Actual source code: plexland.c
1: #include <../src/mat/impls/aij/seq/aij.h>
2: #include <petsc/private/dmpleximpl.h>
3: #include <petsclandau.h>
4: #include <petscts.h>
5: #include <petscdmforest.h>
6: #include <petscdmcomposite.h>
8: /* Landau collision operator */
10: /* relativistic terms */
11: #if defined(PETSC_USE_REAL_SINGLE)
12: #define SPEED_OF_LIGHT 2.99792458e8F
13: #define C_0(v0) (SPEED_OF_LIGHT / v0) /* needed for relativistic tensor on all architectures */
14: #else
15: #define SPEED_OF_LIGHT 2.99792458e8
16: #define C_0(v0) (SPEED_OF_LIGHT / v0) /* needed for relativistic tensor on all architectures */
17: #endif
19: #include "land_tensors.h"
21: #if defined(PETSC_HAVE_OPENMP)
22: #include <omp.h>
23: #endif
25: static PetscErrorCode LandauGPUMapsDestroy(void *ptr)
26: {
27: P4estVertexMaps *maps = (P4estVertexMaps *)ptr;
28: PetscFunctionBegin;
29: // free device data
30: if (maps[0].deviceType != LANDAU_CPU) {
31: #if defined(PETSC_HAVE_KOKKOS)
32: if (maps[0].deviceType == LANDAU_KOKKOS) {
33: PetscCall(LandauKokkosDestroyMatMaps(maps, maps[0].numgrids)); // implies Kokkos does
34: }
35: #endif
36: }
37: // free host data
38: for (PetscInt grid = 0; grid < maps[0].numgrids; grid++) {
39: PetscCall(PetscFree(maps[grid].c_maps));
40: PetscCall(PetscFree(maps[grid].gIdx));
41: }
42: PetscCall(PetscFree(maps));
44: PetscFunctionReturn(PETSC_SUCCESS);
45: }
46: static PetscErrorCode energy_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
47: {
48: PetscReal v2 = 0;
49: PetscFunctionBegin;
50: /* compute v^2 / 2 */
51: for (int i = 0; i < dim; ++i) v2 += x[i] * x[i];
52: /* evaluate the Maxwellian */
53: u[0] = v2 / 2;
54: PetscFunctionReturn(PETSC_SUCCESS);
55: }
57: /* needs double */
58: static PetscErrorCode gamma_m1_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
59: {
60: PetscReal *c2_0_arr = ((PetscReal *)actx);
61: double u2 = 0, c02 = (double)*c2_0_arr, xx;
63: PetscFunctionBegin;
64: /* compute u^2 / 2 */
65: for (int i = 0; i < dim; ++i) u2 += x[i] * x[i];
66: /* gamma - 1 = g_eps, for conditioning and we only take derivatives */
67: xx = u2 / c02;
68: #if defined(PETSC_USE_DEBUG)
69: u[0] = PetscSqrtReal(1. + xx);
70: #else
71: u[0] = xx / (PetscSqrtReal(1. + xx) + 1.) - 1.; // better conditioned. -1 might help condition and only used for derivative
72: #endif
73: PetscFunctionReturn(PETSC_SUCCESS);
74: }
76: /*
77: LandauFormJacobian_Internal - Evaluates Jacobian matrix.
79: Input Parameters:
80: . globX - input vector
81: . actx - optional user-defined context
82: . dim - dimension
84: Output Parameter:
85: . J0acP - Jacobian matrix filled, not created
86: */
87: static PetscErrorCode LandauFormJacobian_Internal(Vec a_X, Mat JacP, const PetscInt dim, PetscReal shift, void *a_ctx)
88: {
89: LandauCtx *ctx = (LandauCtx *)a_ctx;
90: PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nb;
91: PetscQuadrature quad;
92: PetscReal Eq_m[LANDAU_MAX_SPECIES]; // could be static data w/o quench (ex2)
93: PetscScalar *cellClosure = NULL;
94: const PetscScalar *xdata = NULL;
95: PetscDS prob;
96: PetscContainer container;
97: P4estVertexMaps *maps;
98: Mat subJ[LANDAU_MAX_GRIDS * LANDAU_MAX_BATCH_SZ];
100: PetscFunctionBegin;
103: PetscAssertPointer(ctx, 5);
104: /* check for matrix container for GPU assembly. Support CPU assembly for debugging */
105: PetscCheck(ctx->plex[0] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
106: PetscCall(PetscLogEventBegin(ctx->events[10], 0, 0, 0, 0));
107: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
108: PetscCall(PetscObjectQuery((PetscObject)JacP, "assembly_maps", (PetscObject *)&container));
109: if (container) {
110: PetscCheck(ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "maps but no GPU assembly");
111: PetscCall(PetscContainerGetPointer(container, (void **)&maps));
112: PetscCheck(maps, ctx->comm, PETSC_ERR_ARG_WRONG, "empty GPU matrix container");
113: for (PetscInt i = 0; i < ctx->num_grids * ctx->batch_sz; i++) subJ[i] = NULL;
114: } else {
115: PetscCheck(!ctx->gpu_assembly, ctx->comm, PETSC_ERR_ARG_WRONG, "No maps but GPU assembly");
116: for (PetscInt tid = 0; tid < ctx->batch_sz; tid++) {
117: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCreateMatrix(ctx->plex[grid], &subJ[LAND_PACK_IDX(tid, grid)]));
118: }
119: maps = NULL;
120: }
121: // 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)
122: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
123: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
124: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
125: PetscCheck(Nq <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nq, LANDAU_MAX_NQND);
126: PetscCheck(Nb <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nb = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nb, LANDAU_MAX_NQND);
127: // get metadata for collecting dynamic data
128: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
129: PetscInt cStart, cEnd;
130: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
131: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
132: numCells[grid] = cEnd - cStart; // grids can have different topology
133: }
134: PetscCall(PetscLogEventEnd(ctx->events[10], 0, 0, 0, 0));
135: 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 */
136: DM pack;
137: PetscCall(VecGetDM(a_X, &pack));
138: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "pack has no DM");
139: PetscCall(PetscLogEventBegin(ctx->events[1], 0, 0, 0, 0));
140: for (PetscInt fieldA = 0; fieldA < ctx->num_species; fieldA++) {
141: Eq_m[fieldA] = ctx->Ez * ctx->t_0 * ctx->charges[fieldA] / (ctx->v_0 * ctx->masses[fieldA]); /* normalize dimensionless */
142: if (dim == 2) Eq_m[fieldA] *= 2 * PETSC_PI; /* add the 2pi term that is not in Landau */
143: }
144: if (!ctx->gpu_assembly) {
145: Vec *locXArray, *globXArray;
146: PetscScalar *cellClosure_it;
147: PetscInt cellClosure_sz = 0, nDMs, Nf[LANDAU_MAX_GRIDS];
148: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
149: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
150: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
151: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
152: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
153: }
154: /* count cellClosure size */
155: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
156: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) cellClosure_sz += Nb * Nf[grid] * numCells[grid];
157: PetscCall(PetscMalloc1(cellClosure_sz * ctx->batch_sz, &cellClosure));
158: cellClosure_it = cellClosure;
159: PetscCall(PetscMalloc(sizeof(*locXArray) * nDMs, &locXArray));
160: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
161: PetscCall(DMCompositeGetLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
162: PetscCall(DMCompositeGetAccessArray(pack, a_X, nDMs, NULL, globXArray));
163: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP (once)
164: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
165: Vec locX = locXArray[LAND_PACK_IDX(b_id, grid)], globX = globXArray[LAND_PACK_IDX(b_id, grid)], locX2;
166: PetscInt cStart, cEnd, ei;
167: PetscCall(VecDuplicate(locX, &locX2));
168: PetscCall(DMGlobalToLocalBegin(ctx->plex[grid], globX, INSERT_VALUES, locX2));
169: PetscCall(DMGlobalToLocalEnd(ctx->plex[grid], globX, INSERT_VALUES, locX2));
170: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
171: for (ei = cStart; ei < cEnd; ++ei) {
172: PetscScalar *coef = NULL;
173: PetscCall(DMPlexVecGetClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
174: PetscCall(PetscMemcpy(cellClosure_it, coef, Nb * Nf[grid] * sizeof(*cellClosure_it))); /* change if LandauIPReal != PetscScalar */
175: PetscCall(DMPlexVecRestoreClosure(ctx->plex[grid], section[grid], locX2, ei, NULL, &coef));
176: cellClosure_it += Nb * Nf[grid];
177: }
178: PetscCall(VecDestroy(&locX2));
179: }
180: }
181: 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),
182: cellClosure_sz * ctx->batch_sz);
183: PetscCall(DMCompositeRestoreLocalAccessArray(pack, a_X, nDMs, NULL, locXArray));
184: PetscCall(DMCompositeRestoreAccessArray(pack, a_X, nDMs, NULL, globXArray));
185: PetscCall(PetscFree(locXArray));
186: PetscCall(PetscFree(globXArray));
187: xdata = NULL;
188: } else {
189: PetscMemType mtype;
190: if (ctx->jacobian_field_major_order) { // get data in batch ordering
191: PetscCall(VecScatterBegin(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
192: PetscCall(VecScatterEnd(ctx->plex_batch, a_X, ctx->work_vec, INSERT_VALUES, SCATTER_FORWARD));
193: PetscCall(VecGetArrayReadAndMemType(ctx->work_vec, &xdata, &mtype));
194: } else {
195: PetscCall(VecGetArrayReadAndMemType(a_X, &xdata, &mtype));
196: }
197: PetscCheck(mtype == PETSC_MEMTYPE_HOST || ctx->deviceType != LANDAU_CPU, ctx->comm, PETSC_ERR_ARG_WRONG, "CPU run with device data: use -mat_type aij");
198: cellClosure = NULL;
199: }
200: PetscCall(PetscLogEventEnd(ctx->events[1], 0, 0, 0, 0));
201: } else xdata = cellClosure = NULL;
203: /* do it */
204: if (ctx->deviceType == LANDAU_KOKKOS) {
205: #if defined(PETSC_HAVE_KOKKOS)
206: PetscCall(LandauKokkosJacobian(ctx->plex, Nq, Nb, ctx->batch_sz, ctx->num_grids, numCells, Eq_m, cellClosure, xdata, &ctx->SData_d, shift, ctx->events, ctx->mat_offset, ctx->species_offset, subJ, JacP));
207: #else
208: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
209: #endif
210: } else { /* CPU version */
211: PetscTabulation *Tf; // used for CPU and print info. Same on all grids and all species
212: PetscInt ip_offset[LANDAU_MAX_GRIDS + 1], ipf_offset[LANDAU_MAX_GRIDS + 1], elem_offset[LANDAU_MAX_GRIDS + 1], IPf_sz_glb, IPf_sz_tot, num_grids = ctx->num_grids, Nf[LANDAU_MAX_GRIDS];
213: PetscReal *ff, *dudx, *dudy, *dudz, *invJ_a = (PetscReal *)ctx->SData_d.invJ, *xx = (PetscReal *)ctx->SData_d.x, *yy = (PetscReal *)ctx->SData_d.y, *zz = (PetscReal *)ctx->SData_d.z, *ww = (PetscReal *)ctx->SData_d.w;
214: PetscReal *nu_alpha = (PetscReal *)ctx->SData_d.alpha, *nu_beta = (PetscReal *)ctx->SData_d.beta, *invMass = (PetscReal *)ctx->SData_d.invMass;
215: PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
216: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
217: PetscScalar *coo_vals = NULL;
218: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
219: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
220: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
221: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
222: }
223: /* count IPf size, etc */
224: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
225: const PetscReal *const BB = Tf[0]->T[0], *const DD = Tf[0]->T[1];
226: ip_offset[0] = ipf_offset[0] = elem_offset[0] = 0;
227: for (PetscInt grid = 0; grid < num_grids; grid++) {
228: PetscInt nfloc = ctx->species_offset[grid + 1] - ctx->species_offset[grid];
229: elem_offset[grid + 1] = elem_offset[grid] + numCells[grid];
230: ip_offset[grid + 1] = ip_offset[grid] + numCells[grid] * Nq;
231: ipf_offset[grid + 1] = ipf_offset[grid] + Nq * nfloc * numCells[grid];
232: }
233: IPf_sz_glb = ipf_offset[num_grids];
234: IPf_sz_tot = IPf_sz_glb * ctx->batch_sz;
235: // prep COO
236: {
237: PetscCall(PetscMalloc1(ctx->SData_d.coo_size, &coo_vals)); // allocate every time?
238: PetscCall(PetscInfo(ctx->plex[0], "COO Allocate %" PetscInt_FMT " values\n", (PetscInt)ctx->SData_d.coo_size));
239: }
240: if (shift == 0.0) { /* compute dynamic data f and df and init data for Jacobian */
241: #if defined(PETSC_HAVE_THREADSAFETY)
242: double starttime, endtime;
243: starttime = MPI_Wtime();
244: #endif
245: PetscCall(PetscLogEventBegin(ctx->events[8], 0, 0, 0, 0));
246: PetscCall(PetscMalloc4(IPf_sz_tot, &ff, IPf_sz_tot, &dudx, IPf_sz_tot, &dudy, dim == 3 ? IPf_sz_tot : 0, &dudz));
247: // F df/dx
248: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
249: 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
250: // find my grid:
251: PetscInt grid = 0;
252: while (b_elem_idx >= elem_offset[grid + 1]) grid++; // yuck search for grid
253: {
254: 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];
255: 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];
256: PetscScalar *coef, coef_buff[LANDAU_MAX_SPECIES * LANDAU_MAX_NQND];
257: PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim]; // ingJ is static data on batch 0
258: PetscInt b, f, q;
259: if (cellClosure) {
260: coef = &cellClosure[b_id * IPf_sz_glb + ipf_offset[grid] + loc_elem * Nb * loc_Nf]; // this is const
261: } else {
262: coef = coef_buff;
263: for (f = 0; f < loc_Nf; ++f) {
264: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][f][0];
265: for (b = 0; b < Nb; ++b) {
266: PetscInt idx = Idxs[b];
267: if (idx >= 0) {
268: coef[f * Nb + b] = xdata[idx + moffset];
269: } else {
270: idx = -idx - 1;
271: coef[f * Nb + b] = 0;
272: for (q = 0; q < maps[grid].num_face; q++) {
273: PetscInt id = maps[grid].c_maps[idx][q].gid;
274: PetscScalar scale = maps[grid].c_maps[idx][q].scale;
275: coef[f * Nb + b] += scale * xdata[id + moffset];
276: }
277: }
278: }
279: }
280: }
281: /* get f and df */
282: for (PetscInt qi = 0; qi < Nq; qi++) {
283: const PetscReal *invJ = &invJe[qi * dim * dim];
284: const PetscReal *Bq = &BB[qi * Nb];
285: const PetscReal *Dq = &DD[qi * Nb * dim];
286: PetscReal u_x[LANDAU_DIM];
287: /* get f & df */
288: for (f = 0; f < loc_Nf; ++f) {
289: const PetscInt idx = b_id * IPf_sz_glb + ipf_offset[grid] + f * loc_nip + loc_elem * Nq + qi;
290: PetscInt b, e;
291: PetscReal refSpaceDer[LANDAU_DIM];
292: ff[idx] = 0.0;
293: for (int d = 0; d < LANDAU_DIM; ++d) refSpaceDer[d] = 0.0;
294: for (b = 0; b < Nb; ++b) {
295: const PetscInt cidx = b;
296: ff[idx] += Bq[cidx] * PetscRealPart(coef[f * Nb + cidx]);
297: for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[cidx * dim + d] * PetscRealPart(coef[f * Nb + cidx]);
298: }
299: for (int d = 0; d < LANDAU_DIM; ++d) {
300: for (e = 0, u_x[d] = 0.0; e < LANDAU_DIM; ++e) u_x[d] += invJ[e * dim + d] * refSpaceDer[e];
301: }
302: dudx[idx] = u_x[0];
303: dudy[idx] = u_x[1];
304: #if LANDAU_DIM == 3
305: dudz[idx] = u_x[2];
306: #endif
307: }
308: } // q
309: } // grid
310: } // grid*batch
311: PetscCall(PetscLogEventEnd(ctx->events[8], 0, 0, 0, 0));
312: #if defined(PETSC_HAVE_THREADSAFETY)
313: endtime = MPI_Wtime();
314: if (ctx->stage) ctx->times[LANDAU_F_DF] += (endtime - starttime);
315: #endif
316: } // Jacobian setup
317: // assemble Jacobian (or mass)
318: for (PetscInt tid = 0; tid < ctx->batch_sz * elem_offset[num_grids]; tid++) { // for each element
319: const PetscInt b_Nelem = elem_offset[num_grids];
320: const PetscInt glb_elem_idx = tid % b_Nelem, b_id = tid / b_Nelem;
321: PetscInt grid = 0;
322: #if defined(PETSC_HAVE_THREADSAFETY)
323: double starttime, endtime;
324: starttime = MPI_Wtime();
325: #endif
326: while (glb_elem_idx >= elem_offset[grid + 1]) grid++;
327: {
328: const PetscInt loc_Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], loc_elem = glb_elem_idx - elem_offset[grid];
329: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset), totDim = loc_Nf * Nq, elemMatSize = totDim * totDim;
330: PetscScalar *elemMat;
331: const PetscReal *invJe = &invJ_a[(ip_offset[grid] + loc_elem * Nq) * dim * dim];
332: PetscCall(PetscMalloc1(elemMatSize, &elemMat));
333: PetscCall(PetscMemzero(elemMat, elemMatSize * sizeof(*elemMat)));
334: if (shift == 0.0) { // Jacobian
335: PetscCall(PetscLogEventBegin(ctx->events[4], 0, 0, 0, 0));
336: } else { // mass
337: PetscCall(PetscLogEventBegin(ctx->events[16], 0, 0, 0, 0));
338: }
339: for (PetscInt qj = 0; qj < Nq; ++qj) {
340: const PetscInt jpidx_glb = ip_offset[grid] + qj + loc_elem * Nq;
341: 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
342: PetscInt d, d2, dp, d3, IPf_idx;
343: if (shift == 0.0) { // Jacobian
344: const PetscReal *const invJj = &invJe[qj * dim * dim];
345: 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];
346: const PetscReal vj[3] = {xx[jpidx_glb], yy[jpidx_glb], zz ? zz[jpidx_glb] : 0}, wj = ww[jpidx_glb];
347: // create g2 & g3
348: for (d = 0; d < LANDAU_DIM; d++) { // clear accumulation data D & K
349: gg2_temp[d] = 0;
350: for (d2 = 0; d2 < LANDAU_DIM; d2++) gg3_temp[d][d2] = 0;
351: }
352: /* inner beta reduction */
353: IPf_idx = 0;
354: 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
355: PetscInt nip_loc_r = numCells[grid_r] * Nq, Nfloc_r = Nf[grid_r];
356: for (PetscInt ei_r = 0, loc_fdf_idx = 0; ei_r < numCells[grid_r]; ++ei_r) {
357: for (PetscInt qi = 0; qi < Nq; qi++, ipidx++, loc_fdf_idx++) {
358: const PetscReal wi = ww[ipidx], x = xx[ipidx], y = yy[ipidx];
359: PetscReal temp1[3] = {0, 0, 0}, temp2 = 0;
360: #if LANDAU_DIM == 2
361: 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.;
362: LandauTensor2D(vj, x, y, Ud, Uk, mask);
363: #else
364: 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.;
365: if (ctx->use_relativistic_corrections) {
366: LandauTensor3DRelativistic(vj, x, y, z, U, mask, C_0(ctx->v_0));
367: } else {
368: LandauTensor3D(vj, x, y, z, U, mask);
369: }
370: #endif
371: for (int f = 0; f < Nfloc_r; ++f) {
372: 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;
373: temp1[0] += dudx[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
374: temp1[1] += dudy[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
375: #if LANDAU_DIM == 3
376: temp1[2] += dudz[idx] * nu_beta[f + f_off] * invMass[f + f_off] * (*lambdas)[grid][grid_r];
377: #endif
378: temp2 += ff[idx] * nu_beta[f + f_off] * (*lambdas)[grid][grid_r];
379: }
380: temp1[0] *= wi;
381: temp1[1] *= wi;
382: #if LANDAU_DIM == 3
383: temp1[2] *= wi;
384: #endif
385: temp2 *= wi;
386: #if LANDAU_DIM == 2
387: for (d2 = 0; d2 < 2; d2++) {
388: for (d3 = 0; d3 < 2; ++d3) {
389: /* K = U * grad(f): g2=e: i,A */
390: gg2_temp[d2] += Uk[d2][d3] * temp1[d3];
391: /* D = -U * (I \kron (fx)): g3=f: i,j,A */
392: gg3_temp[d2][d3] += Ud[d2][d3] * temp2;
393: }
394: }
395: #else
396: for (d2 = 0; d2 < 3; ++d2) {
397: for (d3 = 0; d3 < 3; ++d3) {
398: /* K = U * grad(f): g2 = e: i,A */
399: gg2_temp[d2] += U[d2][d3] * temp1[d3];
400: /* D = -U * (I \kron (fx)): g3 = f: i,j,A */
401: gg3_temp[d2][d3] += U[d2][d3] * temp2;
402: }
403: }
404: #endif
405: } // qi
406: } // ei_r
407: IPf_idx += nip_loc_r * Nfloc_r;
408: } /* grid_r - IPs */
409: 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);
410: // add alpha and put in gg2/3
411: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) {
412: for (d2 = 0; d2 < LANDAU_DIM; d2++) {
413: gg2[fieldA][d2] = gg2_temp[d2] * nu_alpha[fieldA + f_off];
414: for (d3 = 0; d3 < LANDAU_DIM; d3++) gg3[fieldA][d2][d3] = -gg3_temp[d2][d3] * nu_alpha[fieldA + f_off] * invMass[fieldA + f_off];
415: }
416: }
417: /* add electric field term once per IP */
418: for (PetscInt fieldA = 0, f_off = ctx->species_offset[grid]; fieldA < loc_Nf; ++fieldA) gg2[fieldA][LANDAU_DIM - 1] += Eq_m[fieldA + f_off];
419: /* Jacobian transform - g2, g3 */
420: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
421: for (d = 0; d < dim; ++d) {
422: g2[fieldA][d] = 0.0;
423: for (d2 = 0; d2 < dim; ++d2) {
424: g2[fieldA][d] += invJj[d * dim + d2] * gg2[fieldA][d2];
425: g3[fieldA][d][d2] = 0.0;
426: for (d3 = 0; d3 < dim; ++d3) {
427: for (dp = 0; dp < dim; ++dp) g3[fieldA][d][d2] += invJj[d * dim + d3] * gg3[fieldA][d3][dp] * invJj[d2 * dim + dp];
428: }
429: g3[fieldA][d][d2] *= wj;
430: }
431: g2[fieldA][d] *= wj;
432: }
433: }
434: } else { // mass
435: PetscReal wj = ww[jpidx_glb];
436: /* Jacobian transform - g0 */
437: for (PetscInt fieldA = 0; fieldA < loc_Nf; ++fieldA) {
438: if (dim == 2) {
439: g0[fieldA] = wj * shift * 2. * PETSC_PI; // move this to below and remove g0
440: } else {
441: g0[fieldA] = wj * shift; // move this to below and remove g0
442: }
443: }
444: }
445: /* FE matrix construction */
446: {
447: PetscInt fieldA, d, f, d2, g;
448: const PetscReal *BJq = &BB[qj * Nb], *DIq = &DD[qj * Nb * dim];
449: /* assemble - on the diagonal (I,I) */
450: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
451: for (f = 0; f < Nb; f++) {
452: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
453: for (g = 0; g < Nb; ++g) {
454: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
455: const PetscInt fOff = i * totDim + j;
456: if (shift == 0.0) {
457: for (d = 0; d < dim; ++d) {
458: elemMat[fOff] += DIq[f * dim + d] * g2[fieldA][d] * BJq[g];
459: for (d2 = 0; d2 < dim; ++d2) elemMat[fOff] += DIq[f * dim + d] * g3[fieldA][d][d2] * DIq[g * dim + d2];
460: }
461: } else { // mass
462: elemMat[fOff] += BJq[f] * g0[fieldA] * BJq[g];
463: }
464: }
465: }
466: }
467: }
468: } /* qj loop */
469: if (shift == 0.0) { // Jacobian
470: PetscCall(PetscLogEventEnd(ctx->events[4], 0, 0, 0, 0));
471: } else {
472: PetscCall(PetscLogEventEnd(ctx->events[16], 0, 0, 0, 0));
473: }
474: #if defined(PETSC_HAVE_THREADSAFETY)
475: endtime = MPI_Wtime();
476: if (ctx->stage) ctx->times[LANDAU_KERNEL] += (endtime - starttime);
477: #endif
478: /* assemble matrix */
479: if (!container) {
480: PetscInt cStart;
481: PetscCall(PetscLogEventBegin(ctx->events[6], 0, 0, 0, 0));
482: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, NULL));
483: PetscCall(DMPlexMatSetClosure(ctx->plex[grid], section[grid], globsection[grid], subJ[LAND_PACK_IDX(b_id, grid)], loc_elem + cStart, elemMat, ADD_VALUES));
484: PetscCall(PetscLogEventEnd(ctx->events[6], 0, 0, 0, 0));
485: } else { // GPU like assembly for debugging
486: 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];
487: 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};
488: LandauIdx *coo_elem_offsets = (LandauIdx *)ctx->SData_d.coo_elem_offsets, *coo_elem_fullNb = (LandauIdx *)ctx->SData_d.coo_elem_fullNb, (*coo_elem_point_offsets)[LANDAU_MAX_NQND + 1] = (LandauIdx(*)[LANDAU_MAX_NQND + 1]) ctx->SData_d.coo_elem_point_offsets;
489: /* assemble - from the diagonal (I,I) in this format for DMPlexMatSetClosure */
490: for (fieldA = 0; fieldA < loc_Nf; fieldA++) {
491: LandauIdx *const Idxs = &maps[grid].gIdx[loc_elem][fieldA][0];
492: for (f = 0; f < Nb; f++) {
493: PetscInt idx = Idxs[f];
494: if (idx >= 0) {
495: nr = 1;
496: rows0[0] = idx;
497: row_scale[0] = 1.;
498: } else {
499: idx = -idx - 1;
500: for (q = 0, nr = 0; q < maps[grid].num_face; q++, nr++) {
501: if (maps[grid].c_maps[idx][q].gid < 0) break;
502: rows0[q] = maps[grid].c_maps[idx][q].gid;
503: row_scale[q] = maps[grid].c_maps[idx][q].scale;
504: }
505: }
506: for (g = 0; g < Nb; ++g) {
507: idx = Idxs[g];
508: if (idx >= 0) {
509: nc = 1;
510: cols0[0] = idx;
511: col_scale[0] = 1.;
512: } else {
513: idx = -idx - 1;
514: nc = maps[grid].num_face;
515: for (q = 0, nc = 0; q < maps[grid].num_face; q++, nc++) {
516: if (maps[grid].c_maps[idx][q].gid < 0) break;
517: cols0[q] = maps[grid].c_maps[idx][q].gid;
518: col_scale[q] = maps[grid].c_maps[idx][q].scale;
519: }
520: }
521: const PetscInt i = fieldA * Nb + f; /* Element matrix row */
522: const PetscInt j = fieldA * Nb + g; /* Element matrix column */
523: const PetscScalar Aij = elemMat[i * totDim + j];
524: if (coo_vals) { // mirror (i,j) in CreateStaticGPUData
525: const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
526: 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];
527: for (int q = 0, idx2 = idx0; q < nr; q++) {
528: for (int d = 0; d < nc; d++, idx2++) coo_vals[idx2] = row_scale[q] * col_scale[d] * Aij;
529: }
530: } else {
531: for (q = 0; q < nr; q++) rows[q] = rows0[q] + moffset;
532: for (d = 0; d < nc; d++) cols[d] = cols0[d] + moffset;
533: for (q = 0; q < nr; q++) {
534: for (d = 0; d < nc; d++) vals[q * nc + d] = row_scale[q] * col_scale[d] * Aij;
535: }
536: PetscCall(MatSetValues(JacP, nr, rows, nc, cols, vals, ADD_VALUES));
537: }
538: }
539: }
540: }
541: }
542: if (loc_elem == -1) {
543: PetscCall(PetscPrintf(ctx->comm, "CPU Element matrix\n"));
544: for (int d = 0; d < totDim; ++d) {
545: for (int f = 0; f < totDim; ++f) PetscCall(PetscPrintf(ctx->comm, " %12.5e", (double)PetscRealPart(elemMat[d * totDim + f])));
546: PetscCall(PetscPrintf(ctx->comm, "\n"));
547: }
548: exit(12);
549: }
550: PetscCall(PetscFree(elemMat));
551: } /* grid */
552: } /* outer element & batch loop */
553: if (shift == 0.0) { // mass
554: PetscCall(PetscFree4(ff, dudx, dudy, dudz));
555: }
556: if (!container) { // 'CPU' assembly move nest matrix to global JacP
557: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // OpenMP
558: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
559: 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];
560: PetscInt nloc, nzl, colbuf[1024], row;
561: const PetscInt *cols;
562: const PetscScalar *vals;
563: Mat B = subJ[LAND_PACK_IDX(b_id, grid)];
564: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
565: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
566: PetscCall(MatGetSize(B, &nloc, NULL));
567: for (int i = 0; i < nloc; i++) {
568: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
569: PetscCheck(nzl <= 1024, PetscObjectComm((PetscObject)B), PETSC_ERR_PLIB, "Row too big: %" PetscInt_FMT, nzl);
570: for (int j = 0; j < nzl; j++) colbuf[j] = moffset + cols[j];
571: row = moffset + i;
572: PetscCall(MatSetValues(JacP, 1, &row, nzl, colbuf, vals, ADD_VALUES));
573: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
574: }
575: PetscCall(MatDestroy(&B));
576: }
577: }
578: }
579: if (coo_vals) {
580: PetscCall(MatSetValuesCOO(JacP, coo_vals, ADD_VALUES));
581: PetscCall(PetscFree(coo_vals));
582: }
583: } /* CPU version */
584: PetscCall(MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY));
585: PetscCall(MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY));
586: /* clean up */
587: if (cellClosure) PetscCall(PetscFree(cellClosure));
588: if (xdata) PetscCall(VecRestoreArrayReadAndMemType(a_X, &xdata));
589: PetscFunctionReturn(PETSC_SUCCESS);
590: }
592: static PetscErrorCode GeometryDMLandau(DM base, PetscInt point, PetscInt dim, const PetscReal abc[], PetscReal xyz[], void *a_ctx)
593: {
594: PetscReal r = abc[0], z = abc[1];
596: PetscFunctionBegin;
597: xyz[0] = r;
598: xyz[1] = z;
599: if (dim == 3) xyz[2] = abc[2];
601: PetscFunctionReturn(PETSC_SUCCESS);
602: }
604: /* create DMComposite of meshes for each species group */
605: static PetscErrorCode LandauDMCreateVMeshes(MPI_Comm comm_self, const PetscInt dim, const char prefix[], LandauCtx *ctx, DM pack)
606: {
607: PetscFunctionBegin;
608: { /* p4est, quads */
609: /* Create plex mesh of Landau domain */
610: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
611: PetscReal par_radius = ctx->radius_par[grid], perp_radius = ctx->radius_perp[grid];
612: if (!ctx->sphere && !ctx->simplex) { // 2 or 3D (only 3D option)
613: PetscReal lo[] = {-perp_radius, -par_radius, -par_radius}, hi[] = {perp_radius, par_radius, par_radius};
614: DMBoundaryType periodicity[3] = {DM_BOUNDARY_NONE, dim == 2 ? DM_BOUNDARY_NONE : DM_BOUNDARY_NONE, DM_BOUNDARY_NONE};
615: if (dim == 2) lo[0] = 0;
616: else {
617: lo[1] = -perp_radius;
618: hi[1] = perp_radius; // 3D y is a perp
619: }
620: 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
621: PetscCall(DMLocalizeCoordinates(ctx->plex[grid])); /* needed for periodic */
622: if (dim == 3) PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "cube"));
623: else PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "half-plane"));
624: } else if (dim == 2) {
625: size_t len;
626: PetscCall(PetscStrlen(ctx->filename, &len));
627: if (len) {
628: Vec coords;
629: PetscScalar *x;
630: PetscInt N;
631: char str[] = "-dm_landau_view_file_0";
632: str[21] += grid;
633: PetscCall(DMPlexCreateFromFile(comm_self, ctx->filename, "plexland.c", PETSC_TRUE, &ctx->plex[grid]));
634: PetscCall(DMPlexOrient(ctx->plex[grid]));
635: PetscCall(DMGetCoordinatesLocal(ctx->plex[grid], &coords));
636: PetscCall(VecGetSize(coords, &N));
637: PetscCall(VecGetArray(coords, &x));
638: /* scale by domain size */
639: for (PetscInt i = 0; i < N; i += 2) {
640: x[i + 0] *= ctx->radius_perp[grid];
641: x[i + 1] *= ctx->radius_par[grid];
642: }
643: PetscCall(VecRestoreArray(coords, &x));
644: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], ctx->filename));
645: PetscCall(PetscInfo(ctx->plex[grid], "%d) Read %s mesh file (%s)\n", (int)grid, ctx->filename, str));
646: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, str));
647: } else {
648: PetscInt numCells = ctx->simplex ? 12 : 6, cell_size = ctx->simplex ? 3 : 4, j;
649: const PetscInt numVerts = 11;
650: PetscInt cellsT[][4] = {
651: {0, 1, 6, 5 },
652: {1, 2, 7, 6 },
653: {2, 3, 8, 7 },
654: {3, 4, 9, 8 },
655: {5, 6, 7, 10},
656: {10, 7, 8, 9 }
657: };
658: PetscInt cellsS[][3] = {
659: {0, 1, 6 },
660: {1, 2, 6 },
661: {6, 2, 7 },
662: {7, 2, 8 },
663: {8, 2, 3 },
664: {8, 3, 4 },
665: {0, 6, 5 },
666: {5, 6, 7 },
667: {5, 7, 10},
668: {10, 7, 9 },
669: {9, 7, 8 },
670: {9, 8, 4 }
671: };
672: const PetscInt *pcell = (const PetscInt *)(ctx->simplex ? &cellsS[0][0] : &cellsT[0][0]);
673: PetscReal coords[11][2], *flatCoords = (PetscReal *)&coords[0][0];
674: PetscReal rad = ctx->radius[grid];
675: for (j = 0; j < 5; j++) { // outside edge
676: PetscReal z, r, theta = -PETSC_PI / 2 + (j % 5) * PETSC_PI / 4;
677: r = rad * PetscCosReal(theta);
678: coords[j][0] = r;
679: z = rad * PetscSinReal(theta);
680: coords[j][1] = z;
681: }
682: coords[j][0] = 0;
683: coords[j++][1] = -rad * ctx->sphere_inner_radius_90degree;
684: coords[j][0] = rad * ctx->sphere_inner_radius_45degree;
685: coords[j++][1] = -rad * ctx->sphere_inner_radius_45degree;
686: coords[j][0] = rad * ctx->sphere_inner_radius_90degree;
687: coords[j++][1] = 0;
688: coords[j][0] = rad * ctx->sphere_inner_radius_45degree;
689: coords[j++][1] = rad * ctx->sphere_inner_radius_45degree;
690: coords[j][0] = 0;
691: coords[j++][1] = rad * ctx->sphere_inner_radius_90degree;
692: coords[j][0] = 0;
693: coords[j++][1] = 0;
694: PetscCall(DMPlexCreateFromCellListPetsc(comm_self, 2, numCells, numVerts, cell_size, ctx->interpolate, pcell, 2, flatCoords, &ctx->plex[grid]));
695: PetscCall(PetscObjectSetName((PetscObject)ctx->plex[grid], "semi-circle"));
696: PetscCall(PetscInfo(ctx->plex[grid], "\t%" PetscInt_FMT ") Make circle %s mesh\n", grid, ctx->simplex ? "simplex" : "tensor"));
697: }
698: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Velocity space meshes does not support 3V cubed sphere or simplex");
699: PetscCall(DMSetFromOptions(ctx->plex[grid]));
700: } // grid loop
701: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)pack, prefix));
702: { /* convert to p4est (or whatever), wait for discretization to create pack */
703: char convType[256];
704: PetscBool flg;
706: PetscOptionsBegin(ctx->comm, prefix, "Mesh conversion options", "DMPLEX");
707: PetscCall(PetscOptionsFList("-dm_landau_type", "Convert DMPlex to another format (p4est)", "plexland.c", DMList, DMPLEX, convType, 256, &flg));
708: PetscOptionsEnd();
709: if (flg) {
710: ctx->use_p4est = PETSC_TRUE; /* flag for Forest */
711: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
712: DM dmforest;
713: PetscCall(DMConvert(ctx->plex[grid], convType, &dmforest));
714: if (dmforest) {
715: PetscBool isForest;
716: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)dmforest, prefix));
717: PetscCall(DMIsForest(dmforest, &isForest));
718: if (isForest) {
719: if (ctx->sphere) PetscCall(DMForestSetBaseCoordinateMapping(dmforest, GeometryDMLandau, ctx));
720: PetscCall(DMDestroy(&ctx->plex[grid]));
721: ctx->plex[grid] = dmforest; // Forest for adaptivity
722: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Converted to non Forest?");
723: } else SETERRQ(ctx->comm, PETSC_ERR_PLIB, "Convert failed?");
724: }
725: } else ctx->use_p4est = PETSC_FALSE; /* flag for Forest */
726: }
727: } /* non-file */
728: PetscCall(DMSetDimension(pack, dim));
729: PetscCall(PetscObjectSetName((PetscObject)pack, "Mesh"));
730: PetscCall(DMSetApplicationContext(pack, ctx));
732: PetscFunctionReturn(PETSC_SUCCESS);
733: }
735: static PetscErrorCode SetupDS(DM pack, PetscInt dim, PetscInt grid, LandauCtx *ctx)
736: {
737: PetscInt ii, i0;
738: char buf[256];
739: PetscSection section;
741: PetscFunctionBegin;
742: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
743: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "e"));
744: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "i%" PetscInt_FMT, ii));
745: /* Setup Discretization - FEM */
746: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, ctx->simplex, NULL, PETSC_DECIDE, &ctx->fe[ii]));
747: PetscCall(PetscObjectSetName((PetscObject)ctx->fe[ii], buf));
748: PetscCall(DMSetField(ctx->plex[grid], i0, NULL, (PetscObject)ctx->fe[ii]));
749: }
750: PetscCall(DMCreateDS(ctx->plex[grid]));
751: PetscCall(DMGetSection(ctx->plex[grid], §ion));
752: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
753: if (ii == 0) PetscCall(PetscSNPrintf(buf, sizeof(buf), "se"));
754: else PetscCall(PetscSNPrintf(buf, sizeof(buf), "si%" PetscInt_FMT, ii));
755: PetscCall(PetscSectionSetComponentName(section, i0, 0, buf));
756: }
757: PetscFunctionReturn(PETSC_SUCCESS);
758: }
760: /* Define a Maxwellian function for testing out the operator. */
762: /* Using cartesian velocity space coordinates, the particle */
763: /* density, [1/m^3], is defined according to */
765: /* $$ n=\int_{R^3} dv^3 \left(\frac{m}{2\pi T}\right)^{3/2}\exp [- mv^2/(2T)] $$ */
767: /* Using some constant, c, we normalize the velocity vector into a */
768: /* dimensionless variable according to v=c*x. Thus the density, $n$, becomes */
770: /* $$ n=\int_{R^3} dx^3 \left(\frac{mc^2}{2\pi T}\right)^{3/2}\exp [- mc^2/(2T)*x^2] $$ */
772: /* Defining $\theta=2T/mc^2$, we thus find that the probability density */
773: /* for finding the particle within the interval in a box dx^3 around x is */
775: /* f(x;\theta)=\left(\frac{1}{\pi\theta}\right)^{3/2} \exp [ -x^2/\theta ] */
777: typedef struct {
778: PetscReal v_0;
779: PetscReal kT_m;
780: PetscReal n;
781: PetscReal shift;
782: } MaxwellianCtx;
784: static PetscErrorCode maxwellian(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf_dummy, PetscScalar *u, void *actx)
785: {
786: MaxwellianCtx *mctx = (MaxwellianCtx *)actx;
787: PetscInt i;
788: PetscReal v2 = 0, theta = 2 * mctx->kT_m / (mctx->v_0 * mctx->v_0), shift; /* theta = 2kT/mc^2 */
789: PetscFunctionBegin;
790: /* compute the exponents, v^2 */
791: for (i = 0; i < dim; ++i) v2 += x[i] * x[i];
792: /* evaluate the Maxwellian */
793: if (mctx->shift < 0) shift = -mctx->shift;
794: else {
795: u[0] = mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
796: shift = mctx->shift;
797: }
798: if (shift != 0.) {
799: v2 = 0;
800: for (i = 0; i < dim - 1; ++i) v2 += x[i] * x[i];
801: v2 += (x[dim - 1] - shift) * (x[dim - 1] - shift);
802: /* evaluate the shifted Maxwellian */
803: u[0] += mctx->n * PetscPowReal(PETSC_PI * theta, -1.5) * (PetscExpReal(-v2 / theta));
804: }
805: PetscFunctionReturn(PETSC_SUCCESS);
806: }
808: /*@
809: DMPlexLandauAddMaxwellians - Add a Maxwellian distribution to a state
811: Collective
813: Input Parameters:
814: + dm - The mesh (local)
815: . time - Current time
816: . temps - Temperatures of each species (global)
817: . ns - Number density of each species (global)
818: . grid - index into current grid - just used for offset into `temp` and `ns`
819: . b_id - batch index
820: . n_batch - number of batches
821: - actx - Landau context
823: Output Parameter:
824: . X - The state (local to this grid)
826: Level: beginner
828: .seealso: `DMPlexLandauCreateVelocitySpace()`
829: @*/
830: PetscErrorCode DMPlexLandauAddMaxwellians(DM dm, Vec X, PetscReal time, PetscReal temps[], PetscReal ns[], PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
831: {
832: LandauCtx *ctx = (LandauCtx *)actx;
833: PetscErrorCode (*initu[LANDAU_MAX_SPECIES])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
834: PetscInt dim;
835: MaxwellianCtx *mctxs[LANDAU_MAX_SPECIES], data[LANDAU_MAX_SPECIES];
837: PetscFunctionBegin;
838: PetscCall(DMGetDimension(dm, &dim));
839: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
840: for (PetscInt ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
841: mctxs[i0] = &data[i0];
842: data[i0].v_0 = ctx->v_0; // v_0 same for all grids
843: data[i0].kT_m = ctx->k * temps[ii] / ctx->masses[ii]; /* kT/m */
844: data[i0].n = ns[ii];
845: initu[i0] = maxwellian;
846: data[i0].shift = 0;
847: }
848: data[0].shift = ctx->electronShift;
849: /* need to make ADD_ALL_VALUES work - TODO */
850: PetscCall(DMProjectFunction(dm, time, initu, (void **)mctxs, INSERT_ALL_VALUES, X));
851: PetscFunctionReturn(PETSC_SUCCESS);
852: }
854: /*
855: LandauSetInitialCondition - Adds Maxwellians with context
857: Collective
859: Input Parameters:
860: . dm - The mesh
861: - grid - index into current grid - just used for offset into temp and ns
862: . b_id - batch index
863: - n_batch - number of batches
864: + actx - Landau context with T and n
866: Output Parameter:
867: . X - The state
869: Level: beginner
871: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauAddMaxwellians()`
872: */
873: static PetscErrorCode LandauSetInitialCondition(DM dm, Vec X, PetscInt grid, PetscInt b_id, PetscInt n_batch, void *actx)
874: {
875: LandauCtx *ctx = (LandauCtx *)actx;
876: PetscFunctionBegin;
877: if (!ctx) PetscCall(DMGetApplicationContext(dm, &ctx));
878: PetscCall(VecZeroEntries(X));
879: PetscCall(DMPlexLandauAddMaxwellians(dm, X, 0.0, ctx->thermal_temps, ctx->n, grid, b_id, n_batch, ctx));
880: PetscFunctionReturn(PETSC_SUCCESS);
881: }
883: // adapt a level once. Forest in/out
884: #if defined(PETSC_USE_INFO)
885: static const char *s_refine_names[] = {"RE", "Z1", "Origin", "Z2", "Uniform"};
886: #endif
887: static PetscErrorCode adaptToleranceFEM(PetscFE fem, Vec sol, PetscInt type, PetscInt grid, LandauCtx *ctx, DM *newForest)
888: {
889: DM forest, plex, adaptedDM = NULL;
890: PetscDS prob;
891: PetscBool isForest;
892: PetscQuadrature quad;
893: PetscInt Nq, Nb, *Nb2, cStart, cEnd, c, dim, qj, k;
894: DMLabel adaptLabel = NULL;
896: PetscFunctionBegin;
897: forest = ctx->plex[grid];
898: PetscCall(DMCreateDS(forest));
899: PetscCall(DMGetDS(forest, &prob));
900: PetscCall(DMGetDimension(forest, &dim));
901: PetscCall(DMIsForest(forest, &isForest));
902: PetscCheck(isForest, ctx->comm, PETSC_ERR_ARG_WRONG, "! Forest");
903: PetscCall(DMConvert(forest, DMPLEX, &plex));
904: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
905: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "adapt", &adaptLabel));
906: PetscCall(PetscFEGetQuadrature(fem, &quad));
907: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL));
908: PetscCheck(Nq <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nq, LANDAU_MAX_NQND);
909: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
910: PetscCall(PetscDSGetDimensions(prob, &Nb2));
911: PetscCheck(Nb2[0] == Nb, ctx->comm, PETSC_ERR_ARG_WRONG, " Nb = %" PetscInt_FMT " != Nb (%d)", Nb, (int)Nb2[0]);
912: PetscCheck(Nb <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nb = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nb, LANDAU_MAX_NQND);
913: PetscCall(PetscInfo(sol, "%" PetscInt_FMT ") Refine phase: %s\n", grid, s_refine_names[type]));
914: if (type == 4) {
915: for (c = cStart; c < cEnd; c++) PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
916: } else if (type == 2) {
917: PetscInt rCellIdx[8], nr = 0, nrmax = (dim == 3) ? 8 : 2;
918: PetscReal minRad = PETSC_INFINITY, r;
919: for (c = cStart; c < cEnd; c++) {
920: PetscReal tt, v0[LANDAU_MAX_NQND * 3], detJ[LANDAU_MAX_NQND];
921: PetscCall(DMPlexComputeCellGeometryFEM(plex, c, quad, v0, NULL, NULL, detJ));
922: for (qj = 0; qj < Nq; ++qj) {
923: tt = PetscSqr(v0[dim * qj + 0]) + PetscSqr(v0[dim * qj + 1]) + PetscSqr(((dim == 3) ? v0[dim * qj + 2] : 0));
924: r = PetscSqrtReal(tt);
925: if (r < minRad - PETSC_SQRT_MACHINE_EPSILON * 10.) {
926: minRad = r;
927: nr = 0;
928: rCellIdx[nr++] = c;
929: 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));
930: } else if ((r - minRad) < PETSC_SQRT_MACHINE_EPSILON * 100. && nr < nrmax) {
931: for (k = 0; k < nr; k++)
932: if (c == rCellIdx[k]) break;
933: if (k == nr) {
934: rCellIdx[nr++] = c;
935: 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)));
936: }
937: }
938: }
939: }
940: for (k = 0; k < nr; k++) PetscCall(DMLabelSetValue(adaptLabel, rCellIdx[k], DM_ADAPT_REFINE));
941: 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));
942: } else if (type == 0 || type == 1 || type == 3) { /* refine along r=0 axis */
943: PetscScalar *coef = NULL;
944: Vec coords;
945: PetscInt csize, Nv, d, nz, nrefined = 0;
946: DM cdm;
947: PetscSection cs;
948: PetscCall(DMGetCoordinatesLocal(forest, &coords));
949: PetscCall(DMGetCoordinateDM(forest, &cdm));
950: PetscCall(DMGetLocalSection(cdm, &cs));
951: for (c = cStart; c < cEnd; c++) {
952: PetscInt doit = 0, outside = 0;
953: PetscCall(DMPlexVecGetClosure(cdm, cs, coords, c, &csize, &coef));
954: Nv = csize / dim;
955: for (nz = d = 0; d < Nv; d++) {
956: PetscReal z = PetscRealPart(coef[d * dim + (dim - 1)]), x = PetscSqr(PetscRealPart(coef[d * dim + 0])) + ((dim == 3) ? PetscSqr(PetscRealPart(coef[d * dim + 1])) : 0);
957: x = PetscSqrtReal(x);
958: if (type == 0) {
959: 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 */
960: } else if (type == 1 && (z > ctx->vperp0_radius1 || z < -ctx->vperp0_radius1)) {
961: outside++; /* don't refine outside electron refine radius */
962: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
963: } else if (type == 3 && (z > ctx->vperp0_radius2 || z < -ctx->vperp0_radius2)) {
964: outside++; /* refine r=0 cells on refinement front */
965: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") (debug) found %s cells\n", grid, s_refine_names[type]));
966: }
967: if (x < PETSC_MACHINE_EPSILON * 10. && (type != 0 || ctx->re_radius > PETSC_SQRT_MACHINE_EPSILON)) nz++;
968: }
969: PetscCall(DMPlexVecRestoreClosure(cdm, cs, coords, c, &csize, &coef));
970: if (doit || (outside < Nv && nz)) {
971: PetscCall(DMLabelSetValue(adaptLabel, c, DM_ADAPT_REFINE));
972: nrefined++;
973: }
974: }
975: PetscCall(PetscInfo(sol, "\t%" PetscInt_FMT ") Refined %" PetscInt_FMT " cells\n", grid, nrefined));
976: }
977: PetscCall(DMDestroy(&plex));
978: PetscCall(DMAdaptLabel(forest, adaptLabel, &adaptedDM));
979: PetscCall(DMLabelDestroy(&adaptLabel));
980: *newForest = adaptedDM;
981: if (adaptedDM) {
982: if (isForest) {
983: PetscCall(DMForestSetAdaptivityForest(adaptedDM, NULL)); // ????
984: }
985: PetscCall(DMConvert(adaptedDM, DMPLEX, &plex));
986: PetscCall(DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd));
987: PetscCall(PetscInfo(sol, "\t\t\t\t%" PetscInt_FMT ") %" PetscInt_FMT " cells, %" PetscInt_FMT " total quadrature points\n", grid, cEnd - cStart, Nq * (cEnd - cStart)));
988: PetscCall(DMDestroy(&plex));
989: } else *newForest = NULL;
990: PetscFunctionReturn(PETSC_SUCCESS);
991: }
993: // forest goes in (ctx->plex[grid]), plex comes out
994: static PetscErrorCode adapt(PetscInt grid, LandauCtx *ctx, Vec *uu)
995: {
996: PetscInt adaptIter;
998: PetscFunctionBegin;
999: 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]};
1000: for (type = 0; type < 5; type++) {
1001: for (adaptIter = 0; adaptIter < limits[type]; adaptIter++) {
1002: DM newForest = NULL;
1003: PetscCall(adaptToleranceFEM(ctx->fe[0], *uu, type, grid, ctx, &newForest));
1004: if (newForest) {
1005: PetscCall(DMDestroy(&ctx->plex[grid]));
1006: PetscCall(VecDestroy(uu));
1007: PetscCall(DMCreateGlobalVector(newForest, uu));
1008: PetscCall(PetscObjectSetName((PetscObject)*uu, "uAMR"));
1009: PetscCall(LandauSetInitialCondition(newForest, *uu, grid, 0, 1, ctx));
1010: ctx->plex[grid] = newForest;
1011: } else {
1012: PetscCall(PetscInfo(*uu, "No refinement\n"));
1013: }
1014: }
1015: }
1016: PetscFunctionReturn(PETSC_SUCCESS);
1017: }
1019: // make log(Lambdas) from NRL Plasma formulary
1020: static PetscErrorCode makeLambdas(LandauCtx *ctx)
1021: {
1022: PetscFunctionBegin;
1023: for (PetscInt gridi = 0; gridi < ctx->num_grids; gridi++) {
1024: int iii = ctx->species_offset[gridi];
1025: PetscReal Ti_ev = (ctx->thermal_temps[iii] / 1.1604525e7) * 1000; // convert (back) to eV
1026: PetscReal ni = ctx->n[iii] * ctx->n_0;
1027: for (PetscInt gridj = gridi; gridj < ctx->num_grids; gridj++) {
1028: PetscInt jjj = ctx->species_offset[gridj];
1029: PetscReal Zj = ctx->charges[jjj] / 1.6022e-19;
1030: if (gridi == 0) {
1031: if (gridj == 0) { // lam_ee
1032: ctx->lambdas[gridi][gridj] = 23.5 - PetscLogReal(PetscSqrtReal(ni) * PetscPowReal(Ti_ev, -1.25)) - PetscSqrtReal(1e-5 + PetscSqr(PetscLogReal(Ti_ev) - 2) / 16);
1033: } else { // lam_ei == lam_ie
1034: if (10 * Zj * Zj > Ti_ev) {
1035: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 23 - PetscLogReal(PetscSqrtReal(ni) * Zj * PetscPowReal(Ti_ev, -1.5));
1036: } else {
1037: ctx->lambdas[gridi][gridj] = ctx->lambdas[gridj][gridi] = 24 - PetscLogReal(PetscSqrtReal(ni) / Ti_ev);
1038: }
1039: }
1040: } else { // lam_ii'
1041: PetscReal mui = ctx->masses[iii] / 1.6720e-27, Zi = ctx->charges[iii] / 1.6022e-19;
1042: PetscReal Tj_ev = (ctx->thermal_temps[jjj] / 1.1604525e7) * 1000; // convert (back) to eV
1043: PetscReal muj = ctx->masses[jjj] / 1.6720e-27;
1044: PetscReal nj = ctx->n[jjj] * ctx->n_0;
1045: 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));
1046: }
1047: }
1048: }
1049: //PetscReal v0 = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1050: PetscFunctionReturn(PETSC_SUCCESS);
1051: }
1053: static PetscErrorCode ProcessOptions(LandauCtx *ctx, const char prefix[])
1054: {
1055: PetscBool flg, fileflg;
1056: PetscInt ii, nt, nm, nc, num_species_grid[LANDAU_MAX_GRIDS], non_dim_grid;
1057: PetscReal lnLam = 10;
1058: DM dummy;
1060: PetscFunctionBegin;
1061: PetscCall(DMCreate(ctx->comm, &dummy));
1062: /* get options - initialize context */
1063: ctx->verbose = 1; // should be 0 for silent compliance
1064: ctx->batch_sz = 1;
1065: ctx->batch_view_idx = 0;
1066: ctx->interpolate = PETSC_TRUE;
1067: ctx->gpu_assembly = PETSC_TRUE;
1068: ctx->norm_state = 0;
1069: ctx->electronShift = 0;
1070: ctx->M = NULL;
1071: ctx->J = NULL;
1072: /* geometry and grids */
1073: ctx->sphere = PETSC_FALSE;
1074: ctx->use_p4est = PETSC_FALSE;
1075: ctx->simplex = PETSC_FALSE;
1076: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1077: ctx->radius[grid] = 5.; /* thermal radius (velocity) */
1078: ctx->radius_perp[grid] = 5.; /* thermal radius (velocity) */
1079: ctx->radius_par[grid] = 5.; /* thermal radius (velocity) */
1080: ctx->numAMRRefine[grid] = 0;
1081: ctx->postAMRRefine[grid] = 0;
1082: ctx->species_offset[grid + 1] = 1; // one species default
1083: num_species_grid[grid] = 0;
1084: ctx->plex[grid] = NULL; /* cache as expensive to Convert */
1085: }
1086: ctx->species_offset[0] = 0;
1087: ctx->re_radius = 0.;
1088: ctx->vperp0_radius1 = 0;
1089: ctx->vperp0_radius2 = 0;
1090: ctx->nZRefine1 = 0;
1091: ctx->nZRefine2 = 0;
1092: ctx->numRERefine = 0;
1093: num_species_grid[0] = 1; // one species default
1094: /* species - [0] electrons, [1] one ion species eg, duetarium, [2] heavy impurity ion, ... */
1095: ctx->charges[0] = -1; /* electron charge (MKS) */
1096: ctx->masses[0] = 1 / 1835.469965278441013; /* temporary value in proton mass */
1097: ctx->n[0] = 1;
1098: ctx->v_0 = 1; /* thermal velocity, we could start with a scale != 1 */
1099: ctx->thermal_temps[0] = 1;
1100: /* constants, etc. */
1101: ctx->epsilon0 = 8.8542e-12; /* permittivity of free space (MKS) F/m */
1102: ctx->k = 1.38064852e-23; /* Boltzmann constant (MKS) J/K */
1103: ctx->n_0 = 1.e20; /* typical plasma n, but could set it to 1 */
1104: ctx->Ez = 0;
1105: for (PetscInt grid = 0; grid < LANDAU_NUM_TIMERS; grid++) ctx->times[grid] = 0;
1106: for (PetscInt ii = 0; ii < LANDAU_DIM; ii++) ctx->cells0[ii] = 2;
1107: if (LANDAU_DIM == 2) ctx->cells0[0] = 1;
1108: ctx->use_matrix_mass = PETSC_FALSE;
1109: ctx->use_relativistic_corrections = PETSC_FALSE;
1110: ctx->use_energy_tensor_trick = PETSC_FALSE; /* Use Eero's trick for energy conservation v --> grad(v^2/2) */
1111: ctx->SData_d.w = NULL;
1112: ctx->SData_d.x = NULL;
1113: ctx->SData_d.y = NULL;
1114: ctx->SData_d.z = NULL;
1115: ctx->SData_d.invJ = NULL;
1116: ctx->jacobian_field_major_order = PETSC_FALSE;
1117: ctx->SData_d.coo_elem_offsets = NULL;
1118: ctx->SData_d.coo_elem_point_offsets = NULL;
1119: ctx->SData_d.coo_elem_fullNb = NULL;
1120: ctx->SData_d.coo_size = 0;
1121: PetscOptionsBegin(ctx->comm, prefix, "Options for Fokker-Plank-Landau collision operator", "none");
1122: #if defined(PETSC_HAVE_KOKKOS)
1123: ctx->deviceType = LANDAU_KOKKOS;
1124: PetscCall(PetscStrncpy(ctx->filename, "kokkos", sizeof(ctx->filename)));
1125: #else
1126: ctx->deviceType = LANDAU_CPU;
1127: PetscCall(PetscStrncpy(ctx->filename, "cpu", sizeof(ctx->filename)));
1128: #endif
1129: PetscCall(PetscOptionsString("-dm_landau_device_type", "Use kernels on 'cpu' 'kokkos'", "plexland.c", ctx->filename, ctx->filename, sizeof(ctx->filename), NULL));
1130: PetscCall(PetscStrcmp("cpu", ctx->filename, &flg));
1131: if (flg) {
1132: ctx->deviceType = LANDAU_CPU;
1133: } else {
1134: PetscCall(PetscStrcmp("kokkos", ctx->filename, &flg));
1135: if (flg) ctx->deviceType = LANDAU_KOKKOS;
1136: else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_device_type %s", ctx->filename);
1137: }
1138: ctx->filename[0] = '\0';
1139: PetscCall(PetscOptionsString("-dm_landau_filename", "file to read mesh from", "plexland.c", ctx->filename, ctx->filename, sizeof(ctx->filename), &fileflg));
1140: PetscCall(PetscOptionsReal("-dm_landau_electron_shift", "Shift in thermal velocity of electrons", "none", ctx->electronShift, &ctx->electronShift, NULL));
1141: PetscCall(PetscOptionsInt("-dm_landau_verbose", "Level of verbosity output", "plexland.c", ctx->verbose, &ctx->verbose, NULL));
1142: PetscCall(PetscOptionsInt("-dm_landau_batch_size", "Number of 'vertices' to batch", "ex2.c", ctx->batch_sz, &ctx->batch_sz, NULL));
1143: 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);
1144: 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));
1145: 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);
1146: PetscCall(PetscOptionsReal("-dm_landau_Ez", "Initial parallel electric field in unites of Conner-Hastie critical field", "plexland.c", ctx->Ez, &ctx->Ez, NULL));
1147: PetscCall(PetscOptionsReal("-dm_landau_n_0", "Normalization constant for number density", "plexland.c", ctx->n_0, &ctx->n_0, NULL));
1148: 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));
1149: PetscCall(PetscOptionsBool("-dm_landau_use_relativistic_corrections", "Use relativistic corrections", "plexland.c", ctx->use_relativistic_corrections, &ctx->use_relativistic_corrections, NULL));
1150: PetscCall(PetscOptionsBool("-dm_landau_simplex", "Use simplex elements", "plexland.c", ctx->simplex, &ctx->simplex, NULL));
1151: if (LANDAU_DIM == 2 && ctx->use_relativistic_corrections) ctx->use_relativistic_corrections = PETSC_FALSE; // should warn
1152: 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,
1153: &ctx->use_energy_tensor_trick, NULL));
1155: /* get num species with temperature, set defaults */
1156: for (ii = 1; ii < LANDAU_MAX_SPECIES; ii++) {
1157: ctx->thermal_temps[ii] = 1;
1158: ctx->charges[ii] = 1;
1159: ctx->masses[ii] = 1;
1160: ctx->n[ii] = 1;
1161: }
1162: nt = LANDAU_MAX_SPECIES;
1163: 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));
1164: if (flg) {
1165: PetscCall(PetscInfo(dummy, "num_species set to number of thermal temps provided (%" PetscInt_FMT ")\n", nt));
1166: ctx->num_species = nt;
1167: } else SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_thermal_temps ,t1,t2,.. must be provided to set the number of species");
1168: for (ii = 0; ii < ctx->num_species; ii++) ctx->thermal_temps[ii] *= 1.1604525e7; /* convert to Kelvin */
1169: nm = LANDAU_MAX_SPECIES - 1;
1170: 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));
1171: 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);
1172: nm = LANDAU_MAX_SPECIES;
1173: PetscCall(PetscOptionsRealArray("-dm_landau_n", "Number density of each species = n_s * n_0", "plexland.c", ctx->n, &nm, &flg));
1174: 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);
1175: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] *= 1.6720e-27; /* scale by proton mass kg */
1176: ctx->masses[0] = 9.10938356e-31; /* electron mass kg (should be about right already) */
1177: nc = LANDAU_MAX_SPECIES - 1;
1178: 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));
1179: 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);
1180: for (ii = 0; ii < LANDAU_MAX_SPECIES; ii++) ctx->charges[ii] *= 1.6022e-19; /* electron/proton charge (MKS) */
1181: /* geometry and grids */
1182: nt = LANDAU_MAX_GRIDS;
1183: 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));
1184: if (flg) {
1185: ctx->num_grids = nt;
1186: for (ii = nt = 0; ii < ctx->num_grids; ii++) nt += num_species_grid[ii];
1187: 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,
1188: ctx->num_grids, LANDAU_MAX_GRIDS);
1189: } else {
1190: if (ctx->num_species > LANDAU_MAX_GRIDS) {
1191: num_species_grid[0] = 1;
1192: num_species_grid[1] = ctx->num_species - 1;
1193: ctx->num_grids = 2;
1194: } else {
1195: ctx->num_grids = ctx->num_species;
1196: for (ii = 0; ii < ctx->num_grids; ii++) num_species_grid[ii] = 1;
1197: }
1198: }
1199: 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];
1200: 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],
1201: ctx->num_species);
1202: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1203: int iii = ctx->species_offset[grid]; // normalize with first (arbitrary) species on grid
1204: ctx->thermal_speed[grid] = PetscSqrtReal(ctx->k * ctx->thermal_temps[iii] / ctx->masses[iii]); /* arbitrary units for non-dimensionalization: plasma formulary def */
1205: }
1206: // get lambdas here because we need them for t_0 etc
1207: PetscCall(PetscOptionsReal("-dm_landau_ln_lambda", "Universal cross section parameter. Default uses NRL formulas", "plexland.c", lnLam, &lnLam, &flg));
1208: if (flg) {
1209: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1210: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) ctx->lambdas[gridj][grid] = lnLam; /* cross section ratio large - small angle collisions */
1211: }
1212: } else {
1213: PetscCall(makeLambdas(ctx));
1214: }
1215: non_dim_grid = 0;
1216: 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));
1217: if (non_dim_grid != 0) PetscCall(PetscInfo(dummy, "Normalization grid set to %" PetscInt_FMT ", but non-default not well verified\n", non_dim_grid));
1218: 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);
1219: ctx->v_0 = ctx->thermal_speed[non_dim_grid]; /* arbitrary units for non dimensionalization: global mean velocity in 1D of electrons */
1220: ctx->m_0 = ctx->masses[non_dim_grid]; /* arbitrary reference mass, electrons */
1221: 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 */
1222: /* domain */
1223: nt = LANDAU_MAX_GRIDS;
1224: PetscCall(PetscOptionsRealArray("-dm_landau_domain_radius", "Phase space size in units of thermal velocity of grid", "plexland.c", ctx->radius, &nt, &flg));
1225: if (flg) {
1226: 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);
1227: while (nt--) ctx->radius_par[nt] = ctx->radius_perp[nt] = ctx->radius[nt];
1228: } else {
1229: nt = LANDAU_MAX_GRIDS;
1230: 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));
1231: 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);
1232: 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));
1233: 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);
1234: }
1235: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1236: if (flg && ctx->radius[grid] <= 0) { /* negative is ratio of c - need to set par and perp with this -- todo */
1237: if (ctx->radius[grid] == 0) ctx->radius[grid] = 0.75;
1238: else ctx->radius[grid] = -ctx->radius[grid];
1239: 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)
1240: PetscCall(PetscInfo(dummy, "Change domain radius to %g for grid %" PetscInt_FMT "\n", (double)ctx->radius[grid], grid));
1241: }
1242: ctx->radius[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1243: ctx->radius_perp[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1244: ctx->radius_par[grid] *= ctx->thermal_speed[grid] / ctx->v_0; // scale domain by thermal radius relative to v_0
1245: }
1246: /* amr parameters */
1247: if (!fileflg) {
1248: nt = LANDAU_MAX_GRIDS;
1249: 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));
1250: 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);
1251: nt = LANDAU_MAX_GRIDS;
1252: PetscCall(PetscOptionsIntArray("-dm_landau_amr_post_refine", "Number of levels to uniformly refine after AMR", "plexland.c", ctx->postAMRRefine, &nt, &flg));
1253: for (ii = 1; ii < ctx->num_grids; ii++) ctx->postAMRRefine[ii] = ctx->postAMRRefine[0]; // all grids the same now
1254: 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));
1255: 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));
1256: 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));
1257: 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));
1258: 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));
1259: 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));
1260: /* spherical domain (not used) */
1261: PetscCall(PetscOptionsBool("-dm_landau_sphere", "use sphere/semi-circle domain instead of rectangle", "plexland.c", ctx->sphere, &ctx->sphere, NULL));
1262: if (ctx->sphere || ctx->simplex) {
1263: ctx->sphere_inner_radius_90degree = 0.40;
1264: ctx->sphere_inner_radius_45degree = 0.35;
1265: PetscCall(PetscOptionsReal("-dm_landau_sphere_inner_radius_90degree_scale", "Scaling of radius for inner circle on 90 degree grid", "plexland.c", ctx->sphere_inner_radius_90degree, &ctx->sphere_inner_radius_90degree, NULL));
1266: PetscCall(PetscOptionsReal("-dm_landau_sphere_inner_radius_45degree_scale", "Scaling of radius for inner circle on 45 degree grid", "plexland.c", ctx->sphere_inner_radius_45degree, &ctx->sphere_inner_radius_45degree, NULL));
1267: } else {
1268: nt = LANDAU_DIM;
1269: PetscCall(PetscOptionsIntArray("-dm_landau_num_cells", "Number of cells in each dimension of base grid", "plexland.c", ctx->cells0, &nt, &flg));
1270: }
1271: }
1272: /* processing options */
1273: PetscCall(PetscOptionsBool("-dm_landau_gpu_assembly", "Assemble Jacobian on GPU", "plexland.c", ctx->gpu_assembly, &ctx->gpu_assembly, NULL));
1274: 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));
1275: 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");
1276: PetscCheck(!ctx->jacobian_field_major_order, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1277: PetscOptionsEnd();
1279: for (ii = ctx->num_species; ii < LANDAU_MAX_SPECIES; ii++) ctx->masses[ii] = ctx->thermal_temps[ii] = ctx->charges[ii] = 0;
1280: if (ctx->verbose != 0) {
1281: 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)));
1282: 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)));
1283: 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)));
1284: 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],
1285: (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));
1286: 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]));
1287: 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]));
1288: if (ctx->use_relativistic_corrections) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nUse relativistic corrections\n"));
1289: else PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1290: }
1291: PetscCall(DMDestroy(&dummy));
1292: {
1293: PetscMPIInt rank;
1294: PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
1295: ctx->stage = 0;
1296: PetscCall(PetscLogEventRegister("Landau Create", DM_CLASSID, &ctx->events[13])); /* 13 */
1297: PetscCall(PetscLogEventRegister(" GPU ass. setup", DM_CLASSID, &ctx->events[2])); /* 2 */
1298: PetscCall(PetscLogEventRegister(" Build matrix", DM_CLASSID, &ctx->events[12])); /* 12 */
1299: PetscCall(PetscLogEventRegister(" Assembly maps", DM_CLASSID, &ctx->events[15])); /* 15 */
1300: PetscCall(PetscLogEventRegister("Landau Mass mat", DM_CLASSID, &ctx->events[14])); /* 14 */
1301: PetscCall(PetscLogEventRegister("Landau Operator", DM_CLASSID, &ctx->events[11])); /* 11 */
1302: PetscCall(PetscLogEventRegister("Landau Jacobian", DM_CLASSID, &ctx->events[0])); /* 0 */
1303: PetscCall(PetscLogEventRegister("Landau Mass", DM_CLASSID, &ctx->events[9])); /* 9 */
1304: PetscCall(PetscLogEventRegister(" Preamble", DM_CLASSID, &ctx->events[10])); /* 10 */
1305: PetscCall(PetscLogEventRegister(" static IP Data", DM_CLASSID, &ctx->events[7])); /* 7 */
1306: PetscCall(PetscLogEventRegister(" dynamic IP-Jac", DM_CLASSID, &ctx->events[1])); /* 1 */
1307: PetscCall(PetscLogEventRegister(" Kernel-init", DM_CLASSID, &ctx->events[3])); /* 3 */
1308: PetscCall(PetscLogEventRegister(" Jac-f-df (GPU)", DM_CLASSID, &ctx->events[8])); /* 8 */
1309: PetscCall(PetscLogEventRegister(" J Kernel (GPU)", DM_CLASSID, &ctx->events[4])); /* 4 */
1310: PetscCall(PetscLogEventRegister(" M Kernel (GPU)", DM_CLASSID, &ctx->events[16])); /* 16 */
1311: PetscCall(PetscLogEventRegister(" Copy to CPU", DM_CLASSID, &ctx->events[5])); /* 5 */
1312: PetscCall(PetscLogEventRegister(" CPU assemble", DM_CLASSID, &ctx->events[6])); /* 6 */
1314: if (rank) { /* turn off output stuff for duplicate runs - do we need to add the prefix to all this? */
1315: PetscCall(PetscOptionsClearValue(NULL, "-snes_converged_reason"));
1316: PetscCall(PetscOptionsClearValue(NULL, "-ksp_converged_reason"));
1317: PetscCall(PetscOptionsClearValue(NULL, "-snes_monitor"));
1318: PetscCall(PetscOptionsClearValue(NULL, "-ksp_monitor"));
1319: PetscCall(PetscOptionsClearValue(NULL, "-ts_monitor"));
1320: PetscCall(PetscOptionsClearValue(NULL, "-ts_view"));
1321: PetscCall(PetscOptionsClearValue(NULL, "-ts_adapt_monitor"));
1322: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_dm_view"));
1323: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_amr_vec_view"));
1324: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_dm_view"));
1325: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mass_view"));
1326: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_jacobian_view"));
1327: PetscCall(PetscOptionsClearValue(NULL, "-dm_landau_mat_view"));
1328: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_converged_reason"));
1329: PetscCall(PetscOptionsClearValue(NULL, "-pc_bjkokkos_ksp_monitor"));
1330: PetscCall(PetscOptionsClearValue(NULL, "-"));
1331: PetscCall(PetscOptionsClearValue(NULL, "-info"));
1332: }
1333: }
1334: PetscFunctionReturn(PETSC_SUCCESS);
1335: }
1337: static PetscErrorCode CreateStaticData(PetscInt dim, IS grid_batch_is_inv[], LandauCtx *ctx)
1338: {
1339: PetscSection section[LANDAU_MAX_GRIDS], globsection[LANDAU_MAX_GRIDS];
1340: PetscQuadrature quad;
1341: const PetscReal *quadWeights;
1342: PetscReal invMass[LANDAU_MAX_SPECIES], nu_alpha[LANDAU_MAX_SPECIES], nu_beta[LANDAU_MAX_SPECIES];
1343: PetscInt numCells[LANDAU_MAX_GRIDS], Nq, Nb, Nf[LANDAU_MAX_GRIDS], ncellsTot = 0, MAP_BF_SIZE = 64 * LANDAU_DIM * LANDAU_DIM * LANDAU_MAX_Q_FACE * LANDAU_MAX_SPECIES;
1344: PetscTabulation *Tf;
1345: PetscDS prob;
1347: PetscFunctionBegin;
1348: PetscCall(PetscFEGetDimension(ctx->fe[0], &Nb));
1349: PetscCheck(Nb <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nb = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nb, LANDAU_MAX_NQND);
1350: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1351: for (PetscInt ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++) {
1352: invMass[ii] = ctx->m_0 / ctx->masses[ii];
1353: nu_alpha[ii] = PetscSqr(ctx->charges[ii] / ctx->m_0) * ctx->m_0 / ctx->masses[ii];
1354: nu_beta[ii] = PetscSqr(ctx->charges[ii] / ctx->epsilon0) / (8 * PETSC_PI) * ctx->t_0 * ctx->n_0 / PetscPowReal(ctx->v_0, 3);
1355: }
1356: }
1357: if (ctx->verbose == 4) {
1358: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "nu_alpha: "));
1359: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1360: int iii = ctx->species_offset[grid];
1361: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_alpha[ii]));
1362: }
1363: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_beta: "));
1364: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1365: int iii = ctx->species_offset[grid];
1366: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %e", (double)nu_beta[ii]));
1367: }
1368: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\nnu_alpha[i]*nu_beta[j]*lambda[i][j]:\n"));
1369: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1370: int iii = ctx->species_offset[grid];
1371: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) {
1372: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1373: int jjj = ctx->species_offset[gridj];
1374: 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])));
1375: }
1376: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1377: }
1378: }
1379: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "lambda[i][j]:\n"));
1380: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1381: int iii = ctx->species_offset[grid];
1382: for (PetscInt ii = iii; ii < ctx->species_offset[grid + 1]; ii++) {
1383: for (PetscInt gridj = 0; gridj < ctx->num_grids; gridj++) {
1384: int jjj = ctx->species_offset[gridj];
1385: for (PetscInt jj = jjj; jj < ctx->species_offset[gridj + 1]; jj++) PetscCall(PetscPrintf(PETSC_COMM_WORLD, " %14.9e", (double)ctx->lambdas[grid][gridj]));
1386: }
1387: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
1388: }
1389: }
1390: }
1391: PetscCall(DMGetDS(ctx->plex[0], &prob)); // same DS for all grids
1392: PetscCall(PetscDSGetTabulation(prob, &Tf)); // Bf, &Df same for all grids
1393: /* DS, Tab and quad is same on all grids */
1394: PetscCheck(ctx->plex[0], ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1395: PetscCall(PetscFEGetQuadrature(ctx->fe[0], &quad));
1396: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, &quadWeights));
1397: PetscCheck(Nq <= LANDAU_MAX_NQND, ctx->comm, PETSC_ERR_ARG_WRONG, "Order too high. Nq = %" PetscInt_FMT " > LANDAU_MAX_NQND (%d)", Nq, LANDAU_MAX_NQND);
1398: /* setup each grid */
1399: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1400: PetscInt cStart, cEnd;
1401: PetscCheck(ctx->plex[grid] != NULL, ctx->comm, PETSC_ERR_ARG_WRONG, "Plex not created");
1402: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1403: numCells[grid] = cEnd - cStart; // grids can have different topology
1404: PetscCall(DMGetLocalSection(ctx->plex[grid], §ion[grid]));
1405: PetscCall(DMGetGlobalSection(ctx->plex[grid], &globsection[grid]));
1406: PetscCall(PetscSectionGetNumFields(section[grid], &Nf[grid]));
1407: ncellsTot += numCells[grid];
1408: }
1409: /* create GPU assembly data */
1410: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1411: PetscContainer container;
1412: PetscScalar *elemMatrix, *elMat;
1413: pointInterpolationP4est(*pointMaps)[LANDAU_MAX_Q_FACE];
1414: P4estVertexMaps *maps;
1415: const PetscInt *plex_batch = NULL, elMatSz = Nb * Nb * ctx->num_species * ctx->num_species;
1416: LandauIdx *coo_elem_offsets = NULL, *coo_elem_fullNb = NULL, (*coo_elem_point_offsets)[LANDAU_MAX_NQND + 1] = NULL;
1417: /* create GPU assembly data */
1418: PetscCall(PetscInfo(ctx->plex[0], "Make GPU maps %d\n", 1));
1419: PetscCall(PetscLogEventBegin(ctx->events[2], 0, 0, 0, 0));
1420: PetscCall(PetscMalloc(sizeof(*maps) * ctx->num_grids, &maps));
1421: PetscCall(PetscMalloc(sizeof(*pointMaps) * MAP_BF_SIZE, &pointMaps));
1422: PetscCall(PetscMalloc(sizeof(*elemMatrix) * elMatSz, &elemMatrix));
1424: { // setup COO assembly -- put COO metadata directly in ctx->SData_d
1425: PetscCall(PetscMalloc3(ncellsTot + 1, &coo_elem_offsets, ncellsTot, &coo_elem_fullNb, ncellsTot, &coo_elem_point_offsets)); // array of integer pointers
1426: coo_elem_offsets[0] = 0; // finish later
1427: PetscCall(PetscInfo(ctx->plex[0], "COO initialization, %" PetscInt_FMT " cells\n", ncellsTot));
1428: ctx->SData_d.coo_n_cellsTot = ncellsTot;
1429: ctx->SData_d.coo_elem_offsets = (void *)coo_elem_offsets;
1430: ctx->SData_d.coo_elem_fullNb = (void *)coo_elem_fullNb;
1431: ctx->SData_d.coo_elem_point_offsets = (void *)coo_elem_point_offsets;
1432: }
1434: ctx->SData_d.coo_max_fullnb = 0;
1435: for (PetscInt grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1436: PetscInt cStart, cEnd, Nfloc = Nf[grid], totDim = Nfloc * Nb;
1437: if (grid_batch_is_inv[grid]) PetscCall(ISGetIndices(grid_batch_is_inv[grid], &plex_batch));
1438: PetscCheck(!plex_batch, ctx->comm, PETSC_ERR_ARG_WRONG, "-dm_landau_jacobian_field_major_order DEPRECATED");
1439: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1440: // make maps
1441: maps[grid].d_self = NULL;
1442: maps[grid].num_elements = numCells[grid];
1443: maps[grid].num_face = (PetscInt)(pow(Nq, 1. / ((double)dim)) + .001); // Q
1444: maps[grid].num_face = (PetscInt)(pow(maps[grid].num_face, (double)(dim - 1)) + .001); // Q^2
1445: maps[grid].num_reduced = 0;
1446: maps[grid].deviceType = ctx->deviceType;
1447: maps[grid].numgrids = ctx->num_grids;
1448: // count reduced and get
1449: PetscCall(PetscMalloc(maps[grid].num_elements * sizeof(*maps[grid].gIdx), &maps[grid].gIdx));
1450: for (int ej = cStart, eidx = 0; ej < cEnd; ++ej, ++eidx, glb_elem_idx++) {
1451: if (coo_elem_offsets) coo_elem_offsets[glb_elem_idx + 1] = coo_elem_offsets[glb_elem_idx]; // start with last one, then add
1452: for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1453: int fullNb = 0;
1454: for (int q = 0; q < Nb; ++q) {
1455: PetscInt numindices, *indices;
1456: PetscScalar *valuesOrig = elMat = elemMatrix;
1457: PetscCall(PetscArrayzero(elMat, totDim * totDim));
1458: elMat[(fieldA * Nb + q) * totDim + fieldA * Nb + q] = 1;
1459: PetscCall(DMPlexGetClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat));
1460: if (ctx->simplex) {
1461: PetscCheck(numindices == Nb, ctx->comm, PETSC_ERR_ARG_WRONG, "numindices != Nb numindices=%d Nb=%d", (int)numindices, (int)Nb);
1462: for (int q = 0; q < numindices; ++q) { maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)indices[q]; }
1463: fullNb++;
1464: } else {
1465: for (PetscInt f = 0; f < numindices; ++f) { // look for a non-zero on the diagonal (is this too complicated for simplices?)
1466: if (PetscAbs(PetscRealPart(elMat[f * numindices + f])) > PETSC_MACHINE_EPSILON) {
1467: // found it
1468: if (PetscAbs(PetscRealPart(elMat[f * numindices + f] - 1.)) < PETSC_MACHINE_EPSILON) { // normal vertex 1.0
1469: if (plex_batch) {
1470: maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)plex_batch[indices[f]];
1471: } else {
1472: maps[grid].gIdx[eidx][fieldA][q] = (LandauIdx)indices[f];
1473: }
1474: fullNb++;
1475: } else { //found a constraint
1476: int jj = 0;
1477: PetscReal sum = 0;
1478: const PetscInt ff = f;
1479: maps[grid].gIdx[eidx][fieldA][q] = -maps[grid].num_reduced - 1; // store (-)index: id = -(idx+1): idx = -id - 1
1480: PetscCheck(!ctx->simplex, ctx->comm, PETSC_ERR_ARG_WRONG, "No constraints with simplex");
1481: do { // constraints are continuous in Plex - exploit that here
1482: int ii; // get 'scale'
1483: 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
1484: 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
1485: pointMaps[maps[grid].num_reduced][jj].scale += PetscRealPart(elMat[f * numindices + ff + ii]);
1486: }
1487: }
1488: sum += pointMaps[maps[grid].num_reduced][jj].scale; // diagnostic
1489: // get 'gid'
1490: if (pointMaps[maps[grid].num_reduced][jj].scale == 0) pointMaps[maps[grid].num_reduced][jj].gid = -1; // 3D has Q and Q^2 interps
1491: else {
1492: if (plex_batch) {
1493: pointMaps[maps[grid].num_reduced][jj].gid = plex_batch[indices[f]];
1494: } else {
1495: pointMaps[maps[grid].num_reduced][jj].gid = indices[f];
1496: }
1497: fullNb++;
1498: }
1499: } while (++jj < maps[grid].num_face && ++f < numindices); // jj is incremented if we hit the end
1500: while (jj < maps[grid].num_face) {
1501: pointMaps[maps[grid].num_reduced][jj].scale = 0;
1502: pointMaps[maps[grid].num_reduced][jj].gid = -1;
1503: jj++;
1504: }
1505: if (PetscAbs(sum - 1.0) > 10 * PETSC_MACHINE_EPSILON) { // debug
1506: int d, f;
1507: PetscReal tmp = 0;
1508: 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));
1509: for (d = 0, tmp = 0; d < numindices; ++d) {
1510: if (tmp != 0 && PetscAbs(tmp - 1.0) > 10 * PETSC_MACHINE_EPSILON) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%3d) %3" PetscInt_FMT ": ", d, indices[d]));
1511: for (f = 0; f < numindices; ++f) tmp += PetscRealPart(elMat[d * numindices + f]);
1512: if (tmp != 0) PetscCall(PetscPrintf(ctx->comm, " | %22.16e\n", (double)tmp));
1513: }
1514: }
1515: maps[grid].num_reduced++;
1516: 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);
1517: }
1518: break;
1519: }
1520: }
1521: } // !simplex
1522: // cleanup
1523: PetscCall(DMPlexRestoreClosureIndices(ctx->plex[grid], section[grid], globsection[grid], ej, PETSC_TRUE, &numindices, &indices, NULL, (PetscScalar **)&elMat));
1524: if (elMat != valuesOrig) PetscCall(DMRestoreWorkArray(ctx->plex[grid], numindices * numindices, MPIU_SCALAR, &elMat));
1525: }
1526: { // setup COO assembly
1527: coo_elem_offsets[glb_elem_idx + 1] += fullNb * fullNb; // one species block, adds a block for each species, on this element in this grid
1528: if (fieldA == 0) { // cache full Nb for this element, on this grid per species
1529: coo_elem_fullNb[glb_elem_idx] = fullNb;
1530: if (fullNb > ctx->SData_d.coo_max_fullnb) ctx->SData_d.coo_max_fullnb = fullNb;
1531: } 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);
1532: }
1533: } // field
1534: } // cell
1535: // allocate and copy point data maps[grid].gIdx[eidx][field][q]
1536: PetscCall(PetscMalloc(maps[grid].num_reduced * sizeof(*maps[grid].c_maps), &maps[grid].c_maps));
1537: for (int ej = 0; ej < maps[grid].num_reduced; ++ej) {
1538: for (int q = 0; q < maps[grid].num_face; ++q) {
1539: maps[grid].c_maps[ej][q].scale = pointMaps[ej][q].scale;
1540: maps[grid].c_maps[ej][q].gid = pointMaps[ej][q].gid;
1541: }
1542: }
1543: #if defined(PETSC_HAVE_KOKKOS)
1544: if (ctx->deviceType == LANDAU_KOKKOS) {
1545: PetscCall(LandauKokkosCreateMatMaps(maps, pointMaps, Nf, grid)); // implies Kokkos does
1546: }
1547: #endif
1548: if (plex_batch) {
1549: PetscCall(ISRestoreIndices(grid_batch_is_inv[grid], &plex_batch));
1550: PetscCall(ISDestroy(&grid_batch_is_inv[grid])); // we are done with this
1551: }
1552: } /* grids */
1553: // finish COO
1554: { // setup COO assembly
1555: PetscInt *oor, *ooc;
1556: ctx->SData_d.coo_size = coo_elem_offsets[ncellsTot] * ctx->batch_sz;
1557: PetscCall(PetscMalloc2(ctx->SData_d.coo_size, &oor, ctx->SData_d.coo_size, &ooc));
1558: for (int i = 0; i < ctx->SData_d.coo_size; i++) oor[i] = ooc[i] = -1;
1559: // get
1560: for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1561: for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1562: const int fullNb = coo_elem_fullNb[glb_elem_idx];
1563: 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
1564: coo_elem_point_offsets[glb_elem_idx][0] = 0;
1565: for (int f = 0, cnt2 = 0; f < Nb; f++) {
1566: int idx = Idxs[f];
1567: coo_elem_point_offsets[glb_elem_idx][f + 1] = coo_elem_point_offsets[glb_elem_idx][f]; // start at last
1568: if (idx >= 0) {
1569: cnt2++;
1570: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1571: } else {
1572: idx = -idx - 1;
1573: for (int q = 0; q < maps[grid].num_face; q++) {
1574: if (maps[grid].c_maps[idx][q].gid < 0) break;
1575: cnt2++;
1576: coo_elem_point_offsets[glb_elem_idx][f + 1]++; // inc
1577: }
1578: }
1579: PetscCheck(cnt2 <= fullNb, PETSC_COMM_SELF, PETSC_ERR_PLIB, "wrong count %d < %d", fullNb, cnt2);
1580: }
1581: 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);
1582: }
1583: }
1584: // set
1585: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1586: for (int grid = 0, glb_elem_idx = 0; grid < ctx->num_grids; grid++) {
1587: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1588: for (int ej = 0; ej < numCells[grid]; ++ej, glb_elem_idx++) {
1589: const int fullNb = coo_elem_fullNb[glb_elem_idx], fullNb2 = fullNb * fullNb;
1590: // set (i,j)
1591: for (int fieldA = 0; fieldA < Nf[grid]; fieldA++) {
1592: const LandauIdx *const Idxs = &maps[grid].gIdx[ej][fieldA][0];
1593: int rows[LANDAU_MAX_Q_FACE], cols[LANDAU_MAX_Q_FACE];
1594: for (int f = 0; f < Nb; ++f) {
1595: const int nr = coo_elem_point_offsets[glb_elem_idx][f + 1] - coo_elem_point_offsets[glb_elem_idx][f];
1596: if (nr == 1) rows[0] = Idxs[f];
1597: else {
1598: const int idx = -Idxs[f] - 1;
1599: for (int q = 0; q < nr; q++) rows[q] = maps[grid].c_maps[idx][q].gid;
1600: }
1601: for (int g = 0; g < Nb; ++g) {
1602: const int nc = coo_elem_point_offsets[glb_elem_idx][g + 1] - coo_elem_point_offsets[glb_elem_idx][g];
1603: if (nc == 1) cols[0] = Idxs[g];
1604: else {
1605: const int idx = -Idxs[g] - 1;
1606: for (int q = 0; q < nc; q++) cols[q] = maps[grid].c_maps[idx][q].gid;
1607: }
1608: 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];
1609: for (int q = 0, idx = idx0; q < nr; q++) {
1610: for (int d = 0; d < nc; d++, idx++) {
1611: oor[idx] = rows[q] + moffset;
1612: ooc[idx] = cols[d] + moffset;
1613: }
1614: }
1615: }
1616: }
1617: }
1618: } // cell
1619: } // grid
1620: } // batch
1621: PetscCall(MatSetPreallocationCOO(ctx->J, ctx->SData_d.coo_size, oor, ooc));
1622: PetscCall(PetscFree2(oor, ooc));
1623: }
1624: PetscCall(PetscFree(pointMaps));
1625: PetscCall(PetscFree(elemMatrix));
1626: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
1627: PetscCall(PetscContainerSetPointer(container, (void *)maps));
1628: PetscCall(PetscContainerSetUserDestroy(container, LandauGPUMapsDestroy));
1629: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "assembly_maps", (PetscObject)container));
1630: PetscCall(PetscContainerDestroy(&container));
1631: PetscCall(PetscLogEventEnd(ctx->events[2], 0, 0, 0, 0));
1632: } // end GPU assembly
1633: { /* create static point data, Jacobian called first, only one vertex copy */
1634: PetscReal *invJe, *ww, *xx, *yy, *zz = NULL, *invJ_a;
1635: PetscInt outer_ipidx, outer_ej, grid, nip_glb = 0;
1636: PetscFE fe;
1637: PetscCall(PetscLogEventBegin(ctx->events[7], 0, 0, 0, 0));
1638: PetscCall(PetscInfo(ctx->plex[0], "Initialize static data\n"));
1639: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) nip_glb += Nq * numCells[grid];
1640: /* collect f data, first time is for Jacobian, but make mass now */
1641: if (ctx->verbose != 0) {
1642: PetscInt ncells = 0, N;
1643: PetscCall(MatGetSize(ctx->J, &N, NULL));
1644: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) ncells += numCells[grid];
1645: 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,
1646: ctx->num_species, Nb, dim, N));
1647: }
1648: PetscCall(PetscMalloc4(nip_glb, &ww, nip_glb, &xx, nip_glb, &yy, nip_glb * dim * dim, &invJ_a));
1649: if (dim == 3) PetscCall(PetscMalloc1(nip_glb, &zz));
1650: if (ctx->use_energy_tensor_trick) {
1651: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, ctx->simplex, NULL, PETSC_DECIDE, &fe));
1652: PetscCall(PetscObjectSetName((PetscObject)fe, "energy"));
1653: }
1654: /* init each grids static data - no batch */
1655: for (grid = 0, outer_ipidx = 0, outer_ej = 0; grid < ctx->num_grids; grid++) { // OpenMP (once)
1656: Vec v2_2 = NULL; // projected function: v^2/2 for non-relativistic, gamma... for relativistic
1657: PetscSection e_section;
1658: DM dmEnergy;
1659: PetscInt cStart, cEnd, ej;
1661: PetscCall(DMPlexGetHeightStratum(ctx->plex[grid], 0, &cStart, &cEnd));
1662: // prep energy trick, get v^2 / 2 vector
1663: if (ctx->use_energy_tensor_trick) {
1664: PetscErrorCode (*energyf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {ctx->use_relativistic_corrections ? gamma_m1_f : energy_f};
1665: Vec glob_v2;
1666: PetscReal *c2_0[1], data[1] = {PetscSqr(C_0(ctx->v_0))};
1668: PetscCall(DMClone(ctx->plex[grid], &dmEnergy));
1669: PetscCall(PetscObjectSetName((PetscObject)dmEnergy, "energy"));
1670: PetscCall(DMSetField(dmEnergy, 0, NULL, (PetscObject)fe));
1671: PetscCall(DMCreateDS(dmEnergy));
1672: PetscCall(DMGetSection(dmEnergy, &e_section));
1673: PetscCall(DMGetGlobalVector(dmEnergy, &glob_v2));
1674: PetscCall(PetscObjectSetName((PetscObject)glob_v2, "trick"));
1675: c2_0[0] = &data[0];
1676: PetscCall(DMProjectFunction(dmEnergy, 0., energyf, (void **)c2_0, INSERT_ALL_VALUES, glob_v2));
1677: PetscCall(DMGetLocalVector(dmEnergy, &v2_2));
1678: PetscCall(VecZeroEntries(v2_2)); /* zero BCs so don't set */
1679: PetscCall(DMGlobalToLocalBegin(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1680: PetscCall(DMGlobalToLocalEnd(dmEnergy, glob_v2, INSERT_VALUES, v2_2));
1681: PetscCall(DMViewFromOptions(dmEnergy, NULL, "-energy_dm_view"));
1682: PetscCall(VecViewFromOptions(glob_v2, NULL, "-energy_vec_view"));
1683: PetscCall(DMRestoreGlobalVector(dmEnergy, &glob_v2));
1684: }
1685: /* append part of the IP data for each grid */
1686: for (ej = 0; ej < numCells[grid]; ++ej, ++outer_ej) {
1687: PetscScalar *coefs = NULL;
1688: PetscReal vj[LANDAU_MAX_NQND * LANDAU_DIM], detJj[LANDAU_MAX_NQND], Jdummy[LANDAU_MAX_NQND * LANDAU_DIM * LANDAU_DIM], c0 = C_0(ctx->v_0), c02 = PetscSqr(c0);
1689: invJe = invJ_a + outer_ej * Nq * dim * dim;
1690: PetscCall(DMPlexComputeCellGeometryFEM(ctx->plex[grid], ej + cStart, quad, vj, Jdummy, invJe, detJj));
1691: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecGetClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1692: /* create static point data */
1693: for (PetscInt qj = 0; qj < Nq; qj++, outer_ipidx++) {
1694: const PetscInt gidx = outer_ipidx;
1695: const PetscReal *invJ = &invJe[qj * dim * dim];
1696: ww[gidx] = detJj[qj] * quadWeights[qj];
1697: if (dim == 2) ww[gidx] *= vj[qj * dim + 0]; /* cylindrical coordinate, w/o 2pi */
1698: // get xx, yy, zz
1699: if (ctx->use_energy_tensor_trick) {
1700: double refSpaceDer[3], eGradPhi[3];
1701: const PetscReal *const DD = Tf[0]->T[1];
1702: const PetscReal *Dq = &DD[qj * Nb * dim];
1703: for (int d = 0; d < 3; ++d) refSpaceDer[d] = eGradPhi[d] = 0.0;
1704: for (int b = 0; b < Nb; ++b) {
1705: for (int d = 0; d < dim; ++d) refSpaceDer[d] += Dq[b * dim + d] * PetscRealPart(coefs[b]);
1706: }
1707: xx[gidx] = 1e10;
1708: if (ctx->use_relativistic_corrections) {
1709: double dg2_c2 = 0;
1710: //for (int d = 0; d < dim; ++d) refSpaceDer[d] *= c02;
1711: for (int d = 0; d < dim; ++d) dg2_c2 += PetscSqr(refSpaceDer[d]);
1712: dg2_c2 *= (double)c02;
1713: if (dg2_c2 >= .999) {
1714: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1715: yy[gidx] = vj[qj * dim + 1];
1716: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1717: 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]));
1718: } else {
1719: PetscReal fact = c02 / PetscSqrtReal(1. - dg2_c2);
1720: for (int d = 0; d < dim; ++d) refSpaceDer[d] *= fact;
1721: // could test with other point u' that (grad - grad') * U (refSpaceDer, refSpaceDer') == 0
1722: }
1723: }
1724: if (xx[gidx] == 1e10) {
1725: for (int d = 0; d < dim; ++d) {
1726: for (int e = 0; e < dim; ++e) eGradPhi[d] += invJ[e * dim + d] * refSpaceDer[e];
1727: }
1728: xx[gidx] = eGradPhi[0];
1729: yy[gidx] = eGradPhi[1];
1730: if (dim == 3) zz[gidx] = eGradPhi[2];
1731: }
1732: } else {
1733: xx[gidx] = vj[qj * dim + 0]; /* coordinate */
1734: yy[gidx] = vj[qj * dim + 1];
1735: if (dim == 3) zz[gidx] = vj[qj * dim + 2];
1736: }
1737: } /* q */
1738: if (ctx->use_energy_tensor_trick) PetscCall(DMPlexVecRestoreClosure(dmEnergy, e_section, v2_2, ej + cStart, NULL, &coefs));
1739: } /* ej */
1740: if (ctx->use_energy_tensor_trick) {
1741: PetscCall(DMRestoreLocalVector(dmEnergy, &v2_2));
1742: PetscCall(DMDestroy(&dmEnergy));
1743: }
1744: } /* grid */
1745: if (ctx->use_energy_tensor_trick) PetscCall(PetscFEDestroy(&fe));
1746: /* cache static data */
1747: if (ctx->deviceType == LANDAU_KOKKOS) {
1748: #if defined(PETSC_HAVE_KOKKOS)
1749: PetscCall(LandauKokkosStaticDataSet(ctx->plex[0], Nq, Nb, ctx->batch_sz, ctx->num_grids, numCells, ctx->species_offset, ctx->mat_offset, nu_alpha, nu_beta, invMass, (PetscReal *)ctx->lambdas, invJ_a, xx, yy, zz, ww, &ctx->SData_d));
1750: #else
1751: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type kokkos not built");
1752: #endif
1753: /* free */
1754: PetscCall(PetscFree4(ww, xx, yy, invJ_a));
1755: if (dim == 3) PetscCall(PetscFree(zz));
1756: } else { /* CPU version, just copy in, only use part */
1757: 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 ?
1758: ctx->SData_d.w = (void *)ww;
1759: ctx->SData_d.x = (void *)xx;
1760: ctx->SData_d.y = (void *)yy;
1761: ctx->SData_d.z = (void *)zz;
1762: ctx->SData_d.invJ = (void *)invJ_a;
1763: 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));
1764: for (PetscInt ii = 0; ii < ctx->num_species; ii++) {
1765: nu_alpha_p[ii] = nu_alpha[ii];
1766: nu_beta_p[ii] = nu_beta[ii];
1767: invMass_p[ii] = invMass[ii];
1768: }
1769: ctx->SData_d.alpha = (void *)nu_alpha_p;
1770: ctx->SData_d.beta = (void *)nu_beta_p;
1771: ctx->SData_d.invMass = (void *)invMass_p;
1772: ctx->SData_d.lambdas = (void *)lambdas_p;
1773: for (PetscInt grid = 0; grid < LANDAU_MAX_GRIDS; grid++) {
1774: PetscReal(*lambdas)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS] = (PetscReal(*)[LANDAU_MAX_GRIDS][LANDAU_MAX_GRIDS])ctx->SData_d.lambdas;
1775: for (PetscInt gridj = 0; gridj < LANDAU_MAX_GRIDS; gridj++) { (*lambdas)[grid][gridj] = ctx->lambdas[grid][gridj]; }
1776: }
1777: }
1778: PetscCall(PetscLogEventEnd(ctx->events[7], 0, 0, 0, 0));
1779: } // initialize
1780: PetscFunctionReturn(PETSC_SUCCESS);
1781: }
1783: /* < v, u > */
1784: 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[])
1785: {
1786: g0[0] = 1.;
1787: }
1789: /* < v, u > */
1790: 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[])
1791: {
1792: static double ttt = 1e-12;
1793: g0[0] = ttt++;
1794: }
1796: /* < v, u > */
1797: 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[])
1798: {
1799: g0[0] = 2. * PETSC_PI * x[0];
1800: }
1802: static PetscErrorCode MatrixNfDestroy(void *ptr)
1803: {
1804: PetscInt *nf = (PetscInt *)ptr;
1805: PetscFunctionBegin;
1806: PetscCall(PetscFree(nf));
1807: PetscFunctionReturn(PETSC_SUCCESS);
1808: }
1810: /*
1811: LandauCreateJacobianMatrix - creates ctx->J with without real data. Hard to keep sparse.
1812: - Like DMPlexLandauCreateMassMatrix. Should remove one and combine
1813: - has old support for field major ordering
1814: */
1815: static PetscErrorCode LandauCreateJacobianMatrix(MPI_Comm comm, Vec X, IS grid_batch_is_inv[LANDAU_MAX_GRIDS], LandauCtx *ctx)
1816: {
1817: PetscInt *idxs = NULL;
1818: Mat subM[LANDAU_MAX_GRIDS];
1820: PetscFunctionBegin;
1821: if (!ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
1822: PetscFunctionReturn(PETSC_SUCCESS);
1823: }
1824: // get the RCM for this grid to separate out species into blocks -- create 'idxs' & 'ctx->batch_is' -- not used
1825: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) PetscCall(PetscMalloc1(ctx->mat_offset[ctx->num_grids] * ctx->batch_sz, &idxs));
1826: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1827: const PetscInt *values, n = ctx->mat_offset[grid + 1] - ctx->mat_offset[grid];
1828: Mat gMat;
1829: DM massDM;
1830: PetscDS prob;
1831: Vec tvec;
1832: // get "mass" matrix for reordering
1833: PetscCall(DMClone(ctx->plex[grid], &massDM));
1834: PetscCall(DMCopyFields(ctx->plex[grid], massDM));
1835: PetscCall(DMCreateDS(massDM));
1836: PetscCall(DMGetDS(massDM, &prob));
1837: 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));
1838: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only")); // this trick is need to both sparsify the matrix and avoid runtime error
1839: PetscCall(DMCreateMatrix(massDM, &gMat));
1840: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
1841: PetscCall(MatSetOption(gMat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
1842: PetscCall(MatSetOption(gMat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
1843: PetscCall(DMCreateLocalVector(ctx->plex[grid], &tvec));
1844: PetscCall(DMPlexSNESComputeJacobianFEM(massDM, tvec, gMat, gMat, ctx));
1845: PetscCall(MatViewFromOptions(gMat, NULL, "-dm_landau_reorder_mat_view"));
1846: PetscCall(DMDestroy(&massDM));
1847: PetscCall(VecDestroy(&tvec));
1848: subM[grid] = gMat;
1849: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1850: MatOrderingType rtype = MATORDERINGRCM;
1851: IS isrow, isicol;
1852: PetscCall(MatGetOrdering(gMat, rtype, &isrow, &isicol));
1853: PetscCall(ISInvertPermutation(isrow, PETSC_DECIDE, &grid_batch_is_inv[grid]));
1854: PetscCall(ISGetIndices(isrow, &values));
1855: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
1856: #if !defined(LANDAU_SPECIES_MAJOR)
1857: PetscInt N = ctx->mat_offset[ctx->num_grids], n0 = ctx->mat_offset[grid] + b_id * N;
1858: for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1859: #else
1860: PetscInt n0 = ctx->mat_offset[grid] * ctx->batch_sz + b_id * n;
1861: for (int ii = 0; ii < n; ++ii) idxs[n0 + ii] = values[ii] + n0;
1862: #endif
1863: }
1864: PetscCall(ISRestoreIndices(isrow, &values));
1865: PetscCall(ISDestroy(&isrow));
1866: PetscCall(ISDestroy(&isicol));
1867: }
1868: }
1869: 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));
1870: // get a block matrix
1871: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1872: Mat B = subM[grid];
1873: PetscInt nloc, nzl, *colbuf, row, COL_BF_SIZE = 1024;
1874: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1875: PetscCall(MatGetSize(B, &nloc, NULL));
1876: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
1877: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
1878: const PetscInt *cols;
1879: const PetscScalar *vals;
1880: for (int i = 0; i < nloc; i++) {
1881: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
1882: if (nzl > COL_BF_SIZE) {
1883: PetscCall(PetscFree(colbuf));
1884: 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));
1885: COL_BF_SIZE = nzl;
1886: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
1887: }
1888: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
1889: for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
1890: row = i + moffset;
1891: PetscCall(MatSetValues(ctx->J, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
1892: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
1893: }
1894: }
1895: PetscCall(PetscFree(colbuf));
1896: }
1897: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
1898: PetscCall(MatAssemblyBegin(ctx->J, MAT_FINAL_ASSEMBLY));
1899: PetscCall(MatAssemblyEnd(ctx->J, MAT_FINAL_ASSEMBLY));
1901: // debug
1902: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_mat_view"));
1903: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
1904: Mat mat_block_order;
1905: PetscCall(MatCreateSubMatrix(ctx->J, ctx->batch_is, ctx->batch_is, MAT_INITIAL_MATRIX, &mat_block_order)); // use MatPermute
1906: PetscCall(MatViewFromOptions(mat_block_order, NULL, "-dm_landau_mat_view"));
1907: PetscCall(MatDestroy(&mat_block_order));
1908: PetscCall(VecScatterCreate(X, ctx->batch_is, X, NULL, &ctx->plex_batch));
1909: PetscCall(VecDuplicate(X, &ctx->work_vec));
1910: }
1912: PetscFunctionReturn(PETSC_SUCCESS);
1913: }
1915: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat);
1916: /*@C
1917: DMPlexLandauCreateVelocitySpace - Create a `DMPLEX` velocity space mesh
1919: Collective
1921: Input Parameters:
1922: + comm - The MPI communicator
1923: . dim - velocity space dimension (2 for axisymmetric, 3 for full 3X + 3V solver)
1924: - prefix - prefix for options (not tested)
1926: Output Parameters:
1927: + pack - The `DM` object representing the mesh
1928: . X - A vector (user destroys)
1929: - J - Optional matrix (object destroys)
1931: Level: beginner
1933: .seealso: `DMPlexCreate()`, `DMPlexLandauDestroyVelocitySpace()`
1934: @*/
1935: PetscErrorCode DMPlexLandauCreateVelocitySpace(MPI_Comm comm, PetscInt dim, const char prefix[], Vec *X, Mat *J, DM *pack)
1936: {
1937: LandauCtx *ctx;
1938: Vec Xsub[LANDAU_MAX_GRIDS];
1939: IS grid_batch_is_inv[LANDAU_MAX_GRIDS];
1941: PetscFunctionBegin;
1942: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Only 2D and 3D supported");
1943: PetscCheck(LANDAU_DIM == dim, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " != LANDAU_DIM %d", dim, LANDAU_DIM);
1944: PetscCall(PetscNew(&ctx));
1945: ctx->comm = comm; /* used for diagnostics and global errors */
1946: /* process options */
1947: PetscCall(ProcessOptions(ctx, prefix));
1948: if (dim == 2) ctx->use_relativistic_corrections = PETSC_FALSE;
1949: /* Create Mesh */
1950: PetscCall(DMCompositeCreate(PETSC_COMM_SELF, pack));
1951: PetscCall(PetscLogEventBegin(ctx->events[13], 0, 0, 0, 0));
1952: PetscCall(PetscLogEventBegin(ctx->events[15], 0, 0, 0, 0));
1953: PetscCall(LandauDMCreateVMeshes(PETSC_COMM_SELF, dim, prefix, ctx, *pack)); // creates grids (Forest of AMR)
1954: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1955: /* create FEM */
1956: PetscCall(SetupDS(ctx->plex[grid], dim, grid, ctx));
1957: /* set initial state */
1958: PetscCall(DMCreateGlobalVector(ctx->plex[grid], &Xsub[grid]));
1959: PetscCall(PetscObjectSetName((PetscObject)Xsub[grid], "u_orig"));
1960: /* initial static refinement, no solve */
1961: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, 0, 1, ctx));
1962: /* forest refinement - forest goes in (if forest), plex comes out */
1963: if (ctx->use_p4est) {
1964: DM plex;
1965: PetscCall(adapt(grid, ctx, &Xsub[grid])); // forest goes in, plex comes out
1966: PetscCall(DMViewFromOptions(ctx->plex[grid], NULL, "-dm_landau_amr_dm_view")); // need to differentiate - todo
1967: PetscCall(VecViewFromOptions(Xsub[grid], NULL, "-dm_landau_amr_vec_view"));
1968: // convert to plex, all done with this level
1969: PetscCall(DMConvert(ctx->plex[grid], DMPLEX, &plex));
1970: PetscCall(DMDestroy(&ctx->plex[grid]));
1971: ctx->plex[grid] = plex;
1972: }
1973: #if !defined(LANDAU_SPECIES_MAJOR)
1974: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
1975: #else
1976: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
1977: PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
1978: }
1979: #endif
1980: PetscCall(DMSetApplicationContext(ctx->plex[grid], ctx));
1981: }
1982: #if !defined(LANDAU_SPECIES_MAJOR)
1983: // stack the batched DMs, could do it all here!!! b_id=0
1984: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
1985: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(*pack, ctx->plex[grid]));
1986: }
1987: #endif
1988: // create ctx->mat_offset
1989: ctx->mat_offset[0] = 0;
1990: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
1991: PetscInt n;
1992: PetscCall(VecGetLocalSize(Xsub[grid], &n));
1993: ctx->mat_offset[grid + 1] = ctx->mat_offset[grid] + n;
1994: }
1995: // creat DM & Jac
1996: PetscCall(DMSetApplicationContext(*pack, ctx));
1997: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
1998: PetscCall(DMCreateMatrix(*pack, &ctx->J));
1999: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2000: PetscCall(MatSetOption(ctx->J, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2001: PetscCall(MatSetOption(ctx->J, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2002: PetscCall(PetscObjectSetName((PetscObject)ctx->J, "Jac"));
2003: // construct initial conditions in X
2004: PetscCall(DMCreateGlobalVector(*pack, X));
2005: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2006: PetscInt n;
2007: PetscCall(VecGetLocalSize(Xsub[grid], &n));
2008: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2009: PetscScalar const *values;
2010: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2011: PetscCall(LandauSetInitialCondition(ctx->plex[grid], Xsub[grid], grid, b_id, ctx->batch_sz, ctx));
2012: PetscCall(VecGetArrayRead(Xsub[grid], &values)); // Drop whole grid in Plex ordering
2013: for (int i = 0, idx = moffset; i < n; i++, idx++) PetscCall(VecSetValue(*X, idx, values[i], INSERT_VALUES));
2014: PetscCall(VecRestoreArrayRead(Xsub[grid], &values));
2015: }
2016: }
2017: // cleanup
2018: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(VecDestroy(&Xsub[grid]));
2019: /* check for correct matrix type */
2020: if (ctx->gpu_assembly) { /* we need GPU object with GPU assembly */
2021: PetscBool flg;
2022: if (ctx->deviceType == LANDAU_KOKKOS) {
2023: PetscCall(PetscObjectTypeCompareAny((PetscObject)ctx->J, &flg, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, MATAIJKOKKOS, ""));
2024: #if defined(PETSC_HAVE_KOKKOS)
2025: 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'");
2026: #else
2027: 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'");
2028: #endif
2029: }
2030: }
2031: PetscCall(PetscLogEventEnd(ctx->events[15], 0, 0, 0, 0));
2033: // create field major ordering
2034: ctx->work_vec = NULL;
2035: ctx->plex_batch = NULL;
2036: ctx->batch_is = NULL;
2037: for (int i = 0; i < LANDAU_MAX_GRIDS; i++) grid_batch_is_inv[i] = NULL;
2038: PetscCall(PetscLogEventBegin(ctx->events[12], 0, 0, 0, 0));
2039: PetscCall(LandauCreateJacobianMatrix(comm, *X, grid_batch_is_inv, ctx));
2040: PetscCall(PetscLogEventEnd(ctx->events[12], 0, 0, 0, 0));
2042: // create AMR GPU assembly maps and static GPU data
2043: PetscCall(CreateStaticData(dim, grid_batch_is_inv, ctx));
2045: PetscCall(PetscLogEventEnd(ctx->events[13], 0, 0, 0, 0));
2047: // create mass matrix
2048: PetscCall(DMPlexLandauCreateMassMatrix(*pack, NULL));
2050: if (J) *J = ctx->J;
2052: if (ctx->gpu_assembly && ctx->jacobian_field_major_order) {
2053: PetscContainer container;
2054: // cache ctx for KSP with batch/field major Jacobian ordering -ksp_type gmres/etc -dm_landau_jacobian_field_major_order
2055: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2056: PetscCall(PetscContainerSetPointer(container, (void *)ctx));
2057: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "LandauCtx", (PetscObject)container));
2058: PetscCall(PetscContainerDestroy(&container));
2059: // batch solvers need to map -- can batch solvers work
2060: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2061: PetscCall(PetscContainerSetPointer(container, (void *)ctx->plex_batch));
2062: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "plex_batch_is", (PetscObject)container));
2063: PetscCall(PetscContainerDestroy(&container));
2064: }
2065: // for batch solvers
2066: {
2067: PetscContainer container;
2068: PetscInt *pNf;
2069: PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container));
2070: PetscCall(PetscMalloc1(sizeof(*pNf), &pNf));
2071: *pNf = ctx->batch_sz;
2072: PetscCall(PetscContainerSetPointer(container, (void *)pNf));
2073: PetscCall(PetscContainerSetUserDestroy(container, MatrixNfDestroy));
2074: PetscCall(PetscObjectCompose((PetscObject)ctx->J, "batch size", (PetscObject)container));
2075: PetscCall(PetscContainerDestroy(&container));
2076: }
2078: PetscFunctionReturn(PETSC_SUCCESS);
2079: }
2081: /*@C
2082: DMPlexLandauAccess - Access to the distribution function with user callback
2084: Collective
2086: Input Parameters:
2087: + pack - the `DMCOMPOSITE`
2088: . func - call back function
2089: - user_ctx - user context
2091: Input/Output Parameter:
2092: . X - Vector to data to
2094: Level: advanced
2096: .seealso: `DMPlexLandauCreateVelocitySpace()`
2097: @*/
2098: PetscErrorCode DMPlexLandauAccess(DM pack, Vec X, PetscErrorCode (*func)(DM, Vec, PetscInt, PetscInt, PetscInt, void *), void *user_ctx)
2099: {
2100: LandauCtx *ctx;
2101: PetscFunctionBegin;
2102: PetscCall(DMGetApplicationContext(pack, &ctx)); // uses ctx->num_grids; ctx->plex[grid]; ctx->batch_sz; ctx->mat_offset
2103: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2104: PetscInt dim, n;
2105: PetscCall(DMGetDimension(pack, &dim));
2106: for (PetscInt sp = ctx->species_offset[grid], i0 = 0; sp < ctx->species_offset[grid + 1]; sp++, i0++) {
2107: Vec vec;
2108: PetscInt vf[1] = {i0};
2109: IS vis;
2110: DM vdm;
2111: PetscCall(DMCreateSubDM(ctx->plex[grid], 1, vf, &vis, &vdm));
2112: PetscCall(DMSetApplicationContext(vdm, ctx)); // the user might want this
2113: PetscCall(DMCreateGlobalVector(vdm, &vec));
2114: PetscCall(VecGetSize(vec, &n));
2115: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2116: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2117: PetscCall(VecZeroEntries(vec));
2118: /* Add your data with 'dm' for species 'sp' to 'vec' */
2119: PetscCall(func(vdm, vec, i0, grid, b_id, user_ctx));
2120: /* add to global */
2121: PetscScalar const *values;
2122: const PetscInt *offsets;
2123: PetscCall(VecGetArrayRead(vec, &values));
2124: PetscCall(ISGetIndices(vis, &offsets));
2125: for (int i = 0; i < n; i++) PetscCall(VecSetValue(X, moffset + offsets[i], values[i], ADD_VALUES));
2126: PetscCall(VecRestoreArrayRead(vec, &values));
2127: PetscCall(ISRestoreIndices(vis, &offsets));
2128: } // batch
2129: PetscCall(VecDestroy(&vec));
2130: PetscCall(ISDestroy(&vis));
2131: PetscCall(DMDestroy(&vdm));
2132: }
2133: } // grid
2134: PetscFunctionReturn(PETSC_SUCCESS);
2135: }
2137: /*@
2138: DMPlexLandauDestroyVelocitySpace - Destroy a `DMPLEX` velocity space mesh
2140: Collective
2142: Input/Output Parameters:
2143: . dm - the `DM` to destroy
2145: Level: beginner
2147: .seealso: `DMPlexLandauCreateVelocitySpace()`
2148: @*/
2149: PetscErrorCode DMPlexLandauDestroyVelocitySpace(DM *dm)
2150: {
2151: LandauCtx *ctx;
2152: PetscFunctionBegin;
2153: PetscCall(DMGetApplicationContext(*dm, &ctx));
2154: PetscCall(MatDestroy(&ctx->M));
2155: PetscCall(MatDestroy(&ctx->J));
2156: for (PetscInt ii = 0; ii < ctx->num_species; ii++) PetscCall(PetscFEDestroy(&ctx->fe[ii]));
2157: PetscCall(ISDestroy(&ctx->batch_is));
2158: PetscCall(VecDestroy(&ctx->work_vec));
2159: PetscCall(VecScatterDestroy(&ctx->plex_batch));
2160: if (ctx->deviceType == LANDAU_KOKKOS) {
2161: #if defined(PETSC_HAVE_KOKKOS)
2162: PetscCall(LandauKokkosStaticDataClear(&ctx->SData_d));
2163: #else
2164: SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONG, "-landau_device_type %s not built", "kokkos");
2165: #endif
2166: } else {
2167: if (ctx->SData_d.x) { /* in a CPU run */
2168: 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;
2169: LandauIdx *coo_elem_offsets = (LandauIdx *)ctx->SData_d.coo_elem_offsets, *coo_elem_fullNb = (LandauIdx *)ctx->SData_d.coo_elem_fullNb, (*coo_elem_point_offsets)[LANDAU_MAX_NQND + 1] = (LandauIdx(*)[LANDAU_MAX_NQND + 1]) ctx->SData_d.coo_elem_point_offsets;
2170: PetscCall(PetscFree4(ww, xx, yy, invJ));
2171: if (zz) PetscCall(PetscFree(zz));
2172: if (coo_elem_offsets) {
2173: PetscCall(PetscFree3(coo_elem_offsets, coo_elem_fullNb, coo_elem_point_offsets)); // could be NULL
2174: }
2175: PetscCall(PetscFree4(ctx->SData_d.alpha, ctx->SData_d.beta, ctx->SData_d.invMass, ctx->SData_d.lambdas));
2176: }
2177: }
2179: if (ctx->times[LANDAU_MATRIX_TOTAL] > 0) { // OMP timings
2180: PetscCall(PetscPrintf(ctx->comm, "TSStep N 1.0 %10.3e\n", ctx->times[LANDAU_EX2_TSSOLVE]));
2181: 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));
2182: PetscCall(PetscPrintf(ctx->comm, "3: Landau: %10.3e\n", ctx->times[LANDAU_MATRIX_TOTAL]));
2183: PetscCall(PetscPrintf(ctx->comm, "Landau Jacobian %" PetscInt_FMT " 1.0 %10.3e\n", (PetscInt)ctx->times[LANDAU_JACOBIAN_COUNT], ctx->times[LANDAU_JACOBIAN]));
2184: PetscCall(PetscPrintf(ctx->comm, "Landau Operator N 1.0 %10.3e\n", ctx->times[LANDAU_OPERATOR]));
2185: PetscCall(PetscPrintf(ctx->comm, "Landau Mass N 1.0 %10.3e\n", ctx->times[LANDAU_MASS]));
2186: PetscCall(PetscPrintf(ctx->comm, " Jac-f-df (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_F_DF]));
2187: PetscCall(PetscPrintf(ctx->comm, " Kernel (GPU) N 1.0 %10.3e\n", ctx->times[LANDAU_KERNEL]));
2188: PetscCall(PetscPrintf(ctx->comm, "MatLUFactorNum X 1.0 %10.3e\n", ctx->times[KSP_FACTOR]));
2189: PetscCall(PetscPrintf(ctx->comm, "MatSolve X 1.0 %10.3e\n", ctx->times[KSP_SOLVE]));
2190: }
2191: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMDestroy(&ctx->plex[grid]));
2192: PetscCall(PetscFree(ctx));
2193: PetscCall(DMDestroy(dm));
2194: PetscFunctionReturn(PETSC_SUCCESS);
2195: }
2197: /* < v, ru > */
2198: 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)
2199: {
2200: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2201: f0[0] = u[ii];
2202: }
2204: /* < v, ru > */
2205: 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)
2206: {
2207: PetscInt ii = (PetscInt)PetscRealPart(constants[0]), jj = (PetscInt)PetscRealPart(constants[1]);
2208: f0[0] = x[jj] * u[ii]; /* x momentum */
2209: }
2211: 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)
2212: {
2213: PetscInt i, ii = (PetscInt)PetscRealPart(constants[0]);
2214: double tmp1 = 0.;
2215: for (i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2216: f0[0] = tmp1 * u[ii];
2217: }
2219: static PetscErrorCode gamma_n_f(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *actx)
2220: {
2221: const PetscReal *c2_0_arr = ((PetscReal *)actx);
2222: const PetscReal c02 = c2_0_arr[0];
2224: PetscFunctionBegin;
2225: for (int s = 0; s < Nf; s++) {
2226: PetscReal tmp1 = 0.;
2227: for (int i = 0; i < dim; ++i) tmp1 += x[i] * x[i];
2228: #if defined(PETSC_USE_DEBUG)
2229: u[s] = PetscSqrtReal(1. + tmp1 / c02); // u[0] = PetscSqrtReal(1. + xx);
2230: #else
2231: {
2232: PetscReal xx = tmp1 / c02;
2233: u[s] = xx / (PetscSqrtReal(1. + xx) + 1.); // better conditioned = xx/(PetscSqrtReal(1. + xx) + 1.)
2234: }
2235: #endif
2236: }
2237: PetscFunctionReturn(PETSC_SUCCESS);
2238: }
2240: /* < v, ru > */
2241: 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)
2242: {
2243: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2244: f0[0] = 2. * PETSC_PI * x[0] * u[ii];
2245: }
2247: /* < v, ru > */
2248: 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)
2249: {
2250: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2251: f0[0] = 2. * PETSC_PI * x[0] * x[1] * u[ii];
2252: }
2254: 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)
2255: {
2256: PetscInt ii = (PetscInt)PetscRealPart(constants[0]);
2257: f0[0] = 2. * PETSC_PI * x[0] * (x[0] * x[0] + x[1] * x[1]) * u[ii];
2258: }
2260: /*@
2261: DMPlexLandauPrintNorms - collects moments and prints them
2263: Collective
2265: Input Parameters:
2266: + X - the state
2267: - stepi - current step to print
2269: Level: beginner
2271: .seealso: `DMPlexLandauCreateVelocitySpace()`
2272: @*/
2273: PetscErrorCode DMPlexLandauPrintNorms(Vec X, PetscInt stepi)
2274: {
2275: LandauCtx *ctx;
2276: PetscDS prob;
2277: DM pack;
2278: PetscInt cStart, cEnd, dim, ii, i0, nDMs;
2279: PetscScalar xmomentumtot = 0, ymomentumtot = 0, zmomentumtot = 0, energytot = 0, densitytot = 0, tt[LANDAU_MAX_SPECIES];
2280: PetscScalar xmomentum[LANDAU_MAX_SPECIES], ymomentum[LANDAU_MAX_SPECIES], zmomentum[LANDAU_MAX_SPECIES], energy[LANDAU_MAX_SPECIES], density[LANDAU_MAX_SPECIES];
2281: Vec *globXArray;
2283: PetscFunctionBegin;
2284: PetscCall(VecGetDM(X, &pack));
2285: PetscCheck(pack, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Vector has no DM");
2286: PetscCall(DMGetDimension(pack, &dim));
2287: PetscCheck(dim == 2 || dim == 3, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " not in [2,3]", dim);
2288: PetscCall(DMGetApplicationContext(pack, &ctx));
2289: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2290: /* print momentum and energy */
2291: PetscCall(DMCompositeGetNumberDM(pack, &nDMs));
2292: 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);
2293: PetscCall(PetscMalloc(sizeof(*globXArray) * nDMs, &globXArray));
2294: PetscCall(DMCompositeGetAccessArray(pack, X, nDMs, NULL, globXArray));
2295: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2296: Vec Xloc = globXArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2297: PetscCall(DMGetDS(ctx->plex[grid], &prob));
2298: for (ii = ctx->species_offset[grid], i0 = 0; ii < ctx->species_offset[grid + 1]; ii++, i0++) {
2299: PetscScalar user[2] = {(PetscScalar)i0, (PetscScalar)ctx->charges[ii]};
2300: PetscCall(PetscDSSetConstants(prob, 2, user));
2301: if (dim == 2) { /* 2/3X + 3V (cylindrical coordinates) */
2302: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rden));
2303: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2304: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2305: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rmom));
2306: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2307: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2308: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_rv2));
2309: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2310: energy[ii] = tt[0] * 0.5 * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2311: zmomentumtot += zmomentum[ii];
2312: energytot += energy[ii];
2313: densitytot += density[ii];
2314: 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])));
2315: } else { /* 2/3Xloc + 3V */
2316: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_den));
2317: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2318: density[ii] = tt[0] * ctx->n_0 * ctx->charges[ii];
2319: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_mom));
2320: user[1] = 0;
2321: PetscCall(PetscDSSetConstants(prob, 2, user));
2322: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2323: xmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2324: user[1] = 1;
2325: PetscCall(PetscDSSetConstants(prob, 2, user));
2326: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2327: ymomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2328: user[1] = 2;
2329: PetscCall(PetscDSSetConstants(prob, 2, user));
2330: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2331: zmomentum[ii] = tt[0] * ctx->n_0 * ctx->v_0 * ctx->masses[ii];
2332: if (ctx->use_relativistic_corrections) {
2333: /* gamma * M * f */
2334: if (ii == 0 && grid == 0) { // do all at once
2335: Vec Mf, globGamma, *globMfArray, *globGammaArray;
2336: PetscErrorCode (*gammaf[1])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *) = {gamma_n_f};
2337: PetscReal *c2_0[1], data[1];
2339: PetscCall(VecDuplicate(X, &globGamma));
2340: PetscCall(VecDuplicate(X, &Mf));
2341: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globMfArray));
2342: PetscCall(PetscMalloc(sizeof(*globMfArray) * nDMs, &globGammaArray));
2343: /* M * f */
2344: PetscCall(MatMult(ctx->M, X, Mf));
2345: /* gamma */
2346: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2347: 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
2348: Vec v1 = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)];
2349: data[0] = PetscSqr(C_0(ctx->v_0));
2350: c2_0[0] = &data[0];
2351: PetscCall(DMProjectFunction(ctx->plex[grid], 0., gammaf, (void **)c2_0, INSERT_ALL_VALUES, v1));
2352: }
2353: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2354: /* gamma * Mf */
2355: PetscCall(DMCompositeGetAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2356: PetscCall(DMCompositeGetAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2357: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) { // yes a grid loop in a grid loop to print nice
2358: PetscInt Nf = ctx->species_offset[grid + 1] - ctx->species_offset[grid], N, bs;
2359: Vec Mfsub = globMfArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], Gsub = globGammaArray[LAND_PACK_IDX(ctx->batch_view_idx, grid)], v1, v2;
2360: // get each component
2361: PetscCall(VecGetSize(Mfsub, &N));
2362: PetscCall(VecCreate(ctx->comm, &v1));
2363: PetscCall(VecSetSizes(v1, PETSC_DECIDE, N / Nf));
2364: PetscCall(VecCreate(ctx->comm, &v2));
2365: PetscCall(VecSetSizes(v2, PETSC_DECIDE, N / Nf));
2366: PetscCall(VecSetFromOptions(v1)); // ???
2367: PetscCall(VecSetFromOptions(v2));
2368: // get each component
2369: PetscCall(VecGetBlockSize(Gsub, &bs));
2370: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT " in Gsub", bs, Nf);
2371: PetscCall(VecGetBlockSize(Mfsub, &bs));
2372: PetscCheck(bs == Nf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "bs %" PetscInt_FMT " != num_species %" PetscInt_FMT, bs, Nf);
2373: for (int i = 0, ix = ctx->species_offset[grid]; i < Nf; i++, ix++) {
2374: PetscScalar val;
2375: PetscCall(VecStrideGather(Gsub, i, v1, INSERT_VALUES)); // this is not right -- TODO
2376: PetscCall(VecStrideGather(Mfsub, i, v2, INSERT_VALUES));
2377: PetscCall(VecDot(v1, v2, &val));
2378: energy[ix] = PetscRealPart(val) * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ix];
2379: }
2380: PetscCall(VecDestroy(&v1));
2381: PetscCall(VecDestroy(&v2));
2382: } /* grids */
2383: PetscCall(DMCompositeRestoreAccessArray(pack, globGamma, nDMs, NULL, globGammaArray));
2384: PetscCall(DMCompositeRestoreAccessArray(pack, Mf, nDMs, NULL, globMfArray));
2385: PetscCall(PetscFree(globGammaArray));
2386: PetscCall(PetscFree(globMfArray));
2387: PetscCall(VecDestroy(&globGamma));
2388: PetscCall(VecDestroy(&Mf));
2389: }
2390: } else {
2391: PetscCall(PetscDSSetObjective(prob, 0, &f0_s_v2));
2392: PetscCall(DMPlexComputeIntegralFEM(ctx->plex[grid], Xloc, tt, ctx));
2393: energy[ii] = 0.5 * tt[0] * ctx->n_0 * ctx->v_0 * ctx->v_0 * ctx->masses[ii];
2394: }
2395: 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])));
2396: xmomentumtot += xmomentum[ii];
2397: ymomentumtot += ymomentum[ii];
2398: zmomentumtot += zmomentum[ii];
2399: energytot += energy[ii];
2400: densitytot += density[ii];
2401: }
2402: if (ctx->num_species > 1) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2403: }
2404: }
2405: PetscCall(DMCompositeRestoreAccessArray(pack, X, nDMs, NULL, globXArray));
2406: PetscCall(PetscFree(globXArray));
2407: /* totals */
2408: PetscCall(DMPlexGetHeightStratum(ctx->plex[0], 0, &cStart, &cEnd));
2409: if (ctx->num_species > 1) {
2410: if (dim == 2) {
2411: 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),
2412: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2413: } else {
2414: 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),
2415: (double)(ctx->masses[1] / ctx->masses[0]), cEnd - cStart));
2416: }
2417: } else PetscCall(PetscPrintf(PETSC_COMM_WORLD, " -- %" PetscInt_FMT " cells", cEnd - cStart));
2418: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "\n"));
2419: PetscFunctionReturn(PETSC_SUCCESS);
2420: }
2422: /*@
2423: DMPlexLandauCreateMassMatrix - Create mass matrix for Landau in Plex space (not field major order of Jacobian)
2424: - puts mass matrix into ctx->M
2426: Collective
2428: Input Parameter:
2429: . pack - the `DM` object. Puts matrix in Landau context M field
2431: Output Parameter:
2432: . Amat - The mass matrix (optional), mass matrix is added to the `DM` context
2434: Level: beginner
2436: .seealso: `DMPlexLandauCreateVelocitySpace()`
2437: @*/
2438: PetscErrorCode DMPlexLandauCreateMassMatrix(DM pack, Mat *Amat)
2439: {
2440: DM mass_pack, massDM[LANDAU_MAX_GRIDS];
2441: PetscDS prob;
2442: PetscInt ii, dim, N1 = 1, N2;
2443: LandauCtx *ctx;
2444: Mat packM, subM[LANDAU_MAX_GRIDS];
2446: PetscFunctionBegin;
2448: if (Amat) PetscAssertPointer(Amat, 2);
2449: PetscCall(DMGetApplicationContext(pack, &ctx));
2450: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2451: PetscCall(PetscLogEventBegin(ctx->events[14], 0, 0, 0, 0));
2452: PetscCall(DMGetDimension(pack, &dim));
2453: PetscCall(DMCompositeCreate(PetscObjectComm((PetscObject)pack), &mass_pack));
2454: /* create pack mass matrix */
2455: for (PetscInt grid = 0, ix = 0; grid < ctx->num_grids; grid++) {
2456: PetscCall(DMClone(ctx->plex[grid], &massDM[grid]));
2457: PetscCall(DMCopyFields(ctx->plex[grid], massDM[grid]));
2458: PetscCall(DMCreateDS(massDM[grid]));
2459: PetscCall(DMGetDS(massDM[grid], &prob));
2460: for (ix = 0, ii = ctx->species_offset[grid]; ii < ctx->species_offset[grid + 1]; ii++, ix++) {
2461: if (dim == 3) PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_1, NULL, NULL, NULL));
2462: else PetscCall(PetscDSSetJacobian(prob, ix, ix, g0_r, NULL, NULL, NULL));
2463: }
2464: #if !defined(LANDAU_SPECIES_MAJOR)
2465: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2466: #else
2467: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) { // add batch size DMs for this species grid
2468: PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2469: }
2470: #endif
2471: PetscCall(DMCreateMatrix(massDM[grid], &subM[grid]));
2472: }
2473: #if !defined(LANDAU_SPECIES_MAJOR)
2474: // stack the batched DMs
2475: for (PetscInt b_id = 1; b_id < ctx->batch_sz; b_id++) {
2476: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(DMCompositeAddDM(mass_pack, massDM[grid]));
2477: }
2478: #endif
2479: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only"));
2480: PetscCall(DMCreateMatrix(mass_pack, &packM));
2481: PetscCall(PetscOptionsInsertString(NULL, "-dm_preallocate_only false"));
2482: PetscCall(MatSetOption(packM, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE));
2483: PetscCall(MatSetOption(packM, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
2484: PetscCall(DMDestroy(&mass_pack));
2485: /* make mass matrix for each block */
2486: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2487: Vec locX;
2488: DM plex = massDM[grid];
2489: PetscCall(DMGetLocalVector(plex, &locX));
2490: /* Mass matrix is independent of the input, so no need to fill locX */
2491: PetscCall(DMPlexSNESComputeJacobianFEM(plex, locX, subM[grid], subM[grid], ctx));
2492: PetscCall(DMRestoreLocalVector(plex, &locX));
2493: PetscCall(DMDestroy(&massDM[grid]));
2494: }
2495: PetscCall(MatGetSize(ctx->J, &N1, NULL));
2496: PetscCall(MatGetSize(packM, &N2, NULL));
2497: PetscCheck(N1 == N2, PetscObjectComm((PetscObject)pack), PETSC_ERR_PLIB, "Incorrect matrix sizes: |Jacobian| = %" PetscInt_FMT ", |Mass|=%" PetscInt_FMT, N1, N2);
2498: /* assemble block diagonals */
2499: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) {
2500: Mat B = subM[grid];
2501: PetscInt nloc, nzl, *colbuf, COL_BF_SIZE = 1024, row;
2502: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2503: PetscCall(MatGetSize(B, &nloc, NULL));
2504: for (PetscInt b_id = 0; b_id < ctx->batch_sz; b_id++) {
2505: const PetscInt moffset = LAND_MOFFSET(b_id, grid, ctx->batch_sz, ctx->num_grids, ctx->mat_offset);
2506: const PetscInt *cols;
2507: const PetscScalar *vals;
2508: for (int i = 0; i < nloc; i++) {
2509: PetscCall(MatGetRow(B, i, &nzl, NULL, NULL));
2510: if (nzl > COL_BF_SIZE) {
2511: PetscCall(PetscFree(colbuf));
2512: PetscCall(PetscInfo(pack, "Realloc buffer %" PetscInt_FMT " to %" PetscInt_FMT " (row size %" PetscInt_FMT ") \n", COL_BF_SIZE, 2 * COL_BF_SIZE, nzl));
2513: COL_BF_SIZE = nzl;
2514: PetscCall(PetscMalloc(sizeof(*colbuf) * COL_BF_SIZE, &colbuf));
2515: }
2516: PetscCall(MatGetRow(B, i, &nzl, &cols, &vals));
2517: for (int j = 0; j < nzl; j++) colbuf[j] = cols[j] + moffset;
2518: row = i + moffset;
2519: PetscCall(MatSetValues(packM, 1, &row, nzl, colbuf, vals, INSERT_VALUES));
2520: PetscCall(MatRestoreRow(B, i, &nzl, &cols, &vals));
2521: }
2522: }
2523: PetscCall(PetscFree(colbuf));
2524: }
2525: // cleanup
2526: for (PetscInt grid = 0; grid < ctx->num_grids; grid++) PetscCall(MatDestroy(&subM[grid]));
2527: PetscCall(MatAssemblyBegin(packM, MAT_FINAL_ASSEMBLY));
2528: PetscCall(MatAssemblyEnd(packM, MAT_FINAL_ASSEMBLY));
2529: PetscCall(PetscObjectSetName((PetscObject)packM, "mass"));
2530: PetscCall(MatViewFromOptions(packM, NULL, "-dm_landau_mass_view"));
2531: ctx->M = packM;
2532: if (Amat) *Amat = packM;
2533: PetscCall(PetscLogEventEnd(ctx->events[14], 0, 0, 0, 0));
2534: PetscFunctionReturn(PETSC_SUCCESS);
2535: }
2537: /*@
2538: DMPlexLandauIFunction - `TS` residual calculation, confusingly this computes the Jacobian w/o mass
2540: Collective
2542: Input Parameters:
2543: + ts - The time stepping context
2544: . time_dummy - current time (not used)
2545: . X - Current state
2546: . X_t - Time derivative of current state
2547: - actx - Landau context
2549: Output Parameter:
2550: . F - The residual
2552: Level: beginner
2554: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIJacobian()`
2555: @*/
2556: PetscErrorCode DMPlexLandauIFunction(TS ts, PetscReal time_dummy, Vec X, Vec X_t, Vec F, void *actx)
2557: {
2558: LandauCtx *ctx = (LandauCtx *)actx;
2559: PetscInt dim;
2560: DM pack;
2561: #if defined(PETSC_HAVE_THREADSAFETY)
2562: double starttime, endtime;
2563: #endif
2564: PetscObjectState state;
2566: PetscFunctionBegin;
2567: PetscCall(TSGetDM(ts, &pack));
2568: PetscCall(DMGetApplicationContext(pack, &ctx));
2569: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2570: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2571: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2572: PetscCall(PetscLogEventBegin(ctx->events[0], 0, 0, 0, 0));
2573: #if defined(PETSC_HAVE_THREADSAFETY)
2574: starttime = MPI_Wtime();
2575: #endif
2576: PetscCall(DMGetDimension(pack, &dim));
2577: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2578: if (state != ctx->norm_state) {
2579: PetscCall(PetscInfo(ts, "Create Landau Jacobian t=%g J.state %" PetscInt64_FMT " --> %" PetscInt64_FMT "\n", (double)time_dummy, ctx->norm_state, state));
2580: PetscCall(MatZeroEntries(ctx->J));
2581: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, 0.0, (void *)ctx));
2582: PetscCall(MatViewFromOptions(ctx->J, NULL, "-dm_landau_jacobian_view"));
2583: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2584: ctx->norm_state = state;
2585: } else {
2586: PetscCall(PetscInfo(ts, "WARNING Skip forming Jacobian, has not changed %" PetscInt64_FMT "\n", state));
2587: }
2588: /* mat vec for op */
2589: PetscCall(MatMult(ctx->J, X, F)); /* C*f */
2590: /* add time term */
2591: if (X_t) PetscCall(MatMultAdd(ctx->M, X_t, F, F));
2592: #if defined(PETSC_HAVE_THREADSAFETY)
2593: if (ctx->stage) {
2594: endtime = MPI_Wtime();
2595: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2596: ctx->times[LANDAU_JACOBIAN] += (endtime - starttime);
2597: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2598: ctx->times[LANDAU_JACOBIAN_COUNT] += 1;
2599: }
2600: #endif
2601: PetscCall(PetscLogEventEnd(ctx->events[0], 0, 0, 0, 0));
2602: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2603: if (ctx->stage) PetscCall(PetscLogStagePop());
2604: PetscFunctionReturn(PETSC_SUCCESS);
2605: }
2607: /*@
2608: DMPlexLandauIJacobian - `TS` Jacobian construction, confusingly this adds mass
2610: Collective
2612: Input Parameters:
2613: + ts - The time stepping context
2614: . time_dummy - current time (not used)
2615: . X - Current state
2616: . U_tdummy - Time derivative of current state (not used)
2617: . shift - shift for du/dt term
2618: - actx - Landau context
2620: Output Parameters:
2621: + Amat - Jacobian
2622: - Pmat - same as Amat
2624: Level: beginner
2626: .seealso: `DMPlexLandauCreateVelocitySpace()`, `DMPlexLandauIFunction()`
2627: @*/
2628: PetscErrorCode DMPlexLandauIJacobian(TS ts, PetscReal time_dummy, Vec X, Vec U_tdummy, PetscReal shift, Mat Amat, Mat Pmat, void *actx)
2629: {
2630: LandauCtx *ctx = NULL;
2631: PetscInt dim;
2632: DM pack;
2633: #if defined(PETSC_HAVE_THREADSAFETY)
2634: double starttime, endtime;
2635: #endif
2636: PetscObjectState state;
2638: PetscFunctionBegin;
2639: PetscCall(TSGetDM(ts, &pack));
2640: PetscCall(DMGetApplicationContext(pack, &ctx));
2641: PetscCheck(ctx, PETSC_COMM_SELF, PETSC_ERR_PLIB, "no context");
2642: PetscCheck(Amat == Pmat && Amat == ctx->J, ctx->comm, PETSC_ERR_PLIB, "Amat!=Pmat || Amat!=ctx->J");
2643: PetscCall(DMGetDimension(pack, &dim));
2644: /* get collision Jacobian into A */
2645: if (ctx->stage) PetscCall(PetscLogStagePush(ctx->stage));
2646: PetscCall(PetscLogEventBegin(ctx->events[11], 0, 0, 0, 0));
2647: PetscCall(PetscLogEventBegin(ctx->events[9], 0, 0, 0, 0));
2648: #if defined(PETSC_HAVE_THREADSAFETY)
2649: starttime = MPI_Wtime();
2650: #endif
2651: PetscCall(PetscInfo(ts, "Adding mass to Jacobian t=%g, shift=%g\n", (double)time_dummy, (double)shift));
2652: PetscCheck(shift != 0.0, ctx->comm, PETSC_ERR_PLIB, "zero shift");
2653: PetscCall(PetscObjectStateGet((PetscObject)ctx->J, &state));
2654: PetscCheck(state == ctx->norm_state, ctx->comm, PETSC_ERR_PLIB, "wrong state, %" PetscInt64_FMT " %" PetscInt64_FMT "", ctx->norm_state, state);
2655: if (!ctx->use_matrix_mass) {
2656: PetscCall(LandauFormJacobian_Internal(X, ctx->J, dim, shift, (void *)ctx));
2657: } else { /* add mass */
2658: PetscCall(MatAXPY(Pmat, shift, ctx->M, SAME_NONZERO_PATTERN));
2659: }
2660: #if defined(PETSC_HAVE_THREADSAFETY)
2661: if (ctx->stage) {
2662: endtime = MPI_Wtime();
2663: ctx->times[LANDAU_OPERATOR] += (endtime - starttime);
2664: ctx->times[LANDAU_MASS] += (endtime - starttime);
2665: ctx->times[LANDAU_MATRIX_TOTAL] += (endtime - starttime);
2666: }
2667: #endif
2668: PetscCall(PetscLogEventEnd(ctx->events[9], 0, 0, 0, 0));
2669: PetscCall(PetscLogEventEnd(ctx->events[11], 0, 0, 0, 0));
2670: if (ctx->stage) PetscCall(PetscLogStagePop());
2671: PetscFunctionReturn(PETSC_SUCCESS);
2672: }