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 8 /* data for runaway electron model */ 9 typedef struct REctx_struct { 10 PetscErrorCode (*test)(TS, Vec, DM, PetscInt, PetscReal, PetscBool, LandauCtx *, struct REctx_struct *); 11 PetscErrorCode (*impuritySrcRate)(PetscReal, PetscReal *, LandauCtx*); 12 PetscErrorCode (*E)(Vec, Vec, PetscInt, PetscReal, LandauCtx*, PetscReal *); 13 PetscReal T_cold; /* temperature of newly ionized electrons and impurity ions */ 14 PetscReal ion_potential; /* ionization potential of impurity */ 15 PetscReal Ne_ion; /* effective number of electrons shed in ioization of impurity */ 16 PetscReal Ez_initial; 17 PetscReal L; /* inductance */ 18 Vec X_0; 19 PetscInt imp_idx; /* index for impurity ionizing sink */ 20 PetscReal pulse_start; 21 PetscReal pulse_width; 22 PetscReal pulse_rate; 23 PetscReal current_rate; 24 PetscInt plotIdx; 25 PetscInt plotStep; 26 PetscInt idx; /* cache */ 27 PetscReal j; /* cache */ 28 PetscReal plotDt; 29 PetscBool plotting; 30 PetscBool use_spitzer_eta; 31 Vec imp_src; 32 } REctx; 33 34 static const PetscReal kev_joul = 6.241506479963235e+15; /* 1/1000e */ 35 36 #define RE_CUT 5. 37 /* < v, u_re * v * q > */ 38 static void f0_j_re(PetscInt dim, PetscInt Nf, PetscInt NfAux, 39 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 40 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 41 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 42 { 43 PetscReal n_e = PetscRealPart(u[0]); 44 if (dim==2) { 45 if (x[1] > RE_CUT || x[1] < -RE_CUT) { /* simply a cutoff for REs. v_|| > 3 v(T_e) */ 46 *f0 = n_e * 2.*PETSC_PI*x[0] * x[1] * constants[0]; /* n * r * v_|| * q */ 47 } else { 48 *f0 = 0; 49 } 50 } else { 51 if (x[2] > RE_CUT || x[2] < -RE_CUT) { /* simply a cutoff for REs. v_|| > 3 v(T_e) */ 52 *f0 = n_e * x[2] * constants[0]; 53 } else { 54 *f0 = 0; 55 } 56 } 57 } 58 59 /* sum < v, u*v*q > */ 60 static void f0_jz_sum(PetscInt dim, PetscInt Nf, PetscInt NfAux, 61 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 62 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 63 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 64 { 65 PetscInt ii; 66 f0[0] = 0; 67 if (dim==2) { 68 for (ii=0;ii<numConstants;ii++) f0[0] += u[ii] * 2.*PETSC_PI*x[0] * x[1] * constants[ii]; /* n * r * v_|| * q */ 69 } else { 70 for (ii=0;ii<numConstants;ii++) f0[0] += u[ii] * x[2] * constants[ii]; /* n * v_|| * q */ 71 } 72 } 73 74 /* < v, n_e > */ 75 static void f0_n(PetscInt dim, PetscInt Nf, PetscInt NfAux, 76 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 77 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 78 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 79 { 80 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 81 if (dim==2) f0[0] = 2.*PETSC_PI*x[0]*u[ii]; 82 else { 83 f0[0] = u[ii]; 84 } 85 } 86 87 /* < v, n_e v_|| > */ 88 static void f0_vz(PetscInt dim, PetscInt Nf, PetscInt NfAux, 89 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 90 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 91 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 92 { 93 PetscInt ii = (PetscInt)PetscRealPart(constants[0]); 94 if (dim==2) f0[0] = u[ii] * 2.*PETSC_PI*x[0] * x[1]; /* n r v_|| */ 95 else { 96 f0[0] = u[ii] * x[2]; /* n v_|| */ 97 } 98 } 99 100 /* < v, n_e (v-shift) > */ 101 static void f0_ve_shift(PetscInt dim, PetscInt Nf, PetscInt NfAux, 102 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 103 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 104 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 105 { 106 PetscReal vz = numConstants==1 ? PetscRealPart(constants[0]) : 0; 107 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 */ 108 else { 109 *f0 = u[0] * PetscSqrtReal(x[0]*x[0] + x[1]*x[1] + (x[2]-vz)*(x[2]-vz)); /* n v */ 110 } 111 } 112 113 static PetscErrorCode getTe_kev(DM plex, Vec X, PetscReal *a_n, PetscReal *a_Tkev) 114 { 115 PetscErrorCode ierr; 116 LandauCtx *ctx; 117 118 PetscFunctionBeginUser; 119 ierr = DMGetApplicationContext(plex, &ctx);CHKERRQ(ierr); 120 { 121 PetscDS prob; 122 PetscReal v2, v, n; 123 PetscScalar tt[LANDAU_MAX_SPECIES],user[2] = {0.,ctx->charges[0]}, vz; 124 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 125 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 126 ierr = PetscDSSetObjective(prob, 0, &f0_n);CHKERRQ(ierr); 127 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 128 n = ctx->n_0*PetscRealPart(tt[0]); 129 ierr = PetscDSSetObjective(prob, 0, &f0_vz);CHKERRQ(ierr); 130 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 131 vz = ctx->n_0*PetscRealPart(tt[0])/n; /* non-dimensional */ 132 /* remove drift */ 133 ierr = PetscDSSetConstants(prob, 1, &vz);CHKERRQ(ierr); 134 ierr = PetscDSSetObjective(prob, 0, &f0_ve_shift);CHKERRQ(ierr); 135 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 136 v = ctx->n_0*ctx->v_0*PetscRealPart(tt[0])/n; /* remove number density to get velocity */ 137 v2 = PetscSqr(v); /* use real space: m^2 / s^2 */ 138 if (a_Tkev) *a_Tkev = (v2*ctx->masses[0]*PETSC_PI/8)*kev_joul; /* temperature in kev */ 139 if (a_n) *a_n = n; 140 } 141 PetscFunctionReturn(0); 142 } 143 /* CalculateE - Calculate the electric field */ 144 /* T -- Electron temperature */ 145 /* n -- Electron density */ 146 /* lnLambda -- */ 147 /* eps0 -- */ 148 /* E -- output E, input \hat E */ 149 static PetscReal CalculateE(PetscReal Tev, PetscReal n, PetscReal lnLambda, PetscReal eps0, PetscReal *E) 150 { 151 PetscReal c,e,m; 152 153 PetscFunctionBegin; 154 c = 299792458; 155 e = 1.602176e-19; 156 m = 9.10938e-31; 157 if (1) { 158 double Ec, Ehat = *E, betath = PetscSqrtReal(2*Tev*e/(m*c*c)), j0 = Ehat * 7/(PetscSqrtReal(2)*2) * PetscPowReal(betath,3) * n * e * c; 159 Ec = n*lnLambda*PetscPowReal(e,3) / (4*PETSC_PI*PetscPowReal(eps0,2)*m*c*c); 160 *E = Ec; 161 PetscPrintf(PETSC_COMM_WORLD, "CalculateE j0=%g Ec = %g\n",j0,Ec); 162 } else { 163 PetscReal Ed, vth; 164 vth = PetscSqrtReal(8*Tev*e/(m*PETSC_PI)); 165 Ed = n*lnLambda*PetscPowReal(e,3) / (4*PETSC_PI*PetscPowReal(eps0,2)*m*vth*vth); 166 *E = Ed; 167 } 168 PetscFunctionReturn(0); 169 } 170 171 static PetscReal Spitzer(PetscReal m_e, PetscReal e, PetscReal Z, PetscReal epsilon0, PetscReal lnLam, PetscReal kTe_joules) 172 { 173 PetscReal Fz = (1+1.198*Z+0.222*Z*Z)/(1+2.966*Z+0.753*Z*Z), eta; 174 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); 175 return eta; 176 } 177 178 /* */ 179 static PetscErrorCode testNone(TS ts, Vec X, DM plex, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx) 180 { 181 PetscFunctionBeginUser; 182 PetscFunctionReturn(0); 183 } 184 185 /* */ 186 static PetscErrorCode testSpitzer(TS ts, Vec X, DM plex, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx) 187 { 188 PetscErrorCode ierr; 189 PetscInt ii; 190 PetscDS prob; 191 static PetscReal old_ratio = 1e10; 192 TSConvergedReason reason; 193 PetscReal J,J_re,spit_eta,Te_kev=0,E,ratio,Z,n_e,v,v2; 194 PetscScalar user[2] = {0.,ctx->charges[0]}, constants[LANDAU_MAX_SPECIES],tt[LANDAU_MAX_SPECIES],vz; 195 196 PetscFunctionBeginUser; 197 if (ctx->num_species<2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "ctx->num_species %D < 2",ctx->num_species); 198 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 199 /* get current */ 200 for (ii=0;ii<ctx->num_species;ii++) constants[ii] = ctx->charges[ii]; 201 ierr = PetscDSSetConstants(prob, ctx->num_species, constants);CHKERRQ(ierr); 202 ierr = PetscDSSetObjective(prob, 0, &f0_jz_sum);CHKERRQ(ierr); 203 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 204 J = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]); 205 /* get N_e */ 206 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 207 ierr = PetscDSSetObjective(prob, 0, &f0_n);CHKERRQ(ierr); 208 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 209 n_e = PetscRealPart(tt[0])*ctx->n_0; 210 /* Z */ 211 Z = -ctx->charges[1]/ctx->charges[0]; 212 if (rectx->imp_idx!=1 && ctx->charges[rectx->imp_idx]!=ctx->charges[1]) { 213 PetscReal Znew, n_i1,n_ix; 214 user[0] = 1.0; 215 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 216 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 217 n_i1 = PetscRealPart(tt[0])*ctx->n_0; 218 user[0] = (PetscScalar)rectx->imp_idx; 219 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 220 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 221 n_ix = PetscRealPart(tt[0])*ctx->n_0; 222 Znew = -(ctx->charges[1]*n_i1 + ctx->charges[rectx->imp_idx]*n_ix)/(ctx->charges[0]*(n_i1 + n_ix)); 223 Z = Znew; 224 } 225 /* remove drift */ 226 if (1) { 227 user[0] = .0; 228 ierr = PetscDSSetConstants(prob, 2, user);CHKERRQ(ierr); 229 ierr = PetscDSSetObjective(prob, 0, &f0_vz);CHKERRQ(ierr); 230 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 231 vz = ctx->n_0*PetscRealPart(tt[0])/n_e; /* non-dimensional */ 232 } else vz = 0; 233 /* thermal velocity */ 234 ierr = PetscDSSetConstants(prob, 1, &vz);CHKERRQ(ierr); 235 ierr = PetscDSSetObjective(prob, 0, &f0_ve_shift);CHKERRQ(ierr); 236 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 237 v = ctx->n_0*ctx->v_0*PetscRealPart(tt[0])/n_e; /* remove number density to get velocity */ 238 v2 = PetscSqr(v); /* use real space: m^2 / s^2 */ 239 Te_kev = (v2*ctx->masses[0]*PETSC_PI/8)*kev_joul; /* temperature in kev */ 240 //ierr = getTe_kev(plex, X, NULL, &Te_kev);CHKERRQ(ierr); 241 spit_eta = Spitzer(ctx->masses[0],-ctx->charges[0],Z,ctx->epsilon0,ctx->lnLam,Te_kev/kev_joul); /* kev --> J (kT) */ 242 if (rectx->use_spitzer_eta) E = ctx->Ez = spit_eta*J; 243 else E = ctx->Ez; /* keep real E */ 244 if (0) { 245 ierr = PetscDSSetConstants(prob, 1, &constants[0]);CHKERRQ(ierr); 246 ierr = PetscDSSetObjective(prob, 0, &f0_j_re);CHKERRQ(ierr); 247 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 248 } else tt[0] = 0; 249 J_re = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]); 250 251 ratio = E/J/spit_eta; 252 if (stepi>10 && !rectx->use_spitzer_eta && old_ratio-ratio < 1.e-4 && ratio > 0.97 && ratio < 1.03) { 253 ierr = PetscPrintf(PETSC_COMM_WORLD,"switch to E spitzer spitzer-eta:E/J= %20.13e %20.13e\n",spit_eta,ctx->Ez/J);CHKERRQ(ierr); 254 rectx->pulse_start = time + rectx->plotDt - 1.e-5; /* start (pulse) quench, at next test */ 255 rectx->use_spitzer_eta = PETSC_TRUE; 256 /* ierr = TSSetConvergedReason(ts, TS_CONVERGED_USER);CHKERRQ(ierr); */ 257 } 258 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s %4D) time=%10.3e 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\n", 259 "testSpitzer",stepi,time,n_e/ctx->n_0,ctx->Ez,J,J_re,100*J_re/J,Te_kev,Z,ratio,old_ratio-ratio, 260 rectx->use_spitzer_eta ? "using Spitzer eta*J E" : "constant E");CHKERRQ(ierr); 261 ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); 262 old_ratio = ratio; 263 PetscFunctionReturn(0); 264 } 265 266 static const double ppp = 2; 267 static void f0_0_diff_lp(PetscInt dim, PetscInt Nf, PetscInt NfAux, 268 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 269 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 270 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 271 { 272 LandauCtx *ctx = (LandauCtx *)constants; 273 REctx *rectx = (REctx*)ctx->data; 274 PetscInt ii = rectx->idx, i; 275 const PetscReal kT_m = ctx->k*ctx->thermal_temps[ii]/ctx->masses[ii]; /* kT/m */ 276 const PetscReal n = ctx->n[ii]; 277 PetscReal diff, f_maxwell, v2 = 0, theta = 2*kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 278 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 279 f_maxwell = n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 280 diff = 2.*PETSC_PI*x[0]*(PetscRealPart(u[ii]) - f_maxwell); 281 f0[0] = PetscPowReal(diff,ppp); 282 } 283 static void f0_0_maxwellian_lp(PetscInt dim, PetscInt Nf, PetscInt NfAux, 284 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 285 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 286 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0) 287 { 288 LandauCtx *ctx = (LandauCtx *)constants; 289 REctx *rectx = (REctx*)ctx->data; 290 PetscInt ii = rectx->idx, i; 291 const PetscReal kT_m = ctx->k*ctx->thermal_temps[ii]/ctx->masses[ii]; /* kT/m */ 292 const PetscReal n = ctx->n[ii]; 293 PetscReal f_maxwell, v2 = 0, theta = 2*kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */ 294 for (i = 0; i < dim; ++i) v2 += x[i]*x[i]; 295 f_maxwell = 2.*PETSC_PI*x[0] * n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta)); 296 f0[0] = PetscPowReal(f_maxwell,ppp); 297 } 298 299 /* */ 300 static PetscErrorCode testStable(TS ts, Vec X, DM plex, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx) 301 { 302 PetscErrorCode ierr; 303 PetscDS prob; 304 Vec X2; 305 PetscReal ediff,idiff=0,lpm0,lpm1=1; 306 PetscScalar tt[LANDAU_MAX_SPECIES]; 307 DM dm; 308 309 PetscFunctionBeginUser; 310 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 311 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 312 ierr = VecDuplicate(X,&X2);CHKERRQ(ierr); 313 ierr = VecCopy(X,X2);CHKERRQ(ierr); 314 if (!rectx->X_0) { 315 ierr = VecDuplicate(X,&rectx->X_0);CHKERRQ(ierr); 316 ierr = VecCopy(X,rectx->X_0);CHKERRQ(ierr); 317 } 318 ierr = VecAXPY(X,-1.0,rectx->X_0);CHKERRQ(ierr); 319 ierr = PetscDSSetConstants(prob, sizeof(LandauCtx)/sizeof(PetscScalar), (PetscScalar*)ctx);CHKERRQ(ierr); 320 rectx->idx = 0; 321 ierr = PetscDSSetObjective(prob, 0, &f0_0_diff_lp);CHKERRQ(ierr); 322 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 323 ediff = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 324 ierr = PetscDSSetObjective(prob, 0, &f0_0_maxwellian_lp);CHKERRQ(ierr); 325 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 326 lpm0 = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 327 if (ctx->num_species>1) { 328 rectx->idx = 1; 329 ierr = PetscDSSetObjective(prob, 0, &f0_0_diff_lp);CHKERRQ(ierr); 330 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 331 idiff = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 332 ierr = PetscDSSetObjective(prob, 0, &f0_0_maxwellian_lp);CHKERRQ(ierr); 333 ierr = DMPlexComputeIntegralFEM(plex,X2,tt,NULL);CHKERRQ(ierr); 334 lpm1 = PetscPowReal(PetscRealPart(tt[0]),1./ppp); 335 } 336 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); 337 /* view */ 338 ierr = VecViewFromOptions(X,NULL,"-vec_view_diff");CHKERRQ(ierr); 339 ierr = VecCopy(X2,X);CHKERRQ(ierr); 340 ierr = VecDestroy(&X2);CHKERRQ(ierr); 341 if (islast) { 342 ierr = VecDestroy(&rectx->X_0);CHKERRQ(ierr); 343 rectx->X_0 = NULL; 344 } 345 PetscFunctionReturn(0); 346 } 347 348 /* E = eta_spitzer(Te-vz)*J */ 349 static PetscErrorCode ESpitzer(Vec X, Vec X_t, PetscInt stepi, PetscReal time, LandauCtx *ctx, PetscReal *a_E) 350 { 351 PetscErrorCode ierr; 352 PetscInt ii; 353 PetscReal spit_eta,Te_kev,J,ratio; 354 PetscScalar tt[LANDAU_MAX_SPECIES], constants[LANDAU_MAX_SPECIES]; 355 PetscDS prob; 356 DM dm,plex; 357 REctx *rectx = (REctx*)ctx->data; 358 359 PetscFunctionBeginUser; 360 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "ESpitzer is obsolete"); 361 for (ii=0;ii<ctx->num_species;ii++) constants[ii] = ctx->charges[ii]; 362 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 363 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 364 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 365 /* J */ 366 ierr = PetscDSSetConstants(prob, ctx->num_species, constants);CHKERRQ(ierr); 367 ierr = PetscDSSetObjective(prob, 0, &f0_jz_sum);CHKERRQ(ierr); 368 ierr = DMPlexComputeIntegralFEM(plex,X,tt,NULL);CHKERRQ(ierr); 369 J = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]); 370 ierr = getTe_kev(plex, X, NULL, &Te_kev);CHKERRQ(ierr); 371 spit_eta = Spitzer(ctx->masses[0],-ctx->charges[0],-ctx->charges[1]/ctx->charges[0],ctx->epsilon0,ctx->lnLam,Te_kev/kev_joul); /* kev --> J (kT) */ 372 *a_E = ctx->Ez; /* no change */ 373 if (!rectx->use_spitzer_eta && stepi > 10) { 374 static PetscReal old_ratio = 1e10; 375 ratio = *a_E/J/spit_eta; 376 if ((ratio < 1.01 && ratio > 0.99) || (old_ratio <= ratio && ratio < 1.03 && ratio > 0.97) || (old_ratio-ratio) < 1.e-4) { 377 rectx->j = J; 378 rectx->pulse_start = time + 1.; /* start quench, next time step, should use dt */ 379 } 380 ierr = PetscPrintf(PETSC_COMM_WORLD,"\t\t%D) t=%10.3e ESpitzer E/J vs spitzer ratio=%20.13e J=%10.3e E=%10.3e spit_eta=%10.3e Te_kev=%10.3e %s\n",stepi,time,ratio, J, *a_E, spit_eta, Te_kev, rectx->use_spitzer_eta ? " switch to Spitzer E" : " keep testing");CHKERRQ(ierr); 381 old_ratio = ratio; 382 } else if (rectx->use_spitzer_eta) { 383 /* set E */ 384 *a_E = spit_eta*J; 385 ierr = PetscPrintf(PETSC_COMM_WORLD,"\t%D) use ESpitzer E=%10.3e J=%10.3e Te_kev=%10.3e spit_eta=%10.3e t=%g\n",stepi,*a_E,J,Te_kev,spit_eta,time);CHKERRQ(ierr); 386 } else { 387 ierr = PetscPrintf(PETSC_COMM_WORLD,"\t\t\t%D) ESpitzer delay E=%10.3e J=%10.3e Te_kev=%10.3e spit_eta=%10.3e t=%g ratio=%20.13e\n",stepi,*a_E,J,Te_kev,spit_eta,time,ctx->Ez/J/spit_eta);CHKERRQ(ierr); 388 } 389 /* cleanup */ 390 ierr = DMDestroy(&plex);CHKERRQ(ierr); 391 PetscFunctionReturn(0); 392 } 393 394 static PetscErrorCode EInduction(Vec X, Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E) 395 { 396 REctx *rectx = (REctx*)ctx->data; 397 PetscErrorCode ierr; 398 PetscInt ii; 399 DM dm,plex; 400 PetscScalar tt[LANDAU_MAX_SPECIES], constants[LANDAU_MAX_SPECIES]; 401 PetscReal dJ_dt; 402 PetscDS prob; 403 404 PetscFunctionBeginUser; 405 for (ii=0;ii<ctx->num_species;ii++) constants[ii] = ctx->charges[ii]; 406 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 407 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 408 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 409 /* get d current / dt */ 410 ierr = PetscDSSetConstants(prob, ctx->num_species, constants);CHKERRQ(ierr); 411 ierr = PetscDSSetObjective(prob, 0, &f0_jz_sum);CHKERRQ(ierr); 412 if (!X_t) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "X_t"); 413 ierr = DMPlexComputeIntegralFEM(plex,X_t,tt,NULL);CHKERRQ(ierr); 414 dJ_dt = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0])/ctx->t_0; 415 /* E induction */ 416 *a_E = -rectx->L*dJ_dt + rectx->Ez_initial; 417 ierr = DMDestroy(&plex);CHKERRQ(ierr); 418 PetscFunctionReturn(0); 419 } 420 421 static PetscErrorCode EConstant(Vec X, Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E) 422 { 423 PetscFunctionBeginUser; 424 *a_E = ctx->Ez; 425 PetscFunctionReturn(0); 426 } 427 428 static PetscErrorCode ENone(Vec X, Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E) 429 { 430 PetscFunctionBeginUser; 431 *a_E = 0; 432 PetscFunctionReturn(0); 433 } 434 435 /* ------------------------------------------------------------------- */ 436 /* 437 FormSource - Evaluates source terms F(t). 438 439 Input Parameters: 440 . ts - the TS context 441 . time - 442 . X_dummmy - input vector 443 . dummy - optional user-defined context, as set by SNESSetFunction() 444 445 Output Parameter: 446 . F - function vector 447 */ 448 static PetscErrorCode FormSource(TS ts,PetscReal ftime,Vec X_dummmy, Vec F,void *dummy) 449 { 450 PetscReal new_imp_rate; 451 LandauCtx *ctx; 452 DM dm,plex; 453 PetscErrorCode ierr; 454 REctx *rectx; 455 456 PetscFunctionBeginUser; 457 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 458 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 459 rectx = (REctx*)ctx->data; 460 /* check for impurities */ 461 ierr = rectx->impuritySrcRate(ftime,&new_imp_rate,ctx);CHKERRQ(ierr); 462 if (new_imp_rate != 0) { 463 if (new_imp_rate != rectx->current_rate) { 464 PetscInt ii; 465 PetscReal dne_dt,dni_dt,tilda_ns[LANDAU_MAX_SPECIES],temps[LANDAU_MAX_SPECIES]; 466 PetscDS prob; /* diagnostics only */ 467 rectx->current_rate = new_imp_rate; 468 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 469 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 470 dni_dt = new_imp_rate /* *ctx->t_0 */; /* fully ionized immediately, no normalize, stay in non-dim */ 471 dne_dt = new_imp_rate*rectx->Ne_ion/* *ctx->t_0 */; 472 ierr = PetscPrintf(PETSC_COMM_WORLD, "\tFormSource: have 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); 473 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) tilda_ns[ii] = 0; 474 for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) temps[ii] = 1; 475 tilda_ns[0] = dne_dt; tilda_ns[rectx->imp_idx] = dni_dt; 476 temps[0] = rectx->T_cold; temps[rectx->imp_idx] = rectx->T_cold; 477 /* add it */ 478 if (!rectx->imp_src) { 479 ierr = DMCreateGlobalVector(dm, &rectx->imp_src);CHKERRQ(ierr); 480 ierr = PetscObjectSetName((PetscObject)rectx->imp_src, "source");CHKERRQ(ierr); 481 } 482 ierr = VecZeroEntries(rectx->imp_src);CHKERRQ(ierr); 483 ierr = LandauAddMaxwellians(plex,rectx->imp_src,ftime,temps,tilda_ns,ctx);CHKERRQ(ierr); 484 /* clean up */ 485 ierr = DMDestroy(&plex);CHKERRQ(ierr); 486 if (0) { 487 KSP ksp; 488 Vec S; 489 ierr = KSPCreate(PETSC_COMM_SELF,&ksp);CHKERRQ(ierr); 490 ierr = KSPSetOptionsPrefix(ksp,"mass_");CHKERRQ(ierr); /* stokes */ 491 ierr = KSPSetOperators(ksp,ctx->M,ctx->M);CHKERRQ(ierr); 492 ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); 493 ierr = DMCreateGlobalVector(dm, &S);CHKERRQ(ierr); 494 ierr = KSPSolve(ksp,rectx->imp_src,S);CHKERRQ(ierr); 495 ierr = VecCopy(S,rectx->imp_src);CHKERRQ(ierr); 496 ierr = VecDestroy(&S);CHKERRQ(ierr); 497 } 498 ierr = VecViewFromOptions(rectx->imp_src,NULL,"-vec_view_sources");CHKERRQ(ierr); 499 } 500 ierr = VecCopy(rectx->imp_src,F);CHKERRQ(ierr); 501 } else { 502 if (rectx->current_rate != 0 && rectx->imp_src) { 503 ierr = VecZeroEntries(rectx->imp_src);CHKERRQ(ierr); 504 } 505 ierr = VecZeroEntries(F);CHKERRQ(ierr); 506 rectx->current_rate = 0; 507 } 508 PetscFunctionReturn(0); 509 } 510 PetscErrorCode Monitor(TS ts, PetscInt stepi, PetscReal time, Vec X, void *actx) 511 { 512 LandauCtx *ctx = (LandauCtx*) actx; /* user-defined application context */ 513 REctx *rectx = (REctx*)ctx->data; 514 DM dm,plex; 515 PetscDS prob; 516 TSConvergedReason reason; 517 PetscErrorCode ierr; 518 519 PetscFunctionBeginUser; 520 ierr = VecGetDM(X, &dm);CHKERRQ(ierr); 521 if (stepi > rectx->plotStep && rectx->plotting) { 522 rectx->plotting = PETSC_FALSE; /* was doing diagnostics, now done */ 523 rectx->plotIdx++; 524 } 525 /* view */ 526 ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); 527 if (time/rectx->plotDt >= (PetscReal)rectx->plotIdx || reason) { 528 if (reason || stepi==0) { 529 /* print norms */ 530 ierr = LandauPrintNorms(X, stepi);CHKERRQ(ierr); 531 } 532 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 533 ierr = DMGetDS(plex, &prob);CHKERRQ(ierr); 534 /* diagnostics + change E field with Sptizer (not just a momitor now!) */ 535 ierr = rectx->test(ts,X,plex,stepi,time,reason ? PETSC_TRUE : PETSC_FALSE, ctx, rectx);CHKERRQ(ierr); 536 ierr = DMDestroy(&plex);CHKERRQ(ierr); 537 /* view */ 538 ierr = DMSetOutputSequenceNumber(dm, rectx->plotIdx, time*ctx->t_0);CHKERRQ(ierr); 539 ierr = VecViewFromOptions(X,NULL,"-vec_view");CHKERRQ(ierr); 540 rectx->plotStep = stepi; 541 rectx->plotting = PETSC_TRUE; 542 } 543 /* parallel check */ 544 if (reason) { 545 PetscReal val,rval; 546 PetscMPIInt rank; 547 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRMPI(ierr); 548 ierr = TSGetSolution(ts, &X);CHKERRQ(ierr); 549 ierr = VecNorm(X,NORM_2,&val);CHKERRQ(ierr); 550 ierr = MPIU_Allreduce(&val,&rval,1,MPIU_REAL,MPIU_MAX,PETSC_COMM_WORLD);CHKERRQ(ierr); 551 if (rval != val) { 552 ierr = PetscPrintf(PETSC_COMM_SELF, " ***** [%D] ERROR max |x| = %22.15e, my |x| = %22.15e diff=%e\n",rank,rval,val,rval-val);CHKERRQ(ierr); 553 } else { 554 ierr = PetscPrintf(PETSC_COMM_WORLD, "[%D] parallel consistency check OK\n",rank);CHKERRQ(ierr); 555 } 556 } 557 rectx->idx = 0; 558 PetscFunctionReturn(0); 559 } 560 561 PetscErrorCode PreStep(TS ts) 562 { 563 PetscErrorCode ierr; 564 LandauCtx *ctx; 565 REctx *rectx; 566 DM dm; 567 PetscInt stepi; 568 PetscReal time; 569 Vec X; 570 571 PetscFunctionBeginUser; 572 /* check seed RE run */ 573 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 574 ierr = TSGetTime(ts,&time);CHKERRQ(ierr); 575 ierr = TSGetSolution(ts,&X);CHKERRQ(ierr); 576 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 577 rectx = (REctx*)ctx->data; 578 ierr = TSGetStepNumber(ts, &stepi);CHKERRQ(ierr); 579 /* update E */ 580 ierr = rectx->E(X, NULL, stepi, time, ctx, &ctx->Ez);CHKERRQ(ierr); 581 PetscFunctionReturn(0); 582 } 583 584 /* 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) */ 585 static PetscErrorCode stepSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx) 586 { 587 REctx *rectx = (REctx*)ctx->data; 588 589 PetscFunctionBeginUser; 590 if (time >= rectx->pulse_start) *rho = rectx->pulse_rate; 591 else *rho = 0.; 592 PetscFunctionReturn(0); 593 } 594 static PetscErrorCode zeroSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx) 595 { 596 PetscFunctionBeginUser; 597 *rho = 0.; 598 PetscFunctionReturn(0); 599 } 600 static PetscErrorCode pulseSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx) 601 { 602 REctx *rectx = (REctx*)ctx->data; 603 604 PetscFunctionBeginUser; 605 if (rectx->pulse_start == PETSC_MAX_REAL) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"'-ex2_pulse_start_time X' must be used with '-ex2_impurity_source_type pulse'"); 606 if (time < rectx->pulse_start || time > rectx->pulse_start + 3*rectx->pulse_width) *rho = 0; 607 /* else if (0) { */ 608 /* 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); */ 609 /* *rho = rectx->pulse_rate * (cycle / (stop - start)) / (1 + PetscExpReal(steep*(PetscSinReal(2*PETSC_PI*((t - start)/cycle + xi)) - PetscSinReal(2*PETSC_PI*xi)))); */ 610 /* } else if (0) { */ 611 /* double x = 2*(time - rectx->pulse_start)/(3*rectx->pulse_width) - 1; */ 612 /* if (x==1 || x==-1) *rho = 0; */ 613 /* else *rho = rectx->pulse_rate * PetscExpReal(-1/(1-x*x)); */ 614 /* } */ 615 else { 616 double x = PetscSinReal((time-rectx->pulse_start)/(3*rectx->pulse_width)*2*PETSC_PI - PETSC_PI/2) + 1; /* 0:2, integrates to 1.0 */ 617 *rho = rectx->pulse_rate * x / (3*rectx->pulse_width); 618 if (!rectx->use_spitzer_eta) rectx->use_spitzer_eta = PETSC_TRUE; /* use it next time */ 619 } 620 PetscFunctionReturn(0); 621 } 622 623 #undef __FUNCT__ 624 #define __FUNCT__ "ProcessREOptions" 625 static PetscErrorCode ProcessREOptions(REctx *rectx, const LandauCtx *ctx, DM dm, const char prefix[]) 626 { 627 PetscErrorCode ierr; 628 PetscFunctionList plist = NULL, testlist = NULL, elist = NULL; 629 char pname[256],testname[256],ename[256]; 630 DM dummy; 631 PetscBool Connor_E = PETSC_FALSE; 632 633 PetscFunctionBeginUser; 634 ierr = DMCreate(PETSC_COMM_WORLD,&dummy);CHKERRQ(ierr); 635 rectx->Ne_ion = 1; /* number of electrons given up by impurity ion */ 636 rectx->T_cold = .005; /* kev */ 637 rectx->ion_potential = 15; /* ev */ 638 rectx->L = 2; 639 rectx->X_0 = NULL; 640 rectx->imp_idx = ctx->num_species - 1; /* default ionized impurity as last one */ 641 rectx->pulse_start = PETSC_MAX_REAL; 642 rectx->pulse_width = 1; 643 rectx->plotStep = PETSC_MAX_INT; 644 rectx->pulse_rate = 1.e-1; 645 rectx->current_rate = 0; 646 rectx->plotIdx = 0; 647 rectx->imp_src = 0; 648 rectx->j = 0; 649 rectx->plotDt = 1.0; 650 rectx->plotting = PETSC_TRUE; 651 rectx->use_spitzer_eta = PETSC_FALSE; 652 rectx->idx = 0; 653 /* Register the available impurity sources */ 654 ierr = PetscFunctionListAdd(&plist,"step",&stepSrc);CHKERRQ(ierr); 655 ierr = PetscFunctionListAdd(&plist,"none",&zeroSrc);CHKERRQ(ierr); 656 ierr = PetscFunctionListAdd(&plist,"pulse",&pulseSrc);CHKERRQ(ierr); 657 ierr = PetscStrcpy(pname,"none");CHKERRQ(ierr); 658 ierr = PetscFunctionListAdd(&testlist,"none",&testNone);CHKERRQ(ierr); 659 ierr = PetscFunctionListAdd(&testlist,"spitzer",&testSpitzer);CHKERRQ(ierr); 660 ierr = PetscFunctionListAdd(&testlist,"stable",&testStable);CHKERRQ(ierr); 661 ierr = PetscStrcpy(testname,"none");CHKERRQ(ierr); 662 ierr = PetscFunctionListAdd(&elist,"none",&ENone);CHKERRQ(ierr); 663 ierr = PetscFunctionListAdd(&elist,"spitzer",&ESpitzer);CHKERRQ(ierr); 664 ierr = PetscFunctionListAdd(&elist,"induction",&EInduction);CHKERRQ(ierr); 665 ierr = PetscFunctionListAdd(&elist,"constant",&EConstant);CHKERRQ(ierr); 666 ierr = PetscStrcpy(ename,"constant");CHKERRQ(ierr); 667 668 ierr = PetscOptionsBegin(PETSC_COMM_SELF, prefix, "Options for Runaway/seed electron model", "none");CHKERRQ(ierr); 669 ierr = PetscOptionsReal("-ex2_plot_dt", "Plotting interval", "xgc_dmplex.c", rectx->plotDt, &rectx->plotDt, NULL);CHKERRQ(ierr); 670 if (rectx->plotDt < 0) rectx->plotDt = 1e30; 671 if (rectx->plotDt == 0) rectx->plotDt = 1e-30; 672 ierr = PetscOptionsFList("-ex2_impurity_source_type","Name of impurity source to run","",plist,pname,pname,sizeof(pname),NULL);CHKERRQ(ierr); 673 ierr = PetscOptionsFList("-ex2_test_type","Name of test to run","",testlist,testname,testname,sizeof(testname),NULL);CHKERRQ(ierr); 674 ierr = PetscOptionsInt("-ex2_impurity_index", "index of sink for impurities", "none", rectx->imp_idx, &rectx->imp_idx, NULL);CHKERRQ(ierr); 675 if ((rectx->imp_idx >= ctx->num_species || rectx->imp_idx < 1) && ctx->num_species > 1) SETERRQ1(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); 676 ierr = PetscOptionsFList("-ex2_e_field_type","Electric field type","",elist,ename,ename,sizeof(ename),NULL);CHKERRQ(ierr); 677 rectx->Ne_ion = -ctx->charges[rectx->imp_idx]/ctx->charges[0]; 678 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); 679 ierr = PetscOptionsReal("-ex2_pulse_start_time","Time at which pulse happens for 'pulse' source","none",rectx->pulse_start,&rectx->pulse_start, NULL);CHKERRQ(ierr); 680 ierr = PetscOptionsReal("-ex2_pulse_width_time","Width of pulse 'pulse' source","none",rectx->pulse_width,&rectx->pulse_width, NULL);CHKERRQ(ierr); 681 ierr = PetscOptionsReal("-ex2_pulse_rate","Number density of pulse for 'pulse' source","none",rectx->pulse_rate,&rectx->pulse_rate, NULL);CHKERRQ(ierr); 682 rectx->T_cold *= 1.16e7; /* convert to Kelvin */ 683 ierr = PetscOptionsReal("-ex2_ion_potential","Potential to ionize impurity (should be array) in ev","none",rectx->ion_potential,&rectx->ion_potential, NULL);CHKERRQ(ierr); 684 ierr = PetscOptionsReal("-ex2_inductance","Inductance E feild","none",rectx->L,&rectx->L, NULL);CHKERRQ(ierr); 685 ierr = PetscOptionsBool("-ex2_connor_e_field_units","Scale Ex but Connor-Hastie E_c","none",Connor_E,&Connor_E, NULL);CHKERRQ(ierr); 686 ierr = PetscInfo5(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); 687 ierr = PetscOptionsEnd();CHKERRQ(ierr); 688 /* get impurity source rate function */ 689 ierr = PetscFunctionListFind(plist,pname,&rectx->impuritySrcRate);CHKERRQ(ierr); 690 if (!rectx->impuritySrcRate) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No impurity source function found '%s'",pname); 691 ierr = PetscFunctionListFind(testlist,testname,&rectx->test);CHKERRQ(ierr); 692 if (!rectx->test) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No test found '%s'",testname); 693 ierr = PetscFunctionListFind(elist,ename,&rectx->E);CHKERRQ(ierr); 694 if (!rectx->E) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No E field function found '%s'",ename); 695 ierr = PetscFunctionListDestroy(&plist);CHKERRQ(ierr); 696 ierr = PetscFunctionListDestroy(&testlist);CHKERRQ(ierr); 697 ierr = PetscFunctionListDestroy(&elist);CHKERRQ(ierr); 698 { 699 PetscMPIInt rank; 700 ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRMPI(ierr); 701 if (rank) { /* turn off output stuff for duplicate runs */ 702 ierr = PetscOptionsClearValue(NULL,"-dm_view");CHKERRQ(ierr); 703 ierr = PetscOptionsClearValue(NULL,"-vec_view");CHKERRQ(ierr); 704 ierr = PetscOptionsClearValue(NULL,"-dm_view_diff");CHKERRQ(ierr); 705 ierr = PetscOptionsClearValue(NULL,"-vec_view_diff");CHKERRQ(ierr); 706 ierr = PetscOptionsClearValue(NULL,"-dm_view_sources");CHKERRQ(ierr); 707 ierr = PetscOptionsClearValue(NULL,"-vec_view_sources");CHKERRQ(ierr); 708 } 709 } 710 /* convert E from Connor-Hastie E_c units to real if doing Spitzer E */ 711 if (Connor_E) { 712 PetscReal E = ctx->Ez, Tev = ctx->thermal_temps[0]*8.621738e-5, n = ctx->n_0*ctx->n[0]; 713 CalculateE(Tev, n, ctx->lnLam, ctx->epsilon0, &E); 714 ((LandauCtx*)ctx)->Ez *= E; 715 } 716 ierr = DMDestroy(&dummy);CHKERRQ(ierr); 717 PetscFunctionReturn(0); 718 } 719 720 int main(int argc, char **argv) 721 { 722 DM dm; 723 Vec X; 724 PetscErrorCode ierr; 725 PetscInt dim = 2; 726 TS ts; 727 Mat J; 728 PetscDS prob; 729 LandauCtx *ctx; 730 REctx *rectx; 731 #if defined PETSC_USE_LOG 732 PetscLogStage stage; 733 #endif 734 ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; 735 ierr = PetscOptionsGetInt(NULL,NULL, "-dim", &dim, NULL);CHKERRQ(ierr); 736 /* Create a mesh */ 737 ierr = LandauCreateVelocitySpace(PETSC_COMM_SELF, dim, "", &X, &J, &dm);CHKERRQ(ierr); 738 ierr = LandauCreateMassMatrix(dm, NULL);CHKERRQ(ierr); 739 ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); 740 ierr = DMSetUp(dm);CHKERRQ(ierr); 741 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 742 /* context */ 743 ierr = PetscNew(&rectx);CHKERRQ(ierr); 744 ctx->data = rectx; 745 ierr = ProcessREOptions(rectx,ctx,dm,"");CHKERRQ(ierr); 746 ierr = DMSetOutputSequenceNumber(dm, 0, 0.0);CHKERRQ(ierr); 747 ierr = DMViewFromOptions(dm,NULL,"-dm_view");CHKERRQ(ierr); 748 ierr = DMViewFromOptions(dm,NULL,"-dm_view_sources");CHKERRQ(ierr); 749 ierr = DMViewFromOptions(dm,NULL,"-dm_view_diff");CHKERRQ(ierr); 750 /* Create timestepping solver context */ 751 ierr = TSCreate(PETSC_COMM_SELF,&ts);CHKERRQ(ierr); 752 ierr = TSSetDM(ts,dm);CHKERRQ(ierr); 753 ierr = TSSetIFunction(ts,NULL,LandauIFunction,NULL);CHKERRQ(ierr); 754 ierr = TSSetIJacobian(ts,J,J,LandauIJacobian,NULL);CHKERRQ(ierr); 755 ierr = TSSetRHSFunction(ts,NULL,FormSource,NULL);CHKERRQ(ierr); 756 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 757 ierr = TSSetSolution(ts,X);CHKERRQ(ierr); 758 ierr = TSSetApplicationContext(ts, ctx);CHKERRQ(ierr); 759 ierr = TSMonitorSet(ts,Monitor,ctx,NULL);CHKERRQ(ierr); 760 ierr = TSSetPreStep(ts,PreStep);CHKERRQ(ierr); 761 rectx->Ez_initial = ctx->Ez; /* cache for induction caclulation - applied E field */ 762 if (1) { /* warm up an test just LandauIJacobian */ 763 Vec vec; 764 PetscInt nsteps; 765 PetscReal dt; 766 ierr = PetscLogStageRegister("Warmup", &stage);CHKERRQ(ierr); 767 ierr = PetscLogStagePush(stage);CHKERRQ(ierr); 768 ierr = VecDuplicate(X,&vec);CHKERRQ(ierr); 769 ierr = VecCopy(X,vec);CHKERRQ(ierr); 770 ierr = TSGetMaxSteps(ts,&nsteps); 771 ierr = TSGetTimeStep(ts,&dt);CHKERRQ(ierr); 772 ierr = TSSetMaxSteps(ts,1); 773 ierr = TSSetSolution(ts,vec);CHKERRQ(ierr); 774 ierr = TSSolve(ts,vec);CHKERRQ(ierr); 775 ierr = TSSetMaxSteps(ts,nsteps); 776 ierr = TSSetStepNumber(ts,0);CHKERRQ(ierr); 777 ierr = TSSetTime(ts,0);CHKERRQ(ierr); 778 ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); 779 ierr = TSSetSolution(ts,X);CHKERRQ(ierr); 780 rectx->plotIdx = 0; 781 rectx->plotting = PETSC_TRUE; 782 ierr = PetscLogStagePop();CHKERRQ(ierr); 783 ierr = VecDestroy(&vec);CHKERRQ(ierr); 784 } 785 ierr = VecViewFromOptions(X,NULL,"-vec_view");CHKERRQ(ierr); // inital condition (monitor plots after step) 786 /* go */ 787 ierr = PetscLogStageRegister("Solve", &stage);CHKERRQ(ierr); 788 ierr = PetscLogStagePush(stage);CHKERRQ(ierr); 789 ierr = TSSolve(ts,X);CHKERRQ(ierr); 790 ierr = PetscLogStagePop();CHKERRQ(ierr); 791 /* clean up */ 792 ierr = LandauDestroyVelocitySpace(&dm);CHKERRQ(ierr); 793 ierr = TSDestroy(&ts);CHKERRQ(ierr); 794 ierr = VecDestroy(&X);CHKERRQ(ierr); 795 if (rectx->imp_src) { 796 ierr = VecDestroy(&rectx->imp_src);CHKERRQ(ierr); 797 } 798 ierr = PetscFree(rectx);CHKERRQ(ierr); 799 ierr = PetscFinalize(); 800 return ierr; 801 } 802 803 /*TEST 804 test: 805 suffix: 0 806 requires: p4est !complex double 807 args: -dm_landau_Ez 0 -petscspace_degree 2 -petscspace_poly_tensor 1 -dm_landau_type p4est -info :dm,tsadapt -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 -pc_type lu -ksp_type preonly -dm_landau_amr_levels_max 9 -dm_landau_domain_radius -.75 -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 1 -dm_preallocate_only -dm_landau_gpu_assembly false 808 809 test: 810 suffix: kokkos 811 requires: p4est !complex double kokkos_kernels !define(PETSC_USE_CTABLE) 812 args: -dm_landau_Ez 0 -petscspace_degree 2 -petscspace_poly_tensor 1 -dm_landau_type p4est -info :dm,tsadapt -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 -pc_type lu -ksp_type preonly -dm_landau_amr_levels_max 9 -dm_landau_domain_radius -.75 -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 1 -dm_preallocate_only -dm_landau_device_type kokkos -dm_landau_gpu_assembly true -dm_mat_type aijkokkos -dm_vec_type kokkos 813 814 TEST*/ 815