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 Parameter:
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 *nu_alpha = (PetscReal *)ctx->SData_d.alpha, *nu_beta = (PetscReal *)ctx->SData_d.beta, *invMass = (PetscReal *)ctx->SData_d.invMass;
227: PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
228: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
229: PetscScalar *coo_vals = NULL;
230: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
231: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
232: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
233: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
234: }
235: /* count IPf size, etc */
236: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
237: const PetscReal *const BB = Tf[0]->T[0], *const DD = Tf[0]->T[1];
238: ip_offset[0] = ipf_offset[0] = elem_offset[0] = 0;
239: for (PetscInt grid = 0; grid < num_grids; grid++) {
240: PetscInt nfloc = ctx->species_offset[grid + 1] - ctx->species_offset[grid];
241: elem_offset[grid + 1] = elem_offset[grid] + numCells[grid];
242: ip_offset[grid + 1] = ip_offset[grid] + numCells[grid] * Nq;
243: ipf_offset[grid + 1] = ipf_offset[grid] + Nq * nfloc * numCells[grid];
244: }
245: IPf_sz_glb = ipf_offset[num_grids];
246: IPf_sz_tot = IPf_sz_glb * ctx->batch_sz;
247: // prep COO
248: if (ctx->coo_assembly) {
249: PetscCall(PetscMalloc1(ctx->SData_d.coo_size, &coo_vals)); // allocate every time?
250: PetscCall(PetscInfo(ctx->plex[0], "COO Allocate %" PetscInt_FMT " values\n", (PetscInt)ctx->SData_d.coo_size));
251: }
252: if (shift == 0.0) { /* compute dynamic data f and df and init data for Jacobian */
253: #if defined(PETSC_HAVE_THREADSAFETY)
254: double starttime, endtime;
255: starttime = MPI_Wtime();
256: #endif
257: PetscCall(PetscLogEventBegin(ctx->events[8], 0, 0, 0, 0));
258: PetscCall(PetscMalloc4(IPf_sz_tot, &ff, IPf_sz_tot, &dudx, IPf_sz_tot, &dudy, dim == 3 ? IPf_sz_tot : 0, &dudz));
259: // F df/dx
260: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
261: 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
262: // find my grid:
263: PetscInt grid = 0;
264: while (b_elem_idx >= elem_offset[grid + 1]) grid++; // yuck search for grid
265: {
266: 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];
267: 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];
268: PetscScalar *coef, coef_buff[LANDAU_MAX_SPECIES * LANDAU_MAX_NQ];
269: PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim]; // ingJ is static data on batch 0
270: PetscInt b, f, q;
271: if (cellClosure) {
272: coef = &cellClosure[b_id * IPf_sz_glb + ipf_offset[grid] + loc_elem * Nb * loc_Nf]; // this is const
273: } else {
274: coef = coef_buff;
275: for (f = 0; f < loc_Nf; ++f) {
276: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][f][0];
277: for (b = 0; b < Nb; ++b) {
278: PetscInt idx = Idxs[b];
279: if (idx >= 0) {
280: coef[f * Nb + b] = xdata[idx + moffset];
281: } else {
282: idx = -idx - 1;
283: coef[f * Nb + b] = 0;
284: for (q = 0; q < maps[grid].num_face; q++) {
285: PetscInt id = maps[grid].c_maps[idx][q].gid;
286: PetscScalar scale = maps[grid].c_maps[idx][q].scale;
287: coef[f * Nb + b] += scale * xdata[id + moffset];
288: }
289: }
290: }
291: }
292: }
293: /* get f and df */
294: for (PetscInt qi = 0; qi < Nq; qi++) {
295: const PetscReal *invJ = &invJe[qi * dim * dim];
296: const PetscReal *Bq = &BB[qi * Nb];
297: const PetscReal *Dq = &DD[qi * Nb * dim];
298: PetscReal u_x[LANDAU_DIM];
299: /* get f & df */
300: for (f = 0; f < loc_Nf; ++f) {
301: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid] + f * loc_nip + loc_elem * Nq + qi;
302: PetscInt b, e;
303: PetscReal refSpaceDer[LANDAU_DIM];
304: ff[idx] = 0.0;
305: for (int d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0;
306: for (b = 0; b < Nb; ++b) {
307: const PetscInt cidx = b;
308: ff[idx] += Bq[cidx] * PetscRealPart(coef[f * Nb + cidx]);
309: for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx * dim + d] * PetscRealPart(coef[f * Nb + cidx]);
310: }
311: for (int d = 0; d < LANDAU_DIM; ++d) {
312: for (e = 0, u_x[d] = 0.0; e < LANDAU_DIM; ++e) u_x[d] += invJ[e * dim + d] * refSpaceDer[e];
313: }
314: dudx[idx] = u_x[0];
315: dudy[idx] = u_x[1];
316: #if LANDAU_DIM == 3
317: dudz[idx] = u_x[2];
318: #endif
319: }
320: } // q
321: } // grid
322: } // grid*batch
323: PetscCall(PetscLogEventEnd(ctx->events[8], 0, 0, 0, 0));
324: #if defined(PETSC_HAVE_THREADSAFETY)
325: endtime = MPI_Wtime();
326: if (ctx->stage) ctx->times[LANDAU_F_DF] += (endtime - starttime);
327: #endif
328: } // Jacobian setup
329: // assemble Jacobian (or mass)
330: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
331: const PetscInt b_Nelem = elem_offset[num_grids];
332: const PetscInt glb_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem;
333: PetscInt grid = 0;
334: #if defined(PETSC_HAVE_THREADSAFETY)
335: double starttime, endtime;
336: starttime = MPI_Wtime();
337: #endif
338: while (glb_elem_idx >= elem_offset[grid + 1]) grid++;
339: {
340: const PetscInt loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = glb_elem_idx - elem_offset[grid];
341: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset), totDim = loc_Nf * Nq, elemMatSize = totDim * totDim;
342: PetscScalar *elemMat;
343: const PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim];
344: PetscCall(PetscMalloc1(elemMatSize, &elemMat));
345: PetscCall(PetscMemzero(elemMat, elemMatSize * sizeof(*elemMat)));
346: if (shift == 0.0) { // Jacobian
347: PetscCall(PetscLogEventBegin(ctx->events[4], 0, 0, 0, 0));
348: } else { // mass
349: PetscCall(PetscLogEventBegin(ctx->events[16], 0, 0, 0, 0));
350: }
351: for (PetscInt qj = 0; qj < Nq; ++qj) {
352: const PetscInt jpidx_glb = ip_offset[grid] + qj + loc_elem * Nq;
353: 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
354: PetscInt d, d2, dp, d3, IPf_idx;
355: if (shift == 0.0) { // Jacobian
356: const PetscReal *const invJj = &invJe[qj * dim * dim];
357: 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];
358: const PetscReal vj[3] = {xx[jpidx_glb], yy[jpidx_glb], zz ? zz[jpidx_glb] : 0}, wj = ww[jpidx_glb];
359: // create g2 & g3
360: for (d = 0; d < LANDAU_DIM; d++) { // clear accumulation data D & K
361: gg2_temp[d] = 0;
362: for (d2 = 0; d2 < LANDAU_DIM; d2++) gg3_temp[d][d2] = 0;
363: }
364: /* inner beta reduction */
365: IPf_idx = 0;
366: 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
367: PetscInt nip_loc_r = numCells[grid_r] * Nq, Nfloc_r = Nf[grid_r];
368: for (PetscInt ei_r = 0, loc_fdf_idx = 0; ei_r < numCells[grid_r]; ++ei_r) {
369: for (PetscInt qi = 0; qi < Nq; qi++, ipidx++, loc_fdf_idx++) {
370: const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx];
371: PetscReal temp1[3] = {0, 0, 0}, temp2 = 0;
372: #if LANDAU_DIM == 2
373: 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.;
374: LandauTensor2D(vj, x, y, Ud, Uk, mask);
375: #else
376: 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.;
377: if (ctx->use_relativistic_corrections) {
378: LandauTensor3DRelativistic(vj, x, y, z, U, mask, C_0(ctx->v_0));
379: } else {
380: LandauTensor3D(vj, x, y, z, U, mask);
381: }
382: #endif
383: for (int f = 0; f < Nfloc_r; ++f) {
384: 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;
385: temp1[0] += dudx[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
386: temp1[1] += dudy[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
387: #if LANDAU_DIM == 3
388: temp1[2] += dudz[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
389: #endif
390: temp2 += ff[idx] * nu_beta[f + f_off] * (*lambdas)[grid][grid_r];
391: }
392: temp1[0] *= wi;
393: temp1[1] *= wi;
394: #if LANDAU_DIM == 3
395: temp1[2] *= wi;
396: #endif
397: temp2 *= wi;
398: #if LANDAU_DIM == 2
399: for (d2 = 0; d2 < 2; d2++) {
400: for (d3 = 0; d3 < 2; ++d3) {
401: /* K = U * grad(f): g2=e: i,A */
402: gg2_temp[d2] += Uk[d2][d3] * temp1[d3];
403: /* D = -U * (I \kron (fx)): g3=f: i,j,A */
404: gg3_temp[d2][d3] += Ud[d2][d3] * temp2;
405: }
406: }
407: #else
408: for (d2 = 0; d2 < 3; ++d2) {
409: for (d3 = 0; d3 < 3; ++d3) {
410: /* K = U * grad(f): g2 = e: i,A */
411: gg2_temp[d2] += U[d2][d3] * temp1[d3];
412: /* D = -U * (I \kron (fx)): g3 = f: i,j,A */
413: gg3_temp[d2][d3] += U[d2][d3] * temp2;
414: }
415: }
416: #endif
417: } // qi
418: } // ei_r
419: IPf_idx += nip_loc_r * Nfloc_r;
420: } /* grid_r - IPs */
421: 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);
422: // add alpha and put in gg2/3
423: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) {
424: for (d2 = 0; d2 < LANDAU_DIM; d2++) {
425: gg2[fieldA][d2] = gg2_temp[d2] * nu_alpha[fieldA + f_off];
426: for (d3 = 0; d3 < LANDAU_DIM; d3++) gg3[fieldA][d2][d3] = -gg3_temp[d2][d3] * nu_alpha[fieldA + f_off] * invMass[fieldA + f_off];
427: }
428: }
429: /* add electric field term once per IP */
430: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) gg2[fieldA][LANDAU_DIM - 1] += Eq_m[fieldA + f_off];
431: /* Jacobian transform - g2, g3 */
432: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
433: for (d = 0; d < dim; ++d) {
434: g2[fieldA][d] = 0.0;
435: for (d2 = 0; d2 < dim; ++d2) {
436: g2[fieldA][d] += invJj[d * dim + d2] * gg2[fieldA][d2];
437: g3[fieldA][d][d2] = 0.0;
438: for (d3 = 0; d3 < dim; ++d3) {
439: for (dp = 0; dp < dim; ++dp) g3[fieldA][d][d2] += invJj[d * dim + d3] * gg3[fieldA][d3][dp] * invJj[d2 * dim + dp];
440: }
441: g3[fieldA][d][d2] *= wj;
442: }
443: g2[fieldA][d] *= wj;
444: }
445: }
446: } else { // mass
447: PetscReal wj = ww[jpidx_glb];
448: /* Jacobian transform - g0 */
449: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
450: if (dim == 2) {
451: g0[fieldA] = wj * shift * 2. * PETSC_PI; // move this to below and remove g0
452: } else {
453: g0[fieldA] = wj * shift; // move this to below and remove g0
454: }
455: }
456: }
457: /* FE matrix construction */
458: {
459: PetscInt fieldA, d, f, d2, g;
460: const PetscReal *BJq = &BB[qj * Nb], *DIq = &DD[qj * Nb * dim];
461: /* assemble - on the diagonal (I,I) */
462: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
463: for (f = 0; f < Nb; f++) {
464: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
465: for (g = 0; g < Nb; ++g) {
466: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
467: const PetscInt fOff = i * totDim + j;
468: if (shift == 0.0) {
469: for (d = 0; d < dim; ++d) {
470: elemMat[fOff] += DIq[f * dim + d] * g2[fieldA][d] * BJq[g];
471: for (d2 = 0; d2 < dim; ++d2) elemMat[fOff] += DIq[f * dim + d] * g3[fieldA][d][d2] * DIq[g * dim + d2];
472: }
473: } else { // mass
474: elemMat[fOff] += BJq[f] * g0[fieldA] * BJq[g];
475: }
476: }
477: }
478: }
479: }
480: } /* qj loop */
481: if (shift == 0.0) { // Jacobian
482: PetscCall(PetscLogEventEnd(ctx->events[4], 0, 0, 0, 0));
483: } else {
484: PetscCall(PetscLogEventEnd(ctx->events[16], 0, 0, 0, 0));
485: }
486: #if defined(PETSC_HAVE_THREADSAFETY)
487: endtime = MPI_Wtime();
488: if (ctx->stage) ctx->times[LANDAU_KERNEL] += (endtime - starttime);
489: #endif
490: /* assemble matrix */
491: if (!container) {
492: PetscInt cStart;
493: PetscCall(PetscLogEventBegin(ctx->events[6], 0, 0, 0, 0));
494: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, NULL));
495: PetscCall(DMPlexMatSetClosure(ctx->plex[grid], section[grid], globsection[grid], subJ[LAND_PACK_IDX(b_id, grid)], loc_elem + cStart, elemMat, ADD_VALUES));
496: PetscCall(PetscLogEventEnd(ctx->events[6], 0, 0, 0, 0));
497: } else { // GPU like assembly for debugging
498: 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];
499: 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};
500: 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;
501: /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */
502: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
503: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][fieldA][0];
504: for (f = 0; f < Nb; f++) {
505: PetscInt idx = Idxs[f];
506: if (idx >= 0) {
507: nr = 1;
508: rows0[0] = idx;
509: row_scale[0] = 1.;
510: } else {
511: idx = -idx - 1;
512: for (q = 0, nr = 0; q < maps[grid].num_face; q++, nr++) {
513: if (maps[grid].c_maps[idx][q].gid < 0) break;
514: rows0[q] = maps[grid].c_maps[idx][q].gid;
515: row_scale[q] = maps[grid].c_maps[idx][q].scale;
516: }
517: }
518: for (g = 0; g < Nb; ++g) {
519: idx = Idxs[g];
520: if (idx >= 0) {
521: nc = 1;
522: cols0[0] = idx;
523: col_scale[0] = 1.;
524: } else {
525: idx = -idx - 1;
526: nc = maps[grid].num_face;
527: for (q = 0, nc = 0; q < maps[grid].num_face; q++, nc++) {
528: if (maps[grid].c_maps[idx][q].gid < 0) break;
529: cols0[q] = maps[grid].c_maps[idx][q].gid;
530: col_scale[q] = maps[grid].c_maps[idx][q].scale;
531: }
532: }
533: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
534: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
535: const PetscScalar Aij = elemMat[i * totDim + j];
536: if (coo_vals) { // mirror (i,j) in CreateStaticGPUData
537: const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
538: 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];
539: for (int q = 0, idx2 = idx0; q < nr; q++) {
540: for (int d = 0; d < nc; d++, idx2++) coo_vals[idx2] = row_scale[q] * col_scale[d] * Aij;
541: }
542: } else {
543: for (q = 0; q < nr; q++) rows[q] = rows0[q] + moffset;
544: for (d = 0; d < nc; d++) cols[d] = cols0[d] + moffset;
545: for (q = 0; q < nr; q++) {
546: for (d = 0; d < nc; d++) vals[q * nc + d] = row_scale[q] * col_scale[d] * Aij;
547: }
548: PetscCall(MatSetValues(JacP, nr, rows, nc, cols, vals, ADD_VALUES));
549: }
550: }
551: }
552: }
553: }
554: if (loc_elem == -1) {
555: PetscCall(PetscPrintf(ctx->comm, "CPU Element matrix\n"));
556: for (int d = 0; d < totDim; ++d) {
557: for (int f = 0; f < totDim; ++f) PetscCall(PetscPrintf(ctx->comm, " %12.5e", (double)PetscRealPart(elemMat[d * totDim + f])));
558: PetscCall(PetscPrintf(ctx->comm, "\n"));
559: }
560: exit(12);
561: }
562: PetscCall(PetscFree(elemMat));
563: } /* grid */
564: } /* outer element & batch loop */
565: if (shift == 0.0) { // mass
566: PetscCall(PetscFree4(ff, dudx, dudy, dudz));
567: }
568: if (!container) { // 'CPU' assembly move nest matrix to global JacP
569: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP
570: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
571: 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];
572: PetscInt nloc, nzl, colbuf[1024], row;
573: const PetscInt *cols;
574: const PetscScalar *vals;
575: Mat B = subJ[LAND_PACK_IDX(b_id, grid)];
576: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
577: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
578: PetscCall(MatGetSize(B, &nloc, NULL));
579: for (int i = 0; i < nloc; i++) {
580: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
581: PetscCheck(nzl <= 1024, PetscObjectComm((PetscObject)B), PETSC_ERR_PLIB, "Row too big: %" PetscInt_FMT, nzl);
582: for (int j = 0; j < nzl; j++) colbuf[j] = moffset + cols[j];
583: row = moffset + i;
584: PetscCall(MatSetValues(JacP, 1, &row, nzl, colbuf, vals, ADD_VALUES));
585: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
586: }
587: PetscCall(MatDestroy(&B));
588: }
589: }
590: }
591: if (coo_vals) {
592: PetscCall(MatSetValuesCOO(JacP, coo_vals, ADD_VALUES));
593: PetscCall(PetscFree(coo_vals));
594: }
595: } /* CPU version */
596: PetscCall(MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY));
597: PetscCall(MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY));
598: /* clean up */
599: if (cellClosure) PetscCall(PetscFree(cellClosure));
600: if (xdata) PetscCall(VecRestoreArrayReadAndMemType(a_X, &xdata));
601: PetscFunctionReturn(PETSC_SUCCESS);
602: }
604: static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx)
605: {
606: PetscReal r = abc[0], z = abc[1];
608: PetscFunctionBegin;
609: xyz[0] = r;
610: xyz[1] = z;
611: if (dim == 3) xyz[2] = abc[2];
613: PetscFunctionReturn(PETSC_SUCCESS);
614: }
616: /* create DMComposite of meshes for each species group */
617: static PetscErrorCode LandauDMCreateVMeshes(MPI_Comm comm_self, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM pack)
618: {
619: PetscFunctionBegin;
620: { /* p4est, quads */
621: /* Create plex mesh of Landau domain */
622: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
623: PetscReal par_radius = ctx->radius_par[grid], perp_radius = ctx->radius_perp[grid];
624: if (!ctx->sphere) {
625: PetscReal lo[] = {-perp_radius, -par_radius, -par_radius}, hi[] = {perp_radius, par_radius, par_radius};
626: DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim == 2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
627: if (dim == 2) lo[0] = 0;
628: else {
629: lo[1] = -perp_radius;
630: hi[1] = perp_radius; // 3D y is a perp
631: }
632: PetscCall(DMPlexCreateBoxMesh(comm_self, dim, PETSC_FALSE, ctx->cells0, lo, hi, periodicity, PETSC_TRUE, &ctx->plex[grid])); // todo: make composite and create dm[grid] here
633: PetscCall(DMLocalizeCoordinates(ctx->plex[grid])); /* needed for periodic */
634: if (dim == 3) PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cube"));
635: else PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "half-plane"));
636: } else if (dim == 2) {
637: PetscInt numCells, cells[16][4], i, j;
638: PetscInt numVerts;
639: PetscReal *flatCoords = NULL;
640: PetscInt *flatCells = NULL, *pcell;
641: numCells = 10;
642: numVerts = 16;
643: int cells2[][4] = {
644: {0, 1, 6, 5 },
645: {1, 2, 7, 6 },
646: {2, 3, 8, 7 },
647: {3, 4, 9, 8 },
648: {5, 6, 11, 10},
649: {6, 7, 12, 11},
650: {7, 8, 13, 12},
651: {8, 9, 14, 13},
652: {10, 11, 12, 15},
653: {12, 13, 14, 15}
654: };
655: for (i = 0; i < numCells; i++)
656: for (j = 0; j < 4; j++) cells[i][j] = cells2[i][j];
657: PetscCall(PetscMalloc2(numVerts * 2, &flatCoords, numCells * 4, &flatCells));
658: {
659: PetscReal(*coords)[2] = (PetscReal(*)[2])flatCoords;
660: for (j = 0; j < numVerts - 1; j++) {
661: PetscReal z, r, theta = -PETSC_PI / 2 + (j % 5) * PETSC_PI / 4;
662: PetscReal rad = ctx->radius[grid];
663: z = rad * PetscSinReal(theta);
664: coords[j][1] = z;
665: r = rad * PetscCosReal(theta);
666: coords[j][0] = r;
667: }
668: coords[numVerts - 1][0] = coords[numVerts - 1][1] = 0;
669: }
670: for (j = 0, pcell = flatCells; j < numCells; j++, pcell += 4) {
671: pcell[0] = cells[j][0];
672: pcell[1] = cells[j][1];
673: pcell[2] = cells[j][2];
674: pcell[3] = cells[j][3];
675: }
676: PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 2, numCells, numVerts, 4, ctx->interpolate, flatCells, 2, flatCoords, &ctx->plex[grid]));
677: PetscCall(PetscFree2(flatCoords, flatCells));
678: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "semi-circle"));
679: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Velocity space meshes does not support cubed sphere");
681: PetscCall(DMSetFromOptions(ctx->plex[grid]));
682: } // grid loop
683: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)pack, prefix));
685: { /* convert to p4est (or whatever), wait for discretization to create pack */
686: char convType[256];
687: PetscBool flg;
689: PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");
690: PetscCall(PetscOptionsFList("-dm_landau_type", "Convert DMPlex to another format (p4est)", "plexland.c", DMList, DMPLEX, convType, 256, &flg));
691: PetscOptionsEnd();
692: if (flg) {
693: ctx->use_p4est = PETSC_TRUE; /* flag for Forest */
694: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
695: DM dmforest;
696: PetscCall(DMConvert(ctx->plex[grid], convType, &dmforest));
697: if (dmforest) {
698: PetscBool isForest;
699: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dmforest, prefix));
700: PetscCall(DMIsForest(dmforest, &isForest));
701: if (isForest) {
702: if (ctx->sphere) PetscCall(DMForestSetBaseCoordinateMapping(dmforest, GeometryDMLandau, ctx));
703: PetscCall(DMDestroy(&ctx->plex[grid]));
704: ctx->plex[grid] = dmforest; // Forest for adaptivity
705: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Converted to non Forest?");
706: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Convert failed?");
707: }
708: } else ctx->use_p4est = PETSC_FALSE; /* flag for Forest */
709: }
710: } /* non-file */
711: PetscCall(DMSetDimension(pack, dim));
712: PetscCall(PetscObjectSetName((PetscObject)pack, "Mesh"));
713: PetscCall(DMSetApplicationContext(pack, ctx));
715: PetscFunctionReturn(PETSC_SUCCESS);
716: }
718: static PetscErrorCode SetupDS(DM pack, PetscInt dim, PetscInt grid, LandauCtx *ctx)
719: {
720: PetscInt ii, i0;
721: char buf[256];
722: PetscSection section;
724: PetscFunctionBegin;
725: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
726: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "e"));
727: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "i%" PetscInt_FMT, ii));
728: /* Setup Discretization - FEM */
729: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &ctx->fe[ii]));
730: PetscCall(PetscObjectSetName((PetscObject)ctx->fe[ii], buf));
731: PetscCall(DMSetField(ctx->plex[grid], i0, NULL, (PetscObject)ctx->fe[ii]));
732: }
733: PetscCall(DMCreateDS(ctx->plex[grid]));
734: PetscCall(DMGetSection(ctx->plex[grid], §ion));
735: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
736: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "se"));
737: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "si%" PetscInt_FMT, ii));
738: PetscCall(PetscSectionSetComponentName(section, i0, 0, buf));
739: }
740: PetscFunctionReturn(PETSC_SUCCESS);
741: }
743: /* Define a Maxwellian function for testing out the operator. */
745: /* Using cartesian velocity space coordinates, the particle */
746: /* density, [1/m^3], is defined according to */
748: /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */
750: /* Using some constant, c, we normalize the velocity vector into a */
751: /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */
753: /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */
755: /* Defining $\theta=2T/mc^2$, we thus find that the probability density */
756: /* for finding the particle within the interval in a box dx^3 around x is */
758: /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */
760: typedef struct {
761: PetscReal v_0;
762: PetscReal kT_m;
763: PetscReal n;
764: PetscReal shift;
765: } MaxwellianCtx;
767: static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
768: {
769: MaxwellianCtx *mctx = (MaxwellianCtx *)actx;
770: PetscInt i;
771: PetscReal v2 = 0, theta = 2 * mctx->kT_m / (mctx->v_0 * mctx->v_0), shift; /* theta = 2kT/mc^2 */
772: PetscFunctionBegin;
773: /* compute the exponents, v^2 */
774: for (i = 0; i < dim; ++i) v2 += x[i] * x[i];
775: /* evaluate the Maxwellian */
776: if (mctx->shift < 0) shift = -mctx->shift;
777: else {
778: u[0] = mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
779: shift = mctx->shift;
780: }
781: if (shift != 0.) {
782: v2 = 0;
783: for (i = 0; i < dim - 1; ++i) v2 += x[i] * x[i];
784: v2 += (x[dim - 1] - shift) * (x[dim - 1] - shift);
785: /* evaluate the shifted Maxwellian */
786: u[0] += mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
787: }
788: PetscFunctionReturn(PETSC_SUCCESS);
789: }
791: /*@
792: DMPlexLandauAddMaxwellians - Add a Maxwellian distribution to a state
794: Collective
796: Input Parameters:
797: . dm - The mesh (local)
798: + time - Current time
799: - temps - Temperatures of each species (global)
800: . ns - Number density of each species (global)
801: - grid - index into current grid - just used for offset into temp and ns
802: . b_id - batch index
803: - n_batch - number of batches
804: + actx - Landau context
806: Output Parameter:
807: . X - The state (local to this grid)
809: Level: beginner
811: .keywords: mesh
812: .seealso: `DMPlexLandauCreateVelocitySpace()`
813: @*/
814: PetscErrorCode DMPlexLandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
815: {
816: LandauCtx *ctx = (LandauCtx *)actx;
817: PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
818: PetscInt dim;
819: MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES];
821: PetscFunctionBegin;
822: PetscCall(DMGetDimension(dm, &dim));
823: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
824: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
825: mctxs[i0] = &data[i0];
826: data[i0].v_0 = ctx->v_0; // v_0 same for all grids
827: data[i0].kT_m = ctx->k * temps[ii] / ctx->masses[ii]; /* kT/m */
828: data[i0].n = ns[ii];
829: initu[i0] = maxwellian;
830: data[i0].shift = 0;
831: }
832: data[0].shift = ctx->electronShift;
833: /* need to make ADD_ALL_VALUES work - TODO */
834: PetscCall(DMProjectFunction(dm, time, initu, (void **)mctxs, INSERT_ALL_VALUES, X));
835: PetscFunctionReturn(PETSC_SUCCESS);
836: }
838: /*
839: LandauSetInitialCondition - Addes Maxwellians with context
841: Collective
843: Input Parameters:
844: . dm - The mesh
845: - grid - index into current grid - just used for offset into temp and ns
846: . b_id - batch index
847: - n_batch - number of batches
848: + actx - Landau context with T and n
850: Output Parameter:
851: . X - The state
853: Level: beginner
855: .keywords: mesh
856: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauAddMaxwellians()`
857: */
858: static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
859: {
860: LandauCtx *ctx = (LandauCtx *)actx;
861: PetscFunctionBegin;
862: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
863: PetscCall(VecZeroEntries(X));
864: PetscCall(DMPlexLandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, grid, b_id, n_batch, ctx));
865: PetscFunctionReturn(PETSC_SUCCESS);
866: }
868: // adapt a level once. Forest in/out
869: #if defined(PETSC_USE_INFO)
870: static const char *s_refine_names[] = {"RE", "Z1", "Origin", "Z2", "Uniform"};
871: #endif
872: static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscInt type, PetscInt grid, LandauCtx *ctx, DM *newForest)
873: {
874: DM forest, plex, adaptedDM = NULL;
875: PetscDS prob;
876: PetscBool isForest;
877: PetscQuadrature quad;
878: PetscInt Nq, *Nb, cStart, cEnd, c, dim, qj, k;
879: DMLabel adaptLabel = NULL;
881: PetscFunctionBegin;
882: forest = ctx->plex[grid];
883: PetscCall(DMCreateDS(forest));
884: PetscCall(DMGetDS(forest, &prob));
885: PetscCall(DMGetDimension(forest, &dim));
886: PetscCall(DMIsForest(forest, &isForest));
887: PetscCheck(isForest, ctx->comm, PETSC_ERR_ARG_WRONG, "! Forest");
888: PetscCall(DMConvert(forest, DMPLEX, &plex));
889: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
890: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "adapt", &adaptLabel));
891: PetscCall(PetscFEGetQuadrature(fem, &quad));
892: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
893: 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);
894: PetscCall(PetscDSGetDimensions(prob, &Nb));
895: PetscCall(PetscInfo(sol, "%" PetscInt_FMT ") Refine phase: %s\n", grid, s_refine_names[type]));
896: if (type == 4) {
897: for (c = cStart; c < cEnd; c++) PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
898: } else if (type == 2) {
899: PetscInt rCellIdx[8], nr = 0, nrmax = (dim == 3) ? 8 : 2;
900: PetscReal minRad = PETSC_INFINITY, r;
901: for (c = cStart; c < cEnd; c++) {
902: PetscReal tt, v0[LANDAU_MAX_NQ * 3], detJ[LANDAU_MAX_NQ];
903: PetscCall(DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ));
904: for (qj = 0; qj < Nq; ++qj) {
905: tt = PetscSqr(v0[dim * qj + 0]) + PetscSqr(v0[dim * qj + 1]) + PetscSqr(((dim == 3) ? v0[dim * qj + 2] : 0));
906: r = PetscSqrtReal(tt);
907: if (r < minRad - PETSC_SQRT_MACHINE_EPSILON * 10.) {
908: minRad = r;
909: nr = 0;
910: rCellIdx[nr++] = c;
911: PetscCall(PetscInfo(sol, "\t\t%" PetscInt_FMT ") Found first inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT "\n", grid, (double)r, c, qj + 1, Nq));
912: } else if ((r - minRad) < PETSC_SQRT_MACHINE_EPSILON * 100. && nr < nrmax) {
913: for (k = 0; k < nr; k++)
914: if (c == rCellIdx[k]) break;
915: if (k == nr) {
916: rCellIdx[nr++] = c;
917: PetscCall(PetscInfo(sol, "\t\t\t%" PetscInt_FMT ") Found another inner r=%e, cell %" PetscInt_FMT ", qp %" PetscInt_FMT "/%" PetscInt_FMT ", d=%e\n", grid, (double)r, c, qj + 1, Nq, (double)(r - minRad)));
918: }
919: }
920: }
921: }
922: for (k = 0; k < nr; k++) PetscCall(DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE));
923: PetscCall(PetscInfo(sol, "\t\t\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " origin cells %" PetscInt_FMT ",%" PetscInt_FMT " r=%g\n", grid, nr, rCellIdx[0], rCellIdx[1], (double)minRad));
924: } else if (type == 0 || type == 1 || type == 3) { /* refine along r=0 axis */
925: PetscScalar *coef = NULL;
926: Vec coords;
927: PetscInt csize, Nv, d, nz, nrefined = 0;
928: DM cdm;
929: PetscSection cs;
930: PetscCall(DMGetCoordinatesLocal(forest, &coords));
931: PetscCall(DMGetCoordinateDM(forest, &cdm));
932: PetscCall(DMGetLocalSection(cdm, &cs));
933: for (c = cStart; c < cEnd; c++) {
934: PetscInt doit = 0, outside = 0;
935: PetscCall(DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef));
936: Nv = csize / dim;
937: for (nz = d = 0; d < Nv; d++) {
938: PetscReal z = PetscRealPart(coef[d * dim + (dim - 1)]), x = PetscSqr(PetscRealPart(coef[d * dim + 0])) + ((dim == 3) ? PetscSqr(PetscRealPart(coef[d * dim + 1])) : 0);
939: x = PetscSqrtReal(x);
940: if (type == 0) {
941: if (ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON && (z < -PETSC_MACHINE_EPSILON * 10. || z > ctx->re_radius + PETSC_MACHINE_EPSILON * 10.)) outside++; /* first pass don't refine bottom */
942: } else if (type == 1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) {
943: outside++; /* don't refine outside electron refine radius */
944: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
945: } else if (type == 3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) {
946: outside++; /* refine r=0 cells on refinement front */
947: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
948: }
949: if (x < PETSC_MACHINE_EPSILON * 10. && (type != 0 || ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON)) nz++;
950: }
951: PetscCall(DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef));
952: if (doit || (outside < Nv && nz)) {
953: PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
954: nrefined++;
955: }
956: }
957: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " cells\n", grid, nrefined));
958: }
959: PetscCall(DMDestroy(&plex));
960: PetscCall(DMAdaptLabel(forest, adaptLabel, &adaptedDM));
961: PetscCall(DMLabelDestroy(&adaptLabel));
962: *newForest = adaptedDM;
963: if (adaptedDM) {
964: if (isForest) {
965: PetscCall(DMForestSetAdaptivityForest(adaptedDM, NULL)); // ????
966: }
967: PetscCall(DMConvert(adaptedDM, DMPLEX, &plex));
968: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
969: PetscCall(PetscInfo(sol, "\t\t\t\t%" PetscInt_FMT ") %" PetscInt_FMT " cells, %" PetscInt_FMT " total quadrature points\n", grid, cEnd - cStart, Nq * (cEnd - cStart)));
970: PetscCall(DMDestroy(&plex));
971: } else *newForest = NULL;
972: PetscFunctionReturn(PETSC_SUCCESS);
973: }
975: // forest goes in (ctx->plex[grid]), plex comes out
976: static PetscErrorCode adapt(PetscInt grid, LandauCtx *ctx, Vec *uu)
977: {
978: PetscInt adaptIter;
980: PetscFunctionBegin;
981: 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]};
982: for (type = 0; type < 5; type++) {
983: for (adaptIter = 0; adaptIter < limits[type]; adaptIter++) {
984: DM newForest = NULL;
985: PetscCall(adaptToleranceFEM(ctx->fe[0], *uu, type, grid, ctx, &newForest));
986: if (newForest) {
987: PetscCall(DMDestroy(&ctx->plex[grid]));
988: PetscCall(VecDestroy(uu));
989: PetscCall(DMCreateGlobalVector(newForest, uu));
990: PetscCall(PetscObjectSetName((PetscObject)*uu, "uAMR"));
991: PetscCall(LandauSetInitialCondition(newForest, *uu, grid, 0, 1, ctx));
992: ctx->plex[grid] = newForest;
993: } else {
994: PetscCall(PetscInfo(*uu, "No refinement\n"));
995: }
996: }
997: }
998: PetscFunctionReturn(PETSC_SUCCESS);
999: }
1001: // make log(Lambdas) from NRL Plasma formulary
1002: static PetscErrorCode makeLambdas(LandauCtx *ctx)
1003: {
1004: PetscFunctionBegin;
1005: for (PetscInt gridi = 0; gridi < ctx->num_grids; gridi++) {
1006: int iii = ctx->species_offset[gridi];
1007: PetscReal Ti_ev = (ctx->thermal_temps[iii] / 1.1604525e7) * 1000; // convert (back) to eV
1008: PetscReal ni = ctx->n[iii] * ctx->n_0;
1009: for (PetscInt gridj = gridi; gridj < ctx->num_grids; gridj++) {
1010: PetscInt jjj = ctx->species_offset[gridj];
1011: PetscReal Zj = ctx->charges[jjj] / 1.6022e-19;
1012: if (gridi == 0) {
1013: if (gridj == 0) { // lam_ee
1014: ctx->lambdas[gridi][gridj] = 23.5 - PetscLogReal(PetscSqrtReal(ni) * PetscPowReal(Ti_ev, -1.25)) - PetscSqrtReal(1e-5 + PetscSqr(PetscLogReal(Ti_ev) - 2) / 16);
1015: } else { // lam_ei == lam_ie
1016: if (10 * Zj * Zj > Ti_ev) {
1017: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(PetscSqrtReal(ni) * Zj * PetscPowReal(Ti_ev, -1.5));
1018: } else {
1019: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 24 - PetscLogReal(PetscSqrtReal(ni) / Ti_ev);
1020: }
1021: }
1022: } else { // lam_ii'
1023: PetscReal mui = ctx->masses[iii] / 1.6720e-27, Zi = ctx->charges[iii] / 1.6022e-19;
1024: PetscReal Tj_ev = (ctx->thermal_temps[jjj] / 1.1604525e7) * 1000; // convert (back) to eV
1025: PetscReal muj = ctx->masses[jjj] / 1.6720e-27;
1026: PetscReal nj = ctx->n[jjj] * ctx->n_0;
1027: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(Zi * Zj * (mui + muj) / (mui * Tj_ev + muj * Ti_ev) * PetscSqrtReal(ni * Zi * Zi / Ti_ev + nj * Zj * Zj / Tj_ev));
1028: }
1029: }
1030: }
1031: //PetscReal v0 = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1032: PetscFunctionReturn(PETSC_SUCCESS);
1033: }
1035: static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[])
1036: {
1037: PetscBool flg, sph_flg;
1038: PetscInt ii, nt, nm, nc, num_species_grid[LANDAU_MAX_GRIDS], non_dim_grid;
1039: PetscReal v0_grid[LANDAU_MAX_GRIDS], lnLam = 10;
1040: DM dummy;
1042: PetscFunctionBegin;
1043: PetscCall(DMCreate(ctx->comm, &dummy));
1044: /* get options - initialize context */
1045: ctx->verbose = 1; // should be 0 for silent compliance
1046: #if defined(PETSC_HAVE_THREADSAFETY) && defined(PETSC_HAVE_OPENMP)
1047: ctx->batch_sz = PetscNumOMPThreads;
1048: #else
1049: ctx->batch_sz = 1;
1050: #endif
1051: ctx->batch_view_idx = 0;
1052: ctx->interpolate = PETSC_TRUE;
1053: ctx->gpu_assembly = PETSC_TRUE;
1054: ctx->norm_state = 0;
1055: ctx->electronShift = 0;
1056: ctx->M = NULL;
1057: ctx->J = NULL;
1058: /* geometry and grids */
1059: ctx->sphere = PETSC_FALSE;
1060: ctx->use_p4est = PETSC_FALSE;
1061: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1062: ctx->radius[grid] = 5.; /* thermal radius (velocity) */
1063: ctx->radius_perp[grid] = 5.; /* thermal radius (velocity) */
1064: ctx->radius_par[grid] = 5.; /* thermal radius (velocity) */
1065: ctx->numAMRRefine[grid] = 0;
1066: ctx->postAMRRefine[grid] = 0;
1067: ctx->species_offset[grid + 1] = 1; // one species default
1068: num_species_grid[grid] = 0;
1069: ctx->plex[grid] = NULL; /* cache as expensive to Convert */
1070: }
1071: ctx->species_offset[0] = 0;
1072: ctx->re_radius = 0.;
1073: ctx->vperp0_radius1 = 0;
1074: ctx->vperp0_radius2 = 0;
1075: ctx->nZRefine1 = 0;
1076: ctx->nZRefine2 = 0;
1077: ctx->numRERefine = 0;
1078: num_species_grid[0] = 1; // one species default
1079: /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */
1080: ctx->charges[0] = -1; /* electron charge (MKS) */
1081: ctx->masses[0] = 1 / 1835.469965278441013; /* temporary value in proton mass */
1082: ctx->n[0] = 1;
1083: ctx->v_0 = 1; /* thermal velocity, we could start with a scale != 1 */
1084: ctx->thermal_temps[0] = 1;
1085: /* constants, etc. */
1086: ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */
1087: ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */
1088: ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */
1089: ctx->Ez = 0;
1090: for (PetscInt grid = 0; grid < LANDAU_NUM_TIMERS; grid++) ctx->times[grid] = 0;
1091: for (PetscInt ii = 0; ii < LANDAU_DIM; ii++) ctx->cells0[ii] = 2;
1092: if (LANDAU_DIM == 2) ctx->cells0[0] = 1;
1093: ctx->use_matrix_mass = PETSC_FALSE;
1094: ctx->use_relativistic_corrections = PETSC_FALSE;
1095: ctx->use_energy_tensor_trick = PETSC_FALSE; /* Use Eero's trick for energy conservation v --> grad(v^2/2) */
1096: ctx->SData_d.w = NULL;
1097: ctx->SData_d.x = NULL;
1098: ctx->SData_d.y = NULL;
1099: ctx->SData_d.z = NULL;
1100: ctx->SData_d.invJ = NULL;
1101: ctx->jacobian_field_major_order = PETSC_FALSE;
1102: ctx->SData_d.coo_elem_offsets = NULL;
1103: ctx->SData_d.coo_elem_point_offsets = NULL;
1104: ctx->coo_assembly = PETSC_FALSE;
1105: ctx->SData_d.coo_elem_fullNb = NULL;
1106: ctx->SData_d.coo_size = 0;
1107: PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");
1108: {
1109: char opstring[256];
1110: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
1111: ctx->deviceType = LANDAU_KOKKOS;
1112: PetscCall(PetscStrncpy(opstring, "kokkos", sizeof(opstring)));
1113: #elif defined(PETSC_HAVE_CUDA)
1114: ctx->deviceType = LANDAU_CUDA;
1115: PetscCall(PetscStrncpy(opstring, "cuda", sizeof(opstring)));
1116: #else
1117: ctx->deviceType = LANDAU_CPU;
1118: PetscCall(PetscStrncpy(opstring, "cpu", sizeof(opstring)));
1119: #endif
1120: PetscCall(PetscOptionsString("-dm_landau_device_type", "Use kernels on 'cpu', 'cuda', or 'kokkos'", "plexland.c", opstring, opstring, sizeof(opstring), NULL));
1121: PetscCall(PetscStrcmp("cpu", opstring, &flg));
1122: if (flg) {
1123: ctx->deviceType = LANDAU_CPU;
1124: } else {
1125: PetscCall(PetscStrcmp("cuda", opstring, &flg));
1126: if (flg) {
1127: ctx->deviceType = LANDAU_CUDA;
1128: } else {
1129: PetscCall(PetscStrcmp("kokkos", opstring, &flg));
1130: if (flg) ctx->deviceType = LANDAU_KOKKOS;
1131: else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_device_type %s", opstring);
1132: }
1133: }
1134: }
1135: PetscCall(PetscOptionsReal("-dm_landau_electron_shift", "Shift in thermal velocity of electrons", "none", ctx->electronShift, &ctx->electronShift, NULL));
1136: PetscCall(PetscOptionsInt("-dm_landau_verbose", "Level of verbosity output", "plexland.c", ctx->verbose, &ctx->verbose, NULL));
1137: PetscCall(PetscOptionsInt("-dm_landau_batch_size", "Number of 'vertices' to batch", "ex2.c", ctx->batch_sz, &ctx->batch_sz, NULL));
1138: 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);
1139: 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));
1140: 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);
1141: PetscCall(PetscOptionsReal("-dm_landau_Ez", "Initial parallel electric field in unites of Conner-Hastie critical field", "plexland.c", ctx->Ez, &ctx->Ez, NULL));
1142: PetscCall(PetscOptionsReal("-dm_landau_n_0", "Normalization constant for number density", "plexland.c", ctx->n_0, &ctx->n_0, NULL));
1143: 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));
1144: PetscCall(PetscOptionsBool("-dm_landau_use_relativistic_corrections", "Use relativistic corrections", "plexland.c", ctx->use_relativistic_corrections, &ctx->use_relativistic_corrections, NULL));
1145: if (LANDAU_DIM == 2 && ctx->use_relativistic_corrections) ctx->use_relativistic_corrections = PETSC_FALSE; // should warn
1146: 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,
1147: &ctx->use_energy_tensor_trick, NULL));
1149: /* get num species with temperature, set defaults */
1150: for (ii = 1; ii < LANDAU_MAX_SPECIES; ii++) {
1151: ctx->thermal_temps[ii] = 1;
1152: ctx->charges[ii] = 1;
1153: ctx->masses[ii] = 1;
1154: ctx->n[ii] = 1;
1155: }
1156: nt = LANDAU_MAX_SPECIES;
1157: 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));
1158: if (flg) {
1159: PetscCall(PetscInfo(dummy, "num_species set to number of thermal temps provided (%" PetscInt_FMT ")\n", nt));
1160: ctx->num_species = nt;
1161: } else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species");
1162: for (ii = 0; ii < ctx->num_species; ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */
1163: nm = LANDAU_MAX_SPECIES - 1;
1164: 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));
1165: 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);
1166: nm = LANDAU_MAX_SPECIES;
1167: PetscCall(PetscOptionsRealArray("-dm_landau_n", "Number density of each species = n_s * n_0", "plexland.c", ctx->n, &nm, &flg));
1168: 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);
1169: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */
1170: ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */
1171: nc = LANDAU_MAX_SPECIES - 1;
1172: 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));
1173: 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);
1174: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */
1175: /* geometry and grids */
1176: nt = LANDAU_MAX_GRIDS;
1177: 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));
1178: if (flg) {
1179: ctx->num_grids = nt;
1180: for (ii = nt = 0; ii < ctx->num_grids; ii++) nt += num_species_grid[ii];
1181: 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,
1182: ctx->num_grids, LANDAU_MAX_GRIDS);
1183: } else {
1184: ctx->num_grids = 1; // go back to a single grid run
1185: num_species_grid[0] = ctx->num_species;
1186: }
1187: 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];
1188: 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],
1189: ctx->num_species);
1190: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1191: int iii = ctx->species_offset[grid]; // normalize with first (arbitrary) species on grid
1192: v0_grid[grid] = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1193: }
1194: // get lambdas here because we need them for t_0 etc
1195: PetscCall(PetscOptionsReal("-dm_landau_ln_lambda", "Universal cross section parameter. Default uses NRL formulas", "plexland.c", lnLam, &lnLam, &flg));
1196: if (flg) {
1197: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1198: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) ctx->lambdas[gridj][grid] = lnLam; /* cross section ratio large - small angle collisions */
1199: }
1200: } else {
1201: PetscCall(makeLambdas(ctx));
1202: }
1203: non_dim_grid = 0;
1204: PetscCall(PetscOptionsInt("-dm_landau_normalization_grid", "Index of grid to use for setting v_0, m_0, t_0. (Not recommended)", "plexland.c", non_dim_grid, &non_dim_grid, &flg));
1205: if (non_dim_grid != 0) PetscCall(PetscInfo(dummy, "Normalization grid set to %" PetscInt_FMT ", but non-default not well verified\n", non_dim_grid));
1206: PetscCheck(non_dim_grid >= 0 && non_dim_grid < ctx->num_species, ctx->comm, PETSC_ERR_ARG_WRONG, "Normalization grid wrong: %" PetscInt_FMT, non_dim_grid);
1207: ctx->v_0 = v0_grid[non_dim_grid]; /* arbitrary units for non dimensionalization: global mean velocity in 1D of electrons */
1208: ctx->m_0 = ctx->masses[non_dim_grid]; /* arbitrary reference mass, electrons */
1209: ctx->t_0 = 8 * PETSC_PI * PetscSqr(ctx->epsilon0 * ctx->m_0 / PetscSqr(ctx->charges[non_dim_grid])) / ctx->lambdas[non_dim_grid][non_dim_grid] / ctx->n_0 * PetscPowReal(ctx->v_0, 3); /* note, this t_0 makes nu[non_dim_grid,non_dim_grid]=1 */
1210: /* domain */
1211: nt = LANDAU_MAX_GRIDS;
1212: PetscCall(PetscOptionsRealArray("-dm_landau_domain_radius", "Phase space size in units of thermal velocity of grid", "plexland.c", ctx->radius, &nt, &flg));
1213: if (flg) {
1214: 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);
1215: while (nt--) ctx->radius_par[nt] = ctx->radius_perp[nt] = ctx->radius[nt];
1216: } else {
1217: nt = LANDAU_MAX_GRIDS;
1218: 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));
1219: 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);
1220: 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));
1221: 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);
1222: }
1223: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1224: if (flg && ctx->radius[grid] <= 0) { /* negative is ratio of c - need to set par and perp with this -- todo */
1225: if (ctx->radius[grid] == 0) ctx->radius[grid] = 0.75;
1226: else ctx->radius[grid] = -ctx->radius[grid];
1227: 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)
1228: PetscCall(PetscInfo(dummy, "Change domain radius to %g for grid %" PetscInt_FMT "\n", (double)ctx->radius[grid], grid));
1229: }
1230: ctx->radius[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1231: ctx->radius_perp[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1232: ctx->radius_par[grid] *= v0_grid[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1233: }
1234: /* amr parameters */
1235: nt = LANDAU_DIM;
1236: PetscCall(PetscOptionsIntArray("-dm_landau_num_cells", "Number of cells in each dimension of base grid", "plexland.c", ctx->cells0, &nt, &flg));
1237: nt = LANDAU_MAX_GRIDS;
1238: 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));
1239: 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);
1240: nt = LANDAU_MAX_GRIDS;
1241: PetscCall(PetscOptionsIntArray("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &nt, &flg));
1242: for (ii = 1; ii < ctx->num_grids; ii++) ctx->postAMRRefine[ii] = ctx->postAMRRefine[0]; // all grids the same now
1243: 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));
1244: PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine_pre", "Number of levels to refine along v_perp=0 before origin refine", "plexland.c", ctx->nZRefine1, &ctx->nZRefine1, &flg));
1245: PetscCall(PetscOptionsInt("-dm_landau_amr_z_refine_post", "Number of levels to refine along v_perp=0 after origin refine", "plexland.c", ctx->nZRefine2, &ctx->nZRefine2, &flg));
1246: 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));
1247: PetscCall(PetscOptionsReal("-dm_landau_z_radius_pre", "velocity range to refine r=0 axis (for electrons)", "plexland.c", ctx->vperp0_radius1, &ctx->vperp0_radius1, &flg));
1248: PetscCall(PetscOptionsReal("-dm_landau_z_radius_post", "velocity range to refine r=0 axis (for electrons) after origin AMR", "plexland.c", ctx->vperp0_radius2, &ctx->vperp0_radius2, &flg));
1249: /* spherical domain (not used) */
1250: PetscCall(PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, &sph_flg));
1251: /* processing options */
1252: PetscCall(PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL));
1253: if (ctx->deviceType == LANDAU_CPU || ctx->deviceType == LANDAU_KOKKOS) { // make Kokkos
1254: PetscCall(PetscOptionsBool("-dm_landau_coo_assembly", "Assemble Jacobian with Kokkos on 'device'", "plexland.c", ctx->coo_assembly, &ctx->coo_assembly, NULL));
1255: 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);
1256: }
1257: 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));
1258: 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");
1259: PetscCheck(!ctx->jacobian_field_major_order, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1260: PetscOptionsEnd();
1262: for (ii = ctx->num_species; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0;
1263: if (ctx->verbose != 0) {
1264: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "masses: e=%10.3e; ions in proton mass units: %10.3e %10.3e ...\n", (double)ctx->masses[0], (double)(ctx->masses[1] / 1.6720e-27), (double)(ctx->num_species > 2 ? ctx->masses[2] / 1.6720e-27 : 0)));
1265: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "charges: e=%10.3e; charges in elementary units: %10.3e %10.3e\n", (double)ctx->charges[0], (double)(-ctx->charges[1] / ctx->charges[0]), (double)(ctx->num_species > 2 ? -ctx->charges[2] / ctx->charges[0] : 0)));
1266: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "n: e: %10.3e i: %10.3e %10.3e\n", (double)ctx->n[0], (double)ctx->n[1], (double)(ctx->num_species > 2 ? ctx->n[2] : 0)));
1267: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "thermal T (K): e=%10.3e i=%10.3e %10.3e. Normalization grid %d: v_0=%10.3e (%10.3ec) n_0=%10.3e t_0=%10.3e %" PetscInt_FMT " batched, view batch %" PetscInt_FMT "\n", (double)ctx->thermal_temps[0],
1268: (double)ctx->thermal_temps[1], (double)((ctx->num_species > 2) ? ctx->thermal_temps[2] : 0), (int)non_dim_grid, (double)ctx->v_0, (double)(ctx->v_0 / SPEED_OF_LIGHT), (double)ctx->n_0, (double)ctx->t_0, ctx->batch_sz, ctx->batch_view_idx));
1269: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Domain radius (AMR levels) grid %d: par=%10.3e perp=%10.3e (%" PetscInt_FMT ") ", 0, (double)ctx->radius_par[0], (double)ctx->radius_perp[0], ctx->numAMRRefine[0]));
1270: for (ii = 1; ii < ctx->num_grids; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, ", %" PetscInt_FMT ": par=%10.3e perp=%10.3e (%" PetscInt_FMT ") ", ii, (double)ctx->radius_par[ii], (double)ctx->radius_perp[ii], ctx->numAMRRefine[ii]));
1271: if (ctx->use_relativistic_corrections) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nUse relativistic corrections\n"));
1272: else PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1273: }
1274: PetscCall(DMDestroy(&dummy));
1275: {
1276: PetscMPIInt rank;
1277: PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
1278: ctx->stage = 0;
1279: PetscCall(PetscLogEventRegister("Landau Create", DM_CLASSID, &ctx->events[13])); /* 13 */
1280: PetscCall(PetscLogEventRegister(" GPU ass. setup", DM_CLASSID, &ctx->events[2])); /* 2 */
1281: PetscCall(PetscLogEventRegister(" Build matrix", DM_CLASSID, &ctx->events[12])); /* 12 */
1282: PetscCall(PetscLogEventRegister(" Assembly maps", DM_CLASSID, &ctx->events[15])); /* 15 */
1283: PetscCall(PetscLogEventRegister("Landau Mass mat", DM_CLASSID, &ctx->events[14])); /* 14 */
1284: PetscCall(PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11])); /* 11 */
1285: PetscCall(PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0])); /* 0 */
1286: PetscCall(PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9])); /* 9 */
1287: PetscCall(PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10])); /* 10 */
1288: PetscCall(PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7])); /* 7 */
1289: PetscCall(PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1])); /* 1 */
1290: PetscCall(PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3])); /* 3 */
1291: PetscCall(PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8])); /* 8 */
1292: PetscCall(PetscLogEventRegister(" J Kernel (GPU)", DM_CLASSID, &ctx->events[4])); /* 4 */
1293: PetscCall(PetscLogEventRegister(" M Kernel (GPU)", DM_CLASSID, &ctx->events[16])); /* 16 */
1294: PetscCall(PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5])); /* 5 */
1295: PetscCall(PetscLogEventRegister(" CPU assemble", DM_CLASSID, &ctx->events[6])); /* 6 */
1297: if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */
1298: PetscCall(PetscOptionsClearValue(NULL, "-snes_converged_reason"));
1299: PetscCall(PetscOptionsClearValue(NULL, "-ksp_converged_reason"));
1300: PetscCall(PetscOptionsClearValue(NULL, "-snes_monitor"));
1301: PetscCall(PetscOptionsClearValue(NULL, "-ksp_monitor"));
1302: PetscCall(PetscOptionsClearValue(NULL, "-ts_monitor"));
1303: PetscCall(PetscOptionsClearValue(NULL, "-ts_view"));
1304: PetscCall(PetscOptionsClearValue(NULL, "-ts_adapt_monitor"));
1305: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_dm_view"));
1306: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_vec_view"));
1307: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_dm_view"));
1308: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_view"));
1309: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_jacobian_view"));
1310: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mat_view"));
1311: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_converged_reason"));
1312: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_monitor"));
1313: PetscCall(PetscOptionsClearValue(NULL, "-"));
1314: PetscCall(PetscOptionsClearValue(NULL, "-info"));
1315: }
1316: }
1317: PetscFunctionReturn(PETSC_SUCCESS);
1318: }
1320: static PetscErrorCode CreateStaticData(PetscInt dim, IS grid_batch_is_inv[], LandauCtx *ctx)
1321: {
1322: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
1323: PetscQuadrature quad;
1324: const PetscReal *quadWeights;
1325: PetscReal invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES];
1326: 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;
1327: PetscTabulation *Tf;
1328: PetscDS prob;
1330: PetscFunctionBegin;
1331: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1332: for (PetscInt ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++) {
1333: invMass[ii] = ctx->m_0 / ctx->masses[ii];
1334: nu_alpha[ii] = PetscSqr(ctx->charges[ii] / ctx->m_0) * ctx->m_0 / ctx->masses[ii];
1335: nu_beta[ii] = PetscSqr(ctx->charges[ii] / ctx->epsilon0) / (8 * PETSC_PI) * ctx->t_0 * ctx->n_0 / PetscPowReal(ctx->v_0, 3);
1336: }
1337: }
1338: if (ctx->verbose == 4) {
1339: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "nu_alpha: "));
1340: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1341: int iii = ctx->species_offset[grid];
1342: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_alpha[ii]));
1343: }
1344: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_beta: "));
1345: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1346: int iii = ctx->species_offset[grid];
1347: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_beta[ii]));
1348: }
1349: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_alpha[i]*nu_beta[j]*lambda[i][j]:\n"));
1350: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1351: int iii = ctx->species_offset[grid];
1352: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) {
1353: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1354: int jjj = ctx->species_offset[gridj];
1355: for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)(nu_alpha[ii] * nu_beta[jj] * ctx->lambdas[grid][gridj])));
1356: }
1357: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1358: }
1359: }
1360: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "lambda[i][j]:\n"));
1361: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1362: int iii = ctx->species_offset[grid];
1363: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) {
1364: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1365: int jjj = ctx->species_offset[gridj];
1366: for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)ctx->lambdas[grid][gridj]));
1367: }
1368: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1369: }
1370: }
1371: }
1372: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
1373: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
1374: /* DS, Tab and quad is same on all grids */
1375: PetscCheck(ctx->plex[0], ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1376: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
1377: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights));
1378: 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);
1379: /* setup each grid */
1380: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1381: PetscInt cStart, cEnd;
1382: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1383: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1384: numCells[grid] = cEnd - cStart; // grids can have different topology
1385: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
1386: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
1387: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
1388: ncellsTot += numCells[grid];
1389: }
1390: /* create GPU assembly data */
1391: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1392: PetscContainer container;
1393: PetscScalar *elemMatrix, *elMat;
1394: pointInterpolationP4est(*pointMaps)[LANDAU_MAX_Q_FACE];
1395: P4estVertexMaps *maps;
1396: const PetscInt *plex_batch = NULL, Nb = Nq, elMatSz = Nq * Nq * ctx->num_species * ctx->num_species; // tensor elements;
1397: LandauIdx *coo_elem_offsets = NULL, *coo_elem_fullNb = NULL, (*coo_elem_point_offsets)[LANDAU_MAX_NQ + 1] = NULL;
1398: /* create GPU assembly data */
1399: PetscCall(PetscInfo(ctx->plex[0], "Make GPU maps %d\n", 1));
1400: PetscCall(PetscLogEventBegin(ctx->events[2], 0, 0, 0, 0));
1401: PetscCall(PetscMalloc(sizeof(*maps) * ctx->num_grids, &maps));
1402: PetscCall(PetscMalloc(sizeof(*pointMaps) * MAP_BF_SIZE, &pointMaps));
1403: PetscCall(PetscMalloc(sizeof(*elemMatrix) * elMatSz, &elemMatrix));
1405: if (ctx->coo_assembly) { // setup COO assembly -- put COO metadata directly in ctx->SData_d
1406: PetscCall(PetscMalloc3(ncellsTot + 1, &coo_elem_offsets, ncellsTot, &coo_elem_fullNb, ncellsTot, &coo_elem_point_offsets)); // array of integer pointers
1407: coo_elem_offsets[0] = 0; // finish later
1408: PetscCall(PetscInfo(ctx->plex[0], "COO initialization, %" PetscInt_FMT " cells\n", ncellsTot));
1409: ctx->SData_d.coo_n_cellsTot = ncellsTot;
1410: ctx->SData_d.coo_elem_offsets = (void *)coo_elem_offsets;
1411: ctx->SData_d.coo_elem_fullNb = (void *)coo_elem_fullNb;
1412: ctx->SData_d.coo_elem_point_offsets = (void *)coo_elem_point_offsets;
1413: } else {
1414: ctx->SData_d.coo_elem_offsets = ctx->SData_d.coo_elem_fullNb = NULL;
1415: ctx->SData_d.coo_elem_point_offsets = NULL;
1416: ctx->SData_d.coo_n_cellsTot = 0;
1417: }
1419: ctx->SData_d.coo_max_fullnb = 0;
1420: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1421: PetscInt cStart, cEnd, Nfloc = Nf[grid], totDim = Nfloc * Nq;
1422: if (grid_batch_is_inv[grid]) PetscCall(ISGetIndices(grid_batch_is_inv[grid], &plex_batch));
1423: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1424: // make maps
1425: maps[grid].d_self = NULL;
1426: maps[grid].num_elements = numCells[grid];
1427: maps[grid].num_face = (PetscInt)(pow(Nq, 1. / ((double)dim)) + .001); // Q
1428: maps[grid].num_face = (PetscInt)(pow(maps[grid].num_face, (double)(dim - 1)) + .001); // Q^2
1429: maps[grid].num_reduced = 0;
1430: maps[grid].deviceType = ctx->deviceType;
1431: maps[grid].numgrids = ctx->num_grids;
1432: // count reduced and get
1433: PetscCall(PetscMalloc(maps[grid].num_elements * sizeof(*maps[grid].gIdx), &maps[grid].gIdx));
1434: for (int ej = cStart, eidx = 0; ej < cEnd; ++ej, ++eidx, glb_elem_idx++) {
1435: if (coo_elem_offsets) coo_elem_offsets[glb_elem_idx + 1] = coo_elem_offsets[glb_elem_idx]; // start with last one, then add
1436: for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1437: int fullNb = 0;
1438: for (int q = 0; q < Nb; ++q) {
1439: PetscInt numindices, *indices;
1440: PetscScalar *valuesOrig = elMat = elemMatrix;
1441: PetscCall(PetscArrayzero(elMat, totDim * totDim));
1442: elMat[(fieldA * Nb + q) * totDim + fieldA * Nb + q] = 1;
1443: PetscCall(DMPlexGetClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat));
1444: for (PetscInt f = 0; f < numindices; ++f) { // look for a non-zero on the diagonal
1445: if (PetscAbs(PetscRealPart(elMat[f * numindices + f])) > PETSC_MACHINE_EPSILON) {
1446: // found it
1447: if (PetscAbs(PetscRealPart(elMat[f * numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { // normal vertex 1.0
1448: if (plex_batch) {
1449: maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)plex_batch[indices[f]];
1450: } else {
1451: maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)indices[f];
1452: }
1453: fullNb++;
1454: } else { //found a constraint
1455: int jj = 0;
1456: PetscReal sum = 0;
1457: const PetscInt ff = f;
1458: maps[grid].gIdx[eidx][fieldA][q] = -maps[grid].num_reduced - 1; // store (-)index: id = -(idx+1): idx = -id - 1
1460: do { // constraints are continuous in Plex - exploit that here
1461: int ii; // get 'scale'
1462: 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
1463: 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
1464: pointMaps[maps[grid].num_reduced][jj].scale += PetscRealPart(elMat[f * numindices + ff + ii]);
1465: }
1466: }
1467: sum += pointMaps[maps[grid].num_reduced][jj].scale; // diagnostic
1468: // get 'gid'
1469: if (pointMaps[maps[grid].num_reduced][jj].scale == 0) pointMaps[maps[grid].num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps
1470: else {
1471: if (plex_batch) {
1472: pointMaps[maps[grid].num_reduced][jj].gid = plex_batch[indices[f]];
1473: } else {
1474: pointMaps[maps[grid].num_reduced][jj].gid = indices[f];
1475: }
1476: fullNb++;
1477: }
1478: } while (++jj < maps[grid].num_face && ++f < numindices); // jj is incremented if we hit the end
1479: while (jj < maps[grid].num_face) {
1480: pointMaps[maps[grid].num_reduced][jj].scale = 0;
1481: pointMaps[maps[grid].num_reduced][jj].gid = -1;
1482: jj++;
1483: }
1484: if (PetscAbs(sum - 1.0) > 10 * PETSC_MACHINE_EPSILON) { // debug
1485: int d, f;
1486: PetscReal tmp = 0;
1487: 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));
1488: for (d = 0, tmp = 0; d < numindices; ++d) {
1489: if (tmp != 0 && PetscAbs(tmp - 1.0) > 10 * PETSC_MACHINE_EPSILON) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3d) %3" PetscInt_FMT ": ", d, indices[d]));
1490: for (f = 0; f < numindices; ++f) tmp += PetscRealPart(elMat[d * numindices + f]);
1491: if (tmp != 0) PetscCall(PetscPrintf(ctx->comm, " | %22.16e\n", (double)tmp));
1492: }
1493: }
1494: maps[grid].num_reduced++;
1495: 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);
1496: }
1497: break;
1498: }
1499: }
1500: // cleanup
1501: PetscCall(DMPlexRestoreClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat));
1502: if (elMat != valuesOrig) PetscCall(DMRestoreWorkArray(ctx->plex[grid], numindices * numindices, MPIU_SCALAR, &elMat));
1503: }
1504: if (ctx->coo_assembly) { // setup COO assembly
1505: coo_elem_offsets[glb_elem_idx + 1] += fullNb * fullNb; // one species block, adds a block for each species, on this element in this grid
1506: if (fieldA == 0) { // cache full Nb for this element, on this grid per species
1507: coo_elem_fullNb[glb_elem_idx] = fullNb;
1508: if (fullNb > ctx->SData_d.coo_max_fullnb) ctx->SData_d.coo_max_fullnb = fullNb;
1509: } 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);
1510: }
1511: } // field
1512: } // cell
1513: // allocate and copy point data maps[grid].gIdx[eidx][field][q]
1514: PetscCall(PetscMalloc(maps[grid].num_reduced * sizeof(*maps[grid].c_maps), &maps[grid].c_maps));
1515: for (int ej = 0; ej < maps[grid].num_reduced; ++ej) {
1516: for (int q = 0; q < maps[grid].num_face; ++q) {
1517: maps[grid].c_maps[ej][q].scale = pointMaps[ej][q].scale;
1518: maps[grid].c_maps[ej][q].gid = pointMaps[ej][q].gid;
1519: }
1520: }
1521: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
1522: if (ctx->deviceType == LANDAU_KOKKOS) {
1523: PetscCall(LandauKokkosCreateMatMaps(maps, pointMaps, Nf, Nq, grid)); // implies Kokkos does
1524: } // else could be CUDA
1525: #endif
1526: #if defined(PETSC_HAVE_CUDA)
1527: if (ctx->deviceType == LANDAU_CUDA) PetscCall(LandauCUDACreateMatMaps(maps, pointMaps, Nf, Nq, grid));
1528: #endif
1529: if (plex_batch) {
1530: PetscCall(ISRestoreIndices(grid_batch_is_inv[grid], &plex_batch));
1531: PetscCall(ISDestroy(&grid_batch_is_inv[grid])); // we are done with this
1532: }
1533: } /* grids */
1534: // finish COO
1535: if (ctx->coo_assembly) { // setup COO assembly
1536: PetscInt *oor, *ooc;
1537: ctx->SData_d.coo_size = coo_elem_offsets[ncellsTot] * ctx->batch_sz;
1538: PetscCall(PetscMalloc2(ctx->SData_d.coo_size, &oor, ctx->SData_d.coo_size, &ooc));
1539: for (int i = 0; i < ctx->SData_d.coo_size; i++) oor[i] = ooc[i] = -1;
1540: // get
1541: for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1542: for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1543: const int fullNb = coo_elem_fullNb[glb_elem_idx];
1544: 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
1545: coo_elem_point_offsets[glb_elem_idx][0] = 0;
1546: for (int f = 0, cnt2 = 0; f < Nb; f++) {
1547: int idx = Idxs[f];
1548: coo_elem_point_offsets[glb_elem_idx][f + 1] = coo_elem_point_offsets[glb_elem_idx][f]; // start at last
1549: if (idx >= 0) {
1550: cnt2++;
1551: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1552: } else {
1553: idx = -idx - 1;
1554: for (int q = 0; q < maps[grid].num_face; q++) {
1555: if (maps[grid].c_maps[idx][q].gid < 0) break;
1556: cnt2++;
1557: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1558: }
1559: }
1560: PetscCheck(cnt2 <= fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "wrong count %d < %d", fullNb, cnt2);
1561: }
1562: 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);
1563: }
1564: }
1565: // set
1566: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1567: for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1568: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1569: for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1570: const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
1571: // set (i,j)
1572: for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1573: const LandauIdx *const Idxs = &maps[grid].gIdx[ej][fieldA][0];
1574: int rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE];
1575: for (int f = 0; f < Nb; ++f) {
1576: const int nr = coo_elem_point_offsets[glb_elem_idx][f + 1] - coo_elem_point_offsets[glb_elem_idx][f];
1577: if (nr == 1) rows[0] = Idxs[f];
1578: else {
1579: const int idx = -Idxs[f] - 1;
1580: for (int q = 0; q < nr; q++) rows[q] = maps[grid].c_maps[idx][q].gid;
1581: }
1582: for (int g = 0; g < Nb; ++g) {
1583: const int nc = coo_elem_point_offsets[glb_elem_idx][g + 1] - coo_elem_point_offsets[glb_elem_idx][g];
1584: if (nc == 1) cols[0] = Idxs[g];
1585: else {
1586: const int idx = -Idxs[g] - 1;
1587: for (int q = 0; q < nc; q++) cols[q] = maps[grid].c_maps[idx][q].gid;
1588: }
1589: 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];
1590: for (int q = 0, idx = idx0; q < nr; q++) {
1591: for (int d = 0; d < nc; d++, idx++) {
1592: oor[idx] = rows[q] + moffset;
1593: ooc[idx] = cols[d] + moffset;
1594: }
1595: }
1596: }
1597: }
1598: }
1599: } // cell
1600: } // grid
1601: } // batch
1602: PetscCall(MatSetPreallocationCOO(ctx->J, ctx->SData_d.coo_size, oor, ooc));
1603: PetscCall(PetscFree2(oor, ooc));
1604: }
1605: PetscCall(PetscFree(pointMaps));
1606: PetscCall(PetscFree(elemMatrix));
1607: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
1608: PetscCall(PetscContainerSetPointer(container, (void *)maps));
1609: PetscCall(PetscContainerSetUserDestroy(container, LandauGPUMapsDestroy));
1610: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "assembly_maps", (PetscObject)container));
1611: PetscCall(PetscContainerDestroy(&container));
1612: PetscCall(PetscLogEventEnd(ctx->events[2], 0, 0, 0, 0));
1613: } // end GPU assembly
1614: { /* create static point data, Jacobian called first, only one vertex copy */
1615: PetscReal *invJe, *ww, *xx, *yy, *zz = NULL, *invJ_a;
1616: PetscInt outer_ipidx, outer_ej, grid, nip_glb = 0;
1617: PetscFE fe;
1618: const PetscInt Nb = Nq;
1619: PetscCall(PetscLogEventBegin(ctx->events[7], 0, 0, 0, 0));
1620: PetscCall(PetscInfo(ctx->plex[0], "Initialize static data\n"));
1621: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) nip_glb += Nq * numCells[grid];
1622: /* collect f data, first time is for Jacobian, but make mass now */
1623: if (ctx->verbose != 0) {
1624: PetscInt ncells = 0, N;
1625: PetscCall(MatGetSize(ctx->J, &N, NULL));
1626: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ncells += numCells[grid];
1627: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%d) %s %" PetscInt_FMT " IPs, %" PetscInt_FMT " cells total, Nb=%" PetscInt_FMT ", Nq=%" PetscInt_FMT ", dim=%" PetscInt_FMT ", Tab: Nb=%" PetscInt_FMT " Nf=%" PetscInt_FMT " Np=%" PetscInt_FMT " cdim=%" PetscInt_FMT " N=%" PetscInt_FMT "\n", 0, "FormLandau", nip_glb, ncells, Nb, Nq, dim, Nb,
1628: ctx->num_species, Nb, dim, N));
1629: }
1630: PetscCall(PetscMalloc4(nip_glb, &ww, nip_glb, &xx, nip_glb, &yy, nip_glb * dim * dim, &invJ_a));
1631: if (dim == 3) PetscCall(PetscMalloc1(nip_glb, &zz));
1632: if (ctx->use_energy_tensor_trick) {
1633: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, PETSC_FALSE, NULL, PETSC_DECIDE, &fe));
1634: PetscCall(PetscObjectSetName((PetscObject)fe, "energy"));
1635: }
1636: /* init each grids static data - no batch */
1637: for (grid = 0, outer_ipidx = 0, outer_ej = 0; grid < ctx->num_grids; grid++) { // OpenMP (once)
1638: Vec v2_2 = NULL; // projected function: v^2/2 for non-relativistic, gamma... for relativistic
1639: PetscSection e_section;
1640: DM dmEnergy;
1641: PetscInt cStart, cEnd, ej;
1643: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1644: // prep energy trick, get v^2 / 2 vector
1645: if (ctx->use_energy_tensor_trick) {
1646: PetscErrorCode (*energyf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {ctx->use_relativistic_corrections ? gamma_m1_f : energy_f};
1647: Vec glob_v2;
1648: PetscReal *c2_0[1], data[1] = {PetscSqr(C_0(ctx->v_0))};
1650: PetscCall(DMClone(ctx->plex[grid], &dmEnergy));
1651: PetscCall(PetscObjectSetName((PetscObject)dmEnergy, "energy"));
1652: PetscCall(DMSetField(dmEnergy, 0, NULL, (PetscObject)fe));
1653: PetscCall(DMCreateDS(dmEnergy));
1654: PetscCall(DMGetSection(dmEnergy, &e_section));
1655: PetscCall(DMGetGlobalVector(dmEnergy, &glob_v2));
1656: PetscCall(PetscObjectSetName((PetscObject)glob_v2, "trick"));
1657: c2_0[0] = &data[0];
1658: PetscCall(DMProjectFunction(dmEnergy, 0., energyf, (void **)c2_0, INSERT_ALL_VALUES, glob_v2));
1659: PetscCall(DMGetLocalVector(dmEnergy, &v2_2));
1660: PetscCall(VecZeroEntries(v2_2)); /* zero BCs so don't set */
1661: PetscCall(DMGlobalToLocalBegin(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1662: PetscCall(DMGlobalToLocalEnd(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1663: PetscCall(DMViewFromOptions(dmEnergy, NULL, "-energy_dm_view"));
1664: PetscCall(VecViewFromOptions(glob_v2, NULL, "-energy_vec_view"));
1665: PetscCall(DMRestoreGlobalVector(dmEnergy, &glob_v2));
1666: }
1667: /* append part of the IP data for each grid */
1668: for (ej = 0; ej < numCells[grid]; ++ej, ++outer_ej) {
1669: PetscScalar *coefs = NULL;
1670: 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);
1671: invJe = invJ_a + outer_ej * Nq * dim * dim;
1672: PetscCall(DMPlexComputeCellGeometryFEM(ctx->plex[grid], ej + cStart, quad, vj, Jdummy, invJe, detJj));
1673: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecGetClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1674: /* create static point data */
1675: for (PetscInt qj = 0; qj < Nq; qj++, outer_ipidx++) {
1676: const PetscInt gidx = outer_ipidx;
1677: const PetscReal *invJ = &invJe[qj * dim * dim];
1678: ww[gidx] = detJj[qj] * quadWeights[qj];
1679: if (dim == 2) ww[gidx] *= vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */
1680: // get xx, yy, zz
1681: if (ctx->use_energy_tensor_trick) {
1682: double refSpaceDer[3], eGradPhi[3];
1683: const PetscReal *const DD = Tf[0]->T[1];
1684: const PetscReal *Dq = &DD[qj * Nb * dim];
1685: for (int d = 0; d < 3; ++d) refSpaceDer[d] = eGradPhi[d] = 0.0;
1686: for (int b = 0; b < Nb; ++b) {
1687: for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[b * dim + d] * PetscRealPart(coefs[b]);
1688: }
1689: xx[gidx] = 1e10;
1690: if (ctx->use_relativistic_corrections) {
1691: double dg2_c2 = 0;
1692: //for (int d = 0; d < dim; ++d) refSpaceDer[d] *= c02;
1693: for (int d = 0; d < dim; ++d) dg2_c2 += PetscSqr(refSpaceDer[d]);
1694: dg2_c2 *= (double)c02;
1695: if (dg2_c2 >= .999) {
1696: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1697: yy[gidx] = vj[qj * dim + 1];
1698: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1699: 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]));
1700: } else {
1701: PetscReal fact = c02 / PetscSqrtReal(1. - dg2_c2);
1702: for (int d = 0; d < dim; ++d) refSpaceDer[d] *= fact;
1703: // could test with other point u' that (grad - grad') * U (refSpaceDer, refSpaceDer') == 0
1704: }
1705: }
1706: if (xx[gidx] == 1e10) {
1707: for (int d = 0; d < dim; ++d) {
1708: for (int e = 0; e < dim; ++e) eGradPhi[d] += invJ[e * dim + d] * refSpaceDer[e];
1709: }
1710: xx[gidx] = eGradPhi[0];
1711: yy[gidx] = eGradPhi[1];
1712: if (dim == 3) zz[gidx] = eGradPhi[2];
1713: }
1714: } else {
1715: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1716: yy[gidx] = vj[qj * dim + 1];
1717: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1718: }
1719: } /* q */
1720: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecRestoreClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1721: } /* ej */
1722: if (ctx->use_energy_tensor_trick) {
1723: PetscCall(DMRestoreLocalVector(dmEnergy, &v2_2));
1724: PetscCall(DMDestroy(&dmEnergy));
1725: }
1726: } /* grid */
1727: if (ctx->use_energy_tensor_trick) PetscCall(PetscFEDestroy(&fe));
1728: /* cache static data */
1729: if (ctx->deviceType == LANDAU_CUDA || ctx->deviceType == LANDAU_KOKKOS) {
1730: #if defined(PETSC_HAVE_CUDA) || defined(PETSC_HAVE_KOKKOS_KERNELS)
1731: if (ctx->deviceType == LANDAU_CUDA) {
1732: #if defined(PETSC_HAVE_CUDA)
1733: PetscCall(LandauCUDAStaticDataSet(ctx->plex[0], Nq, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, (PetscReal *)ctx->lambdas, invJ_a, xx, yy, zz, ww, &ctx->SData_d));
1734: #else
1735: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type cuda not built");
1736: #endif
1737: } else if (ctx->deviceType == LANDAU_KOKKOS) {
1738: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
1739: PetscCall(LandauKokkosStaticDataSet(ctx->plex[0], Nq, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, (PetscReal *)ctx->lambdas, invJ_a, xx, yy, zz, ww, &ctx->SData_d));
1740: #else
1741: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type kokkos not built");
1742: #endif
1743: }
1744: #endif
1745: /* free */
1746: PetscCall(PetscFree4(ww, xx, yy, invJ_a));
1747: if (dim == 3) PetscCall(PetscFree(zz));
1748: } else { /* CPU version, just copy in, only use part */
1749: PetscReal *nu_alpha_p = (PetscReal *)ctx->SData_d.alpha, *nu_beta_p = (PetscReal *)ctx->SData_d.beta, *invMass_p = (PetscReal *)ctx->SData_d.invMass, *lambdas_p = NULL; // why set these ?
1750: ctx->SData_d.w = (void *)ww;
1751: ctx->SData_d.x = (void *)xx;
1752: ctx->SData_d.y = (void *)yy;
1753: ctx->SData_d.z = (void *)zz;
1754: ctx->SData_d.invJ = (void *)invJ_a;
1755: PetscCall(PetscMalloc4(ctx->num_species, &nu_alpha_p, ctx->num_species, &nu_beta_p, ctx->num_species, &invMass_p, LANDAU_MAX_GRIDS * LANDAU_MAX_GRIDS, &lambdas_p));
1756: for (PetscInt ii = 0; ii < ctx->num_species; ii++) {
1757: nu_alpha_p[ii] = nu_alpha[ii];
1758: nu_beta_p[ii] = nu_beta[ii];
1759: invMass_p[ii] = invMass[ii];
1760: }
1761: ctx->SData_d.alpha = (void *)nu_alpha_p;
1762: ctx->SData_d.beta = (void *)nu_beta_p;
1763: ctx->SData_d.invMass = (void *)invMass_p;
1764: ctx->SData_d.lambdas = (void *)lambdas_p;
1765: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1766: PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
1767: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) { (*lambdas)[grid][gridj] = ctx->lambdas[grid][gridj]; }
1768: }
1769: }
1770: PetscCall(PetscLogEventEnd(ctx->events[7], 0, 0, 0, 0));
1771: } // initialize
1772: PetscFunctionReturn(PETSC_SUCCESS);
1773: }
1775: /* < v, u > */
1776: 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[])
1777: {
1778: g0[0] = 1.;
1779: }
1781: /* < v, u > */
1782: 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[])
1783: {
1784: static double ttt = 1e-12;
1785: g0[0] = ttt++;
1786: }
1788: /* < v, u > */
1789: 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[])
1790: {
1791: g0[0] = 2. * PETSC_PI * x[0];
1792: }
1794: static PetscErrorCode MatrixNfDestroy(void *ptr)
1795: {
1796: PetscInt *nf = (PetscInt *)ptr;
1797: PetscFunctionBegin;
1798: PetscCall(PetscFree(nf));
1799: PetscFunctionReturn(PETSC_SUCCESS);
1800: }
1802: /*
1803: LandauCreateJacobianMatrix - creates ctx->J with without real data. Hard to keep sparse.
1804: - Like DMPlexLandauCreateMassMatrix. Should remove one and combine
1805: - has old support for field major ordering
1806: */
1807: static PetscErrorCode LandauCreateJacobianMatrix(MPI_Comm comm, Vec X, IS grid_batch_is_inv[LANDAU_MAX_GRIDS], LandauCtx *ctx)
1808: {
1809: PetscInt *idxs = NULL;
1810: Mat subM[LANDAU_MAX_GRIDS];
1812: PetscFunctionBegin;
1813: if (!ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1814: PetscFunctionReturn(PETSC_SUCCESS);
1815: }
1816: // get the RCM for this grid to separate out species into blocks -- create 'idxs' & 'ctx->batch_is' -- not used
1817: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(PetscMalloc1(ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, &idxs));
1818: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1819: const PetscInt *values, n = ctx->mat_offset[grid + 1] - ctx->mat_offset[grid];
1820: Mat gMat;
1821: DM massDM;
1822: PetscDS prob;
1823: Vec tvec;
1824: // get "mass" matrix for reordering
1825: PetscCall(DMClone(ctx->plex[grid], &massDM));
1826: PetscCall(DMCopyFields(ctx->plex[grid], massDM));
1827: PetscCall(DMCreateDS(massDM));
1828: PetscCall(DMGetDS(massDM, &prob));
1829: 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));
1830: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); // this trick is need to both sparsify the matrix and avoid runtime error
1831: PetscCall(DMCreateMatrix(massDM, &gMat));
1832: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
1833: PetscCall(MatSetOption(gMat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
1834: PetscCall(MatSetOption(gMat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
1835: PetscCall(DMCreateLocalVector(ctx->plex[grid], &tvec));
1836: PetscCall(DMPlexSNESComputeJacobianFEM(massDM, tvec, gMat, gMat, ctx));
1837: PetscCall(MatViewFromOptions(gMat, NULL, "-dm_landau_reorder_mat_view"));
1838: PetscCall(DMDestroy(&massDM));
1839: PetscCall(VecDestroy(&tvec));
1840: subM[grid] = gMat;
1841: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1842: MatOrderingType rtype = MATORDERINGRCM;
1843: IS isrow, isicol;
1844: PetscCall(MatGetOrdering(gMat, rtype, &isrow, &isicol));
1845: PetscCall(ISInvertPermutation(isrow, PETSC_DECIDE, &grid_batch_is_inv[grid]));
1846: PetscCall(ISGetIndices(isrow, &values));
1847: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
1848: #if !defined(LANDAU_SPECIES_MAJOR)
1849: PetscInt N = ctx->mat_offset[ctx->num_grids], n0 = ctx->mat_offset[grid] + b_id * N;
1850: for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1851: #else
1852: PetscInt n0 = ctx->mat_offset[grid] * ctx->batch_sz + b_id * n;
1853: for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1854: #endif
1855: }
1856: PetscCall(ISRestoreIndices(isrow, &values));
1857: PetscCall(ISDestroy(&isrow));
1858: PetscCall(ISDestroy(&isicol));
1859: }
1860: }
1861: 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));
1862: // get a block matrix
1863: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1864: Mat B = subM[grid];
1865: PetscInt nloc, nzl, *colbuf, row, COL_BF_SIZE = 1024;
1866: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1867: PetscCall(MatGetSize(B, &nloc, NULL));
1868: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1869: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1870: const PetscInt *cols;
1871: const PetscScalar *vals;
1872: for (int i = 0; i < nloc; i++) {
1873: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
1874: if (nzl > COL_BF_SIZE) {
1875: PetscCall(PetscFree(colbuf));
1876: 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));
1877: COL_BF_SIZE = nzl;
1878: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1879: }
1880: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
1881: for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
1882: row = i + moffset;
1883: PetscCall(MatSetValues(ctx->J, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
1884: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
1885: }
1886: }
1887: PetscCall(PetscFree(colbuf));
1888: }
1889: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
1890: PetscCall(MatAssemblyBegin(ctx->J, MAT_FINAL_ASSEMBLY));
1891: PetscCall(MatAssemblyEnd(ctx->J, MAT_FINAL_ASSEMBLY));
1893: // debug
1894: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_mat_view"));
1895: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1896: Mat mat_block_order;
1897: PetscCall(MatCreateSubMatrix(ctx->J, ctx->batch_is, ctx->batch_is, MAT_INITIAL_MATRIX, &mat_block_order)); // use MatPermute
1898: PetscCall(MatViewFromOptions(mat_block_order, NULL, "-dm_landau_mat_view"));
1899: PetscCall(MatDestroy(&mat_block_order));
1900: PetscCall(VecScatterCreate(X, ctx->batch_is, X, NULL, &ctx->plex_batch));
1901: PetscCall(VecDuplicate(X, &ctx->work_vec));
1902: }
1904: PetscFunctionReturn(PETSC_SUCCESS);
1905: }
1907: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat);
1908: /*@C
1909: DMPlexLandauCreateVelocitySpace - Create a DMPlex velocity space mesh
1911: Collective
1913: Input Parameters:
1914: + comm - The MPI communicator
1915: . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver)
1916: - prefix - prefix for options (not tested)
1918: Output Parameter:
1919: . pack - The DM object representing the mesh
1920: + X - A vector (user destroys)
1921: - J - Optional matrix (object destroys)
1923: Level: beginner
1925: .keywords: mesh
1926: .seealso: `DMPlexCreate()`, `DMPlexLandauDestroyVelocitySpace()`
1927: @*/
1928: PetscErrorCode DMPlexLandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *pack)
1929: {
1930: LandauCtx *ctx;
1931: Vec Xsub[LANDAU_MAX_GRIDS];
1932: IS grid_batch_is_inv[LANDAU_MAX_GRIDS];
1934: PetscFunctionBegin;
1935: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported");
1936: PetscCheck(LANDAU_DIM == dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " != LANDAU_DIM %d", dim, LANDAU_DIM);
1937: PetscCall(PetscNew(&ctx));
1938: ctx->comm = comm; /* used for diagnostics and global errors */
1939: /* process options */
1940: PetscCall(ProcessOptions(ctx, prefix));
1941: if (dim == 2) ctx->use_relativistic_corrections = PETSC_FALSE;
1942: /* Create Mesh */
1943: PetscCall(DMCompositeCreate(PETSC_COMM_SELF, pack));
1944: PetscCall(PetscLogEventBegin(ctx->events[13], 0, 0, 0, 0));
1945: PetscCall(PetscLogEventBegin(ctx->events[15], 0, 0, 0, 0));
1946: PetscCall(LandauDMCreateVMeshes(PETSC_COMM_SELF, dim, prefix, ctx, *pack)); // creates grids (Forest of AMR)
1947: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1948: /* create FEM */
1949: PetscCall(SetupDS(ctx->plex[grid], dim, grid, ctx));
1950: /* set initial state */
1951: PetscCall(DMCreateGlobalVector(ctx->plex[grid], &Xsub[grid]));
1952: PetscCall(PetscObjectSetName((PetscObject)Xsub[grid], "u_orig"));
1953: /* initial static refinement, no solve */
1954: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, 0, 1, ctx));
1955: /* forest refinement - forest goes in (if forest), plex comes out */
1956: if (ctx->use_p4est) {
1957: DM plex;
1958: PetscCall(adapt(grid, ctx, &Xsub[grid])); // forest goes in, plex comes out
1959: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, "-dm_landau_amr_dm_view")); // need to differentiate - todo
1960: PetscCall(VecViewFromOptions(Xsub[grid], NULL, "-dm_landau_amr_vec_view"));
1961: // convert to plex, all done with this level
1962: PetscCall(DMConvert(ctx->plex[grid], DMPLEX, &plex));
1963: PetscCall(DMDestroy(&ctx->plex[grid]));
1964: ctx->plex[grid] = plex;
1965: }
1966: #if !defined(LANDAU_SPECIES_MAJOR)
1967: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
1968: #else
1969: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
1970: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
1971: }
1972: #endif
1973: PetscCall(DMSetApplicationContext(ctx->plex[grid], ctx));
1974: }
1975: #if !defined(LANDAU_SPECIES_MAJOR)
1976: // stack the batched DMs, could do it all here!!! b_id=0
1977: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
1978: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
1979: }
1980: #endif
1981: // create ctx->mat_offset
1982: ctx->mat_offset[0] = 0;
1983: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1984: PetscInt n;
1985: PetscCall(VecGetLocalSize(Xsub[grid], &n));
1986: ctx->mat_offset[grid + 1] = ctx->mat_offset[grid] + n;
1987: }
1988: // creat DM & Jac
1989: PetscCall(DMSetApplicationContext(*pack, ctx));
1990: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
1991: PetscCall(DMCreateMatrix(*pack, &ctx->J));
1992: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
1993: PetscCall(MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
1994: PetscCall(MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
1995: PetscCall(PetscObjectSetName((PetscObject)ctx->J, "Jac"));
1996: // construct initial conditions in X
1997: PetscCall(DMCreateGlobalVector(*pack, X));
1998: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1999: PetscInt n;
2000: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2001: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2002: PetscScalar const *values;
2003: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2004: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, b_id, ctx->batch_sz, ctx));
2005: PetscCall(VecGetArrayRead(Xsub[grid], &values)); // Drop whole grid in Plex ordering
2006: for (int i = 0, idx = moffset; i < n; i++, idx++) PetscCall(VecSetValue(*X, idx, values[i], INSERT_VALUES));
2007: PetscCall(VecRestoreArrayRead(Xsub[grid], &values));
2008: }
2009: }
2010: // cleanup
2011: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(VecDestroy(&Xsub[grid]));
2012: /* check for correct matrix type */
2013: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
2014: PetscBool flg;
2015: if (ctx->deviceType == LANDAU_CUDA) {
2016: PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJCUSPARSE, MATMPIAIJCUSPARSE, MATAIJCUSPARSE, ""));
2017: 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'");
2018: } else if (ctx->deviceType == LANDAU_KOKKOS) {
2019: PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, MATAIJKOKKOS, ""));
2020: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
2021: 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'");
2022: #else
2023: 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'");
2024: #endif
2025: }
2026: }
2027: PetscCall(PetscLogEventEnd(ctx->events[15], 0, 0, 0, 0));
2029: // create field major ordering
2030: ctx->work_vec = NULL;
2031: ctx->plex_batch = NULL;
2032: ctx->batch_is = NULL;
2033: for (int i = 0; i < LANDAU_MAX_GRIDS; i++) grid_batch_is_inv[i] = NULL;
2034: PetscCall(PetscLogEventBegin(ctx->events[12], 0, 0, 0, 0));
2035: PetscCall(LandauCreateJacobianMatrix(comm, *X, grid_batch_is_inv, ctx));
2036: PetscCall(PetscLogEventEnd(ctx->events[12], 0, 0, 0, 0));
2038: // create AMR GPU assembly maps and static GPU data
2039: PetscCall(CreateStaticData(dim, grid_batch_is_inv, ctx));
2041: PetscCall(PetscLogEventEnd(ctx->events[13], 0, 0, 0, 0));
2043: // create mass matrix
2044: PetscCall(DMPlexLandauCreateMassMatrix(*pack, NULL));
2046: if (J) *J = ctx->J;
2048: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
2049: PetscContainer container;
2050: // cache ctx for KSP with batch/field major Jacobian ordering -ksp_type gmres/etc -dm_landau_jacobian_field_major_order
2051: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2052: PetscCall(PetscContainerSetPointer(container, (void *)ctx));
2053: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "LandauCtx", (PetscObject)container));
2054: PetscCall(PetscContainerDestroy(&container));
2055: // batch solvers need to map -- can batch solvers work
2056: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2057: PetscCall(PetscContainerSetPointer(container, (void *)ctx->plex_batch));
2058: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "plex_batch_is", (PetscObject)container));
2059: PetscCall(PetscContainerDestroy(&container));
2060: }
2061: // for batch solvers
2062: {
2063: PetscContainer container;
2064: PetscInt *pNf;
2065: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2066: PetscCall(PetscMalloc1(sizeof(*pNf), &pNf));
2067: *pNf = ctx->batch_sz;
2068: PetscCall(PetscContainerSetPointer(container, (void *)pNf));
2069: PetscCall(PetscContainerSetUserDestroy(container, MatrixNfDestroy));
2070: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "batch size", (PetscObject)container));
2071: PetscCall(PetscContainerDestroy(&container));
2072: }
2074: PetscFunctionReturn(PETSC_SUCCESS);
2075: }
2077: /*@
2078: DMPlexLandauAccess - Access to the distribution function with user callback
2080: Collective
2082: Input Parameters:
2083: . pack - the DMComposite
2084: + func - call back function
2085: . user_ctx - user context
2087: Input/Output Parameter:
2088: . X - Vector to data to
2090: Level: advanced
2092: .keywords: mesh
2093: .seealso: `DMPlexLandauCreateVelocitySpace()`
2094: @*/
2095: PetscErrorCode DMPlexLandauAccess(DM pack, Vec X, PetscErrorCode (*func)(DM, Vec, PetscInt, PetscInt, PetscInt, void *), void *user_ctx)
2096: {
2097: LandauCtx *ctx;
2098: PetscFunctionBegin;
2099: PetscCall(DMGetApplicationContext(pack, &ctx)); // uses ctx->num_grids; ctx->plex[grid]; ctx->batch_sz; ctx->mat_offset
2100: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2101: PetscInt dim, n;
2102: PetscCall(DMGetDimension(pack, &dim));
2103: for (PetscInt sp = ctx->species_offset[grid], i0 = 0; sp < ctx->species_offset[grid + 1]; sp++, i0++) {
2104: Vec vec;
2105: PetscInt vf[1] = {i0};
2106: IS vis;
2107: DM vdm;
2108: PetscCall(DMCreateSubDM(ctx->plex[grid], 1, vf, &vis, &vdm));
2109: PetscCall(DMSetApplicationContext(vdm, ctx)); // the user might want this
2110: PetscCall(DMCreateGlobalVector(vdm, &vec));
2111: PetscCall(VecGetSize(vec, &n));
2112: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2113: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2114: PetscCall(VecZeroEntries(vec));
2115: /* Add your data with 'dm' for species 'sp' to 'vec' */
2116: PetscCall(func(vdm, vec, i0, grid, b_id, user_ctx));
2117: /* add to global */
2118: PetscScalar const *values;
2119: const PetscInt *offsets;
2120: PetscCall(VecGetArrayRead(vec, &values));
2121: PetscCall(ISGetIndices(vis, &offsets));
2122: for (int i = 0; i < n; i++) PetscCall(VecSetValue(X, moffset + offsets[i], values[i], ADD_VALUES));
2123: PetscCall(VecRestoreArrayRead(vec, &values));
2124: PetscCall(ISRestoreIndices(vis, &offsets));
2125: } // batch
2126: PetscCall(VecDestroy(&vec));
2127: PetscCall(ISDestroy(&vis));
2128: PetscCall(DMDestroy(&vdm));
2129: }
2130: } // grid
2131: PetscFunctionReturn(PETSC_SUCCESS);
2132: }
2134: /*@
2135: DMPlexLandauDestroyVelocitySpace - Destroy a DMPlex velocity space mesh
2137: Collective
2139: Input/Output Parameters:
2140: . dm - the dm to destroy
2142: Level: beginner
2144: .keywords: mesh
2145: .seealso: `DMPlexLandauCreateVelocitySpace()`
2146: @*/
2147: PetscErrorCode DMPlexLandauDestroyVelocitySpace(DM *dm)
2148: {
2149: LandauCtx *ctx;
2150: PetscFunctionBegin;
2151: PetscCall(DMGetApplicationContext(*dm, &ctx));
2152: PetscCall(MatDestroy(&ctx->M));
2153: PetscCall(MatDestroy(&ctx->J));
2154: for (PetscInt ii = 0; ii < ctx->num_species; ii++) PetscCall(PetscFEDestroy(&ctx->fe[ii]));
2155: PetscCall(ISDestroy(&ctx->batch_is));
2156: PetscCall(VecDestroy(&ctx->work_vec));
2157: PetscCall(VecScatterDestroy(&ctx->plex_batch));
2158: if (ctx->deviceType == LANDAU_CUDA) {
2159: #if defined(PETSC_HAVE_CUDA)
2160: PetscCall(LandauCUDAStaticDataClear(&ctx->SData_d));
2161: #else
2162: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "cuda");
2163: #endif
2164: } else if (ctx->deviceType == LANDAU_KOKKOS) {
2165: #if defined(PETSC_HAVE_KOKKOS_KERNELS)
2166: PetscCall(LandauKokkosStaticDataClear(&ctx->SData_d));
2167: #else
2168: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
2169: #endif
2170: } else {
2171: if (ctx->SData_d.x) { /* in a CPU run */
2172: 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;
2173: 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;
2174: PetscCall(PetscFree4(ww, xx, yy, invJ));
2175: if (zz) PetscCall(PetscFree(zz));
2176: if (coo_elem_offsets) {
2177: PetscCall(PetscFree3(coo_elem_offsets, coo_elem_fullNb, coo_elem_point_offsets)); // could be NULL
2178: }
2179: PetscCall(PetscFree4(ctx->SData_d.alpha, ctx->SData_d.beta, ctx->SData_d.invMass, ctx->SData_d.lambdas));
2180: }
2181: }
2183: if (ctx->times[LANDAU_MATRIX_TOTAL] > 0) { // OMP timings
2184: PetscCall(PetscPrintf(ctx->comm, "TSStep N 1.0 %10.3e\n", ctx->times[LANDAU_EX2_TSSOLVE]));
2185: 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));
2186: PetscCall(PetscPrintf(ctx->comm, "3: Landau: %10.3e\n", ctx->times[LANDAU_MATRIX_TOTAL]));
2187: PetscCall(PetscPrintf(ctx->comm, "Landau Jacobian %" PetscInt_FMT " 1.0 %10.3e\n", (PetscInt)ctx->times[LANDAU_JACOBIAN_COUNT], ctx->times[LANDAU_JACOBIAN]));
2188: PetscCall(PetscPrintf(ctx->comm, "Landau Operator N 1.0 %10.3e\n", ctx->times[LANDAU_OPERATOR]));
2189: PetscCall(PetscPrintf(ctx->comm, "Landau Mass N 1.0 %10.3e\n", ctx->times[LANDAU_MASS]));
2190: PetscCall(PetscPrintf(ctx->comm, " Jac-f-df (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_F_DF]));
2191: PetscCall(PetscPrintf(ctx->comm, " Kernel (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_KERNEL]));
2192: PetscCall(PetscPrintf(ctx->comm, "MatLUFactorNum X 1.0 %10.3e\n", ctx->times[KSP_FACTOR]));
2193: PetscCall(PetscPrintf(ctx->comm, "MatSolve X 1.0 %10.3e\n", ctx->times[KSP_SOLVE]));
2194: }
2195: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMDestroy(&ctx->plex[grid]));
2196: PetscCall(PetscFree(ctx));
2197: PetscCall(DMDestroy(dm));
2198: PetscFunctionReturn(PETSC_SUCCESS);
2199: }
2201: /* < v, ru > */
2202: 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)
2203: {
2204: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2205: f0[0] = u[ii];
2206: }
2208: /* < v, ru > */
2209: 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)
2210: {
2211: PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]);
2212: f0[0] = x[jj] * u[ii]; /* x momentum */
2213: }
2215: 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)
2216: {
2217: PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]);
2218: double tmp1 = 0.;
2219: for (i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2220: f0[0] = tmp1 * u[ii];
2221: }
2223: static PetscErrorCode gamma_n_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *actx)
2224: {
2225: const PetscReal *c2_0_arr = ((PetscReal *)actx);
2226: const PetscReal c02 = c2_0_arr[0];
2228: PetscFunctionBegin;
2229: for (int s = 0; s < Nf; s++) {
2230: PetscReal tmp1 = 0.;
2231: for (int i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2232: #if defined(PETSC_USE_DEBUG)
2233: u[s] = PetscSqrtReal(1. + tmp1 / c02); // u[0] = PetscSqrtReal(1. + xx);
2234: #else
2235: {
2236: PetscReal xx = tmp1 / c02;
2237: u[s] = xx / (PetscSqrtReal(1. + xx) + 1.); // better conditioned = xx/(PetscSqrtReal(1. + xx) + 1.)
2238: }
2239: #endif
2240: }
2241: PetscFunctionReturn(PETSC_SUCCESS);
2242: }
2244: /* < v, ru > */
2245: 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)
2246: {
2247: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2248: f0[0] = 2. * PETSC_PI * x[0] * u[ii];
2249: }
2251: /* < v, ru > */
2252: 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)
2253: {
2254: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2255: f0[0] = 2. * PETSC_PI * x[0] * x[1] * u[ii];
2256: }
2258: 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)
2259: {
2260: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2261: f0[0] = 2. * PETSC_PI * x[0] * (x[0] * x[0] + x[1] * x[1]) * u[ii];
2262: }
2264: /*@
2265: DMPlexLandauPrintNorms - collects moments and prints them
2267: Collective
2269: Input Parameters:
2270: + X - the state
2271: - stepi - current step to print
2273: Level: beginner
2275: .keywords: mesh
2276: .seealso: `DMPlexLandauCreateVelocitySpace()`
2277: @*/
2278: PetscErrorCode DMPlexLandauPrintNorms(Vec X, PetscInt stepi)
2279: {
2280: LandauCtx *ctx;
2281: PetscDS prob;
2282: DM pack;
2283: PetscInt cStart, cEnd, dim, ii, i0, nDMs;
2284: PetscScalar xmomentumtot = 0, ymomentumtot = 0, zmomentumtot = 0, energytot = 0, densitytot = 0, tt[LANDAU_MAX_SPECIES];
2285: PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES];
2286: Vec *globXArray;
2288: PetscFunctionBegin;
2289: PetscCall(VecGetDM(X, &pack));
2290: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Vector has no DM");
2291: PetscCall(DMGetDimension(pack, &dim));
2292: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " not in [2,3]", dim);
2293: PetscCall(DMGetApplicationContext(pack, &ctx));
2294: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2295: /* print momentum and energy */
2296: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
2297: 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);
2298: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
2299: PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, globXArray));
2300: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2301: Vec Xloc = globXArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2302: PetscCall(DMGetDS(ctx->plex[grid], &prob));
2303: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
2304: PetscScalar user[2] = {(PetscScalar)i0, (PetscScalar)ctx->charges[ii]};
2305: PetscCall(PetscDSSetConstants(prob, 2, user));
2306: if (dim == 2) { /* 2/3X + 3V (cylindrical coordinates) */
2307: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rden));
2308: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2309: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2310: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rmom));
2311: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2312: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2313: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rv2));
2314: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2315: energy[ii] = tt[0] * 0.5 * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2316: zmomentumtot += zmomentum[ii];
2317: energytot += energy[ii];
2318: densitytot += density[ii];
2319: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3" PetscInt_FMT ") species-%" PetscInt_FMT ": charge density= %20.13e z-momentum= %20.13e energy= %20.13e", stepi, ii, (double)PetscRealPart(density[ii]), (double)PetscRealPart(zmomentum[ii]), (double)PetscRealPart(energy[ii])));
2320: } else { /* 2/3Xloc + 3V */
2321: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_den));
2322: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2323: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2324: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_mom));
2325: user[1] = 0;
2326: PetscCall(PetscDSSetConstants(prob, 2, user));
2327: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2328: xmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2329: user[1] = 1;
2330: PetscCall(PetscDSSetConstants(prob, 2, user));
2331: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2332: ymomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2333: user[1] = 2;
2334: PetscCall(PetscDSSetConstants(prob, 2, user));
2335: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2336: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2337: if (ctx->use_relativistic_corrections) {
2338: /* gamma * M * f */
2339: if (ii == 0 && grid == 0) { // do all at once
2340: Vec Mf, globGamma, *globMfArray, *globGammaArray;
2341: PetscErrorCode (*gammaf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {gamma_n_f};
2342: PetscReal *c2_0[1], data[1];
2344: PetscCall(VecDuplicate(X, &globGamma));
2345: PetscCall(VecDuplicate(X, &Mf));
2346: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globMfArray));
2347: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globGammaArray));
2348: /* M * f */
2349: PetscCall(MatMult(ctx->M, X, Mf));
2350: /* gamma */
2351: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2352: 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
2353: Vec v1 = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2354: data[0] = PetscSqr(C_0(ctx->v_0));
2355: c2_0[0] = &data[0];
2356: PetscCall(DMProjectFunction(ctx->plex[grid], 0., gammaf, (void **)c2_0, INSERT_ALL_VALUES, v1));
2357: }
2358: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2359: /* gamma * Mf */
2360: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2361: PetscCall(DMCompositeGetAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2362: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice
2363: PetscInt Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], N, bs;
2364: Vec Mfsub = globMfArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], Gsub = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], v1, v2;
2365: // get each component
2366: PetscCall(VecGetSize(Mfsub, &N));
2367: PetscCall(VecCreate(ctx->comm, &v1));
2368: PetscCall(VecSetSizes(v1, PETSC_DECIDE, N / Nf));
2369: PetscCall(VecCreate(ctx->comm, &v2));
2370: PetscCall(VecSetSizes(v2, PETSC_DECIDE, N / Nf));
2371: PetscCall(VecSetFromOptions(v1)); // ???
2372: PetscCall(VecSetFromOptions(v2));
2373: // get each component
2374: PetscCall(VecGetBlockSize(Gsub, &bs));
2375: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT " in Gsub", bs, Nf);
2376: PetscCall(VecGetBlockSize(Mfsub, &bs));
2377: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT, bs, Nf);
2378: for (int i = 0, ix = ctx->species_offset[grid]; i < Nf; i++, ix++) {
2379: PetscScalar val;
2380: PetscCall(VecStrideGather(Gsub, i, v1, INSERT_VALUES)); // this is not right -- TODO
2381: PetscCall(VecStrideGather(Mfsub, i, v2, INSERT_VALUES));
2382: PetscCall(VecDot(v1, v2, &val));
2383: energy[ix] = PetscRealPart(val) * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ix];
2384: }
2385: PetscCall(VecDestroy(&v1));
2386: PetscCall(VecDestroy(&v2));
2387: } /* grids */
2388: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2389: PetscCall(DMCompositeRestoreAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2390: PetscCall(PetscFree(globGammaArray));
2391: PetscCall(PetscFree(globMfArray));
2392: PetscCall(VecDestroy(&globGamma));
2393: PetscCall(VecDestroy(&Mf));
2394: }
2395: } else {
2396: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_v2));
2397: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2398: energy[ii] = 0.5 * tt[0] * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2399: }
2400: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3" PetscInt_FMT ") species %" PetscInt_FMT ": density=%20.13e, x-momentum=%20.13e, y-momentum=%20.13e, z-momentum=%20.13e, energy=%21.13e", stepi, ii, (double)PetscRealPart(density[ii]), (double)PetscRealPart(xmomentum[ii]), (double)PetscRealPart(ymomentum[ii]), (double)PetscRealPart(zmomentum[ii]), (double)PetscRealPart(energy[ii])));
2401: xmomentumtot += xmomentum[ii];
2402: ymomentumtot += ymomentum[ii];
2403: zmomentumtot += zmomentum[ii];
2404: energytot += energy[ii];
2405: densitytot += density[ii];
2406: }
2407: if (ctx->num_species > 1) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2408: }
2409: }
2410: PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, globXArray));
2411: PetscCall(PetscFree(globXArray));
2412: /* totals */
2413: PetscCall(DMPlexGetHeightStratum(ctx->plex[0], 0, &cStart, &cEnd));
2414: if (ctx->num_species > 1) {
2415: if (dim == 2) {
2416: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\t%3" PetscInt_FMT ") Total: charge density=%21.13e, momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %" PetscInt_FMT " cells on electron grid)", stepi, (double)PetscRealPart(densitytot), (double)PetscRealPart(zmomentumtot), (double)PetscRealPart(energytot),
2417: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2418: } else {
2419: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\t%3" PetscInt_FMT ") Total: charge density=%21.13e, x-momentum=%21.13e, y-momentum=%21.13e, z-momentum=%21.13e, energy=%21.13e (m_i[0]/m_e = %g, %" PetscInt_FMT " cells)", stepi, (double)PetscRealPart(densitytot), (double)PetscRealPart(xmomentumtot), (double)PetscRealPart(ymomentumtot), (double)PetscRealPart(zmomentumtot), (double)PetscRealPart(energytot),
2420: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2421: }
2422: } else PetscCall(PetscPrintf(PETSC_COMM_WORLD, " -- %" PetscInt_FMT " cells", cEnd - cStart));
2423: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2424: PetscFunctionReturn(PETSC_SUCCESS);
2425: }
2427: /*@
2428: DMPlexLandauCreateMassMatrix - Create mass matrix for Landau in Plex space (not field major order of Jacobian)
2429: - puts mass matrix into ctx->M
2431: Collective
2433: Input Parameter:
2434: . pack - the DM object. Puts matrix in Landau context M field
2436: Output Parameter:
2437: . Amat - The mass matrix (optional), mass matrix is added to the DM context
2439: Level: beginner
2441: .keywords: mesh
2442: .seealso: `DMPlexLandauCreateVelocitySpace()`
2443: @*/
2444: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat)
2445: {
2446: DM mass_pack, massDM[LANDAU_MAX_GRIDS];
2447: PetscDS prob;
2448: PetscInt ii, dim, N1 = 1, N2;
2449: LandauCtx *ctx;
2450: Mat packM, subM[LANDAU_MAX_GRIDS];
2452: PetscFunctionBegin;
2455: PetscCall(DMGetApplicationContext(pack, &ctx));
2456: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2457: PetscCall(PetscLogEventBegin(ctx->events[14], 0, 0, 0, 0));
2458: PetscCall(DMGetDimension(pack, &dim));
2459: PetscCall(DMCompositeCreate(PetscObjectComm((PetscObject)pack), &mass_pack));
2460: /* create pack mass matrix */
2461: for (PetscInt grid = 0, ix = 0; grid < ctx->num_grids; grid++) {
2462: PetscCall(DMClone(ctx->plex[grid], &massDM[grid]));
2463: PetscCall(DMCopyFields(ctx->plex[grid], massDM[grid]));
2464: PetscCall(DMCreateDS(massDM[grid]));
2465: PetscCall(DMGetDS(massDM[grid], &prob));
2466: for (ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) {
2467: if (dim == 3) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_1, NULL, NULL, NULL));
2468: else PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_r, NULL, NULL, NULL));
2469: }
2470: #if !defined(LANDAU_SPECIES_MAJOR)
2471: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2472: #else
2473: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2474: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2475: }
2476: #endif
2477: PetscCall(DMCreateMatrix(massDM[grid], &subM[grid]));
2478: }
2479: #if !defined(LANDAU_SPECIES_MAJOR)
2480: // stack the batched DMs
2481: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2482: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2483: }
2484: #endif
2485: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2486: PetscCall(DMCreateMatrix(mass_pack, &packM));
2487: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2488: PetscCall(MatSetOption(packM, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2489: PetscCall(MatSetOption(packM, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2490: PetscCall(DMDestroy(&mass_pack));
2491: /* make mass matrix for each block */
2492: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2493: Vec locX;
2494: DM plex = massDM[grid];
2495: PetscCall(DMGetLocalVector(plex, &locX));
2496: /* Mass matrix is independent of the input, so no need to fill locX */
2497: PetscCall(DMPlexSNESComputeJacobianFEM(plex, locX, subM[grid], subM[grid], ctx));
2498: PetscCall(DMRestoreLocalVector(plex, &locX));
2499: PetscCall(DMDestroy(&massDM[grid]));
2500: }
2501: PetscCall(MatGetSize(ctx->J, &N1, NULL));
2502: PetscCall(MatGetSize(packM, &N2, NULL));
2503: PetscCheck(N1 == N2, PetscObjectComm((PetscObject)pack), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %" PetscInt_FMT ", |Mass|=%" PetscInt_FMT, N1, N2);
2504: /* assemble block diagonals */
2505: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2506: Mat B = subM[grid];
2507: PetscInt nloc, nzl, *colbuf, COL_BF_SIZE = 1024, row;
2508: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2509: PetscCall(MatGetSize(B, &nloc, NULL));
2510: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2511: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2512: const PetscInt *cols;
2513: const PetscScalar *vals;
2514: for (int i = 0; i < nloc; i++) {
2515: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
2516: if (nzl > COL_BF_SIZE) {
2517: PetscCall(PetscFree(colbuf));
2518: PetscCall(PetscInfo(pack, "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl));
2519: COL_BF_SIZE = nzl;
2520: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2521: }
2522: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
2523: for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
2524: row = i + moffset;
2525: PetscCall(MatSetValues(packM, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
2526: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
2527: }
2528: }
2529: PetscCall(PetscFree(colbuf));
2530: }
2531: // cleanup
2532: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
2533: PetscCall(MatAssemblyBegin(packM, MAT_FINAL_ASSEMBLY));
2534: PetscCall(MatAssemblyEnd(packM, MAT_FINAL_ASSEMBLY));
2535: PetscCall(PetscObjectSetName((PetscObject)packM, "mass"));
2536: PetscCall(MatViewFromOptions(packM, NULL, "-dm_landau_mass_view"));
2537: ctx->M = packM;
2538: if (Amat) *Amat = packM;
2539: PetscCall(PetscLogEventEnd(ctx->events[14], 0, 0, 0, 0));
2540: PetscFunctionReturn(PETSC_SUCCESS);
2541: }
2543: /*@
2544: DMPlexLandauIFunction - TS residual calculation, confusingly this computes the Jacobian w/o mass
2546: Collective
2548: Input Parameters:
2549: + TS - The time stepping context
2550: . time_dummy - current time (not used)
2551: . X - Current state
2552: . X_t - Time derivative of current state
2553: - actx - Landau context
2555: Output Parameter:
2556: . F - The residual
2558: Level: beginner
2560: .keywords: mesh
2561: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIJacobian()`
2562: @*/
2563: PetscErrorCode DMPlexLandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx)
2564: {
2565: LandauCtx *ctx = (LandauCtx *)actx;
2566: PetscInt dim;
2567: DM pack;
2568: #if defined(PETSC_HAVE_THREADSAFETY)
2569: double starttime, endtime;
2570: #endif
2571: PetscObjectState state;
2573: PetscFunctionBegin;
2574: PetscCall(TSGetDM(ts, &pack));
2575: PetscCall(DMGetApplicationContext(pack, &ctx));
2576: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2577: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2578: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2579: PetscCall(PetscLogEventBegin(ctx->events[0], 0, 0, 0, 0));
2580: #if defined(PETSC_HAVE_THREADSAFETY)
2581: starttime = MPI_Wtime();
2582: #endif
2583: PetscCall(DMGetDimension(pack, &dim));
2584: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2585: if (state != ctx->norm_state) {
2586: PetscCall(PetscInfo(ts, "Create Landau Jacobian t=%g J.state %" PetscInt64_FMT " --> %" PetscInt64_FMT "\n", (double)time_dummy, ctx->norm_state, state));
2587: PetscCall(MatZeroEntries(ctx->J));
2588: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, 0.0, (void *)ctx));
2589: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_jacobian_view"));
2590: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2591: ctx->norm_state = state;
2592: } else {
2593: PetscCall(PetscInfo(ts, "WARNING Skip forming Jacobian, has not changed %" PetscInt64_FMT "\n", state));
2594: }
2595: /* mat vec for op */
2596: PetscCall(MatMult(ctx->J, X, F)); /* C*f */
2597: /* add time term */
2598: if (X_t) PetscCall(MatMultAdd(ctx->M, X_t, F, F));
2599: #if defined(PETSC_HAVE_THREADSAFETY)
2600: if (ctx->stage) {
2601: endtime = MPI_Wtime();
2602: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2603: ctx->times[LANDAU_JACOBIAN] += (endtime - starttime);
2604: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2605: ctx->times[LANDAU_JACOBIAN_COUNT] += 1;
2606: }
2607: #endif
2608: PetscCall(PetscLogEventEnd(ctx->events[0], 0, 0, 0, 0));
2609: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2610: if (ctx->stage) PetscCall(PetscLogStagePop());
2611: PetscFunctionReturn(PETSC_SUCCESS);
2612: }
2614: /*@
2615: DMPlexLandauIJacobian - TS Jacobian construction, confusingly this adds mass
2617: Collective
2619: Input Parameters:
2620: + TS - The time stepping context
2621: . time_dummy - current time (not used)
2622: . X - Current state
2623: . U_tdummy - Time derivative of current state (not used)
2624: . shift - shift for du/dt term
2625: - actx - Landau context
2627: Output Parameters:
2628: + Amat - Jacobian
2629: - Pmat - same as Amat
2631: Level: beginner
2633: .keywords: mesh
2634: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIFunction()`
2635: @*/
2636: PetscErrorCode DMPlexLandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx)
2637: {
2638: LandauCtx *ctx = NULL;
2639: PetscInt dim;
2640: DM pack;
2641: #if defined(PETSC_HAVE_THREADSAFETY)
2642: double starttime, endtime;
2643: #endif
2644: PetscObjectState state;
2646: PetscFunctionBegin;
2647: PetscCall(TSGetDM(ts, &pack));
2648: PetscCall(DMGetApplicationContext(pack, &ctx));
2649: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2650: PetscCheck(Amat == Pmat && Amat == ctx->J, ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J");
2651: PetscCall(DMGetDimension(pack, &dim));
2652: /* get collision Jacobian into A */
2653: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2654: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2655: PetscCall(PetscLogEventBegin(ctx->events[9], 0, 0, 0, 0));
2656: #if defined(PETSC_HAVE_THREADSAFETY)
2657: starttime = MPI_Wtime();
2658: #endif
2659: PetscCall(PetscInfo(ts, "Adding mass to Jacobian t=%g, shift=%g\n", (double)time_dummy, (double)shift));
2660: PetscCheck(shift != 0.0, ctx->comm, PETSC_ERR_PLIB, "zero shift");
2661: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2662: PetscCheck(state == ctx->norm_state, ctx->comm, PETSC_ERR_PLIB, "wrong state, %" PetscInt64_FMT " %" PetscInt64_FMT "", ctx->norm_state, state);
2663: if (!ctx->use_matrix_mass) {
2664: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, shift, (void *)ctx));
2665: } else { /* add mass */
2666: PetscCall(MatAXPY(Pmat, shift, ctx->M, SAME_NONZERO_PATTERN));
2667: }
2668: #if defined(PETSC_HAVE_THREADSAFETY)
2669: if (ctx->stage) {
2670: endtime = MPI_Wtime();
2671: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2672: ctx->times[LANDAU_MASS] += (endtime - starttime);
2673: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2674: }
2675: #endif
2676: PetscCall(PetscLogEventEnd(ctx->events[9], 0, 0, 0, 0));
2677: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2678: if (ctx->stage) PetscCall(PetscLogStagePop());
2679: PetscFunctionReturn(PETSC_SUCCESS);
2680: }