Actual source code: plexland.c
1: #include <../src/mat/impls/aij/seq/aij.h>
2: #include <petsc/private/dmpleximpl.h>
3: #include <petsclandau.h>
4: #include <petscts.h>
5: #include <petscdmforest.h>
6: #include <petscdmcomposite.h>
8: /* Landau collision operator */
10: /* relativistic terms */
11: #if defined(PETSC_USE_REAL_SINGLE)
12: #define SPEED_OF_LIGHT 2.99792458e8F
13: #define C_0(v0) (SPEED_OF_LIGHT / v0) /* needed for relativistic tensor on all architectures */
14: #else
15: #define SPEED_OF_LIGHT 2.99792458e8
16: #define C_0(v0) (SPEED_OF_LIGHT / v0) /* needed for relativistic tensor on all architectures */
17: #endif
19: #include "land_tensors.h"
21: #if defined(PETSC_HAVE_OPENMP)
22: #include <omp.h>
23: #endif
25: static PetscErrorCode LandauGPUMapsDestroy(void **ptr)
26: {
27: P4estVertexMaps *maps = (P4estVertexMaps *)*ptr;
29: PetscFunctionBegin;
30: // free device data
31: if (maps[0].deviceType != LANDAU_CPU) {
32: #if defined(PETSC_HAVE_KOKKOS)
33: if (maps[0].deviceType == LANDAU_KOKKOS) {
34: PetscCall(LandauKokkosDestroyMatMaps(maps, maps[0].numgrids)); // implies Kokkos does
35: }
36: #endif
37: }
38: // free host data
39: for (PetscInt grid = 0; grid < maps[0].numgrids; grid++) {
40: PetscCall(PetscFree(maps[grid].c_maps));
41: PetscCall(PetscFree(maps[grid].gIdx));
42: }
43: PetscCall(PetscFree(maps));
44: PetscFunctionReturn(PETSC_SUCCESS);
45: }
46: static PetscErrorCode energy_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
47: {
48: PetscReal v2 = 0;
50: PetscFunctionBegin;
51: /* compute v^2 / 2 */
52: for (PetscInt i = 0; i < dim; ++i) v2 += x[i] * x[i];
53: /* evaluate the Maxwellian */
54: u[0] = v2 / 2;
55: PetscFunctionReturn(PETSC_SUCCESS);
56: }
58: /* needs double */
59: static PetscErrorCode gamma_m1_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
60: {
61: PetscReal *c2_0_arr = ((PetscReal *)actx);
62: double u2 = 0, c02 = (double)*c2_0_arr, xx;
64: PetscFunctionBegin;
65: /* compute u^2 / 2 */
66: for (PetscInt i = 0; i < dim; ++i) u2 += x[i] * x[i];
67: /* gamma - 1 = g_eps, for conditioning and we only take derivatives */
68: xx = u2 / c02;
69: #if defined(PETSC_USE_DEBUG)
70: u[0] = PetscSqrtReal(1. + xx);
71: #else
72: u[0] = xx / (PetscSqrtReal(1. + xx) + 1.) - 1.; // better conditioned. -1 might help condition and only used for derivative
73: #endif
74: PetscFunctionReturn(PETSC_SUCCESS);
75: }
77: /*
78: LandauFormJacobian_Internal - Evaluates Jacobian matrix.
80: Input Parameters:
81: . globX - input vector
82: . actx - optional user-defined context
83: . dim - dimension
85: Output Parameter:
86: . J0acP - Jacobian matrix filled, not created
87: */
88: static PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, PetscReal shift, void *a_ctx)
89: {
90: LandauCtx *ctx = (LandauCtx *)a_ctx;
91: PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nb;
92: PetscQuadrature quad;
93: PetscReal Eq_m[LANDAU_MAX_SPECIES]; // could be static data w/o quench (ex2)
94: PetscScalar *cellClosure = NULL;
95: const PetscScalar *xdata = NULL;
96: PetscDS prob;
97: PetscContainer container;
98: P4estVertexMaps *maps;
99: Mat subJ[LANDAU_MAX_GRIDS * LANDAU_MAX_BATCH_SZ];
101: PetscFunctionBegin;
104: PetscAssertPointer(ctx, 5);
105: /* check for matrix container for GPU assembly. Support CPU assembly for debugging */
106: PetscCheck(ctx->plex[0] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
107: PetscCall(PetscLogEventBegin(ctx->events[10], 0, 0, 0, 0));
108: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
109: PetscCall(PetscObjectQuery((PetscObject)JacP, "assembly_maps", (PetscObject *)&container));
110: if (container) {
111: PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "maps but no GPU assembly");
112: PetscCall(PetscContainerGetPointer(container, (void **)&maps));
113: PetscCheck(maps, ctx->comm, PETSC_ERR_ARG_WRONG, "empty GPU matrix container");
114: for (PetscInt i = 0; i < ctx->num_grids * ctx->batch_sz; i++) subJ[i] = NULL;
115: } else {
116: PetscCheck(!ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "No maps but GPU assembly");
117: for (PetscInt tid = 0; tid < ctx->batch_sz; tid++) {
118: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCreateMatrix(ctx->plex[grid], &subJ[LAND_PACK_IDX(tid, grid)]));
119: }
120: maps = NULL;
121: }
122: // get dynamic data (Eq is odd, for quench and Spitzer test) for CPU assembly and raw data for Jacobian GPU assembly. Get host numCells[], Nq (yuck)
123: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
124: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
125: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
126: PetscCheck(Nq <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nq, LANDAU_MAX_NQND);
127: PetscCheck(Nb <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nb = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nb, LANDAU_MAX_NQND);
128: // get metadata for collecting dynamic data
129: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
130: PetscInt cStart, cEnd;
131: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
132: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
133: numCells[grid] = cEnd - cStart; // grids can have different topology
134: }
135: PetscCall(PetscLogEventEnd(ctx->events[10], 0, 0, 0, 0));
136: if (shift == 0) { /* create dynamic point data: f_alpha for closure of each cell (cellClosure[nbatch,ngrids,ncells[g],f[Nb,ns[g]]]) or xdata */
137: DM pack;
138: PetscCall(VecGetDM(a_X, &pack));
139: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "pack has no DM");
140: PetscCall(PetscLogEventBegin(ctx->events[1], 0, 0, 0, 0));
141: for (PetscInt fieldA = 0; fieldA < ctx->num_species; fieldA++) {
142: Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */
143: if (dim == 2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */
144: }
145: if (!ctx->gpu_assembly) {
146: Vec *locXArray, *globXArray;
147: PetscScalar *cellClosure_it;
148: PetscInt cellClosure_sz = 0, nDMs, Nf[LANDAU_MAX_GRIDS];
149: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
150: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
151: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
152: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
153: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
154: }
155: /* count cellClosure size */
156: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
157: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) cellClosure_sz += Nb * Nf[grid] * numCells[grid];
158: PetscCall(PetscMalloc1(cellClosure_sz * ctx->batch_sz, &cellClosure));
159: cellClosure_it = cellClosure;
160: PetscCall(PetscMalloc(sizeof(*locXArray) * nDMs, &locXArray));
161: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
162: PetscCall(DMCompositeGetLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
163: PetscCall(DMCompositeGetAccessArray(pack, a_X, nDMs, NULL, globXArray));
164: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP (once)
165: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
166: Vec locX = locXArray[LAND_PACK_IDX(b_id, grid)], globX = globXArray[LAND_PACK_IDX(b_id, grid)], locX2;
167: PetscInt cStart, cEnd, ei;
168: PetscCall(VecDuplicate(locX, &locX2));
169: PetscCall(DMGlobalToLocalBegin(ctx->plex[grid], globX, INSERT_VALUES, locX2));
170: PetscCall(DMGlobalToLocalEnd(ctx->plex[grid], globX, INSERT_VALUES, locX2));
171: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
172: for (ei = cStart; ei < cEnd; ++ei) {
173: PetscScalar *coef = NULL;
174: PetscCall(DMPlexVecGetClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
175: PetscCall(PetscMemcpy(cellClosure_it, coef, Nb * Nf[grid] * sizeof(*cellClosure_it))); /* change if LandauIPReal != PetscScalar */
176: PetscCall(DMPlexVecRestoreClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
177: cellClosure_it += Nb * Nf[grid];
178: }
179: PetscCall(VecDestroy(&locX2));
180: }
181: }
182: PetscCheck(cellClosure_it - cellClosure == cellClosure_sz * ctx->batch_sz, PETSC_COMM_SELF, PETSC_ERR_PLIB, "iteration wrong %" PetscCount_FMT " != cellClosure_sz = %" PetscInt_FMT, cellClosure_it - cellClosure, cellClosure_sz * ctx->batch_sz);
183: PetscCall(DMCompositeRestoreLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
184: PetscCall(DMCompositeRestoreAccessArray(pack, a_X, nDMs, NULL, globXArray));
185: PetscCall(PetscFree(locXArray));
186: PetscCall(PetscFree(globXArray));
187: xdata = NULL;
188: } else {
189: PetscMemType mtype;
190: if (ctx->jacobian_field_major_order) { // get data in batch ordering
191: PetscCall(VecScatterBegin(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
192: PetscCall(VecScatterEnd(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
193: PetscCall(VecGetArrayReadAndMemType(ctx->work_vec, &xdata, &mtype));
194: } else {
195: PetscCall(VecGetArrayReadAndMemType(a_X, &xdata, &mtype));
196: }
197: PetscCheck(mtype == PETSC_MEMTYPE_HOST || ctx->deviceType != LANDAU_CPU, ctx->comm, PETSC_ERR_ARG_WRONG, "CPU run with device data: use -mat_type aij");
198: cellClosure = NULL;
199: }
200: PetscCall(PetscLogEventEnd(ctx->events[1], 0, 0, 0, 0));
201: } else xdata = cellClosure = NULL;
203: /* do it */
204: if (ctx->deviceType == LANDAU_KOKKOS) {
205: #if defined(PETSC_HAVE_KOKKOS)
206: PetscCall(LandauKokkosJacobian(ctx->plex, Nq, Nb, ctx->batch_sz, ctx->num_grids, numCells, Eq_m, cellClosure, xdata, &ctx->SData_d, shift, ctx->events, ctx->mat_offset, ctx->species_offset, subJ, JacP));
207: #else
208: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
209: #endif
210: } else { /* CPU version */
211: PetscTabulation *Tf; // used for CPU and print info. Same on all grids and all species
212: PetscInt ip_offset[LANDAU_MAX_GRIDS + 1], ipf_offset[LANDAU_MAX_GRIDS + 1], elem_offset[LANDAU_MAX_GRIDS + 1], IPf_sz_glb, IPf_sz_tot, num_grids = ctx->num_grids, Nf[LANDAU_MAX_GRIDS];
213: PetscReal *ff, *dudx, *dudy, *dudz, *invJ_a = (PetscReal *)ctx->SData_d.invJ, *xx = (PetscReal *)ctx->SData_d.x, *yy = (PetscReal *)ctx->SData_d.y, *zz = (PetscReal *)ctx->SData_d.z, *ww = (PetscReal *)ctx->SData_d.w;
214: PetscReal *nu_alpha = (PetscReal *)ctx->SData_d.alpha, *nu_beta = (PetscReal *)ctx->SData_d.beta, *invMass = (PetscReal *)ctx->SData_d.invMass;
215: PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
216: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
217: PetscScalar *coo_vals = NULL;
218: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
219: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
220: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
221: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
222: }
223: /* count IPf size, etc */
224: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
225: const PetscReal *const BB = Tf[0]->T[0], *const DD = Tf[0]->T[1];
226: ip_offset[0] = ipf_offset[0] = elem_offset[0] = 0;
227: for (PetscInt grid = 0; grid < num_grids; grid++) {
228: PetscInt nfloc = ctx->species_offset[grid + 1] - ctx->species_offset[grid];
229: elem_offset[grid + 1] = elem_offset[grid] + numCells[grid];
230: ip_offset[grid + 1] = ip_offset[grid] + numCells[grid] * Nq;
231: ipf_offset[grid + 1] = ipf_offset[grid] + Nq * nfloc * numCells[grid];
232: }
233: IPf_sz_glb = ipf_offset[num_grids];
234: IPf_sz_tot = IPf_sz_glb * ctx->batch_sz;
235: // prep COO
236: PetscCall(PetscMalloc1(ctx->SData_d.coo_size, &coo_vals)); // allocate every time?
237: if (shift == 0.0) { /* compute dynamic data f and df and init data for Jacobian */
238: #if defined(PETSC_HAVE_THREADSAFETY)
239: double starttime, endtime;
240: starttime = MPI_Wtime();
241: #endif
242: PetscCall(PetscLogEventBegin(ctx->events[8], 0, 0, 0, 0));
243: PetscCall(PetscMalloc4(IPf_sz_tot, &ff, IPf_sz_tot, &dudx, IPf_sz_tot, &dudy, (dim == 3 ? IPf_sz_tot : 0), &dudz));
244: // F df/dx
245: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
246: const PetscInt b_Nelem = elem_offset[num_grids], b_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem; // b_id == OMP thd_id in batch
247: // find my grid:
248: PetscInt grid = 0;
249: while (b_elem_idx >= elem_offset[grid + 1]) grid++; // yuck search for grid
250: {
251: const PetscInt loc_nip = numCells[grid] * Nq, loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = b_elem_idx - elem_offset[grid];
252: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); //b_id*b_N + ctx->mat_offset[grid];
253: PetscScalar *coef, coef_buff[LANDAU_MAX_SPECIES * LANDAU_MAX_NQND];
254: PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim]; // ingJ is static data on batch 0
255: PetscInt b, f, q;
256: if (cellClosure) {
257: coef = &cellClosure[b_id * IPf_sz_glb + ipf_offset[grid] + loc_elem * Nb * loc_Nf]; // this is const
258: } else {
259: coef = coef_buff;
260: for (f = 0; f < loc_Nf; ++f) {
261: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][f][0];
262: for (b = 0; b < Nb; ++b) {
263: PetscInt idx = Idxs[b];
264: if (idx >= 0) {
265: coef[f * Nb + b] = xdata[idx + moffset];
266: } else {
267: idx = -idx - 1;
268: coef[f * Nb + b] = 0;
269: for (q = 0; q < maps[grid].num_face; q++) {
270: PetscInt id = maps[grid].c_maps[idx][q].gid;
271: PetscScalar scale = maps[grid].c_maps[idx][q].scale;
272: coef[f * Nb + b] += scale * xdata[id + moffset];
273: }
274: }
275: }
276: }
277: }
278: /* get f and df */
279: for (PetscInt qi = 0; qi < Nq; qi++) {
280: const PetscReal *invJ = &invJe[qi * dim * dim];
281: const PetscReal *Bq = &BB[qi * Nb];
282: const PetscReal *Dq = &DD[qi * Nb * dim];
283: PetscReal u_x[LANDAU_DIM];
284: /* get f & df */
285: for (f = 0; f < loc_Nf; ++f) {
286: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid] + f * loc_nip + loc_elem * Nq + qi;
287: PetscInt b, e;
288: PetscReal refSpaceDer[LANDAU_DIM];
289: ff[idx] = 0.0;
290: for (PetscInt d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0;
291: for (b = 0; b < Nb; ++b) {
292: const PetscInt cidx = b;
293: ff[idx] += Bq[cidx] * PetscRealPart(coef[f * Nb + cidx]);
294: for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx * dim + d] * PetscRealPart(coef[f * Nb + cidx]);
295: }
296: for (PetscInt d = 0; d < LANDAU_DIM; ++d) {
297: for (e = 0, u_x[d] = 0.0; e < LANDAU_DIM; ++e) u_x[d] += invJ[e * dim + d] * refSpaceDer[e];
298: }
299: dudx[idx] = u_x[0];
300: dudy[idx] = u_x[1];
301: #if LANDAU_DIM == 3
302: dudz[idx] = u_x[2];
303: #endif
304: }
305: } // q
306: } // grid
307: } // grid*batch
308: PetscCall(PetscLogEventEnd(ctx->events[8], 0, 0, 0, 0));
309: #if defined(PETSC_HAVE_THREADSAFETY)
310: endtime = MPI_Wtime();
311: if (ctx->stage) ctx->times[LANDAU_F_DF] += (endtime - starttime);
312: #endif
313: } // Jacobian setup
314: // assemble Jacobian (or mass)
315: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
316: const PetscInt b_Nelem = elem_offset[num_grids];
317: const PetscInt glb_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem;
318: PetscInt grid = 0;
319: #if defined(PETSC_HAVE_THREADSAFETY)
320: double starttime, endtime;
321: starttime = MPI_Wtime();
322: #endif
323: while (glb_elem_idx >= elem_offset[grid + 1]) grid++;
324: {
325: const PetscInt loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = glb_elem_idx - elem_offset[grid];
326: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset), totDim = loc_Nf * Nq, elemMatSize = totDim * totDim;
327: PetscScalar *elemMat;
328: const PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim];
329: PetscCall(PetscMalloc1(elemMatSize, &elemMat));
330: PetscCall(PetscMemzero(elemMat, elemMatSize * sizeof(*elemMat)));
331: if (shift == 0.0) { // Jacobian
332: PetscCall(PetscLogEventBegin(ctx->events[4], 0, 0, 0, 0));
333: } else { // mass
334: PetscCall(PetscLogEventBegin(ctx->events[16], 0, 0, 0, 0));
335: }
336: for (PetscInt qj = 0; qj < Nq; ++qj) {
337: const PetscInt jpidx_glb = ip_offset[grid] + qj + loc_elem * Nq;
338: PetscReal g0[LANDAU_MAX_SPECIES], g2[LANDAU_MAX_SPECIES][LANDAU_DIM], g3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM]; // could make a LANDAU_MAX_SPECIES_GRID ~ number of ions - 1
339: PetscInt d, d2, dp, d3, IPf_idx;
340: if (shift == 0.0) { // Jacobian
341: const PetscReal *const invJj = &invJe[qj * dim * dim];
342: PetscReal gg2[LANDAU_MAX_SPECIES][LANDAU_DIM], gg3[LANDAU_MAX_SPECIES][LANDAU_DIM][LANDAU_DIM], gg2_temp[LANDAU_DIM], gg3_temp[LANDAU_DIM][LANDAU_DIM];
343: const PetscReal vj[3] = {xx[jpidx_glb], yy[jpidx_glb], zz ? zz[jpidx_glb] : 0}, wj = ww[jpidx_glb];
344: // create g2 & g3
345: for (d = 0; d < LANDAU_DIM; d++) { // clear accumulation data D & K
346: gg2_temp[d] = 0;
347: for (d2 = 0; d2 < LANDAU_DIM; d2++) gg3_temp[d][d2] = 0;
348: }
349: /* inner beta reduction */
350: IPf_idx = 0;
351: for (PetscInt grid_r = 0, f_off = 0, ipidx = 0; grid_r < ctx->num_grids; grid_r++, f_off = ctx->species_offset[grid_r]) { // IPf_idx += nip_loc_r*Nfloc_r
352: PetscInt nip_loc_r = numCells[grid_r] * Nq, Nfloc_r = Nf[grid_r];
353: for (PetscInt ei_r = 0, loc_fdf_idx = 0; ei_r < numCells[grid_r]; ++ei_r) {
354: for (PetscInt qi = 0; qi < Nq; qi++, ipidx++, loc_fdf_idx++) {
355: const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx];
356: PetscReal temp1[3] = {0, 0, 0}, temp2 = 0;
357: #if LANDAU_DIM == 2
358: PetscReal Ud[2][2], Uk[2][2], mask = (PetscAbs(vj[0] - x) < 100 * PETSC_SQRT_MACHINE_EPSILON && PetscAbs(vj[1] - y) < 100 * PETSC_SQRT_MACHINE_EPSILON) ? 0. : 1.;
359: LandauTensor2D(vj, x, y, Ud, Uk, mask);
360: #else
361: PetscReal U[3][3], z = zz[ipidx], mask = (PetscAbs(vj[0] - x) < 100 * PETSC_SQRT_MACHINE_EPSILON && PetscAbs(vj[1] - y) < 100 * PETSC_SQRT_MACHINE_EPSILON && PetscAbs(vj[2] - z) < 100 * PETSC_SQRT_MACHINE_EPSILON) ? 0. : 1.;
362: if (ctx->use_relativistic_corrections) {
363: LandauTensor3DRelativistic(vj, x, y, z, U, mask, C_0(ctx->v_0));
364: } else {
365: LandauTensor3D(vj, x, y, z, U, mask);
366: }
367: #endif
368: for (PetscInt f = 0; f < Nfloc_r; ++f) {
369: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid_r] + f * nip_loc_r + ei_r * Nq + qi; // IPf_idx + f*nip_loc_r + loc_fdf_idx;
370: temp1[0] += dudx[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
371: temp1[1] += dudy[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
372: #if LANDAU_DIM == 3
373: temp1[2] += dudz[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
374: #endif
375: temp2 += ff[idx] * nu_beta[f + f_off] * (*lambdas)[grid][grid_r];
376: }
377: temp1[0] *= wi;
378: temp1[1] *= wi;
379: #if LANDAU_DIM == 3
380: temp1[2] *= wi;
381: #endif
382: temp2 *= wi;
383: #if LANDAU_DIM == 2
384: for (d2 = 0; d2 < 2; d2++) {
385: for (d3 = 0; d3 < 2; ++d3) {
386: /* K = U * grad(f): g2=e: i,A */
387: gg2_temp[d2] += Uk[d2][d3] * temp1[d3];
388: /* D = -U * (I \kron (fx)): g3=f: i,j,A */
389: gg3_temp[d2][d3] += Ud[d2][d3] * temp2;
390: }
391: }
392: #else
393: for (d2 = 0; d2 < 3; ++d2) {
394: for (d3 = 0; d3 < 3; ++d3) {
395: /* K = U * grad(f): g2 = e: i,A */
396: gg2_temp[d2] += U[d2][d3] * temp1[d3];
397: /* D = -U * (I \kron (fx)): g3 = f: i,j,A */
398: gg3_temp[d2][d3] += U[d2][d3] * temp2;
399: }
400: }
401: #endif
402: } // qi
403: } // ei_r
404: IPf_idx += nip_loc_r * Nfloc_r;
405: } /* grid_r - IPs */
406: PetscCheck(IPf_idx == IPf_sz_glb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "IPf_idx != IPf_sz %" PetscInt_FMT " %" PetscInt_FMT, IPf_idx, IPf_sz_glb);
407: // add alpha and put in gg2/3
408: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) {
409: for (d2 = 0; d2 < LANDAU_DIM; d2++) {
410: gg2[fieldA][d2] = gg2_temp[d2] * nu_alpha[fieldA + f_off];
411: for (d3 = 0; d3 < LANDAU_DIM; d3++) gg3[fieldA][d2][d3] = -gg3_temp[d2][d3] * nu_alpha[fieldA + f_off] * invMass[fieldA + f_off];
412: }
413: }
414: /* add electric field term once per IP */
415: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) gg2[fieldA][LANDAU_DIM - 1] += Eq_m[fieldA + f_off];
416: /* Jacobian transform - g2, g3 */
417: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
418: for (d = 0; d < dim; ++d) {
419: g2[fieldA][d] = 0.0;
420: for (d2 = 0; d2 < dim; ++d2) {
421: g2[fieldA][d] += invJj[d * dim + d2] * gg2[fieldA][d2];
422: g3[fieldA][d][d2] = 0.0;
423: for (d3 = 0; d3 < dim; ++d3) {
424: for (dp = 0; dp < dim; ++dp) g3[fieldA][d][d2] += invJj[d * dim + d3] * gg3[fieldA][d3][dp] * invJj[d2 * dim + dp];
425: }
426: g3[fieldA][d][d2] *= wj;
427: }
428: g2[fieldA][d] *= wj;
429: }
430: }
431: } else { // mass
432: PetscReal wj = ww[jpidx_glb];
433: /* Jacobian transform - g0 */
434: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
435: if (dim == 2) {
436: g0[fieldA] = wj * shift * 2. * PETSC_PI; // move this to below and remove g0
437: } else {
438: g0[fieldA] = wj * shift; // move this to below and remove g0
439: }
440: }
441: }
442: /* FE matrix construction */
443: {
444: PetscInt fieldA, d, f, d2, g;
445: const PetscReal *BJq = &BB[qj * Nb], *DIq = &DD[qj * Nb * dim];
446: /* assemble - on the diagonal (I,I) */
447: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
448: for (f = 0; f < Nb; f++) {
449: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
450: for (g = 0; g < Nb; ++g) {
451: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
452: const PetscInt fOff = i * totDim + j;
453: if (shift == 0.0) {
454: for (d = 0; d < dim; ++d) {
455: elemMat[fOff] += DIq[f * dim + d] * g2[fieldA][d] * BJq[g];
456: for (d2 = 0; d2 < dim; ++d2) elemMat[fOff] += DIq[f * dim + d] * g3[fieldA][d][d2] * DIq[g * dim + d2];
457: }
458: } else { // mass
459: elemMat[fOff] += BJq[f] * g0[fieldA] * BJq[g];
460: }
461: }
462: }
463: }
464: }
465: } /* qj loop */
466: if (shift == 0.0) { // Jacobian
467: PetscCall(PetscLogEventEnd(ctx->events[4], 0, 0, 0, 0));
468: } else {
469: PetscCall(PetscLogEventEnd(ctx->events[16], 0, 0, 0, 0));
470: }
471: #if defined(PETSC_HAVE_THREADSAFETY)
472: endtime = MPI_Wtime();
473: if (ctx->stage) ctx->times[LANDAU_KERNEL] += (endtime - starttime);
474: #endif
475: /* assemble matrix */
476: if (!container) {
477: PetscInt cStart;
478: PetscCall(PetscLogEventBegin(ctx->events[6], 0, 0, 0, 0));
479: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, NULL));
480: PetscCall(DMPlexMatSetClosure(ctx->plex[grid], section[grid], globsection[grid], subJ[LAND_PACK_IDX(b_id, grid)], loc_elem + cStart, elemMat, ADD_VALUES));
481: PetscCall(PetscLogEventEnd(ctx->events[6], 0, 0, 0, 0));
482: } else { // GPU like assembly for debugging
483: PetscInt fieldA, q, f, g, d, nr, nc, rows0[LANDAU_MAX_Q_FACE] = {0}, cols0[LANDAU_MAX_Q_FACE] = {0}, rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE];
484: PetscScalar vals[LANDAU_MAX_Q_FACE * LANDAU_MAX_Q_FACE] = {0}, row_scale[LANDAU_MAX_Q_FACE] = {0}, col_scale[LANDAU_MAX_Q_FACE] = {0};
485: LandauIdx *coo_elem_offsets = (LandauIdx *)ctx->SData_d.coo_elem_offsets, *coo_elem_fullNb = (LandauIdx *)ctx->SData_d.coo_elem_fullNb, (*coo_elem_point_offsets)[LANDAU_MAX_NQND + 1] = (LandauIdx(*)[LANDAU_MAX_NQND + 1]) ctx->SData_d.coo_elem_point_offsets;
486: /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */
487: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
488: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][fieldA][0];
489: for (f = 0; f < Nb; f++) {
490: PetscInt idx = Idxs[f];
491: if (idx >= 0) {
492: nr = 1;
493: rows0[0] = idx;
494: row_scale[0] = 1.;
495: } else {
496: idx = -idx - 1;
497: for (q = 0, nr = 0; q < maps[grid].num_face; q++, nr++) {
498: if (maps[grid].c_maps[idx][q].gid < 0) break;
499: rows0[q] = maps[grid].c_maps[idx][q].gid;
500: row_scale[q] = maps[grid].c_maps[idx][q].scale;
501: }
502: }
503: for (g = 0; g < Nb; ++g) {
504: idx = Idxs[g];
505: if (idx >= 0) {
506: nc = 1;
507: cols0[0] = idx;
508: col_scale[0] = 1.;
509: } else {
510: idx = -idx - 1;
511: nc = maps[grid].num_face;
512: for (q = 0, nc = 0; q < maps[grid].num_face; q++, nc++) {
513: if (maps[grid].c_maps[idx][q].gid < 0) break;
514: cols0[q] = maps[grid].c_maps[idx][q].gid;
515: col_scale[q] = maps[grid].c_maps[idx][q].scale;
516: }
517: }
518: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
519: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
520: const PetscScalar Aij = elemMat[i * totDim + j];
521: if (coo_vals) { // mirror (i,j) in CreateStaticGPUData
522: const PetscInt fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
523: const PetscInt idx0 = b_id * coo_elem_offsets[elem_offset[num_grids]] + coo_elem_offsets[glb_elem_idx] + fieldA * fullNb2 + fullNb * coo_elem_point_offsets[glb_elem_idx][f] + nr * coo_elem_point_offsets[glb_elem_idx][g];
524: for (PetscInt q = 0, idx2 = idx0; q < nr; q++) {
525: for (PetscInt d = 0; d < nc; d++, idx2++) coo_vals[idx2] = row_scale[q] * col_scale[d] * Aij;
526: }
527: } else {
528: for (q = 0; q < nr; q++) rows[q] = rows0[q] + moffset;
529: for (d = 0; d < nc; d++) cols[d] = cols0[d] + moffset;
530: for (q = 0; q < nr; q++) {
531: for (d = 0; d < nc; d++) vals[q * nc + d] = row_scale[q] * col_scale[d] * Aij;
532: }
533: PetscCall(MatSetValues(JacP, nr, rows, nc, cols, vals, ADD_VALUES));
534: }
535: }
536: }
537: }
538: }
539: if (loc_elem == -1) {
540: PetscCall(PetscPrintf(ctx->comm, "CPU Element matrix\n"));
541: for (PetscInt d = 0; d < totDim; ++d) {
542: for (PetscInt f = 0; f < totDim; ++f) PetscCall(PetscPrintf(ctx->comm, " %12.5e", (double)PetscRealPart(elemMat[d * totDim + f])));
543: PetscCall(PetscPrintf(ctx->comm, "\n"));
544: }
545: exit(12);
546: }
547: PetscCall(PetscFree(elemMat));
548: } /* grid */
549: } /* outer element & batch loop */
550: if (shift == 0.0) { // mass
551: PetscCall(PetscFree4(ff, dudx, dudy, dudz));
552: }
553: if (!container) { // 'CPU' assembly move nest matrix to global JacP
554: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP
555: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
556: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset); // b_id*b_N + ctx->mat_offset[grid];
557: PetscInt nloc, nzl, colbuf[1024], row;
558: const PetscInt *cols;
559: const PetscScalar *vals;
560: Mat B = subJ[LAND_PACK_IDX(b_id, grid)];
561: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
562: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
563: PetscCall(MatGetSize(B, &nloc, NULL));
564: for (PetscInt i = 0; i < nloc; i++) {
565: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
566: PetscCheck(nzl <= 1024, PetscObjectComm((PetscObject)B), PETSC_ERR_PLIB, "Row too big: %" PetscInt_FMT, nzl);
567: for (PetscInt j = 0; j < nzl; j++) colbuf[j] = moffset + cols[j];
568: row = moffset + i;
569: PetscCall(MatSetValues(JacP, 1, &row, nzl, colbuf, vals, ADD_VALUES));
570: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
571: }
572: PetscCall(MatDestroy(&B));
573: }
574: }
575: }
576: if (coo_vals) {
577: PetscCall(MatSetValuesCOO(JacP, coo_vals, ADD_VALUES));
578: PetscCall(PetscFree(coo_vals));
579: }
580: } /* CPU version */
581: PetscCall(MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY));
582: PetscCall(MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY));
583: /* clean up */
584: if (cellClosure) PetscCall(PetscFree(cellClosure));
585: if (xdata) PetscCall(VecRestoreArrayReadAndMemType(a_X, &xdata));
586: PetscFunctionReturn(PETSC_SUCCESS);
587: }
589: static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx)
590: {
591: PetscReal r = abc[0], z = abc[1];
592: LandauCtx *ctx = (LandauCtx *)a_ctx;
594: PetscFunctionBegin;
595: if (ctx->sphere && dim == 3) { // make sphere: works for one AMR and Q2
596: PetscInt nzero = 0, idx = 0;
597: xyz[0] = r;
598: xyz[1] = z;
599: xyz[2] = abc[2];
600: for (PetscInt i = 0; i < 3; i++) {
601: if (PetscAbs(xyz[i]) < PETSC_SQRT_MACHINE_EPSILON) nzero++;
602: else idx = i;
603: }
604: if (nzero == 2) xyz[idx] *= 1.732050807568877; // sqrt(3)
605: else if (nzero == 1) {
606: for (PetscInt i = 0; i < 3; i++) xyz[i] *= 1.224744871391589; // sqrt(3/2)
607: }
608: } else {
609: xyz[0] = r;
610: xyz[1] = z;
611: if (dim == 3) xyz[2] = abc[2];
612: }
613: PetscFunctionReturn(PETSC_SUCCESS);
614: }
616: /* create DMComposite of meshes for each species group */
617: static PetscErrorCode LandauDMCreateVMeshes(MPI_Comm comm_self, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM pack)
618: {
619: PetscFunctionBegin;
620: { /* p4est, quads */
621: /* Create plex mesh of Landau domain */
622: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
623: PetscReal par_radius = ctx->radius_par[grid], perp_radius = ctx->radius_perp[grid];
624: if (!ctx->sphere && !ctx->simplex) { // 2 or 3D (only 3D option)
625: PetscReal lo[] = {-perp_radius, -par_radius, -par_radius}, hi[] = {perp_radius, par_radius, par_radius};
626: DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim == 2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
627: if (dim == 2) lo[0] = 0;
628: else {
629: lo[1] = -perp_radius;
630: hi[1] = perp_radius; // 3D y is a perp
631: }
632: PetscCall(DMPlexCreateBoxMesh(comm_self, dim, PETSC_FALSE, ctx->cells0, lo, hi, periodicity, PETSC_TRUE, 0, PETSC_TRUE, &ctx->plex[grid])); // TODO: make composite and create dm[grid] here
633: PetscCall(DMLocalizeCoordinates(ctx->plex[grid])); /* needed for periodic */
634: if (dim == 3) PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cube"));
635: else PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "half-plane"));
636: } else if (dim == 2) {
637: size_t len;
638: PetscCall(PetscStrlen(ctx->filename, &len));
639: if (len) {
640: Vec coords;
641: PetscScalar *x;
642: PetscInt N;
643: char str[] = "-dm_landau_view_file_0";
644: str[21] += grid;
645: PetscCall(DMPlexCreateFromFile(comm_self, ctx->filename, "plexland.c", PETSC_TRUE, &ctx->plex[grid]));
646: PetscCall(DMPlexOrient(ctx->plex[grid]));
647: PetscCall(DMGetCoordinatesLocal(ctx->plex[grid], &coords));
648: PetscCall(VecGetSize(coords, &N));
649: PetscCall(VecGetArray(coords, &x));
650: /* scale by domain size */
651: for (PetscInt i = 0; i < N; i += 2) {
652: x[i + 0] *= ctx->radius_perp[grid];
653: x[i + 1] *= ctx->radius_par[grid];
654: }
655: PetscCall(VecRestoreArray(coords, &x));
656: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], ctx->filename));
657: PetscCall(PetscInfo(ctx->plex[grid], "%" PetscInt_FMT ") Read %s mesh file (%s)\n", grid, ctx->filename, str));
658: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, str));
659: } else { // simplex forces a sphere
660: PetscInt numCells = ctx->simplex ? 12 : 6, cell_size = ctx->simplex ? 3 : 4, j;
661: const PetscInt numVerts = 11;
662: PetscInt cellsT[][4] = {
663: {0, 1, 6, 5 },
664: {1, 2, 7, 6 },
665: {2, 3, 8, 7 },
666: {3, 4, 9, 8 },
667: {5, 6, 7, 10},
668: {10, 7, 8, 9 }
669: };
670: PetscInt cellsS[][3] = {
671: {0, 1, 6 },
672: {1, 2, 6 },
673: {6, 2, 7 },
674: {7, 2, 8 },
675: {8, 2, 3 },
676: {8, 3, 4 },
677: {0, 6, 5 },
678: {5, 6, 7 },
679: {5, 7, 10},
680: {10, 7, 9 },
681: {9, 7, 8 },
682: {9, 8, 4 }
683: };
684: const PetscInt *pcell = (const PetscInt *)(ctx->simplex ? &cellsS[0][0] : &cellsT[0][0]);
685: PetscReal coords[11][2], *flatCoords = &coords[0][0];
686: PetscReal rad = ctx->radius[grid];
687: for (j = 0; j < 5; j++) { // outside edge
688: PetscReal z, r, theta = -PETSC_PI / 2 + (j % 5) * PETSC_PI / 4;
689: r = rad * PetscCosReal(theta);
690: coords[j][0] = r;
691: z = rad * PetscSinReal(theta);
692: coords[j][1] = z;
693: }
694: coords[j][0] = 0;
695: coords[j++][1] = -rad * ctx->sphere_inner_radius_90degree[grid];
696: coords[j][0] = rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
697: coords[j++][1] = -rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
698: coords[j][0] = rad * ctx->sphere_inner_radius_90degree[grid];
699: coords[j++][1] = 0;
700: coords[j][0] = rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
701: coords[j++][1] = rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
702: coords[j][0] = 0;
703: coords[j++][1] = rad * ctx->sphere_inner_radius_90degree[grid];
704: coords[j][0] = 0;
705: coords[j++][1] = 0;
706: PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 2, numCells, numVerts, cell_size, ctx->interpolate, pcell, 2, flatCoords, &ctx->plex[grid]));
707: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "semi-circle"));
708: PetscCall(PetscInfo(ctx->plex[grid], "\t%" PetscInt_FMT ") Make circle %s mesh\n", grid, ctx->simplex ? "simplex" : "tensor"));
709: }
710: } else {
711: PetscCheck(dim == 3 && ctx->sphere && !ctx->simplex, ctx->comm, PETSC_ERR_ARG_WRONG, "not: dim == 3 && ctx->sphere && !ctx->simplex");
712: PetscReal rad = ctx->radius[grid] / 1.732050807568877, inner_rad = rad * ctx->sphere_inner_radius_45degree[grid], outer_rad = rad;
713: const PetscInt numCells = 7, cell_size = 8, numVerts = 16;
714: const PetscInt cells[][8] = {
715: {0, 3, 2, 1, 4, 5, 6, 7 },
716: {0, 4, 5, 1, 8, 9, 13, 12},
717: {1, 5, 6, 2, 9, 10, 14, 13},
718: {2, 6, 7, 3, 10, 11, 15, 14},
719: {0, 3, 7, 4, 8, 12, 15, 11},
720: {0, 1, 2, 3, 8, 11, 10, 9 },
721: {4, 7, 6, 5, 12, 13, 14, 15}
722: };
723: PetscReal coords[16 /* numVerts */][3];
724: for (PetscInt j = 0; j < 4; j++) { // inner edge, low
725: coords[j][0] = inner_rad * (j == 0 || j == 3 ? 1 : -1);
726: coords[j][1] = inner_rad * (j / 2 < 1 ? 1 : -1);
727: coords[j][2] = inner_rad * -1;
728: }
729: for (PetscInt j = 0, jj = 4; j < 4; j++, jj++) { // inner edge, hi
730: coords[jj][0] = inner_rad * (j == 0 || j == 3 ? 1 : -1);
731: coords[jj][1] = inner_rad * (j / 2 < 1 ? 1 : -1);
732: coords[jj][2] = inner_rad * 1;
733: }
734: for (PetscInt j = 0, jj = 8; j < 4; j++, jj++) { // outer edge, low
735: coords[jj][0] = outer_rad * (j == 0 || j == 3 ? 1 : -1);
736: coords[jj][1] = outer_rad * (j / 2 < 1 ? 1 : -1);
737: coords[jj][2] = outer_rad * -1;
738: }
739: for (PetscInt j = 0, jj = 12; j < 4; j++, jj++) { // outer edge, hi
740: coords[jj][0] = outer_rad * (j == 0 || j == 3 ? 1 : -1);
741: coords[jj][1] = outer_rad * (j / 2 < 1 ? 1 : -1);
742: coords[jj][2] = outer_rad * 1;
743: }
744: PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 3, numCells, numVerts, cell_size, ctx->interpolate, (const PetscInt *)cells, 3, (const PetscReal *)coords, &ctx->plex[grid]));
745: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cubed sphere"));
746: PetscCall(PetscInfo(ctx->plex[grid], "\t%" PetscInt_FMT ") Make cubed sphere %s mesh\n", grid, ctx->simplex ? "simplex" : "tensor"));
747: }
748: PetscCall(DMSetFromOptions(ctx->plex[grid]));
749: } // grid loop
750: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)pack, prefix));
751: { /* convert to p4est (or whatever), wait for discretization to create pack */
752: char convType[256];
753: PetscBool flg;
755: PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");
756: PetscCall(PetscOptionsFList("-dm_landau_type", "Convert DMPlex to another format (p4est)", "plexland.c", DMList, DMPLEX, convType, 256, &flg));
757: PetscOptionsEnd();
758: if (flg) {
759: ctx->use_p4est = PETSC_TRUE; /* flag for Forest */
760: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
761: DM dmforest;
762: PetscCall(DMConvert(ctx->plex[grid], convType, &dmforest));
763: if (dmforest) {
764: PetscBool isForest;
765: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dmforest, prefix));
766: PetscCall(DMIsForest(dmforest, &isForest));
767: if (isForest) {
768: if (ctx->sphere) PetscCall(DMForestSetBaseCoordinateMapping(dmforest, GeometryDMLandau, ctx));
769: PetscCall(DMDestroy(&ctx->plex[grid]));
770: ctx->plex[grid] = dmforest; // Forest for adaptivity
771: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Converted to non Forest?");
772: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Convert failed?");
773: }
774: } else ctx->use_p4est = PETSC_FALSE; /* flag for Forest */
775: }
776: } /* non-file */
777: PetscCall(DMSetDimension(pack, dim));
778: PetscCall(PetscObjectSetName((PetscObject)pack, "Mesh"));
779: PetscCall(DMSetApplicationContext(pack, ctx));
780: PetscFunctionReturn(PETSC_SUCCESS);
781: }
783: static PetscErrorCode SetupDS(DM pack, PetscInt dim, PetscInt grid, LandauCtx *ctx)
784: {
785: PetscInt ii, i0;
786: char buf[256];
787: PetscSection section;
789: PetscFunctionBegin;
790: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
791: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "e"));
792: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "i%" PetscInt_FMT, ii));
793: /* Setup Discretization - FEM */
794: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, ctx->simplex, NULL, PETSC_DECIDE, &ctx->fe[ii]));
795: PetscCall(PetscObjectSetName((PetscObject)ctx->fe[ii], buf));
796: PetscCall(DMSetField(ctx->plex[grid], i0, NULL, (PetscObject)ctx->fe[ii]));
797: }
798: PetscCall(DMCreateDS(ctx->plex[grid]));
799: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion));
800: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
801: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "se"));
802: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "si%" PetscInt_FMT, ii));
803: PetscCall(PetscSectionSetComponentName(section, i0, 0, buf));
804: }
805: PetscFunctionReturn(PETSC_SUCCESS);
806: }
808: /* Define a Maxwellian function for testing out the operator. */
810: /* Using cartesian velocity space coordinates, the particle */
811: /* density, [1/m^3], is defined according to */
813: /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */
815: /* Using some constant, c, we normalize the velocity vector into a */
816: /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */
818: /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */
820: /* Defining $\theta=2T/mc^2$, we thus find that the probability density */
821: /* for finding the particle within the interval in a box dx^3 around x is */
823: /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */
825: typedef struct {
826: PetscReal v_0;
827: PetscReal kT_m;
828: PetscReal n;
829: PetscReal shift;
830: } MaxwellianCtx;
832: static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
833: {
834: MaxwellianCtx *mctx = (MaxwellianCtx *)actx;
835: PetscInt i;
836: PetscReal v2 = 0, theta = 2 * mctx->kT_m / (mctx->v_0 * mctx->v_0), shift; /* theta = 2kT/mc^2 */
838: PetscFunctionBegin;
839: /* compute the exponents, v^2 */
840: for (i = 0; i < dim; ++i) v2 += x[i] * x[i];
841: /* evaluate the Maxwellian */
842: if (mctx->shift < 0) shift = -mctx->shift;
843: else {
844: u[0] = mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
845: shift = mctx->shift;
846: }
847: if (shift != 0.) {
848: v2 = 0;
849: for (i = 0; i < dim - 1; ++i) v2 += x[i] * x[i];
850: v2 += (x[dim - 1] - shift) * (x[dim - 1] - shift);
851: /* evaluate the shifted Maxwellian */
852: u[0] += mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
853: }
854: PetscFunctionReturn(PETSC_SUCCESS);
855: }
857: /*@
858: DMPlexLandauAddMaxwellians - Add a Maxwellian distribution to a state
860: Collective
862: Input Parameters:
863: + dm - The mesh (local)
864: . time - Current time
865: . temps - Temperatures of each species (global)
866: . ns - Number density of each species (global)
867: . grid - index into current grid - just used for offset into `temp` and `ns`
868: . b_id - batch index
869: . n_batch - number of batches
870: - actx - Landau context
872: Output Parameter:
873: . X - The state (local to this grid)
875: Level: beginner
877: .seealso: `DMPlexLandauCreateVelocitySpace()`
878: @*/
879: PetscErrorCode DMPlexLandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
880: {
881: LandauCtx *ctx = (LandauCtx *)actx;
882: PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
883: PetscInt dim;
884: MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES];
886: PetscFunctionBegin;
887: PetscCall(DMGetDimension(dm, &dim));
888: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
889: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
890: mctxs[i0] = &data[i0];
891: data[i0].v_0 = ctx->v_0; // v_0 same for all grids
892: data[i0].kT_m = ctx->k * temps[ii] / ctx->masses[ii]; /* kT/m */
893: data[i0].n = ns[ii];
894: initu[i0] = maxwellian;
895: data[i0].shift = 0;
896: }
897: data[0].shift = ctx->electronShift;
898: /* need to make ADD_ALL_VALUES work - TODO */
899: PetscCall(DMProjectFunction(dm, time, initu, (void **)mctxs, INSERT_ALL_VALUES, X));
900: PetscFunctionReturn(PETSC_SUCCESS);
901: }
903: /*
904: LandauSetInitialCondition - Adds Maxwellians with context
906: Collective
908: Input Parameters:
909: . dm - The mesh
910: - grid - index into current grid - just used for offset into temp and ns
911: . b_id - batch index
912: - n_batch - number of batches
913: + actx - Landau context with T and n
915: Output Parameter:
916: . X - The state
918: Level: beginner
920: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauAddMaxwellians()`
921: */
922: static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
923: {
924: LandauCtx *ctx = (LandauCtx *)actx;
926: PetscFunctionBegin;
927: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
928: PetscCall(VecZeroEntries(X));
929: PetscCall(DMPlexLandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, grid, b_id, n_batch, ctx));
930: PetscFunctionReturn(PETSC_SUCCESS);
931: }
933: // adapt a level once. Forest in/out
934: #if defined(PETSC_USE_INFO)
935: static const char *s_refine_names[] = {"RE", "Z1", "Origin", "Z2", "Uniform"};
936: #endif
937: static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscInt type, PetscInt grid, LandauCtx *ctx, DM *newForest)
938: {
939: DM forest, plex, adaptedDM = NULL;
940: PetscDS prob;
941: PetscBool isForest;
942: PetscQuadrature quad;
943: PetscInt Nq, Nb, *Nb2, cStart, cEnd, c, dim, qj, k;
944: DMLabel adaptLabel = NULL;
946: PetscFunctionBegin;
947: forest = ctx->plex[grid];
948: PetscCall(DMCreateDS(forest));
949: PetscCall(DMGetDS(forest, &prob));
950: PetscCall(DMGetDimension(forest, &dim));
951: PetscCall(DMIsForest(forest, &isForest));
952: PetscCheck(isForest, ctx->comm, PETSC_ERR_ARG_WRONG, "! Forest");
953: PetscCall(DMConvert(forest, DMPLEX, &plex));
954: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
955: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "adapt", &adaptLabel));
956: PetscCall(PetscFEGetQuadrature(fem, &quad));
957: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
958: PetscCheck(Nq <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nq, LANDAU_MAX_NQND);
959: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
960: PetscCall(PetscDSGetDimensions(prob, &Nb2));
961: PetscCheck(Nb2[0] == Nb, ctx->comm, PETSC_ERR_ARG_WRONG, " Nb = %" PetscInt_FMT " != Nb (%" PetscInt_FMT ")", Nb, Nb2[0]);
962: PetscCheck(Nb <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nb = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nb, LANDAU_MAX_NQND);
963: PetscCall(PetscInfo(sol, "%" PetscInt_FMT ") Refine phase: %s\n", grid, s_refine_names[type]));
964: if (type == 4) {
965: for (c = cStart; c < cEnd; c++) PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
966: } else if (type == 2) {
967: PetscInt rCellIdx[8], nr = 0, nrmax = (dim == 3) ? 8 : 2;
968: PetscReal minRad = PETSC_INFINITY, r;
969: for (c = cStart; c < cEnd; c++) {
970: PetscReal tt, v0[LANDAU_MAX_NQND * 3], J[LANDAU_MAX_NQND * 9], invJ[LANDAU_MAX_NQND * 9], detJ[LANDAU_MAX_NQND];
971: PetscCall(DMPlexComputeCellGeometryFEM(plex, c, quad, v0, J, invJ, detJ));
972: (void)J;
973: (void)invJ;
974: for (qj = 0; qj < Nq; ++qj) {
975: tt = PetscSqr(v0[dim * qj + 0]) + PetscSqr(v0[dim * qj + 1]) + PetscSqr((dim == 3) ? v0[dim * qj + 2] : 0);
976: r = PetscSqrtReal(tt);
977: if (r < minRad - PETSC_SQRT_MACHINE_EPSILON * 10.) {
978: minRad = r;
979: nr = 0;
980: rCellIdx[nr++] = c;
981: PetscCall(PetscInfo(sol, "\t\t%" PetscInt_FMT ") Found first inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT "\n", grid, (double)r, c, qj + 1, Nq));
982: } else if ((r - minRad) < PETSC_SQRT_MACHINE_EPSILON * 100. && nr < nrmax) {
983: for (k = 0; k < nr; k++)
984: if (c == rCellIdx[k]) break;
985: if (k == nr) {
986: rCellIdx[nr++] = c;
987: PetscCall(PetscInfo(sol, "\t\t\t%" PetscInt_FMT ") Found another inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT ", d=%e\n", grid, (double)r, c, qj + 1, Nq, (double)(r - minRad)));
988: }
989: }
990: }
991: }
992: for (k = 0; k < nr; k++) PetscCall(DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE));
993: PetscCall(PetscInfo(sol, "\t\t\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " origin cells %" PetscInt_FMT ",%" PetscInt_FMT " r=%g\n", grid, nr, rCellIdx[0], rCellIdx[1], (double)minRad));
994: } else if (type == 0 || type == 1 || type == 3) { /* refine along r=0 axis */
995: PetscScalar *coef = NULL;
996: Vec coords;
997: PetscInt csize, Nv, d, nz, nrefined = 0;
998: DM cdm;
999: PetscSection cs;
1000: PetscCall(DMGetCoordinatesLocal(forest, &coords));
1001: PetscCall(DMGetCoordinateDM(forest, &cdm));
1002: PetscCall(DMGetLocalSection(cdm, &cs));
1003: for (c = cStart; c < cEnd; c++) {
1004: PetscInt doit = 0, outside = 0;
1005: PetscCall(DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef));
1006: Nv = csize / dim;
1007: for (nz = d = 0; d < Nv; d++) {
1008: PetscReal z = PetscRealPart(coef[d * dim + (dim - 1)]), x = PetscSqr(PetscRealPart(coef[d * dim + 0])) + ((dim == 3) ? PetscSqr(PetscRealPart(coef[d * dim + 1])) : 0);
1009: x = PetscSqrtReal(x);
1010: if (type == 0) {
1011: if (ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON && (z < -PETSC_MACHINE_EPSILON * 10. || z > ctx->re_radius + PETSC_MACHINE_EPSILON * 10.)) outside++; /* first pass don't refine bottom */
1012: } else if (type == 1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) {
1013: outside++; /* don't refine outside electron refine radius */
1014: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
1015: } else if (type == 3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) {
1016: outside++; /* refine r=0 cells on refinement front */
1017: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
1018: }
1019: if (x < PETSC_MACHINE_EPSILON * 10. && (type != 0 || ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON)) nz++;
1020: }
1021: PetscCall(DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef));
1022: if (doit || (outside < Nv && nz)) {
1023: PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
1024: nrefined++;
1025: }
1026: }
1027: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " cells\n", grid, nrefined));
1028: }
1029: PetscCall(DMDestroy(&plex));
1030: PetscCall(DMAdaptLabel(forest, adaptLabel, &adaptedDM));
1031: PetscCall(DMLabelDestroy(&adaptLabel));
1032: *newForest = adaptedDM;
1033: if (adaptedDM) {
1034: if (isForest) {
1035: PetscCall(DMForestSetAdaptivityForest(adaptedDM, NULL)); // ????
1036: }
1037: PetscCall(DMConvert(adaptedDM, DMPLEX, &plex));
1038: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
1039: PetscCall(PetscInfo(sol, "\t\t\t\t%" PetscInt_FMT ") %" PetscInt_FMT " cells, %" PetscInt_FMT " total quadrature points\n", grid, cEnd - cStart, Nq * (cEnd - cStart)));
1040: PetscCall(DMDestroy(&plex));
1041: } else *newForest = NULL;
1042: PetscFunctionReturn(PETSC_SUCCESS);
1043: }
1045: // forest goes in (ctx->plex[grid]), plex comes out
1046: static PetscErrorCode adapt(PetscInt grid, LandauCtx *ctx, Vec *uu)
1047: {
1048: PetscInt adaptIter;
1050: PetscFunctionBegin;
1051: PetscInt type, limits[5] = {(grid == 0) ? ctx->numRERefine : 0, (grid == 0) ? ctx->nZRefine1 : 0, ctx->numAMRRefine[grid], (grid == 0) ? ctx->nZRefine2 : 0, ctx->postAMRRefine[grid]};
1052: for (type = 0; type < 5; type++) {
1053: for (adaptIter = 0; adaptIter < limits[type]; adaptIter++) {
1054: DM newForest = NULL;
1055: PetscCall(adaptToleranceFEM(ctx->fe[0], *uu, type, grid, ctx, &newForest));
1056: if (newForest) {
1057: PetscCall(DMDestroy(&ctx->plex[grid]));
1058: PetscCall(VecDestroy(uu));
1059: PetscCall(DMCreateGlobalVector(newForest, uu));
1060: PetscCall(LandauSetInitialCondition(newForest, *uu, grid, 0, 1, ctx));
1061: ctx->plex[grid] = newForest;
1062: } else {
1063: PetscCall(PetscInfo(*uu, "No refinement\n"));
1064: }
1065: }
1066: }
1067: PetscCall(PetscObjectSetName((PetscObject)*uu, "uAMR"));
1068: PetscFunctionReturn(PETSC_SUCCESS);
1069: }
1071: // make log(Lambdas) from NRL Plasma formulary
1072: static PetscErrorCode makeLambdas(LandauCtx *ctx)
1073: {
1074: PetscFunctionBegin;
1075: for (PetscInt gridi = 0; gridi < ctx->num_grids; gridi++) {
1076: PetscInt iii = ctx->species_offset[gridi];
1077: PetscReal Ti_ev = (ctx->thermal_temps[iii] / 1.1604525e7) * 1000; // convert (back) to eV
1078: PetscReal ni = ctx->n[iii] * ctx->n_0;
1079: for (PetscInt gridj = gridi; gridj < ctx->num_grids; gridj++) {
1080: PetscInt jjj = ctx->species_offset[gridj];
1081: PetscReal Zj = ctx->charges[jjj] / 1.6022e-19;
1082: if (gridi == 0) {
1083: if (gridj == 0) { // lam_ee
1084: ctx->lambdas[gridi][gridj] = 23.5 - PetscLogReal(PetscSqrtReal(ni) * PetscPowReal(Ti_ev, -1.25)) - PetscSqrtReal(1e-5 + PetscSqr(PetscLogReal(Ti_ev) - 2) / 16);
1085: } else { // lam_ei == lam_ie
1086: if (10 * Zj * Zj > Ti_ev) {
1087: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(PetscSqrtReal(ni) * Zj * PetscPowReal(Ti_ev, -1.5));
1088: } else {
1089: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 24 - PetscLogReal(PetscSqrtReal(ni) / Ti_ev);
1090: }
1091: }
1092: } else { // lam_ii'
1093: PetscReal mui = ctx->masses[iii] / 1.6720e-27, Zi = ctx->charges[iii] / 1.6022e-19;
1094: PetscReal Tj_ev = (ctx->thermal_temps[jjj] / 1.1604525e7) * 1000; // convert (back) to eV
1095: PetscReal muj = ctx->masses[jjj] / 1.6720e-27;
1096: PetscReal nj = ctx->n[jjj] * ctx->n_0;
1097: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(Zi * Zj * (mui + muj) / (mui * Tj_ev + muj * Ti_ev) * PetscSqrtReal(ni * Zi * Zi / Ti_ev + nj * Zj * Zj / Tj_ev));
1098: }
1099: }
1100: }
1101: //PetscReal v0 = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1102: PetscFunctionReturn(PETSC_SUCCESS);
1103: }
1105: static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[])
1106: {
1107: PetscBool flg, fileflg;
1108: PetscInt ii, nt, nm, nc, num_species_grid[LANDAU_MAX_GRIDS], non_dim_grid;
1109: PetscReal lnLam = 10;
1110: DM dummy;
1112: PetscFunctionBegin;
1113: PetscCall(DMCreate(ctx->comm, &dummy));
1114: /* get options - initialize context */
1115: ctx->verbose = 1; // should be 0 for silent compliance
1116: ctx->batch_sz = 1;
1117: ctx->batch_view_idx = 0;
1118: ctx->interpolate = PETSC_TRUE;
1119: ctx->gpu_assembly = PETSC_TRUE;
1120: ctx->norm_state = 0;
1121: ctx->electronShift = 0;
1122: ctx->M = NULL;
1123: ctx->J = NULL;
1124: /* geometry and grids */
1125: ctx->sphere = PETSC_FALSE;
1126: ctx->use_p4est = PETSC_FALSE;
1127: ctx->simplex = PETSC_FALSE;
1128: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1129: ctx->radius[grid] = 5.; /* thermal radius (velocity) */
1130: ctx->radius_perp[grid] = 5.; /* thermal radius (velocity) */
1131: ctx->radius_par[grid] = 5.; /* thermal radius (velocity) */
1132: ctx->numAMRRefine[grid] = 0;
1133: ctx->postAMRRefine[grid] = 0;
1134: ctx->species_offset[grid + 1] = 1; // one species default
1135: num_species_grid[grid] = 0;
1136: ctx->plex[grid] = NULL; /* cache as expensive to Convert */
1137: }
1138: ctx->species_offset[0] = 0;
1139: ctx->re_radius = 0.;
1140: ctx->vperp0_radius1 = 0;
1141: ctx->vperp0_radius2 = 0;
1142: ctx->nZRefine1 = 0;
1143: ctx->nZRefine2 = 0;
1144: ctx->numRERefine = 0;
1145: num_species_grid[0] = 1; // one species default
1146: /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */
1147: ctx->charges[0] = -1; /* electron charge (MKS) */
1148: ctx->masses[0] = 1 / 1835.469965278441013; /* temporary value in proton mass */
1149: ctx->n[0] = 1;
1150: ctx->v_0 = 1; /* thermal velocity, we could start with a scale != 1 */
1151: ctx->thermal_temps[0] = 1;
1152: /* constants, etc. */
1153: ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */
1154: ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */
1155: ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */
1156: ctx->Ez = 0;
1157: for (PetscInt grid = 0; grid < LANDAU_NUM_TIMERS; grid++) ctx->times[grid] = 0;
1158: for (PetscInt ii = 0; ii < LANDAU_DIM; ii++) ctx->cells0[ii] = 2;
1159: if (LANDAU_DIM == 2) ctx->cells0[0] = 1;
1160: ctx->use_matrix_mass = PETSC_FALSE;
1161: ctx->use_relativistic_corrections = PETSC_FALSE;
1162: ctx->use_energy_tensor_trick = PETSC_FALSE; /* Use Eero's trick for energy conservation v --> grad(v^2/2) */
1163: ctx->SData_d.w = NULL;
1164: ctx->SData_d.x = NULL;
1165: ctx->SData_d.y = NULL;
1166: ctx->SData_d.z = NULL;
1167: ctx->SData_d.invJ = NULL;
1168: ctx->jacobian_field_major_order = PETSC_FALSE;
1169: ctx->SData_d.coo_elem_offsets = NULL;
1170: ctx->SData_d.coo_elem_point_offsets = NULL;
1171: ctx->SData_d.coo_elem_fullNb = NULL;
1172: ctx->SData_d.coo_size = 0;
1173: PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");
1174: #if defined(PETSC_HAVE_KOKKOS)
1175: ctx->deviceType = LANDAU_KOKKOS;
1176: PetscCall(PetscStrncpy(ctx->filename, "kokkos", sizeof(ctx->filename)));
1177: #else
1178: ctx->deviceType = LANDAU_CPU;
1179: PetscCall(PetscStrncpy(ctx->filename, "cpu", sizeof(ctx->filename)));
1180: #endif
1181: PetscCall(PetscOptionsString("-dm_landau_device_type", "Use kernels on 'cpu' 'kokkos'", "plexland.c", ctx->filename, ctx->filename, sizeof(ctx->filename), NULL));
1182: PetscCall(PetscStrcmp("cpu", ctx->filename, &flg));
1183: if (flg) {
1184: ctx->deviceType = LANDAU_CPU;
1185: } else {
1186: PetscCall(PetscStrcmp("kokkos", ctx->filename, &flg));
1187: if (flg) ctx->deviceType = LANDAU_KOKKOS;
1188: else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_device_type %s", ctx->filename);
1189: }
1190: ctx->filename[0] = '\0';
1191: PetscCall(PetscOptionsString("-dm_landau_filename", "file to read mesh from", "plexland.c", ctx->filename, ctx->filename, sizeof(ctx->filename), &fileflg));
1192: PetscCall(PetscOptionsReal("-dm_landau_electron_shift", "Shift in thermal velocity of electrons", "none", ctx->electronShift, &ctx->electronShift, NULL));
1193: PetscCall(PetscOptionsInt("-dm_landau_verbose", "Level of verbosity output", "plexland.c", ctx->verbose, &ctx->verbose, NULL));
1194: PetscCall(PetscOptionsInt("-dm_landau_batch_size", "Number of 'vertices' to batch", "ex2.c", ctx->batch_sz, &ctx->batch_sz, NULL));
1195: PetscCheck(LANDAU_MAX_BATCH_SZ >= ctx->batch_sz, ctx->comm, PETSC_ERR_ARG_WRONG, "LANDAU_MAX_BATCH_SZ %d < ctx->batch_sz %" PetscInt_FMT, LANDAU_MAX_BATCH_SZ, ctx->batch_sz);
1196: PetscCall(PetscOptionsInt("-dm_landau_batch_view_idx", "Index of batch for diagnostics like plotting", "ex2.c", ctx->batch_view_idx, &ctx->batch_view_idx, NULL));
1197: PetscCheck(ctx->batch_view_idx < ctx->batch_sz, ctx->comm, PETSC_ERR_ARG_WRONG, "-ctx->batch_view_idx %" PetscInt_FMT " > ctx->batch_sz %" PetscInt_FMT, ctx->batch_view_idx, ctx->batch_sz);
1198: PetscCall(PetscOptionsReal("-dm_landau_Ez", "Initial parallel electric field in unites of Conner-Hastie critical field", "plexland.c", ctx->Ez, &ctx->Ez, NULL));
1199: PetscCall(PetscOptionsReal("-dm_landau_n_0", "Normalization constant for number density", "plexland.c", ctx->n_0, &ctx->n_0, NULL));
1200: PetscCall(PetscOptionsBool("-dm_landau_use_mataxpy_mass", "Use fast but slightly fragile MATAXPY to add mass term", "plexland.c", ctx->use_matrix_mass, &ctx->use_matrix_mass, NULL));
1201: PetscCall(PetscOptionsBool("-dm_landau_use_relativistic_corrections", "Use relativistic corrections", "plexland.c", ctx->use_relativistic_corrections, &ctx->use_relativistic_corrections, NULL));
1202: PetscCall(PetscOptionsBool("-dm_landau_simplex", "Use simplex elements", "plexland.c", ctx->simplex, &ctx->simplex, NULL));
1203: PetscCall(PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, NULL));
1204: if (LANDAU_DIM == 2 && ctx->use_relativistic_corrections) ctx->use_relativistic_corrections = PETSC_FALSE; // should warn
1205: PetscCall(PetscOptionsBool("-dm_landau_use_energy_tensor_trick", "Use Eero's trick of using grad(v^2/2) instead of v as args to Landau tensor to conserve energy with relativistic corrections and Q1 elements", "plexland.c", ctx->use_energy_tensor_trick,
1206: &ctx->use_energy_tensor_trick, NULL));
1208: /* get num species with temperature, set defaults */
1209: for (ii = 1; ii < LANDAU_MAX_SPECIES; ii++) {
1210: ctx->thermal_temps[ii] = 1;
1211: ctx->charges[ii] = 1;
1212: ctx->masses[ii] = 1;
1213: ctx->n[ii] = 1;
1214: }
1215: nt = LANDAU_MAX_SPECIES;
1216: PetscCall(PetscOptionsRealArray("-dm_landau_thermal_temps", "Temperature of each species [e,i_0,i_1,...] in keV (must be set to set number of species)", "plexland.c", ctx->thermal_temps, &nt, &flg));
1217: if (flg) {
1218: PetscCall(PetscInfo(dummy, "num_species set to number of thermal temps provided (%" PetscInt_FMT ")\n", nt));
1219: ctx->num_species = nt;
1220: } else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species");
1221: for (ii = 0; ii < ctx->num_species; ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */
1222: nm = LANDAU_MAX_SPECIES - 1;
1223: PetscCall(PetscOptionsRealArray("-dm_landau_ion_masses", "Mass of each species in units of proton mass [i_0=2,i_1=40...]", "plexland.c", &ctx->masses[1], &nm, &flg));
1224: PetscCheck(!flg || nm == ctx->num_species - 1, ctx->comm, PETSC_ERR_ARG_WRONG, "num ion masses %" PetscInt_FMT " != num species %" PetscInt_FMT, nm, ctx->num_species - 1);
1225: nm = LANDAU_MAX_SPECIES;
1226: PetscCall(PetscOptionsRealArray("-dm_landau_n", "Number density of each species = n_s * n_0", "plexland.c", ctx->n, &nm, &flg));
1227: PetscCheck(!flg || nm == ctx->num_species, ctx->comm, PETSC_ERR_ARG_WRONG, "wrong num n: %" PetscInt_FMT " != num species %" PetscInt_FMT, nm, ctx->num_species);
1228: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */
1229: ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */
1230: nc = LANDAU_MAX_SPECIES - 1;
1231: PetscCall(PetscOptionsRealArray("-dm_landau_ion_charges", "Charge of each species in units of proton charge [i_0=2,i_1=18,...]", "plexland.c", &ctx->charges[1], &nc, &flg));
1232: if (flg) PetscCheck(nc == ctx->num_species - 1, ctx->comm, PETSC_ERR_ARG_WRONG, "num charges %" PetscInt_FMT " != num species %" PetscInt_FMT, nc, ctx->num_species - 1);
1233: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */
1234: /* geometry and grids */
1235: nt = LANDAU_MAX_GRIDS;
1236: PetscCall(PetscOptionsIntArray("-dm_landau_num_species_grid", "Number of species on each grid: [ 1, ....] or [S, 0 ....] for single grid", "plexland.c", num_species_grid, &nt, &flg));
1237: if (flg) {
1238: ctx->num_grids = nt;
1239: for (ii = nt = 0; ii < ctx->num_grids; ii++) nt += num_species_grid[ii];
1240: PetscCheck(ctx->num_species == nt, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_num_species_grid: sum %" PetscInt_FMT " != num_species = %" PetscInt_FMT ". %" PetscInt_FMT " grids (check that number of grids <= LANDAU_MAX_GRIDS = %d)", nt, ctx->num_species,
1241: ctx->num_grids, LANDAU_MAX_GRIDS);
1242: } else {
1243: if (ctx->num_species > LANDAU_MAX_GRIDS) {
1244: num_species_grid[0] = 1;
1245: num_species_grid[1] = ctx->num_species - 1;
1246: ctx->num_grids = 2;
1247: } else {
1248: ctx->num_grids = ctx->num_species;
1249: for (ii = 0; ii < ctx->num_grids; ii++) num_species_grid[ii] = 1;
1250: }
1251: }
1252: for (ctx->species_offset[0] = ii = 0; ii < ctx->num_grids; ii++) ctx->species_offset[ii + 1] = ctx->species_offset[ii] + num_species_grid[ii];
1253: PetscCheck(ctx->species_offset[ctx->num_grids] == ctx->num_species, ctx->comm, PETSC_ERR_ARG_WRONG, "ctx->species_offset[ctx->num_grids] %" PetscInt_FMT " != ctx->num_species = %" PetscInt_FMT " ???????????", ctx->species_offset[ctx->num_grids],
1254: ctx->num_species);
1255: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1256: PetscInt iii = ctx->species_offset[grid]; // normalize with first (arbitrary) species on grid
1257: ctx->thermal_speed[grid] = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1258: }
1259: // get lambdas here because we need them for t_0 etc
1260: PetscCall(PetscOptionsReal("-dm_landau_ln_lambda", "Universal cross section parameter. Default uses NRL formulas", "plexland.c", lnLam, &lnLam, &flg));
1261: if (flg) {
1262: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1263: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) ctx->lambdas[gridj][grid] = lnLam; /* cross section ratio large - small angle collisions */
1264: }
1265: } else {
1266: PetscCall(makeLambdas(ctx));
1267: }
1268: non_dim_grid = 0;
1269: PetscCall(PetscOptionsInt("-dm_landau_normalization_grid", "Index of grid to use for setting v_0, m_0, t_0. (Not recommended)", "plexland.c", non_dim_grid, &non_dim_grid, &flg));
1270: if (non_dim_grid != 0) PetscCall(PetscInfo(dummy, "Normalization grid set to %" PetscInt_FMT ", but non-default not well verified\n", non_dim_grid));
1271: PetscCheck(non_dim_grid >= 0 && non_dim_grid < ctx->num_species, ctx->comm, PETSC_ERR_ARG_WRONG, "Normalization grid wrong: %" PetscInt_FMT, non_dim_grid);
1272: ctx->v_0 = ctx->thermal_speed[non_dim_grid]; /* arbitrary units for non dimensionalization: global mean velocity in 1D of electrons */
1273: ctx->m_0 = ctx->masses[non_dim_grid]; /* arbitrary reference mass, electrons */
1274: ctx->t_0 = 8 * PETSC_PI * PetscSqr(ctx->epsilon0 * ctx->m_0 / PetscSqr(ctx->charges[non_dim_grid])) / ctx->lambdas[non_dim_grid][non_dim_grid] / ctx->n_0 * PetscPowReal(ctx->v_0, 3); /* note, this t_0 makes nu[non_dim_grid,non_dim_grid]=1 */
1275: /* domain */
1276: nt = LANDAU_MAX_GRIDS;
1277: PetscCall(PetscOptionsRealArray("-dm_landau_domain_radius", "Phase space size in units of thermal velocity of grid", "plexland.c", ctx->radius, &nt, &flg));
1278: if (flg) {
1279: PetscCheck(nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_domain_radius: given %" PetscInt_FMT " radius != number grids %" PetscInt_FMT, nt, ctx->num_grids);
1280: while (nt--) ctx->radius_par[nt] = ctx->radius_perp[nt] = ctx->radius[nt];
1281: } else {
1282: nt = LANDAU_MAX_GRIDS;
1283: PetscCall(PetscOptionsRealArray("-dm_landau_domain_max_par", "Parallel velocity domain size in units of thermal velocity of grid", "plexland.c", ctx->radius_par, &nt, &flg));
1284: if (flg) PetscCheck(nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_domain_max_par: given %" PetscInt_FMT " radius != number grids %" PetscInt_FMT, nt, ctx->num_grids);
1285: PetscCall(PetscOptionsRealArray("-dm_landau_domain_max_perp", "Perpendicular velocity domain size in units of thermal velocity of grid", "plexland.c", ctx->radius_perp, &nt, &flg));
1286: if (flg) PetscCheck(nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_domain_max_perp: given %" PetscInt_FMT " radius != number grids %" PetscInt_FMT, nt, ctx->num_grids);
1287: }
1288: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1289: if (flg && ctx->radius[grid] <= 0) { /* negative is ratio of c - need to set par and perp with this -- todo */
1290: if (ctx->radius[grid] == 0) ctx->radius[grid] = 0.75;
1291: else ctx->radius[grid] = -ctx->radius[grid];
1292: ctx->radius[grid] = ctx->radius[grid] * SPEED_OF_LIGHT / ctx->v_0; // use any species on grid to normalize (v_0 same for all on grid)
1293: PetscCall(PetscInfo(dummy, "Change domain radius to %g for grid %" PetscInt_FMT "\n", (double)ctx->radius[grid], grid));
1294: }
1295: ctx->radius[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1296: ctx->radius_perp[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1297: ctx->radius_par[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1298: }
1299: /* amr parameters */
1300: if (!fileflg) {
1301: nt = LANDAU_MAX_GRIDS;
1302: PetscCall(PetscOptionsIntArray("-dm_landau_amr_levels_max", "Number of AMR levels of refinement around origin, after (RE) refinements along z", "plexland.c", ctx->numAMRRefine, &nt, &flg));
1303: PetscCheck(!flg || nt >= ctx->num_grids, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_amr_levels_max: given %" PetscInt_FMT " != number grids %" PetscInt_FMT, nt, ctx->num_grids);
1304: nt = LANDAU_MAX_GRIDS;
1305: PetscCall(PetscOptionsIntArray("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &nt, &flg));
1306: for (ii = 1; ii < ctx->num_grids; ii++) ctx->postAMRRefine[ii] = ctx->postAMRRefine[0]; // all grids the same now
1307: PetscCall(PetscOptionsInt("-dm_landau_amr_re_levels", "Number of levels to refine along v_perp=0, z>0", "plexland.c", ctx->numRERefine, &ctx->numRERefine, &flg));
1308: PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine_pre", "Number of levels to refine along v_perp=0 before origin refine", "plexland.c", ctx->nZRefine1, &ctx->nZRefine1, &flg));
1309: PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine_post", "Number of levels to refine along v_perp=0 after origin refine", "plexland.c", ctx->nZRefine2, &ctx->nZRefine2, &flg));
1310: PetscCall(PetscOptionsReal("-dm_landau_re_radius", "velocity range to refine on positive (z>0) r=0 axis for runaways", "plexland.c", ctx->re_radius, &ctx->re_radius, &flg));
1311: PetscCall(PetscOptionsReal("-dm_landau_z_radius_pre", "velocity range to refine r=0 axis (for electrons)", "plexland.c", ctx->vperp0_radius1, &ctx->vperp0_radius1, &flg));
1312: PetscCall(PetscOptionsReal("-dm_landau_z_radius_post", "velocity range to refine r=0 axis (for electrons) after origin AMR", "plexland.c", ctx->vperp0_radius2, &ctx->vperp0_radius2, &flg));
1313: /* spherical domain */
1314: if (ctx->sphere || ctx->simplex) {
1315: ctx->sphere_uniform_normal = PETSC_FALSE;
1316: PetscCall(PetscOptionsBool("-dm_landau_sphere_uniform_normal", "Scaling of circle radius to get uniform particles per cell with Maxwellians (not used)", "plexland.c", ctx->sphere_uniform_normal, &ctx->sphere_uniform_normal, NULL));
1317: if (!ctx->sphere_uniform_normal) { // true
1318: nt = LANDAU_MAX_GRIDS;
1319: PetscCall(PetscOptionsRealArray("-dm_landau_sphere_inner_radius_90degree_scale", "Scaling of radius for inner circle on 90 degree grid", "plexland.c", ctx->sphere_inner_radius_90degree, &nt, &flg));
1320: if (flg && nt < ctx->num_grids) {
1321: for (PetscInt grid = nt; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_90degree[grid] = ctx->sphere_inner_radius_90degree[0];
1322: } else if (!flg || nt == 0) {
1323: if (LANDAU_DIM == 2) {
1324: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_90degree[grid] = 0.4; // optimized for R=5, Q4, AMR=0
1325: } else {
1326: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_90degree[grid] = 0.577 * 0.40;
1327: }
1328: }
1329: nt = LANDAU_MAX_GRIDS;
1330: PetscCall(PetscOptionsRealArray("-dm_landau_sphere_inner_radius_45degree_scale", "Scaling of radius for inner circle on 45 degree grid", "plexland.c", ctx->sphere_inner_radius_45degree, &nt, &flg));
1331: if (flg && nt < ctx->num_grids) {
1332: for (PetscInt grid = nt; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_45degree[grid] = ctx->sphere_inner_radius_45degree[0];
1333: } else if (!flg || nt == 0) {
1334: if (LANDAU_DIM == 2) {
1335: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_45degree[grid] = 0.45; // optimized for R=5, Q4, AMR=0
1336: } else {
1337: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_45degree[grid] = 0.4; // 3D sphere
1338: }
1339: }
1340: if (ctx->sphere) PetscCall(PetscInfo(ctx->plex[0], "sphere : , 45 degree scaling = %g; 90 degree scaling = %g\n", (double)ctx->sphere_inner_radius_45degree[0], (double)ctx->sphere_inner_radius_90degree[0]));
1341: } else {
1342: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1343: switch (ctx->numAMRRefine[grid]) {
1344: case 0:
1345: case 1:
1346: case 2:
1347: case 3:
1348: default:
1349: if (LANDAU_DIM == 2) {
1350: ctx->sphere_inner_radius_90degree[grid] = 0.40;
1351: ctx->sphere_inner_radius_45degree[grid] = 0.45;
1352: } else {
1353: ctx->sphere_inner_radius_45degree[grid] = 0.25;
1354: }
1355: }
1356: }
1357: }
1358: } else {
1359: nt = LANDAU_DIM;
1360: PetscCall(PetscOptionsIntArray("-dm_landau_num_cells", "Number of cells in each dimension of base grid", "plexland.c", ctx->cells0, &nt, &flg));
1361: }
1362: }
1363: /* processing options */
1364: PetscCall(PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL));
1365: PetscCall(PetscOptionsBool("-dm_landau_jacobian_field_major_order", "Reorder Jacobian for GPU assembly with field major, or block diagonal, ordering (DEPRECATED)", "plexland.c", ctx->jacobian_field_major_order, &ctx->jacobian_field_major_order, NULL));
1366: if (ctx->jacobian_field_major_order) PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order requires -dm_landau_gpu_assembly");
1367: PetscCheck(!ctx->jacobian_field_major_order, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1368: PetscOptionsEnd();
1370: for (ii = ctx->num_species; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0;
1371: if (ctx->verbose != 0) {
1372: PetscReal pmassunit = PetscRealConstant(1.6720e-27);
1374: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "masses: e=%10.3e; ions in proton mass units: %10.3e %10.3e ...\n", (double)ctx->masses[0], (double)(ctx->masses[1] / pmassunit), (double)(ctx->num_species > 2 ? ctx->masses[2] / pmassunit : 0)));
1375: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "charges: e=%10.3e; charges in elementary units: %10.3e %10.3e\n", (double)ctx->charges[0], (double)(-ctx->charges[1] / ctx->charges[0]), (double)(ctx->num_species > 2 ? -ctx->charges[2] / ctx->charges[0] : 0)));
1376: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "n: e: %10.3e i: %10.3e %10.3e\n", (double)ctx->n[0], (double)ctx->n[1], (double)(ctx->num_species > 2 ? ctx->n[2] : 0)));
1377: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "thermal T (K): e=%10.3e i=%10.3e %10.3e. Normalization grid %" PetscInt_FMT ": v_0=%10.3e (%10.3ec) n_0=%10.3e t_0=%10.3e %" PetscInt_FMT " batched, view batch %" PetscInt_FMT "\n", (double)ctx->thermal_temps[0],
1378: (double)ctx->thermal_temps[1], (double)((ctx->num_species > 2) ? ctx->thermal_temps[2] : 0), non_dim_grid, (double)ctx->v_0, (double)(ctx->v_0 / SPEED_OF_LIGHT), (double)ctx->n_0, (double)ctx->t_0, ctx->batch_sz, ctx->batch_view_idx));
1379: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Domain radius (AMR levels) grid %d: par=%10.3e perp=%10.3e (%" PetscInt_FMT ") ", 0, (double)ctx->radius_par[0], (double)ctx->radius_perp[0], ctx->numAMRRefine[0]));
1380: for (ii = 1; ii < ctx->num_grids; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, ", %" PetscInt_FMT ": par=%10.3e perp=%10.3e (%" PetscInt_FMT ") ", ii, (double)ctx->radius_par[ii], (double)ctx->radius_perp[ii], ctx->numAMRRefine[ii]));
1381: if (ctx->use_relativistic_corrections) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nUse relativistic corrections\n"));
1382: else PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1383: }
1384: PetscCall(DMDestroy(&dummy));
1385: {
1386: PetscMPIInt rank;
1387: PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
1388: ctx->stage = 0;
1389: PetscCall(PetscLogEventRegister("Landau Create", DM_CLASSID, &ctx->events[13])); /* 13 */
1390: PetscCall(PetscLogEventRegister(" GPU ass. setup", DM_CLASSID, &ctx->events[2])); /* 2 */
1391: PetscCall(PetscLogEventRegister(" Build matrix", DM_CLASSID, &ctx->events[12])); /* 12 */
1392: PetscCall(PetscLogEventRegister(" Assembly maps", DM_CLASSID, &ctx->events[15])); /* 15 */
1393: PetscCall(PetscLogEventRegister("Landau Mass mat", DM_CLASSID, &ctx->events[14])); /* 14 */
1394: PetscCall(PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11])); /* 11 */
1395: PetscCall(PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0])); /* 0 */
1396: PetscCall(PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9])); /* 9 */
1397: PetscCall(PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10])); /* 10 */
1398: PetscCall(PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7])); /* 7 */
1399: PetscCall(PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1])); /* 1 */
1400: PetscCall(PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3])); /* 3 */
1401: PetscCall(PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8])); /* 8 */
1402: PetscCall(PetscLogEventRegister(" J Kernel (GPU)", DM_CLASSID, &ctx->events[4])); /* 4 */
1403: PetscCall(PetscLogEventRegister(" M Kernel (GPU)", DM_CLASSID, &ctx->events[16])); /* 16 */
1404: PetscCall(PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5])); /* 5 */
1405: PetscCall(PetscLogEventRegister(" CPU assemble", DM_CLASSID, &ctx->events[6])); /* 6 */
1407: if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */
1408: PetscCall(PetscOptionsClearValue(NULL, "-snes_converged_reason"));
1409: PetscCall(PetscOptionsClearValue(NULL, "-ksp_converged_reason"));
1410: PetscCall(PetscOptionsClearValue(NULL, "-snes_monitor"));
1411: PetscCall(PetscOptionsClearValue(NULL, "-ksp_monitor"));
1412: PetscCall(PetscOptionsClearValue(NULL, "-ts_monitor"));
1413: PetscCall(PetscOptionsClearValue(NULL, "-ts_view"));
1414: PetscCall(PetscOptionsClearValue(NULL, "-ts_adapt_monitor"));
1415: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_dm_view"));
1416: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_vec_view"));
1417: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_dm_view"));
1418: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_view"));
1419: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_jacobian_view"));
1420: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mat_view"));
1421: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_converged_reason"));
1422: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_monitor"));
1423: PetscCall(PetscOptionsClearValue(NULL, "-"));
1424: PetscCall(PetscOptionsClearValue(NULL, "-info"));
1425: }
1426: }
1427: PetscFunctionReturn(PETSC_SUCCESS);
1428: }
1430: static PetscErrorCode CreateStaticData(PetscInt dim, IS grid_batch_is_inv[], LandauCtx *ctx)
1431: {
1432: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
1433: PetscQuadrature quad;
1434: const PetscReal *quadWeights;
1435: PetscReal invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES];
1436: PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nb, Nf[LANDAU_MAX_GRIDS], ncellsTot = 0, MAP_BF_SIZE = 64 * LANDAU_DIM * LANDAU_DIM * LANDAU_MAX_Q_FACE * LANDAU_MAX_SPECIES;
1437: PetscTabulation *Tf;
1438: PetscDS prob;
1440: PetscFunctionBegin;
1441: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
1442: PetscCheck(Nb <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nb = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nb, LANDAU_MAX_NQND);
1443: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1444: for (PetscInt ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++) {
1445: invMass[ii] = ctx->m_0 / ctx->masses[ii];
1446: nu_alpha[ii] = PetscSqr(ctx->charges[ii] / ctx->m_0) * ctx->m_0 / ctx->masses[ii];
1447: nu_beta[ii] = PetscSqr(ctx->charges[ii] / ctx->epsilon0) / (8 * PETSC_PI) * ctx->t_0 * ctx->n_0 / PetscPowReal(ctx->v_0, 3);
1448: }
1449: }
1450: if (ctx->verbose == 4) {
1451: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "nu_alpha: "));
1452: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1453: PetscInt iii = ctx->species_offset[grid];
1454: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_alpha[ii]));
1455: }
1456: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_beta: "));
1457: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1458: PetscInt iii = ctx->species_offset[grid];
1459: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_beta[ii]));
1460: }
1461: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_alpha[i]*nu_beta[j]*lambda[i][j]:\n"));
1462: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1463: PetscInt iii = ctx->species_offset[grid];
1464: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) {
1465: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1466: PetscInt jjj = ctx->species_offset[gridj];
1467: for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)(nu_alpha[ii] * nu_beta[jj] * ctx->lambdas[grid][gridj])));
1468: }
1469: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1470: }
1471: }
1472: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "lambda[i][j]:\n"));
1473: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1474: PetscInt iii = ctx->species_offset[grid];
1475: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) {
1476: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1477: PetscInt jjj = ctx->species_offset[gridj];
1478: for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)ctx->lambdas[grid][gridj]));
1479: }
1480: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1481: }
1482: }
1483: }
1484: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
1485: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
1486: /* DS, Tab and quad is same on all grids */
1487: PetscCheck(ctx->plex[0], ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1488: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
1489: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights));
1490: PetscCheck(Nq <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nq, LANDAU_MAX_NQND);
1491: /* setup each grid */
1492: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1493: PetscInt cStart, cEnd;
1494: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1495: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1496: numCells[grid] = cEnd - cStart; // grids can have different topology
1497: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
1498: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
1499: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
1500: ncellsTot += numCells[grid];
1501: }
1502: /* create GPU assembly data */
1503: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1504: PetscContainer container;
1505: PetscScalar *elemMatrix, *elMat;
1506: pointInterpolationP4est(*pointMaps)[LANDAU_MAX_Q_FACE];
1507: P4estVertexMaps *maps;
1508: const PetscInt *plex_batch = NULL, elMatSz = Nb * Nb * ctx->num_species * ctx->num_species;
1509: LandauIdx *coo_elem_offsets = NULL, *coo_elem_fullNb = NULL, (*coo_elem_point_offsets)[LANDAU_MAX_NQND + 1] = NULL;
1510: /* create GPU assembly data */
1511: PetscCall(PetscInfo(ctx->plex[0], "Make GPU maps %d\n", 1));
1512: PetscCall(PetscLogEventBegin(ctx->events[2], 0, 0, 0, 0));
1513: PetscCall(PetscMalloc(sizeof(*maps) * ctx->num_grids, &maps));
1514: PetscCall(PetscMalloc(sizeof(*pointMaps) * MAP_BF_SIZE, &pointMaps));
1515: PetscCall(PetscMalloc(sizeof(*elemMatrix) * elMatSz, &elemMatrix));
1517: { // setup COO assembly -- put COO metadata directly in ctx->SData_d
1518: PetscCall(PetscMalloc3(ncellsTot + 1, &coo_elem_offsets, ncellsTot, &coo_elem_fullNb, ncellsTot, &coo_elem_point_offsets)); // array of integer pointers
1519: coo_elem_offsets[0] = 0; // finish later
1520: PetscCall(PetscInfo(ctx->plex[0], "COO initialization, %" PetscInt_FMT " cells\n", ncellsTot));
1521: ctx->SData_d.coo_n_cellsTot = ncellsTot;
1522: ctx->SData_d.coo_elem_offsets = (void *)coo_elem_offsets;
1523: ctx->SData_d.coo_elem_fullNb = (void *)coo_elem_fullNb;
1524: ctx->SData_d.coo_elem_point_offsets = (void *)coo_elem_point_offsets;
1525: }
1527: ctx->SData_d.coo_max_fullnb = 0;
1528: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1529: PetscInt cStart, cEnd, Nfloc = Nf[grid], totDim = Nfloc * Nb;
1530: if (grid_batch_is_inv[grid]) PetscCall(ISGetIndices(grid_batch_is_inv[grid], &plex_batch));
1531: PetscCheck(!plex_batch, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1532: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1533: // make maps
1534: maps[grid].d_self = NULL;
1535: maps[grid].num_elements = numCells[grid];
1536: maps[grid].num_face = (PetscInt)(pow(Nq, 1. / ((double)dim)) + .001); // Q
1537: maps[grid].num_face = (PetscInt)(pow(maps[grid].num_face, (double)(dim - 1)) + .001); // Q^2
1538: maps[grid].num_reduced = 0;
1539: maps[grid].deviceType = ctx->deviceType;
1540: maps[grid].numgrids = ctx->num_grids;
1541: // count reduced and get
1542: PetscCall(PetscMalloc(maps[grid].num_elements * sizeof(*maps[grid].gIdx), &maps[grid].gIdx));
1543: for (PetscInt ej = cStart, eidx = 0; ej < cEnd; ++ej, ++eidx, glb_elem_idx++) {
1544: if (coo_elem_offsets) coo_elem_offsets[glb_elem_idx + 1] = coo_elem_offsets[glb_elem_idx]; // start with last one, then add
1545: for (PetscInt fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1546: PetscInt fullNb = 0;
1547: for (PetscInt q = 0; q < Nb; ++q) {
1548: PetscInt numindices, *indices;
1549: PetscScalar *valuesOrig = elMat = elemMatrix;
1550: PetscCall(PetscArrayzero(elMat, totDim * totDim));
1551: elMat[(fieldA * Nb + q) * totDim + fieldA * Nb + q] = 1;
1552: PetscCall(DMPlexGetClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, &elMat));
1553: if (ctx->simplex) {
1554: PetscCheck(numindices == Nb, ctx->comm, PETSC_ERR_ARG_WRONG, "numindices != Nb numindices=%" PetscInt_FMT " Nb=%" PetscInt_FMT, numindices, Nb);
1555: for (PetscInt q = 0; q < numindices; ++q) { maps[grid].gIdx[eidx][fieldA][q] = indices[q]; }
1556: fullNb++;
1557: } else {
1558: for (PetscInt f = 0; f < numindices; ++f) { // look for a non-zero on the diagonal (is this too complicated for simplices?)
1559: if (PetscAbs(PetscRealPart(elMat[f * numindices + f])) > PETSC_MACHINE_EPSILON) {
1560: // found it
1561: if (PetscAbs(PetscRealPart(elMat[f * numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { // normal vertex 1.0
1562: if (plex_batch) {
1563: maps[grid].gIdx[eidx][fieldA][q] = plex_batch[indices[f]];
1564: } else {
1565: maps[grid].gIdx[eidx][fieldA][q] = indices[f];
1566: }
1567: fullNb++;
1568: } else { //found a constraint
1569: PetscInt jj = 0;
1570: PetscReal sum = 0;
1571: const PetscInt ff = f;
1572: maps[grid].gIdx[eidx][fieldA][q] = -maps[grid].num_reduced - 1; // store (-)index: id = -(idx+1): idx = -id - 1
1573: PetscCheck(!ctx->simplex, ctx->comm, PETSC_ERR_ARG_WRONG, "No constraints with simplex");
1574: do { // constraints are continuous in Plex - exploit that here
1575: PetscInt ii; // get 'scale'
1576: for (ii = 0, pointMaps[maps[grid].num_reduced][jj].scale = 0; ii < maps[grid].num_face; ii++) { // sum row of outer product to recover vector value
1577: if (ff + ii < numindices) { // 3D has Q and Q^2 interps so might run off end. We could test that elMat[f*numindices + ff + ii] > 0, and break if not
1578: pointMaps[maps[grid].num_reduced][jj].scale += PetscRealPart(elMat[f * numindices + ff + ii]);
1579: }
1580: }
1581: sum += pointMaps[maps[grid].num_reduced][jj].scale; // diagnostic
1582: // get 'gid'
1583: if (pointMaps[maps[grid].num_reduced][jj].scale == 0) pointMaps[maps[grid].num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps
1584: else {
1585: if (plex_batch) {
1586: pointMaps[maps[grid].num_reduced][jj].gid = plex_batch[indices[f]];
1587: } else {
1588: pointMaps[maps[grid].num_reduced][jj].gid = indices[f];
1589: }
1590: fullNb++;
1591: }
1592: } while (++jj < maps[grid].num_face && ++f < numindices); // jj is incremented if we hit the end
1593: while (jj < maps[grid].num_face) {
1594: pointMaps[maps[grid].num_reduced][jj].scale = 0;
1595: pointMaps[maps[grid].num_reduced][jj].gid = -1;
1596: jj++;
1597: }
1598: if (PetscAbs(sum - 1.0) > 10 * PETSC_MACHINE_EPSILON) { // debug
1599: PetscInt d, f;
1600: PetscReal tmp = 0;
1601: PetscCall(
1602: PetscPrintf(PETSC_COMM_SELF, "\t\t%" PetscInt_FMT ".%" PetscInt_FMT ".%" PetscInt_FMT ") ERROR total I = %22.16e (LANDAU_MAX_Q_FACE=%d, #face=%" PetscInt_FMT ")\n", eidx, q, fieldA, (double)sum, LANDAU_MAX_Q_FACE, maps[grid].num_face));
1603: for (d = 0, tmp = 0; d < numindices; ++d) {
1604: if (tmp != 0 && PetscAbs(tmp - 1.0) > 10 * PETSC_MACHINE_EPSILON) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3" PetscInt_FMT ") %3" PetscInt_FMT ": ", d, indices[d]));
1605: for (f = 0; f < numindices; ++f) tmp += PetscRealPart(elMat[d * numindices + f]);
1606: if (tmp != 0) PetscCall(PetscPrintf(ctx->comm, " | %22.16e\n", (double)tmp));
1607: }
1608: }
1609: maps[grid].num_reduced++;
1610: PetscCheck(maps[grid].num_reduced < MAP_BF_SIZE, PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps[grid].num_reduced %" PetscInt_FMT " > %" PetscInt_FMT, maps[grid].num_reduced, MAP_BF_SIZE);
1611: }
1612: break;
1613: }
1614: }
1615: } // !simplex
1616: // cleanup
1617: PetscCall(DMPlexRestoreClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, &elMat));
1618: if (elMat != valuesOrig) PetscCall(DMRestoreWorkArray(ctx->plex[grid], numindices * numindices, MPIU_SCALAR, &elMat));
1619: }
1620: { // setup COO assembly
1621: coo_elem_offsets[glb_elem_idx + 1] += fullNb * fullNb; // one species block, adds a block for each species, on this element in this grid
1622: if (fieldA == 0) { // cache full Nb for this element, on this grid per species
1623: coo_elem_fullNb[glb_elem_idx] = fullNb;
1624: if (fullNb > ctx->SData_d.coo_max_fullnb) ctx->SData_d.coo_max_fullnb = fullNb;
1625: } else PetscCheck(coo_elem_fullNb[glb_elem_idx] == fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "full element size change with species %" PetscInt_FMT " %" PetscInt_FMT, coo_elem_fullNb[glb_elem_idx], fullNb);
1626: }
1627: } // field
1628: } // cell
1629: // allocate and copy point data maps[grid].gIdx[eidx][field][q]
1630: PetscCall(PetscMalloc(maps[grid].num_reduced * sizeof(*maps[grid].c_maps), &maps[grid].c_maps));
1631: for (PetscInt ej = 0; ej < maps[grid].num_reduced; ++ej) {
1632: for (PetscInt q = 0; q < maps[grid].num_face; ++q) {
1633: maps[grid].c_maps[ej][q].scale = pointMaps[ej][q].scale;
1634: maps[grid].c_maps[ej][q].gid = pointMaps[ej][q].gid;
1635: }
1636: }
1637: #if defined(PETSC_HAVE_KOKKOS)
1638: if (ctx->deviceType == LANDAU_KOKKOS) {
1639: PetscCall(LandauKokkosCreateMatMaps(maps, pointMaps, Nf, grid)); // implies Kokkos does
1640: }
1641: #endif
1642: if (plex_batch) {
1643: PetscCall(ISRestoreIndices(grid_batch_is_inv[grid], &plex_batch));
1644: PetscCall(ISDestroy(&grid_batch_is_inv[grid])); // we are done with this
1645: }
1646: } /* grids */
1647: // finish COO
1648: { // setup COO assembly
1649: PetscInt *oor, *ooc;
1650: ctx->SData_d.coo_size = coo_elem_offsets[ncellsTot] * ctx->batch_sz;
1651: PetscCall(PetscMalloc2(ctx->SData_d.coo_size, &oor, ctx->SData_d.coo_size, &ooc));
1652: for (PetscInt i = 0; i < ctx->SData_d.coo_size; i++) oor[i] = ooc[i] = -1;
1653: // get
1654: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1655: for (PetscInt ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1656: const PetscInt fullNb = coo_elem_fullNb[glb_elem_idx];
1657: const LandauIdx *const Idxs = &maps[grid].gIdx[ej][0][0]; // just use field-0 maps, They should be the same but this is just for COO storage
1658: coo_elem_point_offsets[glb_elem_idx][0] = 0;
1659: for (PetscInt f = 0, cnt2 = 0; f < Nb; f++) {
1660: PetscInt idx = Idxs[f];
1661: coo_elem_point_offsets[glb_elem_idx][f + 1] = coo_elem_point_offsets[glb_elem_idx][f]; // start at last
1662: if (idx >= 0) {
1663: cnt2++;
1664: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1665: } else {
1666: idx = -idx - 1;
1667: for (PetscInt q = 0; q < maps[grid].num_face; q++) {
1668: if (maps[grid].c_maps[idx][q].gid < 0) break;
1669: cnt2++;
1670: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1671: }
1672: }
1673: PetscCheck(cnt2 <= fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "wrong count %" PetscInt_FMT " < %" PetscInt_FMT, fullNb, cnt2);
1674: }
1675: PetscCheck(coo_elem_point_offsets[glb_elem_idx][Nb] == fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "coo_elem_point_offsets size %" PetscInt_FMT " != fullNb=%" PetscInt_FMT, coo_elem_point_offsets[glb_elem_idx][Nb], fullNb);
1676: }
1677: }
1678: // set
1679: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1680: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1681: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1682: for (PetscInt ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1683: const PetscInt fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
1684: // set (i,j)
1685: for (PetscInt fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1686: const LandauIdx *const Idxs = &maps[grid].gIdx[ej][fieldA][0];
1687: PetscInt rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE];
1688: for (PetscInt f = 0; f < Nb; ++f) {
1689: const PetscInt nr = coo_elem_point_offsets[glb_elem_idx][f + 1] - coo_elem_point_offsets[glb_elem_idx][f];
1690: if (nr == 1) rows[0] = Idxs[f];
1691: else {
1692: const PetscInt idx = -Idxs[f] - 1;
1693: for (PetscInt q = 0; q < nr; q++) rows[q] = maps[grid].c_maps[idx][q].gid;
1694: }
1695: for (PetscInt g = 0; g < Nb; ++g) {
1696: const PetscInt nc = coo_elem_point_offsets[glb_elem_idx][g + 1] - coo_elem_point_offsets[glb_elem_idx][g];
1697: if (nc == 1) cols[0] = Idxs[g];
1698: else {
1699: const PetscInt idx = -Idxs[g] - 1;
1700: for (PetscInt q = 0; q < nc; q++) cols[q] = maps[grid].c_maps[idx][q].gid;
1701: }
1702: const PetscInt idx0 = b_id * coo_elem_offsets[ncellsTot] + coo_elem_offsets[glb_elem_idx] + fieldA * fullNb2 + fullNb * coo_elem_point_offsets[glb_elem_idx][f] + nr * coo_elem_point_offsets[glb_elem_idx][g];
1703: for (PetscInt q = 0, idx = idx0; q < nr; q++) {
1704: for (PetscInt d = 0; d < nc; d++, idx++) {
1705: oor[idx] = rows[q] + moffset;
1706: ooc[idx] = cols[d] + moffset;
1707: }
1708: }
1709: }
1710: }
1711: }
1712: } // cell
1713: } // grid
1714: } // batch
1715: PetscCall(MatSetPreallocationCOO(ctx->J, ctx->SData_d.coo_size, oor, ooc));
1716: PetscCall(PetscFree2(oor, ooc));
1717: }
1718: PetscCall(PetscFree(pointMaps));
1719: PetscCall(PetscFree(elemMatrix));
1720: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
1721: PetscCall(PetscContainerSetPointer(container, (void *)maps));
1722: PetscCall(PetscContainerSetCtxDestroy(container, LandauGPUMapsDestroy));
1723: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "assembly_maps", (PetscObject)container));
1724: PetscCall(PetscContainerDestroy(&container));
1725: PetscCall(PetscLogEventEnd(ctx->events[2], 0, 0, 0, 0));
1726: } // end GPU assembly
1727: { /* create static point data, Jacobian called first, only one vertex copy */
1728: PetscReal *invJe, *ww, *xx, *yy, *zz = NULL, *invJ_a;
1729: PetscInt outer_ipidx, outer_ej, grid, nip_glb = 0;
1730: PetscFE fe;
1731: PetscCall(PetscLogEventBegin(ctx->events[7], 0, 0, 0, 0));
1732: PetscCall(PetscInfo(ctx->plex[0], "Initialize static data\n"));
1733: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) nip_glb += Nq * numCells[grid];
1734: /* collect f data, first time is for Jacobian, but make mass now */
1735: if (ctx->verbose != 0) {
1736: PetscInt ncells = 0, N;
1737: MatInfo info;
1738: PetscCall(MatGetInfo(ctx->J, MAT_LOCAL, &info));
1739: PetscCall(MatGetSize(ctx->J, &N, NULL));
1740: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ncells += numCells[grid];
1741: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%d) %s %" PetscInt_FMT " IPs, %" PetscInt_FMT " cells total, Nb=%" PetscInt_FMT ", Nq=%" PetscInt_FMT ", dim=%" PetscInt_FMT ", Tab: Nb=%" PetscInt_FMT " Nf=%" PetscInt_FMT " Np=%" PetscInt_FMT " cdim=%" PetscInt_FMT " N=%" PetscInt_FMT " nnz= %" PetscInt_FMT "\n", 0, "FormLandau", nip_glb, ncells, Nb, Nq, dim, Nb,
1742: ctx->num_species, Nb, dim, N, (PetscInt)info.nz_used));
1743: }
1744: PetscCall(PetscMalloc4(nip_glb, &ww, nip_glb, &xx, nip_glb, &yy, nip_glb * dim * dim, &invJ_a));
1745: if (dim == 3) PetscCall(PetscMalloc1(nip_glb, &zz));
1746: if (ctx->use_energy_tensor_trick) {
1747: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, ctx->simplex, NULL, PETSC_DECIDE, &fe));
1748: PetscCall(PetscObjectSetName((PetscObject)fe, "energy"));
1749: }
1750: /* init each grids static data - no batch */
1751: for (grid = 0, outer_ipidx = 0, outer_ej = 0; grid < ctx->num_grids; grid++) { // OpenMP (once)
1752: Vec v2_2 = NULL; // projected function: v^2/2 for non-relativistic, gamma... for relativistic
1753: PetscSection e_section;
1754: DM dmEnergy;
1755: PetscInt cStart, cEnd, ej;
1757: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1758: // prep energy trick, get v^2 / 2 vector
1759: if (ctx->use_energy_tensor_trick) {
1760: PetscErrorCode (*energyf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {ctx->use_relativistic_corrections ? gamma_m1_f : energy_f};
1761: Vec glob_v2;
1762: PetscReal *c2_0[1], data[1] = {PetscSqr(C_0(ctx->v_0))};
1764: PetscCall(DMClone(ctx->plex[grid], &dmEnergy));
1765: PetscCall(PetscObjectSetName((PetscObject)dmEnergy, "energy"));
1766: PetscCall(DMSetField(dmEnergy, 0, NULL, (PetscObject)fe));
1767: PetscCall(DMCreateDS(dmEnergy));
1768: PetscCall(DMGetLocalSection(dmEnergy, &e_section));
1769: PetscCall(DMGetGlobalVector(dmEnergy, &glob_v2));
1770: PetscCall(PetscObjectSetName((PetscObject)glob_v2, "trick"));
1771: c2_0[0] = &data[0];
1772: PetscCall(DMProjectFunction(dmEnergy, 0., energyf, (void **)c2_0, INSERT_ALL_VALUES, glob_v2));
1773: PetscCall(DMGetLocalVector(dmEnergy, &v2_2));
1774: PetscCall(VecZeroEntries(v2_2)); /* zero BCs so don't set */
1775: PetscCall(DMGlobalToLocalBegin(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1776: PetscCall(DMGlobalToLocalEnd(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1777: PetscCall(DMViewFromOptions(dmEnergy, NULL, "-energy_dm_view"));
1778: PetscCall(VecViewFromOptions(glob_v2, NULL, "-energy_vec_view"));
1779: PetscCall(DMRestoreGlobalVector(dmEnergy, &glob_v2));
1780: }
1781: /* append part of the IP data for each grid */
1782: for (ej = 0; ej < numCells[grid]; ++ej, ++outer_ej) {
1783: PetscScalar *coefs = NULL;
1784: PetscReal vj[LANDAU_MAX_NQND * LANDAU_DIM], detJj[LANDAU_MAX_NQND], Jdummy[LANDAU_MAX_NQND * LANDAU_DIM * LANDAU_DIM], c0 = C_0(ctx->v_0), c02 = PetscSqr(c0);
1785: invJe = invJ_a + outer_ej * Nq * dim * dim;
1786: PetscCall(DMPlexComputeCellGeometryFEM(ctx->plex[grid], ej + cStart, quad, vj, Jdummy, invJe, detJj));
1787: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecGetClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1788: /* create static point data */
1789: for (PetscInt qj = 0; qj < Nq; qj++, outer_ipidx++) {
1790: const PetscInt gidx = outer_ipidx;
1791: const PetscReal *invJ = &invJe[qj * dim * dim];
1792: ww[gidx] = detJj[qj] * quadWeights[qj];
1793: if (dim == 2) ww[gidx] *= vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */
1794: // get xx, yy, zz
1795: if (ctx->use_energy_tensor_trick) {
1796: double refSpaceDer[3], eGradPhi[3];
1797: const PetscReal *const DD = Tf[0]->T[1];
1798: const PetscReal *Dq = &DD[qj * Nb * dim];
1799: for (PetscInt d = 0; d < 3; ++d) refSpaceDer[d] = eGradPhi[d] = 0.0;
1800: for (PetscInt b = 0; b < Nb; ++b) {
1801: for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] += Dq[b * dim + d] * PetscRealPart(coefs[b]);
1802: }
1803: xx[gidx] = 1e10;
1804: if (ctx->use_relativistic_corrections) {
1805: double dg2_c2 = 0;
1806: //for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] *= c02;
1807: for (PetscInt d = 0; d < dim; ++d) dg2_c2 += PetscSqr(refSpaceDer[d]);
1808: dg2_c2 *= (double)c02;
1809: if (dg2_c2 >= .999) {
1810: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1811: yy[gidx] = vj[qj * dim + 1];
1812: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1813: PetscCall(PetscPrintf(ctx->comm, "Error: %12.5e %" PetscInt_FMT ".%" PetscInt_FMT ") dg2/c02 = %12.5e x= %12.5e %12.5e %12.5e\n", (double)PetscSqrtReal(xx[gidx] * xx[gidx] + yy[gidx] * yy[gidx] + zz[gidx] * zz[gidx]), ej, qj, dg2_c2, (double)xx[gidx], (double)yy[gidx], (double)zz[gidx]));
1814: } else {
1815: PetscReal fact = c02 / PetscSqrtReal(1. - dg2_c2);
1816: for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] *= fact;
1817: // could test with other point u' that (grad - grad') * U (refSpaceDer, refSpaceDer') == 0
1818: }
1819: }
1820: if (xx[gidx] == 1e10) {
1821: for (PetscInt d = 0; d < dim; ++d) {
1822: for (PetscInt e = 0; e < dim; ++e) eGradPhi[d] += invJ[e * dim + d] * refSpaceDer[e];
1823: }
1824: xx[gidx] = eGradPhi[0];
1825: yy[gidx] = eGradPhi[1];
1826: if (dim == 3) zz[gidx] = eGradPhi[2];
1827: }
1828: } else {
1829: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1830: yy[gidx] = vj[qj * dim + 1];
1831: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1832: }
1833: } /* q */
1834: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecRestoreClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1835: } /* ej */
1836: if (ctx->use_energy_tensor_trick) {
1837: PetscCall(DMRestoreLocalVector(dmEnergy, &v2_2));
1838: PetscCall(DMDestroy(&dmEnergy));
1839: }
1840: } /* grid */
1841: if (ctx->use_energy_tensor_trick) PetscCall(PetscFEDestroy(&fe));
1842: /* cache static data */
1843: if (ctx->deviceType == LANDAU_KOKKOS) {
1844: #if defined(PETSC_HAVE_KOKKOS)
1845: PetscCall(LandauKokkosStaticDataSet(ctx->plex[0], Nq, Nb, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, (PetscReal *)ctx->lambdas, invJ_a, xx, yy, zz, ww, &ctx->SData_d));
1846: /* free */
1847: PetscCall(PetscFree4(ww, xx, yy, invJ_a));
1848: if (dim == 3) PetscCall(PetscFree(zz));
1849: #else
1850: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type kokkos not built");
1851: #endif
1852: } else { /* CPU version, just copy in, only use part */
1853: PetscReal *nu_alpha_p = (PetscReal *)ctx->SData_d.alpha, *nu_beta_p = (PetscReal *)ctx->SData_d.beta, *invMass_p = (PetscReal *)ctx->SData_d.invMass, *lambdas_p = NULL; // why set these ?
1854: ctx->SData_d.w = (void *)ww;
1855: ctx->SData_d.x = (void *)xx;
1856: ctx->SData_d.y = (void *)yy;
1857: ctx->SData_d.z = (void *)zz;
1858: ctx->SData_d.invJ = (void *)invJ_a;
1859: PetscCall(PetscMalloc4(ctx->num_species, &nu_alpha_p, ctx->num_species, &nu_beta_p, ctx->num_species, &invMass_p, LANDAU_MAX_GRIDS * LANDAU_MAX_GRIDS, &lambdas_p));
1860: for (PetscInt ii = 0; ii < ctx->num_species; ii++) {
1861: nu_alpha_p[ii] = nu_alpha[ii];
1862: nu_beta_p[ii] = nu_beta[ii];
1863: invMass_p[ii] = invMass[ii];
1864: }
1865: ctx->SData_d.alpha = (void *)nu_alpha_p;
1866: ctx->SData_d.beta = (void *)nu_beta_p;
1867: ctx->SData_d.invMass = (void *)invMass_p;
1868: ctx->SData_d.lambdas = (void *)lambdas_p;
1869: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1870: PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
1871: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) { (*lambdas)[grid][gridj] = ctx->lambdas[grid][gridj]; }
1872: }
1873: }
1874: PetscCall(PetscLogEventEnd(ctx->events[7], 0, 0, 0, 0));
1875: } // initialize
1876: PetscFunctionReturn(PETSC_SUCCESS);
1877: }
1879: /* < v, u > */
1880: static void g0_1(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, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[])
1881: {
1882: g0[0] = 1.;
1883: }
1885: /* < v, u > */
1886: static void g0_fake(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, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[])
1887: {
1888: static double ttt = 1e-12;
1889: g0[0] = ttt++;
1890: }
1892: /* < v, u > */
1893: static void g0_r(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, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[])
1894: {
1895: g0[0] = 2. * PETSC_PI * x[0];
1896: }
1898: /*
1899: LandauCreateJacobianMatrix - creates ctx->J with without real data. Hard to keep sparse.
1900: - Like DMPlexLandauCreateMassMatrix. Should remove one and combine
1901: - has old support for field major ordering
1902: */
1903: static PetscErrorCode LandauCreateJacobianMatrix(MPI_Comm comm, Vec X, IS grid_batch_is_inv[LANDAU_MAX_GRIDS], LandauCtx *ctx)
1904: {
1905: PetscInt *idxs = NULL;
1906: Mat subM[LANDAU_MAX_GRIDS];
1908: PetscFunctionBegin;
1909: if (!ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1910: PetscFunctionReturn(PETSC_SUCCESS);
1911: }
1912: // get the RCM for this grid to separate out species into blocks -- create 'idxs' & 'ctx->batch_is' -- not used
1913: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(PetscMalloc1(ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, &idxs));
1914: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1915: const PetscInt *values, n = ctx->mat_offset[grid + 1] - ctx->mat_offset[grid];
1916: Mat gMat;
1917: DM massDM;
1918: PetscDS prob;
1919: Vec tvec;
1920: // get "mass" matrix for reordering
1921: PetscCall(DMClone(ctx->plex[grid], &massDM));
1922: PetscCall(DMCopyFields(ctx->plex[grid], PETSC_DETERMINE, PETSC_DETERMINE, massDM));
1923: PetscCall(DMCreateDS(massDM));
1924: PetscCall(DMGetDS(massDM, &prob));
1925: for (PetscInt ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_fake, NULL, NULL, NULL));
1926: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); // this trick is need to both sparsify the matrix and avoid runtime error
1927: PetscCall(DMCreateMatrix(massDM, &gMat));
1928: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
1929: PetscCall(MatSetOption(gMat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
1930: PetscCall(MatSetOption(gMat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
1931: PetscCall(DMCreateLocalVector(ctx->plex[grid], &tvec));
1932: PetscCall(DMPlexSNESComputeJacobianFEM(massDM, tvec, gMat, gMat, ctx));
1933: PetscCall(MatViewFromOptions(gMat, NULL, "-dm_landau_reorder_mat_view"));
1934: PetscCall(DMDestroy(&massDM));
1935: PetscCall(VecDestroy(&tvec));
1936: subM[grid] = gMat;
1937: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1938: MatOrderingType rtype = MATORDERINGRCM;
1939: IS isrow, isicol;
1940: PetscCall(MatGetOrdering(gMat, rtype, &isrow, &isicol));
1941: PetscCall(ISInvertPermutation(isrow, PETSC_DECIDE, &grid_batch_is_inv[grid]));
1942: PetscCall(ISGetIndices(isrow, &values));
1943: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
1944: #if !defined(LANDAU_SPECIES_MAJOR)
1945: PetscInt N = ctx->mat_offset[ctx->num_grids], n0 = ctx->mat_offset[grid] + b_id * N;
1946: for (PetscInt ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1947: #else
1948: PetscInt n0 = ctx->mat_offset[grid] * ctx->batch_sz + b_id * n;
1949: for (PetscInt ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1950: #endif
1951: }
1952: PetscCall(ISRestoreIndices(isrow, &values));
1953: PetscCall(ISDestroy(&isrow));
1954: PetscCall(ISDestroy(&isicol));
1955: }
1956: }
1957: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(ISCreateGeneral(comm, ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, idxs, PETSC_OWN_POINTER, &ctx->batch_is));
1958: // get a block matrix
1959: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1960: Mat B = subM[grid];
1961: PetscInt nloc, nzl, *colbuf, row, COL_BF_SIZE = 1024;
1962: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1963: PetscCall(MatGetSize(B, &nloc, NULL));
1964: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1965: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1966: const PetscInt *cols;
1967: const PetscScalar *vals;
1968: for (PetscInt i = 0; i < nloc; i++) {
1969: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
1970: if (nzl > COL_BF_SIZE) {
1971: PetscCall(PetscFree(colbuf));
1972: PetscCall(PetscInfo(ctx->plex[grid], "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl));
1973: COL_BF_SIZE = nzl;
1974: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1975: }
1976: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
1977: for (PetscInt j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
1978: row = i + moffset;
1979: PetscCall(MatSetValues(ctx->J, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
1980: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
1981: }
1982: }
1983: PetscCall(PetscFree(colbuf));
1984: }
1985: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
1986: PetscCall(MatAssemblyBegin(ctx->J, MAT_FINAL_ASSEMBLY));
1987: PetscCall(MatAssemblyEnd(ctx->J, MAT_FINAL_ASSEMBLY));
1989: // debug
1990: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_mat_view"));
1991: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1992: Mat mat_block_order;
1993: PetscCall(MatCreateSubMatrix(ctx->J, ctx->batch_is, ctx->batch_is, MAT_INITIAL_MATRIX, &mat_block_order)); // use MatPermute
1994: PetscCall(MatViewFromOptions(mat_block_order, NULL, "-dm_landau_mat_view"));
1995: PetscCall(MatDestroy(&mat_block_order));
1996: PetscCall(VecScatterCreate(X, ctx->batch_is, X, NULL, &ctx->plex_batch));
1997: PetscCall(VecDuplicate(X, &ctx->work_vec));
1998: }
1999: PetscFunctionReturn(PETSC_SUCCESS);
2000: }
2002: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat);
2003: /*@C
2004: DMPlexLandauCreateVelocitySpace - Create a `DMPLEX` velocity space mesh
2006: Collective
2008: Input Parameters:
2009: + comm - The MPI communicator
2010: . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver)
2011: - prefix - prefix for options (not tested)
2013: Output Parameters:
2014: + pack - The `DM` object representing the mesh
2015: . X - A vector (user destroys)
2016: - J - Optional matrix (object destroys)
2018: Level: beginner
2020: .seealso: `DMPlexCreate()`, `DMPlexLandauDestroyVelocitySpace()`
2021: @*/
2022: PetscErrorCode DMPlexLandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *pack)
2023: {
2024: LandauCtx *ctx;
2025: Vec Xsub[LANDAU_MAX_GRIDS];
2026: IS grid_batch_is_inv[LANDAU_MAX_GRIDS];
2028: PetscFunctionBegin;
2029: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported");
2030: PetscCheck(LANDAU_DIM == dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " != LANDAU_DIM %d", dim, LANDAU_DIM);
2031: PetscCall(PetscNew(&ctx));
2032: ctx->comm = comm; /* used for diagnostics and global errors */
2033: /* process options */
2034: PetscCall(ProcessOptions(ctx, prefix));
2035: if (dim == 2) ctx->use_relativistic_corrections = PETSC_FALSE;
2036: /* Create Mesh */
2037: PetscCall(DMCompositeCreate(PETSC_COMM_SELF, pack));
2038: PetscCall(PetscLogEventBegin(ctx->events[13], 0, 0, 0, 0));
2039: PetscCall(PetscLogEventBegin(ctx->events[15], 0, 0, 0, 0));
2040: PetscCall(LandauDMCreateVMeshes(PETSC_COMM_SELF, dim, prefix, ctx, *pack)); // creates grids (Forest of AMR)
2041: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2042: /* create FEM */
2043: PetscCall(SetupDS(ctx->plex[grid], dim, grid, ctx));
2044: /* set initial state */
2045: PetscCall(DMCreateGlobalVector(ctx->plex[grid], &Xsub[grid]));
2046: PetscCall(PetscObjectSetName((PetscObject)Xsub[grid], "u_orig"));
2047: /* initial static refinement, no solve */
2048: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, 0, 1, ctx));
2049: /* forest refinement - forest goes in (if forest), plex comes out */
2050: if (ctx->use_p4est) {
2051: DM plex;
2052: PetscCall(adapt(grid, ctx, &Xsub[grid])); // forest goes in, plex comes out
2053: if (grid == 0) {
2054: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, "-dm_landau_amr_dm_view")); // need to differentiate - todo
2055: PetscCall(VecViewFromOptions(Xsub[grid], NULL, "-dm_landau_amr_vec_view"));
2056: }
2057: // convert to plex, all done with this level
2058: PetscCall(DMConvert(ctx->plex[grid], DMPLEX, &plex));
2059: PetscCall(DMDestroy(&ctx->plex[grid]));
2060: ctx->plex[grid] = plex;
2061: }
2062: #if !defined(LANDAU_SPECIES_MAJOR)
2063: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2064: #else
2065: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2066: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2067: }
2068: #endif
2069: PetscCall(DMSetApplicationContext(ctx->plex[grid], ctx));
2070: }
2071: #if !defined(LANDAU_SPECIES_MAJOR)
2072: // stack the batched DMs, could do it all here!!! b_id=0
2073: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2074: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2075: }
2076: #endif
2077: // create ctx->mat_offset
2078: ctx->mat_offset[0] = 0;
2079: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2080: PetscInt n;
2081: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2082: ctx->mat_offset[grid + 1] = ctx->mat_offset[grid] + n;
2083: }
2084: // creat DM & Jac
2085: PetscCall(DMSetApplicationContext(*pack, ctx));
2086: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2087: PetscCall(DMCreateMatrix(*pack, &ctx->J));
2088: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2089: PetscCall(MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2090: PetscCall(MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2091: PetscCall(PetscObjectSetName((PetscObject)ctx->J, "Jac"));
2092: // construct initial conditions in X
2093: PetscCall(DMCreateGlobalVector(*pack, X));
2094: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2095: PetscInt n;
2096: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2097: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2098: PetscScalar const *values;
2099: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2100: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, b_id, ctx->batch_sz, ctx));
2101: PetscCall(VecGetArrayRead(Xsub[grid], &values)); // Drop whole grid in Plex ordering
2102: for (PetscInt i = 0, idx = moffset; i < n; i++, idx++) PetscCall(VecSetValue(*X, idx, values[i], INSERT_VALUES));
2103: PetscCall(VecRestoreArrayRead(Xsub[grid], &values));
2104: }
2105: }
2106: // cleanup
2107: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(VecDestroy(&Xsub[grid]));
2108: /* check for correct matrix type */
2109: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
2110: PetscBool flg;
2111: if (ctx->deviceType == LANDAU_KOKKOS) {
2112: PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, MATAIJKOKKOS, ""));
2113: #if defined(PETSC_HAVE_KOKKOS)
2114: PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "must use '-dm_mat_type aijkokkos -dm_vec_type kokkos' for GPU assembly and Kokkos or use '-dm_landau_device_type cpu'");
2115: #else
2116: PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "must configure with '--download-kokkos-kernels' for GPU assembly and Kokkos or use '-dm_landau_device_type cpu'");
2117: #endif
2118: }
2119: }
2120: PetscCall(PetscLogEventEnd(ctx->events[15], 0, 0, 0, 0));
2122: // create field major ordering
2123: ctx->work_vec = NULL;
2124: ctx->plex_batch = NULL;
2125: ctx->batch_is = NULL;
2126: for (PetscInt i = 0; i < LANDAU_MAX_GRIDS; i++) grid_batch_is_inv[i] = NULL;
2127: PetscCall(PetscLogEventBegin(ctx->events[12], 0, 0, 0, 0));
2128: PetscCall(LandauCreateJacobianMatrix(comm, *X, grid_batch_is_inv, ctx));
2129: PetscCall(PetscLogEventEnd(ctx->events[12], 0, 0, 0, 0));
2131: // create AMR GPU assembly maps and static GPU data
2132: PetscCall(CreateStaticData(dim, grid_batch_is_inv, ctx));
2134: PetscCall(PetscLogEventEnd(ctx->events[13], 0, 0, 0, 0));
2136: // create mass matrix
2137: PetscCall(DMPlexLandauCreateMassMatrix(*pack, NULL));
2139: if (J) *J = ctx->J;
2141: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
2142: PetscContainer container;
2143: // cache ctx for KSP with batch/field major Jacobian ordering -ksp_type gmres/etc -dm_landau_jacobian_field_major_order
2144: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2145: PetscCall(PetscContainerSetPointer(container, (void *)ctx));
2146: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "LandauCtx", (PetscObject)container));
2147: PetscCall(PetscContainerDestroy(&container));
2148: // batch solvers need to map -- can batch solvers work
2149: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2150: PetscCall(PetscContainerSetPointer(container, (void *)ctx->plex_batch));
2151: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "plex_batch_is", (PetscObject)container));
2152: PetscCall(PetscContainerDestroy(&container));
2153: }
2154: // for batch solvers
2155: {
2156: PetscContainer container;
2157: PetscInt *pNf;
2158: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2159: PetscCall(PetscMalloc1(sizeof(*pNf), &pNf));
2160: *pNf = ctx->batch_sz;
2161: PetscCall(PetscContainerSetPointer(container, (void *)pNf));
2162: PetscCall(PetscContainerSetCtxDestroy(container, PetscCtxDestroyDefault));
2163: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "batch size", (PetscObject)container));
2164: PetscCall(PetscContainerDestroy(&container));
2165: }
2166: PetscFunctionReturn(PETSC_SUCCESS);
2167: }
2169: /*@C
2170: DMPlexLandauAccess - Access to the distribution function with user callback
2172: Collective
2174: Input Parameters:
2175: + pack - the `DMCOMPOSITE`
2176: . func - call back function
2177: - user_ctx - user context
2179: Input/Output Parameter:
2180: . X - Vector to data to
2182: Level: advanced
2184: .seealso: `DMPlexLandauCreateVelocitySpace()`
2185: @*/
2186: PetscErrorCode DMPlexLandauAccess(DM pack, Vec X, PetscErrorCode (*func)(DM, Vec, PetscInt, PetscInt, PetscInt, void *), void *user_ctx)
2187: {
2188: LandauCtx *ctx;
2190: PetscFunctionBegin;
2191: PetscCall(DMGetApplicationContext(pack, &ctx)); // uses ctx->num_grids; ctx->plex[grid]; ctx->batch_sz; ctx->mat_offset
2192: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2193: PetscInt dim, n;
2194: PetscCall(DMGetDimension(pack, &dim));
2195: for (PetscInt sp = ctx->species_offset[grid], i0 = 0; sp < ctx->species_offset[grid + 1]; sp++, i0++) {
2196: Vec vec;
2197: PetscInt vf[1] = {i0};
2198: IS vis;
2199: DM vdm;
2200: PetscCall(DMCreateSubDM(ctx->plex[grid], 1, vf, &vis, &vdm));
2201: PetscCall(DMSetApplicationContext(vdm, ctx)); // the user might want this
2202: PetscCall(DMCreateGlobalVector(vdm, &vec));
2203: PetscCall(VecGetSize(vec, &n));
2204: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2205: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2206: PetscCall(VecZeroEntries(vec));
2207: /* Add your data with 'dm' for species 'sp' to 'vec' */
2208: PetscCall(func(vdm, vec, i0, grid, b_id, user_ctx));
2209: /* add to global */
2210: PetscScalar const *values;
2211: const PetscInt *offsets;
2212: PetscCall(VecGetArrayRead(vec, &values));
2213: PetscCall(ISGetIndices(vis, &offsets));
2214: for (PetscInt i = 0; i < n; i++) PetscCall(VecSetValue(X, moffset + offsets[i], values[i], ADD_VALUES));
2215: PetscCall(VecRestoreArrayRead(vec, &values));
2216: PetscCall(ISRestoreIndices(vis, &offsets));
2217: } // batch
2218: PetscCall(VecDestroy(&vec));
2219: PetscCall(ISDestroy(&vis));
2220: PetscCall(DMDestroy(&vdm));
2221: }
2222: } // grid
2223: PetscFunctionReturn(PETSC_SUCCESS);
2224: }
2226: /*@
2227: DMPlexLandauDestroyVelocitySpace - Destroy a `DMPLEX` velocity space mesh
2229: Collective
2231: Input/Output Parameters:
2232: . dm - the `DM` to destroy
2234: Level: beginner
2236: .seealso: `DMPlexLandauCreateVelocitySpace()`
2237: @*/
2238: PetscErrorCode DMPlexLandauDestroyVelocitySpace(DM *dm)
2239: {
2240: LandauCtx *ctx;
2242: PetscFunctionBegin;
2243: PetscCall(DMGetApplicationContext(*dm, &ctx));
2244: PetscCall(MatDestroy(&ctx->M));
2245: PetscCall(MatDestroy(&ctx->J));
2246: for (PetscInt ii = 0; ii < ctx->num_species; ii++) PetscCall(PetscFEDestroy(&ctx->fe[ii]));
2247: PetscCall(ISDestroy(&ctx->batch_is));
2248: PetscCall(VecDestroy(&ctx->work_vec));
2249: PetscCall(VecScatterDestroy(&ctx->plex_batch));
2250: if (ctx->deviceType == LANDAU_KOKKOS) {
2251: #if defined(PETSC_HAVE_KOKKOS)
2252: PetscCall(LandauKokkosStaticDataClear(&ctx->SData_d));
2253: #else
2254: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
2255: #endif
2256: } else {
2257: if (ctx->SData_d.x) { /* in a CPU run */
2258: PetscReal *invJ = (PetscReal *)ctx->SData_d.invJ, *xx = (PetscReal *)ctx->SData_d.x, *yy = (PetscReal *)ctx->SData_d.y, *zz = (PetscReal *)ctx->SData_d.z, *ww = (PetscReal *)ctx->SData_d.w;
2259: LandauIdx *coo_elem_offsets = (LandauIdx *)ctx->SData_d.coo_elem_offsets, *coo_elem_fullNb = (LandauIdx *)ctx->SData_d.coo_elem_fullNb, (*coo_elem_point_offsets)[LANDAU_MAX_NQND + 1] = (LandauIdx(*)[LANDAU_MAX_NQND + 1]) ctx->SData_d.coo_elem_point_offsets;
2260: PetscCall(PetscFree4(ww, xx, yy, invJ));
2261: if (zz) PetscCall(PetscFree(zz));
2262: if (coo_elem_offsets) {
2263: PetscCall(PetscFree3(coo_elem_offsets, coo_elem_fullNb, coo_elem_point_offsets)); // could be NULL
2264: }
2265: PetscCall(PetscFree4(ctx->SData_d.alpha, ctx->SData_d.beta, ctx->SData_d.invMass, ctx->SData_d.lambdas));
2266: }
2267: }
2269: if (ctx->times[LANDAU_MATRIX_TOTAL] > 0) { // OMP timings
2270: PetscCall(PetscPrintf(ctx->comm, "TSStep N 1.0 %10.3e\n", ctx->times[LANDAU_EX2_TSSOLVE]));
2271: PetscCall(PetscPrintf(ctx->comm, "2: Solve: %10.3e with %" PetscInt_FMT " threads\n", ctx->times[LANDAU_EX2_TSSOLVE] - ctx->times[LANDAU_MATRIX_TOTAL], ctx->batch_sz));
2272: PetscCall(PetscPrintf(ctx->comm, "3: Landau: %10.3e\n", ctx->times[LANDAU_MATRIX_TOTAL]));
2273: PetscCall(PetscPrintf(ctx->comm, "Landau Jacobian %" PetscInt_FMT " 1.0 %10.3e\n", (PetscInt)ctx->times[LANDAU_JACOBIAN_COUNT], ctx->times[LANDAU_JACOBIAN]));
2274: PetscCall(PetscPrintf(ctx->comm, "Landau Operator N 1.0 %10.3e\n", ctx->times[LANDAU_OPERATOR]));
2275: PetscCall(PetscPrintf(ctx->comm, "Landau Mass N 1.0 %10.3e\n", ctx->times[LANDAU_MASS]));
2276: PetscCall(PetscPrintf(ctx->comm, " Jac-f-df (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_F_DF]));
2277: PetscCall(PetscPrintf(ctx->comm, " Kernel (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_KERNEL]));
2278: PetscCall(PetscPrintf(ctx->comm, "MatLUFactorNum X 1.0 %10.3e\n", ctx->times[KSP_FACTOR]));
2279: PetscCall(PetscPrintf(ctx->comm, "MatSolve X 1.0 %10.3e\n", ctx->times[KSP_SOLVE]));
2280: }
2281: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMDestroy(&ctx->plex[grid]));
2282: PetscCall(PetscFree(ctx));
2283: PetscCall(DMDestroy(dm));
2284: PetscFunctionReturn(PETSC_SUCCESS);
2285: }
2287: /* < v, ru > */
2288: static void f0_s_den(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)
2289: {
2290: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2291: f0[0] = u[ii];
2292: }
2294: /* < v, ru > */
2295: static void f0_s_mom(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)
2296: {
2297: PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]);
2298: f0[0] = x[jj] * u[ii]; /* x momentum */
2299: }
2301: static void f0_s_v2(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)
2302: {
2303: PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]);
2304: double tmp1 = 0.;
2305: for (i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2306: f0[0] = tmp1 * u[ii];
2307: }
2309: static PetscErrorCode gamma_n_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *actx)
2310: {
2311: const PetscReal *c2_0_arr = ((PetscReal *)actx);
2312: const PetscReal c02 = c2_0_arr[0];
2314: PetscFunctionBegin;
2315: for (PetscInt s = 0; s < Nf; s++) {
2316: PetscReal tmp1 = 0.;
2317: for (PetscInt i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2318: #if defined(PETSC_USE_DEBUG)
2319: u[s] = PetscSqrtReal(1. + tmp1 / c02); // u[0] = PetscSqrtReal(1. + xx);
2320: #else
2321: {
2322: PetscReal xx = tmp1 / c02;
2323: u[s] = xx / (PetscSqrtReal(1. + xx) + 1.); // better conditioned = xx/(PetscSqrtReal(1. + xx) + 1.)
2324: }
2325: #endif
2326: }
2327: PetscFunctionReturn(PETSC_SUCCESS);
2328: }
2330: /* < v, ru > */
2331: static void f0_s_rden(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)
2332: {
2333: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2334: f0[0] = 2. * PETSC_PI * x[0] * u[ii];
2335: }
2337: /* < v, ru > */
2338: static void f0_s_rmom(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)
2339: {
2340: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2341: f0[0] = 2. * PETSC_PI * x[0] * x[1] * u[ii];
2342: }
2344: static void f0_s_rv2(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)
2345: {
2346: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2347: f0[0] = 2. * PETSC_PI * x[0] * (x[0] * x[0] + x[1] * x[1]) * u[ii];
2348: }
2350: /*@
2351: DMPlexLandauPrintNorms - collects moments and prints them
2353: Collective
2355: Input Parameters:
2356: + X - the state
2357: - stepi - current step to print
2359: Level: beginner
2361: .seealso: `DMPlexLandauCreateVelocitySpace()`
2362: @*/
2363: PetscErrorCode DMPlexLandauPrintNorms(Vec X, PetscInt stepi)
2364: {
2365: LandauCtx *ctx;
2366: PetscDS prob;
2367: DM pack;
2368: PetscInt cStart, cEnd, dim, ii, i0, nDMs;
2369: PetscScalar xmomentumtot = 0, ymomentumtot = 0, zmomentumtot = 0, energytot = 0, densitytot = 0, tt[LANDAU_MAX_SPECIES];
2370: PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES];
2371: Vec *globXArray;
2373: PetscFunctionBegin;
2374: PetscCall(VecGetDM(X, &pack));
2375: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Vector has no DM");
2376: PetscCall(DMGetDimension(pack, &dim));
2377: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " not in [2,3]", dim);
2378: PetscCall(DMGetApplicationContext(pack, &ctx));
2379: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2380: /* print momentum and energy */
2381: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
2382: PetscCheck(nDMs == ctx->num_grids * ctx->batch_sz, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "#DM wrong %" PetscInt_FMT " %" PetscInt_FMT, nDMs, ctx->num_grids * ctx->batch_sz);
2383: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
2384: PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, globXArray));
2385: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2386: Vec Xloc = globXArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2387: PetscCall(DMGetDS(ctx->plex[grid], &prob));
2388: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
2389: PetscScalar user[2] = {(PetscScalar)i0, ctx->charges[ii]};
2390: PetscCall(PetscDSSetConstants(prob, 2, user));
2391: if (dim == 2) { /* 2/3X + 3V (cylindrical coordinates) */
2392: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rden));
2393: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2394: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2395: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rmom));
2396: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2397: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2398: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rv2));
2399: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2400: energy[ii] = tt[0] * 0.5 * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2401: zmomentumtot += zmomentum[ii];
2402: energytot += energy[ii];
2403: densitytot += density[ii];
2404: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3" PetscInt_FMT ") species-%" PetscInt_FMT ": charge density= %20.13e z-momentum= %20.13e energy= %20.13e", stepi, ii, (double)PetscRealPart(density[ii]), (double)PetscRealPart(zmomentum[ii]), (double)PetscRealPart(energy[ii])));
2405: } else { /* 2/3Xloc + 3V */
2406: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_den));
2407: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2408: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2409: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_mom));
2410: user[1] = 0;
2411: PetscCall(PetscDSSetConstants(prob, 2, user));
2412: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2413: xmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2414: user[1] = 1;
2415: PetscCall(PetscDSSetConstants(prob, 2, user));
2416: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2417: ymomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2418: user[1] = 2;
2419: PetscCall(PetscDSSetConstants(prob, 2, user));
2420: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2421: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2422: if (ctx->use_relativistic_corrections) {
2423: /* gamma * M * f */
2424: if (ii == 0 && grid == 0) { // do all at once
2425: Vec Mf, globGamma, *globMfArray, *globGammaArray;
2426: PetscErrorCode (*gammaf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {gamma_n_f};
2427: PetscReal *c2_0[1], data[1];
2429: PetscCall(VecDuplicate(X, &globGamma));
2430: PetscCall(VecDuplicate(X, &Mf));
2431: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globMfArray));
2432: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globGammaArray));
2433: /* M * f */
2434: PetscCall(MatMult(ctx->M, X, Mf));
2435: /* gamma */
2436: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2437: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice, need to fix for batching
2438: Vec v1 = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2439: data[0] = PetscSqr(C_0(ctx->v_0));
2440: c2_0[0] = &data[0];
2441: PetscCall(DMProjectFunction(ctx->plex[grid], 0., gammaf, (void **)c2_0, INSERT_ALL_VALUES, v1));
2442: }
2443: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2444: /* gamma * Mf */
2445: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2446: PetscCall(DMCompositeGetAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2447: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice
2448: PetscInt Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], N, bs;
2449: Vec Mfsub = globMfArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], Gsub = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], v1, v2;
2450: // get each component
2451: PetscCall(VecGetSize(Mfsub, &N));
2452: PetscCall(VecCreate(ctx->comm, &v1));
2453: PetscCall(VecSetSizes(v1, PETSC_DECIDE, N / Nf));
2454: PetscCall(VecCreate(ctx->comm, &v2));
2455: PetscCall(VecSetSizes(v2, PETSC_DECIDE, N / Nf));
2456: PetscCall(VecSetFromOptions(v1)); // ???
2457: PetscCall(VecSetFromOptions(v2));
2458: // get each component
2459: PetscCall(VecGetBlockSize(Gsub, &bs));
2460: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT " in Gsub", bs, Nf);
2461: PetscCall(VecGetBlockSize(Mfsub, &bs));
2462: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT, bs, Nf);
2463: for (PetscInt i = 0, ix = ctx->species_offset[grid]; i < Nf; i++, ix++) {
2464: PetscScalar val;
2465: PetscCall(VecStrideGather(Gsub, i, v1, INSERT_VALUES)); // this is not right -- TODO
2466: PetscCall(VecStrideGather(Mfsub, i, v2, INSERT_VALUES));
2467: PetscCall(VecDot(v1, v2, &val));
2468: energy[ix] = PetscRealPart(val) * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ix];
2469: }
2470: PetscCall(VecDestroy(&v1));
2471: PetscCall(VecDestroy(&v2));
2472: } /* grids */
2473: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2474: PetscCall(DMCompositeRestoreAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2475: PetscCall(PetscFree(globGammaArray));
2476: PetscCall(PetscFree(globMfArray));
2477: PetscCall(VecDestroy(&globGamma));
2478: PetscCall(VecDestroy(&Mf));
2479: }
2480: } else {
2481: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_v2));
2482: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2483: energy[ii] = 0.5 * tt[0] * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2484: }
2485: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3" PetscInt_FMT ") species %" PetscInt_FMT ": density=%20.13e, x-momentum=%20.13e, y-momentum=%20.13e, z-momentum=%20.13e, energy=%21.13e", stepi, ii, (double)PetscRealPart(density[ii]), (double)PetscRealPart(xmomentum[ii]), (double)PetscRealPart(ymomentum[ii]), (double)PetscRealPart(zmomentum[ii]), (double)PetscRealPart(energy[ii])));
2486: xmomentumtot += xmomentum[ii];
2487: ymomentumtot += ymomentum[ii];
2488: zmomentumtot += zmomentum[ii];
2489: energytot += energy[ii];
2490: densitytot += density[ii];
2491: }
2492: if (ctx->num_species > 1) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2493: }
2494: }
2495: PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, globXArray));
2496: PetscCall(PetscFree(globXArray));
2497: /* totals */
2498: PetscCall(DMPlexGetHeightStratum(ctx->plex[0], 0, &cStart, &cEnd));
2499: if (ctx->num_species > 1) {
2500: if (dim == 2) {
2501: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\t%3" PetscInt_FMT ") Total: charge density=%21.13e, momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %" PetscInt_FMT " cells on electron grid)", stepi, (double)PetscRealPart(densitytot), (double)PetscRealPart(zmomentumtot), (double)PetscRealPart(energytot),
2502: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2503: } else {
2504: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\t%3" PetscInt_FMT ") Total: charge density=%21.13e, x-momentum=%21.13e, y-momentum=%21.13e, z-momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %" PetscInt_FMT " cells)", stepi, (double)PetscRealPart(densitytot), (double)PetscRealPart(xmomentumtot), (double)PetscRealPart(ymomentumtot), (double)PetscRealPart(zmomentumtot), (double)PetscRealPart(energytot),
2505: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2506: }
2507: } else PetscCall(PetscPrintf(PETSC_COMM_WORLD, " -- %" PetscInt_FMT " cells", cEnd - cStart));
2508: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2509: PetscFunctionReturn(PETSC_SUCCESS);
2510: }
2512: /*@
2513: DMPlexLandauCreateMassMatrix - Create mass matrix for Landau in Plex space (not field major order of Jacobian)
2514: - puts mass matrix into ctx->M
2516: Collective
2518: Input Parameter:
2519: . pack - the `DM` object. Puts matrix in Landau context M field
2521: Output Parameter:
2522: . Amat - The mass matrix (optional), mass matrix is added to the `DM` context
2524: Level: beginner
2526: .seealso: `DMPlexLandauCreateVelocitySpace()`
2527: @*/
2528: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat)
2529: {
2530: DM mass_pack, massDM[LANDAU_MAX_GRIDS];
2531: PetscDS prob;
2532: PetscInt ii, dim, N1 = 1, N2;
2533: LandauCtx *ctx;
2534: Mat packM, subM[LANDAU_MAX_GRIDS];
2536: PetscFunctionBegin;
2538: if (Amat) PetscAssertPointer(Amat, 2);
2539: PetscCall(DMGetApplicationContext(pack, &ctx));
2540: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2541: PetscCall(PetscLogEventBegin(ctx->events[14], 0, 0, 0, 0));
2542: PetscCall(DMGetDimension(pack, &dim));
2543: PetscCall(DMCompositeCreate(PetscObjectComm((PetscObject)pack), &mass_pack));
2544: /* create pack mass matrix */
2545: for (PetscInt grid = 0, ix = 0; grid < ctx->num_grids; grid++) {
2546: PetscCall(DMClone(ctx->plex[grid], &massDM[grid]));
2547: PetscCall(DMCopyFields(ctx->plex[grid], PETSC_DETERMINE, PETSC_DETERMINE, massDM[grid]));
2548: PetscCall(DMCreateDS(massDM[grid]));
2549: PetscCall(DMGetDS(massDM[grid], &prob));
2550: for (ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) {
2551: if (dim == 3) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_1, NULL, NULL, NULL));
2552: else PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_r, NULL, NULL, NULL));
2553: }
2554: #if !defined(LANDAU_SPECIES_MAJOR)
2555: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2556: #else
2557: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2558: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2559: }
2560: #endif
2561: PetscCall(DMCreateMatrix(massDM[grid], &subM[grid]));
2562: }
2563: #if !defined(LANDAU_SPECIES_MAJOR)
2564: // stack the batched DMs
2565: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2566: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2567: }
2568: #endif
2569: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2570: PetscCall(DMCreateMatrix(mass_pack, &packM));
2571: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2572: PetscCall(MatSetOption(packM, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2573: PetscCall(MatSetOption(packM, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2574: PetscCall(DMDestroy(&mass_pack));
2575: /* make mass matrix for each block */
2576: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2577: Vec locX;
2578: DM plex = massDM[grid];
2579: PetscCall(DMGetLocalVector(plex, &locX));
2580: /* Mass matrix is independent of the input, so no need to fill locX */
2581: PetscCall(DMPlexSNESComputeJacobianFEM(plex, locX, subM[grid], subM[grid], ctx));
2582: PetscCall(DMRestoreLocalVector(plex, &locX));
2583: PetscCall(DMDestroy(&massDM[grid]));
2584: }
2585: PetscCall(MatGetSize(ctx->J, &N1, NULL));
2586: PetscCall(MatGetSize(packM, &N2, NULL));
2587: PetscCheck(N1 == N2, PetscObjectComm((PetscObject)pack), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %" PetscInt_FMT ", |Mass|=%" PetscInt_FMT, N1, N2);
2588: /* assemble block diagonals */
2589: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2590: Mat B = subM[grid];
2591: PetscInt nloc, nzl, *colbuf, COL_BF_SIZE = 1024, row;
2592: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2593: PetscCall(MatGetSize(B, &nloc, NULL));
2594: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2595: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2596: const PetscInt *cols;
2597: const PetscScalar *vals;
2598: for (PetscInt i = 0; i < nloc; i++) {
2599: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
2600: if (nzl > COL_BF_SIZE) {
2601: PetscCall(PetscFree(colbuf));
2602: PetscCall(PetscInfo(pack, "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl));
2603: COL_BF_SIZE = nzl;
2604: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2605: }
2606: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
2607: for (PetscInt j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
2608: row = i + moffset;
2609: PetscCall(MatSetValues(packM, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
2610: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
2611: }
2612: }
2613: PetscCall(PetscFree(colbuf));
2614: }
2615: // cleanup
2616: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
2617: PetscCall(MatAssemblyBegin(packM, MAT_FINAL_ASSEMBLY));
2618: PetscCall(MatAssemblyEnd(packM, MAT_FINAL_ASSEMBLY));
2619: PetscCall(PetscObjectSetName((PetscObject)packM, "mass"));
2620: PetscCall(MatViewFromOptions(packM, NULL, "-dm_landau_mass_view"));
2621: ctx->M = packM;
2622: if (Amat) *Amat = packM;
2623: PetscCall(PetscLogEventEnd(ctx->events[14], 0, 0, 0, 0));
2624: PetscFunctionReturn(PETSC_SUCCESS);
2625: }
2627: /*@
2628: DMPlexLandauIFunction - `TS` residual calculation, confusingly this computes the Jacobian w/o mass
2630: Collective
2632: Input Parameters:
2633: + ts - The time stepping context
2634: . time_dummy - current time (not used)
2635: . X - Current state
2636: . X_t - Time derivative of current state
2637: - actx - Landau context
2639: Output Parameter:
2640: . F - The residual
2642: Level: beginner
2644: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIJacobian()`
2645: @*/
2646: PetscErrorCode DMPlexLandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx)
2647: {
2648: LandauCtx *ctx = (LandauCtx *)actx;
2649: PetscInt dim;
2650: DM pack;
2651: #if defined(PETSC_HAVE_THREADSAFETY)
2652: double starttime, endtime;
2653: #endif
2654: PetscObjectState state;
2656: PetscFunctionBegin;
2657: PetscCall(TSGetDM(ts, &pack));
2658: PetscCall(DMGetApplicationContext(pack, &ctx));
2659: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2660: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2661: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2662: PetscCall(PetscLogEventBegin(ctx->events[0], 0, 0, 0, 0));
2663: #if defined(PETSC_HAVE_THREADSAFETY)
2664: starttime = MPI_Wtime();
2665: #endif
2666: PetscCall(DMGetDimension(pack, &dim));
2667: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2668: if (state != ctx->norm_state) {
2669: PetscCall(MatZeroEntries(ctx->J));
2670: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, 0.0, (void *)ctx));
2671: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_jacobian_view"));
2672: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2673: ctx->norm_state = state;
2674: } else {
2675: PetscCall(PetscInfo(ts, "WARNING Skip forming Jacobian, has not changed %" PetscInt64_FMT "\n", state));
2676: }
2677: /* mat vec for op */
2678: PetscCall(MatMult(ctx->J, X, F)); /* C*f */
2679: /* add time term */
2680: if (X_t) PetscCall(MatMultAdd(ctx->M, X_t, F, F));
2681: #if defined(PETSC_HAVE_THREADSAFETY)
2682: if (ctx->stage) {
2683: endtime = MPI_Wtime();
2684: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2685: ctx->times[LANDAU_JACOBIAN] += (endtime - starttime);
2686: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2687: ctx->times[LANDAU_JACOBIAN_COUNT] += 1;
2688: }
2689: #endif
2690: PetscCall(PetscLogEventEnd(ctx->events[0], 0, 0, 0, 0));
2691: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2692: if (ctx->stage) PetscCall(PetscLogStagePop());
2693: PetscFunctionReturn(PETSC_SUCCESS);
2694: }
2696: /*@
2697: DMPlexLandauIJacobian - `TS` Jacobian construction, confusingly this adds mass
2699: Collective
2701: Input Parameters:
2702: + ts - The time stepping context
2703: . time_dummy - current time (not used)
2704: . X - Current state
2705: . U_tdummy - Time derivative of current state (not used)
2706: . shift - shift for du/dt term
2707: - actx - Landau context
2709: Output Parameters:
2710: + Amat - Jacobian
2711: - Pmat - same as Amat
2713: Level: beginner
2715: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIFunction()`
2716: @*/
2717: PetscErrorCode DMPlexLandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx)
2718: {
2719: LandauCtx *ctx = NULL;
2720: PetscInt dim;
2721: DM pack;
2722: #if defined(PETSC_HAVE_THREADSAFETY)
2723: double starttime, endtime;
2724: #endif
2725: PetscObjectState state;
2727: PetscFunctionBegin;
2728: PetscCall(TSGetDM(ts, &pack));
2729: PetscCall(DMGetApplicationContext(pack, &ctx));
2730: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2731: PetscCheck(Amat == Pmat && Amat == ctx->J, ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J");
2732: PetscCall(DMGetDimension(pack, &dim));
2733: /* get collision Jacobian into A */
2734: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2735: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2736: PetscCall(PetscLogEventBegin(ctx->events[9], 0, 0, 0, 0));
2737: #if defined(PETSC_HAVE_THREADSAFETY)
2738: starttime = MPI_Wtime();
2739: #endif
2740: PetscCheck(shift != 0.0, ctx->comm, PETSC_ERR_PLIB, "zero shift");
2741: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2742: PetscCheck(state == ctx->norm_state, ctx->comm, PETSC_ERR_PLIB, "wrong state, %" PetscInt64_FMT " %" PetscInt64_FMT, ctx->norm_state, state);
2743: if (!ctx->use_matrix_mass) {
2744: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, shift, (void *)ctx));
2745: } else { /* add mass */
2746: PetscCall(MatAXPY(Pmat, shift, ctx->M, SAME_NONZERO_PATTERN));
2747: }
2748: #if defined(PETSC_HAVE_THREADSAFETY)
2749: if (ctx->stage) {
2750: endtime = MPI_Wtime();
2751: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2752: ctx->times[LANDAU_MASS] += (endtime - starttime);
2753: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2754: }
2755: #endif
2756: PetscCall(PetscLogEventEnd(ctx->events[9], 0, 0, 0, 0));
2757: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2758: if (ctx->stage) PetscCall(PetscLogStagePop());
2759: PetscFunctionReturn(PETSC_SUCCESS);
2760: }