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: #define PETSC_THREAD_SYNC
20: #include "land_tensors.h"
22: #if defined(PETSC_HAVE_OPENMP)
23: #include <omp.h>
24: #endif
26: static PetscErrorCode LandauGPUMapsDestroy(void *ptr)
27: {
28: P4estVertexMaps *maps = (P4estVertexMaps *)ptr;
29: PetscFunctionBegin;
30: // free device data
31: if (maps[0].deviceType != LANDAU_CPU) {
32: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
33: if (maps[0].deviceType == LANDAU_KOKKOS) {
34: PetscCall(LandauKokkosDestroyMatMaps(maps, maps[0].numgrids)); // implies Kokkos does
35: } // else could be CUDA
36: #elif defined(PETSC_HAVE_CUDA)
37: if (maps[0].deviceType == LANDAU_CUDA) {
38: PetscCall(LandauCUDADestroyMatMaps(maps, maps[0].numgrids));
39: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps->deviceType %d ?????", maps->deviceType);
40: #endif
41: }
42: // free host data
43: for (PetscInt grid = 0; grid < maps[0].numgrids; grid++) {
44: PetscCall(PetscFree(maps[grid].c_maps));
45: PetscCall(PetscFree(maps[grid].gIdx));
46: }
47: PetscCall(PetscFree(maps));
49: PetscFunctionReturn(PETSC_SUCCESS);
50: }
51: static PetscErrorCode energy_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
52: {
53: PetscReal v2 = 0;
54: PetscFunctionBegin;
55: /* compute v^2 / 2 */
56: for (int i = 0; i < dim; ++i) v2 += x[i] * x[i];
57: /* evaluate the Maxwellian */
58: u[0] = v2 / 2;
59: PetscFunctionReturn(PETSC_SUCCESS);
60: }
62: /* needs double */
63: static PetscErrorCode gamma_m1_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
64: {
65: PetscReal *c2_0_arr = ((PetscReal *)actx);
66: double u2 = 0, c02 = (double)*c2_0_arr, xx;
68: PetscFunctionBegin;
69: /* compute u^2 / 2 */
70: for (int i = 0; i < dim; ++i) u2 += x[i] * x[i];
71: /* gamma - 1 = g_eps, for conditioning and we only take derivatives */
72: xx = u2 / c02;
73: #if defined(PETSC_USE_DEBUG)
74: u[0] = PetscSqrtReal(1. + xx);
75: #else
76: u[0] = xx / (PetscSqrtReal(1. + xx) + 1.) - 1.; // better conditioned. -1 might help condition and only used for derivative
77: #endif
78: PetscFunctionReturn(PETSC_SUCCESS);
79: }
81: /*
82: LandauFormJacobian_Internal - Evaluates Jacobian matrix.
84: Input Parameters:
85: . globX - input vector
86: . actx - optional user-defined context
87: . dim - dimension
89: Output Parameters:
90: . J0acP - Jacobian matrix filled, not created
91: */
92: static PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, PetscReal shift, void *a_ctx)
93: {
94: LandauCtx *ctx = (LandauCtx *)a_ctx;
95: PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nb;
96: PetscQuadrature quad;
97: PetscReal Eq_m[LANDAU_MAX_SPECIES]; // could be static data w/o quench (ex2)
98: PetscScalar *cellClosure = NULL;
99: const PetscScalar *xdata = NULL;
100: PetscDS prob;
101: PetscContainer container;
102: P4estVertexMaps *maps;
103: Mat subJ[LANDAU_MAX_GRIDS * LANDAU_MAX_BATCH_SZ];
105: PetscFunctionBegin;
109: /* check for matrix container for GPU assembly. Support CPU assembly for debugging */
110: PetscCheck(ctx->plex[0] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
111: PetscCall(PetscLogEventBegin(ctx->events[10], 0, 0, 0, 0));
112: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
113: PetscCall(PetscObjectQuery((PetscObject)JacP, "assembly_maps", (PetscObject *)&container));
114: if (container) {
115: PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "maps but no GPU assembly");
116: PetscCall(PetscContainerGetPointer(container, (void **)&maps));
117: PetscCheck(maps, ctx->comm, PETSC_ERR_ARG_WRONG, "empty GPU matrix container");
118: for (PetscInt i = 0; i < ctx->num_grids * ctx->batch_sz; i++) subJ[i] = NULL;
119: } else {
120: PetscCheck(!ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "No maps but GPU assembly");
121: for (PetscInt tid = 0; tid < ctx->batch_sz; tid++) {
122: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCreateMatrix(ctx->plex[grid], &subJ[LAND_PACK_IDX(tid, grid)]));
123: }
124: maps = NULL;
125: }
126: // 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)
127: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
128: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
129: Nb = Nq;
130: PetscCheck(Nq <= LANDAU_MAX_NQ, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQ (%d)", Nq, LANDAU_MAX_NQ);
131: // get metadata for collecting dynamic data
132: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
133: PetscInt cStart, cEnd;
134: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
135: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
136: numCells[grid] = cEnd - cStart; // grids can have different topology
137: }
138: PetscCall(PetscLogEventEnd(ctx->events[10], 0, 0, 0, 0));
139: 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 */
140: DM pack;
141: PetscCall(VecGetDM(a_X, &pack));
142: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "pack has no DM");
143: PetscCall(PetscLogEventBegin(ctx->events[1], 0, 0, 0, 0));
144: for (PetscInt fieldA = 0; fieldA < ctx->num_species; fieldA++) {
145: Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */
146: if (dim == 2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */
147: }
148: if (!ctx->gpu_assembly) {
149: Vec *locXArray, *globXArray;
150: PetscScalar *cellClosure_it;
151: PetscInt cellClosure_sz = 0, nDMs, Nf[LANDAU_MAX_GRIDS];
152: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
153: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
154: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
155: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
156: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
157: }
158: /* count cellClosure size */
159: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
160: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) cellClosure_sz += Nb * Nf[grid] * numCells[grid];
161: PetscCall(PetscMalloc1(cellClosure_sz * ctx->batch_sz, &cellClosure));
162: cellClosure_it = cellClosure;
163: PetscCall(PetscMalloc(sizeof(*locXArray) * nDMs, &locXArray));
164: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
165: PetscCall(DMCompositeGetLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
166: PetscCall(DMCompositeGetAccessArray(pack, a_X, nDMs, NULL, globXArray));
167: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP (once)
168: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
169: Vec locX = locXArray[LAND_PACK_IDX(b_id, grid)], globX = globXArray[LAND_PACK_IDX(b_id, grid)], locX2;
170: PetscInt cStart, cEnd, ei;
171: PetscCall(VecDuplicate(locX, &locX2));
172: PetscCall(DMGlobalToLocalBegin(ctx->plex[grid], globX, INSERT_VALUES, locX2));
173: PetscCall(DMGlobalToLocalEnd(ctx->plex[grid], globX, INSERT_VALUES, locX2));
174: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
175: for (ei = cStart; ei < cEnd; ++ei) {
176: PetscScalar *coef = NULL;
177: PetscCall(DMPlexVecGetClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
178: PetscCall(PetscMemcpy(cellClosure_it, coef, Nb * Nf[grid] * sizeof(*cellClosure_it))); /* change if LandauIPReal != PetscScalar */
179: PetscCall(DMPlexVecRestoreClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
180: cellClosure_it += Nb * Nf[grid];
181: }
182: PetscCall(VecDestroy(&locX2));
183: }
184: }
185: PetscCheck(cellClosure_it - cellClosure == cellClosure_sz * ctx->batch_sz, PETSC_COMM_SELF, PETSC_ERR_PLIB, "iteration wrong %" PetscCount_FMT " != cellClosure_sz = %" PetscInt_FMT, (PetscCount)(cellClosure_it - cellClosure),
186: cellClosure_sz * ctx->batch_sz);
187: PetscCall(DMCompositeRestoreLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
188: PetscCall(DMCompositeRestoreAccessArray(pack, a_X, nDMs, NULL, globXArray));
189: PetscCall(PetscFree(locXArray));
190: PetscCall(PetscFree(globXArray));
191: xdata = NULL;
192: } else {
193: PetscMemType mtype;
194: if (ctx->jacobian_field_major_order) { // get data in batch ordering
195: PetscCall(VecScatterBegin(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
196: PetscCall(VecScatterEnd(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
197: PetscCall(VecGetArrayReadAndMemType(ctx->work_vec, &xdata, &mtype));
198: } else {
199: PetscCall(VecGetArrayReadAndMemType(a_X, &xdata, &mtype));
200: }
201: PetscCheck(mtype == PETSC_MEMTYPE_HOST || ctx->deviceType != LANDAU_CPU, ctx->comm, PETSC_ERR_ARG_WRONG, "CPU run with device data: use -mat_type aij");
202: cellClosure = NULL;
203: }
204: PetscCall(PetscLogEventEnd(ctx->events[1], 0, 0, 0, 0));
205: } else xdata = cellClosure = NULL;
207: /* do it */
208: if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) {
209: if (ctx->deviceType == LANDAU_CUDA) {
210: #if defined(PETSC_HAVE_CUDA)
211: PetscCall(LandauCUDAJacobian(ctx->plex, Nq, 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));
212: #else
213: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "cuda");
214: #endif
215: } else if (ctx->deviceType == LANDAU_KOKKOS) {
216: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
217: PetscCall(LandauKokkosJacobian(ctx->plex, Nq, 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));
218: #else
219: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
220: #endif
221: }
222: } else { /* CPU version */
223: PetscTabulation *Tf; // used for CPU and print info. Same on all grids and all species
224: 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];
225: 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;
226: PetscReal Eq_m[LANDAU_MAX_SPECIES], invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES];
227: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
228: PetscScalar *coo_vals = NULL;
229: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
230: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
231: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
232: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
233: }
234: /* count IPf size, etc */
235: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
236: const PetscReal *const BB = Tf[0]->T[0], *const DD = Tf[0]->T[1];
237: ip_offset[0] = ipf_offset[0] = elem_offset[0] = 0;
238: for (PetscInt grid = 0; grid < num_grids; grid++) {
239: PetscInt nfloc = ctx->species_offset[grid + 1] - ctx->species_offset[grid];
240: elem_offset[grid + 1] = elem_offset[grid] + numCells[grid];
241: ip_offset[grid + 1] = ip_offset[grid] + numCells[grid] * Nq;
242: ipf_offset[grid + 1] = ipf_offset[grid] + Nq * nfloc * numCells[grid];
243: }
244: IPf_sz_glb = ipf_offset[num_grids];
245: IPf_sz_tot = IPf_sz_glb * ctx->batch_sz;
246: // prep COO
247: if (ctx->coo_assembly) {
248: PetscCall(PetscMalloc1(ctx->SData_d.coo_size, &coo_vals)); // allocate every time?
249: PetscCall(PetscInfo(ctx->plex[0], "COO Allocate %" PetscInt_FMT " values\n", (PetscInt)ctx->SData_d.coo_size));
250: }
251: if (shift == 0.0) { /* compute dynamic data f and df and init data for Jacobian */
252: #if defined(PETSC_HAVE_THREADSAFETY)
253: double starttime, endtime;
254: starttime = MPI_Wtime();
255: #endif
256: PetscCall(PetscLogEventBegin(ctx->events[8], 0, 0, 0, 0));
257: for (PetscInt fieldA = 0; fieldA < ctx->num_species; fieldA++) {
258: invMass[fieldA] = ctx->m_0 / ctx->masses[fieldA];
259: Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */
260: if (dim == 2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */
261: nu_alpha[fieldA] = PetscSqr(ctx->charges[fieldA] / ctx->m_0) * ctx->m_0 / ctx->masses[fieldA];
262: nu_beta[fieldA] = PetscSqr(ctx->charges[fieldA] / ctx->epsilon0) * ctx->lnLam / (8 * PETSC_PI) * ctx->t_0 * ctx->n_0 / PetscPowReal(ctx->v_0, 3);
263: }
264: PetscCall(PetscMalloc4(IPf_sz_tot, &ff, IPf_sz_tot, &dudx, IPf_sz_tot, &dudy, dim == 3 ? IPf_sz_tot : 0, &dudz));
265: // F df/dx
266: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
267: 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
268: // find my grid:
269: PetscInt grid = 0;
270: while (b_elem_idx >= elem_offset[grid + 1]) grid++; // yuck search for grid
271: {
272: 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];
273: 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];
274: PetscScalar *coef, coef_buff[LANDAU_MAX_SPECIES * LANDAU_MAX_NQ];
275: PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim]; // ingJ is static data on batch 0
276: PetscInt b, f, q;
277: if (cellClosure) {
278: coef = &cellClosure[b_id * IPf_sz_glb + ipf_offset[grid] + loc_elem * Nb * loc_Nf]; // this is const
279: } else {
280: coef = coef_buff;
281: for (f = 0; f < loc_Nf; ++f) {
282: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][f][0];
283: for (b = 0; b < Nb; ++b) {
284: PetscInt idx = Idxs[b];
285: if (idx >= 0) {
286: coef[f * Nb + b] = xdata[idx + moffset];
287: } else {
288: idx = -idx - 1;
289: coef[f * Nb + b] = 0;
290: for (q = 0; q < maps[grid].num_face; q++) {
291: PetscInt id = maps[grid].c_maps[idx][q].gid;
292: PetscScalar scale = maps[grid].c_maps[idx][q].scale;
293: coef[f * Nb + b] += scale * xdata[id + moffset];
294: }
295: }
296: }
297: }
298: }
299: /* get f and df */
300: for (PetscInt qi = 0; qi < Nq; qi++) {
301: const PetscReal *invJ = &invJe[qi * dim * dim];
302: const PetscReal *Bq = &BB[qi * Nb];
303: const PetscReal *Dq = &DD[qi * Nb * dim];
304: PetscReal u_x[LANDAU_DIM];
305: /* get f & df */
306: for (f = 0; f < loc_Nf; ++f) {
307: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid] + f * loc_nip + loc_elem * Nq + qi;
308: PetscInt b, e;
309: PetscReal refSpaceDer[LANDAU_DIM];
310: ff[idx] = 0.0;
311: for (int d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0;
312: for (b = 0; b < Nb; ++b) {
313: const PetscInt cidx = b;
314: ff[idx] += Bq[cidx] * PetscRealPart(coef[f * Nb + cidx]);
315: for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx * dim + d] * PetscRealPart(coef[f * Nb + cidx]);
316: }
317: for (int d = 0; d < LANDAU_DIM; ++d) {
318: for (e = 0, u_x[d] = 0.0; e < LANDAU_DIM; ++e) u_x[d] += invJ[e * dim + d] * refSpaceDer[e];
319: }
320: dudx[idx] = u_x[0];
321: dudy[idx] = u_x[1];
322: #if LANDAU_DIM == 3
323: dudz[idx] = u_x[2];
324: #endif
325: }
326: } // q
327: } // grid
328: } // grid*batch
329: PetscCall(PetscLogEventEnd(ctx->events[8], 0, 0, 0, 0));
330: #if defined(PETSC_HAVE_THREADSAFETY)
331: endtime = MPI_Wtime();
332: if (ctx->stage) ctx->times[LANDAU_F_DF] += (endtime - starttime);
333: #endif
334: } // Jacobian setup
335: // assemble Jacobian (or mass)
336: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
337: const PetscInt b_Nelem = elem_offset[num_grids];
338: const PetscInt glb_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem;
339: PetscInt grid = 0;
340: #if defined(PETSC_HAVE_THREADSAFETY)
341: double starttime, endtime;
342: starttime = MPI_Wtime();
343: #endif
344: while (glb_elem_idx >= elem_offset[grid + 1]) grid++;
345: {
346: const PetscInt loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = glb_elem_idx - elem_offset[grid];
347: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset), totDim = loc_Nf * Nq, elemMatSize = totDim * totDim;
348: PetscScalar *elemMat;
349: const PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim];
350: PetscCall(PetscMalloc1(elemMatSize, &elemMat));
351: PetscCall(PetscMemzero(elemMat, elemMatSize * sizeof(*elemMat)));
352: if (shift == 0.0) { // Jacobian
353: PetscCall(PetscLogEventBegin(ctx->events[4], 0, 0, 0, 0));
354: } else { // mass
355: PetscCall(PetscLogEventBegin(ctx->events[16], 0, 0, 0, 0));
356: }
357: for (PetscInt qj = 0; qj < Nq; ++qj) {
358: const PetscInt jpidx_glb = ip_offset[grid] + qj + loc_elem * Nq;
359: 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
360: PetscInt d, d2, dp, d3, IPf_idx;
361: if (shift == 0.0) { // Jacobian
362: const PetscReal *const invJj = &invJe[qj * dim * dim];
363: 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];
364: const PetscReal vj[3] = {xx[jpidx_glb], yy[jpidx_glb], zz ? zz[jpidx_glb] : 0}, wj = ww[jpidx_glb];
365: // create g2 & g3
366: for (d = 0; d < LANDAU_DIM; d++) { // clear accumulation data D & K
367: gg2_temp[d] = 0;
368: for (d2 = 0; d2 < LANDAU_DIM; d2++) gg3_temp[d][d2] = 0;
369: }
370: /* inner beta reduction */
371: IPf_idx = 0;
372: 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
373: PetscInt nip_loc_r = numCells[grid_r] * Nq, Nfloc_r = Nf[grid_r];
374: for (PetscInt ei_r = 0, loc_fdf_idx = 0; ei_r < numCells[grid_r]; ++ei_r) {
375: for (PetscInt qi = 0; qi < Nq; qi++, ipidx++, loc_fdf_idx++) {
376: const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx];
377: PetscReal temp1[3] = {0, 0, 0}, temp2 = 0;
378: #if LANDAU_DIM == 2
379: 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.;
380: LandauTensor2D(vj, x, y, Ud, Uk, mask);
381: #else
382: 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.;
383: if (ctx->use_relativistic_corrections) {
384: LandauTensor3DRelativistic(vj, x, y, z, U, mask, C_0(ctx->v_0));
385: } else {
386: LandauTensor3D(vj, x, y, z, U, mask);
387: }
388: #endif
389: for (int f = 0; f < Nfloc_r; ++f) {
390: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid_r] + f * nip_loc_r + ei_r * Nq + qi; // IPf_idx + f*nip_loc_r + loc_fdf_idx;
391: temp1[0] += dudx[idx] * nu_beta[f + f_off] * invMass[f + f_off];
392: temp1[1] += dudy[idx] * nu_beta[f + f_off] * invMass[f + f_off];
393: #if LANDAU_DIM == 3
394: temp1[2] += dudz[idx] * nu_beta[f + f_off] * invMass[f + f_off];
395: #endif
396: temp2 += ff[idx] * nu_beta[f + f_off];
397: }
398: temp1[0] *= wi;
399: temp1[1] *= wi;
400: #if LANDAU_DIM == 3
401: temp1[2] *= wi;
402: #endif
403: temp2 *= wi;
404: #if LANDAU_DIM == 2
405: for (d2 = 0; d2 < 2; d2++) {
406: for (d3 = 0; d3 < 2; ++d3) {
407: /* K = U * grad(f): g2=e: i,A */
408: gg2_temp[d2] += Uk[d2][d3] * temp1[d3];
409: /* D = -U * (I \kron (fx)): g3=f: i,j,A */
410: gg3_temp[d2][d3] += Ud[d2][d3] * temp2;
411: }
412: }
413: #else
414: for (d2 = 0; d2 < 3; ++d2) {
415: for (d3 = 0; d3 < 3; ++d3) {
416: /* K = U * grad(f): g2 = e: i,A */
417: gg2_temp[d2] += U[d2][d3] * temp1[d3];
418: /* D = -U * (I \kron (fx)): g3 = f: i,j,A */
419: gg3_temp[d2][d3] += U[d2][d3] * temp2;
420: }
421: }
422: #endif
423: } // qi
424: } // ei_r
425: IPf_idx += nip_loc_r * Nfloc_r;
426: } /* grid_r - IPs */
427: 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);
428: // add alpha and put in gg2/3
429: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) {
430: for (d2 = 0; d2 < LANDAU_DIM; d2++) {
431: gg2[fieldA][d2] = gg2_temp[d2] * nu_alpha[fieldA + f_off];
432: for (d3 = 0; d3 < LANDAU_DIM; d3++) gg3[fieldA][d2][d3] = -gg3_temp[d2][d3] * nu_alpha[fieldA + f_off] * invMass[fieldA + f_off];
433: }
434: }
435: /* add electric field term once per IP */
436: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) gg2[fieldA][LANDAU_DIM - 1] += Eq_m[fieldA + f_off];
437: /* Jacobian transform - g2, g3 */
438: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
439: for (d = 0; d < dim; ++d) {
440: g2[fieldA][d] = 0.0;
441: for (d2 = 0; d2 < dim; ++d2) {
442: g2[fieldA][d] += invJj[d * dim + d2] * gg2[fieldA][d2];
443: g3[fieldA][d][d2] = 0.0;
444: for (d3 = 0; d3 < dim; ++d3) {
445: for (dp = 0; dp < dim; ++dp) g3[fieldA][d][d2] += invJj[d * dim + d3] * gg3[fieldA][d3][dp] * invJj[d2 * dim + dp];
446: }
447: g3[fieldA][d][d2] *= wj;
448: }
449: g2[fieldA][d] *= wj;
450: }
451: }
452: } else { // mass
453: PetscReal wj = ww[jpidx_glb];
454: /* Jacobian transform - g0 */
455: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
456: if (dim == 2) {
457: g0[fieldA] = wj * shift * 2. * PETSC_PI; // move this to below and remove g0
458: } else {
459: g0[fieldA] = wj * shift; // move this to below and remove g0
460: }
461: }
462: }
463: /* FE matrix construction */
464: {
465: PetscInt fieldA, d, f, d2, g;
466: const PetscReal *BJq = &BB[qj * Nb], *DIq = &DD[qj * Nb * dim];
467: /* assemble - on the diagonal (I,I) */
468: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
469: for (f = 0; f < Nb; f++) {
470: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
471: for (g = 0; g < Nb; ++g) {
472: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
473: const PetscInt fOff = i * totDim + j;
474: if (shift == 0.0) {
475: for (d = 0; d < dim; ++d) {
476: elemMat[fOff] += DIq[f * dim + d] * g2[fieldA][d] * BJq[g];
477: for (d2 = 0; d2 < dim; ++d2) elemMat[fOff] += DIq[f * dim + d] * g3[fieldA][d][d2] * DIq[g * dim + d2];
478: }
479: } else { // mass
480: elemMat[fOff] += BJq[f] * g0[fieldA] * BJq[g];
481: }
482: }
483: }
484: }
485: }
486: } /* qj loop */
487: if (shift == 0.0) { // Jacobian
488: PetscCall(PetscLogEventEnd(ctx->events[4], 0, 0, 0, 0));
489: } else {
490: PetscCall(PetscLogEventEnd(ctx->events[16], 0, 0, 0, 0));
491: }
492: #if defined(PETSC_HAVE_THREADSAFETY)
493: endtime = MPI_Wtime();
494: if (ctx->stage) ctx->times[LANDAU_KERNEL] += (endtime - starttime);
495: #endif
496: /* assemble matrix */
497: if (!container) {
498: PetscInt cStart;
499: PetscCall(PetscLogEventBegin(ctx->events[6], 0, 0, 0, 0));
500: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, NULL));
501: PetscCall(DMPlexMatSetClosure(ctx->plex[grid], section[grid], globsection[grid], subJ[LAND_PACK_IDX(b_id, grid)], loc_elem + cStart, elemMat, ADD_VALUES));
502: PetscCall(PetscLogEventEnd(ctx->events[6], 0, 0, 0, 0));
503: } else { // GPU like assembly for debugging
504: 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];
505: 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};
506: 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_NQ + 1] = (LandauIdx(*)[LANDAU_MAX_NQ + 1]) ctx->SData_d.coo_elem_point_offsets;
507: /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */
508: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
509: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][fieldA][0];
510: for (f = 0; f < Nb; f++) {
511: PetscInt idx = Idxs[f];
512: if (idx >= 0) {
513: nr = 1;
514: rows0[0] = idx;
515: row_scale[0] = 1.;
516: } else {
517: idx = -idx - 1;
518: for (q = 0, nr = 0; q < maps[grid].num_face; q++, nr++) {
519: if (maps[grid].c_maps[idx][q].gid < 0) break;
520: rows0[q] = maps[grid].c_maps[idx][q].gid;
521: row_scale[q] = maps[grid].c_maps[idx][q].scale;
522: }
523: }
524: for (g = 0; g < Nb; ++g) {
525: idx = Idxs[g];
526: if (idx >= 0) {
527: nc = 1;
528: cols0[0] = idx;
529: col_scale[0] = 1.;
530: } else {
531: idx = -idx - 1;
532: nc = maps[grid].num_face;
533: for (q = 0, nc = 0; q < maps[grid].num_face; q++, nc++) {
534: if (maps[grid].c_maps[idx][q].gid < 0) break;
535: cols0[q] = maps[grid].c_maps[idx][q].gid;
536: col_scale[q] = maps[grid].c_maps[idx][q].scale;
537: }
538: }
539: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
540: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
541: const PetscScalar Aij = elemMat[i * totDim + j];
542: if (coo_vals) { // mirror (i,j) in CreateStaticGPUData
543: const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
544: const int 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];
545: for (int q = 0, idx2 = idx0; q < nr; q++) {
546: for (int d = 0; d < nc; d++, idx2++) coo_vals[idx2] = row_scale[q] * col_scale[d] * Aij;
547: }
548: } else {
549: for (q = 0; q < nr; q++) rows[q] = rows0[q] + moffset;
550: for (d = 0; d < nc; d++) cols[d] = cols0[d] + moffset;
551: for (q = 0; q < nr; q++) {
552: for (d = 0; d < nc; d++) vals[q * nc + d] = row_scale[q] * col_scale[d] * Aij;
553: }
554: PetscCall(MatSetValues(JacP, nr, rows, nc, cols, vals, ADD_VALUES));
555: }
556: }
557: }
558: }
559: }
560: if (loc_elem == -1) {
561: PetscCall(PetscPrintf(ctx->comm, "CPU Element matrix\n"));
562: for (int d = 0; d < totDim; ++d) {
563: for (int f = 0; f < totDim; ++f) PetscCall(PetscPrintf(ctx->comm, " %12.5e", (double)PetscRealPart(elemMat[d * totDim + f])));
564: PetscCall(PetscPrintf(ctx->comm, "\n"));
565: }
566: exit(12);
567: }
568: PetscCall(PetscFree(elemMat));
569: } /* grid */
570: } /* outer element & batch loop */
571: if (shift == 0.0) { // mass
572: PetscCall(PetscFree4(ff, dudx, dudy, dudz));
573: }
574: if (!container) { // 'CPU' assembly move nest matrix to global JacP
575: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP
576: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
577: 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];
578: PetscInt nloc, nzl, colbuf[1024], row;
579: const PetscInt *cols;
580: const PetscScalar *vals;
581: Mat B = subJ[LAND_PACK_IDX(b_id, grid)];
582: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
583: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
584: PetscCall(MatGetSize(B, &nloc, NULL));
585: for (int i = 0; i < nloc; i++) {
586: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
587: PetscCheck(nzl <= 1024, PetscObjectComm((PetscObject)B), PETSC_ERR_PLIB, "Row too big: %" PetscInt_FMT, nzl);
588: for (int j = 0; j < nzl; j++) colbuf[j] = moffset + cols[j];
589: row = moffset + i;
590: PetscCall(MatSetValues(JacP, 1, &row, nzl, colbuf, vals, ADD_VALUES));
591: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
592: }
593: PetscCall(MatDestroy(&B));
594: }
595: }
596: }
597: if (coo_vals) {
598: PetscCall(MatSetValuesCOO(JacP, coo_vals, ADD_VALUES));
599: PetscCall(PetscFree(coo_vals));
600: }
601: } /* CPU version */
602: PetscCall(MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY));
603: PetscCall(MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY));
604: /* clean up */
605: if (cellClosure) PetscCall(PetscFree(cellClosure));
606: if (xdata) PetscCall(VecRestoreArrayReadAndMemType(a_X, &xdata));
607: PetscFunctionReturn(PETSC_SUCCESS);
608: }
610: #if defined(LANDAU_ADD_BCS)
611: static void zero_bc(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 uexact[])
612: {
613: uexact[0] = 0;
614: }
615: #endif
617: #define MATVEC2(__a, __x, __p) \
618: { \
619: int i, j; \
620: for (i = 0.; i < 2; i++) { \
621: __p[i] = 0; \
622: for (j = 0.; j < 2; j++) __p[i] += __a[i][j] * __x[j]; \
623: } \
624: }
625: static void CircleInflate(PetscReal r1, PetscReal r2, PetscReal r0, PetscInt num_sections, PetscReal x, PetscReal y, PetscReal *outX, PetscReal *outY)
626: {
627: PetscReal rr = PetscSqrtReal(x * x + y * y), outfact, efact;
628: if (rr < r1 + PETSC_SQRT_MACHINE_EPSILON) {
629: *outX = x;
630: *outY = y;
631: } else {
632: const PetscReal xy[2] = {x, y}, sinphi = y / rr, cosphi = x / rr;
633: PetscReal cth, sth, xyprime[2], Rth[2][2], rotcos, newrr;
634: if (num_sections == 2) {
635: rotcos = 0.70710678118654;
636: outfact = 1.5;
637: efact = 2.5;
638: /* rotate normalized vector into [-pi/4,pi/4) */
639: if (sinphi >= 0.) { /* top cell, -pi/2 */
640: cth = 0.707106781186548;
641: sth = -0.707106781186548;
642: } else { /* bottom cell -pi/8 */
643: cth = 0.707106781186548;
644: sth = .707106781186548;
645: }
646: } else if (num_sections == 3) {
647: rotcos = 0.86602540378443;
648: outfact = 1.5;
649: efact = 2.5;
650: /* rotate normalized vector into [-pi/6,pi/6) */
651: if (sinphi >= 0.5) { /* top cell, -pi/3 */
652: cth = 0.5;
653: sth = -0.866025403784439;
654: } else if (sinphi >= -.5) { /* mid cell 0 */
655: cth = 1.;
656: sth = .0;
657: } else { /* bottom cell +pi/3 */
658: cth = 0.5;
659: sth = 0.866025403784439;
660: }
661: } else if (num_sections == 4) {
662: rotcos = 0.9238795325112;
663: outfact = 1.5;
664: efact = 3;
665: /* rotate normalized vector into [-pi/8,pi/8) */
666: if (sinphi >= 0.707106781186548) { /* top cell, -3pi/8 */
667: cth = 0.38268343236509;
668: sth = -0.923879532511287;
669: } else if (sinphi >= 0.) { /* mid top cell -pi/8 */
670: cth = 0.923879532511287;
671: sth = -.38268343236509;
672: } else if (sinphi >= -0.707106781186548) { /* mid bottom cell + pi/8 */
673: cth = 0.923879532511287;
674: sth = 0.38268343236509;
675: } else { /* bottom cell + 3pi/8 */
676: cth = 0.38268343236509;
677: sth = .923879532511287;
678: }
679: } else {
680: cth = 0.;
681: sth = 0.;
682: rotcos = 0;
683: efact = 0;
684: }
685: Rth[0][0] = cth;
686: Rth[0][1] = -sth;
687: Rth[1][0] = sth;
688: Rth[1][1] = cth;
689: MATVEC2(Rth, xy, xyprime);
690: if (num_sections == 2) {
691: newrr = xyprime[0] / rotcos;
692: } else {
693: PetscReal newcosphi = xyprime[0] / rr, rin = r1, rout = rr - rin;
694: PetscReal routmax = r0 * rotcos / newcosphi - rin, nroutmax = r0 - rin, routfrac = rout / routmax;
695: newrr = rin + routfrac * nroutmax;
696: }
697: *outX = cosphi * newrr;
698: *outY = sinphi * newrr;
699: /* grade */
700: PetscReal fact, tt, rs, re, rr = PetscSqrtReal(PetscSqr(*outX) + PetscSqr(*outY));
701: if (rr > r2) {
702: rs = r2;
703: re = r0;
704: fact = outfact;
705: } /* outer zone */
706: else {
707: rs = r1;
708: re = r2;
709: fact = efact;
710: } /* electron zone */
711: tt = (rs + PetscPowReal((rr - rs) / (re - rs), fact) * (re - rs)) / rr;
712: *outX *= tt;
713: *outY *= tt;
714: }
715: }
717: static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx)
718: {
719: LandauCtx *ctx = (LandauCtx *)a_ctx;
720: PetscReal r = abc[0], z = abc[1];
721: if (ctx->inflate) {
722: PetscReal absR, absZ;
723: absR = PetscAbs(r);
724: absZ = PetscAbs(z);
725: CircleInflate(ctx->i_radius[0], ctx->e_radius, ctx->radius[0], ctx->num_sections, absR, absZ, &absR, &absZ); // wrong: how do I know what grid I am on?
726: r = (r > 0) ? absR : -absR;
727: z = (z > 0) ? absZ : -absZ;
728: }
729: xyz[0] = r;
730: xyz[1] = z;
731: if (dim == 3) xyz[2] = abc[2];
733: PetscFunctionReturn(PETSC_SUCCESS);
734: }
736: /* create DMComposite of meshes for each species group */
737: static PetscErrorCode LandauDMCreateVMeshes(MPI_Comm comm_self, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM pack)
738: {
739: PetscFunctionBegin;
740: { /* p4est, quads */
741: /* Create plex mesh of Landau domain */
742: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
743: PetscReal par_radius = ctx->radius_par[grid], perp_radius = ctx->radius_perp[grid];
744: if (!ctx->sphere) {
745: PetscReal lo[] = {-perp_radius, -par_radius, -par_radius}, hi[] = {perp_radius, par_radius, par_radius};
746: DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim == 2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
747: if (dim == 2) lo[0] = 0;
748: else {
749: lo[1] = -perp_radius;
750: hi[1] = perp_radius; // 3D y is a perp
751: }
752: PetscCall(DMPlexCreateBoxMesh(comm_self, dim, PETSC_FALSE, ctx->cells0, lo, hi, periodicity, PETSC_TRUE, &ctx->plex[grid])); // todo: make composite and create dm[grid] here
753: PetscCall(DMLocalizeCoordinates(ctx->plex[grid])); /* needed for periodic */
754: if (dim == 3) PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cube"));
755: else PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "half-plane"));
756: } else if (dim == 2) { // sphere is all wrong. should just have one inner radius
757: PetscInt numCells, cells[16][4], i, j;
758: PetscInt numVerts;
759: PetscReal inner_radius1 = ctx->i_radius[grid], inner_radius2 = ctx->e_radius;
760: PetscReal *flatCoords = NULL;
761: PetscInt *flatCells = NULL, *pcell;
762: if (ctx->num_sections == 2) {
763: #if 1
764: numCells = 5;
765: numVerts = 10;
766: int cells2[][4] = {
767: {0, 1, 4, 3},
768: {1, 2, 5, 4},
769: {3, 4, 7, 6},
770: {4, 5, 8, 7},
771: {6, 7, 8, 9}
772: };
773: for (i = 0; i < numCells; i++)
774: for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j];
775: PetscCall(PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells));
776: {
777: PetscReal(*coords)[2] = (PetscReal(*)[2])flatCoords;
778: for (j = 0; j < numVerts - 1; j++) {
779: PetscReal z, r, theta = -PETSC_PI / 2 + (j % 3) * PETSC_PI / 2;
780: PetscReal rad = (j >= 6) ? inner_radius1 : (j >= 3) ? inner_radius2 : ctx->radius[grid];
781: z = rad * PetscSinReal(theta);
782: coords[j][1] = z;
783: r = rad * PetscCosReal(theta);
784: coords[j][0] = r;
785: }
786: coords[numVerts - 1][0] = coords[numVerts - 1][1] = 0;
787: }
788: #else
789: numCells = 4;
790: numVerts = 8;
791: static int cells2[][4] = {
792: {0, 1, 2, 3},
793: {4, 5, 1, 0},
794: {5, 6, 2, 1},
795: {6, 7, 3, 2}
796: };
797: for (i = 0; i < numCells; i++)
798: for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j];
799: PetscCall(loc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells));
800: {
801: PetscReal(*coords)[2] = (PetscReal(*)[2])flatCoords;
802: PetscInt j;
803: for (j = 0; j < 8; j++) {
804: PetscReal z, r;
805: PetscReal theta = -PETSC_PI / 2 + (j % 4) * PETSC_PI / 3.;
806: PetscReal rad = ctx->radius[grid] * ((j < 4) ? 0.5 : 1.0);
807: z = rad * PetscSinReal(theta);
808: coords[j][1] = z;
809: r = rad * PetscCosReal(theta);
810: coords[j][0] = r;
811: }
812: }
813: #endif
814: } else if (ctx->num_sections == 3) {
815: numCells = 7;
816: numVerts = 12;
817: int cells2[][4] = {
818: {0, 1, 5, 4 },
819: {1, 2, 6, 5 },
820: {2, 3, 7, 6 },
821: {4, 5, 9, 8 },
822: {5, 6, 10, 9 },
823: {6, 7, 11, 10},
824: {8, 9, 10, 11}
825: };
826: for (i = 0; i < numCells; i++)
827: for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j];
828: PetscCall(PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells));
829: {
830: PetscReal(*coords)[2] = (PetscReal(*)[2])flatCoords;
831: for (j = 0; j < numVerts; j++) {
832: PetscReal z, r, theta = -PETSC_PI / 2 + (j % 4) * PETSC_PI / 3;
833: PetscReal rad = (j >= 8) ? inner_radius1 : (j >= 4) ? inner_radius2 : ctx->radius[grid];
834: z = rad * PetscSinReal(theta);
835: coords[j][1] = z;
836: r = rad * PetscCosReal(theta);
837: coords[j][0] = r;
838: }
839: }
840: } else if (ctx->num_sections == 4) {
841: numCells = 10;
842: numVerts = 16;
843: int cells2[][4] = {
844: {0, 1, 6, 5 },
845: {1, 2, 7, 6 },
846: {2, 3, 8, 7 },
847: {3, 4, 9, 8 },
848: {5, 6, 11, 10},
849: {6, 7, 12, 11},
850: {7, 8, 13, 12},
851: {8, 9, 14, 13},
852: {10, 11, 12, 15},
853: {12, 13, 14, 15}
854: };
855: for (i = 0; i < numCells; i++)
856: for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j];
857: PetscCall(PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells));
858: {
859: PetscReal(*coords)[2] = (PetscReal(*)[2])flatCoords;
860: for (j = 0; j < numVerts - 1; j++) {
861: PetscReal z, r, theta = -PETSC_PI / 2 + (j % 5) * PETSC_PI / 4;
862: PetscReal rad = (j >= 10) ? inner_radius1 : (j >= 5) ? inner_radius2 : ctx->radius[grid];
863: z = rad * PetscSinReal(theta);
864: coords[j][1] = z;
865: r = rad * PetscCosReal(theta);
866: coords[j][0] = r;
867: }
868: coords[numVerts - 1][0] = coords[numVerts - 1][1] = 0;
869: }
870: } else {
871: numCells = 0;
872: numVerts = 0;
873: }
874: for (j = 0, pcell = flatCells; j < numCells; j++, pcell += 4) {
875: pcell[0] = cells[j][0];
876: pcell[1] = cells[j][1];
877: pcell[2] = cells[j][2];
878: pcell[3] = cells[j][3];
879: }
880: PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 2, numCells, numVerts, 4, ctx->interpolate, flatCells, 2, flatCoords, &ctx->plex[grid]));
881: PetscCall(PetscFree2(flatCoords, flatCells));
882: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "semi-circle"));
883: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Velocity space meshes does not support cubed sphere");
885: PetscCall(DMSetFromOptions(ctx->plex[grid]));
886: } // grid loop
887: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)pack, prefix));
889: { /* convert to p4est (or whatever), wait for discretization to create pack */
890: char convType[256];
891: PetscBool flg;
893: PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");
894: PetscCall(PetscOptionsFList("-dm_landau_type", "Convert DMPlex to another format (p4est)", "plexland.c", DMList, DMPLEX, convType, 256, &flg));
895: PetscOptionsEnd();
896: if (flg) {
897: ctx->use_p4est = PETSC_TRUE; /* flag for Forest */
898: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
899: DM dmforest;
900: PetscCall(DMConvert(ctx->plex[grid], convType, &dmforest));
901: if (dmforest) {
902: PetscBool isForest;
903: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dmforest, prefix));
904: PetscCall(DMIsForest(dmforest, &isForest));
905: if (isForest) {
906: if (ctx->sphere && ctx->inflate) PetscCall(DMForestSetBaseCoordinateMapping(dmforest, GeometryDMLandau, ctx));
907: PetscCall(DMDestroy(&ctx->plex[grid]));
908: ctx->plex[grid] = dmforest; // Forest for adaptivity
909: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Converted to non Forest?");
910: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Convert failed?");
911: }
912: } else ctx->use_p4est = PETSC_FALSE; /* flag for Forest */
913: }
914: } /* non-file */
915: PetscCall(DMSetDimension(pack, dim));
916: PetscCall(PetscObjectSetName((PetscObject)pack, "Mesh"));
917: PetscCall(DMSetApplicationContext(pack, ctx));
919: PetscFunctionReturn(PETSC_SUCCESS);
920: }
922: static PetscErrorCode SetupDS(DM pack, PetscInt dim, PetscInt grid, LandauCtx *ctx)
923: {
924: PetscInt ii, i0;
925: char buf[256];
926: PetscSection section;
928: PetscFunctionBegin;
929: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
930: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "e"));
931: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "i%" PetscInt_FMT, ii));
932: /* Setup Discretization - FEM */
933: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &ctx->fe[ii]));
934: PetscCall(PetscObjectSetName((PetscObject)ctx->fe[ii], buf));
935: PetscCall(DMSetField(ctx->plex[grid], i0, NULL, (PetscObject)ctx->fe[ii]));
936: }
937: PetscCall(DMCreateDS(ctx->plex[grid]));
938: PetscCall(DMGetSection(ctx->plex[grid], §ion));
939: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
940: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "se"));
941: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "si%" PetscInt_FMT, ii));
942: PetscCall(PetscSectionSetComponentName(section, i0, 0, buf));
943: }
944: PetscFunctionReturn(PETSC_SUCCESS);
945: }
947: /* Define a Maxwellian function for testing out the operator. */
949: /* Using cartesian velocity space coordinates, the particle */
950: /* density, [1/m^3], is defined according to */
952: /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */
954: /* Using some constant, c, we normalize the velocity vector into a */
955: /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */
957: /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */
959: /* Defining $\theta=2T/mc^2$, we thus find that the probability density */
960: /* for finding the particle within the interval in a box dx^3 around x is */
962: /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */
964: typedef struct {
965: PetscReal v_0;
966: PetscReal kT_m;
967: PetscReal n;
968: PetscReal shift;
969: } MaxwellianCtx;
971: static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
972: {
973: MaxwellianCtx *mctx = (MaxwellianCtx *)actx;
974: PetscInt i;
975: PetscReal v2 = 0, theta = 2 * mctx->kT_m / (mctx->v_0 * mctx->v_0); /* theta = 2kT/mc^2 */
976: PetscFunctionBegin;
977: /* compute the exponents, v^2 */
978: for (i = 0; i < dim; ++i) v2 += x[i] * x[i];
979: /* evaluate the Maxwellian */
980: u[0] = mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
981: if (mctx->shift != 0.) {
982: v2 = 0;
983: for (i = 0; i < dim - 1; ++i) v2 += x[i] * x[i];
984: v2 += (x[dim - 1] - mctx->shift) * (x[dim - 1] - mctx->shift);
985: /* evaluate the shifted Maxwellian */
986: u[0] += mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
987: }
988: PetscFunctionReturn(PETSC_SUCCESS);
989: }
991: /*@
992: DMPlexLandauAddMaxwellians - Add a Maxwellian distribution to a state
994: Collective
996: Input Parameters:
997: . dm - The mesh (local)
998: + time - Current time
999: - temps - Temperatures of each species (global)
1000: . ns - Number density of each species (global)
1001: - grid - index into current grid - just used for offset into temp and ns
1002: . b_id - batch index
1003: - n_batch - number of batches
1004: + actx - Landau context
1006: Output Parameter:
1007: . X - The state (local to this grid)
1009: Level: beginner
1011: .keywords: mesh
1012: .seealso: `DMPlexLandauCreateVelocitySpace()`
1013: @*/
1014: PetscErrorCode DMPlexLandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
1015: {
1016: LandauCtx *ctx = (LandauCtx *)actx;
1017: PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
1018: PetscInt dim;
1019: MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES];
1021: PetscFunctionBegin;
1022: PetscCall(DMGetDimension(dm, &dim));
1023: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
1024: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
1025: mctxs[i0] = &data[i0];
1026: data[i0].v_0 = ctx->v_0; // v_0 same for all grids
1027: data[i0].kT_m = ctx->k * temps[ii] / ctx->masses[ii]; /* kT/m */
1028: data[i0].n = ns[ii] * (1 + 0.1 * (double)b_id / (double)n_batch); // ramp density up 10% to mimic application, n[0] use for Conner-Hastie
1029: initu[i0] = maxwellian;
1030: data[i0].shift = 0;
1031: }
1032: data[0].shift = ctx->electronShift;
1033: /* need to make ADD_ALL_VALUES work - TODO */
1034: PetscCall(DMProjectFunction(dm, time, initu, (void **)mctxs, INSERT_ALL_VALUES, X));
1035: PetscFunctionReturn(PETSC_SUCCESS);
1036: }
1038: /*
1039: LandauSetInitialCondition - Addes Maxwellians with context
1041: Collective
1043: Input Parameters:
1044: . dm - The mesh
1045: - grid - index into current grid - just used for offset into temp and ns
1046: . b_id - batch index
1047: - n_batch - number of batches
1048: + actx - Landau context with T and n
1050: Output Parameter:
1051: . X - The state
1053: Level: beginner
1055: .keywords: mesh
1056: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauAddMaxwellians()`
1057: */
1058: static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
1059: {
1060: LandauCtx *ctx = (LandauCtx *)actx;
1061: PetscFunctionBegin;
1062: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
1063: PetscCall(VecZeroEntries(X));
1064: PetscCall(DMPlexLandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, grid, b_id, n_batch, ctx));
1065: PetscFunctionReturn(PETSC_SUCCESS);
1066: }
1068: // adapt a level once. Forest in/out
1069: static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscInt type, PetscInt grid, LandauCtx *ctx, DM *newForest)
1070: {
1071: DM forest, plex, adaptedDM = NULL;
1072: PetscDS prob;
1073: PetscBool isForest;
1074: PetscQuadrature quad;
1075: PetscInt Nq, *Nb, cStart, cEnd, c, dim, qj, k;
1076: DMLabel adaptLabel = NULL;
1078: PetscFunctionBegin;
1079: forest = ctx->plex[grid];
1080: PetscCall(DMCreateDS(forest));
1081: PetscCall(DMGetDS(forest, &prob));
1082: PetscCall(DMGetDimension(forest, &dim));
1083: PetscCall(DMIsForest(forest, &isForest));
1084: PetscCheck(isForest, ctx->comm, PETSC_ERR_ARG_WRONG, "! Forest");
1085: PetscCall(DMConvert(forest, DMPLEX, &plex));
1086: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
1087: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "adapt", &adaptLabel));
1088: PetscCall(PetscFEGetQuadrature(fem, &quad));
1089: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
1090: PetscCheck(Nq <= LANDAU_MAX_NQ, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQ (%d)", Nq, LANDAU_MAX_NQ);
1091: PetscCall(PetscDSGetDimensions(prob, &Nb));
1092: if (type == 4) {
1093: for (c = cStart; c < cEnd; c++) PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
1094: PetscCall(PetscInfo(sol, "Phase:%s: Uniform refinement\n", "adaptToleranceFEM"));
1095: } else if (type == 2) {
1096: PetscInt rCellIdx[8], eCellIdx[64], iCellIdx[64], eMaxIdx = -1, iMaxIdx = -1, nr = 0, nrmax = (dim == 3) ? 8 : 2;
1097: PetscReal minRad = PETSC_INFINITY, r, eMinRad = PETSC_INFINITY, iMinRad = PETSC_INFINITY;
1098: for (c = 0; c < 64; c++) eCellIdx[c] = iCellIdx[c] = -1;
1099: for (c = cStart; c < cEnd; c++) {
1100: PetscReal tt, v0[LANDAU_MAX_NQ * 3], detJ[LANDAU_MAX_NQ];
1101: PetscCall(DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ));
1102: for (qj = 0; qj < Nq; ++qj) {
1103: tt = PetscSqr(v0[dim * qj + 0]) + PetscSqr(v0[dim * qj + 1]) + PetscSqr(((dim == 3) ? v0[dim * qj + 2] : 0));
1104: r = PetscSqrtReal(tt);
1105: if (r < minRad - PETSC_SQRT_MACHINE_EPSILON * 10.) {
1106: minRad = r;
1107: nr = 0;
1108: rCellIdx[nr++] = c;
1109: PetscCall(PetscInfo(sol, "\t\tPhase: adaptToleranceFEM Found first inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT "\n", (double)r, c, qj + 1, Nq));
1110: } else if ((r - minRad) < PETSC_SQRT_MACHINE_EPSILON * 100. && nr < nrmax) {
1111: for (k = 0; k < nr; k++)
1112: if (c == rCellIdx[k]) break;
1113: if (k == nr) {
1114: rCellIdx[nr++] = c;
1115: PetscCall(PetscInfo(sol, "\t\t\tPhase: adaptToleranceFEM Found another inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT ", d=%e\n", (double)r, c, qj + 1, Nq, (double)(r - minRad)));
1116: }
1117: }
1118: if (ctx->sphere) {
1119: if ((tt = r - ctx->e_radius) > 0) {
1120: PetscCall(PetscInfo(sol, "\t\t\t %" PetscInt_FMT " cell r=%g\n", c, (double)tt));
1121: if (tt < eMinRad - PETSC_SQRT_MACHINE_EPSILON * 100.) {
1122: eMinRad = tt;
1123: eMaxIdx = 0;
1124: eCellIdx[eMaxIdx++] = c;
1125: } else if (eMaxIdx > 0 && (tt - eMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != eCellIdx[eMaxIdx - 1]) {
1126: eCellIdx[eMaxIdx++] = c;
1127: }
1128: }
1129: if ((tt = r - ctx->i_radius[grid]) > 0) {
1130: if (tt < iMinRad - 1.e-5) {
1131: iMinRad = tt;
1132: iMaxIdx = 0;
1133: iCellIdx[iMaxIdx++] = c;
1134: } else if (iMaxIdx > 0 && (tt - iMinRad) <= PETSC_SQRT_MACHINE_EPSILON && c != iCellIdx[iMaxIdx - 1]) {
1135: iCellIdx[iMaxIdx++] = c;
1136: }
1137: }
1138: }
1139: }
1140: }
1141: for (k = 0; k < nr; k++) PetscCall(DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE));
1142: if (ctx->sphere) {
1143: for (c = 0; c < eMaxIdx; c++) {
1144: PetscCall(DMLabelSetValue(adaptLabel, eCellIdx[c], DM_ADAPT_REFINE));
1145: PetscCall(PetscInfo(sol, "\t\tPhase:%s: refine sphere e cell %" PetscInt_FMT " r=%g\n", "adaptToleranceFEM", eCellIdx[c], (double)eMinRad));
1146: }
1147: for (c = 0; c < iMaxIdx; c++) {
1148: PetscCall(DMLabelSetValue(adaptLabel, iCellIdx[c], DM_ADAPT_REFINE));
1149: PetscCall(PetscInfo(sol, "\t\tPhase:%s: refine sphere i cell %" PetscInt_FMT " r=%g\n", "adaptToleranceFEM", iCellIdx[c], (double)iMinRad));
1150: }
1151: }
1152: PetscCall(PetscInfo(sol, "Phase:%s: Adaptive refine origin cells %" PetscInt_FMT ",%" PetscInt_FMT " r=%g\n", "adaptToleranceFEM", rCellIdx[0], rCellIdx[1], (double)minRad));
1153: } else if (type == 0 || type == 1 || type == 3) { /* refine along r=0 axis */
1154: PetscScalar *coef = NULL;
1155: Vec coords;
1156: PetscInt csize, Nv, d, nz;
1157: DM cdm;
1158: PetscSection cs;
1159: PetscCall(DMGetCoordinatesLocal(forest, &coords));
1160: PetscCall(DMGetCoordinateDM(forest, &cdm));
1161: PetscCall(DMGetLocalSection(cdm, &cs));
1162: for (c = cStart; c < cEnd; c++) {
1163: PetscInt doit = 0, outside = 0;
1164: PetscCall(DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef));
1165: Nv = csize / dim;
1166: for (nz = d = 0; d < Nv; d++) {
1167: PetscReal z = PetscRealPart(coef[d * dim + (dim - 1)]), x = PetscSqr(PetscRealPart(coef[d * dim + 0])) + ((dim == 3) ? PetscSqr(PetscRealPart(coef[d * dim + 1])) : 0);
1168: x = PetscSqrtReal(x);
1169: if (x < PETSC_MACHINE_EPSILON * 10. && PetscAbs(z) < PETSC_MACHINE_EPSILON * 10.) doit = 1; /* refine origin */
1170: else if (type == 0 && (z < -PETSC_MACHINE_EPSILON * 10. || z > ctx->re_radius + PETSC_MACHINE_EPSILON * 10.)) outside++; /* first pass don't refine bottom */
1171: else if (type == 1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) outside++; /* don't refine outside electron refine radius */
1172: else if (type == 3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) outside++; /* don't refine outside ion refine radius */
1173: if (x < PETSC_MACHINE_EPSILON * 10.) nz++;
1174: }
1175: PetscCall(DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef));
1176: if (doit || (outside < Nv && nz)) PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
1177: }
1178: PetscCall(PetscInfo(sol, "Phase:%s: RE refinement\n", "adaptToleranceFEM"));
1179: }
1180: PetscCall(DMDestroy(&plex));
1181: PetscCall(DMAdaptLabel(forest, adaptLabel, &adaptedDM));
1182: PetscCall(DMLabelDestroy(&adaptLabel));
1183: *newForest = adaptedDM;
1184: if (adaptedDM) {
1185: if (isForest) {
1186: PetscCall(DMForestSetAdaptivityForest(adaptedDM, NULL)); // ????
1187: } else exit(33); // ???????
1188: PetscCall(DMConvert(adaptedDM, DMPLEX, &plex));
1189: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
1190: PetscCall(PetscInfo(sol, "\tPhase: adaptToleranceFEM: %" PetscInt_FMT " cells, %" PetscInt_FMT " total quadrature points\n", cEnd - cStart, Nq * (cEnd - cStart)));
1191: PetscCall(DMDestroy(&plex));
1192: } else *newForest = NULL;
1193: PetscFunctionReturn(PETSC_SUCCESS);
1194: }
1196: // forest goes in (ctx->plex[grid]), plex comes out
1197: static PetscErrorCode adapt(PetscInt grid, LandauCtx *ctx, Vec *uu)
1198: {
1199: PetscInt adaptIter;
1201: PetscFunctionBegin;
1202: 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]};
1203: for (type = 0; type < 5; type++) {
1204: for (adaptIter = 0; adaptIter < limits[type]; adaptIter++) {
1205: DM newForest = NULL;
1206: PetscCall(adaptToleranceFEM(ctx->fe[0], *uu, type, grid, ctx, &newForest));
1207: if (newForest) {
1208: PetscCall(DMDestroy(&ctx->plex[grid]));
1209: PetscCall(VecDestroy(uu));
1210: PetscCall(DMCreateGlobalVector(newForest, uu));
1211: PetscCall(PetscObjectSetName((PetscObject)*uu, "uAMR"));
1212: PetscCall(LandauSetInitialCondition(newForest, *uu, grid, 0, 1, ctx));
1213: ctx->plex[grid] = newForest;
1214: } else {
1215: exit(4); // can happen with no AMR and post refinement
1216: }
1217: }
1218: }
1219: PetscFunctionReturn(PETSC_SUCCESS);
1220: }
1222: static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[])
1223: {
1224: PetscBool flg, sph_flg;
1225: PetscInt ii, nt, nm, nc, num_species_grid[LANDAU_MAX_GRIDS];
1226: PetscReal v0_grid[LANDAU_MAX_GRIDS];
1227: DM dummy;
1229: PetscFunctionBegin;
1230: PetscCall(DMCreate(ctx->comm, &dummy));
1231: /* get options - initialize context */
1232: ctx->verbose = 1; // should be 0 for silent compliance
1233: #if defined(PETSC_HAVE_THREADSAFETY) && defined(PETSC_HAVE_OPENMP)
1234: ctx->batch_sz = PetscNumOMPThreads;
1235: #else
1236: ctx->batch_sz = 1;
1237: #endif
1238: ctx->batch_view_idx = 0;
1239: ctx->interpolate = PETSC_TRUE;
1240: ctx->gpu_assembly = PETSC_TRUE;
1241: ctx->norm_state = 0;
1242: ctx->electronShift = 0;
1243: ctx->M = NULL;
1244: ctx->J = NULL;
1245: /* geometry and grids */
1246: ctx->sphere = PETSC_FALSE;
1247: ctx->inflate = PETSC_FALSE;
1248: ctx->use_p4est = PETSC_FALSE;
1249: ctx->num_sections = 3; /* 2, 3 or 4 */
1250: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1251: ctx->radius[grid] = 5.; /* thermal radius (velocity) */
1252: ctx->radius_perp[grid] = 5.; /* thermal radius (velocity) */
1253: ctx->radius_par[grid] = 5.; /* thermal radius (velocity) */
1254: ctx->numAMRRefine[grid] = 5;
1255: ctx->postAMRRefine[grid] = 0;
1256: ctx->species_offset[grid + 1] = 1; // one species default
1257: num_species_grid[grid] = 0;
1258: ctx->plex[grid] = NULL; /* cache as expensive to Convert */
1259: }
1260: ctx->species_offset[0] = 0;
1261: ctx->re_radius = 0.;
1262: ctx->vperp0_radius1 = 0;
1263: ctx->vperp0_radius2 = 0;
1264: ctx->nZRefine1 = 0;
1265: ctx->nZRefine2 = 0;
1266: ctx->numRERefine = 0;
1267: num_species_grid[0] = 1; // one species default
1268: /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */
1269: ctx->charges[0] = -1; /* electron charge (MKS) */
1270: ctx->masses[0] = 1 / 1835.469965278441013; /* temporary value in proton mass */
1271: ctx->n[0] = 1;
1272: ctx->v_0 = 1; /* thermal velocity, we could start with a scale != 1 */
1273: ctx->thermal_temps[0] = 1;
1274: /* constants, etc. */
1275: ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */
1276: ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */
1277: ctx->lnLam = 10; /* cross section ratio large - small angle collisions */
1278: ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */
1279: ctx->Ez = 0;
1280: for (PetscInt grid = 0; grid < LANDAU_NUM_TIMERS; grid++) ctx->times[grid] = 0;
1281: for (PetscInt ii = 0; ii < LANDAU_DIM; ii++) ctx->cells0[ii] = 2;
1282: if (LANDAU_DIM == 2) ctx->cells0[0] = 1;
1283: ctx->use_matrix_mass = PETSC_FALSE;
1284: ctx->use_relativistic_corrections = PETSC_FALSE;
1285: ctx->use_energy_tensor_trick = PETSC_FALSE; /* Use Eero's trick for energy conservation v --> grad(v^2/2) */
1286: ctx->SData_d.w = NULL;
1287: ctx->SData_d.x = NULL;
1288: ctx->SData_d.y = NULL;
1289: ctx->SData_d.z = NULL;
1290: ctx->SData_d.invJ = NULL;
1291: ctx->jacobian_field_major_order = PETSC_FALSE;
1292: ctx->SData_d.coo_elem_offsets = NULL;
1293: ctx->SData_d.coo_elem_point_offsets = NULL;
1294: ctx->coo_assembly = PETSC_FALSE;
1295: ctx->SData_d.coo_elem_fullNb = NULL;
1296: ctx->SData_d.coo_size = 0;
1297: PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");
1298: {
1299: char opstring[256];
1300: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
1301: ctx->deviceType = LANDAU_KOKKOS;
1302: PetscCall(PetscStrcpy(opstring, "kokkos"));
1303: #elif defined(PETSC_HAVE_CUDA)
1304: ctx->deviceType = LANDAU_CUDA;
1305: PetscCall(PetscStrcpy(opstring, "cuda"));
1306: #else
1307: ctx->deviceType = LANDAU_CPU;
1308: PetscCall(PetscStrcpy(opstring, "cpu"));
1309: #endif
1310: PetscCall(PetscOptionsString("-dm_landau_device_type", "Use kernels on 'cpu', 'cuda', or 'kokkos'", "plexland.c", opstring, opstring, sizeof(opstring), NULL));
1311: PetscCall(PetscStrcmp("cpu", opstring, &flg));
1312: if (flg) {
1313: ctx->deviceType = LANDAU_CPU;
1314: } else {
1315: PetscCall(PetscStrcmp("cuda", opstring, &flg));
1316: if (flg) {
1317: ctx->deviceType = LANDAU_CUDA;
1318: } else {
1319: PetscCall(PetscStrcmp("kokkos", opstring, &flg));
1320: if (flg) ctx->deviceType = LANDAU_KOKKOS;
1321: else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_device_type %s", opstring);
1322: }
1323: }
1324: }
1325: PetscCall(PetscOptionsReal("-dm_landau_electron_shift", "Shift in thermal velocity of electrons", "none", ctx->electronShift, &ctx->electronShift, NULL));
1326: PetscCall(PetscOptionsInt("-dm_landau_verbose", "Level of verbosity output", "plexland.c", ctx->verbose, &ctx->verbose, NULL));
1327: PetscCall(PetscOptionsInt("-dm_landau_batch_size", "Number of 'vertices' to batch", "ex2.c", ctx->batch_sz, &ctx->batch_sz, NULL));
1328: PetscCheck(LANDAU_MAX_BATCH_SZ >= ctx->batch_sz, ctx->comm, PETSC_ERR_ARG_WRONG, "LANDAU_MAX_BATCH_SZ %" PetscInt_FMT " < ctx->batch_sz %" PetscInt_FMT, (PetscInt)LANDAU_MAX_BATCH_SZ, ctx->batch_sz);
1329: 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));
1330: 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);
1331: PetscCall(PetscOptionsReal("-dm_landau_Ez", "Initial parallel electric field in unites of Conner-Hastie critical field", "plexland.c", ctx->Ez, &ctx->Ez, NULL));
1332: PetscCall(PetscOptionsReal("-dm_landau_n_0", "Normalization constant for number density", "plexland.c", ctx->n_0, &ctx->n_0, NULL));
1333: PetscCall(PetscOptionsReal("-dm_landau_ln_lambda", "Cross section parameter", "plexland.c", ctx->lnLam, &ctx->lnLam, NULL));
1334: 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));
1335: PetscCall(PetscOptionsBool("-dm_landau_use_relativistic_corrections", "Use relativistic corrections", "plexland.c", ctx->use_relativistic_corrections, &ctx->use_relativistic_corrections, NULL));
1336: 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,
1337: &ctx->use_energy_tensor_trick, NULL));
1339: /* get num species with temperature, set defaults */
1340: for (ii = 1; ii < LANDAU_MAX_SPECIES; ii++) {
1341: ctx->thermal_temps[ii] = 1;
1342: ctx->charges[ii] = 1;
1343: ctx->masses[ii] = 1;
1344: ctx->n[ii] = 1;
1345: }
1346: nt = LANDAU_MAX_SPECIES;
1347: 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));
1348: if (flg) {
1349: PetscCall(PetscInfo(dummy, "num_species set to number of thermal temps provided (%" PetscInt_FMT ")\n", nt));
1350: ctx->num_species = nt;
1351: } else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species");
1352: for (ii = 0; ii < ctx->num_species; ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */
1353: nm = LANDAU_MAX_SPECIES - 1;
1354: 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));
1355: 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);
1356: nm = LANDAU_MAX_SPECIES;
1357: PetscCall(PetscOptionsRealArray("-dm_landau_n", "Number density of each species = n_s * n_0", "plexland.c", ctx->n, &nm, &flg));
1358: 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);
1359: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */
1360: ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */
1361: ctx->m_0 = ctx->masses[0]; /* arbitrary reference mass, electrons */
1362: nc = LANDAU_MAX_SPECIES - 1;
1363: 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));
1364: 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);
1365: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */
1366: /* geometry and grids */
1367: nt = LANDAU_MAX_GRIDS;
1368: 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));
1369: if (flg) {
1370: ctx->num_grids = nt;
1371: for (ii = nt = 0; ii < ctx->num_grids; ii++) nt += num_species_grid[ii];
1372: 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,
1373: ctx->num_grids, LANDAU_MAX_GRIDS);
1374: } else {
1375: ctx->num_grids = 1; // go back to a single grid run
1376: num_species_grid[0] = ctx->num_species;
1377: }
1378: 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];
1379: 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],
1380: ctx->num_species);
1381: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1382: int iii = ctx->species_offset[grid]; // normalize with first (arbitrary) species on grid
1383: v0_grid[grid] = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: mean velocity in 1D of first species on grid */
1384: }
1385: ii = 0;
1386: PetscCall(PetscOptionsInt("-dm_landau_v0_grid", "Index of grid to use for setting v_0 (electrons are default). Not recommended to change", "plexland.c", ii, &ii, NULL));
1387: ctx->v_0 = v0_grid[ii]; /* arbitrary units for non dimensionalization: global mean velocity in 1D of electrons */
1388: ctx->t_0 = 8 * PETSC_PI * PetscSqr(ctx->epsilon0 * ctx->m_0 / PetscSqr(ctx->charges[0])) / ctx->lnLam / ctx->n_0 * PetscPowReal(ctx->v_0, 3); /* note, this t_0 makes nu[0,0]=1 */
1389: /* domain */
1390: nt = LANDAU_MAX_GRIDS;
1391: PetscCall(PetscOptionsRealArray("-dm_landau_domain_radius", "Phase space size in units of thermal velocity of grid", "plexland.c", ctx->radius, &nt, &flg));
1392: if (flg) {
1393: 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);
1394: while (nt--) ctx->radius_par[nt] = ctx->radius_perp[nt] = ctx->radius[nt];
1395: } else {
1396: nt = LANDAU_MAX_GRIDS;
1397: 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));
1398: 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);
1399: 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));
1400: 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);
1401: }
1402: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1403: if (flg && ctx->radius[grid] <= 0) { /* negative is ratio of c - need to set par and perp with this -- todo */
1404: if (ctx->radius[grid] == 0) ctx->radius[grid] = 0.75;
1405: else ctx->radius[grid] = -ctx->radius[grid];
1406: 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)
1407: PetscCall(PetscInfo(dummy, "Change domain radius to %g for grid %" PetscInt_FMT "\n", (double)ctx->radius[grid], grid));
1408: }
1409: ctx->radius[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1410: ctx->radius_perp[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1411: ctx->radius_par[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1412: }
1413: /* amr parameters */
1414: nt = LANDAU_DIM;
1415: PetscCall(PetscOptionsIntArray("-dm_landau_num_cells", "Number of cells in each dimension of base grid", "plexland.c", ctx->cells0, &nt, &flg));
1416: nt = LANDAU_MAX_GRIDS;
1417: 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));
1418: 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);
1419: nt = LANDAU_MAX_GRIDS;
1420: PetscCall(PetscOptionsIntArray("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &nt, &flg));
1421: for (ii = 1; ii < ctx->num_grids; ii++) ctx->postAMRRefine[ii] = ctx->postAMRRefine[0]; // all grids the same now
1422: 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));
1423: PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine1", "Number of levels to refine along v_perp=0", "plexland.c", ctx->nZRefine1, &ctx->nZRefine1, &flg));
1424: PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine2", "Number of levels to refine along v_perp=0", "plexland.c", ctx->nZRefine2, &ctx->nZRefine2, &flg));
1425: 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));
1426: PetscCall(PetscOptionsReal("-dm_landau_z_radius1", "velocity range to refine r=0 axis (for electrons)", "plexland.c", ctx->vperp0_radius1, &ctx->vperp0_radius1, &flg));
1427: PetscCall(PetscOptionsReal("-dm_landau_z_radius2", "velocity range to refine r=0 axis (for ions) after origin AMR", "plexland.c", ctx->vperp0_radius2, &ctx->vperp0_radius2, &flg));
1428: /* spherical domain (not used) */
1429: PetscCall(PetscOptionsInt("-dm_landau_num_sections", "Number of tangential section in (2D) grid, 2, 3, of 4", "plexland.c", ctx->num_sections, &ctx->num_sections, NULL));
1430: PetscCall(PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, &sph_flg));
1431: PetscCall(PetscOptionsBool("-dm_landau_inflate", "With sphere, inflate for curved edges", "plexland.c", ctx->inflate, &ctx->inflate, &flg));
1432: PetscCall(PetscOptionsReal("-dm_landau_e_radius", "Electron thermal velocity, used for circular meshes", "plexland.c", ctx->e_radius, &ctx->e_radius, &flg));
1433: if (flg && !sph_flg) ctx->sphere = PETSC_TRUE; /* you gave me an e radius but did not set sphere, user error really */
1434: if (!flg) ctx->e_radius = 1.5 * PetscSqrtReal(8 * ctx->k * ctx->thermal_temps[0] / ctx->masses[0] / PETSC_PI) / ctx->v_0;
1435: nt = LANDAU_MAX_GRIDS;
1436: PetscCall(PetscOptionsRealArray("-dm_landau_i_radius", "Ion thermal velocity, used for circular meshes", "plexland.c", ctx->i_radius, &nt, &flg));
1437: if (flg && !sph_flg) ctx->sphere = PETSC_TRUE;
1438: if (!flg) {
1439: ctx->i_radius[0] = 1.5 * PetscSqrtReal(8 * ctx->k * ctx->thermal_temps[1] / ctx->masses[1] / PETSC_PI) / ctx->v_0; // need to correct for ion grid domain
1440: }
1441: if (flg) PetscCheck(ctx->num_grids == nt, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_i_radius: %" PetscInt_FMT " != num_species = %" PetscInt_FMT, nt, ctx->num_grids);
1442: if (ctx->sphere) PetscCheck(ctx->e_radius > ctx->i_radius[0], ctx->comm, PETSC_ERR_ARG_WRONG, "bad radii: %g < %g < %g", (double)ctx->i_radius[0], (double)ctx->e_radius, (double)ctx->radius[0]);
1443: /* processing options */
1444: PetscCall(PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL));
1445: if (ctx->deviceType == LANDAU_CPU || ctx->deviceType == LANDAU_KOKKOS) { // make Kokkos
1446: PetscCall(PetscOptionsBool("-dm_landau_coo_assembly", "Assemble Jacobian with Kokkos on 'device'", "plexland.c", ctx->coo_assembly, &ctx->coo_assembly, NULL));
1447: if (ctx->coo_assembly) PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "COO assembly requires 'gpu assembly' even if Kokkos 'CPU' back-end %d", ctx->coo_assembly);
1448: }
1449: 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));
1450: 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");
1451: PetscCheck(!ctx->jacobian_field_major_order, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1452: PetscOptionsEnd();
1454: for (ii = ctx->num_species; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0;
1455: if (ctx->verbose > 0) {
1456: PetscCall(PetscPrintf(ctx->comm, "masses: e=%10.3e; ions in proton mass units: %10.3e %10.3e ...\n", (double)ctx->masses[0], (double)(ctx->masses[1] / 1.6720e-27), (double)(ctx->num_species > 2 ? ctx->masses[2] / 1.6720e-27 : 0)));
1457: PetscCall(PetscPrintf(ctx->comm, "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)));
1458: PetscCall(PetscPrintf(ctx->comm, "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)));
1459: PetscCall(PetscPrintf(ctx->comm, "thermal T (K): e=%10.3e i=%10.3e %10.3e. v_0=%10.3e (%10.3ec) n_0=%10.3e t_0=%10.3e, %s, %s, %" PetscInt_FMT " batched\n", (double)ctx->thermal_temps[0], (double)ctx->thermal_temps[1],
1460: (double)((ctx->num_species > 2) ? ctx->thermal_temps[2] : 0), (double)ctx->v_0, (double)(ctx->v_0 / SPEED_OF_LIGHT), (double)ctx->n_0, (double)ctx->t_0, ctx->use_relativistic_corrections ? "relativistic" : "classical", ctx->use_energy_tensor_trick ? "Use trick" : "Intuitive",
1461: ctx->batch_sz));
1462: PetscCall(PetscPrintf(ctx->comm, "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]));
1463: for (ii = 1; ii < ctx->num_grids; ii++) PetscCall(PetscPrintf(ctx->comm, ", %" PetscInt_FMT ": par=%10.3e, perp=%10.3e (%" PetscInt_FMT ") ", ii, (double)ctx->radius_par[ii], (double)ctx->radius_perp[ii], ctx->numAMRRefine[ii]));
1464: PetscCall(PetscPrintf(ctx->comm, "\n"));
1465: if (ctx->jacobian_field_major_order) {
1466: PetscCall(PetscPrintf(ctx->comm, "Using field major order for GPU Jacobian\n"));
1467: } else {
1468: PetscCall(PetscPrintf(ctx->comm, "Using default Plex order for all matrices\n"));
1469: }
1470: }
1471: PetscCall(DMDestroy(&dummy));
1472: {
1473: PetscMPIInt rank;
1474: PetscCallMPI(MPI_Comm_rank(ctx->comm, &rank));
1475: ctx->stage = 0;
1476: PetscCall(PetscLogEventRegister("Landau Create", DM_CLASSID, &ctx->events[13])); /* 13 */
1477: PetscCall(PetscLogEventRegister(" GPU ass. setup", DM_CLASSID, &ctx->events[2])); /* 2 */
1478: PetscCall(PetscLogEventRegister(" Build matrix", DM_CLASSID, &ctx->events[12])); /* 12 */
1479: PetscCall(PetscLogEventRegister(" Assembly maps", DM_CLASSID, &ctx->events[15])); /* 15 */
1480: PetscCall(PetscLogEventRegister("Landau Mass mat", DM_CLASSID, &ctx->events[14])); /* 14 */
1481: PetscCall(PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11])); /* 11 */
1482: PetscCall(PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0])); /* 0 */
1483: PetscCall(PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9])); /* 9 */
1484: PetscCall(PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10])); /* 10 */
1485: PetscCall(PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7])); /* 7 */
1486: PetscCall(PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1])); /* 1 */
1487: PetscCall(PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3])); /* 3 */
1488: PetscCall(PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8])); /* 8 */
1489: PetscCall(PetscLogEventRegister(" J Kernel (GPU)", DM_CLASSID, &ctx->events[4])); /* 4 */
1490: PetscCall(PetscLogEventRegister(" M Kernel (GPU)", DM_CLASSID, &ctx->events[16])); /* 16 */
1491: PetscCall(PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5])); /* 5 */
1492: PetscCall(PetscLogEventRegister(" CPU assemble", DM_CLASSID, &ctx->events[6])); /* 6 */
1494: if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */
1495: PetscCall(PetscOptionsClearValue(NULL, "-snes_converged_reason"));
1496: PetscCall(PetscOptionsClearValue(NULL, "-ksp_converged_reason"));
1497: PetscCall(PetscOptionsClearValue(NULL, "-snes_monitor"));
1498: PetscCall(PetscOptionsClearValue(NULL, "-ksp_monitor"));
1499: PetscCall(PetscOptionsClearValue(NULL, "-ts_monitor"));
1500: PetscCall(PetscOptionsClearValue(NULL, "-ts_view"));
1501: PetscCall(PetscOptionsClearValue(NULL, "-ts_adapt_monitor"));
1502: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_dm_view"));
1503: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_vec_view"));
1504: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_dm_view"));
1505: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_view"));
1506: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_jacobian_view"));
1507: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mat_view"));
1508: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_converged_reason"));
1509: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_monitor"));
1510: PetscCall(PetscOptionsClearValue(NULL, "-"));
1511: PetscCall(PetscOptionsClearValue(NULL, "-info"));
1512: }
1513: }
1514: PetscFunctionReturn(PETSC_SUCCESS);
1515: }
1517: static PetscErrorCode CreateStaticGPUData(PetscInt dim, IS grid_batch_is_inv[], LandauCtx *ctx)
1518: {
1519: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
1520: PetscQuadrature quad;
1521: const PetscReal *quadWeights;
1522: PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nf[LANDAU_MAX_GRIDS], ncellsTot = 0, MAP_BF_SIZE = 64 * LANDAU_DIM * LANDAU_DIM * LANDAU_MAX_Q_FACE * LANDAU_MAX_SPECIES;
1523: PetscTabulation *Tf;
1524: PetscDS prob;
1526: PetscFunctionBegin;
1527: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
1528: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
1529: /* DS, Tab and quad is same on all grids */
1530: PetscCheck(ctx->plex[0], ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1531: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
1532: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights));
1533: PetscCheck(Nq <= LANDAU_MAX_NQ, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQ (%d)", Nq, LANDAU_MAX_NQ);
1534: /* setup each grid */
1535: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1536: PetscInt cStart, cEnd;
1537: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1538: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1539: numCells[grid] = cEnd - cStart; // grids can have different topology
1540: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
1541: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
1542: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
1543: ncellsTot += numCells[grid];
1544: }
1545: /* create GPU assembly data */
1546: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1547: PetscContainer container;
1548: PetscScalar *elemMatrix, *elMat;
1549: pointInterpolationP4est(*pointMaps)[LANDAU_MAX_Q_FACE];
1550: P4estVertexMaps *maps;
1551: const PetscInt *plex_batch = NULL, Nb = Nq, elMatSz = Nq * Nq * ctx->num_species * ctx->num_species; // tensor elements;
1552: LandauIdx *coo_elem_offsets = NULL, *coo_elem_fullNb = NULL, (*coo_elem_point_offsets)[LANDAU_MAX_NQ + 1] = NULL;
1553: /* create GPU assembly data */
1554: PetscCall(PetscInfo(ctx->plex[0], "Make GPU maps %d\n", 1));
1555: PetscCall(PetscLogEventBegin(ctx->events[2], 0, 0, 0, 0));
1556: PetscCall(PetscMalloc(sizeof(*maps) * ctx->num_grids, &maps));
1557: PetscCall(PetscMalloc(sizeof(*pointMaps) * MAP_BF_SIZE, &pointMaps));
1558: PetscCall(PetscMalloc(sizeof(*elemMatrix) * elMatSz, &elemMatrix));
1560: if (ctx->coo_assembly) { // setup COO assembly -- put COO metadata directly in ctx->SData_d
1561: PetscCall(PetscMalloc3(ncellsTot + 1, &coo_elem_offsets, ncellsTot, &coo_elem_fullNb, ncellsTot, &coo_elem_point_offsets)); // array of integer pointers
1562: coo_elem_offsets[0] = 0; // finish later
1563: PetscCall(PetscInfo(ctx->plex[0], "COO initialization, %" PetscInt_FMT " cells\n", ncellsTot));
1564: ctx->SData_d.coo_n_cellsTot = ncellsTot;
1565: ctx->SData_d.coo_elem_offsets = (void *)coo_elem_offsets;
1566: ctx->SData_d.coo_elem_fullNb = (void *)coo_elem_fullNb;
1567: ctx->SData_d.coo_elem_point_offsets = (void *)coo_elem_point_offsets;
1568: } else {
1569: ctx->SData_d.coo_elem_offsets = ctx->SData_d.coo_elem_fullNb = NULL;
1570: ctx->SData_d.coo_elem_point_offsets = NULL;
1571: ctx->SData_d.coo_n_cellsTot = 0;
1572: }
1574: ctx->SData_d.coo_max_fullnb = 0;
1575: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1576: PetscInt cStart, cEnd, Nfloc = Nf[grid], totDim = Nfloc * Nq;
1577: if (grid_batch_is_inv[grid]) PetscCall(ISGetIndices(grid_batch_is_inv[grid], &plex_batch));
1578: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1579: // make maps
1580: maps[grid].d_self = NULL;
1581: maps[grid].num_elements = numCells[grid];
1582: maps[grid].num_face = (PetscInt)(pow(Nq, 1. / ((double)dim)) + .001); // Q
1583: maps[grid].num_face = (PetscInt)(pow(maps[grid].num_face, (double)(dim - 1)) + .001); // Q^2
1584: maps[grid].num_reduced = 0;
1585: maps[grid].deviceType = ctx->deviceType;
1586: maps[grid].numgrids = ctx->num_grids;
1587: // count reduced and get
1588: PetscCall(PetscMalloc(maps[grid].num_elements * sizeof(*maps[grid].gIdx), &maps[grid].gIdx));
1589: for (int ej = cStart, eidx = 0; ej < cEnd; ++ej, ++eidx, glb_elem_idx++) {
1590: if (coo_elem_offsets) coo_elem_offsets[glb_elem_idx + 1] = coo_elem_offsets[glb_elem_idx]; // start with last one, then add
1591: for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1592: int fullNb = 0;
1593: for (int q = 0; q < Nb; ++q) {
1594: PetscInt numindices, *indices;
1595: PetscScalar *valuesOrig = elMat = elemMatrix;
1596: PetscCall(PetscArrayzero(elMat, totDim * totDim));
1597: elMat[(fieldA * Nb + q) * totDim + fieldA * Nb + q] = 1;
1598: PetscCall(DMPlexGetClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat));
1599: for (PetscInt f = 0; f < numindices; ++f) { // look for a non-zero on the diagonal
1600: if (PetscAbs(PetscRealPart(elMat[f * numindices + f])) > PETSC_MACHINE_EPSILON) {
1601: // found it
1602: if (PetscAbs(PetscRealPart(elMat[f * numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { // normal vertex 1.0
1603: if (plex_batch) {
1604: maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)plex_batch[indices[f]];
1605: } else {
1606: maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)indices[f];
1607: }
1608: fullNb++;
1609: } else { //found a constraint
1610: int jj = 0;
1611: PetscReal sum = 0;
1612: const PetscInt ff = f;
1613: maps[grid].gIdx[eidx][fieldA][q] = -maps[grid].num_reduced - 1; // store (-)index: id = -(idx+1): idx = -id - 1
1615: do { // constraints are continuous in Plex - exploit that here
1616: int ii; // get 'scale'
1617: 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
1618: 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
1619: pointMaps[maps[grid].num_reduced][jj].scale += PetscRealPart(elMat[f * numindices + ff + ii]);
1620: }
1621: }
1622: sum += pointMaps[maps[grid].num_reduced][jj].scale; // diagnostic
1623: // get 'gid'
1624: if (pointMaps[maps[grid].num_reduced][jj].scale == 0) pointMaps[maps[grid].num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps
1625: else {
1626: if (plex_batch) {
1627: pointMaps[maps[grid].num_reduced][jj].gid = plex_batch[indices[f]];
1628: } else {
1629: pointMaps[maps[grid].num_reduced][jj].gid = indices[f];
1630: }
1631: fullNb++;
1632: }
1633: } while (++jj < maps[grid].num_face && ++f < numindices); // jj is incremented if we hit the end
1634: while (jj < maps[grid].num_face) {
1635: pointMaps[maps[grid].num_reduced][jj].scale = 0;
1636: pointMaps[maps[grid].num_reduced][jj].gid = -1;
1637: jj++;
1638: }
1639: if (PetscAbs(sum - 1.0) > 10 * PETSC_MACHINE_EPSILON) { // debug
1640: int d, f;
1641: PetscReal tmp = 0;
1642: PetscCall(PetscPrintf(PETSC_COMM_SELF, "\t\t%d.%d.%d) ERROR total I = %22.16e (LANDAU_MAX_Q_FACE=%d, #face=%d)\n", eidx, q, fieldA, (double)sum, LANDAU_MAX_Q_FACE, maps[grid].num_face));
1643: for (d = 0, tmp = 0; d < numindices; ++d) {
1644: if (tmp != 0 && PetscAbs(tmp - 1.0) > 10 * PETSC_MACHINE_EPSILON) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3d) %3" PetscInt_FMT ": ", d, indices[d]));
1645: for (f = 0; f < numindices; ++f) tmp += PetscRealPart(elMat[d * numindices + f]);
1646: if (tmp != 0) PetscCall(PetscPrintf(ctx->comm, " | %22.16e\n", (double)tmp));
1647: }
1648: }
1649: maps[grid].num_reduced++;
1650: PetscCheck(maps[grid].num_reduced < MAP_BF_SIZE, PETSC_COMM_SELF, PETSC_ERR_PLIB, "maps[grid].num_reduced %d > %" PetscInt_FMT, maps[grid].num_reduced, MAP_BF_SIZE);
1651: }
1652: break;
1653: }
1654: }
1655: // cleanup
1656: PetscCall(DMPlexRestoreClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat));
1657: if (elMat != valuesOrig) PetscCall(DMRestoreWorkArray(ctx->plex[grid], numindices * numindices, MPIU_SCALAR, &elMat));
1658: }
1659: if (ctx->coo_assembly) { // setup COO assembly
1660: coo_elem_offsets[glb_elem_idx + 1] += fullNb * fullNb; // one species block, adds a block for each species, on this element in this grid
1661: if (fieldA == 0) { // cache full Nb for this element, on this grid per species
1662: coo_elem_fullNb[glb_elem_idx] = fullNb;
1663: if (fullNb > ctx->SData_d.coo_max_fullnb) ctx->SData_d.coo_max_fullnb = fullNb;
1664: } else PetscCheck(coo_elem_fullNb[glb_elem_idx] == fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "full element size change with species %d %d", coo_elem_fullNb[glb_elem_idx], fullNb);
1665: }
1666: } // field
1667: } // cell
1668: // allocate and copy point data maps[grid].gIdx[eidx][field][q]
1669: PetscCall(PetscMalloc(maps[grid].num_reduced * sizeof(*maps[grid].c_maps), &maps[grid].c_maps));
1670: for (int ej = 0; ej < maps[grid].num_reduced; ++ej) {
1671: for (int q = 0; q < maps[grid].num_face; ++q) {
1672: maps[grid].c_maps[ej][q].scale = pointMaps[ej][q].scale;
1673: maps[grid].c_maps[ej][q].gid = pointMaps[ej][q].gid;
1674: }
1675: }
1676: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
1677: if (ctx->deviceType == LANDAU_KOKKOS) {
1678: PetscCall(LandauKokkosCreateMatMaps(maps, pointMaps, Nf, Nq, grid)); // implies Kokkos does
1679: } // else could be CUDA
1680: #endif
1681: #if defined(PETSC_HAVE_CUDA)
1682: if (ctx->deviceType == LANDAU_CUDA) PetscCall(LandauCUDACreateMatMaps(maps, pointMaps, Nf, Nq, grid));
1683: #endif
1684: if (plex_batch) {
1685: PetscCall(ISRestoreIndices(grid_batch_is_inv[grid], &plex_batch));
1686: PetscCall(ISDestroy(&grid_batch_is_inv[grid])); // we are done with this
1687: }
1688: } /* grids */
1689: // finish COO
1690: if (ctx->coo_assembly) { // setup COO assembly
1691: PetscInt *oor, *ooc;
1692: ctx->SData_d.coo_size = coo_elem_offsets[ncellsTot] * ctx->batch_sz;
1693: PetscCall(PetscMalloc2(ctx->SData_d.coo_size, &oor, ctx->SData_d.coo_size, &ooc));
1694: for (int i = 0; i < ctx->SData_d.coo_size; i++) oor[i] = ooc[i] = -1;
1695: // get
1696: for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1697: for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1698: const int fullNb = coo_elem_fullNb[glb_elem_idx];
1699: 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
1700: coo_elem_point_offsets[glb_elem_idx][0] = 0;
1701: for (int f = 0, cnt2 = 0; f < Nb; f++) {
1702: int idx = Idxs[f];
1703: coo_elem_point_offsets[glb_elem_idx][f + 1] = coo_elem_point_offsets[glb_elem_idx][f]; // start at last
1704: if (idx >= 0) {
1705: cnt2++;
1706: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1707: } else {
1708: idx = -idx - 1;
1709: for (int q = 0; q < maps[grid].num_face; q++) {
1710: if (maps[grid].c_maps[idx][q].gid < 0) break;
1711: cnt2++;
1712: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1713: }
1714: }
1715: PetscCheck(cnt2 <= fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "wrong count %d < %d", fullNb, cnt2);
1716: }
1717: PetscCheck(coo_elem_point_offsets[glb_elem_idx][Nb] == fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "coo_elem_point_offsets size %d != fullNb=%d", coo_elem_point_offsets[glb_elem_idx][Nb], fullNb);
1718: }
1719: }
1720: // set
1721: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1722: for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1723: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1724: for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1725: const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
1726: // set (i,j)
1727: for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1728: const LandauIdx *const Idxs = &maps[grid].gIdx[ej][fieldA][0];
1729: int rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE];
1730: for (int f = 0; f < Nb; ++f) {
1731: const int nr = coo_elem_point_offsets[glb_elem_idx][f + 1] - coo_elem_point_offsets[glb_elem_idx][f];
1732: if (nr == 1) rows[0] = Idxs[f];
1733: else {
1734: const int idx = -Idxs[f] - 1;
1735: for (int q = 0; q < nr; q++) rows[q] = maps[grid].c_maps[idx][q].gid;
1736: }
1737: for (int g = 0; g < Nb; ++g) {
1738: const int nc = coo_elem_point_offsets[glb_elem_idx][g + 1] - coo_elem_point_offsets[glb_elem_idx][g];
1739: if (nc == 1) cols[0] = Idxs[g];
1740: else {
1741: const int idx = -Idxs[g] - 1;
1742: for (int q = 0; q < nc; q++) cols[q] = maps[grid].c_maps[idx][q].gid;
1743: }
1744: const int 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];
1745: for (int q = 0, idx = idx0; q < nr; q++) {
1746: for (int d = 0; d < nc; d++, idx++) {
1747: oor[idx] = rows[q] + moffset;
1748: ooc[idx] = cols[d] + moffset;
1749: }
1750: }
1751: }
1752: }
1753: }
1754: } // cell
1755: } // grid
1756: } // batch
1757: PetscCall(MatSetPreallocationCOO(ctx->J, ctx->SData_d.coo_size, oor, ooc));
1758: PetscCall(PetscFree2(oor, ooc));
1759: }
1760: PetscCall(PetscFree(pointMaps));
1761: PetscCall(PetscFree(elemMatrix));
1762: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
1763: PetscCall(PetscContainerSetPointer(container, (void *)maps));
1764: PetscCall(PetscContainerSetUserDestroy(container, LandauGPUMapsDestroy));
1765: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "assembly_maps", (PetscObject)container));
1766: PetscCall(PetscContainerDestroy(&container));
1767: PetscCall(PetscLogEventEnd(ctx->events[2], 0, 0, 0, 0));
1768: } // end GPU assembly
1769: { /* create static point data, Jacobian called first, only one vertex copy */
1770: PetscReal *invJe, *ww, *xx, *yy, *zz = NULL, *invJ_a;
1771: PetscInt outer_ipidx, outer_ej, grid, nip_glb = 0;
1772: PetscFE fe;
1773: const PetscInt Nb = Nq;
1774: PetscCall(PetscLogEventBegin(ctx->events[7], 0, 0, 0, 0));
1775: PetscCall(PetscInfo(ctx->plex[0], "Initialize static data\n"));
1776: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) nip_glb += Nq * numCells[grid];
1777: /* collect f data, first time is for Jacobian, but make mass now */
1778: if (ctx->verbose > 0) {
1779: PetscInt ncells = 0, N;
1780: PetscCall(MatGetSize(ctx->J, &N, NULL));
1781: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ncells += numCells[grid];
1782: PetscCall(PetscPrintf(ctx->comm, "%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 "\n", 0, "FormLandau", nip_glb, ncells, Nb, Nq, dim, Nb,
1783: ctx->num_species, Nb, dim, N));
1784: }
1785: PetscCall(PetscMalloc4(nip_glb, &ww, nip_glb, &xx, nip_glb, &yy, nip_glb * dim * dim, &invJ_a));
1786: if (dim == 3) PetscCall(PetscMalloc1(nip_glb, &zz));
1787: if (ctx->use_energy_tensor_trick) {
1788: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &fe));
1789: PetscCall(PetscObjectSetName((PetscObject)fe, "energy"));
1790: }
1791: /* init each grids static data - no batch */
1792: for (grid = 0, outer_ipidx = 0, outer_ej = 0; grid < ctx->num_grids; grid++) { // OpenMP (once)
1793: Vec v2_2 = NULL; // projected function: v^2/2 for non-relativistic, gamma... for relativistic
1794: PetscSection e_section;
1795: DM dmEnergy;
1796: PetscInt cStart, cEnd, ej;
1798: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1799: // prep energy trick, get v^2 / 2 vector
1800: if (ctx->use_energy_tensor_trick) {
1801: PetscErrorCode (*energyf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {ctx->use_relativistic_corrections ? gamma_m1_f : energy_f};
1802: Vec glob_v2;
1803: PetscReal *c2_0[1], data[1] = {PetscSqr(C_0(ctx->v_0))};
1805: PetscCall(DMClone(ctx->plex[grid], &dmEnergy));
1806: PetscCall(PetscObjectSetName((PetscObject)dmEnergy, "energy"));
1807: PetscCall(DMSetField(dmEnergy, 0, NULL, (PetscObject)fe));
1808: PetscCall(DMCreateDS(dmEnergy));
1809: PetscCall(DMGetSection(dmEnergy, &e_section));
1810: PetscCall(DMGetGlobalVector(dmEnergy, &glob_v2));
1811: PetscCall(PetscObjectSetName((PetscObject)glob_v2, "trick"));
1812: c2_0[0] = &data[0];
1813: PetscCall(DMProjectFunction(dmEnergy, 0., energyf, (void **)c2_0, INSERT_ALL_VALUES, glob_v2));
1814: PetscCall(DMGetLocalVector(dmEnergy, &v2_2));
1815: PetscCall(VecZeroEntries(v2_2)); /* zero BCs so don't set */
1816: PetscCall(DMGlobalToLocalBegin(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1817: PetscCall(DMGlobalToLocalEnd(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1818: PetscCall(DMViewFromOptions(dmEnergy, NULL, "-energy_dm_view"));
1819: PetscCall(VecViewFromOptions(glob_v2, NULL, "-energy_vec_view"));
1820: PetscCall(DMRestoreGlobalVector(dmEnergy, &glob_v2));
1821: }
1822: /* append part of the IP data for each grid */
1823: for (ej = 0; ej < numCells[grid]; ++ej, ++outer_ej) {
1824: PetscScalar *coefs = NULL;
1825: PetscReal vj[LANDAU_MAX_NQ * LANDAU_DIM], detJj[LANDAU_MAX_NQ], Jdummy[LANDAU_MAX_NQ * LANDAU_DIM * LANDAU_DIM], c0 = C_0(ctx->v_0), c02 = PetscSqr(c0);
1826: invJe = invJ_a + outer_ej * Nq * dim * dim;
1827: PetscCall(DMPlexComputeCellGeometryFEM(ctx->plex[grid], ej + cStart, quad, vj, Jdummy, invJe, detJj));
1828: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecGetClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1829: /* create static point data */
1830: for (PetscInt qj = 0; qj < Nq; qj++, outer_ipidx++) {
1831: const PetscInt gidx = outer_ipidx;
1832: const PetscReal *invJ = &invJe[qj * dim * dim];
1833: ww[gidx] = detJj[qj] * quadWeights[qj];
1834: if (dim == 2) ww[gidx] *= vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */
1835: // get xx, yy, zz
1836: if (ctx->use_energy_tensor_trick) {
1837: double refSpaceDer[3], eGradPhi[3];
1838: const PetscReal *const DD = Tf[0]->T[1];
1839: const PetscReal *Dq = &DD[qj * Nb * dim];
1840: for (int d = 0; d < 3; ++d) refSpaceDer[d] = eGradPhi[d] = 0.0;
1841: for (int b = 0; b < Nb; ++b) {
1842: for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[b * dim + d] * PetscRealPart(coefs[b]);
1843: }
1844: xx[gidx] = 1e10;
1845: if (ctx->use_relativistic_corrections) {
1846: double dg2_c2 = 0;
1847: //for (int d = 0; d < dim; ++d) refSpaceDer[d] *= c02;
1848: for (int d = 0; d < dim; ++d) dg2_c2 += PetscSqr(refSpaceDer[d]);
1849: dg2_c2 *= (double)c02;
1850: if (dg2_c2 >= .999) {
1851: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1852: yy[gidx] = vj[qj * dim + 1];
1853: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1854: 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]));
1855: } else {
1856: PetscReal fact = c02 / PetscSqrtReal(1. - dg2_c2);
1857: for (int d = 0; d < dim; ++d) refSpaceDer[d] *= fact;
1858: // could test with other point u' that (grad - grad') * U (refSpaceDer, refSpaceDer') == 0
1859: }
1860: }
1861: if (xx[gidx] == 1e10) {
1862: for (int d = 0; d < dim; ++d) {
1863: for (int e = 0; e < dim; ++e) eGradPhi[d] += invJ[e * dim + d] * refSpaceDer[e];
1864: }
1865: xx[gidx] = eGradPhi[0];
1866: yy[gidx] = eGradPhi[1];
1867: if (dim == 3) zz[gidx] = eGradPhi[2];
1868: }
1869: } else {
1870: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1871: yy[gidx] = vj[qj * dim + 1];
1872: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1873: }
1874: } /* q */
1875: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecRestoreClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1876: } /* ej */
1877: if (ctx->use_energy_tensor_trick) {
1878: PetscCall(DMRestoreLocalVector(dmEnergy, &v2_2));
1879: PetscCall(DMDestroy(&dmEnergy));
1880: }
1881: } /* grid */
1882: if (ctx->use_energy_tensor_trick) PetscCall(PetscFEDestroy(&fe));
1883: /* cache static data */
1884: if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) {
1885: #if defined(PETSC_HAVE_CUDA) || defined(PETSC_HAVE_KOKKOS_KERNELS)
1886: PetscReal invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES];
1887: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1888: for (PetscInt ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++) {
1889: invMass[ii] = ctx->m_0 / ctx->masses[ii];
1890: nu_alpha[ii] = PetscSqr(ctx->charges[ii] / ctx->m_0) * ctx->m_0 / ctx->masses[ii];
1891: nu_beta[ii] = PetscSqr(ctx->charges[ii] / ctx->epsilon0) * ctx->lnLam / (8 * PETSC_PI) * ctx->t_0 * ctx->n_0 / PetscPowReal(ctx->v_0, 3);
1892: }
1893: }
1894: if (ctx->deviceType == LANDAU_CUDA) {
1895: #if defined(PETSC_HAVE_CUDA)
1896: PetscCall(LandauCUDAStaticDataSet(ctx->plex[0], Nq, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, invJ_a, xx, yy, zz, ww, &ctx->SData_d));
1897: #else
1898: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type cuda not built");
1899: #endif
1900: } else if (ctx->deviceType == LANDAU_KOKKOS) {
1901: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
1902: PetscCall(LandauKokkosStaticDataSet(ctx->plex[0], Nq, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, invJ_a, xx, yy, zz, ww, &ctx->SData_d));
1903: #else
1904: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type kokkos not built");
1905: #endif
1906: }
1907: #endif
1908: /* free */
1909: PetscCall(PetscFree4(ww, xx, yy, invJ_a));
1910: if (dim == 3) PetscCall(PetscFree(zz));
1911: } else { /* CPU version, just copy in, only use part */
1912: ctx->SData_d.w = (void *)ww;
1913: ctx->SData_d.x = (void *)xx;
1914: ctx->SData_d.y = (void *)yy;
1915: ctx->SData_d.z = (void *)zz;
1916: ctx->SData_d.invJ = (void *)invJ_a;
1917: }
1918: PetscCall(PetscLogEventEnd(ctx->events[7], 0, 0, 0, 0));
1919: } // initialize
1920: PetscFunctionReturn(PETSC_SUCCESS);
1921: }
1923: /* < v, u > */
1924: 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[])
1925: {
1926: g0[0] = 1.;
1927: }
1929: /* < v, u > */
1930: 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[])
1931: {
1932: static double ttt = 1e-12;
1933: g0[0] = ttt++;
1934: }
1936: /* < v, u > */
1937: 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[])
1938: {
1939: g0[0] = 2. * PETSC_PI * x[0];
1940: }
1942: static PetscErrorCode MatrixNfDestroy(void *ptr)
1943: {
1944: PetscInt *nf = (PetscInt *)ptr;
1945: PetscFunctionBegin;
1946: PetscCall(PetscFree(nf));
1947: PetscFunctionReturn(PETSC_SUCCESS);
1948: }
1950: /*
1951: LandauCreateJacobianMatrix - creates ctx->J with without real data. Hard to keep sparse.
1952: - Like DMPlexLandauCreateMassMatrix. Should remove one and combine
1953: - has old support for field major ordering
1954: */
1955: static PetscErrorCode LandauCreateJacobianMatrix(MPI_Comm comm, Vec X, IS grid_batch_is_inv[LANDAU_MAX_GRIDS], LandauCtx *ctx)
1956: {
1957: PetscInt *idxs = NULL;
1958: Mat subM[LANDAU_MAX_GRIDS];
1960: PetscFunctionBegin;
1961: if (!ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1962: PetscFunctionReturn(PETSC_SUCCESS);
1963: }
1964: // get the RCM for this grid to separate out species into blocks -- create 'idxs' & 'ctx->batch_is' -- not used
1965: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(PetscMalloc1(ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, &idxs));
1966: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1967: const PetscInt *values, n = ctx->mat_offset[grid + 1] - ctx->mat_offset[grid];
1968: Mat gMat;
1969: DM massDM;
1970: PetscDS prob;
1971: Vec tvec;
1972: // get "mass" matrix for reordering
1973: PetscCall(DMClone(ctx->plex[grid], &massDM));
1974: PetscCall(DMCopyFields(ctx->plex[grid], massDM));
1975: PetscCall(DMCreateDS(massDM));
1976: PetscCall(DMGetDS(massDM, &prob));
1977: for (int 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));
1978: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); // this trick is need to both sparsify the matrix and avoid runtime error
1979: PetscCall(DMCreateMatrix(massDM, &gMat));
1980: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
1981: PetscCall(MatSetOption(gMat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
1982: PetscCall(MatSetOption(gMat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
1983: PetscCall(DMCreateLocalVector(ctx->plex[grid], &tvec));
1984: PetscCall(DMPlexSNESComputeJacobianFEM(massDM, tvec, gMat, gMat, ctx));
1985: PetscCall(MatViewFromOptions(gMat, NULL, "-dm_landau_reorder_mat_view"));
1986: PetscCall(DMDestroy(&massDM));
1987: PetscCall(VecDestroy(&tvec));
1988: subM[grid] = gMat;
1989: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1990: MatOrderingType rtype = MATORDERINGRCM;
1991: IS isrow, isicol;
1992: PetscCall(MatGetOrdering(gMat, rtype, &isrow, &isicol));
1993: PetscCall(ISInvertPermutation(isrow, PETSC_DECIDE, &grid_batch_is_inv[grid]));
1994: PetscCall(ISGetIndices(isrow, &values));
1995: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
1996: #if !defined(LANDAU_SPECIES_MAJOR)
1997: PetscInt N = ctx->mat_offset[ctx->num_grids], n0 = ctx->mat_offset[grid] + b_id * N;
1998: for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1999: #else
2000: PetscInt n0 = ctx->mat_offset[grid] * ctx->batch_sz + b_id * n;
2001: for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
2002: #endif
2003: }
2004: PetscCall(ISRestoreIndices(isrow, &values));
2005: PetscCall(ISDestroy(&isrow));
2006: PetscCall(ISDestroy(&isicol));
2007: }
2008: }
2009: 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));
2010: // get a block matrix
2011: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2012: Mat B = subM[grid];
2013: PetscInt nloc, nzl, *colbuf, row, COL_BF_SIZE = 1024;
2014: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2015: PetscCall(MatGetSize(B, &nloc, NULL));
2016: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2017: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2018: const PetscInt *cols;
2019: const PetscScalar *vals;
2020: for (int i = 0; i < nloc; i++) {
2021: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
2022: if (nzl > COL_BF_SIZE) {
2023: PetscCall(PetscFree(colbuf));
2024: 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));
2025: COL_BF_SIZE = nzl;
2026: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2027: }
2028: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
2029: for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
2030: row = i + moffset;
2031: PetscCall(MatSetValues(ctx->J, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
2032: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
2033: }
2034: }
2035: PetscCall(PetscFree(colbuf));
2036: }
2037: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
2038: PetscCall(MatAssemblyBegin(ctx->J, MAT_FINAL_ASSEMBLY));
2039: PetscCall(MatAssemblyEnd(ctx->J, MAT_FINAL_ASSEMBLY));
2041: // debug
2042: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_mat_view"));
2043: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
2044: Mat mat_block_order;
2045: PetscCall(MatCreateSubMatrix(ctx->J, ctx->batch_is, ctx->batch_is, MAT_INITIAL_MATRIX, &mat_block_order)); // use MatPermute
2046: PetscCall(MatViewFromOptions(mat_block_order, NULL, "-dm_landau_mat_view"));
2047: PetscCall(MatDestroy(&mat_block_order));
2048: PetscCall(VecScatterCreate(X, ctx->batch_is, X, NULL, &ctx->plex_batch));
2049: PetscCall(VecDuplicate(X, &ctx->work_vec));
2050: }
2052: PetscFunctionReturn(PETSC_SUCCESS);
2053: }
2055: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat);
2056: /*@C
2057: DMPlexLandauCreateVelocitySpace - Create a DMPlex velocity space mesh
2059: Collective
2061: Input Parameters:
2062: + comm - The MPI communicator
2063: . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver)
2064: - prefix - prefix for options (not tested)
2066: Output Parameter:
2067: . pack - The DM object representing the mesh
2068: + X - A vector (user destroys)
2069: - J - Optional matrix (object destroys)
2071: Level: beginner
2073: .keywords: mesh
2074: .seealso: `DMPlexCreate()`, `DMPlexLandauDestroyVelocitySpace()`
2075: @*/
2076: PetscErrorCode DMPlexLandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *pack)
2077: {
2078: LandauCtx *ctx;
2079: Vec Xsub[LANDAU_MAX_GRIDS];
2080: IS grid_batch_is_inv[LANDAU_MAX_GRIDS];
2082: PetscFunctionBegin;
2083: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported");
2084: PetscCheck(LANDAU_DIM == dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " != LANDAU_DIM %d", dim, LANDAU_DIM);
2085: PetscCall(PetscNew(&ctx));
2086: ctx->comm = comm; /* used for diagnostics and global errors */
2087: /* process options */
2088: PetscCall(ProcessOptions(ctx, prefix));
2089: if (dim == 2) ctx->use_relativistic_corrections = PETSC_FALSE;
2090: /* Create Mesh */
2091: PetscCall(DMCompositeCreate(PETSC_COMM_SELF, pack));
2092: PetscCall(PetscLogEventBegin(ctx->events[13], 0, 0, 0, 0));
2093: PetscCall(PetscLogEventBegin(ctx->events[15], 0, 0, 0, 0));
2094: PetscCall(LandauDMCreateVMeshes(PETSC_COMM_SELF, dim, prefix, ctx, *pack)); // creates grids (Forest of AMR)
2095: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2096: /* create FEM */
2097: PetscCall(SetupDS(ctx->plex[grid], dim, grid, ctx));
2098: /* set initial state */
2099: PetscCall(DMCreateGlobalVector(ctx->plex[grid], &Xsub[grid]));
2100: PetscCall(PetscObjectSetName((PetscObject)Xsub[grid], "u_orig"));
2101: /* initial static refinement, no solve */
2102: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, 0, 1, ctx));
2103: /* forest refinement - forest goes in (if forest), plex comes out */
2104: if (ctx->use_p4est) {
2105: DM plex;
2106: PetscCall(adapt(grid, ctx, &Xsub[grid])); // forest goes in, plex comes out
2107: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, "-dm_landau_amr_dm_view")); // need to differentiate - todo
2108: PetscCall(VecViewFromOptions(Xsub[grid], NULL, "-dm_landau_amr_vec_view"));
2109: // convert to plex, all done with this level
2110: PetscCall(DMConvert(ctx->plex[grid], DMPLEX, &plex));
2111: PetscCall(DMDestroy(&ctx->plex[grid]));
2112: ctx->plex[grid] = plex;
2113: }
2114: #if !defined(LANDAU_SPECIES_MAJOR)
2115: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2116: #else
2117: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2118: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2119: }
2120: #endif
2121: PetscCall(DMSetApplicationContext(ctx->plex[grid], ctx));
2122: }
2123: #if !defined(LANDAU_SPECIES_MAJOR)
2124: // stack the batched DMs, could do it all here!!! b_id=0
2125: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2126: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
2127: }
2128: #endif
2129: // create ctx->mat_offset
2130: ctx->mat_offset[0] = 0;
2131: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2132: PetscInt n;
2133: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2134: ctx->mat_offset[grid + 1] = ctx->mat_offset[grid] + n;
2135: }
2136: // creat DM & Jac
2137: PetscCall(DMSetApplicationContext(*pack, ctx));
2138: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2139: PetscCall(DMCreateMatrix(*pack, &ctx->J));
2140: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2141: PetscCall(MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2142: PetscCall(MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2143: PetscCall(PetscObjectSetName((PetscObject)ctx->J, "Jac"));
2144: // construct initial conditions in X
2145: PetscCall(DMCreateGlobalVector(*pack, X));
2146: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2147: PetscInt n;
2148: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2149: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2150: PetscScalar const *values;
2151: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2152: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, b_id, ctx->batch_sz, ctx));
2153: PetscCall(VecGetArrayRead(Xsub[grid], &values)); // Drop whole grid in Plex ordering
2154: for (int i = 0, idx = moffset; i < n; i++, idx++) PetscCall(VecSetValue(*X, idx, values[i], INSERT_VALUES));
2155: PetscCall(VecRestoreArrayRead(Xsub[grid], &values));
2156: }
2157: }
2158: // cleanup
2159: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(VecDestroy(&Xsub[grid]));
2160: /* check for correct matrix type */
2161: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
2162: PetscBool flg;
2163: if (ctx->deviceType == LANDAU_CUDA) {
2164: PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJCUSPARSE, MATMPIAIJCUSPARSE, MATAIJCUSPARSE, ""));
2165: PetscCheck(flg, ctx->comm, PETSC_ERR_ARG_WRONG, "must use '-dm_mat_type aijcusparse -dm_vec_type cuda' for GPU assembly and Cuda or use '-dm_landau_device_type cpu'");
2166: } else if (ctx->deviceType == LANDAU_KOKKOS) {
2167: PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, MATAIJKOKKOS, ""));
2168: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
2169: 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'");
2170: #else
2171: 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'");
2172: #endif
2173: }
2174: }
2175: PetscCall(PetscLogEventEnd(ctx->events[15], 0, 0, 0, 0));
2177: // create field major ordering
2178: ctx->work_vec = NULL;
2179: ctx->plex_batch = NULL;
2180: ctx->batch_is = NULL;
2181: for (int i = 0; i < LANDAU_MAX_GRIDS; i++) grid_batch_is_inv[i] = NULL;
2182: PetscCall(PetscLogEventBegin(ctx->events[12], 0, 0, 0, 0));
2183: PetscCall(LandauCreateJacobianMatrix(comm, *X, grid_batch_is_inv, ctx));
2184: PetscCall(PetscLogEventEnd(ctx->events[12], 0, 0, 0, 0));
2186: // create AMR GPU assembly maps and static GPU data
2187: PetscCall(CreateStaticGPUData(dim, grid_batch_is_inv, ctx));
2189: PetscCall(PetscLogEventEnd(ctx->events[13], 0, 0, 0, 0));
2191: // create mass matrix
2192: PetscCall(DMPlexLandauCreateMassMatrix(*pack, NULL));
2194: if (J) *J = ctx->J;
2196: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
2197: PetscContainer container;
2198: // cache ctx for KSP with batch/field major Jacobian ordering -ksp_type gmres/etc -dm_landau_jacobian_field_major_order
2199: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2200: PetscCall(PetscContainerSetPointer(container, (void *)ctx));
2201: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "LandauCtx", (PetscObject)container));
2202: PetscCall(PetscContainerDestroy(&container));
2203: // batch solvers need to map -- can batch solvers work
2204: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2205: PetscCall(PetscContainerSetPointer(container, (void *)ctx->plex_batch));
2206: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "plex_batch_is", (PetscObject)container));
2207: PetscCall(PetscContainerDestroy(&container));
2208: }
2209: // for batch solvers
2210: {
2211: PetscContainer container;
2212: PetscInt *pNf;
2213: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2214: PetscCall(PetscMalloc1(sizeof(*pNf), &pNf));
2215: *pNf = ctx->batch_sz;
2216: PetscCall(PetscContainerSetPointer(container, (void *)pNf));
2217: PetscCall(PetscContainerSetUserDestroy(container, MatrixNfDestroy));
2218: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "batch size", (PetscObject)container));
2219: PetscCall(PetscContainerDestroy(&container));
2220: }
2222: PetscFunctionReturn(PETSC_SUCCESS);
2223: }
2225: /*@
2226: DMPlexLandauAccess - Access to the distribution function with user callback
2228: Collective
2230: Input Parameters:
2231: . pack - the DMComposite
2232: + func - call back function
2233: . user_ctx - user context
2235: Input/Output Parameters:
2236: + X - Vector to data to
2238: Level: advanced
2240: .keywords: mesh
2241: .seealso: `DMPlexLandauCreateVelocitySpace()`
2242: @*/
2243: PetscErrorCode DMPlexLandauAccess(DM pack, Vec X, PetscErrorCode (*func)(DM, Vec, PetscInt, PetscInt, PetscInt, void *), void *user_ctx)
2244: {
2245: LandauCtx *ctx;
2246: PetscFunctionBegin;
2247: PetscCall(DMGetApplicationContext(pack, &ctx)); // uses ctx->num_grids; ctx->plex[grid]; ctx->batch_sz; ctx->mat_offset
2248: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2249: PetscInt dim, n;
2250: PetscCall(DMGetDimension(pack, &dim));
2251: for (PetscInt sp = ctx->species_offset[grid], i0 = 0; sp < ctx->species_offset[grid + 1]; sp++, i0++) {
2252: Vec vec;
2253: PetscInt vf[1] = {i0};
2254: IS vis;
2255: DM vdm;
2256: PetscCall(DMCreateSubDM(ctx->plex[grid], 1, vf, &vis, &vdm));
2257: PetscCall(DMSetApplicationContext(vdm, ctx)); // the user might want this
2258: PetscCall(DMCreateGlobalVector(vdm, &vec));
2259: PetscCall(VecGetSize(vec, &n));
2260: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2261: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2262: PetscCall(VecZeroEntries(vec));
2263: /* Add your data with 'dm' for species 'sp' to 'vec' */
2264: PetscCall(func(vdm, vec, i0, grid, b_id, user_ctx));
2265: /* add to global */
2266: PetscScalar const *values;
2267: const PetscInt *offsets;
2268: PetscCall(VecGetArrayRead(vec, &values));
2269: PetscCall(ISGetIndices(vis, &offsets));
2270: for (int i = 0; i < n; i++) PetscCall(VecSetValue(X, moffset + offsets[i], values[i], ADD_VALUES));
2271: PetscCall(VecRestoreArrayRead(vec, &values));
2272: PetscCall(ISRestoreIndices(vis, &offsets));
2273: } // batch
2274: PetscCall(VecDestroy(&vec));
2275: PetscCall(ISDestroy(&vis));
2276: PetscCall(DMDestroy(&vdm));
2277: }
2278: } // grid
2279: PetscFunctionReturn(PETSC_SUCCESS);
2280: }
2282: /*@
2283: DMPlexLandauDestroyVelocitySpace - Destroy a DMPlex velocity space mesh
2285: Collective
2287: Input/Output Parameters:
2288: . dm - the dm to destroy
2290: Level: beginner
2292: .keywords: mesh
2293: .seealso: `DMPlexLandauCreateVelocitySpace()`
2294: @*/
2295: PetscErrorCode DMPlexLandauDestroyVelocitySpace(DM *dm)
2296: {
2297: LandauCtx *ctx;
2298: PetscFunctionBegin;
2299: PetscCall(DMGetApplicationContext(*dm, &ctx));
2300: PetscCall(MatDestroy(&ctx->M));
2301: PetscCall(MatDestroy(&ctx->J));
2302: for (PetscInt ii = 0; ii < ctx->num_species; ii++) PetscCall(PetscFEDestroy(&ctx->fe[ii]));
2303: PetscCall(ISDestroy(&ctx->batch_is));
2304: PetscCall(VecDestroy(&ctx->work_vec));
2305: PetscCall(VecScatterDestroy(&ctx->plex_batch));
2306: if (ctx->deviceType == LANDAU_CUDA) {
2307: #if defined(PETSC_HAVE_CUDA)
2308: PetscCall(LandauCUDAStaticDataClear(&ctx->SData_d));
2309: #else
2310: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "cuda");
2311: #endif
2312: } else if (ctx->deviceType == LANDAU_KOKKOS) {
2313: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
2314: PetscCall(LandauKokkosStaticDataClear(&ctx->SData_d));
2315: #else
2316: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
2317: #endif
2318: } else {
2319: if (ctx->SData_d.x) { /* in a CPU run */
2320: 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;
2321: 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_NQ + 1] = (LandauIdx(*)[LANDAU_MAX_NQ + 1]) ctx->SData_d.coo_elem_point_offsets;
2322: PetscCall(PetscFree4(ww, xx, yy, invJ));
2323: if (zz) PetscCall(PetscFree(zz));
2324: if (coo_elem_offsets) {
2325: PetscCall(PetscFree3(coo_elem_offsets, coo_elem_fullNb, coo_elem_point_offsets)); // could be NULL
2326: }
2327: }
2328: }
2330: if (ctx->times[LANDAU_MATRIX_TOTAL] > 0) { // OMP timings
2331: PetscCall(PetscPrintf(ctx->comm, "TSStep N 1.0 %10.3e\n", ctx->times[LANDAU_EX2_TSSOLVE]));
2332: 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));
2333: PetscCall(PetscPrintf(ctx->comm, "3: Landau: %10.3e\n", ctx->times[LANDAU_MATRIX_TOTAL]));
2334: PetscCall(PetscPrintf(ctx->comm, "Landau Jacobian %" PetscInt_FMT " 1.0 %10.3e\n", (PetscInt)ctx->times[LANDAU_JACOBIAN_COUNT], ctx->times[LANDAU_JACOBIAN]));
2335: PetscCall(PetscPrintf(ctx->comm, "Landau Operator N 1.0 %10.3e\n", ctx->times[LANDAU_OPERATOR]));
2336: PetscCall(PetscPrintf(ctx->comm, "Landau Mass N 1.0 %10.3e\n", ctx->times[LANDAU_MASS]));
2337: PetscCall(PetscPrintf(ctx->comm, " Jac-f-df (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_F_DF]));
2338: PetscCall(PetscPrintf(ctx->comm, " Kernel (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_KERNEL]));
2339: PetscCall(PetscPrintf(ctx->comm, "MatLUFactorNum X 1.0 %10.3e\n", ctx->times[KSP_FACTOR]));
2340: PetscCall(PetscPrintf(ctx->comm, "MatSolve X 1.0 %10.3e\n", ctx->times[KSP_SOLVE]));
2341: }
2342: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMDestroy(&ctx->plex[grid]));
2343: PetscCall(PetscFree(ctx));
2344: PetscCall(DMDestroy(dm));
2345: PetscFunctionReturn(PETSC_SUCCESS);
2346: }
2348: /* < v, ru > */
2349: 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)
2350: {
2351: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2352: f0[0] = u[ii];
2353: }
2355: /* < v, ru > */
2356: 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)
2357: {
2358: PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]);
2359: f0[0] = x[jj] * u[ii]; /* x momentum */
2360: }
2362: 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)
2363: {
2364: PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]);
2365: double tmp1 = 0.;
2366: for (i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2367: f0[0] = tmp1 * u[ii];
2368: }
2370: static PetscErrorCode gamma_n_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *actx)
2371: {
2372: const PetscReal *c2_0_arr = ((PetscReal *)actx);
2373: const PetscReal c02 = c2_0_arr[0];
2375: PetscFunctionBegin;
2376: for (int s = 0; s < Nf; s++) {
2377: PetscReal tmp1 = 0.;
2378: for (int i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2379: #if defined(PETSC_USE_DEBUG)
2380: u[s] = PetscSqrtReal(1. + tmp1 / c02); // u[0] = PetscSqrtReal(1. + xx);
2381: #else
2382: {
2383: PetscReal xx = tmp1 / c02;
2384: u[s] = xx / (PetscSqrtReal(1. + xx) + 1.); // better conditioned = xx/(PetscSqrtReal(1. + xx) + 1.)
2385: }
2386: #endif
2387: }
2388: PetscFunctionReturn(PETSC_SUCCESS);
2389: }
2391: /* < v, ru > */
2392: 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)
2393: {
2394: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2395: f0[0] = 2. * PETSC_PI * x[0] * u[ii];
2396: }
2398: /* < v, ru > */
2399: 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)
2400: {
2401: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2402: f0[0] = 2. * PETSC_PI * x[0] * x[1] * u[ii];
2403: }
2405: 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)
2406: {
2407: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2408: f0[0] = 2. * PETSC_PI * x[0] * (x[0] * x[0] + x[1] * x[1]) * u[ii];
2409: }
2411: /*@
2412: DMPlexLandauPrintNorms - collects moments and prints them
2414: Collective
2416: Input Parameters:
2417: + X - the state
2418: - stepi - current step to print
2420: Level: beginner
2422: .keywords: mesh
2423: .seealso: `DMPlexLandauCreateVelocitySpace()`
2424: @*/
2425: PetscErrorCode DMPlexLandauPrintNorms(Vec X, PetscInt stepi)
2426: {
2427: LandauCtx *ctx;
2428: PetscDS prob;
2429: DM pack;
2430: PetscInt cStart, cEnd, dim, ii, i0, nDMs;
2431: PetscScalar xmomentumtot = 0, ymomentumtot = 0, zmomentumtot = 0, energytot = 0, densitytot = 0, tt[LANDAU_MAX_SPECIES];
2432: PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES];
2433: Vec *globXArray;
2435: PetscFunctionBegin;
2436: PetscCall(VecGetDM(X, &pack));
2437: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Vector has no DM");
2438: PetscCall(DMGetDimension(pack, &dim));
2439: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " not in [2,3]", dim);
2440: PetscCall(DMGetApplicationContext(pack, &ctx));
2441: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2442: /* print momentum and energy */
2443: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
2444: 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);
2445: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
2446: PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, globXArray));
2447: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2448: Vec Xloc = globXArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2449: PetscCall(DMGetDS(ctx->plex[grid], &prob));
2450: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
2451: PetscScalar user[2] = {(PetscScalar)i0, (PetscScalar)ctx->charges[ii]};
2452: PetscCall(PetscDSSetConstants(prob, 2, user));
2453: if (dim == 2) { /* 2/3X + 3V (cylindrical coordinates) */
2454: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rden));
2455: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2456: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2457: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rmom));
2458: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2459: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2460: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rv2));
2461: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2462: energy[ii] = tt[0] * 0.5 * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2463: zmomentumtot += zmomentum[ii];
2464: energytot += energy[ii];
2465: densitytot += density[ii];
2466: PetscCall(PetscPrintf(ctx->comm, "%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])));
2467: } else { /* 2/3Xloc + 3V */
2468: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_den));
2469: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2470: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2471: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_mom));
2472: user[1] = 0;
2473: PetscCall(PetscDSSetConstants(prob, 2, user));
2474: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2475: xmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2476: user[1] = 1;
2477: PetscCall(PetscDSSetConstants(prob, 2, user));
2478: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2479: ymomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2480: user[1] = 2;
2481: PetscCall(PetscDSSetConstants(prob, 2, user));
2482: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2483: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2484: if (ctx->use_relativistic_corrections) {
2485: /* gamma * M * f */
2486: if (ii == 0 && grid == 0) { // do all at once
2487: Vec Mf, globGamma, *globMfArray, *globGammaArray;
2488: PetscErrorCode (*gammaf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {gamma_n_f};
2489: PetscReal *c2_0[1], data[1];
2491: PetscCall(VecDuplicate(X, &globGamma));
2492: PetscCall(VecDuplicate(X, &Mf));
2493: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globMfArray));
2494: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globGammaArray));
2495: /* M * f */
2496: PetscCall(MatMult(ctx->M, X, Mf));
2497: /* gamma */
2498: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2499: 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
2500: Vec v1 = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2501: data[0] = PetscSqr(C_0(ctx->v_0));
2502: c2_0[0] = &data[0];
2503: PetscCall(DMProjectFunction(ctx->plex[grid], 0., gammaf, (void **)c2_0, INSERT_ALL_VALUES, v1));
2504: }
2505: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2506: /* gamma * Mf */
2507: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2508: PetscCall(DMCompositeGetAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2509: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice
2510: PetscInt Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], N, bs;
2511: Vec Mfsub = globMfArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], Gsub = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], v1, v2;
2512: // get each component
2513: PetscCall(VecGetSize(Mfsub, &N));
2514: PetscCall(VecCreate(ctx->comm, &v1));
2515: PetscCall(VecSetSizes(v1, PETSC_DECIDE, N / Nf));
2516: PetscCall(VecCreate(ctx->comm, &v2));
2517: PetscCall(VecSetSizes(v2, PETSC_DECIDE, N / Nf));
2518: PetscCall(VecSetFromOptions(v1)); // ???
2519: PetscCall(VecSetFromOptions(v2));
2520: // get each component
2521: PetscCall(VecGetBlockSize(Gsub, &bs));
2522: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT " in Gsub", bs, Nf);
2523: PetscCall(VecGetBlockSize(Mfsub, &bs));
2524: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT, bs, Nf);
2525: for (int i = 0, ix = ctx->species_offset[grid]; i < Nf; i++, ix++) {
2526: PetscScalar val;
2527: PetscCall(VecStrideGather(Gsub, i, v1, INSERT_VALUES)); // this is not right -- TODO
2528: PetscCall(VecStrideGather(Mfsub, i, v2, INSERT_VALUES));
2529: PetscCall(VecDot(v1, v2, &val));
2530: energy[ix] = PetscRealPart(val) * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ix];
2531: }
2532: PetscCall(VecDestroy(&v1));
2533: PetscCall(VecDestroy(&v2));
2534: } /* grids */
2535: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2536: PetscCall(DMCompositeRestoreAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2537: PetscCall(PetscFree(globGammaArray));
2538: PetscCall(PetscFree(globMfArray));
2539: PetscCall(VecDestroy(&globGamma));
2540: PetscCall(VecDestroy(&Mf));
2541: }
2542: } else {
2543: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_v2));
2544: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2545: energy[ii] = 0.5 * tt[0] * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2546: }
2547: PetscCall(PetscPrintf(ctx->comm, "%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])));
2548: xmomentumtot += xmomentum[ii];
2549: ymomentumtot += ymomentum[ii];
2550: zmomentumtot += zmomentum[ii];
2551: energytot += energy[ii];
2552: densitytot += density[ii];
2553: }
2554: if (ctx->num_species > 1) PetscCall(PetscPrintf(ctx->comm, "\n"));
2555: }
2556: }
2557: PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, globXArray));
2558: PetscCall(PetscFree(globXArray));
2559: /* totals */
2560: PetscCall(DMPlexGetHeightStratum(ctx->plex[0], 0, &cStart, &cEnd));
2561: if (ctx->num_species > 1) {
2562: if (dim == 2) {
2563: PetscCall(PetscPrintf(ctx->comm, "\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),
2564: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2565: } else {
2566: PetscCall(PetscPrintf(ctx->comm, "\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),
2567: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2568: }
2569: } else PetscCall(PetscPrintf(ctx->comm, " -- %" PetscInt_FMT " cells", cEnd - cStart));
2570: PetscCall(PetscPrintf(ctx->comm, "\n"));
2571: PetscFunctionReturn(PETSC_SUCCESS);
2572: }
2574: /*@
2575: DMPlexLandauCreateMassMatrix - Create mass matrix for Landau in Plex space (not field major order of Jacobian)
2576: - puts mass matrix into ctx->M
2578: Collective
2580: Input/Output Parameters:
2581: . pack - the DM object. Puts matrix in Landau context M field
2583: Output Parameters:
2584: . Amat - The mass matrix (optional), mass matrix is added to the DM context
2586: Level: beginner
2588: .keywords: mesh
2589: .seealso: `DMPlexLandauCreateVelocitySpace()`
2590: @*/
2591: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat)
2592: {
2593: DM mass_pack, massDM[LANDAU_MAX_GRIDS];
2594: PetscDS prob;
2595: PetscInt ii, dim, N1 = 1, N2;
2596: LandauCtx *ctx;
2597: Mat packM, subM[LANDAU_MAX_GRIDS];
2599: PetscFunctionBegin;
2602: PetscCall(DMGetApplicationContext(pack, &ctx));
2603: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2604: PetscCall(PetscLogEventBegin(ctx->events[14], 0, 0, 0, 0));
2605: PetscCall(DMGetDimension(pack, &dim));
2606: PetscCall(DMCompositeCreate(PetscObjectComm((PetscObject)pack), &mass_pack));
2607: /* create pack mass matrix */
2608: for (PetscInt grid = 0, ix = 0; grid < ctx->num_grids; grid++) {
2609: PetscCall(DMClone(ctx->plex[grid], &massDM[grid]));
2610: PetscCall(DMCopyFields(ctx->plex[grid], massDM[grid]));
2611: PetscCall(DMCreateDS(massDM[grid]));
2612: PetscCall(DMGetDS(massDM[grid], &prob));
2613: for (ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) {
2614: if (dim == 3) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_1, NULL, NULL, NULL));
2615: else PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_r, NULL, NULL, NULL));
2616: }
2617: #if !defined(LANDAU_SPECIES_MAJOR)
2618: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2619: #else
2620: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2621: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2622: }
2623: #endif
2624: PetscCall(DMCreateMatrix(massDM[grid], &subM[grid]));
2625: }
2626: #if !defined(LANDAU_SPECIES_MAJOR)
2627: // stack the batched DMs
2628: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2629: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2630: }
2631: #endif
2632: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2633: PetscCall(DMCreateMatrix(mass_pack, &packM));
2634: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2635: PetscCall(MatSetOption(packM, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2636: PetscCall(MatSetOption(packM, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2637: PetscCall(DMDestroy(&mass_pack));
2638: /* make mass matrix for each block */
2639: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2640: Vec locX;
2641: DM plex = massDM[grid];
2642: PetscCall(DMGetLocalVector(plex, &locX));
2643: /* Mass matrix is independent of the input, so no need to fill locX */
2644: PetscCall(DMPlexSNESComputeJacobianFEM(plex, locX, subM[grid], subM[grid], ctx));
2645: PetscCall(DMRestoreLocalVector(plex, &locX));
2646: PetscCall(DMDestroy(&massDM[grid]));
2647: }
2648: PetscCall(MatGetSize(ctx->J, &N1, NULL));
2649: PetscCall(MatGetSize(packM, &N2, NULL));
2650: PetscCheck(N1 == N2, PetscObjectComm((PetscObject)pack), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %" PetscInt_FMT ", |Mass|=%" PetscInt_FMT, N1, N2);
2651: /* assemble block diagonals */
2652: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2653: Mat B = subM[grid];
2654: PetscInt nloc, nzl, *colbuf, COL_BF_SIZE = 1024, row;
2655: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2656: PetscCall(MatGetSize(B, &nloc, NULL));
2657: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2658: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2659: const PetscInt *cols;
2660: const PetscScalar *vals;
2661: for (int i = 0; i < nloc; i++) {
2662: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
2663: if (nzl > COL_BF_SIZE) {
2664: PetscCall(PetscFree(colbuf));
2665: PetscCall(PetscInfo(pack, "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl));
2666: COL_BF_SIZE = nzl;
2667: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2668: }
2669: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
2670: for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
2671: row = i + moffset;
2672: PetscCall(MatSetValues(packM, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
2673: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
2674: }
2675: }
2676: PetscCall(PetscFree(colbuf));
2677: }
2678: // cleanup
2679: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
2680: PetscCall(MatAssemblyBegin(packM, MAT_FINAL_ASSEMBLY));
2681: PetscCall(MatAssemblyEnd(packM, MAT_FINAL_ASSEMBLY));
2682: PetscCall(PetscObjectSetName((PetscObject)packM, "mass"));
2683: PetscCall(MatViewFromOptions(packM, NULL, "-dm_landau_mass_view"));
2684: ctx->M = packM;
2685: if (Amat) *Amat = packM;
2686: PetscCall(PetscLogEventEnd(ctx->events[14], 0, 0, 0, 0));
2687: PetscFunctionReturn(PETSC_SUCCESS);
2688: }
2690: /*@
2691: DMPlexLandauIFunction - TS residual calculation, confusingly this computes the Jacobian w/o mass
2693: Collective
2695: Input Parameters:
2696: + TS - The time stepping context
2697: . time_dummy - current time (not used)
2698: . X - Current state
2699: . X_t - Time derivative of current state
2700: - actx - Landau context
2702: Output Parameter:
2703: . F - The residual
2705: Level: beginner
2707: .keywords: mesh
2708: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIJacobian()`
2709: @*/
2710: PetscErrorCode DMPlexLandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx)
2711: {
2712: LandauCtx *ctx = (LandauCtx *)actx;
2713: PetscInt dim;
2714: DM pack;
2715: #if defined(PETSC_HAVE_THREADSAFETY)
2716: double starttime, endtime;
2717: #endif
2718: PetscObjectState state;
2720: PetscFunctionBegin;
2721: PetscCall(TSGetDM(ts, &pack));
2722: PetscCall(DMGetApplicationContext(pack, &ctx));
2723: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2724: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2725: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2726: PetscCall(PetscLogEventBegin(ctx->events[0], 0, 0, 0, 0));
2727: #if defined(PETSC_HAVE_THREADSAFETY)
2728: starttime = MPI_Wtime();
2729: #endif
2730: PetscCall(DMGetDimension(pack, &dim));
2731: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2732: if (state != ctx->norm_state) {
2733: PetscCall(PetscInfo(ts, "Create Landau Jacobian t=%g J.state %" PetscInt64_FMT " --> %" PetscInt64_FMT "\n", (double)time_dummy, ctx->norm_state, state));
2734: PetscCall(MatZeroEntries(ctx->J));
2735: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, 0.0, (void *)ctx));
2736: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_jacobian_view"));
2737: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2738: ctx->norm_state = state;
2739: } else {
2740: PetscCall(PetscInfo(ts, "WARNING Skip forming Jacobian, has not changed %" PetscInt64_FMT "\n", state));
2741: }
2742: /* mat vec for op */
2743: PetscCall(MatMult(ctx->J, X, F)); /* C*f */
2744: /* add time term */
2745: if (X_t) PetscCall(MatMultAdd(ctx->M, X_t, F, F));
2746: #if defined(PETSC_HAVE_THREADSAFETY)
2747: if (ctx->stage) {
2748: endtime = MPI_Wtime();
2749: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2750: ctx->times[LANDAU_JACOBIAN] += (endtime - starttime);
2751: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2752: ctx->times[LANDAU_JACOBIAN_COUNT] += 1;
2753: }
2754: #endif
2755: PetscCall(PetscLogEventEnd(ctx->events[0], 0, 0, 0, 0));
2756: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2757: if (ctx->stage) PetscCall(PetscLogStagePop());
2758: PetscFunctionReturn(PETSC_SUCCESS);
2759: }
2761: /*@
2762: DMPlexLandauIJacobian - TS Jacobian construction, confusingly this adds mass
2764: Collective
2766: Input Parameters:
2767: + TS - The time stepping context
2768: . time_dummy - current time (not used)
2769: . X - Current state
2770: . U_tdummy - Time derivative of current state (not used)
2771: . shift - shift for du/dt term
2772: - actx - Landau context
2774: Output Parameters:
2775: + Amat - Jacobian
2776: - Pmat - same as Amat
2778: Level: beginner
2780: .keywords: mesh
2781: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIFunction()`
2782: @*/
2783: PetscErrorCode DMPlexLandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx)
2784: {
2785: LandauCtx *ctx = NULL;
2786: PetscInt dim;
2787: DM pack;
2788: #if defined(PETSC_HAVE_THREADSAFETY)
2789: double starttime, endtime;
2790: #endif
2791: PetscObjectState state;
2793: PetscFunctionBegin;
2794: PetscCall(TSGetDM(ts, &pack));
2795: PetscCall(DMGetApplicationContext(pack, &ctx));
2796: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2797: PetscCheck(Amat == Pmat && Amat == ctx->J, ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J");
2798: PetscCall(DMGetDimension(pack, &dim));
2799: /* get collision Jacobian into A */
2800: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2801: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2802: PetscCall(PetscLogEventBegin(ctx->events[9], 0, 0, 0, 0));
2803: #if defined(PETSC_HAVE_THREADSAFETY)
2804: starttime = MPI_Wtime();
2805: #endif
2806: PetscCall(PetscInfo(ts, "Adding mass to Jacobian t=%g, shift=%g\n", (double)time_dummy, (double)shift));
2807: PetscCheck(shift != 0.0, ctx->comm, PETSC_ERR_PLIB, "zero shift");
2808: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2809: PetscCheck(state == ctx->norm_state, ctx->comm, PETSC_ERR_PLIB, "wrong state, %" PetscInt64_FMT " %" PetscInt64_FMT "", ctx->norm_state, state);
2810: if (!ctx->use_matrix_mass) {
2811: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, shift, (void *)ctx));
2812: } else { /* add mass */
2813: PetscCall(MatAXPY(Pmat, shift, ctx->M, SAME_NONZERO_PATTERN));
2814: }
2815: #if defined(PETSC_HAVE_THREADSAFETY)
2816: if (ctx->stage) {
2817: endtime = MPI_Wtime();
2818: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2819: ctx->times[LANDAU_MASS] += (endtime - starttime);
2820: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2821: }
2822: #endif
2823: PetscCall(PetscLogEventEnd(ctx->events[9], 0, 0, 0, 0));
2824: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2825: if (ctx->stage) PetscCall(PetscLogStagePop());
2826: PetscFunctionReturn(PETSC_SUCCESS);
2827: }