Actual source code: ex1.c

  1: static char help[] = "Landau collision operator with amnisotropic thermalization verification test as per Hager et al.\n 'A fully non-linear multi-species Fokker-Planck-Landau collision operator for simulation of fusion plasma', and "
  2:                      "published as 'A performance portable, fully implicit Landau collision operator with batched linear solvers' https://arxiv.org/abs/2209.03228\n\n";

  4: #include <petscts.h>
  5: #include <petsclandau.h>
  6: #include <petscdmcomposite.h>
  7: #include <petscds.h>

  9: /*
 10:  call back method for DMPlexLandauAccess:

 12: Input Parameters:
 13:  .   dm - a DM for this field
 14:  -   local_field - the local index in the grid for this field
 15:  .   grid - the grid index
 16:  +   b_id - the batch index
 17:  -   vctx - a user context

 19:  Input/Output Parameter:
 20:  .   x - Vector to data to

 22:  */
 23: PetscErrorCode landau_field_print_access_callback(DM dm, Vec x, PetscInt local_field, PetscInt grid, PetscInt b_id, void *vctx)
 24: {
 25:   LandauCtx  *ctx;
 26:   PetscScalar val;
 27:   PetscInt    species;

 29:   PetscFunctionBegin;
 30:   PetscCall(DMGetApplicationContext(dm, &ctx));
 31:   species = ctx->species_offset[grid] + local_field;
 32:   val     = (PetscScalar)(LAND_PACK_IDX(b_id, grid) + (species + 1) * 10);
 33:   PetscCall(VecSet(x, val));
 34:   PetscCall(PetscInfo(dm, "DMPlexLandauAccess user 'add' method to grid %" PetscInt_FMT ", batch %" PetscInt_FMT " and local field %" PetscInt_FMT " with %" PetscInt_FMT " grids\n", grid, b_id, local_field, ctx->num_grids));

 36:   PetscFunctionReturn(PETSC_SUCCESS);
 37: }

 39: static const PetscReal alphai   = 1 / 1.3;
 40: static const PetscReal kev_joul = 6.241506479963235e+15; /* 1/1000e */

 42: // constants: [index of (anisotropic) direction of source, z x[1] shift
 43: /* < v, n_s v_|| > */
 44: static void f0_vz(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
 45: {
 46:   if (dim == 2) f0[0] = u[0] * (2. * PETSC_PI * x[0]) * x[1]; /* n r v_|| */
 47:   else f0[0] = u[0] * x[2];
 48: }
 49: /* < v, n (v-shift)^2 > */
 50: static void f0_v2_par_shift(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
 51: {
 52:   PetscReal vz = PetscRealPart(constants[0]);
 53:   if (dim == 2) *f0 = u[0] * (2. * PETSC_PI * x[0]) * (x[1] - vz) * (x[1] - vz); /* n r v^2_par|perp */
 54:   else *f0 = u[0] * (x[2] - vz) * (x[2] - vz);
 55: }
 56: static void f0_v2_perp(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
 57: {
 58:   if (dim == 2) *f0 = u[0] * (2. * PETSC_PI * x[0]) * x[0] * x[0]; /* n r v^2_perp */
 59:   else *f0 = u[0] * (x[0] * x[0] + x[1] * x[1]);
 60: }
 61: /* < v, n_e > */
 62: static void f0_n(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
 63: {
 64:   if (dim == 2) f0[0] = 2. * PETSC_PI * x[0] * u[0];
 65:   else f0[0] = u[0];
 66: }
 67: static void f0_v2_shift(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
 68: {
 69:   PetscReal vz = PetscRealPart(constants[0]);
 70:   if (dim == 2) f0[0] = u[0] * (2. * PETSC_PI * x[0]) * (x[0] * x[0] + (x[1] - vz) * (x[1] - vz));
 71:   else f0[0] = u[0] * (x[0] * x[0] + x[1] * x[1] + (x[2] - vz) * (x[2] - vz));
 72: }
 73: /* Define a Maxwellian function for testing out the operator. */
 74: typedef struct {
 75:   PetscReal v_0;
 76:   PetscReal kT_m;
 77:   PetscReal n;
 78:   PetscReal shift;
 79:   PetscInt  species;
 80: } MaxwellianCtx;

 82: static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
 83: {
 84:   MaxwellianCtx *mctx  = (MaxwellianCtx *)actx;
 85:   PetscReal      theta = 2 * mctx->kT_m / (mctx->v_0 * mctx->v_0); /* theta = 2kT/mc^2 */
 86:   PetscFunctionBegin;
 87:   /* evaluate the shifted Maxwellian */
 88:   if (dim == 2) u[0] += alphai * mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * PetscExpReal(-(alphai * x[0] * x[0] + (x[1] - mctx->shift) * (x[1] - mctx->shift)) / theta);
 89:   else u[0] += alphai * mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * PetscExpReal(-(alphai * (x[0] * x[0] + x[1] * x[1]) + (x[2] - mctx->shift) * (x[2] - mctx->shift)) / theta);
 90:   PetscFunctionReturn(PETSC_SUCCESS);
 91: }

 93: static PetscErrorCode SetMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], PetscInt grid, PetscReal shifts[], LandauCtx *ctx)
 94: {
 95:   PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
 96:   MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES];
 97:   PetscFunctionBegin;
 98:   if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
 99:   for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
100:     mctxs[i0]        = &data[i0];
101:     data[i0].v_0     = ctx->v_0;                             // v_0 same for all grids
102:     data[i0].kT_m    = ctx->k * temps[ii] / ctx->masses[ii]; /* kT/m = v_th ^ 2*/
103:     data[i0].n       = ns[ii];
104:     initu[i0]        = maxwellian;
105:     data[i0].shift   = 0;
106:     data[i0].species = ii;
107:   }
108:   if (1) {
109:     data[0].shift = -((PetscReal)PetscSign(ctx->charges[ctx->species_offset[grid]])) * ctx->electronShift * ctx->m_0 / ctx->masses[ctx->species_offset[grid]];
110:   } else {
111:     shifts[0]     = 0.5 * PetscSqrtReal(ctx->masses[0] / ctx->masses[1]);
112:     shifts[1]     = 50 * (ctx->masses[0] / ctx->masses[1]);
113:     data[0].shift = ctx->electronShift * shifts[grid] * PetscSqrtReal(data[0].kT_m) / ctx->v_0; // shifts to not matter!!!!
114:   }
115:   PetscCall(DMProjectFunction(dm, time, initu, (void **)mctxs, INSERT_ALL_VALUES, X));
116:   PetscFunctionReturn(PETSC_SUCCESS);
117: }

119: typedef enum {
120:   E_PAR_IDX,
121:   E_PERP_IDX,
122:   I_PAR_IDX,
123:   I_PERP_IDX,
124:   NUM_TEMPS
125: } TemperatureIDX;

127: /* --------------------  Evaluate NRL Function F(x) (analytical solutions exist for this) --------------------- */
128: static PetscReal n_cm3[2] = {0, 0};
129: PetscErrorCode   FormFunction(TS ts, PetscReal tdummy, Vec X, Vec F, void *ptr)
130: {
131:   LandauCtx         *ctx = (LandauCtx *)ptr; /* user-defined application context */
132:   PetscScalar       *f;
133:   const PetscScalar *x;
134:   const PetscReal    k_B = 1.6e-12, e_cgs = 4.8e-10, proton_mass = 9.1094e-28, m_cgs[2] = {proton_mass, proton_mass * ctx->masses[1] / ctx->masses[0]}; // erg/eV, e, m as per NRL;
135:   PetscReal          AA, v_bar_ab, vTe, t1, TeDiff, Te, Ti, Tdiff;

137:   PetscFunctionBeginUser;
138:   PetscCall(VecGetArrayRead(X, &x));
139:   Te = PetscRealPart(2 * x[E_PERP_IDX] + x[E_PAR_IDX]) / 3, Ti = PetscRealPart(2 * x[I_PERP_IDX] + x[I_PAR_IDX]) / 3;
140:   // thermalization from NRL Plasma formulary, assume Z = 1, mu = 2, n_i = n_e
141:   v_bar_ab = 1.8e-19 * PetscSqrtReal(m_cgs[0] * m_cgs[1]) * n_cm3[0] * ctx->lambdas[0][1] * PetscPowReal(m_cgs[0] * Ti + m_cgs[1] * Te, -1.5);
142:   PetscCall(VecGetArray(F, &f));
143:   for (PetscInt ii = 0; ii < 2; ii++) {
144:     PetscReal tPerp = PetscRealPart(x[2 * ii + E_PERP_IDX]), tPar = PetscRealPart(x[2 * ii + E_PAR_IDX]), ff;
145:     TeDiff = tPerp - tPar;
146:     AA     = tPerp / tPar - 1;
147:     if (AA < 0) ff = PetscAtanhReal(PetscSqrtReal(-AA)) / PetscSqrtReal(-AA);
148:     else ff = PetscAtanReal(PetscSqrtReal(AA)) / PetscSqrtReal(AA);
149:     t1 = (-3 + (AA + 3) * ff) / PetscSqr(AA);
150:     //PetscReal vTeB = 8.2e-7 * n_cm3[0] * ctx->lambdas[0][1] * PetscPowReal(Te, -1.5);
151:     vTe = 2 * PetscSqrtReal(PETSC_PI / m_cgs[ii]) * PetscSqr(PetscSqr(e_cgs)) * n_cm3[0] * ctx->lambdas[0][1] * PetscPowReal(PetscRealPart(k_B * x[E_PAR_IDX]), -1.5) * t1;
152:     t1  = vTe * TeDiff; // * 2; // scaling from NRL that makes it fit pretty good

154:     f[2 * ii + E_PAR_IDX]  = 2 * t1; // par
155:     f[2 * ii + E_PERP_IDX] = -t1;    // perp
156:     Tdiff                  = (ii == 0) ? (Ti - Te) : (Te - Ti);
157:     f[2 * ii + E_PAR_IDX] += v_bar_ab * Tdiff;
158:     f[2 * ii + E_PERP_IDX] += v_bar_ab * Tdiff;
159:   }
160:   PetscCall(VecRestoreArrayRead(X, &x));
161:   PetscCall(VecRestoreArray(F, &f));
162:   PetscFunctionReturn(PETSC_SUCCESS);
163: }

165: /* --------------------  Form initial approximation ----------------- */
166: static PetscReal T0[4] = {300, 390, 200, 260};
167: PetscErrorCode   createVec_NRL(LandauCtx *ctx, Vec *vec)
168: {
169:   PetscScalar *x;
170:   Vec          Temps;

172:   PetscFunctionBeginUser;
173:   PetscCall(VecCreateSeq(PETSC_COMM_SELF, NUM_TEMPS, &Temps));
174:   PetscCall(VecGetArray(Temps, &x));
175:   for (PetscInt i = 0; i < NUM_TEMPS; i++) x[i] = T0[i];
176:   PetscCall(VecRestoreArray(Temps, &x));
177:   *vec = Temps;
178:   PetscFunctionReturn(PETSC_SUCCESS);
179: }

181: PetscErrorCode createTS_NRL(LandauCtx *ctx, Vec Temps)
182: {
183:   TSAdapt adapt;
184:   TS      ts;

186:   PetscFunctionBeginUser;
187:   PetscCall(TSCreate(PETSC_COMM_SELF, &ts));
188:   ctx->data = (void *)ts; // 'data' is for applications (eg, monitors)
189:   PetscCall(TSSetApplicationContext(ts, ctx));
190:   PetscCall(TSSetType(ts, TSRK));
191:   PetscCall(TSSetRHSFunction(ts, NULL, FormFunction, ctx));
192:   PetscCall(TSSetSolution(ts, Temps));
193:   PetscCall(TSRKSetType(ts, TSRK2A));
194:   PetscCall(TSSetOptionsPrefix(ts, "nrl_"));
195:   PetscCall(TSSetFromOptions(ts));
196:   PetscCall(TSGetAdapt(ts, &adapt));
197:   PetscCall(TSAdaptSetType(adapt, TSADAPTNONE));
198:   PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP));
199:   PetscCall(TSSetStepNumber(ts, 0));
200:   PetscCall(TSSetMaxSteps(ts, 1));
201:   PetscCall(TSSetTime(ts, 0));

203:   PetscFunctionReturn(PETSC_SUCCESS);
204: }

206: PetscErrorCode Monitor_nrl(TS ts, PetscInt stepi, PetscReal time, Vec X, void *actx)
207: {
208:   const PetscScalar *x;
209:   LandauCtx         *ctx = (LandauCtx *)actx; /* user-defined application context */

211:   PetscFunctionBeginUser;
212:   if (stepi % 100 == 0) {
213:     PetscCall(PetscPrintf(PETSC_COMM_WORLD, "nrl-step %d time= %g ", (int)stepi, (double)(time / ctx->t_0)));
214:     PetscCall(VecGetArrayRead(X, &x));
215:     for (PetscInt i = 0; i < NUM_TEMPS; i++) { PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%g ", (double)PetscRealPart(x[i]))); }
216:     PetscCall(VecRestoreArrayRead(X, &x));
217:     PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
218:   }
219:   PetscFunctionReturn(PETSC_SUCCESS);
220: }

222: PetscErrorCode Monitor(TS ts, PetscInt stepi, PetscReal time, Vec X, void *actx)
223: {
224:   LandauCtx *ctx      = (LandauCtx *)actx; /* user-defined application context */
225:   TS         ts_nrl   = (TS)ctx->data;
226:   PetscInt   printing = 0, logT;

228:   PetscFunctionBeginUser;
229:   if (ctx->verbose > 0) { // hacks to generate sparse data (eg, use '-dm_landau_verbose 1' and '-dm_landau_verbose -1' to get all steps printed)
230:     PetscReal dt;
231:     PetscCall(TSGetTimeStep(ts, &dt));
232:     logT = (PetscInt)PetscLog2Real(time / dt);
233:     if (logT < 0) logT = 0;
234:     ctx->verbose = PetscPowInt(2, logT) / 2;
235:     if (ctx->verbose == 0) ctx->verbose = 1;
236:   }
237:   if (ctx->verbose) {
238:     TSConvergedReason reason;
239:     PetscCall(TSGetConvergedReason(ts, &reason));
240:     if (stepi % ctx->verbose == 0 || reason || stepi == 1 || ctx->verbose < 0) {
241:       PetscInt nDMs, id;
242:       DM       pack;
243:       Vec     *XsubArray = NULL;
244:       printing           = 1;
245:       PetscCall(TSGetDM(ts, &pack));
246:       PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
247:       PetscCall(DMGetOutputSequenceNumber(ctx->plex[0], &id, NULL));
248:       PetscCall(DMSetOutputSequenceNumber(ctx->plex[0], id + 1, time));
249:       PetscCall(DMSetOutputSequenceNumber(ctx->plex[1], id + 1, time));
250:       PetscCall(PetscInfo(pack, "ex1 plot step %" PetscInt_FMT ", time = %g\n", id, (double)time));
251:       PetscCall(PetscMalloc(sizeof(*XsubArray) * nDMs, &XsubArray));
252:       PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, XsubArray)); // read only
253:       PetscCall(VecViewFromOptions(XsubArray[LAND_PACK_IDX(ctx->batch_view_idx, 0)], NULL, "-ex1_vec_view_e"));
254:       PetscCall(VecViewFromOptions(XsubArray[LAND_PACK_IDX(ctx->batch_view_idx, 1)], NULL, "-ex1_vec_view_i"));
255:       // temps
256:       for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
257:         PetscDS     prob;
258:         DM          dm      = ctx->plex[grid];
259:         PetscScalar user[2] = {0, 0}, tt[1];
260:         PetscReal   vz_0 = 0, n, energy, e_perp, e_par, m_s = ctx->masses[ctx->species_offset[grid]];
261:         Vec         Xloc = XsubArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
262:         PetscCall(DMGetDS(dm, &prob));
263:         /* get n */
264:         PetscCall(PetscDSSetObjective(prob, 0, &f0_n));
265:         PetscCall(DMPlexComputeIntegralFEM(dm, Xloc, tt, NULL));
266:         n = PetscRealPart(tt[0]);
267:         /* get vz */
268:         PetscCall(PetscDSSetObjective(prob, 0, &f0_vz));
269:         PetscCall(DMPlexComputeIntegralFEM(dm, Xloc, tt, NULL));
270:         user[0] = vz_0 = PetscRealPart(tt[0]) / n;
271:         /* energy temp */
272:         PetscCall(PetscDSSetConstants(prob, 2, user));
273:         PetscCall(PetscDSSetObjective(prob, 0, &f0_v2_shift));
274:         PetscCall(DMPlexComputeIntegralFEM(dm, Xloc, tt, ctx));
275:         energy = PetscRealPart(tt[0]) * ctx->v_0 * ctx->v_0 * m_s / n / 3; // scale?
276:         energy *= kev_joul * 1000;                                         // T eV
277:         /* energy temp - par */
278:         PetscCall(PetscDSSetConstants(prob, 2, user));
279:         PetscCall(PetscDSSetObjective(prob, 0, &f0_v2_par_shift));
280:         PetscCall(DMPlexComputeIntegralFEM(dm, Xloc, tt, ctx));
281:         e_par = PetscRealPart(tt[0]) * ctx->v_0 * ctx->v_0 * m_s / n;
282:         e_par *= kev_joul * 1000; // eV
283:         /* energy temp - perp */
284:         PetscCall(PetscDSSetConstants(prob, 2, user));
285:         PetscCall(PetscDSSetObjective(prob, 0, &f0_v2_perp));
286:         PetscCall(DMPlexComputeIntegralFEM(dm, Xloc, tt, ctx));
287:         e_perp = PetscRealPart(tt[0]) * ctx->v_0 * ctx->v_0 * m_s / n / 2;
288:         e_perp *= kev_joul * 1000; // eV
289:         if (grid == 0) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "step %4d) time= %e temperature (eV): ", (int)stepi, (double)time));
290:         PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%s T= %9.4e T_par= %9.4e T_perp= %9.4e ", (grid == 0) ? "electron:" : ";ion:", (double)energy, (double)e_par, (double)e_perp));
291:         if (n_cm3[grid] == 0) n_cm3[grid] = ctx->n_0 * n * 1e-6; // does not change m^3 --> cm^3
292:       }
293:       // cleanup
294:       PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, XsubArray));
295:       PetscCall(PetscFree(XsubArray));
296:     }
297:   }
298:   /* evolve NRL data, end line */
299:   if (n_cm3[NUM_TEMPS / 2 - 1] < 0 && ts_nrl) {
300:     PetscCall(TSDestroy(&ts_nrl));
301:     ctx->data = NULL;
302:     if (printing) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nSTOP printing NRL Ts\n"));
303:   } else if (ts_nrl) {
304:     const PetscScalar *x;
305:     PetscReal          dt_real, dt;
306:     Vec                U;
307:     PetscCall(TSGetTimeStep(ts, &dt)); // dt for NEXT time step
308:     dt_real = dt * ctx->t_0;
309:     PetscCall(TSGetSolution(ts_nrl, &U));
310:     if (printing) {
311:       PetscCall(VecGetArrayRead(U, &x));
312:       PetscCall(PetscPrintf(PETSC_COMM_WORLD, "NRL_i_par= %9.4e NRL_i_perp= %9.4e ", (double)PetscRealPart(x[I_PAR_IDX]), (double)PetscRealPart(x[I_PERP_IDX])));
313:       if (n_cm3[0] > 0) {
314:         PetscCall(PetscPrintf(PETSC_COMM_WORLD, "NRL_e_par= %9.4e NRL_e_perp= %9.4e\n", (double)PetscRealPart(x[E_PAR_IDX]), (double)PetscRealPart(x[E_PERP_IDX])));
315:       } else PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
316:       PetscCall(VecRestoreArrayRead(U, &x));
317:     }
318:     // we have the next time step, so need to advance now
319:     PetscCall(TSSetTimeStep(ts_nrl, dt_real));
320:     PetscCall(TSSetMaxSteps(ts_nrl, stepi + 1)); // next step
321:     PetscCall(TSSolve(ts_nrl, NULL));
322:   } else if (printing) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
323:   if (printing) { PetscCall(DMPlexLandauPrintNorms(X, stepi /*id + 1*/)); }

325:   PetscFunctionReturn(PETSC_SUCCESS);
326: }

328: int main(int argc, char **argv)
329: {
330:   DM          pack;
331:   Vec         X;
332:   PetscInt    dim = 2, nDMs;
333:   TS          ts, ts_nrl = NULL;
334:   Mat         J;
335:   Vec        *XsubArray = NULL;
336:   LandauCtx  *ctx;
337:   PetscMPIInt rank;
338:   PetscBool   use_nrl   = PETSC_TRUE;
339:   PetscBool   print_nrl = PETSC_FALSE;
340:   PetscReal   dt0;
341:   PetscFunctionBeginUser;
342:   PetscCall(PetscInitialize(&argc, &argv, NULL, help));
343:   PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
344:   if (rank) { /* turn off output stuff for duplicate runs */
345:     PetscCall(PetscOptionsClearValue(NULL, "-ex1_dm_view_e"));
346:     PetscCall(PetscOptionsClearValue(NULL, "-ex1_dm_view_i"));
347:     PetscCall(PetscOptionsClearValue(NULL, "-ex1_vec_view_e"));
348:     PetscCall(PetscOptionsClearValue(NULL, "-ex1_vec_view_i"));
349:     PetscCall(PetscOptionsClearValue(NULL, "-info"));
350:     PetscCall(PetscOptionsClearValue(NULL, "-snes_converged_reason"));
351:     PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_converged_reason"));
352:     PetscCall(PetscOptionsClearValue(NULL, "-ksp_converged_reason"));
353:     PetscCall(PetscOptionsClearValue(NULL, "-ts_adapt_monitor"));
354:     PetscCall(PetscOptionsClearValue(NULL, "-ts_monitor"));
355:     PetscCall(PetscOptionsClearValue(NULL, "-snes_monitor"));
356:   }
357:   PetscCall(PetscOptionsGetInt(NULL, NULL, "-dim", &dim, NULL));
358:   PetscCall(PetscOptionsGetBool(NULL, NULL, "-use_nrl", &use_nrl, NULL));
359:   PetscCall(PetscOptionsGetBool(NULL, NULL, "-print_nrl", &print_nrl, NULL));
360:   /* Create a mesh */
361:   PetscCall(DMPlexLandauCreateVelocitySpace(PETSC_COMM_SELF, dim, "", &X, &J, &pack));
362:   PetscCall(DMSetUp(pack));
363:   PetscCall(DMGetApplicationContext(pack, &ctx));
364:   PetscCheck(ctx->num_grids == 2, PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Must have two grids: use '-dm_landau_num_species_grid 1,1'");
365:   PetscCheck(ctx->num_species == 2, PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Must have two species: use '-dm_landau_num_species_grid 1,1'");
366:   PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
367:   /* output plot names */
368:   PetscCall(PetscMalloc(sizeof(*XsubArray) * nDMs, &XsubArray));
369:   PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, XsubArray)); // read only
370:   PetscCall(PetscObjectSetName((PetscObject)XsubArray[LAND_PACK_IDX(ctx->batch_view_idx, 0)], 0 == 0 ? "ue" : "ui"));
371:   PetscCall(PetscObjectSetName((PetscObject)XsubArray[LAND_PACK_IDX(ctx->batch_view_idx, 1)], 1 == 0 ? "ue" : "ui"));
372:   /* add bimaxwellian anisotropic test */
373:   for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
374:     for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
375:       PetscReal shifts[2];
376:       PetscCall(SetMaxwellians(ctx->plex[grid], XsubArray[LAND_PACK_IDX(b_id, grid)], 0.0, ctx->thermal_temps, ctx->n, grid, shifts, ctx));
377:     }
378:   }
379:   PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, XsubArray));
380:   PetscCall(PetscFree(XsubArray));
381:   /* plot */
382:   PetscCall(DMSetOutputSequenceNumber(ctx->plex[0], -1, 0.0));
383:   PetscCall(DMSetOutputSequenceNumber(ctx->plex[1], -1, 0.0));
384:   PetscCall(DMViewFromOptions(ctx->plex[0], NULL, "-ex1_dm_view_e"));
385:   PetscCall(DMViewFromOptions(ctx->plex[1], NULL, "-ex1_dm_view_i"));
386:   /* Create timestepping solver context */
387:   PetscCall(TSCreate(PETSC_COMM_SELF, &ts));
388:   PetscCall(TSSetDM(ts, pack));
389:   PetscCall(TSSetIFunction(ts, NULL, DMPlexLandauIFunction, NULL));
390:   PetscCall(TSSetIJacobian(ts, J, J, DMPlexLandauIJacobian, NULL));
391:   PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));
392:   PetscCall(TSSetFromOptions(ts));
393:   PetscCall(TSSetSolution(ts, X));
394:   PetscCall(TSMonitorSet(ts, Monitor, ctx, NULL));
395:   /* Create NRL timestepping */
396:   if (use_nrl || print_nrl) {
397:     Vec NRL_vec;
398:     PetscCall(createVec_NRL(ctx, &NRL_vec));
399:     PetscCall(createTS_NRL(ctx, NRL_vec));
400:     PetscCall(VecDestroy(&NRL_vec));
401:   } else ctx->data = NULL;
402:   /* solve */
403:   PetscCall(TSGetTimeStep(ts, &dt0));
404:   PetscCall(TSSetTime(ts, dt0 / 2));
405:   PetscCall(TSSolve(ts, X));
406:   /* test add field method & output */
407:   PetscCall(DMPlexLandauAccess(pack, X, landau_field_print_access_callback, NULL));
408:   // run NRL in separate TS
409:   ts_nrl = (TS)ctx->data;
410:   if (print_nrl) {
411:     PetscReal    finalTime, dt_real, tstart = dt0 * ctx->t_0 / 2; // hack
412:     Vec          U;
413:     PetscScalar *x;
414:     PetscInt     nsteps;
415:     dt_real = dt0 * ctx->t_0;
416:     PetscCall(TSSetTimeStep(ts_nrl, dt_real));
417:     PetscCall(TSGetTime(ts, &finalTime));
418:     finalTime *= ctx->t_0;
419:     PetscCall(TSSetMaxTime(ts_nrl, finalTime));
420:     nsteps = (PetscInt)(finalTime / dt_real) + 1;
421:     PetscCall(TSSetMaxSteps(ts_nrl, nsteps));
422:     PetscCall(TSSetStepNumber(ts_nrl, 0));
423:     PetscCall(TSSetTime(ts_nrl, tstart));
424:     PetscCall(TSGetSolution(ts_nrl, &U));
425:     PetscCall(VecGetArray(U, &x));
426:     for (PetscInt i = 0; i < NUM_TEMPS; i++) x[i] = T0[i];
427:     PetscCall(VecRestoreArray(U, &x));
428:     PetscCall(TSMonitorSet(ts_nrl, Monitor_nrl, ctx, NULL));
429:     PetscCall(TSSolve(ts_nrl, NULL));
430:   }
431:   /* clean up */
432:   PetscCall(TSDestroy(&ts));
433:   PetscCall(TSDestroy(&ts_nrl));
434:   PetscCall(VecDestroy(&X));
435:   PetscCall(DMPlexLandauDestroyVelocitySpace(&pack));
436:   PetscCall(PetscFinalize());
437:   return 0;
438: }

440: /*TEST
441:   testset:
442:     requires: p4est !complex double defined(PETSC_USE_DMLANDAU_2D)
443:     output_file: output/ex1_0.out
444:     filter: grep -v "DM"
445:     args: -dm_landau_amr_levels_max 0,2 -dm_landau_amr_post_refine 0 -dm_landau_amr_re_levels 2 -dm_landau_domain_radius 6,6 -dm_landau_electron_shift 1.5 -dm_landau_ion_charges 1 -dm_landau_ion_masses 2 -dm_landau_n 1,1 -dm_landau_n_0 1e20 -dm_landau_num_cells 2,4 -dm_landau_num_species_grid 1,1 -dm_landau_re_radius 2 -use_nrl true -print_nrl false -dm_landau_thermal_temps .3,.2 -dm_landau_type p4est -dm_landau_verbose -1 -dm_preallocate_only false -ex1_dm_view_e -ksp_type preonly -pc_type lu -petscspace_degree 3 -snes_converged_reason -snes_rtol 1.e-14 -snes_stol 1.e-14 -ts_adapt_clip .5,1.5 -ts_adapt_dt_max 5 -ts_adapt_monitor -ts_adapt_scale_solve_failed 0.5 -ts_arkimex_type 1bee -ts_dt .01 -ts_max_snes_failures -1 -ts_max_steps 1 -ts_max_time 8 -ts_monitor -ts_rtol 1e-2 -ts_type arkimex
446:     test:
447:       suffix: cpu
448:       args: -dm_landau_device_type cpu -dm_landau_use_relativistic_corrections
449:     test:
450:       suffix: kokkos
451:       requires: kokkos_kernels !defined(PETSC_HAVE_CUDA_CLANG)
452:       args: -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos

454:   testset:
455:     requires: !complex defined(PETSC_USE_DMLANDAU_2D) p4est
456:     args: -dm_landau_type p4est -dm_landau_num_species_grid 1,1 -dm_landau_n 1,1 -dm_landau_thermal_temps 2,1 -dm_landau_ion_charges 1 -dm_landau_ion_masses 2 -petscspace_degree 2 -ts_type beuler -ts_dt .1 -ts_max_steps 1 -dm_landau_verbose 2 -ksp_type preonly -pc_type lu -dm_landau_device_type cpu -use_nrl false -print_nrl -snes_rtol 1.e-14 -snes_stol 1.e-14 -snes_converged_reason -dm_landau_device_type cpu
457:     nsize: 1
458:     test:
459:       suffix: sphere
460:       args: -dm_landau_sphere -dm_landau_amr_levels_max 1,1 -dm_landau_sphere_inner_radius_90degree_scale .55 -dm_landau_sphere_inner_radius_45degree_scale .5
461:     test:
462:       suffix: re
463:       args: -dm_landau_num_cells 4,4 -dm_landau_amr_levels_max 0,2 -dm_landau_z_radius_pre 2.5 -dm_landau_z_radius_post 3.75 -dm_landau_amr_z_refine_pre 1 -dm_landau_amr_z_refine_post 1 -dm_landau_electron_shift 1.25 -info :vec

465: TEST*/