xref: /petsc/src/ts/utils/dmplexlandau/tutorials/ex2.c (revision 419c2fb8d764c7b6d5cfa75a78778d34da486dd3)
1e0eea495SMark static char help[] = "Runaway electron model with Landau collision operator\n\n";
2e0eea495SMark 
3e0eea495SMark #include <petscdmplex.h>
4e0eea495SMark #include <petsclandau.h>
5e0eea495SMark #include <petscts.h>
6e0eea495SMark #include <petscds.h>
78a6f2e61SMark Adams #include <petscdmcomposite.h>
8c3e4dd79SMark Adams #include "petsc/private/petscimpl.h"
9e0eea495SMark 
10*419c2fb8Smarkadams4 #if defined(PETSC_HAVE_CUDA_NVTX)
11*419c2fb8Smarkadams4 #include <nvToolsExt.h>
12*419c2fb8Smarkadams4 #endif
13*419c2fb8Smarkadams4 
14e0eea495SMark /* data for runaway electron model */
15e0eea495SMark typedef struct REctx_struct {
168a6f2e61SMark Adams   PetscErrorCode (*test)(TS, Vec, PetscInt, PetscReal, PetscBool,  LandauCtx *, struct REctx_struct *);
17e0eea495SMark   PetscErrorCode (*impuritySrcRate)(PetscReal, PetscReal *, LandauCtx*);
18e0eea495SMark   PetscErrorCode (*E)(Vec, Vec, PetscInt, PetscReal, LandauCtx*, PetscReal *);
19e0eea495SMark   PetscReal     T_cold;        /* temperature of newly ionized electrons and impurity ions */
20e0eea495SMark   PetscReal     ion_potential; /* ionization potential of impurity */
21e0eea495SMark   PetscReal     Ne_ion;        /* effective number of electrons shed in ioization of impurity */
22e0eea495SMark   PetscReal     Ez_initial;
23e0eea495SMark   PetscReal     L;             /* inductance */
24e0eea495SMark   Vec           X_0;
25e0eea495SMark   PetscInt      imp_idx;       /* index for impurity ionizing sink */
26e0eea495SMark   PetscReal     pulse_start;
27e0eea495SMark   PetscReal     pulse_width;
28e0eea495SMark   PetscReal     pulse_rate;
29e0eea495SMark   PetscReal     current_rate;
30e0eea495SMark   PetscInt      plotIdx;
31e0eea495SMark   PetscInt      plotStep;
32e0eea495SMark   PetscInt      idx; /* cache */
33e0eea495SMark   PetscReal     j; /* cache */
34e0eea495SMark   PetscReal     plotDt;
35e0eea495SMark   PetscBool     plotting;
36e0eea495SMark   PetscBool     use_spitzer_eta;
378a6f2e61SMark Adams   PetscInt      print_period;
388fdabdddSMark Adams   PetscInt      grid_view_idx;
39e0eea495SMark } REctx;
40e0eea495SMark 
41e0eea495SMark static const PetscReal kev_joul = 6.241506479963235e+15; /* 1/1000e */
42e0eea495SMark 
4390d163c9SMark Adams #define RE_CUT 3.
44e0eea495SMark /* < v, u_re * v * q > */
45e0eea495SMark static void f0_j_re(PetscInt dim, PetscInt Nf, PetscInt NfAux,
46e0eea495SMark                     const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
47e0eea495SMark                     const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
48e0eea495SMark                     PetscReal t, const PetscReal x[],  PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
49e0eea495SMark {
50e0eea495SMark   PetscReal n_e = PetscRealPart(u[0]);
51e0eea495SMark   if (dim==2) {
52e0eea495SMark     if (x[1] > RE_CUT || x[1] < -RE_CUT) { /* simply a cutoff for REs. v_|| > 3 v(T_e) */
53e0eea495SMark       *f0 = n_e * 2.*PETSC_PI*x[0] * x[1] * constants[0]; /* n * r * v_|| * q */
54e0eea495SMark     } else {
55e0eea495SMark       *f0 = 0;
56e0eea495SMark     }
57e0eea495SMark   } else {
58e0eea495SMark     if (x[2] > RE_CUT || x[2] < -RE_CUT) { /* simply a cutoff for REs. v_|| > 3 v(T_e) */
59e0eea495SMark       *f0 = n_e                * x[2] * constants[0];
60e0eea495SMark     } else {
61e0eea495SMark       *f0 = 0;
62e0eea495SMark     }
63e0eea495SMark   }
64e0eea495SMark }
65e0eea495SMark 
66e0eea495SMark /* sum < v, u*v*q > */
67e0eea495SMark static void f0_jz_sum(PetscInt dim, PetscInt Nf, PetscInt NfAux,
68e0eea495SMark                       const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
69e0eea495SMark                       const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
708a6f2e61SMark Adams                       PetscReal t, const PetscReal x[],  PetscInt numConstants, const PetscScalar q[], PetscScalar *f0)
71e0eea495SMark {
72e0eea495SMark   PetscInt ii;
73e0eea495SMark   f0[0] = 0;
74e0eea495SMark   if (dim==2) {
758a6f2e61SMark Adams     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 */
76e0eea495SMark   } else {
778a6f2e61SMark Adams     for (ii=0;ii<Nf;ii++) f0[0] += u[ii]                * x[2] * q[ii]; /* n * v_|| * q  * v_0 */
78e0eea495SMark   }
79e0eea495SMark }
80e0eea495SMark 
81e0eea495SMark /* < v, n_e > */
82e0eea495SMark static void f0_n(PetscInt dim, PetscInt Nf, PetscInt NfAux,
83e0eea495SMark                   const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
84e0eea495SMark                   const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
85e0eea495SMark                   PetscReal t, const PetscReal x[],  PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
86e0eea495SMark {
87e0eea495SMark   PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
88e0eea495SMark   if (dim==2) f0[0] = 2.*PETSC_PI*x[0]*u[ii];
89e0eea495SMark   else {
90e0eea495SMark     f0[0] =                        u[ii];
91e0eea495SMark   }
92e0eea495SMark }
93e0eea495SMark 
94e0eea495SMark /* < v, n_e v_|| > */
95e0eea495SMark static void f0_vz(PetscInt dim, PetscInt Nf, PetscInt NfAux,
96e0eea495SMark                    const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
97e0eea495SMark                    const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
98e0eea495SMark                    PetscReal t, const PetscReal x[],  PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
99e0eea495SMark {
100e0eea495SMark   PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
101e0eea495SMark   if (dim==2) f0[0] = u[ii] * 2.*PETSC_PI*x[0] * x[1]; /* n r v_|| */
102e0eea495SMark   else {
103e0eea495SMark     f0[0] =           u[ii] *                x[2]; /* n v_|| */
104e0eea495SMark   }
105e0eea495SMark }
106e0eea495SMark 
107e0eea495SMark /* < v, n_e (v-shift) > */
108e0eea495SMark static void f0_ve_shift(PetscInt dim, PetscInt Nf, PetscInt NfAux,
109e0eea495SMark                          const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
110e0eea495SMark                          const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
111e0eea495SMark                          PetscReal t, const PetscReal x[],  PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
112e0eea495SMark {
1138a6f2e61SMark Adams   PetscReal vz = numConstants>0 ? PetscRealPart(constants[0]) : 0;
114e0eea495SMark   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 */
115e0eea495SMark   else {
116e0eea495SMark     *f0 =           u[0] *                PetscSqrtReal(x[0]*x[0] + x[1]*x[1] + (x[2]-vz)*(x[2]-vz)); /* n v */
117e0eea495SMark   }
118e0eea495SMark }
119e0eea495SMark 
120e0eea495SMark  /* CalculateE - Calculate the electric field  */
121e0eea495SMark  /*  T        -- Electron temperature  */
122e0eea495SMark  /*  n        -- Electron density  */
123e0eea495SMark  /*  lnLambda --   */
124e0eea495SMark  /*  eps0     --  */
125e0eea495SMark  /*  E        -- output E, input \hat E */
126e0eea495SMark static PetscReal CalculateE(PetscReal Tev, PetscReal n, PetscReal lnLambda, PetscReal eps0, PetscReal *E)
127e0eea495SMark {
128e0eea495SMark   PetscReal c,e,m;
129e0eea495SMark 
130e0eea495SMark   PetscFunctionBegin;
131cefb98e8SMark Adams   c = 299792458.0;
132e0eea495SMark   e = 1.602176e-19;
133e0eea495SMark   m = 9.10938e-31;
134e0eea495SMark   if (1) {
135e0eea495SMark     double Ec, Ehat = *E, betath = PetscSqrtReal(2*Tev*e/(m*c*c)), j0 = Ehat * 7/(PetscSqrtReal(2)*2) * PetscPowReal(betath,3) * n * e * c;
136e0eea495SMark     Ec = n*lnLambda*PetscPowReal(e,3) / (4*PETSC_PI*PetscPowReal(eps0,2)*m*c*c);
137e0eea495SMark     *E = Ec;
138e0eea495SMark     PetscPrintf(PETSC_COMM_WORLD, "CalculateE j0=%g Ec = %g\n",j0,Ec);
139e0eea495SMark   } else {
140e0eea495SMark     PetscReal Ed, vth;
141e0eea495SMark     vth = PetscSqrtReal(8*Tev*e/(m*PETSC_PI));
142e0eea495SMark     Ed =  n*lnLambda*PetscPowReal(e,3) / (4*PETSC_PI*PetscPowReal(eps0,2)*m*vth*vth);
143e0eea495SMark     *E = Ed;
144e0eea495SMark   }
145e0eea495SMark   PetscFunctionReturn(0);
146e0eea495SMark }
147e0eea495SMark 
148e0eea495SMark static PetscReal Spitzer(PetscReal m_e, PetscReal e, PetscReal Z, PetscReal epsilon0,  PetscReal lnLam, PetscReal kTe_joules)
149e0eea495SMark {
150e0eea495SMark   PetscReal Fz = (1+1.198*Z+0.222*Z*Z)/(1+2.966*Z+0.753*Z*Z), eta;
151e0eea495SMark   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);
152e0eea495SMark   return eta;
153e0eea495SMark }
154e0eea495SMark 
155e0eea495SMark /*  */
1568a6f2e61SMark Adams static PetscErrorCode testNone(TS ts, Vec X, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx)
157e0eea495SMark {
158e0eea495SMark   PetscFunctionBeginUser;
159e0eea495SMark   PetscFunctionReturn(0);
160e0eea495SMark }
161e0eea495SMark 
162e0eea495SMark /*  */
1638a6f2e61SMark Adams static PetscErrorCode testSpitzer(TS ts, Vec X, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx)
164e0eea495SMark {
165f37ccb5fSMark Adams   PetscInt          ii,nDMs;
166e0eea495SMark   PetscDS           prob;
167a587d139SMark   static PetscReal  old_ratio = 1e10;
168a587d139SMark   TSConvergedReason reason;
169a587d139SMark   PetscReal         J,J_re,spit_eta,Te_kev=0,E,ratio,Z,n_e,v,v2;
1708a6f2e61SMark Adams   PetscScalar       user[2] = {0.,ctx->charges[0]}, q[LANDAU_MAX_SPECIES],tt[LANDAU_MAX_SPECIES],vz;
171930e68a5SMark Adams   PetscReal         dt;
1728a6f2e61SMark Adams   DM                pack, plexe = ctx->plex[0], plexi = (ctx->num_grids==1) ? NULL : ctx->plex[1];
173f37ccb5fSMark Adams   Vec               *XsubArray;
174e0eea495SMark 
175e0eea495SMark   PetscFunctionBeginUser;
17663a3b9bcSJacob Faibussowitsch   PetscCheck(ctx->num_species==2,PETSC_COMM_SELF, PETSC_ERR_PLIB, "ctx->num_species %" PetscInt_FMT " != 2",ctx->num_species);
1779566063dSJacob Faibussowitsch   PetscCall(VecGetDM(X, &pack));
1783c633725SBarry Smith   PetscCheck(pack,PETSC_COMM_SELF, PETSC_ERR_PLIB, "no DM");
1799566063dSJacob Faibussowitsch   PetscCall(DMCompositeGetNumberDM(pack,&nDMs));
18063a3b9bcSJacob Faibussowitsch   PetscCheck(nDMs == ctx->num_grids*ctx->batch_sz,PETSC_COMM_SELF, PETSC_ERR_PLIB, "nDMs != ctx->num_grids*ctx->batch_sz %" PetscInt_FMT " != %" PetscInt_FMT,nDMs,ctx->num_grids*ctx->batch_sz);
1819566063dSJacob Faibussowitsch   PetscCall(PetscMalloc(sizeof(*XsubArray)*nDMs, &XsubArray));
1829566063dSJacob Faibussowitsch   PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, XsubArray)); // read only
1839566063dSJacob Faibussowitsch   PetscCall(TSGetTimeStep(ts,&dt));
1848a6f2e61SMark Adams   /* get current for each grid */
1858a6f2e61SMark Adams   for (ii=0;ii<ctx->num_species;ii++) q[ii] = ctx->charges[ii];
1869566063dSJacob Faibussowitsch   PetscCall(DMGetDS(plexe, &prob));
1879566063dSJacob Faibussowitsch   PetscCall(PetscDSSetConstants(prob, 2, &q[0]));
1889566063dSJacob Faibussowitsch   PetscCall(PetscDSSetObjective(prob, 0, &f0_jz_sum));
1899566063dSJacob Faibussowitsch   PetscCall(DMPlexComputeIntegralFEM(plexe,XsubArray[ LAND_PACK_IDX(ctx->batch_view_idx,0) ],tt,NULL));
190e0eea495SMark   J = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]);
1918fdabdddSMark Adams   if (plexi) { // add first (only) ion
1929566063dSJacob Faibussowitsch     PetscCall(DMGetDS(plexi, &prob));
1939566063dSJacob Faibussowitsch     PetscCall(PetscDSSetConstants(prob, 1, &q[1]));
1949566063dSJacob Faibussowitsch     PetscCall(PetscDSSetObjective(prob, 0, &f0_jz_sum));
1959566063dSJacob Faibussowitsch     PetscCall(DMPlexComputeIntegralFEM(plexi,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,1)],tt,NULL));
1968a6f2e61SMark Adams     J += -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]);
1978a6f2e61SMark Adams   }
198a587d139SMark   /* get N_e */
1999566063dSJacob Faibussowitsch   PetscCall(DMGetDS(plexe, &prob));
2009566063dSJacob Faibussowitsch   PetscCall(PetscDSSetConstants(prob, 1, user));
2019566063dSJacob Faibussowitsch   PetscCall(PetscDSSetObjective(prob, 0, &f0_n));
2029566063dSJacob Faibussowitsch   PetscCall(DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL));
203a587d139SMark   n_e = PetscRealPart(tt[0])*ctx->n_0;
204a587d139SMark   /* Z */
205a587d139SMark   Z = -ctx->charges[1]/ctx->charges[0];
206a587d139SMark   /* remove drift */
2078a6f2e61SMark Adams   if (0) {
2088a6f2e61SMark Adams     user[0] = 0; // electrons
2099566063dSJacob Faibussowitsch     PetscCall(DMGetDS(plexe, &prob));
2109566063dSJacob Faibussowitsch     PetscCall(PetscDSSetConstants(prob, 1, user));
2119566063dSJacob Faibussowitsch     PetscCall(PetscDSSetObjective(prob, 0, &f0_vz));
2129566063dSJacob Faibussowitsch     PetscCall(DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL));
213a587d139SMark     vz = ctx->n_0*PetscRealPart(tt[0])/n_e; /* non-dimensional */
214a587d139SMark   } else vz = 0;
215a587d139SMark   /* thermal velocity */
2169566063dSJacob Faibussowitsch   PetscCall(DMGetDS(plexe, &prob));
2179566063dSJacob Faibussowitsch   PetscCall(PetscDSSetConstants(prob, 1, &vz));
2189566063dSJacob Faibussowitsch   PetscCall(PetscDSSetObjective(prob, 0, &f0_ve_shift));
2199566063dSJacob Faibussowitsch   PetscCall(DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL));
220a587d139SMark   v = ctx->n_0*ctx->v_0*PetscRealPart(tt[0])/n_e;   /* remove number density to get velocity */
221a587d139SMark   v2 = PetscSqr(v);                                    /* use real space: m^2 / s^2 */
222a587d139SMark   Te_kev = (v2*ctx->masses[0]*PETSC_PI/8)*kev_joul;    /* temperature in kev */
223a587d139SMark   spit_eta = Spitzer(ctx->masses[0],-ctx->charges[0],Z,ctx->epsilon0,ctx->lnLam,Te_kev/kev_joul); /* kev --> J (kT) */
2248a6f2e61SMark Adams   if (0) {
2259566063dSJacob Faibussowitsch     PetscCall(DMGetDS(plexe, &prob));
2269566063dSJacob Faibussowitsch     PetscCall(PetscDSSetConstants(prob, 1, q));
2279566063dSJacob Faibussowitsch     PetscCall(PetscDSSetObjective(prob, 0, &f0_j_re));
2289566063dSJacob Faibussowitsch     PetscCall(DMPlexComputeIntegralFEM(plexe,XsubArray[LAND_PACK_IDX(ctx->batch_view_idx,0)],tt,NULL));
229a587d139SMark   } else tt[0] = 0;
230e0eea495SMark   J_re = -ctx->n_0*ctx->v_0*PetscRealPart(tt[0]);
2319566063dSJacob Faibussowitsch   PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, XsubArray)); // read only
2329566063dSJacob Faibussowitsch   PetscCall(PetscFree(XsubArray));
233a587d139SMark 
23490d163c9SMark Adams   if (rectx->use_spitzer_eta) {
23590d163c9SMark Adams     E = ctx->Ez = spit_eta*(rectx->j-J_re);
23690d163c9SMark Adams   } else {
23790d163c9SMark Adams     E = ctx->Ez; /* keep real E */
23890d163c9SMark Adams     rectx->j = J; /* cache */
23990d163c9SMark Adams   }
24090d163c9SMark Adams 
241e0eea495SMark   ratio = E/J/spit_eta;
2428a6f2e61SMark Adams   if (stepi>10 && !rectx->use_spitzer_eta && (
2438a6f2e61SMark Adams         (old_ratio-ratio < 1.e-6))) {
24490d163c9SMark Adams     rectx->pulse_start = time + 0.98*dt;
245a587d139SMark     rectx->use_spitzer_eta = PETSC_TRUE;
246a587d139SMark   }
2479566063dSJacob Faibussowitsch   PetscCall(TSGetConvergedReason(ts,&reason));
2489566063dSJacob Faibussowitsch   PetscCall(TSGetConvergedReason(ts,&reason));
24990d163c9SMark Adams   if ((rectx->plotting) || stepi == 0 || reason || rectx->pulse_start == time + 0.98*dt) {
25063a3b9bcSJacob Faibussowitsch     PetscCall(PetscPrintf(ctx->comm, "testSpitzer: %4" PetscInt_FMT ") 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,(double)time,(double)(n_e/ctx->n_0),(double)ctx->Ez,(double)J,(double)J_re,(double)(100*J_re/J),(double)Te_kev,(double)Z,(double)ratio,(double)(old_ratio-ratio), rectx->use_spitzer_eta ? "using Spitzer eta*J E" : "constant E",rectx->pulse_start != time + 0.98*dt ? "normal" : "transition",(double)spit_eta));
25163a3b9bcSJacob Faibussowitsch     PetscCheck(rectx->pulse_start != (time + 0.98*dt),PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Spitzer complete ratio=%g",(double)ratio);
252930e68a5SMark Adams   }
253e0eea495SMark   old_ratio = ratio;
254e0eea495SMark   PetscFunctionReturn(0);
255e0eea495SMark }
256e0eea495SMark 
257e0eea495SMark static const double ppp = 2;
258e0eea495SMark static void f0_0_diff_lp(PetscInt dim, PetscInt Nf, PetscInt NfAux,
259e0eea495SMark                           const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
260e0eea495SMark                           const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
261e0eea495SMark                           PetscReal t, const PetscReal x[],  PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
262e0eea495SMark {
263e0eea495SMark   LandauCtx       *ctx = (LandauCtx *)constants;
264e0eea495SMark   REctx           *rectx = (REctx*)ctx->data;
265e0eea495SMark   PetscInt        ii = rectx->idx, i;
266e0eea495SMark   const PetscReal kT_m = ctx->k*ctx->thermal_temps[ii]/ctx->masses[ii]; /* kT/m */
267e0eea495SMark   const PetscReal n = ctx->n[ii];
268e0eea495SMark   PetscReal       diff, f_maxwell, v2 = 0, theta = 2*kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */
269e0eea495SMark   for (i = 0; i < dim; ++i) v2 += x[i]*x[i];
270e0eea495SMark   f_maxwell = n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta));
271e0eea495SMark   diff = 2.*PETSC_PI*x[0]*(PetscRealPart(u[ii]) - f_maxwell);
272e0eea495SMark   f0[0] = PetscPowReal(diff,ppp);
273e0eea495SMark }
274e0eea495SMark static void f0_0_maxwellian_lp(PetscInt dim, PetscInt Nf, PetscInt NfAux,
275e0eea495SMark                           const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
276e0eea495SMark                           const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
277e0eea495SMark                           PetscReal t, const PetscReal x[],  PetscInt numConstants, const PetscScalar constants[], PetscScalar *f0)
278e0eea495SMark {
279e0eea495SMark   LandauCtx       *ctx = (LandauCtx *)constants;
280e0eea495SMark   REctx           *rectx = (REctx*)ctx->data;
281e0eea495SMark   PetscInt        ii = rectx->idx, i;
282e0eea495SMark   const PetscReal kT_m = ctx->k*ctx->thermal_temps[ii]/ctx->masses[ii]; /* kT/m */
283e0eea495SMark   const PetscReal n = ctx->n[ii];
284e0eea495SMark   PetscReal       f_maxwell, v2 = 0, theta = 2*kT_m/(ctx->v_0*ctx->v_0); /* theta = 2kT/mc^2 */
285e0eea495SMark   for (i = 0; i < dim; ++i) v2 += x[i]*x[i];
286e0eea495SMark   f_maxwell = 2.*PETSC_PI*x[0] * n*PetscPowReal(PETSC_PI*theta,-1.5)*(PetscExpReal(-v2/theta));
287e0eea495SMark   f0[0] = PetscPowReal(f_maxwell,ppp);
288e0eea495SMark }
289e0eea495SMark 
290e0eea495SMark /*  */
2918a6f2e61SMark Adams static PetscErrorCode testStable(TS ts, Vec X, PetscInt stepi, PetscReal time, PetscBool islast, LandauCtx *ctx, REctx *rectx)
292e0eea495SMark {
293e0eea495SMark   PetscDS           prob;
294e0eea495SMark   Vec               X2;
295e0eea495SMark   PetscReal         ediff,idiff=0,lpm0,lpm1=1;
296e0eea495SMark   PetscScalar       tt[LANDAU_MAX_SPECIES];
2978a6f2e61SMark Adams   DM                dm, plex = ctx->plex[0];
298e0eea495SMark 
299e0eea495SMark   PetscFunctionBeginUser;
3009566063dSJacob Faibussowitsch   PetscCall(VecGetDM(X, &dm));
3019566063dSJacob Faibussowitsch   PetscCall(DMGetDS(plex, &prob));
3029566063dSJacob Faibussowitsch   PetscCall(VecDuplicate(X,&X2));
3039566063dSJacob Faibussowitsch   PetscCall(VecCopy(X,X2));
304e0eea495SMark   if (!rectx->X_0) {
3059566063dSJacob Faibussowitsch     PetscCall(VecDuplicate(X,&rectx->X_0));
3069566063dSJacob Faibussowitsch     PetscCall(VecCopy(X,rectx->X_0));
307e0eea495SMark   }
3089566063dSJacob Faibussowitsch   PetscCall(VecAXPY(X,-1.0,rectx->X_0));
3099566063dSJacob Faibussowitsch   PetscCall(PetscDSSetConstants(prob, sizeof(LandauCtx)/sizeof(PetscScalar), (PetscScalar*)ctx));
310e0eea495SMark   rectx->idx = 0;
3119566063dSJacob Faibussowitsch   PetscCall(PetscDSSetObjective(prob, 0, &f0_0_diff_lp));
3129566063dSJacob Faibussowitsch   PetscCall(DMPlexComputeIntegralFEM(plex,X2,tt,NULL));
313e0eea495SMark   ediff = PetscPowReal(PetscRealPart(tt[0]),1./ppp);
3149566063dSJacob Faibussowitsch   PetscCall(PetscDSSetObjective(prob, 0, &f0_0_maxwellian_lp));
3159566063dSJacob Faibussowitsch   PetscCall(DMPlexComputeIntegralFEM(plex,X2,tt,NULL));
316e0eea495SMark   lpm0 = PetscPowReal(PetscRealPart(tt[0]),1./ppp);
317e0eea495SMark   if (ctx->num_species>1) {
318e0eea495SMark     rectx->idx = 1;
3199566063dSJacob Faibussowitsch     PetscCall(PetscDSSetObjective(prob, 0, &f0_0_diff_lp));
3209566063dSJacob Faibussowitsch     PetscCall(DMPlexComputeIntegralFEM(plex,X2,tt,NULL));
321e0eea495SMark     idiff = PetscPowReal(PetscRealPart(tt[0]),1./ppp);
3229566063dSJacob Faibussowitsch     PetscCall(PetscDSSetObjective(prob, 0, &f0_0_maxwellian_lp));
3239566063dSJacob Faibussowitsch     PetscCall(DMPlexComputeIntegralFEM(plex,X2,tt,NULL));
324e0eea495SMark     lpm1 = PetscPowReal(PetscRealPart(tt[0]),1./ppp);
325e0eea495SMark   }
32663a3b9bcSJacob Faibussowitsch   PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%s %" PetscInt_FMT ") time=%10.3e n-%d norm electrons/max=%20.13e ions/max=%20.13e\n", "----",stepi,(double)time,(int)ppp,(double)(ediff/lpm0),(double)(idiff/lpm1)));
327e0eea495SMark   /* view */
3289566063dSJacob Faibussowitsch   PetscCall(VecCopy(X2,X));
3299566063dSJacob Faibussowitsch   PetscCall(VecDestroy(&X2));
330e0eea495SMark   if (islast) {
3319566063dSJacob Faibussowitsch     PetscCall(VecDestroy(&rectx->X_0));
332e0eea495SMark     rectx->X_0 = NULL;
333e0eea495SMark   }
334e0eea495SMark   PetscFunctionReturn(0);
335e0eea495SMark }
336e0eea495SMark 
337e0eea495SMark static PetscErrorCode EInduction(Vec X, Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E)
338e0eea495SMark {
339e0eea495SMark   REctx             *rectx = (REctx*)ctx->data;
340e0eea495SMark   PetscInt          ii;
341e0eea495SMark   DM                dm,plex;
3428a6f2e61SMark Adams   PetscScalar       tt[LANDAU_MAX_SPECIES], qv0[LANDAU_MAX_SPECIES];
343e0eea495SMark   PetscReal         dJ_dt;
344e0eea495SMark   PetscDS           prob;
345e0eea495SMark 
346e0eea495SMark   PetscFunctionBeginUser;
3478a6f2e61SMark Adams   for (ii=0;ii<ctx->num_species;ii++) qv0[ii] = ctx->charges[ii]*ctx->v_0;
3489566063dSJacob Faibussowitsch   PetscCall(VecGetDM(X, &dm));
3499566063dSJacob Faibussowitsch   PetscCall(DMGetDS(dm, &prob));
3509566063dSJacob Faibussowitsch   PetscCall(DMConvert(dm, DMPLEX, &plex));
351e0eea495SMark   /* get d current / dt */
3529566063dSJacob Faibussowitsch   PetscCall(PetscDSSetConstants(prob, ctx->num_species, qv0));
3539566063dSJacob Faibussowitsch   PetscCall(PetscDSSetObjective(prob, 0, &f0_jz_sum));
3543c633725SBarry Smith   PetscCheck(X_t,PETSC_COMM_SELF, PETSC_ERR_PLIB, "X_t");
3559566063dSJacob Faibussowitsch   PetscCall(DMPlexComputeIntegralFEM(plex,X_t,tt,NULL));
3568a6f2e61SMark Adams   dJ_dt = -ctx->n_0*PetscRealPart(tt[0])/ctx->t_0;
357e0eea495SMark   /* E induction */
358e0eea495SMark   *a_E = -rectx->L*dJ_dt + rectx->Ez_initial;
3599566063dSJacob Faibussowitsch   PetscCall(DMDestroy(&plex));
360e0eea495SMark   PetscFunctionReturn(0);
361e0eea495SMark }
362e0eea495SMark 
363e0eea495SMark static PetscErrorCode EConstant(Vec X,  Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E)
364e0eea495SMark {
365e0eea495SMark   PetscFunctionBeginUser;
366e0eea495SMark   *a_E = ctx->Ez;
367e0eea495SMark   PetscFunctionReturn(0);
368e0eea495SMark }
369e0eea495SMark 
370e0eea495SMark static PetscErrorCode ENone(Vec X,  Vec X_t, PetscInt step, PetscReal time, LandauCtx *ctx, PetscReal *a_E)
371e0eea495SMark {
372e0eea495SMark   PetscFunctionBeginUser;
373e0eea495SMark   *a_E = 0;
374e0eea495SMark   PetscFunctionReturn(0);
375e0eea495SMark }
376e0eea495SMark 
377e0eea495SMark /* ------------------------------------------------------------------- */
378e0eea495SMark /*
379e0eea495SMark    FormSource - Evaluates source terms F(t).
380e0eea495SMark 
381e0eea495SMark    Input Parameters:
382e0eea495SMark .  ts - the TS context
383e0eea495SMark .  time -
384e0eea495SMark .  X_dummmy - input vector
385e0eea495SMark .  dummy - optional user-defined context, as set by SNESSetFunction()
386e0eea495SMark 
387e0eea495SMark    Output Parameter:
388e0eea495SMark .  F - function vector
389e0eea495SMark  */
390e0eea495SMark static PetscErrorCode FormSource(TS ts, PetscReal ftime, Vec X_dummmy, Vec F, void *dummy)
391e0eea495SMark {
392e0eea495SMark   PetscReal      new_imp_rate;
393e0eea495SMark   LandauCtx      *ctx;
3948a6f2e61SMark Adams   DM             pack;
395e0eea495SMark   REctx          *rectx;
396e0eea495SMark 
397e0eea495SMark   PetscFunctionBeginUser;
3989566063dSJacob Faibussowitsch   PetscCall(TSGetDM(ts,&pack));
3999566063dSJacob Faibussowitsch   PetscCall(DMGetApplicationContext(pack, &ctx));
400e0eea495SMark   rectx = (REctx*)ctx->data;
401e0eea495SMark   /* check for impurities */
4029566063dSJacob Faibussowitsch   PetscCall(rectx->impuritySrcRate(ftime,&new_imp_rate,ctx));
403e0eea495SMark   if (new_imp_rate != 0) {
404e0eea495SMark     if (new_imp_rate != rectx->current_rate) {
405e0eea495SMark       PetscInt       ii;
406e0eea495SMark       PetscReal      dne_dt,dni_dt,tilda_ns[LANDAU_MAX_SPECIES],temps[LANDAU_MAX_SPECIES];
4078fdabdddSMark Adams       Vec            globFarray[LANDAU_MAX_GRIDS*LANDAU_MAX_BATCH_SZ];
408e0eea495SMark       rectx->current_rate = new_imp_rate;
409e0eea495SMark       for (ii=1;ii<LANDAU_MAX_SPECIES;ii++) tilda_ns[ii] = 0;
410e0eea495SMark       for (ii=1;ii<LANDAU_MAX_SPECIES;ii++)    temps[ii] = 1;
4118a6f2e61SMark Adams       dni_dt = new_imp_rate               /* *ctx->t_0 */; /* fully ionized immediately, no normalize, stay in non-dim */
4128a6f2e61SMark Adams       dne_dt = new_imp_rate*rectx->Ne_ion /* *ctx->t_0 */;
413e0eea495SMark       tilda_ns[0] = dne_dt;        tilda_ns[rectx->imp_idx] = dni_dt;
414e0eea495SMark       temps[0]    = rectx->T_cold;    temps[rectx->imp_idx] = rectx->T_cold;
41563a3b9bcSJacob Faibussowitsch       PetscCall(PetscInfo(ctx->plex[0], "\tHave new_imp_rate= %10.3e time= %10.3e de/dt= %10.3e di/dt= %10.3e ***\n",(double)new_imp_rate,(double)ftime,(double)dne_dt,(double)dni_dt));
4169566063dSJacob Faibussowitsch       PetscCall(DMCompositeGetAccessArray(pack, F, ctx->num_grids*ctx->batch_sz, NULL, globFarray));
4178a6f2e61SMark Adams       for (PetscInt grid=0 ; grid<ctx->num_grids ; grid++) {
418e0eea495SMark         /* add it */
419c3e4dd79SMark Adams         PetscCall(DMPlexLandauAddMaxwellians(ctx->plex[grid],globFarray[ LAND_PACK_IDX(0,grid) ],ftime,temps,tilda_ns,grid,0,1,ctx));
420e0eea495SMark       }
4218fdabdddSMark Adams       // Does DMCompositeRestoreAccessArray copy the data back? (no)
4229566063dSJacob Faibussowitsch       PetscCall(DMCompositeRestoreAccessArray(pack, F, ctx->num_grids*ctx->batch_sz, NULL, globFarray));
423e0eea495SMark     }
424e0eea495SMark   } else {
4259566063dSJacob Faibussowitsch     PetscCall(VecZeroEntries(F));
426e0eea495SMark     rectx->current_rate = 0;
427e0eea495SMark   }
428e0eea495SMark   PetscFunctionReturn(0);
429e0eea495SMark }
430*419c2fb8Smarkadams4 
431e0eea495SMark PetscErrorCode Monitor(TS ts, PetscInt stepi, PetscReal time, Vec X, void *actx)
432e0eea495SMark {
433e0eea495SMark   LandauCtx         *ctx = (LandauCtx*) actx;   /* user-defined application context */
434e0eea495SMark   REctx             *rectx = (REctx*)ctx->data;
435*419c2fb8Smarkadams4   DM                pack=NULL;
4368fdabdddSMark Adams   Vec               globXArray[LANDAU_MAX_GRIDS*LANDAU_MAX_BATCH_SZ];
437e0eea495SMark   TSConvergedReason reason;
438*419c2fb8Smarkadams4 
439e0eea495SMark   PetscFunctionBeginUser;
440*419c2fb8Smarkadams4   PetscCall(TSGetConvergedReason(ts,&reason));
441*419c2fb8Smarkadams4   if (rectx->grid_view_idx != -1 || (reason && ctx->verbose > 3)) {
4429566063dSJacob Faibussowitsch     PetscCall(VecGetDM(X, &pack));
4439566063dSJacob Faibussowitsch     PetscCall(DMCompositeGetAccessArray(pack, X, ctx->num_grids*ctx->batch_sz, NULL, globXArray));
444*419c2fb8Smarkadams4   }
445e0eea495SMark   if (stepi > rectx->plotStep && rectx->plotting) {
446e0eea495SMark     rectx->plotting = PETSC_FALSE; /* was doing diagnostics, now done */
447e0eea495SMark     rectx->plotIdx++;
448e0eea495SMark   }
449e0eea495SMark   /* view */
450e0eea495SMark   if (time/rectx->plotDt >= (PetscReal)rectx->plotIdx || reason) {
451c3e4dd79SMark Adams     if ((reason || stepi==0 || rectx->plotIdx%rectx->print_period==0) && ctx->verbose > 1) {
452e0eea495SMark       /* print norms */
4539566063dSJacob Faibussowitsch       PetscCall(DMPlexLandauPrintNorms(X, stepi));
454a587d139SMark     }
455930e68a5SMark Adams     if (!rectx->plotting) { /* first step of possible backtracks */
456930e68a5SMark Adams       rectx->plotting = PETSC_TRUE;
457930e68a5SMark Adams       /* diagnostics + change E field with Sptizer (not just a monitor) */
4589566063dSJacob Faibussowitsch       PetscCall(rectx->test(ts,X,stepi,time,reason ? PETSC_TRUE : PETSC_FALSE, ctx, rectx));
459930e68a5SMark Adams     } else {
460930e68a5SMark Adams       PetscPrintf(PETSC_COMM_WORLD, "\t\t ERROR SKIP test spit ------\n");
461930e68a5SMark Adams       rectx->plotting = PETSC_TRUE;
462930e68a5SMark Adams     }
463*419c2fb8Smarkadams4     if (rectx->grid_view_idx != -1) {
4649566063dSJacob Faibussowitsch       PetscCall(PetscObjectSetName((PetscObject) globXArray[ LAND_PACK_IDX(ctx->batch_view_idx,rectx->grid_view_idx) ], rectx->grid_view_idx==0 ? "ue" : "ui"));
465930e68a5SMark Adams       /* view, overwrite step when back tracked */
4669566063dSJacob Faibussowitsch       PetscCall(DMSetOutputSequenceNumber(pack, rectx->plotIdx, time*ctx->t_0));
467*419c2fb8Smarkadams4       PetscCall(VecViewFromOptions(globXArray[ LAND_PACK_IDX(ctx->batch_view_idx, rectx->grid_view_idx) ],NULL,"-ex2_vec_view"));
468*419c2fb8Smarkadams4     }
469e0eea495SMark     rectx->plotStep = stepi;
470930e68a5SMark Adams   } else {
47163a3b9bcSJacob Faibussowitsch     if (rectx->plotting) PetscPrintf(PETSC_COMM_WORLD," ERROR rectx->plotting=%s step %" PetscInt_FMT "\n",PetscBools[rectx->plotting],stepi);
472930e68a5SMark Adams     /* diagnostics + change E field with Sptizer (not just a monitor) - can we lag this? */
4739566063dSJacob Faibussowitsch     PetscCall(rectx->test(ts,X,stepi,time,reason ? PETSC_TRUE : PETSC_FALSE, ctx, rectx));
474e0eea495SMark   }
475f37ccb5fSMark Adams   /* parallel check that only works of all batches are identical */
476f37ccb5fSMark Adams   if (reason && ctx->verbose > 3) {
477e0eea495SMark     PetscReal    val,rval;
478e0eea495SMark     PetscMPIInt  rank;
4799566063dSJacob Faibussowitsch     PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
480f37ccb5fSMark Adams     for (PetscInt grid=0;grid<ctx->num_grids;grid++) {
481f37ccb5fSMark Adams       PetscInt nerrors=0;
482f37ccb5fSMark Adams       for (PetscInt i=0; i<ctx->batch_sz;i++) {
4839566063dSJacob Faibussowitsch         PetscCall(VecNorm(globXArray[ LAND_PACK_IDX(i,grid) ],NORM_2,&val));
484f37ccb5fSMark Adams         if (i==0) rval = val;
485f37ccb5fSMark Adams         else if ((val=PetscAbs(val-rval)/rval) > 1000*PETSC_MACHINE_EPSILON) {
48663a3b9bcSJacob Faibussowitsch           PetscCall(PetscPrintf(PETSC_COMM_SELF, " [%d] Warning %" PetscInt_FMT ".%" PetscInt_FMT ") diff = %2.15e\n",rank,grid,i,(double)val));
487f37ccb5fSMark Adams           nerrors++;
488f37ccb5fSMark Adams         }
489f37ccb5fSMark Adams       }
490f37ccb5fSMark Adams       if (nerrors) {
49163a3b9bcSJacob Faibussowitsch         PetscCall(PetscPrintf(PETSC_COMM_SELF, " ***** [%d] ERROR max %" PetscInt_FMT " errors\n",rank,nerrors));
492e0eea495SMark       } else {
49363a3b9bcSJacob Faibussowitsch         PetscCall(PetscPrintf(PETSC_COMM_WORLD, "[%d] %" PetscInt_FMT ") batch consistency check OK\n",rank,grid));
494f37ccb5fSMark Adams       }
495e0eea495SMark     }
496e0eea495SMark   }
497e0eea495SMark   rectx->idx = 0;
498*419c2fb8Smarkadams4   if (rectx->grid_view_idx != -1 || (reason && ctx->verbose > 3)) {
4999566063dSJacob Faibussowitsch     PetscCall(DMCompositeRestoreAccessArray(pack, X, ctx->num_grids*ctx->batch_sz, NULL, globXArray));
500*419c2fb8Smarkadams4   }
501e0eea495SMark   PetscFunctionReturn(0);
502e0eea495SMark }
503e0eea495SMark 
504e0eea495SMark PetscErrorCode PreStep(TS ts)
505e0eea495SMark {
506e0eea495SMark   LandauCtx      *ctx;
507e0eea495SMark   REctx          *rectx;
508e0eea495SMark   DM             dm;
509e0eea495SMark   PetscInt       stepi;
510e0eea495SMark   PetscReal      time;
511e0eea495SMark   Vec            X;
512e0eea495SMark 
513e0eea495SMark   PetscFunctionBeginUser;
514930e68a5SMark Adams   /* not used */
5159566063dSJacob Faibussowitsch   PetscCall(TSGetDM(ts,&dm));
5169566063dSJacob Faibussowitsch   PetscCall(TSGetTime(ts,&time));
5179566063dSJacob Faibussowitsch   PetscCall(TSGetSolution(ts,&X));
5189566063dSJacob Faibussowitsch   PetscCall(DMGetApplicationContext(dm, &ctx));
519e0eea495SMark   rectx = (REctx*)ctx->data;
5209566063dSJacob Faibussowitsch   PetscCall(TSGetStepNumber(ts, &stepi));
521e0eea495SMark   /* update E */
5229566063dSJacob Faibussowitsch   PetscCall(rectx->E(X, NULL, stepi, time, ctx, &ctx->Ez));
523e0eea495SMark   PetscFunctionReturn(0);
524e0eea495SMark }
525e0eea495SMark 
526e0eea495SMark /* 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) */
527e0eea495SMark static PetscErrorCode stepSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx)
528e0eea495SMark {
529e0eea495SMark   REctx         *rectx = (REctx*)ctx->data;
530e0eea495SMark 
531e0eea495SMark   PetscFunctionBeginUser;
532e0eea495SMark   if (time >= rectx->pulse_start) *rho = rectx->pulse_rate;
533e0eea495SMark   else *rho = 0.;
534e0eea495SMark   PetscFunctionReturn(0);
535e0eea495SMark }
536e0eea495SMark static PetscErrorCode zeroSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx)
537e0eea495SMark {
538e0eea495SMark   PetscFunctionBeginUser;
539e0eea495SMark   *rho = 0.;
540e0eea495SMark   PetscFunctionReturn(0);
541e0eea495SMark }
542e0eea495SMark static PetscErrorCode pulseSrc(PetscReal time, PetscReal *rho, LandauCtx *ctx)
543e0eea495SMark {
544e0eea495SMark   REctx *rectx = (REctx*)ctx->data;
545e0eea495SMark 
546e0eea495SMark   PetscFunctionBeginUser;
54708401ef6SPierre Jolivet   PetscCheck(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'");
548e0eea495SMark   if (time < rectx->pulse_start || time > rectx->pulse_start + 3*rectx->pulse_width) *rho = 0;
549a587d139SMark   else {
550e0eea495SMark     double x = PetscSinReal((time-rectx->pulse_start)/(3*rectx->pulse_width)*2*PETSC_PI - PETSC_PI/2) + 1; /* 0:2, integrates to 1.0 */
551e0eea495SMark     *rho = rectx->pulse_rate * x / (3*rectx->pulse_width);
552a587d139SMark     if (!rectx->use_spitzer_eta) rectx->use_spitzer_eta = PETSC_TRUE; /* use it next time */
553e0eea495SMark   }
554e0eea495SMark   PetscFunctionReturn(0);
555e0eea495SMark }
556e0eea495SMark 
557e0eea495SMark #undef __FUNCT__
558e0eea495SMark #define __FUNCT__ "ProcessREOptions"
559e0eea495SMark static PetscErrorCode ProcessREOptions(REctx *rectx, const LandauCtx *ctx, DM dm, const char prefix[])
560e0eea495SMark {
561e0eea495SMark   PetscFunctionList plist = NULL, testlist = NULL, elist = NULL;
562e0eea495SMark   char              pname[256],testname[256],ename[256];
563930e68a5SMark Adams   DM                dm_dummy;
564a587d139SMark   PetscBool         Connor_E = PETSC_FALSE;
565e0eea495SMark 
566e0eea495SMark   PetscFunctionBeginUser;
5679566063dSJacob Faibussowitsch   PetscCall(DMCreate(PETSC_COMM_WORLD,&dm_dummy));
568e0eea495SMark   rectx->Ne_ion = 1;                 /* number of electrons given up by impurity ion */
569e0eea495SMark   rectx->T_cold = .005;              /* kev */
570e0eea495SMark   rectx->ion_potential = 15;         /* ev */
571e0eea495SMark   rectx->L = 2;
572e0eea495SMark   rectx->X_0 = NULL;
573e0eea495SMark   rectx->imp_idx = ctx->num_species - 1; /* default ionized impurity as last one */
574a587d139SMark   rectx->pulse_start = PETSC_MAX_REAL;
575e0eea495SMark   rectx->pulse_width = 1;
576e0eea495SMark   rectx->plotStep = PETSC_MAX_INT;
577e0eea495SMark   rectx->pulse_rate = 1.e-1;
578e0eea495SMark   rectx->current_rate = 0;
579e0eea495SMark   rectx->plotIdx = 0;
580e0eea495SMark   rectx->j = 0;
581e0eea495SMark   rectx->plotDt = 1.0;
582930e68a5SMark Adams   rectx->plotting = PETSC_FALSE;
583e0eea495SMark   rectx->use_spitzer_eta = PETSC_FALSE;
584e0eea495SMark   rectx->idx = 0;
5858a6f2e61SMark Adams   rectx->print_period = 10;
586*419c2fb8Smarkadams4   rectx->grid_view_idx = -1; // do not get if not needed
587e0eea495SMark   /* Register the available impurity sources */
5889566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&plist,"step",&stepSrc));
5899566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&plist,"none",&zeroSrc));
5909566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&plist,"pulse",&pulseSrc));
5919566063dSJacob Faibussowitsch   PetscCall(PetscStrcpy(pname,"none"));
5929566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&testlist,"none",&testNone));
5939566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&testlist,"spitzer",&testSpitzer));
5949566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&testlist,"stable",&testStable));
5959566063dSJacob Faibussowitsch   PetscCall(PetscStrcpy(testname,"none"));
5969566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&elist,"none",&ENone));
5979566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&elist,"induction",&EInduction));
5989566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListAdd(&elist,"constant",&EConstant));
5999566063dSJacob Faibussowitsch   PetscCall(PetscStrcpy(ename,"constant"));
600e0eea495SMark 
601d0609cedSBarry Smith   PetscOptionsBegin(PETSC_COMM_SELF, prefix, "Options for Runaway/seed electron model", "none");
6029566063dSJacob Faibussowitsch   PetscCall(PetscOptionsReal("-ex2_plot_dt", "Plotting interval", "ex2.c", rectx->plotDt, &rectx->plotDt, NULL));
603e0eea495SMark   if (rectx->plotDt < 0) rectx->plotDt = 1e30;
604e0eea495SMark   if (rectx->plotDt == 0) rectx->plotDt = 1e-30;
6059566063dSJacob Faibussowitsch   PetscCall(PetscOptionsInt("-ex2_print_period", "Plotting interval", "ex2.c", rectx->print_period, &rectx->print_period, NULL));
6069566063dSJacob Faibussowitsch   PetscCall(PetscOptionsInt("-ex2_grid_view_idx", "grid_view_idx", "ex2.c", rectx->grid_view_idx, &rectx->grid_view_idx, NULL));
607*419c2fb8Smarkadams4   PetscCheck(rectx->grid_view_idx < ctx->num_grids || rectx->grid_view_idx == -1,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"rectx->grid_view_idx (%" PetscInt_FMT ") >= ctx->num_grids (%" PetscInt_FMT ")",rectx->imp_idx,ctx->num_grids);
6089566063dSJacob Faibussowitsch   PetscCall(PetscOptionsFList("-ex2_impurity_source_type","Name of impurity source to run","",plist,pname,pname,sizeof(pname),NULL));
6099566063dSJacob Faibussowitsch   PetscCall(PetscOptionsFList("-ex2_test_type","Name of test to run","",testlist,testname,testname,sizeof(testname),NULL));
6109566063dSJacob Faibussowitsch   PetscCall(PetscOptionsInt("-ex2_impurity_index", "index of sink for impurities", "none", rectx->imp_idx, &rectx->imp_idx, NULL));
611cad9d221SBarry Smith   PetscCheck((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 (%" PetscInt_FMT "), must be > 0 && < NS",rectx->imp_idx);
6129566063dSJacob Faibussowitsch   PetscCall(PetscOptionsFList("-ex2_e_field_type","Electric field type","",elist,ename,ename,sizeof(ename),NULL));
613e0eea495SMark   rectx->Ne_ion = -ctx->charges[rectx->imp_idx]/ctx->charges[0];
6149566063dSJacob Faibussowitsch   PetscCall(PetscOptionsReal("-ex2_t_cold","Temperature of cold electron and ions after ionization in keV","none",rectx->T_cold,&rectx->T_cold, NULL));
6159566063dSJacob Faibussowitsch   PetscCall(PetscOptionsReal("-ex2_pulse_start_time","Time at which pulse happens for 'pulse' source","none",rectx->pulse_start,&rectx->pulse_start, NULL));
6169566063dSJacob Faibussowitsch   PetscCall(PetscOptionsReal("-ex2_pulse_width_time","Width of pulse 'pulse' source","none",rectx->pulse_width,&rectx->pulse_width, NULL));
6179566063dSJacob Faibussowitsch   PetscCall(PetscOptionsReal("-ex2_pulse_rate","Number density of pulse for 'pulse' source","none",rectx->pulse_rate,&rectx->pulse_rate, NULL));
618e0eea495SMark   rectx->T_cold *= 1.16e7; /* convert to Kelvin */
6199566063dSJacob Faibussowitsch   PetscCall(PetscOptionsReal("-ex2_ion_potential","Potential to ionize impurity (should be array) in ev","none",rectx->ion_potential,&rectx->ion_potential, NULL));
6209566063dSJacob Faibussowitsch   PetscCall(PetscOptionsReal("-ex2_inductance","Inductance E feild","none",rectx->L,&rectx->L, NULL));
6219566063dSJacob Faibussowitsch   PetscCall(PetscOptionsBool("-ex2_connor_e_field_units","Scale Ex but Connor-Hastie E_c","none",Connor_E,&Connor_E, NULL));
62263a3b9bcSJacob Faibussowitsch   PetscCall(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",(double)rectx->Ne_ion,(double)rectx->T_cold,(double)rectx->ion_potential,(double)ctx->Ez,(double)ctx->v_0));
623d0609cedSBarry Smith   PetscOptionsEnd();
624e0eea495SMark   /* get impurity source rate function */
6259566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListFind(plist,pname,&rectx->impuritySrcRate));
6263c633725SBarry Smith   PetscCheck(rectx->impuritySrcRate,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No impurity source function found '%s'",pname);
6279566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListFind(testlist,testname,&rectx->test));
6283c633725SBarry Smith   PetscCheck(rectx->test,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No test found '%s'",testname);
6299566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListFind(elist,ename,&rectx->E));
6303c633725SBarry Smith   PetscCheck(rectx->E,PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"No E field function found '%s'",ename);
6319566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListDestroy(&plist));
6329566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListDestroy(&testlist));
6339566063dSJacob Faibussowitsch   PetscCall(PetscFunctionListDestroy(&elist));
634930e68a5SMark Adams 
635a587d139SMark   /* convert E from Connor-Hastie E_c units to real if doing Spitzer E */
636a587d139SMark   if (Connor_E) {
637e0eea495SMark     PetscReal E = ctx->Ez, Tev = ctx->thermal_temps[0]*8.621738e-5, n = ctx->n_0*ctx->n[0];
638e0eea495SMark     CalculateE(Tev, n, ctx->lnLam, ctx->epsilon0, &E);
639e0eea495SMark     ((LandauCtx*)ctx)->Ez *= E;
640e0eea495SMark   }
6419566063dSJacob Faibussowitsch   PetscCall(DMDestroy(&dm_dummy));
642e0eea495SMark   PetscFunctionReturn(0);
643e0eea495SMark }
644e0eea495SMark 
645e0eea495SMark int main(int argc, char **argv)
646e0eea495SMark {
6478a6f2e61SMark Adams   DM             pack;
648*419c2fb8Smarkadams4   Vec            X;
649f37ccb5fSMark Adams   PetscInt       dim = 2, nDMs;
650e0eea495SMark   TS             ts;
651e0eea495SMark   Mat            J;
652e0eea495SMark   PetscDS        prob;
653e0eea495SMark   LandauCtx      *ctx;
654e0eea495SMark   REctx          *rectx;
655a587d139SMark #if defined PETSC_USE_LOG
656a587d139SMark   PetscLogStage  stage;
657a587d139SMark #endif
658930e68a5SMark Adams   PetscMPIInt    rank;
6598fdabdddSMark Adams #if defined(PETSC_HAVE_THREADSAFETY)
6608fdabdddSMark Adams   double         starttime, endtime;
6618fdabdddSMark Adams #endif
6629566063dSJacob Faibussowitsch   PetscCall(PetscInitialize(&argc, &argv, NULL,help));
6639566063dSJacob Faibussowitsch   PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
664930e68a5SMark Adams   if (rank) { /* turn off output stuff for duplicate runs */
665*419c2fb8Smarkadams4     PetscCall(PetscOptionsClearValue(NULL,"-ex2_dm_view"));
666*419c2fb8Smarkadams4     PetscCall(PetscOptionsClearValue(NULL,"-ex2_vec_view"));
667*419c2fb8Smarkadams4     PetscCall(PetscOptionsClearValue(NULL,"-ex2_vec_view_init"));
668*419c2fb8Smarkadams4     PetscCall(PetscOptionsClearValue(NULL,"-ex2_dm_view_init"));
6699566063dSJacob Faibussowitsch     PetscCall(PetscOptionsClearValue(NULL,"-info")); /* this does not work */
670930e68a5SMark Adams   }
6719566063dSJacob Faibussowitsch   PetscCall(PetscOptionsGetInt(NULL,NULL, "-dim", &dim, NULL));
672e0eea495SMark   /* Create a mesh */
6739566063dSJacob Faibussowitsch   PetscCall(DMPlexLandauCreateVelocitySpace(PETSC_COMM_WORLD, dim, "", &X, &J, &pack));
6749566063dSJacob Faibussowitsch   PetscCall(DMCompositeGetNumberDM(pack,&nDMs));
6759566063dSJacob Faibussowitsch   PetscCall(PetscObjectSetName((PetscObject)J, "Jacobian"));
6769566063dSJacob Faibussowitsch   PetscCall(PetscObjectSetName((PetscObject)X, "f"));
6779566063dSJacob Faibussowitsch   PetscCall(DMGetApplicationContext(pack, &ctx));
6789566063dSJacob Faibussowitsch   PetscCall(DMSetUp(pack));
679e0eea495SMark   /* context */
6809566063dSJacob Faibussowitsch   PetscCall(PetscNew(&rectx));
681e0eea495SMark   ctx->data = rectx;
6829566063dSJacob Faibussowitsch   PetscCall(ProcessREOptions(rectx,ctx,pack,""));
6839566063dSJacob Faibussowitsch   PetscCall(DMGetDS(pack, &prob));
684*419c2fb8Smarkadams4   if (rectx->grid_view_idx != -1) {
685*419c2fb8Smarkadams4     Vec *XsubArray=NULL;
686*419c2fb8Smarkadams4     PetscCall(PetscMalloc(sizeof(*XsubArray)*nDMs, &XsubArray));
6879566063dSJacob Faibussowitsch     PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, XsubArray)); // read only
6889566063dSJacob Faibussowitsch     PetscCall(PetscObjectSetName((PetscObject) XsubArray[ LAND_PACK_IDX(ctx->batch_view_idx, rectx->grid_view_idx) ], rectx->grid_view_idx==0 ? "ue" : "ui"));
689*419c2fb8Smarkadams4     PetscCall(DMViewFromOptions(ctx->plex[rectx->grid_view_idx],NULL,"-ex2_dm_view"));
690*419c2fb8Smarkadams4     PetscCall(DMViewFromOptions(ctx->plex[rectx->grid_view_idx], NULL,"-ex2_dm_view_init"));
691*419c2fb8Smarkadams4     PetscCall(VecViewFromOptions(XsubArray[ LAND_PACK_IDX(ctx->batch_view_idx,rectx->grid_view_idx) ], NULL,"-ex2_vec_view_init")); // initial condition (monitor plots after step)
6929566063dSJacob Faibussowitsch     PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, XsubArray)); // read only
6939566063dSJacob Faibussowitsch     PetscCall(PetscFree(XsubArray));
694*419c2fb8Smarkadams4   }
6959566063dSJacob Faibussowitsch   PetscCall(DMSetOutputSequenceNumber(pack, 0, 0.0));
696e0eea495SMark   /* Create timestepping solver context */
6979566063dSJacob Faibussowitsch   PetscCall(TSCreate(PETSC_COMM_SELF,&ts));
6989566063dSJacob Faibussowitsch   PetscCall(TSSetDM(ts,pack));
6999566063dSJacob Faibussowitsch   PetscCall(TSSetIFunction(ts,NULL,DMPlexLandauIFunction,NULL));
7009566063dSJacob Faibussowitsch   PetscCall(TSSetIJacobian(ts,J,J,DMPlexLandauIJacobian,NULL));
7019566063dSJacob Faibussowitsch   PetscCall(TSSetRHSFunction(ts,NULL,FormSource,NULL));
7029566063dSJacob Faibussowitsch   PetscCall(TSSetFromOptions(ts));
7039566063dSJacob Faibussowitsch   PetscCall(TSSetSolution(ts,X));
7049566063dSJacob Faibussowitsch   PetscCall(TSSetApplicationContext(ts, ctx));
7059566063dSJacob Faibussowitsch   PetscCall(TSMonitorSet(ts,Monitor,ctx,NULL));
7069566063dSJacob Faibussowitsch   PetscCall(TSSetPreStep(ts,PreStep));
707e0eea495SMark   rectx->Ez_initial = ctx->Ez;       /* cache for induction caclulation - applied E field */
7088594ddcfSMark Adams   if (1) { /* warm up an test just DMPlexLandauIJacobian */
709e0eea495SMark     Vec           vec;
710a587d139SMark     PetscInt      nsteps;
711a587d139SMark     PetscReal     dt;
7129566063dSJacob Faibussowitsch     PetscCall(PetscLogStageRegister("Warmup", &stage));
7139566063dSJacob Faibussowitsch     PetscCall(PetscLogStagePush(stage));
7149566063dSJacob Faibussowitsch     PetscCall(VecDuplicate(X,&vec));
7159566063dSJacob Faibussowitsch     PetscCall(VecCopy(X,vec));
7169566063dSJacob Faibussowitsch     PetscCall(TSGetMaxSteps(ts,&nsteps));
7179566063dSJacob Faibussowitsch     PetscCall(TSGetTimeStep(ts,&dt));
7189566063dSJacob Faibussowitsch     PetscCall(TSSetMaxSteps(ts,1));
7199566063dSJacob Faibussowitsch     PetscCall(TSSolve(ts,X));
7209566063dSJacob Faibussowitsch     PetscCall(TSSetMaxSteps(ts,nsteps));
7219566063dSJacob Faibussowitsch     PetscCall(TSSetStepNumber(ts,0));
7229566063dSJacob Faibussowitsch     PetscCall(TSSetTime(ts,0));
7239566063dSJacob Faibussowitsch     PetscCall(TSSetTimeStep(ts,dt));
724a587d139SMark     rectx->plotIdx = 0;
725930e68a5SMark Adams     rectx->plotting = PETSC_FALSE;
7269566063dSJacob Faibussowitsch     PetscCall(PetscLogStagePop());
7279566063dSJacob Faibussowitsch     PetscCall(VecCopy(vec,X));
7289566063dSJacob Faibussowitsch     PetscCall(VecDestroy(&vec));
729c3e4dd79SMark Adams     PetscCall(PetscObjectStateIncrease((PetscObject)ctx->J));
730e0eea495SMark   }
731e0eea495SMark   /* go */
7329566063dSJacob Faibussowitsch   PetscCall(PetscLogStageRegister("Solve", &stage));
733f37ccb5fSMark Adams   ctx->stage = 0; // lets not use this stage
7348fdabdddSMark Adams #if defined(PETSC_HAVE_THREADSAFETY)
735e607c864SMark Adams   ctx->stage = 1; // not set with thread safety
7368fdabdddSMark Adams #endif
737c3e4dd79SMark Adams   //PetscCall(TSSetSolution(ts,X));
7389566063dSJacob Faibussowitsch   PetscCall(PetscLogStagePush(stage));
7398fdabdddSMark Adams #if defined(PETSC_HAVE_THREADSAFETY)
7408fdabdddSMark Adams   starttime = MPI_Wtime();
7418fdabdddSMark Adams #endif
742*419c2fb8Smarkadams4 #if defined(PETSC_HAVE_CUDA_NVTX)
743*419c2fb8Smarkadams4   nvtxRangePushA("ex2-TSSolve-warm");
744*419c2fb8Smarkadams4 #endif
7459566063dSJacob Faibussowitsch   PetscCall(TSSolve(ts,X));
746*419c2fb8Smarkadams4 #if defined(PETSC_HAVE_CUDA_NVTX)
747*419c2fb8Smarkadams4   nvtxRangePop();
748*419c2fb8Smarkadams4 #endif
7499566063dSJacob Faibussowitsch   PetscCall(PetscLogStagePop());
7508fdabdddSMark Adams #if defined(PETSC_HAVE_THREADSAFETY)
7518fdabdddSMark Adams   endtime = MPI_Wtime();
7528fdabdddSMark Adams   ctx->times[LANDAU_EX2_TSSOLVE] += (endtime - starttime);
7538fdabdddSMark Adams #endif
754e0eea495SMark   /* clean up */
7559566063dSJacob Faibussowitsch   PetscCall(DMPlexLandauDestroyVelocitySpace(&pack));
7569566063dSJacob Faibussowitsch   PetscCall(TSDestroy(&ts));
7579566063dSJacob Faibussowitsch   PetscCall(VecDestroy(&X));
7589566063dSJacob Faibussowitsch   PetscCall(PetscFree(rectx));
7599566063dSJacob Faibussowitsch   PetscCall(PetscFinalize());
760b122ec5aSJacob Faibussowitsch   return 0;
761e0eea495SMark }
762e0eea495SMark 
763e0eea495SMark /*TEST
764a587d139SMark 
7655dac466eSMark Adams   testset:
766984ed092SMark Adams     requires: p4est !complex double defined(PETSC_USE_DMLANDAU_2D)
7675dac466eSMark Adams     output_file: output/ex2_0.out
768c3e4dd79SMark Adams     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 -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 -dm_landau_verbose 2
7695dac466eSMark Adams     test:
7705dac466eSMark Adams       suffix: cpu
771c3e4dd79SMark Adams       args: -dm_landau_device_type cpu -ksp_type bicg -pc_type jacobi
772a587d139SMark     test:
773a587d139SMark       suffix: kokkos
7745dac466eSMark Adams       requires: kokkos_kernels
775c3e4dd79SMark Adams       args: -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos -ksp_type bicg -pc_type jacobi
77690d163c9SMark Adams     test:
77790d163c9SMark Adams       suffix: cuda
7785dac466eSMark Adams       requires: cuda
779c3e4dd79SMark Adams       args: -dm_landau_device_type cuda -dm_mat_type aijcusparse -dm_vec_type cuda -mat_cusparse_use_cpu_solve -ksp_type bicg -pc_type jacobi
780cb25d741SMark Adams     test:
781cb25d741SMark Adams       suffix: kokkos_batch
782cb25d741SMark Adams       requires: kokkos_kernels
783c3e4dd79SMark Adams       args: -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos -ksp_type preonly -pc_type bjkokkos -pc_bjkokkos_ksp_type bicg -pc_bjkokkos_pc_type jacobi
784bfc784b7SMark Adams     test:
785bfc784b7SMark Adams       suffix: kokkos_batch_coo
786bfc784b7SMark Adams       requires: kokkos_kernels
787c3e4dd79SMark Adams       args: -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos -ksp_type preonly -pc_type bjkokkos -pc_bjkokkos_ksp_type bicg -pc_bjkokkos_pc_type jacobi -dm_landau_coo_assembly
78890d163c9SMark Adams 
789e0eea495SMark TEST*/
790