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) PetscCall(LandauKokkosDestroyMatMaps(maps, maps[0].numgrids)); // implies Kokkos does
34: #endif
35: }
36: // free host data
37: for (PetscInt grid = 0; grid < maps[0].numgrids; grid++) {
38: PetscCall(PetscFree(maps[grid].c_maps));
39: PetscCall(PetscFree(maps[grid].gIdx));
40: }
41: PetscCall(PetscFree(maps));
42: PetscFunctionReturn(PETSC_SUCCESS);
43: }
44: static PetscErrorCode energy_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
45: {
46: PetscReal v2 = 0;
48: PetscFunctionBegin;
49: /* compute v^2 / 2 */
50: for (PetscInt i = 0; i < dim; ++i) v2 += x[i] * x[i];
51: /* evaluate the Maxwellian */
52: u[0] = v2 / 2;
53: PetscFunctionReturn(PETSC_SUCCESS);
54: }
56: /* needs double */
57: static PetscErrorCode gamma_m1_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
58: {
59: PetscReal *c2_0_arr = ((PetscReal *)actx);
60: double u2 = 0, c02 = (double)*c2_0_arr, xx;
62: PetscFunctionBegin;
63: /* compute u^2 / 2 */
64: for (PetscInt i = 0; i < dim; ++i) u2 += x[i] * x[i];
65: /* gamma - 1 = g_eps, for conditioning and we only take derivatives */
66: xx = u2 / c02;
67: #if defined(PETSC_USE_DEBUG)
68: u[0] = PetscSqrtReal(1. + xx);
69: #else
70: u[0] = xx / (PetscSqrtReal(1. + xx) + 1.) - 1.; // better conditioned. -1 might help condition and only used for derivative
71: #endif
72: PetscFunctionReturn(PETSC_SUCCESS);
73: }
75: /*
76: LandauFormJacobian_Internal - Evaluates Jacobian matrix.
78: Input Parameters:
79: . globX - input vector
80: . actx - optional user-defined context
81: . dim - dimension
83: Output Parameter:
84: . J0acP - Jacobian matrix filled, not created
85: */
86: static PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, PetscReal shift, void *a_ctx)
87: {
88: LandauCtx *ctx = (LandauCtx *)a_ctx;
89: PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nb;
90: PetscQuadrature quad;
91: PetscReal Eq_m[LANDAU_MAX_SPECIES]; // could be static data w/o quench (ex2)
92: PetscScalar *cellClosure = NULL;
93: const PetscScalar *xdata = NULL;
94: PetscDS prob;
95: PetscContainer container;
96: P4estVertexMaps *maps;
97: Mat subJ[LANDAU_MAX_GRIDS * LANDAU_MAX_BATCH_SZ];
99: PetscFunctionBegin;
102: PetscAssertPointer(ctx, 5);
103: /* check for matrix container for GPU assembly. Support CPU assembly for debugging */
104: PetscCheck(ctx->plex[0] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
105: PetscCall(PetscLogEventBegin(ctx->events[10], 0, 0, 0, 0));
106: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
107: PetscCall(PetscObjectQuery((PetscObject)JacP, "assembly_maps", (PetscObject *)&container));
108: if (container) {
109: PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "maps but no GPU assembly");
110: PetscCall(PetscContainerGetPointer(container, (void **)&maps));
111: PetscCheck(maps, ctx->comm, PETSC_ERR_ARG_WRONG, "empty GPU matrix container");
112: for (PetscInt i = 0; i < ctx->num_grids * ctx->batch_sz; i++) subJ[i] = NULL;
113: } else {
114: PetscCheck(!ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "No maps but GPU assembly");
115: for (PetscInt tid = 0; tid < ctx->batch_sz; tid++) {
116: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCreateMatrix(ctx->plex[grid], &subJ[LAND_PACK_IDX(tid, grid)]));
117: }
118: maps = NULL;
119: }
120: // 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)
121: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
122: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
123: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
124: 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);
125: 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);
126: // get metadata for collecting dynamic data
127: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
128: PetscInt cStart, cEnd;
129: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
130: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
131: numCells[grid] = cEnd - cStart; // grids can have different topology
132: }
133: PetscCall(PetscLogEventEnd(ctx->events[10], 0, 0, 0, 0));
134: 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 */
135: DM pack;
136: PetscCall(VecGetDM(a_X, &pack));
137: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "pack has no DM");
138: PetscCall(PetscLogEventBegin(ctx->events[1], 0, 0, 0, 0));
139: for (PetscInt fieldA = 0; fieldA < ctx->num_species; fieldA++) {
140: Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */
141: if (dim == 2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */
142: }
143: if (!ctx->gpu_assembly) {
144: Vec *locXArray, *globXArray;
145: PetscScalar *cellClosure_it;
146: PetscInt cellClosure_sz = 0, nDMs, Nf[LANDAU_MAX_GRIDS];
147: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
148: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
149: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
150: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
151: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
152: }
153: /* count cellClosure size */
154: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
155: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) cellClosure_sz += Nb * Nf[grid] * numCells[grid];
156: PetscCall(PetscMalloc1(cellClosure_sz * ctx->batch_sz, &cellClosure));
157: cellClosure_it = cellClosure;
158: PetscCall(PetscMalloc(sizeof(*locXArray) * nDMs, &locXArray));
159: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
160: PetscCall(DMCompositeGetLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
161: PetscCall(DMCompositeGetAccessArray(pack, a_X, nDMs, NULL, globXArray));
162: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP (once)
163: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
164: Vec locX = locXArray[LAND_PACK_IDX(b_id, grid)], globX = globXArray[LAND_PACK_IDX(b_id, grid)], locX2;
165: PetscInt cStart, cEnd, ei;
166: PetscCall(VecDuplicate(locX, &locX2));
167: PetscCall(DMGlobalToLocalBegin(ctx->plex[grid], globX, INSERT_VALUES, locX2));
168: PetscCall(DMGlobalToLocalEnd(ctx->plex[grid], globX, INSERT_VALUES, locX2));
169: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
170: for (ei = cStart; ei < cEnd; ++ei) {
171: PetscScalar *coef = NULL;
172: PetscCall(DMPlexVecGetClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
173: PetscCall(PetscMemcpy(cellClosure_it, coef, Nb * Nf[grid] * sizeof(*cellClosure_it))); /* change if LandauIPReal != PetscScalar */
174: PetscCall(DMPlexVecRestoreClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
175: cellClosure_it += Nb * Nf[grid];
176: }
177: PetscCall(VecDestroy(&locX2));
178: }
179: }
180: 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);
181: PetscCall(DMCompositeRestoreLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
182: PetscCall(DMCompositeRestoreAccessArray(pack, a_X, nDMs, NULL, globXArray));
183: PetscCall(PetscFree(locXArray));
184: PetscCall(PetscFree(globXArray));
185: xdata = NULL;
186: } else {
187: PetscMemType mtype;
188: if (ctx->jacobian_field_major_order) { // get data in batch ordering
189: PetscCall(VecScatterBegin(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
190: PetscCall(VecScatterEnd(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
191: PetscCall(VecGetArrayReadAndMemType(ctx->work_vec, &xdata, &mtype));
192: } else {
193: PetscCall(VecGetArrayReadAndMemType(a_X, &xdata, &mtype));
194: }
195: PetscCheck(mtype == PETSC_MEMTYPE_HOST || ctx->deviceType != LANDAU_CPU, ctx->comm, PETSC_ERR_ARG_WRONG, "CPU run with device data: use -mat_type aij");
196: cellClosure = NULL;
197: }
198: PetscCall(PetscLogEventEnd(ctx->events[1], 0, 0, 0, 0));
199: } else xdata = cellClosure = NULL;
201: /* do it */
202: if (ctx->deviceType == LANDAU_KOKKOS) {
203: #if defined(PETSC_HAVE_KOKKOS)
204: 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));
205: #else
206: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
207: #endif
208: } else { /* CPU version */
209: PetscTabulation *Tf; // used for CPU and print info. Same on all grids and all species
210: 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];
211: 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;
212: PetscReal *nu_alpha = (PetscReal *)ctx->SData_d.alpha, *nu_beta = (PetscReal *)ctx->SData_d.beta, *invMass = (PetscReal *)ctx->SData_d.invMass;
213: PetscReal (*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal (*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
214: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
215: PetscScalar *coo_vals = NULL;
216: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
217: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
218: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
219: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
220: }
221: /* count IPf size, etc */
222: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
223: const PetscReal *const BB = Tf[0]->T[0], *const DD = Tf[0]->T[1];
224: ip_offset[0] = ipf_offset[0] = elem_offset[0] = 0;
225: for (PetscInt grid = 0; grid < num_grids; grid++) {
226: PetscInt nfloc = ctx->species_offset[grid + 1] - ctx->species_offset[grid];
227: elem_offset[grid + 1] = elem_offset[grid] + numCells[grid];
228: ip_offset[grid + 1] = ip_offset[grid] + numCells[grid] * Nq;
229: ipf_offset[grid + 1] = ipf_offset[grid] + Nq * nfloc * numCells[grid];
230: }
231: IPf_sz_glb = ipf_offset[num_grids];
232: IPf_sz_tot = IPf_sz_glb * ctx->batch_sz;
233: // prep COO
234: PetscCall(PetscMalloc1(ctx->SData_d.coo_size, &coo_vals)); // allocate every time?
235: if (shift == 0.0) { /* compute dynamic data f and df and init data for Jacobian */
236: #if defined(PETSC_HAVE_THREADSAFETY)
237: double starttime, endtime;
238: starttime = MPI_Wtime();
239: #endif
240: PetscCall(PetscLogEventBegin(ctx->events[8], 0, 0, 0, 0));
241: PetscCall(PetscMalloc4(IPf_sz_tot, &ff, IPf_sz_tot, &dudx, IPf_sz_tot, &dudy, (dim == 3 ? IPf_sz_tot : 0), &dudz));
242: // F df/dx
243: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
244: 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
245: // find my grid:
246: PetscInt grid = 0;
247: while (b_elem_idx >= elem_offset[grid + 1]) grid++; // yuck search for grid
248: {
249: 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];
250: 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];
251: PetscScalar *coef, coef_buff[LANDAU_MAX_SPECIES * LANDAU_MAX_NQND];
252: PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim]; // ingJ is static data on batch 0
253: PetscInt b, f, q;
254: if (cellClosure) {
255: coef = &cellClosure[b_id * IPf_sz_glb + ipf_offset[grid] + loc_elem * Nb * loc_Nf]; // this is const
256: } else {
257: coef = coef_buff;
258: for (f = 0; f < loc_Nf; ++f) {
259: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][f][0];
260: for (b = 0; b < Nb; ++b) {
261: PetscInt idx = Idxs[b];
262: if (idx >= 0) {
263: coef[f * Nb + b] = xdata[idx + moffset];
264: } else {
265: idx = -idx - 1;
266: coef[f * Nb + b] = 0;
267: for (q = 0; q < maps[grid].num_face; q++) {
268: PetscInt id = maps[grid].c_maps[idx][q].gid;
269: PetscScalar scale = maps[grid].c_maps[idx][q].scale;
270: coef[f * Nb + b] += scale * xdata[id + moffset];
271: }
272: }
273: }
274: }
275: }
276: /* get f and df */
277: for (PetscInt qi = 0; qi < Nq; qi++) {
278: const PetscReal *invJ = &invJe[qi * dim * dim];
279: const PetscReal *Bq = &BB[qi * Nb];
280: const PetscReal *Dq = &DD[qi * Nb * dim];
281: PetscReal u_x[LANDAU_DIM];
282: /* get f & df */
283: for (f = 0; f < loc_Nf; ++f) {
284: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid] + f * loc_nip + loc_elem * Nq + qi;
285: PetscInt b, e;
286: PetscReal refSpaceDer[LANDAU_DIM];
287: ff[idx] = 0.0;
288: for (PetscInt d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0;
289: for (b = 0; b < Nb; ++b) {
290: const PetscInt cidx = b;
291: ff[idx] += Bq[cidx] * PetscRealPart(coef[f * Nb + cidx]);
292: for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx * dim + d] * PetscRealPart(coef[f * Nb + cidx]);
293: }
294: for (PetscInt d = 0; d < LANDAU_DIM; ++d) {
295: for (e = 0, u_x[d] = 0.0; e < LANDAU_DIM; ++e) u_x[d] += invJ[e * dim + d] * refSpaceDer[e];
296: }
297: dudx[idx] = u_x[0];
298: dudy[idx] = u_x[1];
299: #if LANDAU_DIM == 3
300: dudz[idx] = u_x[2];
301: #endif
302: }
303: } // q
304: } // grid
305: } // grid*batch
306: PetscCall(PetscLogEventEnd(ctx->events[8], 0, 0, 0, 0));
307: #if defined(PETSC_HAVE_THREADSAFETY)
308: endtime = MPI_Wtime();
309: if (ctx->stage) ctx->times[LANDAU_F_DF] += (endtime - starttime);
310: #endif
311: } // Jacobian setup
312: // assemble Jacobian (or mass)
313: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
314: const PetscInt b_Nelem = elem_offset[num_grids];
315: const PetscInt glb_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem;
316: PetscInt grid = 0;
317: #if defined(PETSC_HAVE_THREADSAFETY)
318: double starttime, endtime;
319: starttime = MPI_Wtime();
320: #endif
321: while (glb_elem_idx >= elem_offset[grid + 1]) grid++;
322: {
323: const PetscInt loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = glb_elem_idx - elem_offset[grid];
324: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset), totDim = loc_Nf * Nq, elemMatSize = totDim * totDim;
325: PetscScalar *elemMat;
326: const PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim];
327: PetscCall(PetscMalloc1(elemMatSize, &elemMat));
328: PetscCall(PetscMemzero(elemMat, elemMatSize * sizeof(*elemMat)));
329: if (shift == 0.0) { // Jacobian
330: PetscCall(PetscLogEventBegin(ctx->events[4], 0, 0, 0, 0));
331: } else { // mass
332: PetscCall(PetscLogEventBegin(ctx->events[16], 0, 0, 0, 0));
333: }
334: for (PetscInt qj = 0; qj < Nq; ++qj) {
335: const PetscInt jpidx_glb = ip_offset[grid] + qj + loc_elem * Nq;
336: 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
337: PetscInt d, d2, dp, d3, IPf_idx;
338: if (shift == 0.0) { // Jacobian
339: const PetscReal *const invJj = &invJe[qj * dim * dim];
340: 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];
341: const PetscReal vj[3] = {xx[jpidx_glb], yy[jpidx_glb], zz ? zz[jpidx_glb] : 0}, wj = ww[jpidx_glb];
342: // create g2 & g3
343: for (d = 0; d < LANDAU_DIM; d++) { // clear accumulation data D & K
344: gg2_temp[d] = 0;
345: for (d2 = 0; d2 < LANDAU_DIM; d2++) gg3_temp[d][d2] = 0;
346: }
347: /* inner beta reduction */
348: IPf_idx = 0;
349: 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
350: PetscInt nip_loc_r = numCells[grid_r] * Nq, Nfloc_r = Nf[grid_r];
351: for (PetscInt ei_r = 0; ei_r < numCells[grid_r]; ++ei_r) {
352: for (PetscInt qi = 0; qi < Nq; qi++, ipidx++) {
353: const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx];
354: PetscReal temp1[3] = {0, 0, 0}, temp2 = 0;
355: #if LANDAU_DIM == 2
356: 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.;
357: LandauTensor2D(vj, x, y, Ud, Uk, mask);
358: #else
359: 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.;
360: if (ctx->use_relativistic_corrections) {
361: LandauTensor3DRelativistic(vj, x, y, z, U, mask, C_0(ctx->v_0));
362: } else {
363: LandauTensor3D(vj, x, y, z, U, mask);
364: }
365: #endif
366: for (PetscInt f = 0; f < Nfloc_r; ++f) {
367: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid_r] + f * nip_loc_r + ei_r * Nq + qi;
369: temp1[0] += dudx[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
370: temp1[1] += dudy[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
371: #if LANDAU_DIM == 3
372: temp1[2] += dudz[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
373: #endif
374: temp2 += ff[idx] * nu_beta[f + f_off] * (*lambdas)[grid][grid_r];
375: }
376: temp1[0] *= wi;
377: temp1[1] *= wi;
378: #if LANDAU_DIM == 3
379: temp1[2] *= wi;
380: #endif
381: temp2 *= wi;
382: #if LANDAU_DIM == 2
383: for (d2 = 0; d2 < 2; d2++) {
384: for (d3 = 0; d3 < 2; ++d3) {
385: /* K = U * grad(f): g2=e: i,A */
386: gg2_temp[d2] += Uk[d2][d3] * temp1[d3];
387: /* D = -U * (I \kron (fx)): g3=f: i,j,A */
388: gg3_temp[d2][d3] += Ud[d2][d3] * temp2;
389: }
390: }
391: #else
392: for (d2 = 0; d2 < 3; ++d2) {
393: for (d3 = 0; d3 < 3; ++d3) {
394: /* K = U * grad(f): g2 = e: i,A */
395: gg2_temp[d2] += U[d2][d3] * temp1[d3];
396: /* D = -U * (I \kron (fx)): g3 = f: i,j,A */
397: gg3_temp[d2][d3] += U[d2][d3] * temp2;
398: }
399: }
400: #endif
401: } // qi
402: } // ei_r
403: IPf_idx += nip_loc_r * Nfloc_r;
404: } /* grid_r - IPs */
405: 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);
406: // add alpha and put in gg2/3
407: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) {
408: for (d2 = 0; d2 < LANDAU_DIM; d2++) {
409: gg2[fieldA][d2] = gg2_temp[d2] * nu_alpha[fieldA + f_off];
410: for (d3 = 0; d3 < LANDAU_DIM; d3++) gg3[fieldA][d2][d3] = -gg3_temp[d2][d3] * nu_alpha[fieldA + f_off] * invMass[fieldA + f_off];
411: }
412: }
413: /* add electric field term once per IP */
414: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) gg2[fieldA][LANDAU_DIM - 1] += Eq_m[fieldA + f_off];
415: /* Jacobian transform - g2, g3 */
416: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
417: for (d = 0; d < dim; ++d) {
418: g2[fieldA][d] = 0.0;
419: for (d2 = 0; d2 < dim; ++d2) {
420: g2[fieldA][d] += invJj[d * dim + d2] * gg2[fieldA][d2];
421: g3[fieldA][d][d2] = 0.0;
422: for (d3 = 0; d3 < dim; ++d3) {
423: for (dp = 0; dp < dim; ++dp) g3[fieldA][d][d2] += invJj[d * dim + d3] * gg3[fieldA][d3][dp] * invJj[d2 * dim + dp];
424: }
425: g3[fieldA][d][d2] *= wj;
426: }
427: g2[fieldA][d] *= wj;
428: }
429: }
430: } else { // mass
431: PetscReal wj = ww[jpidx_glb];
432: /* Jacobian transform - g0 */
433: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
434: if (dim == 2) {
435: g0[fieldA] = wj * shift * 2. * PETSC_PI; // move this to below and remove g0
436: } else {
437: g0[fieldA] = wj * shift; // move this to below and remove g0
438: }
439: }
440: }
441: /* FE matrix construction */
442: {
443: PetscInt fieldA, d, f, d2, g;
444: const PetscReal *BJq = &BB[qj * Nb], *DIq = &DD[qj * Nb * dim];
445: /* assemble - on the diagonal (I,I) */
446: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
447: for (f = 0; f < Nb; f++) {
448: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
449: for (g = 0; g < Nb; ++g) {
450: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
451: const PetscInt fOff = i * totDim + j;
452: if (shift == 0.0) {
453: for (d = 0; d < dim; ++d) {
454: elemMat[fOff] += DIq[f * dim + d] * g2[fieldA][d] * BJq[g];
455: for (d2 = 0; d2 < dim; ++d2) elemMat[fOff] += DIq[f * dim + d] * g3[fieldA][d][d2] * DIq[g * dim + d2];
456: }
457: } else { // mass
458: elemMat[fOff] += BJq[f] * g0[fieldA] * BJq[g];
459: }
460: }
461: }
462: }
463: }
464: } /* qj loop */
465: if (shift == 0.0) { // Jacobian
466: PetscCall(PetscLogEventEnd(ctx->events[4], 0, 0, 0, 0));
467: } else {
468: PetscCall(PetscLogEventEnd(ctx->events[16], 0, 0, 0, 0));
469: }
470: #if defined(PETSC_HAVE_THREADSAFETY)
471: endtime = MPI_Wtime();
472: if (ctx->stage) ctx->times[LANDAU_KERNEL] += (endtime - starttime);
473: #endif
474: /* assemble matrix */
475: if (!container) {
476: PetscInt cStart;
477: PetscCall(PetscLogEventBegin(ctx->events[6], 0, 0, 0, 0));
478: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, NULL));
479: PetscCall(DMPlexMatSetClosure(ctx->plex[grid], section[grid], globsection[grid], subJ[LAND_PACK_IDX(b_id, grid)], loc_elem + cStart, elemMat, ADD_VALUES));
480: PetscCall(PetscLogEventEnd(ctx->events[6], 0, 0, 0, 0));
481: } else { // GPU like assembly for debugging
482: 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];
483: 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};
484: 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;
485: /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */
486: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
487: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][fieldA][0];
488: for (f = 0; f < Nb; f++) {
489: PetscInt idx = Idxs[f];
490: if (idx >= 0) {
491: nr = 1;
492: rows0[0] = idx;
493: row_scale[0] = 1.;
494: } else {
495: idx = -idx - 1;
496: for (q = 0, nr = 0; q < maps[grid].num_face; q++, nr++) {
497: if (maps[grid].c_maps[idx][q].gid < 0) break;
498: rows0[q] = maps[grid].c_maps[idx][q].gid;
499: row_scale[q] = maps[grid].c_maps[idx][q].scale;
500: }
501: }
502: for (g = 0; g < Nb; ++g) {
503: idx = Idxs[g];
504: if (idx >= 0) {
505: nc = 1;
506: cols0[0] = idx;
507: col_scale[0] = 1.;
508: } else {
509: idx = -idx - 1;
510: nc = maps[grid].num_face;
511: for (q = 0, nc = 0; q < maps[grid].num_face; q++, nc++) {
512: if (maps[grid].c_maps[idx][q].gid < 0) break;
513: cols0[q] = maps[grid].c_maps[idx][q].gid;
514: col_scale[q] = maps[grid].c_maps[idx][q].scale;
515: }
516: }
517: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
518: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
519: const PetscScalar Aij = elemMat[i * totDim + j];
520: if (coo_vals) { // mirror (i,j) in CreateStaticGPUData
521: const PetscInt fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
522: 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];
523: for (PetscInt q = 0, idx2 = idx0; q < nr; q++) {
524: for (PetscInt d = 0; d < nc; d++, idx2++) coo_vals[idx2] = row_scale[q] * col_scale[d] * Aij;
525: }
526: } else {
527: for (q = 0; q < nr; q++) rows[q] = rows0[q] + moffset;
528: for (d = 0; d < nc; d++) cols[d] = cols0[d] + moffset;
529: for (q = 0; q < nr; q++) {
530: for (d = 0; d < nc; d++) vals[q * nc + d] = row_scale[q] * col_scale[d] * Aij;
531: }
532: PetscCall(MatSetValues(JacP, nr, rows, nc, cols, vals, ADD_VALUES));
533: }
534: }
535: }
536: }
537: }
538: if (loc_elem == -1) {
539: PetscCall(PetscPrintf(ctx->comm, "CPU Element matrix\n"));
540: for (PetscInt d = 0; d < totDim; ++d) {
541: for (PetscInt f = 0; f < totDim; ++f) PetscCall(PetscPrintf(ctx->comm, " %12.5e", (double)PetscRealPart(elemMat[d * totDim + f])));
542: PetscCall(PetscPrintf(ctx->comm, "\n"));
543: }
544: exit(12);
545: }
546: PetscCall(PetscFree(elemMat));
547: } /* grid */
548: } /* outer element & batch loop */
549: if (shift == 0.0) { // mass
550: PetscCall(PetscFree4(ff, dudx, dudy, dudz));
551: }
552: if (!container) { // 'CPU' assembly move nest matrix to global JacP
553: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP
554: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
555: 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];
556: PetscInt nloc, nzl, colbuf[1024], row;
557: const PetscInt *cols;
558: const PetscScalar *vals;
559: Mat B = subJ[LAND_PACK_IDX(b_id, grid)];
560: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
561: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
562: PetscCall(MatGetSize(B, &nloc, NULL));
563: for (PetscInt i = 0; i < nloc; i++) {
564: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
565: PetscCheck(nzl <= 1024, PetscObjectComm((PetscObject)B), PETSC_ERR_PLIB, "Row too big: %" PetscInt_FMT, nzl);
566: for (PetscInt j = 0; j < nzl; j++) colbuf[j] = moffset + cols[j];
567: row = moffset + i;
568: PetscCall(MatSetValues(JacP, 1, &row, nzl, colbuf, vals, ADD_VALUES));
569: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
570: }
571: PetscCall(MatDestroy(&B));
572: }
573: }
574: }
575: if (coo_vals) {
576: PetscCall(MatSetValuesCOO(JacP, coo_vals, ADD_VALUES));
577: PetscCall(PetscFree(coo_vals));
578: }
579: } /* CPU version */
580: PetscCall(MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY));
581: PetscCall(MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY));
582: /* clean up */
583: if (cellClosure) PetscCall(PetscFree(cellClosure));
584: if (xdata) PetscCall(VecRestoreArrayReadAndMemType(a_X, &xdata));
585: PetscFunctionReturn(PETSC_SUCCESS);
586: }
588: static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx)
589: {
590: PetscReal r = abc[0], z = abc[1];
591: LandauCtx *ctx = (LandauCtx *)a_ctx;
593: PetscFunctionBegin;
594: if (ctx->sphere && dim == 3) { // make sphere: works for one AMR and Q2
595: PetscInt nzero = 0, idx = 0;
596: xyz[0] = r;
597: xyz[1] = z;
598: xyz[2] = abc[2];
599: for (PetscInt i = 0; i < 3; i++) {
600: if (PetscAbs(xyz[i]) < PETSC_SQRT_MACHINE_EPSILON) nzero++;
601: else idx = i;
602: }
603: if (nzero == 2) xyz[idx] *= 1.732050807568877; // sqrt(3)
604: else if (nzero == 1) {
605: for (PetscInt i = 0; i < 3; i++) xyz[i] *= 1.224744871391589; // sqrt(3/2)
606: }
607: } else {
608: xyz[0] = r;
609: xyz[1] = z;
610: if (dim == 3) xyz[2] = abc[2];
611: }
612: PetscFunctionReturn(PETSC_SUCCESS);
613: }
615: /* create DMComposite of meshes for each species group */
616: static PetscErrorCode LandauDMCreateVMeshes(MPI_Comm comm_self, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM pack)
617: {
618: PetscFunctionBegin;
619: { /* p4est, quads */
620: /* Create plex mesh of Landau domain */
621: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
622: PetscReal par_radius = ctx->radius_par[grid], perp_radius = ctx->radius_perp[grid];
623: if (!ctx->sphere && !ctx->simplex) { // 2 or 3D (only 3D option)
624: PetscReal lo[] = {-perp_radius, -par_radius, -par_radius}, hi[] = {perp_radius, par_radius, par_radius};
625: DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim == 2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
626: if (dim == 2) lo[0] = 0;
627: else {
628: lo[1] = -perp_radius;
629: hi[1] = perp_radius; // 3D y is a perp
630: }
631: 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
632: PetscCall(DMLocalizeCoordinates(ctx->plex[grid])); /* needed for periodic */
633: if (dim == 3) PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cube"));
634: else PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "half-plane"));
635: } else if (dim == 2) {
636: size_t len;
637: PetscCall(PetscStrlen(ctx->filename, &len));
638: if (len) {
639: Vec coords;
640: PetscScalar *x;
641: PetscInt N;
642: char str[] = "-dm_landau_view_file_0";
643: str[21] += grid;
644: PetscCall(DMPlexCreateFromFile(comm_self, ctx->filename, "plexland.c", PETSC_TRUE, &ctx->plex[grid]));
645: PetscCall(DMPlexOrient(ctx->plex[grid]));
646: PetscCall(DMGetCoordinatesLocal(ctx->plex[grid], &coords));
647: PetscCall(VecGetSize(coords, &N));
648: PetscCall(VecGetArray(coords, &x));
649: /* scale by domain size */
650: for (PetscInt i = 0; i < N; i += 2) {
651: x[i + 0] *= ctx->radius_perp[grid];
652: x[i + 1] *= ctx->radius_par[grid];
653: }
654: PetscCall(VecRestoreArray(coords, &x));
655: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], ctx->filename));
656: PetscCall(PetscInfo(ctx->plex[grid], "%" PetscInt_FMT ") Read %s mesh file (%s)\n", grid, ctx->filename, str));
657: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, str));
658: } else { // simplex forces a sphere
659: PetscInt numCells = ctx->simplex ? 12 : 6, cell_size = ctx->simplex ? 3 : 4, j;
660: const PetscInt numVerts = 11;
661: PetscInt cellsT[][4] = {
662: {0, 1, 6, 5 },
663: {1, 2, 7, 6 },
664: {2, 3, 8, 7 },
665: {3, 4, 9, 8 },
666: {5, 6, 7, 10},
667: {10, 7, 8, 9 }
668: };
669: PetscInt cellsS[][3] = {
670: {0, 1, 6 },
671: {1, 2, 6 },
672: {6, 2, 7 },
673: {7, 2, 8 },
674: {8, 2, 3 },
675: {8, 3, 4 },
676: {0, 6, 5 },
677: {5, 6, 7 },
678: {5, 7, 10},
679: {10, 7, 9 },
680: {9, 7, 8 },
681: {9, 8, 4 }
682: };
683: const PetscInt *pcell = (const PetscInt *)(ctx->simplex ? &cellsS[0][0] : &cellsT[0][0]);
684: PetscReal coords[11][2], *flatCoords = &coords[0][0];
685: PetscReal rad = ctx->radius[grid];
686: for (j = 0; j < 5; j++) { // outside edge
687: PetscReal z, r, theta = -PETSC_PI / 2 + (j % 5) * PETSC_PI / 4;
688: r = rad * PetscCosReal(theta);
689: coords[j][0] = r;
690: z = rad * PetscSinReal(theta);
691: coords[j][1] = z;
692: }
693: coords[j][0] = 0;
694: coords[j++][1] = -rad * ctx->sphere_inner_radius_90degree[grid];
695: coords[j][0] = rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
696: coords[j++][1] = -rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
697: coords[j][0] = rad * ctx->sphere_inner_radius_90degree[grid];
698: coords[j++][1] = 0;
699: coords[j][0] = rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
700: coords[j++][1] = rad * ctx->sphere_inner_radius_45degree[grid] * 0.707106781186548;
701: coords[j][0] = 0;
702: coords[j++][1] = rad * ctx->sphere_inner_radius_90degree[grid];
703: coords[j][0] = 0;
704: coords[j++][1] = 0;
705: PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 2, numCells, numVerts, cell_size, ctx->interpolate, pcell, 2, flatCoords, &ctx->plex[grid]));
706: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "semi-circle"));
707: PetscCall(PetscInfo(ctx->plex[grid], "\t%" PetscInt_FMT ") Make circle %s mesh\n", grid, ctx->simplex ? "simplex" : "tensor"));
708: }
709: } else {
710: PetscCheck(dim == 3 && ctx->sphere && !ctx->simplex, ctx->comm, PETSC_ERR_ARG_WRONG, "not: dim == 3 && ctx->sphere && !ctx->simplex");
711: PetscReal rad = ctx->radius[grid] / 1.732050807568877, inner_rad = rad * ctx->sphere_inner_radius_45degree[grid], outer_rad = rad;
712: const PetscInt numCells = 7, cell_size = 8, numVerts = 16;
713: const PetscInt cells[][8] = {
714: {0, 3, 2, 1, 4, 5, 6, 7 },
715: {0, 4, 5, 1, 8, 9, 13, 12},
716: {1, 5, 6, 2, 9, 10, 14, 13},
717: {2, 6, 7, 3, 10, 11, 15, 14},
718: {0, 3, 7, 4, 8, 12, 15, 11},
719: {0, 1, 2, 3, 8, 11, 10, 9 },
720: {4, 7, 6, 5, 12, 13, 14, 15}
721: };
722: PetscReal coords[16 /* numVerts */][3];
723: for (PetscInt j = 0; j < 4; j++) { // inner edge, low
724: coords[j][0] = inner_rad * (j == 0 || j == 3 ? 1 : -1);
725: coords[j][1] = inner_rad * (j / 2 < 1 ? 1 : -1);
726: coords[j][2] = inner_rad * -1;
727: }
728: for (PetscInt j = 0, jj = 4; j < 4; j++, jj++) { // inner edge, hi
729: coords[jj][0] = inner_rad * (j == 0 || j == 3 ? 1 : -1);
730: coords[jj][1] = inner_rad * (j / 2 < 1 ? 1 : -1);
731: coords[jj][2] = inner_rad * 1;
732: }
733: for (PetscInt j = 0, jj = 8; j < 4; j++, jj++) { // outer edge, low
734: coords[jj][0] = outer_rad * (j == 0 || j == 3 ? 1 : -1);
735: coords[jj][1] = outer_rad * (j / 2 < 1 ? 1 : -1);
736: coords[jj][2] = outer_rad * -1;
737: }
738: for (PetscInt j = 0, jj = 12; j < 4; j++, jj++) { // outer edge, hi
739: coords[jj][0] = outer_rad * (j == 0 || j == 3 ? 1 : -1);
740: coords[jj][1] = outer_rad * (j / 2 < 1 ? 1 : -1);
741: coords[jj][2] = outer_rad * 1;
742: }
743: PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 3, numCells, numVerts, cell_size, ctx->interpolate, (const PetscInt *)cells, 3, (const PetscReal *)coords, &ctx->plex[grid]));
744: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cubed sphere"));
745: PetscCall(PetscInfo(ctx->plex[grid], "\t%" PetscInt_FMT ") Make cubed sphere %s mesh\n", grid, ctx->simplex ? "simplex" : "tensor"));
746: }
747: PetscCall(DMSetFromOptions(ctx->plex[grid]));
748: } // grid loop
749: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)pack, prefix));
750: { /* convert to p4est (or whatever), wait for discretization to create pack */
751: char convType[256];
752: PetscBool flg;
754: PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");
755: PetscCall(PetscOptionsFList("-dm_landau_type", "Convert DMPlex to another format (p4est)", "plexland.c", DMList, DMPLEX, convType, 256, &flg));
756: PetscOptionsEnd();
757: if (flg) {
758: ctx->use_p4est = PETSC_TRUE; /* flag for Forest */
759: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
760: DM dmforest;
761: PetscBool isForest;
763: PetscCall(DMConvert(ctx->plex[grid], convType, &dmforest));
764: PetscCheck(dmforest, ctx->comm, PETSC_ERR_PLIB, "Convert failed?");
765: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dmforest, prefix));
766: PetscCall(DMIsForest(dmforest, &isForest));
767: PetscCheck(isForest, ctx->comm, PETSC_ERR_PLIB, "Converted to non Forest?");
768: if (ctx->sphere) PetscCall(DMForestSetBaseCoordinateMapping(dmforest, GeometryDMLandau, ctx));
769: PetscCall(DMDestroy(&ctx->plex[grid]));
770: ctx->plex[grid] = dmforest; // Forest for adaptivity
771: }
772: } else ctx->use_p4est = PETSC_FALSE; /* flag for Forest */
773: }
774: } /* non-file */
775: PetscCall(DMSetDimension(pack, dim));
776: PetscCall(PetscObjectSetName((PetscObject)pack, "Mesh"));
777: PetscCall(DMSetApplicationContext(pack, ctx));
778: PetscFunctionReturn(PETSC_SUCCESS);
779: }
781: static PetscErrorCode SetupDS(DM pack, PetscInt dim, PetscInt grid, LandauCtx *ctx)
782: {
783: PetscInt ii, i0;
784: char buf[256];
785: PetscSection section;
787: PetscFunctionBegin;
788: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
789: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "e"));
790: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "i%" PetscInt_FMT, ii));
791: /* Setup Discretization - FEM */
792: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, ctx->simplex, NULL, PETSC_DECIDE, &ctx->fe[ii]));
793: PetscCall(PetscObjectSetName((PetscObject)ctx->fe[ii], buf));
794: PetscCall(DMSetField(ctx->plex[grid], i0, NULL, (PetscObject)ctx->fe[ii]));
795: }
796: PetscCall(DMCreateDS(ctx->plex[grid]));
797: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion));
798: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
799: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "se"));
800: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "si%" PetscInt_FMT, ii));
801: PetscCall(PetscSectionSetComponentName(section, i0, 0, buf));
802: }
803: PetscFunctionReturn(PETSC_SUCCESS);
804: }
806: /* Define a Maxwellian function for testing out the operator. */
808: /* Using cartesian velocity space coordinates, the particle */
809: /* density, [1/m^3], is defined according to */
811: /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */
813: /* Using some constant, c, we normalize the velocity vector into a */
814: /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */
816: /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */
818: /* Defining $\theta=2T/mc^2$, we thus find that the probability density */
819: /* for finding the particle within the interval in a box dx^3 around x is */
821: /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */
823: typedef struct {
824: PetscReal v_0;
825: PetscReal kT_m;
826: PetscReal n;
827: PetscReal shift;
828: } MaxwellianCtx;
830: static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
831: {
832: MaxwellianCtx *mctx = (MaxwellianCtx *)actx;
833: PetscInt i;
834: PetscReal v2 = 0, theta = 2 * mctx->kT_m / (mctx->v_0 * mctx->v_0), shift; /* theta = 2kT/mc^2 */
836: PetscFunctionBegin;
837: /* compute the exponents, v^2 */
838: for (i = 0; i < dim; ++i) v2 += x[i] * x[i];
839: /* evaluate the Maxwellian */
840: if (mctx->shift < 0) shift = -mctx->shift;
841: else {
842: u[0] = mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
843: shift = mctx->shift;
844: }
845: if (shift != 0.) {
846: v2 = 0;
847: for (i = 0; i < dim - 1; ++i) v2 += x[i] * x[i];
848: v2 += (x[dim - 1] - shift) * (x[dim - 1] - shift);
849: /* evaluate the shifted Maxwellian */
850: u[0] += mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
851: }
852: PetscFunctionReturn(PETSC_SUCCESS);
853: }
855: /*@
856: DMPlexLandauAddMaxwellians - Add a Maxwellian distribution to a state
858: Collective
860: Input Parameters:
861: + dm - The mesh (local)
862: . time - Current time
863: . temps - Temperatures of each species (global)
864: . ns - Number density of each species (global)
865: . grid - index into current grid - just used for offset into `temp` and `ns`
866: . b_id - batch index
867: . n_batch - number of batches
868: - actx - Landau context
870: Output Parameter:
871: . X - The state (local to this grid)
873: Level: beginner
875: .seealso: `DMPlexLandauCreateVelocitySpace()`
876: @*/
877: PetscErrorCode DMPlexLandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
878: {
879: LandauCtx *ctx = (LandauCtx *)actx;
880: PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
881: PetscInt dim;
882: MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES];
884: PetscFunctionBegin;
885: PetscCall(DMGetDimension(dm, &dim));
886: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
887: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
888: mctxs[i0] = &data[i0];
889: data[i0].v_0 = ctx->v_0; // v_0 same for all grids
890: data[i0].kT_m = ctx->k * temps[ii] / ctx->masses[ii]; /* kT/m */
891: data[i0].n = ns[ii];
892: initu[i0] = maxwellian;
893: data[i0].shift = 0;
894: }
895: data[0].shift = ctx->electronShift;
896: /* need to make ADD_ALL_VALUES work - TODO */
897: PetscCall(DMProjectFunction(dm, time, initu, (void **)mctxs, INSERT_ALL_VALUES, X));
898: PetscFunctionReturn(PETSC_SUCCESS);
899: }
901: /*
902: LandauSetInitialCondition - Adds Maxwellians with context
904: Collective
906: Input Parameters:
907: . dm - The mesh
908: - grid - index into current grid - just used for offset into temp and ns
909: . b_id - batch index
910: - n_batch - number of batches
911: + actx - Landau context with T and n
913: Output Parameter:
914: . X - The state
916: Level: beginner
918: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauAddMaxwellians()`
919: */
920: static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
921: {
922: LandauCtx *ctx = (LandauCtx *)actx;
924: PetscFunctionBegin;
925: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
926: PetscCall(VecZeroEntries(X));
927: PetscCall(DMPlexLandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, grid, b_id, n_batch, ctx));
928: PetscFunctionReturn(PETSC_SUCCESS);
929: }
931: // adapt a level once. Forest in/out
932: #if defined(PETSC_USE_INFO)
933: static const char *s_refine_names[] = {"RE", "Z1", "Origin", "Z2", "Uniform"};
934: #endif
935: static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscInt type, PetscInt grid, LandauCtx *ctx, DM *newForest)
936: {
937: DM forest, plex, adaptedDM = NULL;
938: PetscDS prob;
939: PetscBool isForest;
940: PetscQuadrature quad;
941: PetscInt Nq, Nb, *Nb2, cStart, cEnd, c, dim, qj, k;
942: DMLabel adaptLabel = NULL;
944: PetscFunctionBegin;
945: forest = ctx->plex[grid];
946: PetscCall(DMCreateDS(forest));
947: PetscCall(DMGetDS(forest, &prob));
948: PetscCall(DMGetDimension(forest, &dim));
949: PetscCall(DMIsForest(forest, &isForest));
950: PetscCheck(isForest, ctx->comm, PETSC_ERR_ARG_WRONG, "! Forest");
951: PetscCall(DMConvert(forest, DMPLEX, &plex));
952: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
953: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "adapt", &adaptLabel));
954: PetscCall(PetscFEGetQuadrature(fem, &quad));
955: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
956: 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);
957: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
958: PetscCall(PetscDSGetDimensions(prob, &Nb2));
959: PetscCheck(Nb2[0] == Nb, ctx->comm, PETSC_ERR_ARG_WRONG, " Nb = %" PetscInt_FMT " != Nb (%" PetscInt_FMT ")", Nb, Nb2[0]);
960: 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);
961: PetscCall(PetscInfo(sol, "%" PetscInt_FMT ") Refine phase: %s\n", grid, s_refine_names[type]));
962: if (type == 4) {
963: for (c = cStart; c < cEnd; c++) PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
964: } else if (type == 2) {
965: PetscInt rCellIdx[8], nr = 0, nrmax = (dim == 3) ? 8 : 2;
966: PetscReal minRad = PETSC_INFINITY, r;
967: for (c = cStart; c < cEnd; c++) {
968: PetscReal tt, v0[LANDAU_MAX_NQND * 3], J[LANDAU_MAX_NQND * 9], invJ[LANDAU_MAX_NQND * 9], detJ[LANDAU_MAX_NQND];
969: PetscCall(DMPlexComputeCellGeometryFEM(plex, c, quad, v0, J, invJ, detJ));
970: (void)J;
971: (void)invJ;
972: for (qj = 0; qj < Nq; ++qj) {
973: tt = PetscSqr(v0[dim * qj + 0]) + PetscSqr(v0[dim * qj + 1]) + PetscSqr((dim == 3) ? v0[dim * qj + 2] : 0);
974: r = PetscSqrtReal(tt);
975: if (r < minRad - PETSC_SQRT_MACHINE_EPSILON * 10.) {
976: minRad = r;
977: nr = 0;
978: rCellIdx[nr++] = c;
979: 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));
980: } else if ((r - minRad) < PETSC_SQRT_MACHINE_EPSILON * 100. && nr < nrmax) {
981: for (k = 0; k < nr; k++)
982: if (c == rCellIdx[k]) break;
983: if (k == nr) {
984: rCellIdx[nr++] = c;
985: 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)));
986: }
987: }
988: }
989: }
990: for (k = 0; k < nr; k++) PetscCall(DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE));
991: 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));
992: } else if (type == 0 || type == 1 || type == 3) { /* refine along r=0 axis */
993: PetscScalar *coef = NULL;
994: Vec coords;
995: PetscInt csize, Nv, d, nz, nrefined = 0;
996: DM cdm;
997: PetscSection cs;
998: PetscCall(DMGetCoordinatesLocal(forest, &coords));
999: PetscCall(DMGetCoordinateDM(forest, &cdm));
1000: PetscCall(DMGetLocalSection(cdm, &cs));
1001: for (c = cStart; c < cEnd; c++) {
1002: PetscInt doit = 0, outside = 0;
1003: PetscCall(DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef));
1004: Nv = csize / dim;
1005: for (nz = d = 0; d < Nv; d++) {
1006: PetscReal z = PetscRealPart(coef[d * dim + (dim - 1)]), x = PetscSqr(PetscRealPart(coef[d * dim + 0])) + ((dim == 3) ? PetscSqr(PetscRealPart(coef[d * dim + 1])) : 0);
1007: x = PetscSqrtReal(x);
1008: if (type == 0) {
1009: 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 */
1010: } else if (type == 1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) {
1011: outside++; /* don't refine outside electron refine radius */
1012: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
1013: } else if (type == 3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) {
1014: outside++; /* refine r=0 cells on refinement front */
1015: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
1016: }
1017: if (x < PETSC_MACHINE_EPSILON * 10. && (type != 0 || ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON)) nz++;
1018: }
1019: PetscCall(DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef));
1020: if (doit || (outside < Nv && nz)) {
1021: PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
1022: nrefined++;
1023: }
1024: }
1025: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " cells\n", grid, nrefined));
1026: }
1027: PetscCall(DMDestroy(&plex));
1028: PetscCall(DMAdaptLabel(forest, adaptLabel, &adaptedDM));
1029: PetscCall(DMLabelDestroy(&adaptLabel));
1030: *newForest = adaptedDM;
1031: if (adaptedDM) {
1032: if (isForest) PetscCall(DMForestSetAdaptivityForest(adaptedDM, NULL)); // ????
1033: PetscCall(DMConvert(adaptedDM, DMPLEX, &plex));
1034: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
1035: PetscCall(PetscInfo(sol, "\t\t\t\t%" PetscInt_FMT ") %" PetscInt_FMT " cells, %" PetscInt_FMT " total quadrature points\n", grid, cEnd - cStart, Nq * (cEnd - cStart)));
1036: PetscCall(DMDestroy(&plex));
1037: } else *newForest = NULL;
1038: PetscFunctionReturn(PETSC_SUCCESS);
1039: }
1041: // forest goes in (ctx->plex[grid]), plex comes out
1042: static PetscErrorCode adapt(PetscInt grid, LandauCtx *ctx, Vec *uu)
1043: {
1044: PetscInt adaptIter;
1046: PetscFunctionBegin;
1047: 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]};
1048: for (type = 0; type < 5; type++) {
1049: for (adaptIter = 0; adaptIter < limits[type]; adaptIter++) {
1050: DM newForest = NULL;
1051: PetscCall(adaptToleranceFEM(ctx->fe[0], *uu, type, grid, ctx, &newForest));
1052: if (newForest) {
1053: PetscCall(DMDestroy(&ctx->plex[grid]));
1054: PetscCall(VecDestroy(uu));
1055: PetscCall(DMCreateGlobalVector(newForest, uu));
1056: PetscCall(LandauSetInitialCondition(newForest, *uu, grid, 0, 1, ctx));
1057: ctx->plex[grid] = newForest;
1058: } else {
1059: PetscCall(PetscInfo(*uu, "No refinement\n"));
1060: }
1061: }
1062: }
1063: PetscCall(PetscObjectSetName((PetscObject)*uu, "uAMR"));
1064: PetscFunctionReturn(PETSC_SUCCESS);
1065: }
1067: // make log(Lambdas) from NRL Plasma formulary
1068: static PetscErrorCode makeLambdas(LandauCtx *ctx)
1069: {
1070: PetscFunctionBegin;
1071: for (PetscInt gridi = 0; gridi < ctx->num_grids; gridi++) {
1072: PetscInt iii = ctx->species_offset[gridi];
1073: PetscReal Ti_ev = (ctx->thermal_temps[iii] / 1.1604525e7) * 1000; // convert (back) to eV
1074: PetscReal ni = ctx->n[iii] * ctx->n_0;
1075: for (PetscInt gridj = gridi; gridj < ctx->num_grids; gridj++) {
1076: PetscInt jjj = ctx->species_offset[gridj];
1077: PetscReal Zj = ctx->charges[jjj] / 1.6022e-19;
1078: if (gridi == 0) {
1079: if (gridj == 0) { // lam_ee
1080: ctx->lambdas[gridi][gridj] = 23.5 - PetscLogReal(PetscSqrtReal(ni) * PetscPowReal(Ti_ev, -1.25)) - PetscSqrtReal(1e-5 + PetscSqr(PetscLogReal(Ti_ev) - 2) / 16);
1081: } else { // lam_ei == lam_ie
1082: if (10 * Zj * Zj > Ti_ev) {
1083: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(PetscSqrtReal(ni) * Zj * PetscPowReal(Ti_ev, -1.5));
1084: } else {
1085: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 24 - PetscLogReal(PetscSqrtReal(ni) / Ti_ev);
1086: }
1087: }
1088: } else { // lam_ii'
1089: PetscReal mui = ctx->masses[iii] / 1.6720e-27, Zi = ctx->charges[iii] / 1.6022e-19;
1090: PetscReal Tj_ev = (ctx->thermal_temps[jjj] / 1.1604525e7) * 1000; // convert (back) to eV
1091: PetscReal muj = ctx->masses[jjj] / 1.6720e-27;
1092: PetscReal nj = ctx->n[jjj] * ctx->n_0;
1093: 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));
1094: }
1095: }
1096: }
1097: //PetscReal v0 = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1098: PetscFunctionReturn(PETSC_SUCCESS);
1099: }
1101: static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[])
1102: {
1103: PetscBool flg, fileflg;
1104: PetscInt ii, nt, nm, nc, num_species_grid[LANDAU_MAX_GRIDS], non_dim_grid;
1105: PetscReal lnLam = 10;
1106: DM dummy;
1108: PetscFunctionBegin;
1109: PetscCall(DMCreate(ctx->comm, &dummy));
1110: /* get options - initialize context */
1111: ctx->verbose = 1; // should be 0 for silent compliance
1112: ctx->batch_sz = 1;
1113: ctx->batch_view_idx = 0;
1114: ctx->interpolate = PETSC_TRUE;
1115: ctx->gpu_assembly = PETSC_TRUE;
1116: ctx->norm_state = 0;
1117: ctx->electronShift = 0;
1118: ctx->M = NULL;
1119: ctx->J = NULL;
1120: /* geometry and grids */
1121: ctx->sphere = PETSC_FALSE;
1122: ctx->use_p4est = PETSC_FALSE;
1123: ctx->simplex = PETSC_FALSE;
1124: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1125: ctx->radius[grid] = 5.; /* thermal radius (velocity) */
1126: ctx->radius_perp[grid] = 5.; /* thermal radius (velocity) */
1127: ctx->radius_par[grid] = 5.; /* thermal radius (velocity) */
1128: ctx->numAMRRefine[grid] = 0;
1129: ctx->postAMRRefine[grid] = 0;
1130: ctx->species_offset[grid + 1] = 1; // one species default
1131: num_species_grid[grid] = 0;
1132: ctx->plex[grid] = NULL; /* cache as expensive to Convert */
1133: }
1134: ctx->species_offset[0] = 0;
1135: ctx->re_radius = 0.;
1136: ctx->vperp0_radius1 = 0;
1137: ctx->vperp0_radius2 = 0;
1138: ctx->nZRefine1 = 0;
1139: ctx->nZRefine2 = 0;
1140: ctx->numRERefine = 0;
1141: num_species_grid[0] = 1; // one species default
1142: /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */
1143: ctx->charges[0] = -1; /* electron charge (MKS) */
1144: ctx->masses[0] = 1 / 1835.469965278441013; /* temporary value in proton mass */
1145: ctx->n[0] = 1;
1146: ctx->v_0 = 1; /* thermal velocity, we could start with a scale != 1 */
1147: ctx->thermal_temps[0] = 1;
1148: /* constants, etc. */
1149: ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */
1150: ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */
1151: ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */
1152: ctx->Ez = 0;
1153: for (PetscInt grid = 0; grid < LANDAU_NUM_TIMERS; grid++) ctx->times[grid] = 0;
1154: for (PetscInt ii = 0; ii < LANDAU_DIM; ii++) ctx->cells0[ii] = 2;
1155: if (LANDAU_DIM == 2) ctx->cells0[0] = 1;
1156: ctx->use_matrix_mass = PETSC_FALSE;
1157: ctx->use_relativistic_corrections = PETSC_FALSE;
1158: ctx->use_energy_tensor_trick = PETSC_FALSE; /* Use Eero's trick for energy conservation v --> grad(v^2/2) */
1159: ctx->SData_d.w = NULL;
1160: ctx->SData_d.x = NULL;
1161: ctx->SData_d.y = NULL;
1162: ctx->SData_d.z = NULL;
1163: ctx->SData_d.invJ = NULL;
1164: ctx->jacobian_field_major_order = PETSC_FALSE;
1165: ctx->SData_d.coo_elem_offsets = NULL;
1166: ctx->SData_d.coo_elem_point_offsets = NULL;
1167: ctx->SData_d.coo_elem_fullNb = NULL;
1168: ctx->SData_d.coo_size = 0;
1169: PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");
1170: #if defined(PETSC_HAVE_KOKKOS)
1171: ctx->deviceType = LANDAU_KOKKOS;
1172: PetscCall(PetscStrncpy(ctx->filename, "kokkos", sizeof(ctx->filename)));
1173: #else
1174: ctx->deviceType = LANDAU_CPU;
1175: PetscCall(PetscStrncpy(ctx->filename, "cpu", sizeof(ctx->filename)));
1176: #endif
1177: PetscCall(PetscOptionsString("-dm_landau_device_type", "Use kernels on 'cpu' 'kokkos'", "plexland.c", ctx->filename, ctx->filename, sizeof(ctx->filename), NULL));
1178: PetscCall(PetscStrcmp("cpu", ctx->filename, &flg));
1179: if (flg) {
1180: ctx->deviceType = LANDAU_CPU;
1181: } else {
1182: PetscCall(PetscStrcmp("kokkos", ctx->filename, &flg));
1183: PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_device_type %s", ctx->filename);
1184: ctx->deviceType = LANDAU_KOKKOS;
1185: }
1186: ctx->filename[0] = '\0';
1187: PetscCall(PetscOptionsString("-dm_landau_filename", "file to read mesh from", "plexland.c", ctx->filename, ctx->filename, sizeof(ctx->filename), &fileflg));
1188: PetscCall(PetscOptionsReal("-dm_landau_electron_shift", "Shift in thermal velocity of electrons", "none", ctx->electronShift, &ctx->electronShift, NULL));
1189: PetscCall(PetscOptionsInt("-dm_landau_verbose", "Level of verbosity output", "plexland.c", ctx->verbose, &ctx->verbose, NULL));
1190: PetscCall(PetscOptionsInt("-dm_landau_batch_size", "Number of 'vertices' to batch", "ex2.c", ctx->batch_sz, &ctx->batch_sz, NULL));
1191: 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);
1192: 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));
1193: 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);
1194: PetscCall(PetscOptionsReal("-dm_landau_Ez", "Initial parallel electric field in unites of Conner-Hastie critical field", "plexland.c", ctx->Ez, &ctx->Ez, NULL));
1195: PetscCall(PetscOptionsReal("-dm_landau_n_0", "Normalization constant for number density", "plexland.c", ctx->n_0, &ctx->n_0, NULL));
1196: 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));
1197: PetscCall(PetscOptionsBool("-dm_landau_use_relativistic_corrections", "Use relativistic corrections", "plexland.c", ctx->use_relativistic_corrections, &ctx->use_relativistic_corrections, NULL));
1198: PetscCall(PetscOptionsBool("-dm_landau_simplex", "Use simplex elements", "plexland.c", ctx->simplex, &ctx->simplex, NULL));
1199: PetscCall(PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, NULL));
1200: if (LANDAU_DIM == 2 && ctx->use_relativistic_corrections) ctx->use_relativistic_corrections = PETSC_FALSE; // should warn
1201: 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,
1202: &ctx->use_energy_tensor_trick, NULL));
1204: /* get num species with temperature, set defaults */
1205: for (ii = 1; ii < LANDAU_MAX_SPECIES; ii++) {
1206: ctx->thermal_temps[ii] = 1;
1207: ctx->charges[ii] = 1;
1208: ctx->masses[ii] = 1;
1209: ctx->n[ii] = 1;
1210: }
1211: nt = LANDAU_MAX_SPECIES;
1212: 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));
1213: PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species");
1214: PetscCall(PetscInfo(dummy, "num_species set to number of thermal temps provided (%" PetscInt_FMT ")\n", nt));
1215: ctx->num_species = nt;
1216: for (ii = 0; ii < ctx->num_species; ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */
1217: nm = LANDAU_MAX_SPECIES - 1;
1218: 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));
1219: 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);
1220: nm = LANDAU_MAX_SPECIES;
1221: PetscCall(PetscOptionsRealArray("-dm_landau_n", "Number density of each species = n_s * n_0", "plexland.c", ctx->n, &nm, &flg));
1222: 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);
1223: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */
1224: ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */
1225: nc = LANDAU_MAX_SPECIES - 1;
1226: 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));
1227: 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);
1228: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */
1229: /* geometry and grids */
1230: nt = LANDAU_MAX_GRIDS;
1231: 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));
1232: if (flg) {
1233: ctx->num_grids = nt;
1234: for (ii = nt = 0; ii < ctx->num_grids; ii++) nt += num_species_grid[ii];
1235: 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,
1236: ctx->num_grids, LANDAU_MAX_GRIDS);
1237: } else {
1238: if (ctx->num_species > LANDAU_MAX_GRIDS) {
1239: num_species_grid[0] = 1;
1240: num_species_grid[1] = ctx->num_species - 1;
1241: ctx->num_grids = 2;
1242: } else {
1243: ctx->num_grids = ctx->num_species;
1244: for (ii = 0; ii < ctx->num_grids; ii++) num_species_grid[ii] = 1;
1245: }
1246: }
1247: 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];
1248: 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],
1249: ctx->num_species);
1250: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1251: PetscInt iii = ctx->species_offset[grid]; // normalize with first (arbitrary) species on grid
1252: ctx->thermal_speed[grid] = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1253: }
1254: // get lambdas here because we need them for t_0 etc
1255: PetscCall(PetscOptionsReal("-dm_landau_ln_lambda", "Universal cross section parameter. Default uses NRL formulas", "plexland.c", lnLam, &lnLam, &flg));
1256: if (flg) {
1257: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1258: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) ctx->lambdas[gridj][grid] = lnLam; /* cross section ratio large - small angle collisions */
1259: }
1260: } else {
1261: PetscCall(makeLambdas(ctx));
1262: }
1263: non_dim_grid = 0;
1264: 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));
1265: if (non_dim_grid != 0) PetscCall(PetscInfo(dummy, "Normalization grid set to %" PetscInt_FMT ", but non-default not well verified\n", non_dim_grid));
1266: 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);
1267: ctx->v_0 = ctx->thermal_speed[non_dim_grid]; /* arbitrary units for non dimensionalization: global mean velocity in 1D of electrons */
1268: ctx->m_0 = ctx->masses[non_dim_grid]; /* arbitrary reference mass, electrons */
1269: 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 */
1270: /* domain */
1271: nt = LANDAU_MAX_GRIDS;
1272: PetscCall(PetscOptionsRealArray("-dm_landau_domain_radius", "Phase space size in units of thermal velocity of grid", "plexland.c", ctx->radius, &nt, &flg));
1273: if (flg) {
1274: 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);
1275: while (nt--) ctx->radius_par[nt] = ctx->radius_perp[nt] = ctx->radius[nt];
1276: } else {
1277: nt = LANDAU_MAX_GRIDS;
1278: 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));
1279: 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);
1280: 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));
1281: 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);
1282: }
1283: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1284: if (flg && ctx->radius[grid] <= 0) { /* negative is ratio of c - need to set par and perp with this -- todo */
1285: if (ctx->radius[grid] == 0) ctx->radius[grid] = 0.75;
1286: else ctx->radius[grid] = -ctx->radius[grid];
1287: 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)
1288: PetscCall(PetscInfo(dummy, "Change domain radius to %g for grid %" PetscInt_FMT "\n", (double)ctx->radius[grid], grid));
1289: }
1290: ctx->radius[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1291: ctx->radius_perp[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1292: ctx->radius_par[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1293: }
1294: /* amr parameters */
1295: if (!fileflg) {
1296: nt = LANDAU_MAX_GRIDS;
1297: 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));
1298: 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);
1299: nt = LANDAU_MAX_GRIDS;
1300: PetscCall(PetscOptionsIntArray("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &nt, &flg));
1301: for (ii = 1; ii < ctx->num_grids; ii++) ctx->postAMRRefine[ii] = ctx->postAMRRefine[0]; // all grids the same now
1302: 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));
1303: 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));
1304: 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));
1305: 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));
1306: 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));
1307: 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));
1308: /* spherical domain */
1309: if (ctx->sphere || ctx->simplex) {
1310: ctx->sphere_uniform_normal = PETSC_FALSE;
1311: 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));
1312: if (!ctx->sphere_uniform_normal) { // true
1313: nt = LANDAU_MAX_GRIDS;
1314: 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));
1315: if (flg && nt < ctx->num_grids) {
1316: for (PetscInt grid = nt; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_90degree[grid] = ctx->sphere_inner_radius_90degree[0];
1317: } else if (!flg || nt == 0) {
1318: if (LANDAU_DIM == 2) {
1319: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_90degree[grid] = 0.4; // optimized for R=5, Q4, AMR=0
1320: } else {
1321: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_90degree[grid] = 0.577 * 0.40;
1322: }
1323: }
1324: nt = LANDAU_MAX_GRIDS;
1325: 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));
1326: if (flg && nt < ctx->num_grids) {
1327: for (PetscInt grid = nt; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_45degree[grid] = ctx->sphere_inner_radius_45degree[0];
1328: } else if (!flg || nt == 0) {
1329: if (LANDAU_DIM == 2) {
1330: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_45degree[grid] = 0.45; // optimized for R=5, Q4, AMR=0
1331: } else {
1332: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ctx->sphere_inner_radius_45degree[grid] = 0.4; // 3D sphere
1333: }
1334: }
1335: 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]));
1336: } else {
1337: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1338: switch (ctx->numAMRRefine[grid]) {
1339: case 0:
1340: case 1:
1341: case 2:
1342: case 3:
1343: default:
1344: if (LANDAU_DIM == 2) {
1345: ctx->sphere_inner_radius_90degree[grid] = 0.40;
1346: ctx->sphere_inner_radius_45degree[grid] = 0.45;
1347: } else {
1348: ctx->sphere_inner_radius_45degree[grid] = 0.25;
1349: }
1350: }
1351: }
1352: }
1353: } else {
1354: nt = LANDAU_DIM;
1355: PetscCall(PetscOptionsIntArray("-dm_landau_num_cells", "Number of cells in each dimension of base grid", "plexland.c", ctx->cells0, &nt, &flg));
1356: }
1357: }
1358: /* processing options */
1359: PetscCall(PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL));
1360: 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));
1361: 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");
1362: PetscCheck(!ctx->jacobian_field_major_order, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1363: PetscOptionsEnd();
1365: for (ii = ctx->num_species; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0;
1366: if (ctx->verbose != 0) {
1367: PetscReal pmassunit = PetscRealConstant(1.6720e-27);
1369: 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)));
1370: 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)));
1371: 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)));
1372: 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],
1373: (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));
1374: 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]));
1375: 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]));
1376: if (ctx->use_relativistic_corrections) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nUse relativistic corrections\n"));
1377: else PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1378: }
1379: PetscCall(DMDestroy(&dummy));
1380: {
1381: PetscMPIInt rank;
1382: PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
1383: ctx->stage = 0;
1384: PetscCall(PetscLogEventRegister("Landau Create", DM_CLASSID, &ctx->events[13])); /* 13 */
1385: PetscCall(PetscLogEventRegister(" GPU ass. setup", DM_CLASSID, &ctx->events[2])); /* 2 */
1386: PetscCall(PetscLogEventRegister(" Build matrix", DM_CLASSID, &ctx->events[12])); /* 12 */
1387: PetscCall(PetscLogEventRegister(" Assembly maps", DM_CLASSID, &ctx->events[15])); /* 15 */
1388: PetscCall(PetscLogEventRegister("Landau Mass mat", DM_CLASSID, &ctx->events[14])); /* 14 */
1389: PetscCall(PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11])); /* 11 */
1390: PetscCall(PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0])); /* 0 */
1391: PetscCall(PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9])); /* 9 */
1392: PetscCall(PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10])); /* 10 */
1393: PetscCall(PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7])); /* 7 */
1394: PetscCall(PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1])); /* 1 */
1395: PetscCall(PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3])); /* 3 */
1396: PetscCall(PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8])); /* 8 */
1397: PetscCall(PetscLogEventRegister(" J Kernel (GPU)", DM_CLASSID, &ctx->events[4])); /* 4 */
1398: PetscCall(PetscLogEventRegister(" M Kernel (GPU)", DM_CLASSID, &ctx->events[16])); /* 16 */
1399: PetscCall(PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5])); /* 5 */
1400: PetscCall(PetscLogEventRegister(" CPU assemble", DM_CLASSID, &ctx->events[6])); /* 6 */
1402: if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */
1403: PetscCall(PetscOptionsClearValue(NULL, "-snes_converged_reason"));
1404: PetscCall(PetscOptionsClearValue(NULL, "-ksp_converged_reason"));
1405: PetscCall(PetscOptionsClearValue(NULL, "-snes_monitor"));
1406: PetscCall(PetscOptionsClearValue(NULL, "-ksp_monitor"));
1407: PetscCall(PetscOptionsClearValue(NULL, "-ts_monitor"));
1408: PetscCall(PetscOptionsClearValue(NULL, "-ts_view"));
1409: PetscCall(PetscOptionsClearValue(NULL, "-ts_adapt_monitor"));
1410: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_dm_view"));
1411: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_vec_view"));
1412: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_dm_view"));
1413: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_view"));
1414: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_jacobian_view"));
1415: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mat_view"));
1416: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_converged_reason"));
1417: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_monitor"));
1418: PetscCall(PetscOptionsClearValue(NULL, "-"));
1419: PetscCall(PetscOptionsClearValue(NULL, "-info"));
1420: }
1421: }
1422: PetscFunctionReturn(PETSC_SUCCESS);
1423: }
1425: static PetscErrorCode CreateStaticData(PetscInt dim, IS grid_batch_is_inv[], LandauCtx *ctx)
1426: {
1427: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
1428: PetscQuadrature quad;
1429: const PetscReal *quadWeights;
1430: PetscReal invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES];
1431: 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;
1432: PetscTabulation *Tf;
1433: PetscDS prob;
1435: PetscFunctionBegin;
1436: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
1437: 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);
1438: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1439: for (PetscInt ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++) {
1440: invMass[ii] = ctx->m_0 / ctx->masses[ii];
1441: nu_alpha[ii] = PetscSqr(ctx->charges[ii] / ctx->m_0) * ctx->m_0 / ctx->masses[ii];
1442: nu_beta[ii] = PetscSqr(ctx->charges[ii] / ctx->epsilon0) / (8 * PETSC_PI) * ctx->t_0 * ctx->n_0 / PetscPowReal(ctx->v_0, 3);
1443: }
1444: }
1445: if (ctx->verbose == 4) {
1446: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "nu_alpha: "));
1447: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1448: PetscInt iii = ctx->species_offset[grid];
1449: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_alpha[ii]));
1450: }
1451: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_beta: "));
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_beta[ii]));
1455: }
1456: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_alpha[i]*nu_beta[j]*lambda[i][j]:\n"));
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++) {
1460: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1461: PetscInt jjj = ctx->species_offset[gridj];
1462: 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])));
1463: }
1464: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1465: }
1466: }
1467: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "lambda[i][j]:\n"));
1468: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1469: PetscInt iii = ctx->species_offset[grid];
1470: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) {
1471: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1472: PetscInt jjj = ctx->species_offset[gridj];
1473: for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)ctx->lambdas[grid][gridj]));
1474: }
1475: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1476: }
1477: }
1478: }
1479: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
1480: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
1481: /* DS, Tab and quad is same on all grids */
1482: PetscCheck(ctx->plex[0], ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1483: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
1484: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights));
1485: 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);
1486: /* setup each grid */
1487: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1488: PetscInt cStart, cEnd;
1489: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1490: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1491: numCells[grid] = cEnd - cStart; // grids can have different topology
1492: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
1493: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
1494: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
1495: ncellsTot += numCells[grid];
1496: }
1497: /* create GPU assembly data */
1498: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1499: PetscContainer container;
1500: PetscScalar *elemMatrix, *elMat;
1501: pointInterpolationP4est(*pointMaps)[LANDAU_MAX_Q_FACE];
1502: P4estVertexMaps *maps;
1503: const PetscInt *plex_batch = NULL, elMatSz = Nb * Nb * ctx->num_species * ctx->num_species;
1504: LandauIdx *coo_elem_offsets = NULL, *coo_elem_fullNb = NULL, (*coo_elem_point_offsets)[LANDAU_MAX_NQND + 1] = NULL;
1505: /* create GPU assembly data */
1506: PetscCall(PetscInfo(ctx->plex[0], "Make GPU maps %d\n", 1));
1507: PetscCall(PetscLogEventBegin(ctx->events[2], 0, 0, 0, 0));
1508: PetscCall(PetscMalloc(sizeof(*maps) * ctx->num_grids, &maps));
1509: PetscCall(PetscMalloc(sizeof(*pointMaps) * MAP_BF_SIZE, &pointMaps));
1510: PetscCall(PetscMalloc(sizeof(*elemMatrix) * elMatSz, &elemMatrix));
1512: { // setup COO assembly -- put COO metadata directly in ctx->SData_d
1513: PetscCall(PetscMalloc3(ncellsTot + 1, &coo_elem_offsets, ncellsTot, &coo_elem_fullNb, ncellsTot, &coo_elem_point_offsets)); // array of integer pointers
1514: coo_elem_offsets[0] = 0; // finish later
1515: PetscCall(PetscInfo(ctx->plex[0], "COO initialization, %" PetscInt_FMT " cells\n", ncellsTot));
1516: ctx->SData_d.coo_n_cellsTot = ncellsTot;
1517: ctx->SData_d.coo_elem_offsets = (void *)coo_elem_offsets;
1518: ctx->SData_d.coo_elem_fullNb = (void *)coo_elem_fullNb;
1519: ctx->SData_d.coo_elem_point_offsets = (void *)coo_elem_point_offsets;
1520: }
1522: ctx->SData_d.coo_max_fullnb = 0;
1523: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1524: PetscInt cStart, cEnd, Nfloc = Nf[grid], totDim = Nfloc * Nb;
1525: if (grid_batch_is_inv[grid]) PetscCall(ISGetIndices(grid_batch_is_inv[grid], &plex_batch));
1526: PetscCheck(!plex_batch, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1527: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1528: // make maps
1529: maps[grid].d_self = NULL;
1530: maps[grid].num_elements = numCells[grid];
1531: maps[grid].num_face = (PetscInt)(pow(Nq, 1. / ((double)dim)) + .001); // Q
1532: maps[grid].num_face = (PetscInt)(pow(maps[grid].num_face, (double)(dim - 1)) + .001); // Q^2
1533: maps[grid].num_reduced = 0;
1534: maps[grid].deviceType = ctx->deviceType;
1535: maps[grid].numgrids = ctx->num_grids;
1536: // count reduced and get
1537: PetscCall(PetscMalloc(maps[grid].num_elements * sizeof(*maps[grid].gIdx), &maps[grid].gIdx));
1538: for (PetscInt ej = cStart, eidx = 0; ej < cEnd; ++ej, ++eidx, glb_elem_idx++) {
1539: if (coo_elem_offsets) coo_elem_offsets[glb_elem_idx + 1] = coo_elem_offsets[glb_elem_idx]; // start with last one, then add
1540: for (PetscInt fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1541: PetscInt fullNb = 0;
1542: for (PetscInt q = 0; q < Nb; ++q) {
1543: PetscInt numindices, *indices;
1544: PetscScalar *valuesOrig = elMat = elemMatrix;
1545: PetscCall(PetscArrayzero(elMat, totDim * totDim));
1546: elMat[(fieldA * Nb + q) * totDim + fieldA * Nb + q] = 1;
1547: PetscCall(DMPlexGetClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, &elMat));
1548: if (ctx->simplex) {
1549: PetscCheck(numindices == Nb, ctx->comm, PETSC_ERR_ARG_WRONG, "numindices != Nb numindices=%" PetscInt_FMT " Nb=%" PetscInt_FMT, numindices, Nb);
1550: for (PetscInt q = 0; q < numindices; ++q) maps[grid].gIdx[eidx][fieldA][q] = indices[q];
1551: fullNb++;
1552: } else {
1553: for (PetscInt f = 0; f < numindices; ++f) { // look for a non-zero on the diagonal (is this too complicated for simplices?)
1554: if (PetscAbs(PetscRealPart(elMat[f * numindices + f])) > PETSC_MACHINE_EPSILON) {
1555: // found it
1556: if (PetscAbs(PetscRealPart(elMat[f * numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { // normal vertex 1.0
1557: if (plex_batch) {
1558: maps[grid].gIdx[eidx][fieldA][q] = plex_batch[indices[f]];
1559: } else {
1560: maps[grid].gIdx[eidx][fieldA][q] = indices[f];
1561: }
1562: fullNb++;
1563: } else { //found a constraint
1564: PetscInt jj = 0;
1565: PetscReal sum = 0;
1566: const PetscInt ff = f;
1567: maps[grid].gIdx[eidx][fieldA][q] = -maps[grid].num_reduced - 1; // store (-)index: id = -(idx+1): idx = -id - 1
1568: PetscCheck(!ctx->simplex, ctx->comm, PETSC_ERR_ARG_WRONG, "No constraints with simplex");
1569: do { // constraints are continuous in Plex - exploit that here
1570: PetscInt ii; // get 'scale'
1571: 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
1572: 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
1573: pointMaps[maps[grid].num_reduced][jj].scale += PetscRealPart(elMat[f * numindices + ff + ii]);
1574: }
1575: }
1576: sum += pointMaps[maps[grid].num_reduced][jj].scale; // diagnostic
1577: // get 'gid'
1578: if (pointMaps[maps[grid].num_reduced][jj].scale == 0) pointMaps[maps[grid].num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps
1579: else {
1580: if (plex_batch) {
1581: pointMaps[maps[grid].num_reduced][jj].gid = plex_batch[indices[f]];
1582: } else {
1583: pointMaps[maps[grid].num_reduced][jj].gid = indices[f];
1584: }
1585: fullNb++;
1586: }
1587: } while (++jj < maps[grid].num_face && ++f < numindices); // jj is incremented if we hit the end
1588: while (jj < maps[grid].num_face) {
1589: pointMaps[maps[grid].num_reduced][jj].scale = 0;
1590: pointMaps[maps[grid].num_reduced][jj].gid = -1;
1591: jj++;
1592: }
1593: if (PetscAbs(sum - 1.0) > 10 * PETSC_MACHINE_EPSILON) { // debug
1594: PetscInt d, f;
1595: PetscReal tmp = 0;
1596: PetscCall(
1597: 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));
1598: for (d = 0, tmp = 0; d < numindices; ++d) {
1599: 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]));
1600: for (f = 0; f < numindices; ++f) tmp += PetscRealPart(elMat[d * numindices + f]);
1601: if (tmp != 0) PetscCall(PetscPrintf(ctx->comm, " | %22.16e\n", (double)tmp));
1602: }
1603: }
1604: maps[grid].num_reduced++;
1605: 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);
1606: }
1607: break;
1608: }
1609: }
1610: } // !simplex
1611: // cleanup
1612: PetscCall(DMPlexRestoreClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, &elMat));
1613: if (elMat != valuesOrig) PetscCall(DMRestoreWorkArray(ctx->plex[grid], numindices * numindices, MPIU_SCALAR, &elMat));
1614: }
1615: { // setup COO assembly
1616: coo_elem_offsets[glb_elem_idx + 1] += fullNb * fullNb; // one species block, adds a block for each species, on this element in this grid
1617: if (fieldA == 0) { // cache full Nb for this element, on this grid per species
1618: coo_elem_fullNb[glb_elem_idx] = fullNb;
1619: if (fullNb > ctx->SData_d.coo_max_fullnb) ctx->SData_d.coo_max_fullnb = fullNb;
1620: } 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);
1621: }
1622: } // field
1623: } // cell
1624: // allocate and copy point data maps[grid].gIdx[eidx][field][q]
1625: PetscCall(PetscMalloc(maps[grid].num_reduced * sizeof(*maps[grid].c_maps), &maps[grid].c_maps));
1626: for (PetscInt ej = 0; ej < maps[grid].num_reduced; ++ej) {
1627: for (PetscInt q = 0; q < maps[grid].num_face; ++q) {
1628: maps[grid].c_maps[ej][q].scale = pointMaps[ej][q].scale;
1629: maps[grid].c_maps[ej][q].gid = pointMaps[ej][q].gid;
1630: }
1631: }
1632: #if defined(PETSC_HAVE_KOKKOS)
1633: if (ctx->deviceType == LANDAU_KOKKOS) PetscCall(LandauKokkosCreateMatMaps(maps, pointMaps, Nf, grid)); // implies Kokkos does
1634: #endif
1635: if (plex_batch) {
1636: PetscCall(ISRestoreIndices(grid_batch_is_inv[grid], &plex_batch));
1637: PetscCall(ISDestroy(&grid_batch_is_inv[grid])); // we are done with this
1638: }
1639: } /* grids */
1640: // finish COO
1641: { // setup COO assembly
1642: PetscInt *oor, *ooc;
1643: ctx->SData_d.coo_size = coo_elem_offsets[ncellsTot] * ctx->batch_sz;
1644: PetscCall(PetscMalloc2(ctx->SData_d.coo_size, &oor, ctx->SData_d.coo_size, &ooc));
1645: for (PetscInt i = 0; i < ctx->SData_d.coo_size; i++) oor[i] = ooc[i] = -1;
1646: // get
1647: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1648: for (PetscInt ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1649: const PetscInt fullNb = coo_elem_fullNb[glb_elem_idx];
1650: 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
1651: coo_elem_point_offsets[glb_elem_idx][0] = 0;
1652: for (PetscInt f = 0, cnt2 = 0; f < Nb; f++) {
1653: PetscInt idx = Idxs[f];
1654: coo_elem_point_offsets[glb_elem_idx][f + 1] = coo_elem_point_offsets[glb_elem_idx][f]; // start at last
1655: if (idx >= 0) {
1656: cnt2++;
1657: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1658: } else {
1659: idx = -idx - 1;
1660: for (PetscInt q = 0; q < maps[grid].num_face; q++) {
1661: if (maps[grid].c_maps[idx][q].gid < 0) break;
1662: cnt2++;
1663: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1664: }
1665: }
1666: PetscCheck(cnt2 <= fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "wrong count %" PetscInt_FMT " < %" PetscInt_FMT, fullNb, cnt2);
1667: }
1668: 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);
1669: }
1670: }
1671: // set
1672: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1673: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1674: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1675: for (PetscInt ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1676: const PetscInt fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
1677: // set (i,j)
1678: for (PetscInt fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1679: const LandauIdx *const Idxs = &maps[grid].gIdx[ej][fieldA][0];
1680: PetscInt rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE];
1681: for (PetscInt f = 0; f < Nb; ++f) {
1682: const PetscInt nr = coo_elem_point_offsets[glb_elem_idx][f + 1] - coo_elem_point_offsets[glb_elem_idx][f];
1683: if (nr == 1) rows[0] = Idxs[f];
1684: else {
1685: const PetscInt idx = -Idxs[f] - 1;
1686: for (PetscInt q = 0; q < nr; q++) rows[q] = maps[grid].c_maps[idx][q].gid;
1687: }
1688: for (PetscInt g = 0; g < Nb; ++g) {
1689: const PetscInt nc = coo_elem_point_offsets[glb_elem_idx][g + 1] - coo_elem_point_offsets[glb_elem_idx][g];
1690: if (nc == 1) cols[0] = Idxs[g];
1691: else {
1692: const PetscInt idx = -Idxs[g] - 1;
1693: for (PetscInt q = 0; q < nc; q++) cols[q] = maps[grid].c_maps[idx][q].gid;
1694: }
1695: 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];
1696: for (PetscInt q = 0, idx = idx0; q < nr; q++) {
1697: for (PetscInt d = 0; d < nc; d++, idx++) {
1698: oor[idx] = rows[q] + moffset;
1699: ooc[idx] = cols[d] + moffset;
1700: }
1701: }
1702: }
1703: }
1704: }
1705: } // cell
1706: } // grid
1707: } // batch
1708: PetscCall(MatSetPreallocationCOO(ctx->J, ctx->SData_d.coo_size, oor, ooc));
1709: PetscCall(PetscFree2(oor, ooc));
1710: }
1711: PetscCall(PetscFree(pointMaps));
1712: PetscCall(PetscFree(elemMatrix));
1713: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
1714: PetscCall(PetscContainerSetPointer(container, (void *)maps));
1715: PetscCall(PetscContainerSetCtxDestroy(container, LandauGPUMapsDestroy));
1716: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "assembly_maps", (PetscObject)container));
1717: PetscCall(PetscContainerDestroy(&container));
1718: PetscCall(PetscLogEventEnd(ctx->events[2], 0, 0, 0, 0));
1719: } // end GPU assembly
1720: { /* create static point data, Jacobian called first, only one vertex copy */
1721: PetscReal *invJe, *ww, *xx, *yy, *zz = NULL, *invJ_a;
1722: PetscInt outer_ipidx, outer_ej, grid, nip_glb = 0;
1723: PetscFE fe;
1724: PetscCall(PetscLogEventBegin(ctx->events[7], 0, 0, 0, 0));
1725: PetscCall(PetscInfo(ctx->plex[0], "Initialize static data\n"));
1726: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) nip_glb += Nq * numCells[grid];
1727: /* collect f data, first time is for Jacobian, but make mass now */
1728: if (ctx->verbose != 0) {
1729: PetscInt ncells = 0, N;
1730: MatInfo info;
1731: PetscCall(MatGetInfo(ctx->J, MAT_LOCAL, &info));
1732: PetscCall(MatGetSize(ctx->J, &N, NULL));
1733: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ncells += numCells[grid];
1734: 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,
1735: ctx->num_species, Nb, dim, N, (PetscInt)info.nz_used));
1736: }
1737: PetscCall(PetscMalloc4(nip_glb, &ww, nip_glb, &xx, nip_glb, &yy, nip_glb * dim * dim, &invJ_a));
1738: if (dim == 3) PetscCall(PetscMalloc1(nip_glb, &zz));
1739: if (ctx->use_energy_tensor_trick) {
1740: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, ctx->simplex, NULL, PETSC_DECIDE, &fe));
1741: PetscCall(PetscObjectSetName((PetscObject)fe, "energy"));
1742: }
1743: /* init each grids static data - no batch */
1744: for (grid = 0, outer_ipidx = 0, outer_ej = 0; grid < ctx->num_grids; grid++) { // OpenMP (once)
1745: Vec v2_2 = NULL; // projected function: v^2/2 for non-relativistic, gamma... for relativistic
1746: PetscSection e_section;
1747: DM dmEnergy;
1748: PetscInt cStart, cEnd, ej;
1750: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1751: // prep energy trick, get v^2 / 2 vector
1752: if (ctx->use_energy_tensor_trick) {
1753: PetscErrorCode (*energyf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {ctx->use_relativistic_corrections ? gamma_m1_f : energy_f};
1754: Vec glob_v2;
1755: PetscReal *c2_0[1], data[1] = {PetscSqr(C_0(ctx->v_0))};
1757: PetscCall(DMClone(ctx->plex[grid], &dmEnergy));
1758: PetscCall(PetscObjectSetName((PetscObject)dmEnergy, "energy"));
1759: PetscCall(DMSetField(dmEnergy, 0, NULL, (PetscObject)fe));
1760: PetscCall(DMCreateDS(dmEnergy));
1761: PetscCall(DMGetLocalSection(dmEnergy, &e_section));
1762: PetscCall(DMGetGlobalVector(dmEnergy, &glob_v2));
1763: PetscCall(PetscObjectSetName((PetscObject)glob_v2, "trick"));
1764: c2_0[0] = &data[0];
1765: PetscCall(DMProjectFunction(dmEnergy, 0., energyf, (void **)c2_0, INSERT_ALL_VALUES, glob_v2));
1766: PetscCall(DMGetLocalVector(dmEnergy, &v2_2));
1767: PetscCall(VecZeroEntries(v2_2)); /* zero BCs so don't set */
1768: PetscCall(DMGlobalToLocalBegin(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1769: PetscCall(DMGlobalToLocalEnd(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1770: PetscCall(DMViewFromOptions(dmEnergy, NULL, "-energy_dm_view"));
1771: PetscCall(VecViewFromOptions(glob_v2, NULL, "-energy_vec_view"));
1772: PetscCall(DMRestoreGlobalVector(dmEnergy, &glob_v2));
1773: }
1774: /* append part of the IP data for each grid */
1775: for (ej = 0; ej < numCells[grid]; ++ej, ++outer_ej) {
1776: PetscScalar *coefs = NULL;
1777: 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);
1778: invJe = invJ_a + outer_ej * Nq * dim * dim;
1779: PetscCall(DMPlexComputeCellGeometryFEM(ctx->plex[grid], ej + cStart, quad, vj, Jdummy, invJe, detJj));
1780: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecGetClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1781: /* create static point data */
1782: for (PetscInt qj = 0; qj < Nq; qj++, outer_ipidx++) {
1783: const PetscInt gidx = outer_ipidx;
1784: const PetscReal *invJ = &invJe[qj * dim * dim];
1785: ww[gidx] = detJj[qj] * quadWeights[qj];
1786: if (dim == 2) ww[gidx] *= vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */
1787: // get xx, yy, zz
1788: if (ctx->use_energy_tensor_trick) {
1789: double refSpaceDer[3], eGradPhi[3];
1790: const PetscReal *const DD = Tf[0]->T[1];
1791: const PetscReal *Dq = &DD[qj * Nb * dim];
1792: for (PetscInt d = 0; d < 3; ++d) refSpaceDer[d] = eGradPhi[d] = 0.0;
1793: for (PetscInt b = 0; b < Nb; ++b) {
1794: for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] += Dq[b * dim + d] * PetscRealPart(coefs[b]);
1795: }
1796: xx[gidx] = 1e10;
1797: if (ctx->use_relativistic_corrections) {
1798: double dg2_c2 = 0;
1799: //for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] *= c02;
1800: for (PetscInt d = 0; d < dim; ++d) dg2_c2 += PetscSqr(refSpaceDer[d]);
1801: dg2_c2 *= (double)c02;
1802: if (dg2_c2 >= .999) {
1803: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1804: yy[gidx] = vj[qj * dim + 1];
1805: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1806: 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]));
1807: } else {
1808: PetscReal fact = c02 / PetscSqrtReal(1. - dg2_c2);
1809: for (PetscInt d = 0; d < dim; ++d) refSpaceDer[d] *= fact;
1810: // could test with other point u' that (grad - grad') * U (refSpaceDer, refSpaceDer') == 0
1811: }
1812: }
1813: if (xx[gidx] == 1e10) {
1814: for (PetscInt d = 0; d < dim; ++d) {
1815: for (PetscInt e = 0; e < dim; ++e) eGradPhi[d] += invJ[e * dim + d] * refSpaceDer[e];
1816: }
1817: xx[gidx] = eGradPhi[0];
1818: yy[gidx] = eGradPhi[1];
1819: if (dim == 3) zz[gidx] = eGradPhi[2];
1820: }
1821: } else {
1822: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1823: yy[gidx] = vj[qj * dim + 1];
1824: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1825: }
1826: } /* q */
1827: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecRestoreClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1828: } /* ej */
1829: if (ctx->use_energy_tensor_trick) {
1830: PetscCall(DMRestoreLocalVector(dmEnergy, &v2_2));
1831: PetscCall(DMDestroy(&dmEnergy));
1832: }
1833: } /* grid */
1834: if (ctx->use_energy_tensor_trick) PetscCall(PetscFEDestroy(&fe));
1835: /* cache static data */
1836: if (ctx->deviceType == LANDAU_KOKKOS) {
1837: #if defined(PETSC_HAVE_KOKKOS)
1838: 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));
1839: /* free */
1840: PetscCall(PetscFree4(ww, xx, yy, invJ_a));
1841: if (dim == 3) PetscCall(PetscFree(zz));
1842: #else
1843: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type kokkos not built");
1844: #endif
1845: } else { /* CPU version, just copy in, only use part */
1846: 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 ?
1847: ctx->SData_d.w = (void *)ww;
1848: ctx->SData_d.x = (void *)xx;
1849: ctx->SData_d.y = (void *)yy;
1850: ctx->SData_d.z = (void *)zz;
1851: ctx->SData_d.invJ = (void *)invJ_a;
1852: 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));
1853: for (PetscInt ii = 0; ii < ctx->num_species; ii++) {
1854: nu_alpha_p[ii] = nu_alpha[ii];
1855: nu_beta_p[ii] = nu_beta[ii];
1856: invMass_p[ii] = invMass[ii];
1857: }
1858: ctx->SData_d.alpha = (void *)nu_alpha_p;
1859: ctx->SData_d.beta = (void *)nu_beta_p;
1860: ctx->SData_d.invMass = (void *)invMass_p;
1861: ctx->SData_d.lambdas = (void *)lambdas_p;
1862: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1863: PetscReal (*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal (*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
1864: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) (*lambdas)[grid][gridj] = ctx->lambdas[grid][gridj];
1865: }
1866: }
1867: PetscCall(PetscLogEventEnd(ctx->events[7], 0, 0, 0, 0));
1868: } // initialize
1869: PetscFunctionReturn(PETSC_SUCCESS);
1870: }
1872: /* < v, u > */
1873: 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[])
1874: {
1875: g0[0] = 1.;
1876: }
1878: /* < v, u > */
1879: 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[])
1880: {
1881: static double ttt = 1e-12;
1882: g0[0] = ttt++;
1883: }
1885: /* < v, u > */
1886: 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[])
1887: {
1888: g0[0] = 2. * PETSC_PI * x[0];
1889: }
1891: /*
1892: LandauCreateJacobianMatrix - creates ctx->J with without real data. Hard to keep sparse.
1893: - Like DMPlexLandauCreateMassMatrix. Should remove one and combine
1894: - has old support for field major ordering
1895: */
1896: static PetscErrorCode LandauCreateJacobianMatrix(MPI_Comm comm, Vec X, IS grid_batch_is_inv[LANDAU_MAX_GRIDS], LandauCtx *ctx)
1897: {
1898: PetscInt *idxs = NULL;
1899: Mat subM[LANDAU_MAX_GRIDS];
1901: PetscFunctionBegin;
1902: if (!ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1903: PetscFunctionReturn(PETSC_SUCCESS);
1904: }
1905: // get the RCM for this grid to separate out species into blocks -- create 'idxs' & 'ctx->batch_is' -- not used
1906: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(PetscMalloc1(ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, &idxs));
1907: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1908: const PetscInt *values, n = ctx->mat_offset[grid + 1] - ctx->mat_offset[grid];
1909: Mat gMat;
1910: DM massDM;
1911: PetscDS prob;
1912: Vec tvec;
1913: // get "mass" matrix for reordering
1914: PetscCall(DMClone(ctx->plex[grid], &massDM));
1915: PetscCall(DMCopyFields(ctx->plex[grid], PETSC_DETERMINE, PETSC_DETERMINE, massDM));
1916: PetscCall(DMCreateDS(massDM));
1917: PetscCall(DMGetDS(massDM, &prob));
1918: 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));
1919: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); // this trick is need to both sparsify the matrix and avoid runtime error
1920: PetscCall(DMCreateMatrix(massDM, &gMat));
1921: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
1922: PetscCall(MatSetOption(gMat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
1923: PetscCall(MatSetOption(gMat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
1924: PetscCall(DMCreateLocalVector(ctx->plex[grid], &tvec));
1925: PetscCall(DMPlexSNESComputeJacobianFEM(massDM, tvec, gMat, gMat, ctx));
1926: PetscCall(MatViewFromOptions(gMat, NULL, "-dm_landau_reorder_mat_view"));
1927: PetscCall(DMDestroy(&massDM));
1928: PetscCall(VecDestroy(&tvec));
1929: subM[grid] = gMat;
1930: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1931: MatOrderingType rtype = MATORDERINGRCM;
1932: IS isrow, isicol;
1933: PetscCall(MatGetOrdering(gMat, rtype, &isrow, &isicol));
1934: PetscCall(ISInvertPermutation(isrow, PETSC_DECIDE, &grid_batch_is_inv[grid]));
1935: PetscCall(ISGetIndices(isrow, &values));
1936: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
1937: #if !defined(LANDAU_SPECIES_MAJOR)
1938: PetscInt N = ctx->mat_offset[ctx->num_grids], n0 = ctx->mat_offset[grid] + b_id * N;
1939: for (PetscInt ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1940: #else
1941: PetscInt n0 = ctx->mat_offset[grid] * ctx->batch_sz + b_id * n;
1942: for (PetscInt ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1943: #endif
1944: }
1945: PetscCall(ISRestoreIndices(isrow, &values));
1946: PetscCall(ISDestroy(&isrow));
1947: PetscCall(ISDestroy(&isicol));
1948: }
1949: }
1950: 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));
1951: // get a block matrix
1952: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1953: Mat B = subM[grid];
1954: PetscInt nloc, nzl, *colbuf, row, COL_BF_SIZE = 1024;
1955: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1956: PetscCall(MatGetSize(B, &nloc, NULL));
1957: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1958: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1959: const PetscInt *cols;
1960: const PetscScalar *vals;
1961: for (PetscInt i = 0; i < nloc; i++) {
1962: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
1963: if (nzl > COL_BF_SIZE) {
1964: PetscCall(PetscFree(colbuf));
1965: 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));
1966: COL_BF_SIZE = nzl;
1967: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1968: }
1969: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
1970: for (PetscInt j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
1971: row = i + moffset;
1972: PetscCall(MatSetValues(ctx->J, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
1973: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
1974: }
1975: }
1976: PetscCall(PetscFree(colbuf));
1977: }
1978: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
1979: PetscCall(MatAssemblyBegin(ctx->J, MAT_FINAL_ASSEMBLY));
1980: PetscCall(MatAssemblyEnd(ctx->J, MAT_FINAL_ASSEMBLY));
1982: // debug
1983: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_mat_view"));
1984: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1985: Mat mat_block_order;
1986: PetscCall(MatCreateSubMatrix(ctx->J, ctx->batch_is, ctx->batch_is, MAT_INITIAL_MATRIX, &mat_block_order)); // use MatPermute
1987: PetscCall(MatViewFromOptions(mat_block_order, NULL, "-dm_landau_mat_view"));
1988: PetscCall(MatDestroy(&mat_block_order));
1989: PetscCall(VecScatterCreate(X, ctx->batch_is, X, NULL, &ctx->plex_batch));
1990: PetscCall(VecDuplicate(X, &ctx->work_vec));
1991: }
1992: PetscFunctionReturn(PETSC_SUCCESS);
1993: }
1995: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat);
1996: /*@C
1997: DMPlexLandauCreateVelocitySpace - Create a `DMPLEX` velocity space mesh
1999: Collective
2001: Input Parameters:
2002: + comm - The MPI communicator
2003: . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver)
2004: - prefix - prefix for options (not tested)
2006: Output Parameters:
2007: + pack - The `DM` object representing the mesh
2008: . X - A vector (user destroys)
2009: - J - Optional matrix (object destroys)
2011: Level: beginner
2013: .seealso: `DMPlexCreate()`, `DMPlexLandauDestroyVelocitySpace()`
2014: @*/
2015: PetscErrorCode DMPlexLandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *pack)
2016: {
2017: LandauCtx *ctx;
2018: Vec Xsub[LANDAU_MAX_GRIDS];
2019: IS grid_batch_is_inv[LANDAU_MAX_GRIDS];
2021: PetscFunctionBegin;
2022: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported");
2023: PetscCheck(LANDAU_DIM == dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " != LANDAU_DIM %d", dim, LANDAU_DIM);
2024: PetscCall(PetscNew(&ctx));
2025: ctx->comm = comm; /* used for diagnostics and global errors */
2026: /* process options */
2027: PetscCall(ProcessOptions(ctx, prefix));
2028: if (dim == 2) ctx->use_relativistic_corrections = PETSC_FALSE;
2029: /* Create Mesh */
2030: PetscCall(DMCompositeCreate(PETSC_COMM_SELF, pack));
2031: PetscCall(PetscLogEventBegin(ctx->events[13], 0, 0, 0, 0));
2032: PetscCall(PetscLogEventBegin(ctx->events[15], 0, 0, 0, 0));
2033: PetscCall(LandauDMCreateVMeshes(PETSC_COMM_SELF, dim, prefix, ctx, *pack)); // creates grids (Forest of AMR)
2034: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2035: /* create FEM */
2036: PetscCall(SetupDS(ctx->plex[grid], dim, grid, ctx));
2037: /* set initial state */
2038: PetscCall(DMCreateGlobalVector(ctx->plex[grid], &Xsub[grid]));
2039: PetscCall(PetscObjectSetName((PetscObject)Xsub[grid], "u_orig"));
2040: /* initial static refinement, no solve */
2041: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, 0, 1, ctx));
2042: /* forest refinement - forest goes in (if forest), plex comes out */
2043: if (ctx->use_p4est) {
2044: DM plex;
2045: PetscCall(adapt(grid, ctx, &Xsub[grid])); // forest goes in, plex comes out
2046: if (grid == 0) {
2047: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, "-dm_landau_amr_dm_view")); // need to differentiate - todo
2048: PetscCall(VecViewFromOptions(Xsub[grid], NULL, "-dm_landau_amr_vec_view"));
2049: }
2050: // convert to plex, all done with this level
2051: PetscCall(DMConvert(ctx->plex[grid], DMPLEX, &plex));
2052: PetscCall(DMDestroy(&ctx->plex[grid]));
2053: ctx->plex[grid] = plex;
2054: }
2055: #if !defined(LANDAU_SPECIES_MAJOR)
2056: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2057: #else
2058: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2059: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2060: }
2061: #endif
2062: PetscCall(DMSetApplicationContext(ctx->plex[grid], ctx));
2063: }
2064: #if !defined(LANDAU_SPECIES_MAJOR)
2065: // stack the batched DMs, could do it all here!!! b_id=0
2066: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2067: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2068: }
2069: #endif
2070: // create ctx->mat_offset
2071: ctx->mat_offset[0] = 0;
2072: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2073: PetscInt n;
2074: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2075: ctx->mat_offset[grid + 1] = ctx->mat_offset[grid] + n;
2076: }
2077: // creat DM & Jac
2078: PetscCall(DMSetApplicationContext(*pack, ctx));
2079: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2080: PetscCall(DMCreateMatrix(*pack, &ctx->J));
2081: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2082: PetscCall(MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2083: PetscCall(MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2084: PetscCall(PetscObjectSetName((PetscObject)ctx->J, "Jac"));
2085: // construct initial conditions in X
2086: PetscCall(DMCreateGlobalVector(*pack, X));
2087: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2088: PetscInt n;
2089: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2090: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2091: PetscScalar const *values;
2092: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2093: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, b_id, ctx->batch_sz, ctx));
2094: PetscCall(VecGetArrayRead(Xsub[grid], &values)); // Drop whole grid in Plex ordering
2095: for (PetscInt i = 0, idx = moffset; i < n; i++, idx++) PetscCall(VecSetValue(*X, idx, values[i], INSERT_VALUES));
2096: PetscCall(VecRestoreArrayRead(Xsub[grid], &values));
2097: }
2098: }
2099: // cleanup
2100: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(VecDestroy(&Xsub[grid]));
2101: /* check for correct matrix type */
2102: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
2103: PetscBool flg;
2104: if (ctx->deviceType == LANDAU_KOKKOS) {
2105: PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, MATAIJKOKKOS, ""));
2106: #if defined(PETSC_HAVE_KOKKOS)
2107: 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'");
2108: #else
2109: 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'");
2110: #endif
2111: }
2112: }
2113: PetscCall(PetscLogEventEnd(ctx->events[15], 0, 0, 0, 0));
2115: // create field major ordering
2116: ctx->work_vec = NULL;
2117: ctx->plex_batch = NULL;
2118: ctx->batch_is = NULL;
2119: for (PetscInt i = 0; i < LANDAU_MAX_GRIDS; i++) grid_batch_is_inv[i] = NULL;
2120: PetscCall(PetscLogEventBegin(ctx->events[12], 0, 0, 0, 0));
2121: PetscCall(LandauCreateJacobianMatrix(comm, *X, grid_batch_is_inv, ctx));
2122: PetscCall(PetscLogEventEnd(ctx->events[12], 0, 0, 0, 0));
2124: // create AMR GPU assembly maps and static GPU data
2125: PetscCall(CreateStaticData(dim, grid_batch_is_inv, ctx));
2127: PetscCall(PetscLogEventEnd(ctx->events[13], 0, 0, 0, 0));
2129: // create mass matrix
2130: PetscCall(DMPlexLandauCreateMassMatrix(*pack, NULL));
2132: if (J) *J = ctx->J;
2134: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
2135: PetscContainer container;
2136: // cache ctx for KSP with batch/field major Jacobian ordering -ksp_type gmres/etc -dm_landau_jacobian_field_major_order
2137: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2138: PetscCall(PetscContainerSetPointer(container, (void *)ctx));
2139: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "LandauCtx", (PetscObject)container));
2140: PetscCall(PetscContainerDestroy(&container));
2141: // batch solvers need to map -- can batch solvers work
2142: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2143: PetscCall(PetscContainerSetPointer(container, (void *)ctx->plex_batch));
2144: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "plex_batch_is", (PetscObject)container));
2145: PetscCall(PetscContainerDestroy(&container));
2146: }
2147: // for batch solvers
2148: {
2149: PetscContainer container;
2150: PetscInt *pNf;
2151: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2152: PetscCall(PetscMalloc1(sizeof(*pNf), &pNf));
2153: *pNf = ctx->batch_sz;
2154: PetscCall(PetscContainerSetPointer(container, (void *)pNf));
2155: PetscCall(PetscContainerSetCtxDestroy(container, PetscCtxDestroyDefault));
2156: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "batch size", (PetscObject)container));
2157: PetscCall(PetscContainerDestroy(&container));
2158: }
2159: PetscFunctionReturn(PETSC_SUCCESS);
2160: }
2162: /*@C
2163: DMPlexLandauAccess - Access to the distribution function with user callback
2165: Collective
2167: Input Parameters:
2168: + pack - the `DMCOMPOSITE`
2169: . func - call back function
2170: - user_ctx - user context
2172: Input/Output Parameter:
2173: . X - Vector to data to
2175: Level: advanced
2177: .seealso: `DMPlexLandauCreateVelocitySpace()`
2178: @*/
2179: PetscErrorCode DMPlexLandauAccess(DM pack, Vec X, PetscErrorCode (*func)(DM, Vec, PetscInt, PetscInt, PetscInt, void *), void *user_ctx)
2180: {
2181: LandauCtx *ctx;
2183: PetscFunctionBegin;
2184: PetscCall(DMGetApplicationContext(pack, &ctx)); // uses ctx->num_grids; ctx->plex[grid]; ctx->batch_sz; ctx->mat_offset
2185: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2186: PetscInt dim, n;
2187: PetscCall(DMGetDimension(pack, &dim));
2188: for (PetscInt sp = ctx->species_offset[grid], i0 = 0; sp < ctx->species_offset[grid + 1]; sp++, i0++) {
2189: Vec vec;
2190: PetscInt vf[1] = {i0};
2191: IS vis;
2192: DM vdm;
2193: PetscCall(DMCreateSubDM(ctx->plex[grid], 1, vf, &vis, &vdm));
2194: PetscCall(DMSetApplicationContext(vdm, ctx)); // the user might want this
2195: PetscCall(DMCreateGlobalVector(vdm, &vec));
2196: PetscCall(VecGetSize(vec, &n));
2197: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2198: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2199: PetscCall(VecZeroEntries(vec));
2200: /* Add your data with 'dm' for species 'sp' to 'vec' */
2201: PetscCall(func(vdm, vec, i0, grid, b_id, user_ctx));
2202: /* add to global */
2203: PetscScalar const *values;
2204: const PetscInt *offsets;
2205: PetscCall(VecGetArrayRead(vec, &values));
2206: PetscCall(ISGetIndices(vis, &offsets));
2207: for (PetscInt i = 0; i < n; i++) PetscCall(VecSetValue(X, moffset + offsets[i], values[i], ADD_VALUES));
2208: PetscCall(VecRestoreArrayRead(vec, &values));
2209: PetscCall(ISRestoreIndices(vis, &offsets));
2210: } // batch
2211: PetscCall(VecDestroy(&vec));
2212: PetscCall(ISDestroy(&vis));
2213: PetscCall(DMDestroy(&vdm));
2214: }
2215: } // grid
2216: PetscFunctionReturn(PETSC_SUCCESS);
2217: }
2219: /*@
2220: DMPlexLandauDestroyVelocitySpace - Destroy a `DMPLEX` velocity space mesh
2222: Collective
2224: Input/Output Parameters:
2225: . dm - the `DM` to destroy
2227: Level: beginner
2229: .seealso: `DMPlexLandauCreateVelocitySpace()`
2230: @*/
2231: PetscErrorCode DMPlexLandauDestroyVelocitySpace(DM *dm)
2232: {
2233: LandauCtx *ctx;
2235: PetscFunctionBegin;
2236: PetscCall(DMGetApplicationContext(*dm, &ctx));
2237: PetscCall(MatDestroy(&ctx->M));
2238: PetscCall(MatDestroy(&ctx->J));
2239: for (PetscInt ii = 0; ii < ctx->num_species; ii++) PetscCall(PetscFEDestroy(&ctx->fe[ii]));
2240: PetscCall(ISDestroy(&ctx->batch_is));
2241: PetscCall(VecDestroy(&ctx->work_vec));
2242: PetscCall(VecScatterDestroy(&ctx->plex_batch));
2243: if (ctx->deviceType == LANDAU_KOKKOS) {
2244: #if defined(PETSC_HAVE_KOKKOS)
2245: PetscCall(LandauKokkosStaticDataClear(&ctx->SData_d));
2246: #else
2247: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
2248: #endif
2249: } else {
2250: if (ctx->SData_d.x) { /* in a CPU run */
2251: 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;
2252: 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;
2253: PetscCall(PetscFree4(ww, xx, yy, invJ));
2254: if (zz) PetscCall(PetscFree(zz));
2255: if (coo_elem_offsets) PetscCall(PetscFree3(coo_elem_offsets, coo_elem_fullNb, coo_elem_point_offsets)); // could be NULL
2256: PetscCall(PetscFree4(ctx->SData_d.alpha, ctx->SData_d.beta, ctx->SData_d.invMass, ctx->SData_d.lambdas));
2257: }
2258: }
2260: if (ctx->times[LANDAU_MATRIX_TOTAL] > 0) { // OMP timings
2261: PetscCall(PetscPrintf(ctx->comm, "TSStep N 1.0 %10.3e\n", ctx->times[LANDAU_EX2_TSSOLVE]));
2262: 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));
2263: PetscCall(PetscPrintf(ctx->comm, "3: Landau: %10.3e\n", ctx->times[LANDAU_MATRIX_TOTAL]));
2264: PetscCall(PetscPrintf(ctx->comm, "Landau Jacobian %" PetscInt_FMT " 1.0 %10.3e\n", (PetscInt)ctx->times[LANDAU_JACOBIAN_COUNT], ctx->times[LANDAU_JACOBIAN]));
2265: PetscCall(PetscPrintf(ctx->comm, "Landau Operator N 1.0 %10.3e\n", ctx->times[LANDAU_OPERATOR]));
2266: PetscCall(PetscPrintf(ctx->comm, "Landau Mass N 1.0 %10.3e\n", ctx->times[LANDAU_MASS]));
2267: PetscCall(PetscPrintf(ctx->comm, " Jac-f-df (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_F_DF]));
2268: PetscCall(PetscPrintf(ctx->comm, " Kernel (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_KERNEL]));
2269: PetscCall(PetscPrintf(ctx->comm, "MatLUFactorNum X 1.0 %10.3e\n", ctx->times[KSP_FACTOR]));
2270: PetscCall(PetscPrintf(ctx->comm, "MatSolve X 1.0 %10.3e\n", ctx->times[KSP_SOLVE]));
2271: }
2272: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMDestroy(&ctx->plex[grid]));
2273: PetscCall(PetscFree(ctx));
2274: PetscCall(DMDestroy(dm));
2275: PetscFunctionReturn(PETSC_SUCCESS);
2276: }
2278: /* < v, ru > */
2279: 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)
2280: {
2281: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2282: f0[0] = u[ii];
2283: }
2285: /* < v, ru > */
2286: 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)
2287: {
2288: PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]);
2289: f0[0] = x[jj] * u[ii]; /* x momentum */
2290: }
2292: 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)
2293: {
2294: PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]);
2295: double tmp1 = 0.;
2296: for (i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2297: f0[0] = tmp1 * u[ii];
2298: }
2300: static PetscErrorCode gamma_n_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *actx)
2301: {
2302: const PetscReal *c2_0_arr = ((PetscReal *)actx);
2303: const PetscReal c02 = c2_0_arr[0];
2305: PetscFunctionBegin;
2306: for (PetscInt s = 0; s < Nf; s++) {
2307: PetscReal tmp1 = 0.;
2308: for (PetscInt i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2309: #if defined(PETSC_USE_DEBUG)
2310: u[s] = PetscSqrtReal(1. + tmp1 / c02); // u[0] = PetscSqrtReal(1. + xx);
2311: #else
2312: {
2313: PetscReal xx = tmp1 / c02;
2314: u[s] = xx / (PetscSqrtReal(1. + xx) + 1.); // better conditioned = xx/(PetscSqrtReal(1. + xx) + 1.)
2315: }
2316: #endif
2317: }
2318: PetscFunctionReturn(PETSC_SUCCESS);
2319: }
2321: /* < v, ru > */
2322: 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)
2323: {
2324: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2325: f0[0] = 2. * PETSC_PI * x[0] * u[ii];
2326: }
2328: /* < v, ru > */
2329: 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)
2330: {
2331: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2332: f0[0] = 2. * PETSC_PI * x[0] * x[1] * u[ii];
2333: }
2335: 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)
2336: {
2337: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2338: f0[0] = 2. * PETSC_PI * x[0] * (x[0] * x[0] + x[1] * x[1]) * u[ii];
2339: }
2341: /*@
2342: DMPlexLandauPrintNorms - collects moments and prints them
2344: Collective
2346: Input Parameters:
2347: + X - the state
2348: - stepi - current step to print
2350: Level: beginner
2352: .seealso: `DMPlexLandauCreateVelocitySpace()`
2353: @*/
2354: PetscErrorCode DMPlexLandauPrintNorms(Vec X, PetscInt stepi)
2355: {
2356: LandauCtx *ctx;
2357: PetscDS prob;
2358: DM pack;
2359: PetscInt cStart, cEnd, dim, ii, i0, nDMs;
2360: PetscScalar xmomentumtot = 0, ymomentumtot = 0, zmomentumtot = 0, energytot = 0, densitytot = 0, tt[LANDAU_MAX_SPECIES];
2361: PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES];
2362: Vec *globXArray;
2364: PetscFunctionBegin;
2365: PetscCall(VecGetDM(X, &pack));
2366: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Vector has no DM");
2367: PetscCall(DMGetDimension(pack, &dim));
2368: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " not in [2,3]", dim);
2369: PetscCall(DMGetApplicationContext(pack, &ctx));
2370: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2371: /* print momentum and energy */
2372: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
2373: 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);
2374: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
2375: PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, globXArray));
2376: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2377: Vec Xloc = globXArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2378: PetscCall(DMGetDS(ctx->plex[grid], &prob));
2379: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
2380: PetscScalar user[2] = {(PetscScalar)i0, ctx->charges[ii]};
2381: PetscCall(PetscDSSetConstants(prob, 2, user));
2382: if (dim == 2) { /* 2/3X + 3V (cylindrical coordinates) */
2383: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rden));
2384: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2385: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2386: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rmom));
2387: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2388: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2389: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rv2));
2390: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2391: energy[ii] = tt[0] * 0.5 * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2392: zmomentumtot += zmomentum[ii];
2393: energytot += energy[ii];
2394: densitytot += density[ii];
2395: 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])));
2396: } else { /* 2/3Xloc + 3V */
2397: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_den));
2398: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2399: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2400: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_mom));
2401: user[1] = 0;
2402: PetscCall(PetscDSSetConstants(prob, 2, user));
2403: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2404: xmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2405: user[1] = 1;
2406: PetscCall(PetscDSSetConstants(prob, 2, user));
2407: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2408: ymomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2409: user[1] = 2;
2410: PetscCall(PetscDSSetConstants(prob, 2, user));
2411: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2412: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2413: if (ctx->use_relativistic_corrections) {
2414: /* gamma * M * f */
2415: if (ii == 0 && grid == 0) { // do all at once
2416: Vec Mf, globGamma, *globMfArray, *globGammaArray;
2417: PetscErrorCode (*gammaf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {gamma_n_f};
2418: PetscReal *c2_0[1], data[1];
2420: PetscCall(VecDuplicate(X, &globGamma));
2421: PetscCall(VecDuplicate(X, &Mf));
2422: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globMfArray));
2423: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globGammaArray));
2424: /* M * f */
2425: PetscCall(MatMult(ctx->M, X, Mf));
2426: /* gamma */
2427: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2428: 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
2429: Vec v1 = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2430: data[0] = PetscSqr(C_0(ctx->v_0));
2431: c2_0[0] = &data[0];
2432: PetscCall(DMProjectFunction(ctx->plex[grid], 0., gammaf, (void **)c2_0, INSERT_ALL_VALUES, v1));
2433: }
2434: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2435: /* gamma * Mf */
2436: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2437: PetscCall(DMCompositeGetAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2438: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice
2439: PetscInt Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], N, bs;
2440: Vec Mfsub = globMfArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], Gsub = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], v1, v2;
2441: // get each component
2442: PetscCall(VecGetSize(Mfsub, &N));
2443: PetscCall(VecCreate(ctx->comm, &v1));
2444: PetscCall(VecSetSizes(v1, PETSC_DECIDE, N / Nf));
2445: PetscCall(VecCreate(ctx->comm, &v2));
2446: PetscCall(VecSetSizes(v2, PETSC_DECIDE, N / Nf));
2447: PetscCall(VecSetFromOptions(v1)); // ???
2448: PetscCall(VecSetFromOptions(v2));
2449: // get each component
2450: PetscCall(VecGetBlockSize(Gsub, &bs));
2451: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT " in Gsub", bs, Nf);
2452: PetscCall(VecGetBlockSize(Mfsub, &bs));
2453: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT, bs, Nf);
2454: for (PetscInt i = 0, ix = ctx->species_offset[grid]; i < Nf; i++, ix++) {
2455: PetscScalar val;
2456: PetscCall(VecStrideGather(Gsub, i, v1, INSERT_VALUES)); // this is not right -- TODO
2457: PetscCall(VecStrideGather(Mfsub, i, v2, INSERT_VALUES));
2458: PetscCall(VecDot(v1, v2, &val));
2459: energy[ix] = PetscRealPart(val) * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ix];
2460: }
2461: PetscCall(VecDestroy(&v1));
2462: PetscCall(VecDestroy(&v2));
2463: } /* grids */
2464: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2465: PetscCall(DMCompositeRestoreAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2466: PetscCall(PetscFree(globGammaArray));
2467: PetscCall(PetscFree(globMfArray));
2468: PetscCall(VecDestroy(&globGamma));
2469: PetscCall(VecDestroy(&Mf));
2470: }
2471: } else {
2472: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_v2));
2473: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2474: energy[ii] = 0.5 * tt[0] * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2475: }
2476: 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])));
2477: xmomentumtot += xmomentum[ii];
2478: ymomentumtot += ymomentum[ii];
2479: zmomentumtot += zmomentum[ii];
2480: energytot += energy[ii];
2481: densitytot += density[ii];
2482: }
2483: if (ctx->num_species > 1) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2484: }
2485: }
2486: PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, globXArray));
2487: PetscCall(PetscFree(globXArray));
2488: /* totals */
2489: PetscCall(DMPlexGetHeightStratum(ctx->plex[0], 0, &cStart, &cEnd));
2490: if (ctx->num_species > 1) {
2491: if (dim == 2) {
2492: 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),
2493: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2494: } else {
2495: 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),
2496: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2497: }
2498: } else PetscCall(PetscPrintf(PETSC_COMM_WORLD, " -- %" PetscInt_FMT " cells", cEnd - cStart));
2499: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2500: PetscFunctionReturn(PETSC_SUCCESS);
2501: }
2503: /*@
2504: DMPlexLandauCreateMassMatrix - Create mass matrix for Landau in Plex space (not field major order of Jacobian)
2505: - puts mass matrix into ctx->M
2507: Collective
2509: Input Parameter:
2510: . pack - the `DM` object. Puts matrix in Landau context M field
2512: Output Parameter:
2513: . Amat - The mass matrix (optional), mass matrix is added to the `DM` context
2515: Level: beginner
2517: .seealso: `DMPlexLandauCreateVelocitySpace()`
2518: @*/
2519: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat)
2520: {
2521: DM mass_pack, massDM[LANDAU_MAX_GRIDS];
2522: PetscDS prob;
2523: PetscInt ii, dim, N1 = 1, N2;
2524: LandauCtx *ctx;
2525: Mat packM, subM[LANDAU_MAX_GRIDS];
2527: PetscFunctionBegin;
2529: if (Amat) PetscAssertPointer(Amat, 2);
2530: PetscCall(DMGetApplicationContext(pack, &ctx));
2531: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2532: PetscCall(PetscLogEventBegin(ctx->events[14], 0, 0, 0, 0));
2533: PetscCall(DMGetDimension(pack, &dim));
2534: PetscCall(DMCompositeCreate(PetscObjectComm((PetscObject)pack), &mass_pack));
2535: /* create pack mass matrix */
2536: for (PetscInt grid = 0, ix = 0; grid < ctx->num_grids; grid++) {
2537: PetscCall(DMClone(ctx->plex[grid], &massDM[grid]));
2538: PetscCall(DMCopyFields(ctx->plex[grid], PETSC_DETERMINE, PETSC_DETERMINE, massDM[grid]));
2539: PetscCall(DMCreateDS(massDM[grid]));
2540: PetscCall(DMGetDS(massDM[grid], &prob));
2541: for (ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) {
2542: if (dim == 3) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_1, NULL, NULL, NULL));
2543: else PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_r, NULL, NULL, NULL));
2544: }
2545: #if !defined(LANDAU_SPECIES_MAJOR)
2546: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2547: #else
2548: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2549: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2550: }
2551: #endif
2552: PetscCall(DMCreateMatrix(massDM[grid], &subM[grid]));
2553: }
2554: #if !defined(LANDAU_SPECIES_MAJOR)
2555: // stack the batched DMs
2556: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2557: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2558: }
2559: #endif
2560: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2561: PetscCall(DMCreateMatrix(mass_pack, &packM));
2562: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2563: PetscCall(MatSetOption(packM, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2564: PetscCall(MatSetOption(packM, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2565: PetscCall(DMDestroy(&mass_pack));
2566: /* make mass matrix for each block */
2567: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2568: Vec locX;
2569: DM plex = massDM[grid];
2570: PetscCall(DMGetLocalVector(plex, &locX));
2571: /* Mass matrix is independent of the input, so no need to fill locX */
2572: PetscCall(DMPlexSNESComputeJacobianFEM(plex, locX, subM[grid], subM[grid], ctx));
2573: PetscCall(DMRestoreLocalVector(plex, &locX));
2574: PetscCall(DMDestroy(&massDM[grid]));
2575: }
2576: PetscCall(MatGetSize(ctx->J, &N1, NULL));
2577: PetscCall(MatGetSize(packM, &N2, NULL));
2578: PetscCheck(N1 == N2, PetscObjectComm((PetscObject)pack), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %" PetscInt_FMT ", |Mass|=%" PetscInt_FMT, N1, N2);
2579: /* assemble block diagonals */
2580: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2581: Mat B = subM[grid];
2582: PetscInt nloc, nzl, *colbuf, COL_BF_SIZE = 1024, row;
2583: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2584: PetscCall(MatGetSize(B, &nloc, NULL));
2585: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2586: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2587: const PetscInt *cols;
2588: const PetscScalar *vals;
2589: for (PetscInt i = 0; i < nloc; i++) {
2590: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
2591: if (nzl > COL_BF_SIZE) {
2592: PetscCall(PetscFree(colbuf));
2593: PetscCall(PetscInfo(pack, "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl));
2594: COL_BF_SIZE = nzl;
2595: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2596: }
2597: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
2598: for (PetscInt j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
2599: row = i + moffset;
2600: PetscCall(MatSetValues(packM, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
2601: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
2602: }
2603: }
2604: PetscCall(PetscFree(colbuf));
2605: }
2606: // cleanup
2607: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
2608: PetscCall(MatAssemblyBegin(packM, MAT_FINAL_ASSEMBLY));
2609: PetscCall(MatAssemblyEnd(packM, MAT_FINAL_ASSEMBLY));
2610: PetscCall(PetscObjectSetName((PetscObject)packM, "mass"));
2611: PetscCall(MatViewFromOptions(packM, NULL, "-dm_landau_mass_view"));
2612: ctx->M = packM;
2613: if (Amat) *Amat = packM;
2614: PetscCall(PetscLogEventEnd(ctx->events[14], 0, 0, 0, 0));
2615: PetscFunctionReturn(PETSC_SUCCESS);
2616: }
2618: /*@
2619: DMPlexLandauIFunction - `TS` residual calculation, confusingly this computes the Jacobian w/o mass
2621: Collective
2623: Input Parameters:
2624: + ts - The time stepping context
2625: . time_dummy - current time (not used)
2626: . X - Current state
2627: . X_t - Time derivative of current state
2628: - actx - Landau context
2630: Output Parameter:
2631: . F - The residual
2633: Level: beginner
2635: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIJacobian()`
2636: @*/
2637: PetscErrorCode DMPlexLandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx)
2638: {
2639: LandauCtx *ctx = (LandauCtx *)actx;
2640: PetscInt dim;
2641: DM pack;
2642: #if defined(PETSC_HAVE_THREADSAFETY)
2643: double starttime, endtime;
2644: #endif
2645: PetscObjectState state;
2647: PetscFunctionBegin;
2648: PetscCall(TSGetDM(ts, &pack));
2649: PetscCall(DMGetApplicationContext(pack, &ctx));
2650: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2651: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2652: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2653: PetscCall(PetscLogEventBegin(ctx->events[0], 0, 0, 0, 0));
2654: #if defined(PETSC_HAVE_THREADSAFETY)
2655: starttime = MPI_Wtime();
2656: #endif
2657: PetscCall(DMGetDimension(pack, &dim));
2658: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2659: if (state != ctx->norm_state) {
2660: PetscCall(MatZeroEntries(ctx->J));
2661: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, 0.0, (void *)ctx));
2662: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_jacobian_view"));
2663: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2664: ctx->norm_state = state;
2665: } else {
2666: PetscCall(PetscInfo(ts, "WARNING Skip forming Jacobian, has not changed %" PetscInt64_FMT "\n", state));
2667: }
2668: /* mat vec for op */
2669: PetscCall(MatMult(ctx->J, X, F)); /* C*f */
2670: /* add time term */
2671: if (X_t) PetscCall(MatMultAdd(ctx->M, X_t, F, F));
2672: #if defined(PETSC_HAVE_THREADSAFETY)
2673: if (ctx->stage) {
2674: endtime = MPI_Wtime();
2675: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2676: ctx->times[LANDAU_JACOBIAN] += (endtime - starttime);
2677: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2678: ctx->times[LANDAU_JACOBIAN_COUNT] += 1;
2679: }
2680: #endif
2681: PetscCall(PetscLogEventEnd(ctx->events[0], 0, 0, 0, 0));
2682: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2683: if (ctx->stage) PetscCall(PetscLogStagePop());
2684: PetscFunctionReturn(PETSC_SUCCESS);
2685: }
2687: /*@
2688: DMPlexLandauIJacobian - `TS` Jacobian construction, confusingly this adds mass
2690: Collective
2692: Input Parameters:
2693: + ts - The time stepping context
2694: . time_dummy - current time (not used)
2695: . X - Current state
2696: . U_tdummy - Time derivative of current state (not used)
2697: . shift - shift for du/dt term
2698: - actx - Landau context
2700: Output Parameters:
2701: + Amat - Jacobian
2702: - Pmat - same as Amat
2704: Level: beginner
2706: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIFunction()`
2707: @*/
2708: PetscErrorCode DMPlexLandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx)
2709: {
2710: LandauCtx *ctx = NULL;
2711: PetscInt dim;
2712: DM pack;
2713: #if defined(PETSC_HAVE_THREADSAFETY)
2714: double starttime, endtime;
2715: #endif
2716: PetscObjectState state;
2718: PetscFunctionBegin;
2719: PetscCall(TSGetDM(ts, &pack));
2720: PetscCall(DMGetApplicationContext(pack, &ctx));
2721: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2722: PetscCheck(Amat == Pmat && Amat == ctx->J, ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J");
2723: PetscCall(DMGetDimension(pack, &dim));
2724: /* get collision Jacobian into A */
2725: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2726: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2727: PetscCall(PetscLogEventBegin(ctx->events[9], 0, 0, 0, 0));
2728: #if defined(PETSC_HAVE_THREADSAFETY)
2729: starttime = MPI_Wtime();
2730: #endif
2731: PetscCheck(shift != 0.0, ctx->comm, PETSC_ERR_PLIB, "zero shift");
2732: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2733: PetscCheck(state == ctx->norm_state, ctx->comm, PETSC_ERR_PLIB, "wrong state, %" PetscInt64_FMT " %" PetscInt64_FMT, ctx->norm_state, state);
2734: if (!ctx->use_matrix_mass) {
2735: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, shift, (void *)ctx));
2736: } else { /* add mass */
2737: PetscCall(MatAXPY(Pmat, shift, ctx->M, SAME_NONZERO_PATTERN));
2738: }
2739: #if defined(PETSC_HAVE_THREADSAFETY)
2740: if (ctx->stage) {
2741: endtime = MPI_Wtime();
2742: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2743: ctx->times[LANDAU_MASS] += (endtime - starttime);
2744: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2745: }
2746: #endif
2747: PetscCall(PetscLogEventEnd(ctx->events[9], 0, 0, 0, 0));
2748: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2749: if (ctx->stage) PetscCall(PetscLogStagePop());
2750: PetscFunctionReturn(PETSC_SUCCESS);
2751: }