKERRQ(ierr); 186 ierr = PetscLogEventBegin(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 187 ierr = PetscLogFlops((PetscLogDouble)Nq*flops);CHKERRQ(ierr); 188 for (qj = 0; qj < Nq; ++qj) { 189 PetscReal g2[1][LANDAU_MAX_SUB_THREAD_BLOCKS][LANDAU_MAX_SPECIES][LANDAU_DIM], g3[1][LANDAU_MAX_SUB_THREAD_BLOCKS][LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM]; 190 const PetscInt nip = numCells*Nq, jpidx = Nq*(ej-cStart) + qj, one = 1, zero = 0; /* length of inner global interation, outer integration point */ 191 landau_inner_integral(zero, one, zero, one, zero, nip, 1, jpidx, Nf, dim, IPData, wiGlob, &invJ[qj*dim*dim], nu_alpha, nu_beta, invMass, Eq_m, ctx->quarter3DDomain, Nq, Nb, qj, qj+1, Tf[0]->T[0], Tf[0]->T[1], elemMat, g2, g3, ej); 192 } /* qj loop */ 193 ierr = PetscLogEventEnd(ctx->events[4],0,0,0,0);CHKERRQ(ierr); 194 195 /* assemble matrix */ 196 ierr = PetscLogEventBegin(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 197 ierr = DMPlexMatSetClosure(plex, section, globsection, JacP, ej, elemMat, ADD_VALUES); 198 if (ej==-1 || ierr) { 199 PetscErrorCode ierr2; 200 ierr2 = PetscPrintf(PETSC_COMM_SELF, "CPU Element matrix\n");CHKERRQ(ierr2); 201 for (d = 0; d < totDim; ++d){ 202 for (f = 0; f < totDim; ++f) {ierr2 = PetscPrintf(PETSC_COMM_SELF," %17.9e", PetscRealPart(elemMat[d*totDim + f]));CHKERRQ(ierr2);} 203 ierr2 = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr2); 204 } 205 } 206 CHKERRQ(ierr); 207 ierr = PetscLogEventEnd(ctx->events[6],0,0,0,0);CHKERRQ(ierr); 208 } /* ej cells loop, not cuda */ 209 } 210 // PetscSleep(2); exit(13); 211 212 /* assemble matrix or vector */ 213 ierr = PetscLogEventBegin(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 214 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 215 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 216 ierr = MatScale(JacP, -1.0);CHKERRQ(ierr); /* The code reflect the papers: du/dt = C, whereas PETSc use the form G(u) = du/dt - C(u) = 0 */ 217 ierr = PetscLogEventEnd(ctx->events[7],0,0,0,0);CHKERRQ(ierr); 218 219 /* clean up */ 220 ierr = PetscFree3(elemMat,wiGlob,invJ_a);CHKERRQ(ierr); 221 ierr = DMDestroy(&plex);CHKERRQ(ierr); 222 ierr = LandauPointDataDestroy(IPData);CHKERRQ(ierr); 223 PetscFunctionReturn(0); 224 } 225 226 #if defined(LANDAU_ADD_BCS) 227 static void zero_bc(PetscInt dim, PetscInt Nf, PetscInt NfAux, 228 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 229 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 230 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar uexact[]) 231 { 232 uexact[0] = 0; 233 } 234 #endif 235 236 #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]; }} 237 static void CircleInflate(PetscReal r1, PetscReal r2, PetscReal r0, PetscInt num_sections, PetscReal x, PetscReal y, 238 PetscReal *outX, PetscReal *outY) 239 { 240 PetscReal rr = PetscSqrtReal(x*x + y*y), outfact, efact; 241 if (rr < r1 + PETSC_SQRT_MACHINE_EPSILON) { 242 *outX = x; *outY = y; 243 } else { 244 const PetscReal xy[2] = {x,y}, sinphi=y/rr, cosphi=x/rr; 245 PetscReal cth,sth,xyprime[2],Rth[2][2],rotcos,newrr; 246 if (num_sections==2) { 247 rotcos = 0.70710678118654; 248 outfact = 1.5; efact = 2.5; 249 /* rotate normalized vector into [-pi/4,pi/4) */ 250 if (sinphi >= 0.) { /* top cell, -pi/2 */ 251 cth = 0.707106781186548; sth = -0.707106781186548; 252 } else { /* bottom cell -pi/8 */ 253 cth = 0.707106781186548; sth = .707106781186548; 254 } 255 } else if (num_sections==3) { 256 rotcos = 0.86602540378443; 257 outfact = 1.5; efact = 2.5; 258 /* rotate normalized vector into [-pi/6,pi/6) */ 259 if (sinphi >= 0.5) { /* top cell, -pi/3 */ 260 cth = 0.5; sth = -0.866025403784439; 261 } else if (sinphi >= -.5) { /* mid cell 0 */ 262 cth = 1.; sth = .0; 263 } else { /* bottom cell +pi/3 */ 264 cth = 0.5; sth = 0.866025403784439; 265 } 266 } else if (num_sections==4) { 267 rotcos = 0.9238795325112; 268 outfact = 1.5; efact = 3; 269 /* rotate normalized vector into [-pi/8,pi/8) */ 270 if (sinphi >= 0.707106781186548) { /* top cell, -3pi/8 */ 271 cth = 0.38268343236509; sth = -0.923879532511287; 272 } else if (sinphi >= 0.) { /* mid top cell -pi/8 */ 273 cth = 0.923879532511287; sth = -.38268343236509; 274 } else if (sinphi >= -0.707106781186548) { /* mid bottom cell + pi/8 */ 275 cth = 0.923879532511287; sth = 0.38268343236509; 276 } else { /* bottom cell + 3pi/8 */ 277 cth = 0.38268343236509; sth = .923879532511287; 278 } 279 } else { 280 cth = 0.; sth = 0.; rotcos = 0; efact = 0; 281 } 282 Rth[0][0] = cth; Rth[0][1] =-sth; 283 Rth[1][0] = sth; Rth[1][1] = cth; 284 MATVEC2(Rth,xy,xyprime); 285 if (num_sections==2) { 286 newrr = xyprime[0]/rotcos; 287 } else { 288 PetscReal newcosphi=xyprime[0]/rr, rin = r1, rout = rr - rin; 289 PetscReal routmax = r0*rotcos/newcosphi - rin, nroutmax = r0 - rin, routfrac = rout/routmax; 290 newrr = rin + routfrac*nroutmax; 291 } 292 *outX = cosphi*newrr; *outY = sinphi*newrr; 293 /* grade */ 294 PetscReal fact,tt,rs,re, rr = PetscSqrtReal(PetscSqr(*outX) + PetscSqr(*outY)); 295 if (rr > r2) { rs = r2; re = r0; fact = outfact;} /* outer zone */ 296 else { rs = r1; re = r2; fact = efact;} /* electron zone */ 297 tt = (rs + PetscPowReal((rr - rs)/(re - rs),fact) * (re-rs)) / rr; 298 *outX *= tt; 299 *outY *= tt; 300 } 301 } 302 303 static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx) 304 { 305 LandauCtx *ctx = (LandauCtx*)a_ctx; 306 PetscReal r = abc[0], z = abc[1]; 307 if (ctx->inflate) { 308 PetscReal absR, absZ; 309 absR = PetscAbsReal(r); 310 absZ = PetscAbsReal(z); 311 CircleInflate(ctx->i_radius,ctx->e_radius,ctx->radius,ctx->num_sections,absR,absZ,&absR,&absZ); 312 r = (r > 0) ? absR : -absR; 313 z = (z > 0) ? absZ : -absZ; 314 } 315 xyz[0] = r; 316 xyz[1] = z; 317 if (dim==3) xyz[2] = abc[2]; 318 319 PetscFunctionReturn(0); 320 } 321 322 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) 323 { 324 PetscReal err = 0.0; 325 PetscInt f = *(PetscInt*)actx, j; 326 PetscFunctionBegin; 327 for (j = 0; j < dim; ++j) { 328 err += PetscSqr(PetscRealPart(u_x[f*dim+j])); 329 } 330 err = PetscRealPart(u[f]); /* just use rho */ 331 *error = volume * err; /* * (ctx->axisymmetric ? 2.*PETSC_PI * r : 1); */ 332 PetscFunctionReturn(0); 333 } 334 335 static PetscErrorCode LandauDMCreateVMesh(MPI_Comm comm, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM *dm) 336 { 337 PetscErrorCode ierr; 338 PetscReal radius = ctx->radius; 339 size_t len; 340 char fname[128] = ""; /* we can add a file if we want */ 341 342 PetscFunctionBegin; 343 /* create DM */ 344 ierr = PetscStrlen(fname, &len);CHKERRQ(ierr); 345 if (len) { 346 PetscInt dim2; 347 ierr = DMPlexCreateFromFile(comm, fname, ctx->interpolate, dm);CHKERRQ(ierr); 348 ierr = DMGetDimension(*dm, &dim2);CHKERRQ(ierr); 349 } else { /* p4est, quads */ 350 /* Create plex mesh of Landau domain */ 351 if (!ctx->sphere) { 352 PetscInt cells[] = {2,2,2}; 353 PetscReal lo[] = {-radius,-radius,-radius}, hi[] = {radius,radius,radius}; 354 DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim==2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 355 if (dim==2) { lo[0] = 0; cells[0] = 1; } 356 else if (ctx->quarter3DDomain) { lo[0] = lo[1] = 0; cells[0] = cells[1] = 2; } 357 ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, cells, lo, hi, periodicity, PETSC_TRUE, dm);CHKERRQ(ierr); 358 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); /* needed for periodic */ 359 if (dim==3) {ierr = PetscObjectSetName((PetscObject) *dm, "cube");CHKERRQ(ierr);} 360 else {ierr = PetscObjectSetName((PetscObject) *dm, "half-plane");CHKERRQ(ierr);} 361 } else if (dim==2) { 362 PetscInt numCells,cells[16][4],i,j; 363 PetscInt numVerts; 364 PetscReal inner_radius1 = ctx->i_radius, inner_radius2 = ctx->e_radius; 365 PetscReal *flatCoords = NULL; 366 PetscInt *flatCells = NULL, *pcell; 367 if (ctx->num_sections==2) { 368 #if 1 369 numCells = 5; 370 numVerts = 10; 371 int cells2[][4] = { {0,1,4,3}, 372 {1,2,5,4}, 373 {3,4,7,6}, 374 {4,5,8,7}, 375 {6,7,8,9} }; 376 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 377 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 378 { 379 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 380 for (j = 0; j < numVerts-1; j++) { 381 PetscReal z, r, theta = -PETSC_PI/2 + (j%3) * PETSC_PI/2; 382 PetscReal rad = (j >= 6) ? inner_radius1 : (j >= 3) ? inner_radius2 : ctx->radius; 383 z = rad * PetscSinReal(theta); 384 coords[j][1] = z; 385 r = rad * PetscCosReal(theta); 386 coords[j][0] = r; 387 } 388 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 389 } 390 #else 391 numCells = 4; 392 numVerts = 8; 393 static int cells2[][4] = {{0,1,2,3}, 394 {4,5,1,0}, 395 {5,6,2,1}, 396 {6,7,3,2}}; 397 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 398 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 399 { 400 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 401 PetscInt j; 402 for (j = 0; j < 8; j++) { 403 PetscReal z, r; 404 PetscReal theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3.; 405 PetscReal rad = ctx->radius * ((j < 4) ? 0.5 : 1.0); 406 z = rad * PetscSinReal(theta); 407 coords[j][1] = z; 408 r = rad * PetscCosReal(theta); 409 coords[j][0] = r; 410 } 411 } 412 #endif 413 } else if (ctx->num_sections==3) { 414 numCells = 7; 415 numVerts = 12; 416 int cells2[][4] = { {0,1,5,4}, 417 {1,2,6,5}, 418 {2,3,7,6}, 419 {4,5,9,8}, 420 {5,6,10,9}, 421 {6,7,11,10}, 422 {8,9,10,11} }; 423 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 424 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 425 { 426 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 427 for (j = 0; j < numVerts; j++) { 428 PetscReal z, r, theta = -PETSC_PI/2 + (j%4) * PETSC_PI/3; 429 PetscReal rad = (j >= 8) ? inner_radius1 : (j >= 4) ? inner_radius2 : ctx->radius; 430 z = rad * PetscSinReal(theta); 431 coords[j][1] = z; 432 r = rad * PetscCosReal(theta); 433 coords[j][0] = r; 434 } 435 } 436 } else if (ctx->num_sections==4) { 437 numCells = 10; 438 numVerts = 16; 439 int cells2[][4] = { {0,1,6,5}, 440 {1,2,7,6}, 441 {2,3,8,7}, 442 {3,4,9,8}, 443 {5,6,11,10}, 444 {6,7,12,11}, 445 {7,8,13,12}, 446 {8,9,14,13}, 447 {10,11,12,15}, 448 {12,13,14,15}}; 449 for (i = 0; i < numCells; i++) for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j]; 450 ierr = PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells);CHKERRQ(ierr); 451 { 452 PetscReal (*coords)[2] = (PetscReal (*) [2]) flatCoords; 453 for (j = 0; j < numVerts-1; j++) { 454 PetscReal z, r, theta = -PETSC_PI/2 + (j%5) * PETSC_PI/4; 455 PetscReal rad = (j >= 10) ? inner_radius1 : (j >= 5) ? inner_radius2 : ctx->radius; 456 z = rad * PetscSinReal(theta); 457 coords[j][1] = z; 458 r = rad * PetscCosReal(theta); 459 coords[j][0] = r; 460 } 461 coords[numVerts-1][0] = coords[numVerts-1][1] = 0; 462 } 463 } else { 464 numCells = 0; 465 numVerts = 0; 466 } 467 for (j = 0, pcell = flatCells; j < numCells; j++, pcell += 4) { 468 pcell[0] = cells[j][0]; pcell[1] = cells[j][1]; 469 pcell[2] = cells[j][2]; pcell[3] = cells[j][3]; 470 } 471 ierr = DMPlexCreateFromCellListPetsc(comm,2,numCells,numVerts,4,ctx->interpolate,flatCells,2,flatCoords,dm);CHKERRQ(ierr); 472 ierr = PetscFree2(flatCoords,flatCells);CHKERRQ(ierr); 473 ierr = PetscObjectSetName((PetscObject) *dm, "semi-circle");CHKERRQ(ierr); 474 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Velocity space meshes does not support cubed sphere"); 475 } 476 ierr = PetscObjectSetOptionsPrefix((PetscObject)*dm,prefix);CHKERRQ(ierr); 477 478 ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); /* Plex refine */ 479 480 { /* p4est? */ 481 char convType[256]; 482 PetscBool flg; 483 ierr = PetscOptionsBegin(PETSC_COMM_WORLD, prefix, "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); 484 ierr = PetscOptionsFList("-dm_landau_type","Convert DMPlex to another format (should not be Plex!)","ex6f.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); 485 ierr = PetscOptionsEnd(); 486 if (flg) { 487 DM dmforest; 488 ierr = DMConvert(*dm,convType,&dmforest);CHKERRQ(ierr); 489 if (dmforest) { 490 PetscBool isForest; 491 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 492 ierr = PetscObjectSetOptionsPrefix((PetscObject)dmforest,prefix);CHKERRQ(ierr); 493 ierr = DMIsForest(dmforest,&isForest);CHKERRQ(ierr); 494 if (isForest) { 495 if (ctx->sphere && ctx->inflate) { 496 ierr = DMForestSetBaseCoordinateMapping(dmforest,GeometryDMLandau,ctx);CHKERRQ(ierr); 497 } 498 if (dmforest->prealloc_only != (*dm)->prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"plex->prealloc_only != dm->prealloc_only"); 499 ierr = DMDestroy(dm);CHKERRQ(ierr); 500 *dm = dmforest; 501 ctx->errorIndicator = ErrorIndicator_Simple; /* flag for Forest */ 502 } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?"); 503 } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?"); 504 } 505 } 506 ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); 507 PetscFunctionReturn(0); 508 } 509 510 static PetscErrorCode SetupDS(DM dm, PetscInt dim, LandauCtx *ctx) 511 { 512 PetscErrorCode ierr; 513 PetscInt ii; 514 PetscFunctionBegin; 515 for (ii=0;ii<ctx->num_species;ii++) { 516 char buf[256]; 517 if (ii==0) ierr = PetscSNPrintf(buf, 256, "e"); 518 else {ierr = PetscSNPrintf(buf, 256, "i%D", ii);CHKERRQ(ierr);} 519 /* Setup Discretization - FEM */ 520 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), dim, 1, ctx->simplex, NULL, PETSC_DECIDE, &ctx->fe[ii]);CHKERRQ(ierr); 521 ierr = PetscObjectSetName((PetscObject) ctx->fe[ii], buf);CHKERRQ(ierr); 522 ierr = DMSetField(dm, ii, NULL, (PetscObject) ctx->fe[ii]);CHKERRQ(ierr); 523 } 524 ierr = DMCreateDS(dm);CHKERRQ(ierr); 525 if (1) { 526 PetscInt ii; 527 PetscSection section; 528 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 529 for (ii=0;ii<ctx->num_species;ii++){ 530 char buf[256]; 531 if (ii==0) ierr = PetscSNPrintf(buf, 256, "se"); 532 else ierr = PetscSNPrintf(buf, 256, "si%D", ii); 533 ierr = PetscSectionSetComponentName(section, ii, 0, buf);CHKERRQ(ierr); 534 } 535 } 536 PetscFunctionReturn(0); 537 } 538 539 /* Define a Maxwellian function for testing out the operator. */ 540 541 /* Using cartesian velocity space coordinates, the particle */ 542 /* density, [1/m^3], is defined according to */ 543 544 /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */ 545 546 /* Using some constant, c, we normalize the velocity vector into a */ 547 /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */ 548 549 /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */ 550 551 /* Defining $\theta=2T/mc^2$, we thus find that the probability density */ 552 /* for finding the particle within the interval in a box dx^3 around x is */ 553 554 /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */ 555 556 typedef struct { 557 LandauCtx *ctx; 558 PetscReal kT_m; 559 PetscReal n; 560 PetscReal shift; 561 } MaxwellianCtx; 562 563 static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx) 564 { 565 MaxwellianCtx *mctx = (MaxwellianCtx*)actx; 566 LandauCtx *ctx = mctx->ctx; 567 PetscInt i; 568 PetscReal v2 = 0, theta = 2*mctx->kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 569 PetscFunctionBegin; 570 /* compute the exponents, v^2 */ 571 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 572 /* evaluate the Maxwellian */ 573 u[0] = mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 574 if (mctx->shift!=0.) { 575 v2 = 0; 576 for (i = 0; i < dim-1; ++i) v2 += x[i]*x[i]; 577 v2 += (x[dim-1]-mctx->shift)*(x[dim-1]-mctx->shift); 578 /* evaluate the shifted Maxwellian */ 579 u[0] += mctx->n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 580 } 581 PetscFunctionReturn(0); 582 } 583 584 /*@ 585 LandauAddMaxwellians - Add a Maxwellian distribution to a state 586 587 Collective on X 588 589 Input Parameters: 590 . dm - The mesh 591 + time - Current time 592 - temps - Temperatures of each species 593 . ns - Number density of each species 594 + actx - Landau context 595 596 Output Parameter: 597 . X - The state 598 599 Level: beginner 600 601 .keywords: mesh 602 .seealso: LandauCreateVelocitySpace() 603 @*/ 604 PetscErrorCode LandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], void *actx) 605 { 606 LandauCtx *ctx = (LandauCtx*)actx; 607 PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar [], void *); 608 PetscErrorCode ierr,ii; 609 PetscInt dim; 610 MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES]; 611 612 PetscFunctionBegin; 613 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 614 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 615 for (ii=0;ii<ctx->num_species;ii++) { 616 mctxs[ii] = &data[ii]; 617 data[ii].ctx = ctx; 618 data[ii].kT_m = ctx->k*temps[ii]/ctx->masses[ii]; /* kT/m */ 619 data[ii].n = ns[ii]; 620 initu[ii] = maxwellian; 621 data[ii].shift = 0; 622 } 623 data[0].shift = ctx->electronShift; 624 /* need to make ADD_ALL_VALUES work - TODO */ 625 ierr = DMProjectFunction(dm, time, initu, (void**)mctxs, INSERT_ALL_VALUES, X);CHKERRQ(ierr); 626 PetscFunctionReturn(0); 627 } 628 629 /* 630 LandauSetInitialCondition - Addes Maxwellians with context 631 632 Collective on X 633 634 Input Parameters: 635 . dm - The mesh 636 + actx - Landau context with T and n 637 638 Output Parameter: 639 . X - The state 640 641 Level: beginner 642 643 .keywords: mesh 644 .seealso: LandauCreateVelocitySpace(), LandauAddMaxwellians() 645 */ 646 static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, void *actx) 647 { 648 LandauCtx *ctx = (LandauCtx*)actx; 649 PetscErrorCode ierr; 650 PetscFunctionBegin; 651 if (!ctx) { ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); } 652 ierr = VecZeroEntries(X);CHKERRQ(ierr); 653 ierr = LandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, ctx);CHKERRQ(ierr); 654 PetscFunctionReturn(0); 655 } 656 657 static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscReal refineTol[], PetscReal coarsenTol[], PetscInt type, LandauCtx *ctx, DM *newDM) 658 { 659 DM dm, plex, adaptedDM = NULL; 660 PetscDS prob; 661 PetscBool isForest; 662 PetscQuadrature quad; 663 PetscInt Nq, *Nb, cStart, cEnd, c, dim, qj, k; 664 DMLabel adaptLabel = NULL; 665 PetscErrorCode ierr; 666 667 PetscFunctionBegin; 668 ierr = VecGetDM(sol, &dm);CHKERRQ(ierr); 669 ierr = DMCreateDS(dm);CHKERRQ(ierr); 670 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 671 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 672 ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr); 673 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 674 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 675 ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr); 676 ierr = PetscFEGetQuadrature(fem, &quad);CHKERRQ(ierr); 677 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 678 if (Nq >LANDAU_MAX_NQ) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Order too high. Nq = %D > LANDAU_MAX_NQ (%D)",Nq,LANDAU_MAX_NQ); 679 ierr = PetscDSGetDimensions(prob, &Nb);CHKERRQ(ierr); 680 if (type==4) { 681 for (c = cStart; c < cEnd; c++) { 682 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 683 } 684 ierr = PetscInfo1(sol, "Phase:%s: Uniform refinement\n","adaptToleranceFEM");CHKERRQ(ierr); 685 } else if (type==2) { 686 PetscInt rCellIdx[8], eCellIdx[64], iCellIdx[64], eMaxIdx = -1, iMaxIdx = -1, nr = 0, nrmax = (dim==3 && !ctx->quarter3DDomain) ? 8 : 2; 687 PetscReal minRad = PETSC_INFINITY, r, eMinRad = PETSC_INFINITY, iMinRad = PETSC_INFINITY; 688 for (c = 0; c < 64; c++) { eCellIdx[c] = iCellIdx[c] = -1; } 689 for (c = cStart; c < cEnd; c++) { 690 PetscReal tt, v0[LANDAU_MAX_NQ*3], detJ[LANDAU_MAX_NQ]; 691 ierr = DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ);CHKERRQ(ierr); 692 for (qj = 0; qj < Nq; ++qj) { 693 tt = PetscSqr(v0[dim*qj+0]) + PetscSqr(v0[dim*qj+1]) + PetscSqr(((dim==3) ? v0[dim*qj+2] : 0)); 694 r = PetscSqrtReal(tt); 695 if (r < minRad - PETSC_SQRT_MACHINE_EPSILON*10.) { 696 minRad = r; 697 nr = 0; 698 rCellIdx[nr++]= c; 699 ierr = PetscInfo4(sol, "\t\tPhase: adaptToleranceFEM Found first inner r=%e, cell %D, qp %D/%D\n", r, c, qj+1, Nq);CHKERRQ(ierr); 700 } else if ((r-minRad) < PETSC_SQRT_MACHINE_EPSILON*100. && nr < nrmax) { 701 for (k=0;k<nr;k++) if (c == rCellIdx[k]) break; 702 if (k==nr) { 703 rCellIdx[nr++]= c; 704 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); 705 } 706 } 707 if (ctx->sphere) { 708 if ((tt=r-ctx->e_radius) > 0) { 709 PetscInfo2(sol, "\t\t\t %D cell r=%g\n",c,tt); 710 if (tt < eMinRad - PETSC_SQRT_MACHINE_EPSILON*100.) { 711 eMinRad = tt; 712 eMaxIdx = 0; 713 eCellIdx[eMaxIdx++] = c; 714 } else if (eMaxIdx > 0 && (tt-eMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != eCellIdx[eMaxIdx-1]) { 715 eCellIdx[eMaxIdx++] = c; 716 } 717 } 718 if ((tt=r-ctx->i_radius) > 0) { 719 if (tt < iMinRad - 1.e-5) { 720 iMinRad = tt; 721 iMaxIdx = 0; 722 iCellIdx[iMaxIdx++] = c; 723 } else if (iMaxIdx > 0 && (tt-iMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != iCellIdx[iMaxIdx-1]) { 724 iCellIdx[iMaxIdx++] = c; 725 } 726 } 727 } 728 } 729 } 730 for (k=0;k<nr;k++) { 731 ierr = DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE);CHKERRQ(ierr); 732 } 733 if (ctx->sphere) { 734 for (c = 0; c < eMaxIdx; c++) { 735 ierr = DMLabelSetValue(adaptLabel, eCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 736 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere e cell %D r=%g\n","adaptToleranceFEM",eCellIdx[c],eMinRad); 737 } 738 for (c = 0; c < iMaxIdx; c++) { 739 ierr = DMLabelSetValue(adaptLabel, iCellIdx[c], DM_ADAPT_REFINE);CHKERRQ(ierr); 740 ierr = PetscInfo3(sol, "\t\tPhase:%s: refine sphere i cell %D r=%g\n","adaptToleranceFEM",iCellIdx[c],iMinRad); 741 } 742 } 743 ierr = PetscInfo4(sol, "Phase:%s: Adaptive refine origin cells %D,%D r=%g\n","adaptToleranceFEM",rCellIdx[0],rCellIdx[1],minRad); 744 } else if (type==0 || type==1 || type==3) { /* refine along r=0 axis */ 745 PetscScalar *coef = NULL; 746 Vec coords; 747 PetscInt csize,Nv,d,nz; 748 DM cdm; 749 PetscSection cs; 750 ierr = DMGetCoordinatesLocal(dm, &coords);CHKERRQ(ierr); 751 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 752 ierr = DMGetLocalSection(cdm, &cs);CHKERRQ(ierr); 753 for (c = cStart; c < cEnd; c++) { 754 PetscInt doit = 0, outside = 0; 755 ierr = DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 756 Nv = csize/dim; 757 for (nz = d = 0; d < Nv; d++) { 758 PetscReal z = PetscRealPart(coef[d*dim + (dim-1)]), x = PetscSqr(PetscRealPart(coef[d*dim + 0])) + ((dim==3) ? PetscSqr(PetscRealPart(coef[d*dim + 1])) : 0); 759 x = PetscSqrtReal(x); 760 if (x < PETSC_MACHINE_EPSILON*10. && PetscAbsReal(z)<PETSC_MACHINE_EPSILON*10.) doit = 1; /* refine origin */ 761 else if (type==0 && (z < -PETSC_MACHINE_EPSILON*10. || z > ctx->re_radius+PETSC_MACHINE_EPSILON*10.)) outside++; /* first pass don't refine bottom */ 762 else if (type==1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) outside++; /* don't refine outside electron refine radius */ 763 else if (type==3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) outside++; /* don't refine outside ion refine radius */ 764 if (x < PETSC_MACHINE_EPSILON*10.) nz++; 765 } 766 ierr = DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef);CHKERRQ(ierr); 767 if (doit || (outside<Nv && nz)) { 768 ierr = DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE);CHKERRQ(ierr); 769 } 770 } 771 ierr = PetscInfo1(sol, "Phase:%s: RE refinement\n","adaptToleranceFEM"); 772 } 773 /* ierr = VecDestroy(&locX);CHKERRQ(ierr); */ 774 ierr = DMDestroy(&plex);CHKERRQ(ierr); 775 ierr = DMAdaptLabel(dm, adaptLabel, &adaptedDM);CHKERRQ(ierr); 776 ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); 777 *newDM = adaptedDM; 778 if (adaptedDM) { 779 if (isForest) { 780 ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr); 781 } 782 ierr = DMConvert(adaptedDM, DMPLEX, &plex);CHKERRQ(ierr); 783 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 784 ierr = PetscInfo2(sol, "\tPhase: adaptToleranceFEM: %D cells, %d total quadrature points\n",cEnd-cStart,Nq*(cEnd-cStart));CHKERRQ(ierr); 785 ierr = DMDestroy(&plex);CHKERRQ(ierr); 786 } 787 PetscFunctionReturn(0); 788 } 789 790 static PetscErrorCode adapt(DM *dm, LandauCtx *ctx, Vec *uu) 791 { 792 PetscErrorCode ierr; 793 PetscInt type, limits[5] = {ctx->numRERefine,ctx->nZRefine1,ctx->maxRefIts,ctx->nZRefine2,ctx->postAMRRefine}; 794 PetscInt adaptIter; 795 796 PetscFunctionBegin; 797 for (type=0;type<5;type++) { 798 for (adaptIter = 0; adaptIter<limits[type];adaptIter++) { 799 DM dmNew = NULL; 800 ierr = adaptToleranceFEM(ctx->fe[0], *uu, ctx->refineTol, ctx->coarsenTol, type, ctx, &dmNew);CHKERRQ(ierr); 801 if (!dmNew) { 802 exit(113); 803 break; 804 } else { 805 ierr = DMDestroy(dm);CHKERRQ(ierr); 806 ierr = VecDestroy(uu);CHKERRQ(ierr); 807 ierr = DMCreateGlobalVector(dmNew,uu);CHKERRQ(ierr); 808 ierr = PetscObjectSetName((PetscObject) *uu, "u");CHKERRQ(ierr); 809 ierr = LandauSetInitialCondition(dmNew, *uu, ctx);CHKERRQ(ierr); 810 *dm = dmNew; 811 } 812 } 813 } 814 PetscFunctionReturn(0); 815 } 816 817 static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[]) 818 { 819 PetscErrorCode ierr; 820 PetscBool flg, sph_flg; 821 PetscInt ii,nt,nm,nc; 822 DM dummy; 823 824 PetscFunctionBegin; 825 ierr = DMCreate(PETSC_COMM_WORLD,&dummy);CHKERRQ(ierr); 826 /* get options - initialize context */ 827 ctx->normJ = 0; 828 ctx->verbose = 1; 829 ctx->interpolate = PETSC_TRUE; 830 ctx->simplex = PETSC_FALSE; 831 ctx->sphere = PETSC_FALSE; 832 ctx->inflate = PETSC_FALSE; 833 ctx->electronShift = 0; 834 ctx->errorIndicator = NULL; 835 ctx->radius = 5.; /* electron thermal radius (velocity) */ 836 ctx->re_radius = 0.; 837 ctx->vperp0_radius1 = 0; 838 ctx->vperp0_radius2 = 0; 839 ctx->e_radius = .1; 840 ctx->i_radius = .01; 841 ctx->maxRefIts = 5; 842 ctx->postAMRRefine = 0; 843 ctx->nZRefine1 = 0; 844 ctx->nZRefine2 = 0; 845 ctx->numRERefine = 0; 846 ctx->num_sections = 3; /* 2, 3 or 4 */ 847 /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */ 848 ctx->charges[0] = -1; /* electron charge (MKS) */ 849 ctx->masses[0] = 1/1835.5; /* temporary value in proton mass */ 850 ctx->n[0] = 1; 851 ctx->thermal_temps[0] = 1; 852 /* constants, etc. */ 853 ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */ 854 ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */ 855 ctx->lnLam = 10; /* cross section ratio large - small angle collisions */ 856 ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */ 857 ctx->Ez = 0; 858 ctx->v_0 = 1; /* in electron thermal velocity */ 859 ctx->subThreadBlockSize = 1; /* for device and maybe OMP */ 860 ctx->quarter3DDomain = PETSC_FALSE; 861 ierr = PetscOptionsBegin(PETSC_COMM_WORLD, prefix, "Options for Fokker-Plank-Landau collision operator", "none");CHKERRQ(ierr); 862 { 863 char opstring[256]; 864 #if defined(PETSC_HAVE_KOKKOS) 865 ctx->deviceType = LANDAU_KOKKOS; 866 ierr = PetscStrcpy(opstring,"kokkos");CHKERRQ(ierr); 867 #if !defined(PETSC_HAVE_CUDA) 868 ctx->subThreadBlockSize = 0; 869 #endif 870 #elif defined(PETSC_HAVE_CUDA) 871 ctx->deviceType = LANDAU_CUDA; 872 ierr = PetscStrcpy(opstring,"cuda");CHKERRQ(ierr); 873 #else 874 ctx->deviceType = LANDAU_CPU; 875 ierr = PetscStrcpy(opstring,"cpu");CHKERRQ(ierr); 876 ctx->subThreadBlockSize = 0; 877 #endif 878 ierr = PetscOptionsString("-dm_landau_device_type","Use kernels on 'cpu', 'cuda', or 'kokkos'","plexland.c",opstring,opstring,256,NULL);CHKERRQ(ierr); 879 ierr = PetscStrcmp("cpu",opstring,&flg);CHKERRQ(ierr); 880 if (flg) { 881 ctx->deviceType = LANDAU_CPU; 882 ctx->subThreadBlockSize = 0; 883 } else { 884 ierr = PetscStrcmp("cuda",opstring,&flg);CHKERRQ(ierr); 885 if (flg) ctx->deviceType = LANDAU_CUDA; 886 else { 887 ierr = PetscStrcmp("kokkos",opstring,&flg);CHKERRQ(ierr); 888 if (flg) ctx->deviceType = LANDAU_KOKKOS; 889 else SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"-dm_landau_device_type %s",opstring); 890 } 891 } 892 } 893 ierr = PetscOptionsReal("-dm_landau_electron_shift","Shift in thermal velocity of electrons","none",ctx->electronShift,&ctx->electronShift, NULL);CHKERRQ(ierr); 894 ierr = PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, &sph_flg);CHKERRQ(ierr); 895 ierr = PetscOptionsBool("-dm_landau_inflate", "With sphere, inflate for curved edges (no AMR)", "plexland.c", ctx->inflate, &ctx->inflate, NULL);CHKERRQ(ierr); 896 /* ierr = PetscOptionsBool("-dm_landau_quarter_3d_domain", "Use symmetry in 3D to model 1/4 of domain", "plexland.c", ctx->quarter3DDomain, &ctx->quarter3DDomain, NULL);CHKERRQ(ierr); */ 897 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); 898 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); 899 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); 900 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); 901 ierr = PetscOptionsInt("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &ctx->postAMRRefine, NULL);CHKERRQ(ierr); 902 ierr = PetscOptionsInt("-dm_landau_verbose", "", "plexland.c", ctx->verbose, &ctx->verbose, NULL);CHKERRQ(ierr); 903 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); 904 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); 905 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); 906 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); 907 ierr = PetscOptionsReal("-dm_landau_n_0","Normalization constant for number density","plexland.c",ctx->n_0,&ctx->n_0, NULL);CHKERRQ(ierr); 908 ierr = PetscOptionsReal("-dm_landau_ln_lambda","Cross section parameter","plexland.c",ctx->lnLam,&ctx->lnLam, NULL);CHKERRQ(ierr); 909 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); 910 ctx->simplex = PETSC_FALSE; 911 /* get num species with tempurature*/ 912 { 913 PetscReal arr[100]; 914 nt = 100; 915 ierr = PetscOptionsRealArray("-dm_landau_thermal_temps", "Temperature of each species [e,i_0,i_1,...] in keV", "plexland.c", arr, &nt, &flg);CHKERRQ(ierr); 916 if (flg && nt > LANDAU_MAX_SPECIES) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"-thermal_temps ,t1,t2,.. number of species %D > MAX %D",nt,LANDAU_MAX_SPECIES); 917 } 918 nt = LANDAU_MAX_SPECIES; 919 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) { 920 ctx->thermal_temps[ii] = 1.; 921 ctx->charges[ii] = 1; 922 ctx->masses[ii] = 1; 923 ctx->n[ii] = (ii==1) ? 1 : 0; 924 } 925 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); 926 if (flg) { 927 PetscInfo1(dummy, "num_species set to number of thermal temps provided (%D)\n",nt); 928 ctx->num_species = nt; 929 } else SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species"); 930 for (ii=0;ii<ctx->num_species;ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */ 931 nm = LANDAU_MAX_SPECIES-1; 932 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); 933 if (flg && nm != ctx->num_species-1) { 934 SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"num ion masses %D != num species %D",nm,ctx->num_species-1); 935 } 936 nm = LANDAU_MAX_SPECIES; 937 ierr = PetscOptionsRealArray("-dm_landau_n", "Normalized (by -n_0) number density of each species", "plexland.c", ctx->n, &nm, &flg);CHKERRQ(ierr); 938 if (flg && nm != ctx->num_species) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"wrong num n: %D != num species %D",nm,ctx->num_species); 939 ctx->n_0 *= ctx->n[0]; /* normalized number density */ 940 for (ii=1;ii<ctx->num_species;ii++) ctx->n[ii] = ctx->n[ii]/ctx->n[0]; 941 ctx->n[0] = 1; 942 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */ 943 ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */ 944 ctx->m_0 = ctx->masses[0]; /* arbitrary reference mass, electrons */ 945 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); 946 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) */ 947 nc = LANDAU_MAX_SPECIES-1; 948 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); 949 if (flg && nc != ctx->num_species-1) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"num charges %D != num species %D",nc,ctx->num_species-1); 950 for (ii=0;ii<LANDAU_MAX_SPECIES;ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */ 951 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 */ 952 /* geometry */ 953 for (ii=0;ii<ctx->num_species;ii++) ctx->refineTol[ii] = PETSC_MAX_REAL; 954 for (ii=0;ii<ctx->num_species;ii++) ctx->coarsenTol[ii] = 0.; 955 ii = LANDAU_MAX_SPECIES; 956 ierr = PetscOptionsRealArray("-dm_landau_refine_tol","tolerance for refining cells in AMR","plexland.c",ctx->refineTol, &ii, &flg);CHKERRQ(ierr); 957 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #refine_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 958 ii = LANDAU_MAX_SPECIES; 959 ierr = PetscOptionsRealArray("-dm_landau_coarsen_tol","tolerance for coarsening cells in AMR","plexland.c",ctx->coarsenTol, &ii, &flg);CHKERRQ(ierr); 960 if (flg && ii != ctx->num_species) ierr = PetscInfo2(dummy, "Phase: Warning, #coarsen_tol %D != num_species %D\n",ii,ctx->num_species);CHKERRQ(ierr); 961 ierr = PetscOptionsReal("-dm_landau_domain_radius","Phase space size in units of electron thermal velocity","plexland.c",ctx->radius,&ctx->radius, &flg);CHKERRQ(ierr); 962 if (flg && ctx->radius <= 0) { /* negative is ratio of c */ 963 if (ctx->radius == 0) ctx->radius = 0.75; 964 else ctx->radius = -ctx->radius; 965 ctx->radius = ctx->radius*299792458/ctx->v_0; 966 ierr = PetscInfo1(dummy, "Change domain radius to %e\n",ctx->radius);CHKERRQ(ierr); 967 } 968 ierr = PetscOptionsReal("-dm_landau_i_radius","Ion thermal velocity, used for circular meshes","plexland.c",ctx->i_radius,&ctx->i_radius, &flg);CHKERRQ(ierr); 969 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an ion radius but did not set sphere, user error really */ 970 if (!flg) { 971 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 */ 972 } 973 ierr = PetscOptionsReal("-dm_landau_e_radius","Electron thermal velocity, used for circular meshes","plexland.c",ctx->e_radius,&ctx->e_radius, &flg);CHKERRQ(ierr); 974 if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an e radius but did not set sphere, user error really */ 975 if (!flg) { 976 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 */ 977 } 978 if (ctx->sphere && (ctx->e_radius <= ctx->i_radius || ctx->radius <= ctx->e_radius)) SETERRQ3(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"bad radii: %g < %g < %g",ctx->i_radius,ctx->e_radius,ctx->radius); 979 ierr = PetscOptionsInt("-dm_landau_sub_thread_block_size", "Number of threads in CUDA integration point subblock", "plexland.c", ctx->subThreadBlockSize, &ctx->subThreadBlockSize, NULL);CHKERRQ(ierr); 980 #if !defined(PETSC_HAVE_KOKKOS) 981 if (ctx->subThreadBlockSize > LANDAU_MAX_SUB_THREAD_BLOCKS) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"num sub threads %D > MAX %d",ctx->subThreadBlockSize,LANDAU_MAX_SUB_THREAD_BLOCKS); 982 #endif 983 ierr = PetscOptionsEnd();CHKERRQ(ierr); 984 for (ii=ctx->num_species;ii<LANDAU_MAX_SPECIES;ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0; 985 if (ctx->verbose > 0) { 986 ierr = PetscPrintf(PETSC_COMM_WORLD, "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); 987 ierr = PetscPrintf(PETSC_COMM_WORLD, "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); 988 ierr = PetscPrintf(PETSC_COMM_WORLD, "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); 989 } 990 ierr = DMDestroy(&dummy);CHKERRQ(ierr); 991 { 992 PetscMPIInt rank; 993 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr); 994 /* PetscLogStage setup_stage; */ 995 ierr = PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[0]);CHKERRQ(ierr); /* 0 */ 996 ierr = PetscLogEventRegister(" Jac-vector", DM_CLASSID, &ctx->events[1]);CHKERRQ(ierr); /* 1 */ 997 ierr = PetscLogEventRegister(" Jac-kern-init", DM_CLASSID, &ctx->events[3]);CHKERRQ(ierr); /* 3 */ 998 ierr = PetscLogEventRegister(" Jac-kernel", DM_CLASSID, &ctx->events[4]);CHKERRQ(ierr); /* 4 */ 999 ierr = PetscLogEventRegister(" Jac-kernel-post", DM_CLASSID, &ctx->events[5]);CHKERRQ(ierr); /* 5 */ 1000 ierr = PetscLogEventRegister(" Jac-assemble", DM_CLASSID, &ctx->events[6]);CHKERRQ(ierr); /* 6 */ 1001 ierr = PetscLogEventRegister(" Jac-end", DM_CLASSID, &ctx->events[7]);CHKERRQ(ierr); /* 7 */ 1002 ierr = PetscLogEventRegister(" Jac-geo-color", DM_CLASSID, &ctx->events[8]);CHKERRQ(ierr); /* 8 */ 1003 ierr = PetscLogEventRegister(" Jac-cuda-sum", DM_CLASSID, &ctx->events[2]);CHKERRQ(ierr); /* 2 */ 1004 ierr = PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[9]);CHKERRQ(ierr); /* 9 */ 1005 if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */ 1006 ierr = PetscOptionsClearValue(NULL,"-snes_converged_reason");CHKERRQ(ierr); 1007 ierr = PetscOptionsClearValue(NULL,"-ksp_converged_reason");CHKERRQ(ierr); 1008 ierr = PetscOptionsClearValue(NULL,"-snes_monitor");CHKERRQ(ierr); 1009 ierr = PetscOptionsClearValue(NULL,"-ksp_monitor");CHKERRQ(ierr); 1010 ierr = PetscOptionsClearValue(NULL,"-ts_monitor");CHKERRQ(ierr); 1011 ierr = PetscOptionsClearValue(NULL,"-ts_adapt_monitor");CHKERRQ(ierr); 1012 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1013 ierr = PetscOptionsClearValue(NULL,"-dm_landau_amr_vec_view");CHKERRQ(ierr); 1014 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1015 ierr = PetscOptionsClearValue(NULL,"-dm_landau_pre_vec_view");CHKERRQ(ierr); 1016 ierr = PetscOptionsClearValue(NULL,"-info");CHKERRQ(ierr); 1017 } 1018 } 1019 PetscFunctionReturn(0); 1020 } 1021 1022 /*@C 1023 LandauCreateVelocitySpace - Create a DMPlex velocity space mesh 1024 1025 Collective on comm 1026 1027 Input Parameters: 1028 + comm - The MPI communicator 1029 . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver) 1030 - prefix - prefix for options 1031 1032 Output Parameter: 1033 . dm - The DM object representing the mesh 1034 + X - A vector (user destroys) 1035 - J - Optional matrix (object destroys) 1036 1037 Level: beginner 1038 1039 .keywords: mesh 1040 .seealso: DMPlexCreate(), LandauDestroyVelocitySpace() 1041 @*/ 1042 PetscErrorCode LandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *dm) 1043 { 1044 PetscMPIInt size; 1045 PetscErrorCode ierr; 1046 LandauCtx *ctx; 1047 PetscBool prealloc_only; 1048 1049 PetscFunctionBegin; 1050 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1051 if (size!=1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Velocity space meshes should be serial (but should work in parallel)"); 1052 if (dim!=2 && dim!=3) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported"); 1053 ctx = (LandauCtx*)malloc(sizeof(LandauCtx)); 1054 /* process options */ 1055 ierr = ProcessOptions(ctx,prefix);CHKERRQ(ierr); 1056 /* Create Mesh */ 1057 ierr = LandauDMCreateVMesh(comm, dim, prefix, ctx, dm);CHKERRQ(ierr); 1058 prealloc_only = (*dm)->prealloc_only; 1059 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_pre_dm_view");CHKERRQ(ierr); 1060 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1061 /* create FEM */ 1062 ierr = SetupDS(*dm,dim,ctx);CHKERRQ(ierr); 1063 /* set initial state */ 1064 ierr = DMCreateGlobalVector(*dm,X);CHKERRQ(ierr); 1065 ierr = PetscObjectSetName((PetscObject) *X, "u");CHKERRQ(ierr); 1066 /* initial static refinement, no solve */ 1067 ierr = LandauSetInitialCondition(*dm, *X, ctx);CHKERRQ(ierr); 1068 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_pre_vec_view");CHKERRQ(ierr); 1069 /* forest refinement */ 1070 if (ctx->errorIndicator) { 1071 /* AMR */ 1072 ierr = adapt(dm,ctx,X);CHKERRQ(ierr); 1073 if ((*dm)->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"(*dm)->prealloc_only != prealloc_only"); 1074 ierr = DMViewFromOptions(*dm,NULL,"-dm_landau_amr_dm_view");CHKERRQ(ierr); 1075 ierr = VecViewFromOptions(*X, NULL, "-dm_landau_amr_vec_view");CHKERRQ(ierr); 1076 } 1077 ierr = DMSetApplicationContext(*dm, ctx);CHKERRQ(ierr); 1078 ctx->dmv = *dm; 1079 if (ctx->dmv->prealloc_only != prealloc_only) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"ctx->dmv->prealloc_only != prealloc_only"); 1080 ierr = DMCreateMatrix(ctx->dmv, &ctx->J);CHKERRQ(ierr); 1081 ierr = MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1082 if (J) *J = ctx->J; 1083 PetscFunctionReturn(0); 1084 } 1085 1086 /*@ 1087 LandauDestroyVelocitySpace - Destroy a DMPlex velocity space mesh 1088 1089 Collective on dm 1090 1091 Input/Output Parameters: 1092 . dm - the dm to destroy 1093 1094 Level: beginner 1095 1096 .keywords: mesh 1097 .seealso: LandauCreateVelocitySpace() 1098 @*/ 1099 PetscErrorCode LandauDestroyVelocitySpace(DM *dm) 1100 { 1101 PetscErrorCode ierr,ii; 1102 LandauCtx *ctx; 1103 PetscContainer container = NULL; 1104 PetscFunctionBegin; 1105 ierr = DMGetApplicationContext(*dm, &ctx);CHKERRQ(ierr); 1106 ierr = PetscObjectQuery((PetscObject)ctx->J,"coloring", (PetscObject*)&container);CHKERRQ(ierr); 1107 if (container) { 1108 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 1109 } 1110 ierr = MatDestroy(&ctx->M);CHKERRQ(ierr); 1111 ierr = MatDestroy(&ctx->J);CHKERRQ(ierr); 1112 for (ii=0;ii<ctx->num_species;ii++) { 1113 ierr = PetscFEDestroy(&ctx->fe[ii]);CHKERRQ(ierr); 1114 } 1115 free(ctx); 1116 ierr = DMDestroy(dm);CHKERRQ(ierr); 1117 PetscFunctionReturn(0); 1118 } 1119 1120 /* < v, ru > */ 1121 static void f0_s_den(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1122 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1123 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1124 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1125 { 1126 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1127 f0[0] = u[ii]; 1128 } 1129 1130 /* < v, ru > */ 1131 static void f0_s_mom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1132 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1133 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1134 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1135 { 1136 PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]); 1137 f0[0] = x[jj]*u[ii]; /* x momentum */ 1138 } 1139 1140 static void f0_s_v2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1141 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1142 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1143 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1144 { 1145 PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]); 1146 double tmp1 = 0.; 1147 for (i = 0; i < dim; ++i) tmp1 += x[i]*x[i]; 1148 f0[0] = tmp1*u[ii]; 1149 } 1150 1151 /* < v, ru > */ 1152 static void f0_s_rden(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1153 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1154 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1155 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1156 { 1157 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1158 f0[0] = 2.*PETSC_PI*x[0]*u[ii]; 1159 } 1160 1161 /* < v, ru > */ 1162 static void f0_s_rmom(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1163 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1164 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1165 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1166 { 1167 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1168 f0[0] = 2.*PETSC_PI*x[0]*x[1]*u[ii]; 1169 } 1170 1171 static void f0_s_rv2(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1172 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1173 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1174 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 1175 { 1176 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 1177 f0[0] = 2.*PETSC_PI*x[0]*(x[0]*x[0] + x[1]*x[1])*u[ii]; 1178 } 1179 1180 /*@ 1181 LandauPrintNorms - collects moments and prints them 1182 1183 Collective on dm 1184 1185 Input Parameters: 1186 + X - the state 1187 - stepi - current step to print 1188 1189 Level: beginner 1190 1191 .keywords: mesh 1192 .seealso: LandauCreateVelocitySpace() 1193 @*/ 1194 PetscErrorCode LandauPrintNorms(Vec X, PetscInt stepi) 1195 { 1196 PetscErrorCode ierr; 1197 LandauCtx *ctx; 1198 PetscDS prob; 1199 DM plex,dm; 1200 PetscInt cStart, cEnd, dim, ii; 1201 PetscScalar xmomentumtot=0, ymomentumtot=0, zmomentumtot=0, energytot=0, densitytot=0, tt[LANDAU_MAX_SPECIES]; 1202 PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES]; 1203 1204 PetscFunctionBegin; 1205 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 1206 if (!dm) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no DM"); 1207 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1208 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1209 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1210 ierr = DMConvert(ctx->dmv, DMPLEX, &plex);CHKERRQ(ierr); 1211 ierr = DMCreateDS(plex);CHKERRQ(ierr); 1212 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 1213 /* print momentum and energy */ 1214 for (ii=0;ii<ctx->num_species;ii++) { 1215 PetscScalar user[2] = { (PetscScalar)ii, (PetscScalar)ctx->charges[ii]}; 1216 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 1217 if (dim==2) { /* 2/3X + 3V (cylindrical coordinates) */ 1218 ierr = PetscDSSetObjective(prob, 0, &f0_s_rden);CHKERRQ(ierr); 1219 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1220 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1221 ierr = PetscDSSetObjective(prob, 0, &f0_s_rmom);CHKERRQ(ierr); 1222 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1223 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1224 ierr = PetscDSSetObjective(prob, 0, &f0_s_rv2);CHKERRQ(ierr); 1225 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1226 energy[ii] = tt[0]*0.5*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1227 zmomentumtot += zmomentum[ii]; 1228 energytot += energy[ii]; 1229 densitytot += density[ii]; 1230 ierr = PetscPrintf(PETSC_COMM_WORLD, "%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); 1231 } else { /* 2/3X + 3V */ 1232 ierr = PetscDSSetObjective(prob, 0, &f0_s_den);CHKERRQ(ierr); 1233 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1234 density[ii] = tt[0]*ctx->n_0*ctx->charges[ii]; 1235 ierr = PetscDSSetObjective(prob, 0, &f0_s_mom);CHKERRQ(ierr); 1236 user[1] = 0; 1237 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1238 xmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1239 user[1] = 1; 1240 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1241 ymomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1242 user[1] = 2; 1243 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1244 zmomentum[ii] = tt[0]*ctx->n_0*ctx->v_0*ctx->masses[ii]; 1245 ierr = PetscDSSetObjective(prob, 0, &f0_s_v2);CHKERRQ(ierr); 1246 ierr = DMPlexComputeIntegralFEM(plex,X,tt,ctx);CHKERRQ(ierr); 1247 energy[ii] = 0.5*tt[0]*ctx->n_0*ctx->v_0*ctx->v_0*ctx->masses[ii]; 1248 ierr = PetscPrintf(PETSC_COMM_WORLD, "%3D) species %D: density=%20.13e, x-momentum=%20.13e, y-momentum=%20.13e, z-momentum=%20.13e, energy=%21.13e", 1249 stepi,ii,PetscRealPart(density[ii]),PetscRealPart(xmomentum[ii]),PetscRealPart(ymomentum[ii]),PetscRealPart(zmomentum[ii]),PetscRealPart(energy[ii]));CHKERRQ(ierr); 1250 xmomentumtot += xmomentum[ii]; 1251 ymomentumtot += ymomentum[ii]; 1252 zmomentumtot += zmomentum[ii]; 1253 energytot += energy[ii]; 1254 densitytot += density[ii]; 1255 } 1256 if (ctx->num_species>1) PetscPrintf(PETSC_COMM_WORLD, "\n"); 1257 } 1258 /* totals */ 1259 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1260 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1261 if (ctx->num_species>1) { 1262 if (dim==2) { 1263 ierr = PetscPrintf(PETSC_COMM_WORLD, "\t%3D) Total: charge density=%21.13e, momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %D cells)", 1264 stepi,PetscRealPart(densitytot),PetscRealPart(zmomentumtot),PetscRealPart(energytot),ctx->masses[1]/ctx->masses[0],cEnd-cStart);CHKERRQ(ierr); 1265 } else { 1266 ierr = PetscPrintf(PETSC_COMM_WORLD, "\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)", 1267 stepi,PetscRealPart(densitytot),PetscRealPart(xmomentumtot),PetscRealPart(ymomentumtot),PetscRealPart(zmomentumtot),PetscRealPart(energytot),ctx->masses[1]/ctx->masses[0],cEnd-cStart);CHKERRQ(ierr); 1268 } 1269 } else { 1270 ierr = PetscPrintf(PETSC_COMM_WORLD, " -- %D cells",cEnd-cStart);CHKERRQ(ierr); 1271 } 1272 if (ctx->verbose > 1) {ierr = PetscPrintf(PETSC_COMM_WORLD,", %D sub (vector) threads\n",ctx->subThreadBlockSize);CHKERRQ(ierr);} 1273 else {ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);} 1274 PetscFunctionReturn(0); 1275 } 1276 1277 static PetscErrorCode destroy_coloring (void *is) 1278 { 1279 ISColoring tmp = (ISColoring)is; 1280 return ISColoringDestroy(&tmp); 1281 } 1282 1283 /*@ 1284 LandauCreateColoring - create a coloring and add to matrix (Landau context used just for 'print' flag, should be in DMPlex) 1285 1286 Collective on JacP 1287 1288 Input Parameters: 1289 + JacP - matrix to add coloring to 1290 - plex - The DM 1291 1292 Output Parameter: 1293 . container - Container with coloring 1294 1295 Level: beginner 1296 1297 .keywords: mesh 1298 .seealso: LandauCreateVelocitySpace() 1299 @*/ 1300 PetscErrorCode LandauCreateColoring(Mat JacP, DM plex, PetscContainer *container) 1301 { 1302 PetscErrorCode ierr; 1303 PetscInt dim,cell,i,ej,nc,Nv,totDim,numGCells,cStart,cEnd; 1304 ISColoring iscoloring = NULL; 1305 Mat G,Q; 1306 PetscScalar ones[128]; 1307 MatColoring mc; 1308 IS *is; 1309 PetscInt csize,colour,j,k; 1310 const PetscInt *indices; 1311 PetscInt numComp[1]; 1312 PetscInt numDof[4]; 1313 PetscFE fe; 1314 DM colordm; 1315 PetscSection csection, section, globalSection; 1316 PetscDS prob; 1317 LandauCtx *ctx; 1318 1319 PetscFunctionBegin; 1320 ierr = DMGetApplicationContext(plex, &ctx);CHKERRQ(ierr); 1321 ierr = DMGetLocalSection(plex, §ion);CHKERRQ(ierr); 1322 ierr = DMGetGlobalSection(plex, &globalSection);CHKERRQ(ierr); 1323 ierr = DMGetDimension(plex, &dim);CHKERRQ(ierr); 1324 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 1325 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1326 ierr = DMPlexGetHeightStratum(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1327 numGCells = cEnd - cStart; 1328 /* create cell centered DM */ 1329 ierr = DMClone(plex, &colordm);CHKERRQ(ierr); 1330 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) plex), dim, 1, PETSC_FALSE, "color_", PETSC_DECIDE, &fe);CHKERRQ(ierr); 1331 ierr = PetscObjectSetName((PetscObject) fe, "color");CHKERRQ(ierr); 1332 ierr = DMSetField(colordm, 0, NULL, (PetscObject)fe);CHKERRQ(ierr); 1333 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 1334 for (i = 0; i < (dim+1); ++i) numDof[i] = 0; 1335 numDof[dim] = 1; 1336 numComp[0] = 1; 1337 ierr = DMPlexCreateSection(colordm, NULL, numComp, numDof, 0, NULL, NULL, NULL, NULL, &csection);CHKERRQ(ierr); 1338 ierr = PetscSectionSetFieldName(csection, 0, "color");CHKERRQ(ierr); 1339 ierr = DMSetLocalSection(colordm, csection);CHKERRQ(ierr); 1340 ierr = DMViewFromOptions(colordm,NULL,"-color_dm_view");CHKERRQ(ierr); 1341 /* get vertex to element map Q and colroing graph G */ 1342 ierr = MatGetSize(JacP,NULL,&Nv);CHKERRQ(ierr); 1343 ierr = MatCreateAIJ(PETSC_COMM_SELF,PETSC_DECIDE,PETSC_DECIDE,numGCells,Nv,totDim,NULL,0,NULL,&Q);CHKERRQ(ierr); 1344 for (i=0;i<128;i++) ones[i] = 1.0; 1345 for (cell = cStart, ej = 0 ; cell < cEnd; ++cell, ++ej) { 1346 PetscInt numindices,*indices; 1347 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1348 if (numindices>128) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many indices. %D > %D",numindices,128); 1349 ierr = MatSetValues(Q,1,&ej,numindices,indices,ones,ADD_VALUES);CHKERRQ(ierr); 1350 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, NULL);CHKERRQ(ierr); 1351 } 1352 ierr = MatAssemblyBegin(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1353 ierr = MatAssemblyEnd(Q, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1354 ierr = MatMatTransposeMult(Q,Q,MAT_INITIAL_MATRIX,4.0,&G);CHKERRQ(ierr); 1355 ierr = PetscObjectSetName((PetscObject) Q, "Q");CHKERRQ(ierr); 1356 ierr = PetscObjectSetName((PetscObject) G, "coloring graph");CHKERRQ(ierr); 1357 ierr = MatViewFromOptions(G,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1358 ierr = MatViewFromOptions(Q,NULL,"-coloring_mat_view");CHKERRQ(ierr); 1359 ierr = MatDestroy(&Q);CHKERRQ(ierr); 1360 /* coloring */ 1361 ierr = MatColoringCreate(G,&mc);CHKERRQ(ierr); 1362 ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr); 1363 ierr = MatColoringSetType(mc,MATCOLORINGJP);CHKERRQ(ierr); 1364 ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr); 1365 ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr); 1366 ierr = MatColoringDestroy(&mc);CHKERRQ(ierr); 1367 /* view */ 1368 ierr = ISColoringViewFromOptions(iscoloring,NULL,"-coloring_is_view");CHKERRQ(ierr); 1369 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1370 if (ctx && ctx->verbose > 5) { 1371 PetscViewer viewer; 1372 Vec color_vec, eidx_vec; 1373 ierr = DMGetGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1374 ierr = DMGetGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1375 for (colour=0; colour<nc; colour++) { 1376 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1377 ierr = ISGetIndices(is[colour],&indices);CHKERRQ(ierr); 1378 for (j=0; j<csize; j++) { 1379 PetscScalar v = (PetscScalar)colour; 1380 k = indices[j]; 1381 ierr = VecSetValues(color_vec,1,&k,&v,INSERT_VALUES); 1382 v = (PetscScalar)k; 1383 ierr = VecSetValues(eidx_vec,1,&k,&v,INSERT_VALUES); 1384 } 1385 ierr = ISRestoreIndices(is[colour],&indices);CHKERRQ(ierr); 1386 } 1387 /* view */ 1388 ierr = PetscViewerVTKOpen(PETSC_COMM_WORLD, "color.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1389 ierr = PetscObjectSetName((PetscObject) color_vec, "color");CHKERRQ(ierr); 1390 ierr = VecView(color_vec, viewer);CHKERRQ(ierr); 1391 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1392 ierr = PetscViewerVTKOpen(PETSC_COMM_WORLD, "eidx.vtu", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr); 1393 ierr = PetscObjectSetName((PetscObject) eidx_vec, "element-idx");CHKERRQ(ierr); 1394 ierr = VecView(eidx_vec, viewer);CHKERRQ(ierr); 1395 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1396 ierr = DMRestoreGlobalVector(colordm, &color_vec);CHKERRQ(ierr); 1397 ierr = DMRestoreGlobalVector(colordm, &eidx_vec);CHKERRQ(ierr); 1398 } 1399 ierr = PetscSectionDestroy(&csection);CHKERRQ(ierr); 1400 ierr = DMDestroy(&colordm);CHKERRQ(ierr); 1401 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1402 ierr = MatDestroy(&G);CHKERRQ(ierr); 1403 /* stash coloring */ 1404 ierr = PetscContainerCreate(PETSC_COMM_SELF, container);CHKERRQ(ierr); 1405 ierr = PetscContainerSetPointer(*container,(void*)iscoloring);CHKERRQ(ierr); 1406 ierr = PetscContainerSetUserDestroy(*container, destroy_coloring);CHKERRQ(ierr); 1407 ierr = PetscObjectCompose((PetscObject)JacP,"coloring",(PetscObject)*container);CHKERRQ(ierr); 1408 if (ctx && ctx->verbose > 0) { 1409 ierr = PetscPrintf(PETSC_COMM_WORLD, "Made coloring with %D colors\n", nc);CHKERRQ(ierr); 1410 } 1411 PetscFunctionReturn(0); 1412 } 1413 1414 PetscErrorCode LandauAssembleOpenMP(PetscInt cStart, PetscInt cEnd, PetscInt totDim, DM plex, PetscSection section, PetscSection globalSection, Mat JacP, PetscScalar elemMats[], PetscContainer container) 1415 { 1416 PetscErrorCode ierr; 1417 IS *is; 1418 PetscInt nc,colour,j; 1419 const PetscInt *clr_idxs; 1420 ISColoring iscoloring; 1421 PetscFunctionBegin; 1422 ierr = PetscContainerGetPointer(container,(void**)&iscoloring);CHKERRQ(ierr); 1423 ierr = ISColoringGetIS(iscoloring,PETSC_USE_POINTER,&nc,&is);CHKERRQ(ierr); 1424 for (colour=0; colour<nc; colour++) { 1425 PetscInt *idx_arr[1024]; /* need to make dynamic for general use */ 1426 PetscScalar *new_el_mats[1024]; 1427 PetscInt idx_size[1024],csize; 1428 ierr = ISGetLocalSize(is[colour],&csize);CHKERRQ(ierr); 1429 if (csize>1024) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "too many elements in color. %D > %D",csize,1024); 1430 ierr = ISGetIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1431 /* get indices and mats */ 1432 for (j=0; j<csize; j++) { 1433 PetscInt cell = cStart + clr_idxs[j]; 1434 PetscInt numindices,*indices; 1435 PetscScalar *elMat = &elemMats[clr_idxs[j]*totDim*totDim]; 1436 PetscScalar *valuesOrig = elMat; 1437 ierr = DMPlexGetClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1438 idx_size[j] = numindices; 1439 ierr = PetscMalloc2(numindices,&idx_arr[j],numindices*numindices,&new_el_mats[j]);CHKERRQ(ierr); 1440 ierr = PetscMemcpy(idx_arr[j],indices,numindices*sizeof(PetscInt));CHKERRQ(ierr); 1441 ierr = PetscMemcpy(new_el_mats[j],elMat,numindices*numindices*sizeof(PetscScalar));CHKERRQ(ierr); 1442 ierr = DMPlexRestoreClosureIndices(plex, section, globalSection, cell, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **) &elMat);CHKERRQ(ierr); 1443 if (elMat != valuesOrig) {ierr = DMRestoreWorkArray(plex, numindices*numindices, MPIU_SCALAR, &elMat);} 1444 } 1445 /* assemble matrix - pragmas break CI ? */ 1446 //#pragma omp parallel default(JacP,idx_size,idx_arr,new_el_mats,colour,clr_idxs) private(j) 1447 //#pragma omp parallel for private(j) 1448 for (j=0; j<csize; j++) { 1449 PetscInt numindices = idx_size[j], *indices = idx_arr[j]; 1450 PetscScalar *elMat = new_el_mats[j]; 1451 MatSetValues(JacP,numindices,indices,numindices,indices,elMat,ADD_VALUES); 1452 } 1453 /* free */ 1454 ierr = ISRestoreIndices(is[colour],&clr_idxs);CHKERRQ(ierr); 1455 for (j=0; j<csize; j++) { 1456 ierr = PetscFree2(idx_arr[j],new_el_mats[j]);CHKERRQ(ierr); 1457 } 1458 } 1459 ierr = ISColoringRestoreIS(iscoloring,PETSC_USE_POINTER,&is);CHKERRQ(ierr); 1460 PetscFunctionReturn(0); 1461 } 1462 1463 /* < v, u > */ 1464 static void g0_1(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1465 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1466 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1467 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1468 { 1469 g0[0] = 1.; 1470 } 1471 1472 /* < v, u > */ 1473 static void g0_r(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1474 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1475 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1476 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 1477 { 1478 g0[0] = 2.*PETSC_PI*x[0]; 1479 } 1480 1481 /*@ 1482 LandauCreateMassMatrix - Create mass matrix for Landau 1483 1484 Collective on dm 1485 1486 Input Parameters: 1487 . dm - the DM object 1488 1489 Output Parameters: 1490 . Amat - The mass matrix (optional), mass matrix is added to the DM context 1491 1492 Level: beginner 1493 1494 .keywords: mesh 1495 .seealso: LandauCreateVelocitySpace() 1496 @*/ 1497 PetscErrorCode LandauCreateMassMatrix(DM dm, Mat *Amat) 1498 { 1499 DM massDM; 1500 PetscDS prob; 1501 PetscInt ii,dim,N1=1,N2; 1502 PetscErrorCode ierr; 1503 LandauCtx *ctx; 1504 Mat M; 1505 1506 PetscFunctionBegin; 1507 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1508 if (Amat) PetscValidPointer(Amat,3); 1509 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1510 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1511 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1512 ierr = DMClone(dm, &massDM);CHKERRQ(ierr); 1513 ierr = DMCopyFields(dm, massDM);CHKERRQ(ierr); 1514 ierr = DMCreateDS(massDM);CHKERRQ(ierr); 1515 ierr = DMGetDS(massDM, &prob);CHKERRQ(ierr); 1516 for (ii=0;ii<ctx->num_species;ii++) { 1517 if (dim==3) {ierr = PetscDSSetJacobian(prob, ii, ii, g0_1, NULL, NULL, NULL);CHKERRQ(ierr);} 1518 else {ierr = PetscDSSetJacobian(prob, ii, ii, g0_r, NULL, NULL, NULL);CHKERRQ(ierr);} 1519 } 1520 ierr = DMViewFromOptions(massDM,NULL,"-dm_landau_mass_dm_view");CHKERRQ(ierr); 1521 ierr = DMCreateMatrix(massDM, &M);CHKERRQ(ierr); 1522 ierr = MatSetOption(M, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 1523 { 1524 Vec locX; 1525 DM plex; 1526 ierr = DMConvert(massDM, DMPLEX, &plex);CHKERRQ(ierr); 1527 ierr = DMGetLocalVector(massDM, &locX);CHKERRQ(ierr); 1528 /* Mass matrix is independent of the input, so no need to fill locX */ 1529 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); 1530 ierr = DMPlexSNESComputeJacobianFEM(plex, locX, M, M, ctx);CHKERRQ(ierr); 1531 ierr = DMRestoreLocalVector(massDM, &locX);CHKERRQ(ierr); 1532 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1533 } 1534 ierr = DMDestroy(&massDM);CHKERRQ(ierr); 1535 ierr = MatGetSize(ctx->J, &N1, NULL);CHKERRQ(ierr); 1536 ierr = MatGetSize(M, &N2, NULL);CHKERRQ(ierr); 1537 if (N1 != N2) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %D, |Mass|=%D",N1,N2); 1538 ierr = PetscObjectSetName((PetscObject)M, "mass");CHKERRQ(ierr); 1539 ierr = MatViewFromOptions(M,NULL,"-dm_landau_mass_mat_view");CHKERRQ(ierr); 1540 ctx->M = M; /* this could be a noop, a = a */ 1541 if (Amat) *Amat = M; 1542 PetscFunctionReturn(0); 1543 } 1544 1545 /*@ 1546 LandauIFunction - TS residual calculation 1547 1548 Collective on ts 1549 1550 Input Parameters: 1551 + TS - The time stepping context 1552 . time_dummy - current time (not used) 1553 - X - Current state 1554 + X_t - Time derivative of current state 1555 . actx - Landau context 1556 1557 Output Parameter: 1558 . F - The residual 1559 1560 Level: beginner 1561 1562 .keywords: mesh 1563 .seealso: LandauCreateVelocitySpace(), LandauIJacobian() 1564 @*/ 1565 PetscErrorCode LandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx) 1566 { 1567 PetscErrorCode ierr; 1568 LandauCtx *ctx=(LandauCtx*)actx; 1569 PetscReal unorm; 1570 PetscInt dim; 1571 DM dm; 1572 1573 PetscFunctionBegin; 1574 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 1575 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1576 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1577 ierr = VecNorm(X,NORM_2,&unorm);CHKERRQ(ierr); 1578 ierr = PetscLogEventBegin(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 1579 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 1580 if (ctx->normJ != unorm) { 1581 ctx->normJ = unorm; 1582 ierr = PetscInfo1(ts, "Create Landau Jacobian t=%g\n",time_dummy);CHKERRQ(ierr); 1583 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,(void*)ctx);CHKERRQ(ierr); 1584 ctx->aux_bool = PETSC_TRUE; /* debug: set flag that we made a new Jacobian */ 1585 } else { 1586 ctx->aux_bool = PETSC_FALSE; 1587 ierr = PetscInfo1(ts, "Skip Landau Jacobian t=%g\n",(double)time_dummy);CHKERRQ(ierr); 1588 } 1589 /* mat vec for op */ 1590 ierr = MatMult(ctx->J,X,F);CHKERRQ(ierr);CHKERRQ(ierr); /* C*f */ 1591 /* add time term */ 1592 if (X_t) { 1593 ierr = MatMultAdd(ctx->M,X_t,F,F);CHKERRQ(ierr); 1594 } 1595 ierr = PetscLogEventEnd(ctx->events[0],0,0,0,0);CHKERRQ(ierr); 1596 PetscFunctionReturn(0); 1597 } 1598 1599 /*@ 1600 LandauIJacobian - TS Jacobian construction 1601 1602 Collective on ts 1603 1604 Input Parameters: 1605 + TS - The time stepping context 1606 . time_dummy - current time (not used) 1607 - X - Current state 1608 + U_tdummy - Time derivative of current state (not used) 1609 . shift - shift for du/dt term 1610 - actx - Landau context 1611 1612 Output Parameter: 1613 . Amat - Jacobian 1614 + Pmat - same as Amat 1615 1616 Level: beginner 1617 1618 .keywords: mesh 1619 .seealso: LandauCreateVelocitySpace(), LandauIFunction() 1620 @*/ 1621 PetscErrorCode LandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx) 1622 { 1623 PetscErrorCode ierr; 1624 LandauCtx *ctx=(LandauCtx*)actx; 1625 PetscReal unorm; 1626 PetscInt dim; 1627 DM dm; 1628 1629 PetscFunctionBegin; 1630 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 1631 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 1632 if (!ctx) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context"); 1633 if (Amat!=Pmat || Amat!=ctx->J) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J"); 1634 ierr = DMGetDimension(ctx->dmv, &dim);CHKERRQ(ierr); 1635 /* get collision Jacobian into A */ 1636 ierr = PetscLogEventBegin(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 1637 ierr = VecNorm(X,NORM_2,&unorm);CHKERRQ(ierr); 1638 if (ctx->normJ!=unorm) { 1639 ierr = PetscInfo2(ts, "Create Landau Jacobian t=%g, shift=%g\n",(double)time_dummy,(double)shift);CHKERRQ(ierr); 1640 ierr = LandauFormJacobian_Internal(X,ctx->J,dim,(void*)ctx);CHKERRQ(ierr); 1641 ctx->normJ = unorm; 1642 ctx->aux_bool = PETSC_TRUE; /* debug: set flag that we made a new Jacobian */ 1643 } else { 1644 ctx->aux_bool = PETSC_FALSE; 1645 ierr = PetscInfo3(ts, "Skip Landau Jacobian t=%g, shift=%g shift*|u|=%20.12e\n",(double)time_dummy,(double)shift,(double)shift*unorm);CHKERRQ(ierr); 1646 } 1647 ierr = MatCopy(ctx->J,Pmat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); // these are the same 1648 { 1649 MatInfo info1, info2; 1650 double nz_1, nz_2; 1651 ierr = MatGetInfo(Pmat,MAT_LOCAL,&info1);CHKERRQ(ierr); 1652 nz_1 = info1.nz_allocated; 1653 ierr = MatGetInfo(ctx->J,MAT_LOCAL,&info2);CHKERRQ(ierr); 1654 nz_2 = info2.nz_allocated; 1655 if (0){ 1656 ierr = PetscInfo2(ts, "\t\tnnz A = %g, nnz M = %g\n",nz_1,nz_2);CHKERRQ(ierr); 1657 } 1658 /* add mass */ 1659 if (nz_1 != nz_2||1) { /* there is a bug wit Q2 elements and this generates an error message instead of diverged solution, need to fix */ 1660 ierr = MatAXPY(Pmat,shift,ctx->M,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); 1661 //SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "nz_1 != nz_2 %g %g",(double)nz_1,(double)nz_2); 1662 } else { 1663 ierr = MatAXPY(Pmat,shift,ctx->M,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 1664 } 1665 } 1666 ierr = PetscLogEventEnd(ctx->events[9],0,0,0,0);CHKERRQ(ierr); 1667 PetscFunctionReturn(0); 1668 } 1669