1 static char help[] = "Runaway electron model with Landau collision operator\n\n"; 2 3 #include <petscdmplex.h> 4 #include <petsclandau.h> 5 #include <petscts.h> 6 #include <petscds.h> 7 #include <petscdmcomposite.h> 8 9 /* data for runaway electron model */ 10 typedef struct REctx_struct { 11 PetscErrorCode (*test)(TS, Vec, PetscInt, PetscReal, PetscBool, LandauCtx *, struct REctx_struct *); 12 PetscErrorCode (*impuritySrcRate)(PetscReal, PetscReal *, LandauCtx*); 13 PetscErrorCode (*E)(Vec, Vec, PetscInt, PetscReal, LandauCtx*, PetscReal *); 14 PetscReal T_cold; /* temperature of newly ionized electrons and impurity ions */ 15 PetscReal ion_potential; /* ionization potential of impurity */ 16 PetscReal Ne_ion; /* effective number of electrons shed in ioization of impurity */ 17 PetscReal Ez_initial; 18 PetscReal L; /* inductance */ 19 Vec X_0; 20 PetscInt imp_idx; /* index for impurity ionizing sink */ 21 PetscReal pulse_start; 22 PetscReal pulse_width; 23 PetscReal pulse_rate; 24 PetscReal current_rate; 25 PetscInt plotIdx; 26 PetscInt plotStep; 27 PetscInt idx; /* cache */ 28 PetscReal j; /* cache */ 29 PetscReal plotDt; 30 PetscBool plotting; 31 PetscBool use_spitzer_eta; 32 PetscInt print_period; 33 PetscInt grid_view_idx; 34 } REctx; 35 36 static const PetscReal kev_joul = 6.241506479963235e+15; /* 1/1000e */ 37 38 #define RE_CUT 3. 39 /* < v, u_re * v * q > */ 40 static void f0_j_re(PetscInt dim, PetscInt Nf, PetscInt NfAux, 41 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 42 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 43 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 44 { 45 PetscReal n_e = PetscRealPart(u[0]); 46 if (dim==2) { 47 if (x[1] > RE_CUT || x[1] < -RE_CUT) { /* simply a cutoff for REs. v_|| > 3 v(T_e) */ 48 *f0 = n_e * 2.*PETSC_PI*x[0] * x[1] * constants[0]; /* n * r * v_|| * q */ 49 } else { 50 *f0 = 0; 51 } 52 } else { 53 if (x[2] > RE_CUT || x[2] < -RE_CUT) { /* simply a cutoff for REs. v_|| > 3 v(T_e) */ 54 *f0 = n_e * x[2] * constants[0]; 55 } else { 56 *f0 = 0; 57 } 58 } 59 } 60 61 /* sum < v, u*v*q > */ 62 static void f0_jz_sum(PetscInt dim, PetscInt Nf, PetscInt NfAux, 63 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 64 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 65 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar q[], PetscScalar *f0) 66 { 67 PetscInt ii; 68 f0[0] = 0; 69 if (dim==2) { 70 for (ii=0;ii<Nf;ii++) f0[0] += u[ii] * 2.*PETSC_PI*x[0] * x[1] * q[ii]; /* n * r * v_|| * q * v_0 */ 71 } else { 72 for (ii=0;ii<Nf;ii++) f0[0] += u[ii] * x[2] * q[ii]; /* n * v_|| * q * v_0 */ 73 } 74 } 75 76 /* < v, n_e > */ 77 static void f0_n(PetscInt dim, PetscInt Nf, PetscInt NfAux, 78 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 79 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 80 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 81 { 82 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 83 if (dim==2) f0[0] = 2.*PETSC_PI*x[0]*u[ii]; 84 else { 85 f0[0] = u[ii]; 86 } 87 } 88 89 /* < v, n_e v_|| > */ 90 static void f0_vz(PetscInt dim, PetscInt Nf, PetscInt NfAux, 91 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 92 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 93 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 94 { 95 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 96 if (dim==2) f0[0] = u[ii] * 2.*PETSC_PI*x[0] * x[1]; /* n r v_|| */ 97 else { 98 f0[0] = u[ii] * x[2]; /* n v_|| */ 99 } 100 } 101 102 /* < v, n_e (v-shift) > */ 103 static void f0_ve_shift(PetscInt dim, PetscInt Nf, PetscInt NfAux, 104 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 105 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 106 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 107 { 108 PetscReal vz = numConstants>0 ? PetscRealPart(constants[0]) : 0; 109 if (dim==2) *f0 = u[0] * 2.*PETSC_PI*x[0] * PetscSqrtReal(x[0]*x[0] + (x[1]-vz)*(x[1]-vz)); /* n r v */ 110 else { 111 *f0 = u[0] * PetscSqrtReal(x[0]*x[0] + x[1]*x[1] + (x[2]-vz)*(x[2]-vz)); /* n v */ 112 } 113 } 114 115 /* CalculateE - Calculate the electric field */ 116 /* T -- Electron temperature */ 117 /* n -- Electron density */ 118 /* lnLambda -- */ 119 /* eps0 -- */ 120 /* E -- output E, input \hat E */ 121 static PetscReal CalculateE(PetscReal Tev, PetscReal n, PetscReal lnLambda, PetscReal eps0, PetscReal *E) 122 { 123 PetscReal c,e,m; 124 125 PetscFunctionBegin; 126 c = 299792458.0; 127 e = 1.602176e-19; 128 m = 9.10938e-31; 129 if (1) { 130 double Ec, Ehat = *E, betath = PetscSqrtReal(2*Tev*e/(m*c*c)), j0 = Ehat * 7/(PetscSqrtReal(2)*2) * PetscPowReal(betath,3) * n * e * c; 131 Ec = n*lnLambda*PetscPowReal(e,3) / (4*PETSC_PI*PetscPowReal(eps0,2)*m*c*c); 132 *E = Ec; 133 PetscPrintf(PETSC_COMM_WORLD, "CalculateE j0=%g Ec = %g\n",j0,Ec); 134 } else { 135 PetscReal Ed, vth; 136 vth = PetscSqrtReal(8*Tev*e/(m*PETSC_PI)); 137 Ed = n*lnLambda*PetscPowReal(e,3) / (4*PETSC_PI*PetscPowReal(eps0,2)*m*vth*vth); 138 *E = Ed; 139 } 140 PetscFunctionReturn(0); 141 } 142 143 static PetscReal Spitzer(PetscReal m_e, PetscReal e, PetscReal Z, PetscReal epsilon0, PetscReal lnLam, PetscReal kTe_joules) 144 { 145 PetscReal Fz = (1+1.198*Z+0.222*Z*Z)/(1+2.966*Z+0.753*Z*Z), eta; 146 eta = Fz*4./3.*PetscSqrtReal(2.*PETSC_PI)*Z*PetscSqrtReal(m_e)*PetscSqr(e)*lnLam*PetscPowReal(4*PETSC_PI*epsilon0,-2.)*PetscPowReal(kTe_joules,-1.5); 147 return eta; 148 } 149 150 /* */ 151 static PetscErrorCode testNone(TS ts, Vec X, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx) 152 { 153 PetscFunctionBeginUser; 154 PetscFunctionReturn(0); 155 } 156 157 /* */ 158 static PetscErrorCode testSpitzer(TS ts, Vec X, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx) 159 { 160 PetscErrorCode ierr; 161 PetscInt ii,nDMs; 162 PetscDS prob; 163 static PetscReal old_ratio = 1e10; 164 TSConvergedReason reason; 165 PetscReal J,J_re,spit_eta,Te_kev=0,E,ratio,Z,n_e,v,v2; 166 PetscScalar user[2] = {0.,ctx->charges[0]}, q[LANDAU_MAX_SPECIES],tt[LANDAU_MAX_SPECIES],vz; 167 PetscReal dt; 168 DM pack, plexe = ctx->plex[0], plexi = (ctx->num_grids==1) ? NULL : ctx->plex[1]; 169 Vec *XsubArray; 170 171 PetscFunctionBeginUser; 172 PetscCheckFalse(ctx->num_species!=2,PETSC_COMM_SELF, PETSC_ERR_PLIB, "ctx->num_species %D != 2",ctx->num_species); 173 ierr = VecGetDM(X, &pack);CHKERRQ(ierr); 174 PetscCheckFalse(!pack,PETSC_COMM_SELF, PETSC_ERR_PLIB, "no DM"); 175 ierr = DMCompositeGetNumberDM(pack,&nDMs);CHKERRQ(ierr); 176 PetscCheckFalse(nDMs != ctx->num_grids*ctx->batch_sz,PETSC_COMM_SELF, PETSC_ERR_PLIB, "nDMs != ctx->num_grids*ctx->batch_sz %D != %D",nDMs,ctx->num_grids*ctx->batch_sz); 177 ierr = PetscMalloc(sizeof(*XsubArray)*nDMs, &XsubArray);CHKERRQ(ierr); 178 ierr = DMCompositeGetAccessArray(pack, X, nDMs, NULL, XsubArray);CHKERRQ(ierr); // read only 179 ierr = TSGetTimeStep(ts,&dt);CHKERRQ(ierr); 180 /* get current for each grid */ 181 for (ii=0;ii<ctx->num_species;ii++) q[ii] = ctx->charges[ii]; 182 ierr = DMGetDS(plexe, &prob);CHKERRQ(ierr); 183 ierr = PetscDSSetConstants(prob, 2, &q[0]);CHKERRQ(ierr); 184 ierr = PetscDSSetObjective(prob, 0, &f0_jz_sum);CHKERRQ(ierr); 185 ierr = DMPlexComputeIntegralFEM(plexe,XsubArray[ LAND_PACK_IDX(ctx->batch_view_idx,0) ],tt,NULL);CHKERRQ(ierr); 186 J = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]); 187 if (plexi) { // add first (only) ion 188 ierr = DMGetDS(plexi, &prob);CHKERRQ(ierr); 189 ierr = PetscDSSetConstants(prob, 1, &q[1]);CHKERRQ(ierr); 190 ierr = PetscDSSetObjective(prob, 0, &f0_jz_sum);CHKERRQ(ierr); 191 ierr = DMPlexComputeIntegralFEM(plexi,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,1)],tt,NULL);CHKERRQ(ierr); 192 J += -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]); 193 } 194 /* get N_e */ 195 ierr = DMGetDS(plexe, &prob);CHKERRQ(ierr); 196 ierr = PetscDSSetConstants(prob, 1, user);CHKERRQ(ierr); 197 ierr = PetscDSSetObjective(prob, 0, &f0_n);CHKERRQ(ierr); 198 ierr = DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL);CHKERRQ(ierr); 199 n_e = PetscRealPart(tt[0])*ctx->n_0; 200 /* Z */ 201 Z = -ctx->charges[1]/ctx->charges[0]; 202 /* remove drift */ 203 if (0) { 204 user[0] = 0; // electrons 205 ierr = DMGetDS(plexe, &prob);CHKERRQ(ierr); 206 ierr = PetscDSSetConstants(prob, 1, user);CHKERRQ(ierr); 207 ierr = PetscDSSetObjective(prob, 0, &f0_vz);CHKERRQ(ierr); 208 ierr = DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL);CHKERRQ(ierr); 209 vz = ctx->n_0*PetscRealPart(tt[0])/n_e; /* non-dimensional */ 210 } else vz = 0; 211 /* thermal velocity */ 212 ierr = DMGetDS(plexe, &prob);CHKERRQ(ierr); 213 ierr = PetscDSSetConstants(prob, 1, &vz);CHKERRQ(ierr); 214 ierr = PetscDSSetObjective(prob, 0, &f0_ve_shift);CHKERRQ(ierr); 215 ierr = DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL);CHKERRQ(ierr); 216 v = ctx->n_0*ctx->v_0*PetscRealPart(tt[0])/n_e; /* remove number density to get velocity */ 217 v2 = PetscSqr(v); /* use real space: m^2 / s^2 */ 218 Te_kev = (v2*ctx->masses[0]*PETSC_PI/8)*kev_joul; /* temperature in kev */ 219 spit_eta = Spitzer(ctx->masses[0],-ctx->charges[0],Z,ctx->epsilon0,ctx->lnLam,Te_kev/kev_joul); /* kev --> J (kT) */ 220 if (0) { 221 ierr = DMGetDS(plexe, &prob);CHKERRQ(ierr); 222 ierr = PetscDSSetConstants(prob, 1, q);CHKERRQ(ierr); 223 ierr = PetscDSSetObjective(prob, 0, &f0_j_re);CHKERRQ(ierr); 224 ierr = DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL);CHKERRQ(ierr); 225 } else tt[0] = 0; 226 J_re = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]); 227 ierr = DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, XsubArray);CHKERRQ(ierr); // read only 228 ierr = PetscFree(XsubArray);CHKERRQ(ierr); 229 230 if (rectx->use_spitzer_eta) { 231 E = ctx->Ez = spit_eta*(rectx->j-J_re); 232 } else { 233 E = ctx->Ez; /* keep real E */ 234 rectx->j = J; /* cache */ 235 } 236 237 ratio = E/J/spit_eta; 238 if (stepi>10 && !rectx->use_spitzer_eta && ( 239 (old_ratio-ratio < 1.e-6))) { 240 rectx->pulse_start = time + 0.98*dt; 241 rectx->use_spitzer_eta = PETSC_TRUE; 242 } 243 ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); 244 ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); 245 if ((rectx->plotting) || stepi == 0 || reason || rectx->pulse_start == time + 0.98*dt) { 246 ierr = PetscPrintf(ctx->comm, "testSpitzer: %4D) time=%11.4e n_e= %10.3e E= %10.3e J= %10.3e J_re= %10.3e %.3g%% Te_kev= %10.3e Z_eff=%g E/J to eta ratio= %g (diff=%g) %s %s spit_eta=%g\n",stepi,time,n_e/ctx->n_0,ctx->Ez,J,J_re,100*J_re/J, Te_kev,Z,ratio,old_ratio-ratio, rectx->use_spitzer_eta ? "using Spitzer eta*J E" : "constant E",rectx->pulse_start != time + 0.98*dt ? "normal" : "transition",spit_eta);CHKERRQ(ierr); 247 PetscCheckFalse(rectx->pulse_start == time + 0.98*dt,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Spitzer complete ratio=%g",ratio); 248 } 249 old_ratio = ratio; 250 PetscFunctionReturn(0); 251 } 252 253 static const double ppp = 2; 254 static void f0_0_diff_lp(PetscInt dim, PetscInt Nf, PetscInt NfAux, 255 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 256 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 257 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 258 { 259 LandauCtx *ctx = (LandauCtx *)constants; 260 REctx *rectx = (REctx*)ctx->data; 261 PetscInt ii = rectx->idx, i; 262 const PetscReal kT_m = ctx->k*ctx->thermal_temps[ii]/ctx->masses[ii]; /* kT/m */ 263 const PetscReal n = ctx->n[ii]; 264 PetscReal diff, f_maxwell, v2 = 0, theta = 2*kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 265 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 266 f_maxwell = n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 267 diff = 2.*PETSC_PI*x[0]*(PetscRealPart(u[ii]) - f_maxwell); 268 f0[0] = PetscPowReal(diff,ppp); 269 } 270 static void f0_0_maxwellian_lp(PetscInt dim, PetscInt Nf, PetscInt NfAux, 271 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 272 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 273 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 274 { 275 LandauCtx *ctx = (LandauCtx *)constants; 276 REctx *rectx = (REctx*)ctx->data; 277 PetscInt ii = rectx->idx, i; 278 const PetscReal kT_m = ctx->k*ctx->thermal_temps[ii]/ctx->masses[ii]; /* kT/m */ 279 const PetscReal n = ctx->n[ii]; 280 PetscReal f_maxwell, v2 = 0, theta = 2*kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 281 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 282 f_maxwell = 2.*PETSC_PI*x[0] * n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 283 f0[0] = PetscPowReal(f_maxwell,ppp); 284 } 285 286 /* */ 287 static PetscErrorCode testStable(TS ts, Vec X, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx) 288 { 289 PetscErrorCode ierr; 290 PetscDS prob; 291 Vec X2; 292 PetscReal ediff,idiff=0,lpm0,lpm1=1; 293 PetscScalar tt[LANDAU_MAX_SPECIES]; 294 DM dm, plex = ctx->plex[0]; 295 296 PetscFunctionBeginUser; 297 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 298 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 299 ierr = VecDuplicate(X,&X2);CHKERRQ(ierr); 300 ierr = VecCopy(X,X2);CHKERRQ(ierr); 301 if (!rectx->X_0) { 302 ierr = VecDuplicate(X,&rectx->X_0);CHKERRQ(ierr); 303 ierr = VecCopy(X,rectx->X_0);CHKERRQ(ierr); 304 } 305 ierr = VecAXPY(X,-1.0,rectx->X_0);CHKERRQ(ierr); 306 ierr = PetscDSSetConstants(prob, sizeof(LandauCtx)/sizeof(PetscScalar), (PetscScalar*)ctx);CHKERRQ(ierr); 307 rectx->idx = 0; 308 ierr = PetscDSSetObjective(prob, 0, &f0_0_diff_lp);CHKERRQ(ierr); 309 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 310 ediff = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 311 ierr = PetscDSSetObjective(prob, 0, &f0_0_maxwellian_lp);CHKERRQ(ierr); 312 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 313 lpm0 = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 314 if (ctx->num_species>1) { 315 rectx->idx = 1; 316 ierr = PetscDSSetObjective(prob, 0, &f0_0_diff_lp);CHKERRQ(ierr); 317 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 318 idiff = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 319 ierr = PetscDSSetObjective(prob, 0, &f0_0_maxwellian_lp);CHKERRQ(ierr); 320 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 321 lpm1 = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 322 } 323 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s %D) time=%10.3e n-%d norm electrons/max=%20.13e ions/max=%20.13e\n", "----",stepi,time,(int)ppp,ediff/lpm0,idiff/lpm1);CHKERRQ(ierr); 324 /* view */ 325 ierr = VecCopy(X2,X);CHKERRQ(ierr); 326 ierr = VecDestroy(&X2);CHKERRQ(ierr); 327 if (islast) { 328 ierr = VecDestroy(&rectx->X_0);CHKERRQ(ierr); 329 rectx->X_0 = NULL; 330 } 331 PetscFunctionReturn(0); 332 } 333 334 static PetscErrorCode EInduction(Vec X, Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E) 335 { 336 REctx *rectx = (REctx*)ctx->data; 337 PetscErrorCode ierr; 338 PetscInt ii; 339 DM dm,plex; 340 PetscScalar tt[LANDAU_MAX_SPECIES], qv0[LANDAU_MAX_SPECIES]; 341 PetscReal dJ_dt; 342 PetscDS prob; 343 344 PetscFunctionBeginUser; 345 for (ii=0;ii<ctx->num_species;ii++) qv0[ii] = ctx->charges[ii]*ctx->v_0; 346 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 347 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 348 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 349 /* get d current / dt */ 350 ierr = PetscDSSetConstants(prob, ctx->num_species, qv0);CHKERRQ(ierr); 351 ierr = PetscDSSetObjective(prob, 0, &f0_jz_sum);CHKERRQ(ierr); 352 PetscCheckFalse(!X_t,PETSC_COMM_SELF, PETSC_ERR_PLIB, "X_t"); 353 ierr = DMPlexComputeIntegralFEM(plex,X_t,tt,NULL);CHKERRQ(ierr); 354 dJ_dt = -ctx->n_0*PetscRealPart(tt[0])/ctx->t_0; 355 /* E induction */ 356 *a_E = -rectx->L*dJ_dt + rectx->Ez_initial; 357 ierr = DMDestroy(&plex);CHKERRQ(ierr); 358 PetscFunctionReturn(0); 359 } 360 361 static PetscErrorCode EConstant(Vec X, Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E) 362 { 363 PetscFunctionBeginUser; 364 *a_E = ctx->Ez; 365 PetscFunctionReturn(0); 366 } 367 368 static PetscErrorCode ENone(Vec X, Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E) 369 { 370 PetscFunctionBeginUser; 371 *a_E = 0; 372 PetscFunctionReturn(0); 373 } 374 375 /* ------------------------------------------------------------------- */ 376 /* 377 FormSource - Evaluates source terms F(t). 378 379 Input Parameters: 380 . ts - the TS context 381 . time - 382 . X_dummmy - input vector 383 . dummy - optional user-defined context, as set by SNESSetFunction() 384 385 Output Parameter: 386 . F - function vector 387 */ 388 static PetscErrorCode FormSource(TS ts, PetscReal ftime, Vec X_dummmy, Vec F, void *dummy) 389 { 390 PetscReal new_imp_rate; 391 LandauCtx *ctx; 392 DM pack; 393 PetscErrorCode ierr; 394 REctx *rectx; 395 396 PetscFunctionBeginUser; 397 ierr = TSGetDM(ts,&pack);CHKERRQ(ierr); 398 ierr = DMGetApplicationContext(pack, &ctx);CHKERRQ(ierr); 399 rectx = (REctx*)ctx->data; 400 /* check for impurities */ 401 ierr = rectx->impuritySrcRate(ftime,&new_imp_rate,ctx);CHKERRQ(ierr); 402 if (new_imp_rate != 0) { 403 if (new_imp_rate != rectx->current_rate) { 404 PetscInt ii; 405 PetscReal dne_dt,dni_dt,tilda_ns[LANDAU_MAX_SPECIES],temps[LANDAU_MAX_SPECIES]; 406 Vec globFarray[LANDAU_MAX_GRIDS*LANDAU_MAX_BATCH_SZ]; 407 rectx->current_rate = new_imp_rate; 408 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) tilda_ns[ii] = 0; 409 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) temps[ii] = 1; 410 dni_dt = new_imp_rate /* *ctx->t_0 */; /* fully ionized immediately, no normalize, stay in non-dim */ 411 dne_dt = new_imp_rate*rectx->Ne_ion /* *ctx->t_0 */; 412 tilda_ns[0] = dne_dt; tilda_ns[rectx->imp_idx] = dni_dt; 413 temps[0] = rectx->T_cold; temps[rectx->imp_idx] = rectx->T_cold; 414 ierr = PetscInfo(ctx->plex[0], "\tHave new_imp_rate= %10.3e time= %10.3e de/dt= %10.3e di/dt= %10.3e ***\n",new_imp_rate,ftime,dne_dt,dni_dt);CHKERRQ(ierr); 415 ierr = DMCompositeGetAccessArray(pack, F, ctx->num_grids*ctx->batch_sz, NULL, globFarray);CHKERRQ(ierr); 416 for (PetscInt grid=0 ; grid<ctx->num_grids ; grid++) { 417 /* add it */ 418 ierr = LandauAddMaxwellians(ctx->plex[grid],globFarray[ LAND_PACK_IDX(0,grid) ],ftime,temps,tilda_ns,grid,0,ctx);CHKERRQ(ierr); 419 ierr = VecViewFromOptions(globFarray[ LAND_PACK_IDX(0,grid) ],NULL,"-vec_view_sources");CHKERRQ(ierr); 420 } 421 // Does DMCompositeRestoreAccessArray copy the data back? (no) 422 ierr = DMCompositeRestoreAccessArray(pack, F, ctx->num_grids*ctx->batch_sz, NULL, globFarray);CHKERRQ(ierr); 423 } 424 } else { 425 ierr = VecZeroEntries(F);CHKERRQ(ierr); 426 rectx->current_rate = 0; 427 } 428 PetscFunctionReturn(0); 429 } 430 PetscErrorCode Monitor(TS ts, PetscInt stepi, PetscReal time, Vec X, void *actx) 431 { 432 LandauCtx *ctx = (LandauCtx*) actx; /* user-defined application context */ 433 REctx *rectx = (REctx*)ctx->data; 434 DM pack; 435 Vec globXArray[LANDAU_MAX_GRIDS*LANDAU_MAX_BATCH_SZ]; 436 TSConvergedReason reason; 437 PetscErrorCode ierr; 438 PetscFunctionBeginUser; 439 ierr = VecGetDM(X, &pack);CHKERRQ(ierr); 440 ierr = DMCompositeGetAccessArray(pack, X, ctx->num_grids*ctx->batch_sz, NULL, globXArray);CHKERRQ(ierr); 441 if (stepi > rectx->plotStep && rectx->plotting) { 442 rectx->plotting = PETSC_FALSE; /* was doing diagnostics, now done */ 443 rectx->plotIdx++; 444 } 445 /* view */ 446 ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); 447 if (time/rectx->plotDt >= (PetscReal)rectx->plotIdx || reason) { 448 if ((reason || stepi==0 || rectx->plotIdx%rectx->print_period==0) && ctx->verbose > 0) { 449 /* print norms */ 450 ierr = LandauPrintNorms(X, stepi);CHKERRQ(ierr); 451 } 452 if (!rectx->plotting) { /* first step of possible backtracks */ 453 rectx->plotting = PETSC_TRUE; 454 /* diagnostics + change E field with Sptizer (not just a monitor) */ 455 ierr = rectx->test(ts,X,stepi,time,reason ? PETSC_TRUE : PETSC_FALSE, ctx, rectx);CHKERRQ(ierr); 456 } else { 457 PetscPrintf(PETSC_COMM_WORLD, "\t\t ERROR SKIP test spit ------\n"); 458 rectx->plotting = PETSC_TRUE; 459 } 460 ierr = PetscObjectSetName((PetscObject) globXArray[ LAND_PACK_IDX(ctx->batch_view_idx,rectx->grid_view_idx) ], rectx->grid_view_idx==0 ? "ue" : "ui");CHKERRQ(ierr); 461 /* view, overwrite step when back tracked */ 462 ierr = DMSetOutputSequenceNumber(pack, rectx->plotIdx, time*ctx->t_0);CHKERRQ(ierr); 463 ierr = VecViewFromOptions(globXArray[ LAND_PACK_IDX(ctx->batch_view_idx, rectx->grid_view_idx) ],NULL,"-vec_view");CHKERRQ(ierr); 464 465 rectx->plotStep = stepi; 466 } else { 467 if (rectx->plotting) PetscPrintf(PETSC_COMM_WORLD," ERROR rectx->plotting=%D step %D\n",rectx->plotting,stepi); 468 /* diagnostics + change E field with Sptizer (not just a monitor) - can we lag this? */ 469 ierr = rectx->test(ts,X,stepi,time,reason ? PETSC_TRUE : PETSC_FALSE, ctx, rectx);CHKERRQ(ierr); 470 } 471 /* parallel check that only works of all batches are identical */ 472 if (reason && ctx->verbose > 3) { 473 PetscReal val,rval; 474 PetscMPIInt rank; 475 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRMPI(ierr); 476 for (PetscInt grid=0;grid<ctx->num_grids;grid++) { 477 PetscInt nerrors=0; 478 for (PetscInt i=0; i<ctx->batch_sz;i++) { 479 ierr = VecNorm(globXArray[ LAND_PACK_IDX(i,grid) ],NORM_2,&val);CHKERRQ(ierr); 480 if (i==0) rval = val; 481 else if ((val=PetscAbs(val-rval)/rval) > 1000*PETSC_MACHINE_EPSILON) { 482 PetscPrintf(PETSC_COMM_SELF, " [%D] Warning %D.%D) diff = %2.15e\n",rank,grid,i,val);CHKERRQ(ierr); 483 nerrors++; 484 } 485 } 486 if (nerrors) { 487 ierr = PetscPrintf(PETSC_COMM_SELF, " ***** [%D] ERROR max %D errors\n",rank,nerrors);CHKERRQ(ierr); 488 } else { 489 ierr = PetscPrintf(PETSC_COMM_WORLD, "[%D] %D) batch consistency check OK\n",rank,grid);CHKERRQ(ierr); 490 } 491 } 492 } 493 rectx->idx = 0; 494 ierr = DMCompositeRestoreAccessArray(pack, X, ctx->num_grids*ctx->batch_sz, NULL, globXArray);CHKERRQ(ierr); 495 PetscFunctionReturn(0); 496 } 497 498 PetscErrorCode PreStep(TS ts) 499 { 500 PetscErrorCode ierr; 501 LandauCtx *ctx; 502 REctx *rectx; 503 DM dm; 504 PetscInt stepi; 505 PetscReal time; 506 Vec X; 507 508 PetscFunctionBeginUser; 509 /* not used */ 510 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 511 ierr = TSGetTime(ts,&time);CHKERRQ(ierr); 512 ierr = TSGetSolution(ts,&X);CHKERRQ(ierr); 513 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 514 rectx = (REctx*)ctx->data; 515 ierr = TSGetStepNumber(ts, &stepi);CHKERRQ(ierr); 516 /* update E */ 517 ierr = rectx->E(X, NULL, stepi, time, ctx, &ctx->Ez);CHKERRQ(ierr); 518 PetscFunctionReturn(0); 519 } 520 521 /* model for source of non-ionized impurities, profile provided by model, in du/dt form in normalized units (tricky because n_0 is normalized with electrons) */ 522 static PetscErrorCode stepSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx) 523 { 524 REctx *rectx = (REctx*)ctx->data; 525 526 PetscFunctionBeginUser; 527 if (time >= rectx->pulse_start) *rho = rectx->pulse_rate; 528 else *rho = 0.; 529 PetscFunctionReturn(0); 530 } 531 static PetscErrorCode zeroSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx) 532 { 533 PetscFunctionBeginUser; 534 *rho = 0.; 535 PetscFunctionReturn(0); 536 } 537 static PetscErrorCode pulseSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx) 538 { 539 REctx *rectx = (REctx*)ctx->data; 540 541 PetscFunctionBeginUser; 542 PetscCheckFalse(rectx->pulse_start == PETSC_MAX_REAL,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"'-ex2_pulse_start_time X' must be used with '-ex2_impurity_source_type pulse'"); 543 if (time < rectx->pulse_start || time > rectx->pulse_start + 3*rectx->pulse_width) *rho = 0; 544 /* else if (0) { */ 545 /* double t = time - rectx->pulse_start, start = rectx->pulse_width, stop = 2*rectx->pulse_width, cycle = 3*rectx->pulse_width, steep = 5, xi = 0.75 - (stop - start)/(2* cycle); */ 546 /* *rho = rectx->pulse_rate * (cycle / (stop - start)) / (1 + PetscExpReal(steep*(PetscSinReal(2*PETSC_PI*((t - start)/cycle + xi)) - PetscSinReal(2*PETSC_PI*xi)))); */ 547 /* } else if (0) { */ 548 /* double x = 2*(time - rectx->pulse_start)/(3*rectx->pulse_width) - 1; */ 549 /* if (x==1 || x==-1) *rho = 0; */ 550 /* else *rho = rectx->pulse_rate * PetscExpReal(-1/(1-x*x)); */ 551 /* } */ 552 else { 553 double x = PetscSinReal((time-rectx->pulse_start)/(3*rectx->pulse_width)*2*PETSC_PI - PETSC_PI/2) + 1; /* 0:2, integrates to 1.0 */ 554 *rho = rectx->pulse_rate * x / (3*rectx->pulse_width); 555 if (!rectx->use_spitzer_eta) rectx->use_spitzer_eta = PETSC_TRUE; /* use it next time */ 556 } 557 PetscFunctionReturn(0); 558 } 559 560 #undef __FUNCT__ 561 #define __FUNCT__ "ProcessREOptions" 562 static PetscErrorCode ProcessREOptions(REctx *rectx, const LandauCtx *ctx, DM dm, const char prefix[]) 563 { 564 PetscErrorCode ierr; 565 PetscFunctionList plist = NULL, testlist = NULL, elist = NULL; 566 char pname[256],testname[256],ename[256]; 567 DM dm_dummy; 568 PetscBool Connor_E = PETSC_FALSE; 569 570 PetscFunctionBeginUser; 571 ierr = DMCreate(PETSC_COMM_WORLD,&dm_dummy);CHKERRQ(ierr); 572 rectx->Ne_ion = 1; /* number of electrons given up by impurity ion */ 573 rectx->T_cold = .005; /* kev */ 574 rectx->ion_potential = 15; /* ev */ 575 rectx->L = 2; 576 rectx->X_0 = NULL; 577 rectx->imp_idx = ctx->num_species - 1; /* default ionized impurity as last one */ 578 rectx->pulse_start = PETSC_MAX_REAL; 579 rectx->pulse_width = 1; 580 rectx->plotStep = PETSC_MAX_INT; 581 rectx->pulse_rate = 1.e-1; 582 rectx->current_rate = 0; 583 rectx->plotIdx = 0; 584 rectx->j = 0; 585 rectx->plotDt = 1.0; 586 rectx->plotting = PETSC_FALSE; 587 rectx->use_spitzer_eta = PETSC_FALSE; 588 rectx->idx = 0; 589 rectx->print_period = 10; 590 rectx->grid_view_idx = 0; 591 /* Register the available impurity sources */ 592 ierr = PetscFunctionListAdd(&plist,"step",&stepSrc);CHKERRQ(ierr); 593 ierr = PetscFunctionListAdd(&plist,"none",&zeroSrc);CHKERRQ(ierr); 594 ierr = PetscFunctionListAdd(&plist,"pulse",&pulseSrc);CHKERRQ(ierr); 595 ierr = PetscStrcpy(pname,"none");CHKERRQ(ierr); 596 ierr = PetscFunctionListAdd(&testlist,"none",&testNone);CHKERRQ(ierr); 597 ierr = PetscFunctionListAdd(&testlist,"spitzer",&testSpitzer);CHKERRQ(ierr); 598 ierr = PetscFunctionListAdd(&testlist,"stable",&testStable);CHKERRQ(ierr); 599 ierr = PetscStrcpy(testname,"none");CHKERRQ(ierr); 600 ierr = PetscFunctionListAdd(&elist,"none",&ENone);CHKERRQ(ierr); 601 ierr = PetscFunctionListAdd(&elist,"induction",&EInduction);CHKERRQ(ierr); 602 ierr = PetscFunctionListAdd(&elist,"constant",&EConstant);CHKERRQ(ierr); 603 ierr = PetscStrcpy(ename,"constant");CHKERRQ(ierr); 604 605 ierr = PetscOptionsBegin(PETSC_COMM_SELF, prefix, "Options for Runaway/seed electron model", "none");CHKERRQ(ierr); 606 ierr = PetscOptionsReal("-ex2_plot_dt", "Plotting interval", "ex2.c", rectx->plotDt, &rectx->plotDt, NULL);CHKERRQ(ierr); 607 if (rectx->plotDt < 0) rectx->plotDt = 1e30; 608 if (rectx->plotDt == 0) rectx->plotDt = 1e-30; 609 ierr = PetscOptionsInt("-ex2_print_period", "Plotting interval", "ex2.c", rectx->print_period, &rectx->print_period, NULL);CHKERRQ(ierr); 610 ierr = PetscOptionsInt("-ex2_grid_view_idx", "grid_view_idx", "ex2.c", rectx->grid_view_idx, &rectx->grid_view_idx, NULL);CHKERRQ(ierr); 611 PetscCheckFalse(rectx->grid_view_idx >= ctx->num_grids,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"rectx->grid_view_idx (%D) >= ctx->num_grids (%D)",rectx->imp_idx,ctx->num_grids); 612 ierr = PetscOptionsFList("-ex2_impurity_source_type","Name of impurity source to run","",plist,pname,pname,sizeof(pname),NULL);CHKERRQ(ierr); 613 ierr = PetscOptionsFList("-ex2_test_type","Name of test to run","",testlist,testname,testname,sizeof(testname),NULL);CHKERRQ(ierr); 614 ierr = PetscOptionsInt("-ex2_impurity_index", "index of sink for impurities", "none", rectx->imp_idx, &rectx->imp_idx, NULL);CHKERRQ(ierr); 615 PetscCheckFalse((rectx->imp_idx >= ctx->num_species || rectx->imp_idx < 1) && ctx->num_species > 1,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"index of sink for impurities ions is out of range (%D), must be > 0 && < NS",rectx->imp_idx); 616 ierr = PetscOptionsFList("-ex2_e_field_type","Electric field type","",elist,ename,ename,sizeof(ename),NULL);CHKERRQ(ierr); 617 rectx->Ne_ion = -ctx->charges[rectx->imp_idx]/ctx->charges[0]; 618 ierr = PetscOptionsReal("-ex2_t_cold","Temperature of cold electron and ions after ionization in keV","none",rectx->T_cold,&rectx->T_cold, NULL);CHKERRQ(ierr); 619 ierr = PetscOptionsReal("-ex2_pulse_start_time","Time at which pulse happens for 'pulse' source","none",rectx->pulse_start,&rectx->pulse_start, NULL);CHKERRQ(ierr); 620 ierr = PetscOptionsReal("-ex2_pulse_width_time","Width of pulse 'pulse' source","none",rectx->pulse_width,&rectx->pulse_width, NULL);CHKERRQ(ierr); 621 ierr = PetscOptionsReal("-ex2_pulse_rate","Number density of pulse for 'pulse' source","none",rectx->pulse_rate,&rectx->pulse_rate, NULL);CHKERRQ(ierr); 622 rectx->T_cold *= 1.16e7; /* convert to Kelvin */ 623 ierr = PetscOptionsReal("-ex2_ion_potential","Potential to ionize impurity (should be array) in ev","none",rectx->ion_potential,&rectx->ion_potential, NULL);CHKERRQ(ierr); 624 ierr = PetscOptionsReal("-ex2_inductance","Inductance E feild","none",rectx->L,&rectx->L, NULL);CHKERRQ(ierr); 625 ierr = PetscOptionsBool("-ex2_connor_e_field_units","Scale Ex but Connor-Hastie E_c","none",Connor_E,&Connor_E, NULL);CHKERRQ(ierr); 626 ierr = PetscInfo(dm_dummy, "Num electrons from ions=%g, T_cold=%10.3e, ion potential=%10.3e, E_z=%10.3e v_0=%10.3e\n",rectx->Ne_ion,rectx->T_cold,rectx->ion_potential,ctx->Ez,ctx->v_0);CHKERRQ(ierr); 627 ierr = PetscOptionsEnd();CHKERRQ(ierr); 628 /* get impurity source rate function */ 629 ierr = PetscFunctionListFind(plist,pname,&rectx->impuritySrcRate);CHKERRQ(ierr); 630 PetscCheckFalse(!rectx->impuritySrcRate,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No impurity source function found '%s'",pname); 631 ierr = PetscFunctionListFind(testlist,testname,&rectx->test);CHKERRQ(ierr); 632 PetscCheckFalse(!rectx->test,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No test found '%s'",testname); 633 ierr = PetscFunctionListFind(elist,ename,&rectx->E);CHKERRQ(ierr); 634 PetscCheckFalse(!rectx->E,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No E field function found '%s'",ename); 635 ierr = PetscFunctionListDestroy(&plist);CHKERRQ(ierr); 636 ierr = PetscFunctionListDestroy(&testlist);CHKERRQ(ierr); 637 ierr = PetscFunctionListDestroy(&elist);CHKERRQ(ierr); 638 639 /* convert E from Connor-Hastie E_c units to real if doing Spitzer E */ 640 if (Connor_E) { 641 PetscReal E = ctx->Ez, Tev = ctx->thermal_temps[0]*8.621738e-5, n = ctx->n_0*ctx->n[0]; 642 CalculateE(Tev, n, ctx->lnLam, ctx->epsilon0, &E); 643 ((LandauCtx*)ctx)->Ez *= E; 644 } 645 ierr = DMDestroy(&dm_dummy);CHKERRQ(ierr); 646 PetscFunctionReturn(0); 647 } 648 649 int main(int argc, char **argv) 650 { 651 DM pack; 652 Vec X,*XsubArray; 653 PetscErrorCode ierr; 654 PetscInt dim = 2, nDMs; 655 TS ts; 656 Mat J; 657 PetscDS prob; 658 LandauCtx *ctx; 659 REctx *rectx; 660 #if defined PETSC_USE_LOG 661 PetscLogStage stage; 662 #endif 663 PetscMPIInt rank; 664 #if defined(PETSC_HAVE_THREADSAFETY) 665 double starttime, endtime; 666 #endif 667 ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; 668 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRMPI(ierr); 669 if (rank) { /* turn off output stuff for duplicate runs */ 670 ierr = PetscOptionsClearValue(NULL,"-dm_view");CHKERRQ(ierr); 671 ierr = PetscOptionsClearValue(NULL,"-vec_view");CHKERRQ(ierr); 672 ierr = PetscOptionsClearValue(NULL,"-dm_view_diff");CHKERRQ(ierr); 673 ierr = PetscOptionsClearValue(NULL,"-vec_view_diff");CHKERRQ(ierr); 674 ierr = PetscOptionsClearValue(NULL,"-dm_view_sources");CHKERRQ(ierr); 675 ierr = PetscOptionsClearValue(NULL,"-vec_view_0");CHKERRQ(ierr); 676 ierr = PetscOptionsClearValue(NULL,"-dm_view_0");CHKERRQ(ierr); 677 ierr = PetscOptionsClearValue(NULL,"-vec_view_sources");CHKERRQ(ierr); 678 ierr = PetscOptionsClearValue(NULL,"-info");CHKERRQ(ierr); /* this does not work */ 679 } 680 ierr = PetscOptionsGetInt(NULL,NULL, "-dim", &dim, NULL);CHKERRQ(ierr); 681 /* Create a mesh */ 682 ierr = LandauCreateVelocitySpace(PETSC_COMM_WORLD, dim, "", &X, &J, &pack);CHKERRQ(ierr); 683 ierr = DMCompositeGetNumberDM(pack,&nDMs);CHKERRQ(ierr); 684 ierr = PetscMalloc(sizeof(*XsubArray)*nDMs, &XsubArray);CHKERRQ(ierr); 685 ierr = PetscObjectSetName((PetscObject)J, "Jacobian");CHKERRQ(ierr); 686 ierr = PetscObjectSetName((PetscObject)X, "f");CHKERRQ(ierr); 687 ierr = DMGetApplicationContext(pack, &ctx);CHKERRQ(ierr); 688 ierr = DMSetUp(pack);CHKERRQ(ierr); 689 /* context */ 690 ierr = PetscNew(&rectx);CHKERRQ(ierr); 691 ctx->data = rectx; 692 ierr = ProcessREOptions(rectx,ctx,pack,"");CHKERRQ(ierr); 693 ierr = DMGetDS(pack, &prob);CHKERRQ(ierr); 694 ierr = DMCompositeGetAccessArray(pack, X, nDMs, NULL, XsubArray);CHKERRQ(ierr); // read only 695 ierr = PetscObjectSetName((PetscObject) XsubArray[ LAND_PACK_IDX(ctx->batch_view_idx, rectx->grid_view_idx) ], rectx->grid_view_idx==0 ? "ue" : "ui");CHKERRQ(ierr); 696 ierr = DMViewFromOptions(ctx->plex[rectx->grid_view_idx],NULL,"-dm_view");CHKERRQ(ierr); 697 ierr = DMViewFromOptions(ctx->plex[rectx->grid_view_idx], NULL,"-dm_view_0");CHKERRQ(ierr); 698 ierr = VecViewFromOptions(XsubArray[ LAND_PACK_IDX(ctx->batch_view_idx,rectx->grid_view_idx) ], NULL,"-vec_view_0");CHKERRQ(ierr); // initial condition (monitor plots after step) 699 ierr = DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, XsubArray);CHKERRQ(ierr); // read only 700 ierr = PetscFree(XsubArray);CHKERRQ(ierr); 701 ierr = VecViewFromOptions(X, NULL,"-vec_view_global");CHKERRQ(ierr); // initial condition (monitor plots after step) 702 ierr = DMSetOutputSequenceNumber(pack, 0, 0.0);CHKERRQ(ierr); 703 /* Create timestepping solver context */ 704 ierr = TSCreate(PETSC_COMM_SELF,&ts);CHKERRQ(ierr); 705 ierr = TSSetDM(ts,pack);CHKERRQ(ierr); 706 ierr = TSSetIFunction(ts,NULL,LandauIFunction,NULL);CHKERRQ(ierr); 707 ierr = TSSetIJacobian(ts,J,J,LandauIJacobian,NULL);CHKERRQ(ierr); 708 ierr = TSSetRHSFunction(ts,NULL,FormSource,NULL);CHKERRQ(ierr); 709 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 710 ierr = TSSetSolution(ts,X);CHKERRQ(ierr); 711 ierr = TSSetApplicationContext(ts, ctx);CHKERRQ(ierr); 712 ierr = TSMonitorSet(ts,Monitor,ctx,NULL);CHKERRQ(ierr); 713 ierr = TSSetPreStep(ts,PreStep);CHKERRQ(ierr); 714 rectx->Ez_initial = ctx->Ez; /* cache for induction caclulation - applied E field */ 715 if (1) { /* warm up an test just LandauIJacobian */ 716 Vec vec; 717 PetscInt nsteps; 718 PetscReal dt; 719 ierr = PetscLogStageRegister("Warmup", &stage);CHKERRQ(ierr); 720 ierr = PetscLogStagePush(stage);CHKERRQ(ierr); 721 ierr = VecDuplicate(X,&vec);CHKERRQ(ierr); 722 ierr = VecCopy(X,vec);CHKERRQ(ierr); 723 ierr = TSGetMaxSteps(ts,&nsteps);CHKERRQ(ierr); 724 ierr = TSGetTimeStep(ts,&dt);CHKERRQ(ierr); 725 ierr = TSSetMaxSteps(ts,1);CHKERRQ(ierr); 726 ierr = TSSolve(ts,X);CHKERRQ(ierr); 727 ierr = TSSetMaxSteps(ts,nsteps);CHKERRQ(ierr); 728 ierr = TSSetStepNumber(ts,0);CHKERRQ(ierr); 729 ierr = TSSetTime(ts,0);CHKERRQ(ierr); 730 ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); 731 rectx->plotIdx = 0; 732 rectx->plotting = PETSC_FALSE; 733 ierr = PetscLogStagePop();CHKERRQ(ierr); 734 ierr = VecCopy(vec,X);CHKERRQ(ierr); 735 ierr = VecDestroy(&vec);CHKERRQ(ierr); 736 ctx->aux_bool = PETSC_FALSE; // flag for not a clean Jacobian 737 } 738 /* go */ 739 ierr = PetscLogStageRegister("Solve", &stage);CHKERRQ(ierr); 740 ctx->stage = 0; // lets not use this stage 741 #if defined(PETSC_HAVE_THREADSAFETY) 742 ctx->stage = 1; // not set with thread safety 743 #endif 744 ierr = TSSetSolution(ts,X);CHKERRQ(ierr); 745 ierr = PetscLogStagePush(stage);CHKERRQ(ierr); 746 #if defined(PETSC_HAVE_THREADSAFETY) 747 starttime = MPI_Wtime(); 748 #endif 749 ierr = TSSolve(ts,X);CHKERRQ(ierr); 750 ierr = PetscLogStagePop();CHKERRQ(ierr); 751 #if defined(PETSC_HAVE_THREADSAFETY) 752 endtime = MPI_Wtime(); 753 ctx->times[LANDAU_EX2_TSSOLVE] += (endtime - starttime); 754 #endif 755 ierr = VecViewFromOptions(X, NULL,"-vec_view_global");CHKERRQ(ierr); 756 /* clean up */ 757 ierr = LandauDestroyVelocitySpace(&pack);CHKERRQ(ierr); 758 ierr = TSDestroy(&ts);CHKERRQ(ierr); 759 ierr = VecDestroy(&X);CHKERRQ(ierr); 760 ierr = PetscFree(rectx);CHKERRQ(ierr); 761 ierr = PetscFinalize(); 762 return ierr; 763 } 764 765 /*TEST 766 767 testset: 768 requires: p4est !complex double 769 output_file: output/ex2_0.out 770 args: -dm_landau_num_species_grid 1,1 -dm_landau_Ez 0 -petscspace_degree 3 -petscspace_poly_tensor 1 -dm_landau_type p4est -dm_landau_ion_masses 2 -dm_landau_ion_charges 1 -dm_landau_thermal_temps 5,5 -dm_landau_n 2,2 -dm_landau_n_0 5e19 -ts_monitor -snes_rtol 1.e-10 -snes_stol 1.e-14 -snes_monitor -snes_converged_reason -snes_max_it 10 -ts_type arkimex -ts_arkimex_type 1bee -ts_max_snes_failures -1 -ts_rtol 1e-3 -ts_dt 1.e-1 -ts_max_time 1 -ts_adapt_clip .5,1.25 -ts_max_steps 2 -ts_adapt_scale_solve_failed 0.75 -ts_adapt_time_step_increase_delay 5 -ksp_type tfqmr -pc_type jacobi -dm_landau_amr_levels_max 2,2 -ex2_impurity_source_type pulse -ex2_pulse_start_time 1e-1 -ex2_pulse_width_time 10 -ex2_pulse_rate 1e-2 -ex2_t_cold .05 -ex2_plot_dt 1e-1 -dm_refine 0 -dm_landau_gpu_assembly true -dm_landau_batch_size 2 771 test: 772 suffix: cpu 773 args: -dm_landau_device_type cpu -ksp_pc_side right 774 test: 775 suffix: kokkos 776 requires: kokkos_kernels 777 args: -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos -ksp_pc_side right 778 test: 779 suffix: cuda 780 requires: cuda 781 args: -dm_landau_device_type cuda -dm_mat_type aijcusparse -dm_vec_type cuda -mat_cusparse_use_cpu_solve -ksp_pc_side right 782 test: 783 suffix: kokkos_batch 784 requires: kokkos_kernels 785 args: -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos -ksp_type preonly -pc_type bjkokkos -pc_bjkokkos_ksp_type tfqmr -pc_bjkokkos_pc_type jacobi 786 test: 787 suffix: kokkos_batch_coo 788 requires: kokkos_kernels 789 args: -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos -ksp_type preonly -pc_type bjkokkos -pc_bjkokkos_ksp_type tfqmr -pc_bjkokkos_pc_type jacobi -dm_landau_use_coo_assembly 790 791 TEST*/ 792