Actual source code: ex4.c
1: static char help[] = "Two-level system for Landau Damping using Vlasov-Poisson equations\n";
3: /*
4: Moment Equations:
6: We will discretize the moment equations using finite elements, and we will project the moments into the finite element space We will use the PFAK method, which guarantees that our FE approximation is weakly equivalent to the true moment. The first moment, number density, is given by
8: \int dx \phi_i n_f = \int dx \phi_i n_p
9: \int dx \phi_i n_f = \int dx \phi_i \int dv f
10: \int dx \phi_i n_f = \int dx \phi_i \int dv \sum_p w_p \delta(x - x_p) \delta(v - v_p)
11: \int dx \phi_i n_f = \int dx \phi_i \sum_p w_p \delta(x - x_p)
12: M n_F = M_p w_p
14: where
16: (M_p){ip} = \phi_i(x_p)
18: which is just a scaled version of the charge density. The second moment, momentum density, is given by
20: \int dx \phi_i p_f = m \int dx \phi_i \int dv v f
21: \int dx \phi_i p_f = m \int dx \phi_i \sum_p w_p \delta(x - x_p) v_p
22: M p_F = M_p v_p w_p
24: And finally the third moment, pressure, is given by
26: \int dx \phi_i pr_f = m \int dx \phi_i \int dv (v - u)^2 f
27: \int dx \phi_i pr_f = m \int dx \phi_i \sum_p w_p \delta(x - x_p) (v_p - u)^2
28: M pr_F = M_p (v_p - u)^2 w_p
29: = M_p (v_p - p_F(x_p) / m n_F(x_p))^2 w_p
30: = M_p (v_p - (\sum_j p_F \phi_j(x_p)) / m (\sum_k n_F \phi_k(x_p)))^2 w_p
32: Here we need all FEM basis functions \phi_i that see that particle p.
34: To run the code with particles sinusoidally perturbed in x space use the test "pp_poisson_bsi_1d_4" or "pp_poisson_bsi_2d_4"
35: According to Lukas, good damping results come at ~16k particles per cell
37: Swarm CellDMs
38: =============
39: Name: "space"
40: Fields: DMSwarmPICField_coor, "velocity"
41: Coordinates: DMSwarmPICField_coor
43: Name: "velocity"
44: Fields: "w_q"
45: Coordinates: "velocity"
47: Name: "moments"
48: Fields: "w_q"
49: Coordinates: DMSwarmPICField_coor
51: Name: "moment fields"
52: Fields: "velocity"
53: Coordinates: DMSwarmPICField_coor
55: To visualize the maximum electric field use
57: -efield_monitor
59: To monitor velocity moments of the distribution use
61: -ptof_pc_type lu -moments_monitor
63: To monitor the particle positions in phase space use
65: -positions_monitor
67: To monitor the charge density, E field, and potential use
69: -poisson_monitor
71: To monitor the remapping field use
73: -remap_uf_view draw
75: To visualize the swarm distribution use
77: -ts_monitor_hg_swarm
79: To visualize the particles, we can use
81: -ts_monitor_sp_swarm -ts_monitor_sp_swarm_retain 0 -ts_monitor_sp_swarm_phase 1 -draw_size 500,500
82: */
83: #include <petsctao.h>
84: #include <petscts.h>
85: #include <petscdmplex.h>
86: #include <petscdmswarm.h>
87: #include <petscfe.h>
88: #include <petscds.h>
89: #include <petscbag.h>
90: #include <petscdraw.h>
91: #include <petsc/private/petscfeimpl.h>
92: #include <petsc/private/dmswarmimpl.h>
93: #include "petscdm.h"
94: #include "petscdmlabel.h"
96: PETSC_EXTERN PetscErrorCode stream(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
97: PETSC_EXTERN PetscErrorCode line(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar[], void *);
99: const char *EMTypes[] = {"primal", "mixed", "coulomb", "none", "EMType", "EM_", NULL};
100: typedef enum {
101: EM_PRIMAL,
102: EM_MIXED,
103: EM_COULOMB,
104: EM_NONE
105: } EMType;
107: typedef enum {
108: V0,
109: X0,
110: T0,
111: M0,
112: Q0,
113: PHI0,
114: POISSON,
115: VLASOV,
116: SIGMA,
117: NUM_CONSTANTS
118: } ConstantType;
120: typedef enum {
121: E_MONITOR_NONE,
122: E_MONITOR_FULL,
123: E_MONITOR_QUIET
124: } EMonitorType;
125: const char *const EMonitorTypes[] = {"NONE", "FULL", "QUIET", "EMonitorType", "E_MONITOR_", NULL};
127: typedef struct {
128: PetscScalar v0; /* Velocity scale, often the thermal velocity */
129: PetscScalar t0; /* Time scale */
130: PetscScalar x0; /* Space scale */
131: PetscScalar m0; /* Mass scale */
132: PetscScalar q0; /* Charge scale */
133: PetscScalar kb;
134: PetscScalar epsi0;
135: PetscScalar phi0; /* Potential scale */
136: PetscScalar poissonNumber; /* Non-Dimensional Poisson Number */
137: PetscScalar vlasovNumber; /* Non-Dimensional Vlasov Number */
138: PetscReal sigma; /* Nondimensional charge per length in x */
139: } Parameter;
141: typedef struct {
142: PetscInt s; // Starting sample (we ignore some in the beginning)
143: PetscInt e; // Ending sample
144: PetscInt per; // Period of fitting
145: const PetscReal *t; // Time for each sample
146: const PetscReal *Emax; // Emax for each sample
147: } EmaxCtx;
149: typedef struct {
150: PetscBag bag; // Problem parameters
151: PetscBool error; // Flag for printing the error
152: PetscInt remapFreq; // Number of timesteps between remapping
153: EMonitorType efield_monitor; // Flag to show electric field monitor
154: PetscBool moment_monitor; // Flag to show distribution moment monitor
155: PetscBool moment_field_monitor; // Flag to show moment field monitor
156: PetscBool positions_monitor; // Flag to show particle positins at each time step
157: PetscBool poisson_monitor; // Flag to display charge, E field, and potential at each solve
158: PetscBool initial_monitor; // Flag to monitor the initial conditions
159: PetscInt velocity_monitor; // Cell to monitor the velocity distribution for
160: PetscBool perturbed_weights; // Uniformly sample x,v space with gaussian weights
161: PetscInt ostep; // Print the energy at each ostep time steps
162: PetscInt numParticles;
163: PetscReal timeScale; /* Nondimensionalizing time scale */
164: PetscReal charges[2]; /* The charges of each species */
165: PetscReal masses[2]; /* The masses of each species */
166: PetscReal thermal_energy[2]; /* Thermal Energy (used to get other constants)*/
167: PetscReal cosine_coefficients[2]; /*(alpha, k)*/
168: PetscReal totalWeight;
169: PetscReal stepSize;
170: PetscInt steps;
171: PetscReal initVel;
172: EMType em; // Type of electrostatic model
173: SNES snes; // EM solver
174: DM dmMom; // The DM for moment fields
175: DM dmN; // The DM for number density fields
176: IS isN; // The IS mapping dmN into dmMom
177: Mat MN; // The finite element mass matrix for number density
178: DM dmP; // The DM for momentum density fields
179: IS isP; // The IS mapping dmP into dmMom
180: Mat MP; // The finite element mass matrix for momentum density
181: DM dmE; // The DM for energy density (pressure) fields
182: IS isE; // The IS mapping dmE into dmMom
183: Mat ME; // The finite element mass matrix for energy density (pressure)
184: DM dmPot; // The DM for potential
185: Mat fftPot; // Fourier Transform operator for the potential
186: Vec fftX, fftY; // FFT vectors with phases added (complex parts)
187: IS fftReal; // The indices for real parts
188: IS isPot; // The IS for potential, or NULL in primal
189: Mat M; // The finite element mass matrix for potential
190: PetscFEGeom *fegeom; // Geometric information for the DM cells
191: PetscDrawHG drawhgic_x; // Histogram of the particle weight in each X cell
192: PetscDrawHG drawhgic_v; // Histogram of the particle weight in each X cell
193: PetscDrawHG drawhgcell_v; // Histogram of the particle weight in a given cell
194: PetscBool validE; // Flag to indicate E-field in swarm is valid
195: PetscReal drawlgEmin; // The minimum lg(E) to plot
196: PetscDrawLG drawlgE; // Logarithm of maximum electric field
197: PetscDrawSP drawspE; // Electric field at particle positions
198: PetscDrawSP drawspX; // Particle positions
199: PetscViewer viewerRho; // Charge density viewer
200: PetscViewer viewerRhoHat; // Charge density Fourier Transform viewer
201: PetscViewer viewerPhi; // Potential viewer
202: PetscViewer viewerN; // Number density viewer
203: PetscViewer viewerP; // Momentum density viewer
204: PetscViewer viewerE; // Energy density (pressure) viewer
205: PetscViewer viewerNRes; // Number density residual viewer
206: PetscViewer viewerPRes; // Momentum density residual viewer
207: PetscViewer viewerERes; // Energy density (pressure) residual viewer
208: PetscDrawLG drawlgMomRes; // Residuals for the moment equations
209: DM swarm; // The particle swarm
210: PetscRandom random; // Used for particle perturbations
211: PetscBool twostream; // Flag for activating 2-stream setup
212: PetscBool checkweights; // Check weight normalization
213: PetscInt checkVRes; // Flag to check/output velocity residuals for nightly tests
214: PetscBool checkLandau; // Check the Landau damping result
215: EmaxCtx emaxCtx; // Information for fit to decay profile
216: PetscReal gamma; // The damping rate for Landau damping
217: PetscReal omega; // The perturbed oscillation frequency for Landau damping
219: PetscLogEvent RhsXEvent, RhsVEvent, ESolveEvent, ETabEvent;
220: } AppCtx;
222: static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
223: {
224: PetscFunctionBeginUser;
225: PetscInt d = 2;
226: PetscInt maxSpecies = 2;
227: options->error = PETSC_FALSE;
228: options->remapFreq = 1;
229: options->efield_monitor = E_MONITOR_NONE;
230: options->moment_monitor = PETSC_FALSE;
231: options->moment_field_monitor = PETSC_FALSE;
232: options->initial_monitor = PETSC_FALSE;
233: options->perturbed_weights = PETSC_FALSE;
234: options->poisson_monitor = PETSC_FALSE;
235: options->positions_monitor = PETSC_FALSE;
236: options->velocity_monitor = -1;
237: options->ostep = 100;
238: options->timeScale = 2.0e-14;
239: options->charges[0] = -1.0;
240: options->charges[1] = 1.0;
241: options->masses[0] = 1.0;
242: options->masses[1] = 1000.0;
243: options->thermal_energy[0] = 1.0;
244: options->thermal_energy[1] = 1.0;
245: options->cosine_coefficients[0] = 0.01;
246: options->cosine_coefficients[1] = 0.5;
247: options->initVel = 1;
248: options->totalWeight = 1.0;
249: options->drawhgic_x = NULL;
250: options->drawhgic_v = NULL;
251: options->drawhgcell_v = NULL;
252: options->validE = PETSC_FALSE;
253: options->drawlgEmin = -6;
254: options->drawlgE = NULL;
255: options->drawspE = NULL;
256: options->drawspX = NULL;
257: options->viewerRho = NULL;
258: options->viewerRhoHat = NULL;
259: options->viewerPhi = NULL;
260: options->viewerN = NULL;
261: options->viewerP = NULL;
262: options->viewerE = NULL;
263: options->viewerNRes = NULL;
264: options->viewerPRes = NULL;
265: options->viewerERes = NULL;
266: options->drawlgMomRes = NULL;
267: options->em = EM_COULOMB;
268: options->snes = NULL;
269: options->dmMom = NULL;
270: options->dmN = NULL;
271: options->MN = NULL;
272: options->dmP = NULL;
273: options->MP = NULL;
274: options->dmE = NULL;
275: options->ME = NULL;
276: options->dmPot = NULL;
277: options->fftPot = NULL;
278: options->fftX = NULL;
279: options->fftY = NULL;
280: options->fftReal = NULL;
281: options->isPot = NULL;
282: options->M = NULL;
283: options->numParticles = 32768;
284: options->twostream = PETSC_FALSE;
285: options->checkweights = PETSC_FALSE;
286: options->checkVRes = 0;
287: options->checkLandau = PETSC_FALSE;
288: options->emaxCtx.s = 50;
289: options->emaxCtx.per = 100;
291: PetscOptionsBegin(comm, "", "Landau Damping and Two Stream options", "DMSWARM");
292: PetscCall(PetscOptionsBool("-error", "Flag to print the error", __FILE__, options->error, &options->error, NULL));
293: PetscCall(PetscOptionsInt("-remap_freq", "Number", __FILE__, options->remapFreq, &options->remapFreq, NULL));
294: PetscCall(PetscOptionsEnum("-efield_monitor", "Flag to record and plot log(max E) over time", __FILE__, EMonitorTypes, (PetscEnum)options->efield_monitor, (PetscEnum *)&options->efield_monitor, NULL));
295: PetscCall(PetscOptionsReal("-efield_min_monitor", "Minimum E field to plot", __FILE__, options->drawlgEmin, &options->drawlgEmin, NULL));
296: PetscCall(PetscOptionsBool("-moments_monitor", "Flag to show moments table", __FILE__, options->moment_monitor, &options->moment_monitor, NULL));
297: PetscCall(PetscOptionsBool("-moment_field_monitor", "Flag to show moment fields", __FILE__, options->moment_field_monitor, &options->moment_field_monitor, NULL));
298: PetscCall(PetscOptionsBool("-ics_monitor", "Flag to show initial condition histograms", __FILE__, options->initial_monitor, &options->initial_monitor, NULL));
299: PetscCall(PetscOptionsBool("-positions_monitor", "The flag to show particle positions", __FILE__, options->positions_monitor, &options->positions_monitor, NULL));
300: PetscCall(PetscOptionsBool("-poisson_monitor", "The flag to show charges, Efield and potential solve", __FILE__, options->poisson_monitor, &options->poisson_monitor, NULL));
301: PetscCall(PetscOptionsInt("-velocity_monitor", "Cell to show velocity histograms", __FILE__, options->velocity_monitor, &options->velocity_monitor, NULL));
302: PetscCall(PetscOptionsBool("-twostream", "Run two stream instability", __FILE__, options->twostream, &options->twostream, NULL));
303: PetscCall(PetscOptionsBool("-perturbed_weights", "Flag to run uniform sampling with perturbed weights", __FILE__, options->perturbed_weights, &options->perturbed_weights, NULL));
304: PetscCall(PetscOptionsBool("-check_weights", "Ensure all particle weights are positive", __FILE__, options->checkweights, &options->checkweights, NULL));
305: PetscCall(PetscOptionsBool("-check_landau", "Check the decay from Landau damping", __FILE__, options->checkLandau, &options->checkLandau, NULL));
306: PetscCall(PetscOptionsInt("-output_step", "Number of time steps between output", __FILE__, options->ostep, &options->ostep, NULL));
307: PetscCall(PetscOptionsReal("-timeScale", "Nondimensionalizing time scale", __FILE__, options->timeScale, &options->timeScale, NULL));
308: PetscCall(PetscOptionsInt("-check_vel_res", "Check particle velocity residuals for nightly tests", __FILE__, options->checkVRes, &options->checkVRes, NULL));
309: PetscCall(PetscOptionsReal("-initial_velocity", "Initial velocity of perturbed particle", __FILE__, options->initVel, &options->initVel, NULL));
310: PetscCall(PetscOptionsReal("-total_weight", "Total weight of all particles", __FILE__, options->totalWeight, &options->totalWeight, NULL));
311: PetscCall(PetscOptionsRealArray("-cosine_coefficients", "Amplitude and frequency of cosine equation used in initialization", __FILE__, options->cosine_coefficients, &d, NULL));
312: PetscCall(PetscOptionsRealArray("-charges", "Species charges", __FILE__, options->charges, &maxSpecies, NULL));
313: PetscCall(PetscOptionsEnum("-em_type", "Type of electrostatic solver", __FILE__, EMTypes, (PetscEnum)options->em, (PetscEnum *)&options->em, NULL));
314: PetscCall(PetscOptionsInt("-emax_start_step", "First time step to use for Emax fits", __FILE__, options->emaxCtx.s, &options->emaxCtx.s, NULL));
315: PetscCall(PetscOptionsInt("-emax_solve_step", "Number of time steps between Emax fits", __FILE__, options->emaxCtx.per, &options->emaxCtx.per, NULL));
316: PetscOptionsEnd();
318: PetscCall(PetscLogEventRegister("RhsX", TS_CLASSID, &options->RhsXEvent));
319: PetscCall(PetscLogEventRegister("RhsV", TS_CLASSID, &options->RhsVEvent));
320: PetscCall(PetscLogEventRegister("ESolve", TS_CLASSID, &options->ESolveEvent));
321: PetscCall(PetscLogEventRegister("ETab", TS_CLASSID, &options->ETabEvent));
322: PetscFunctionReturn(PETSC_SUCCESS);
323: }
325: static PetscErrorCode SetupContext(DM dm, DM sw, AppCtx *user)
326: {
327: MPI_Comm comm;
329: PetscFunctionBeginUser;
330: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
331: if (user->efield_monitor) {
332: PetscDraw draw;
333: PetscDrawAxis axis;
335: if (user->efield_monitor == E_MONITOR_FULL) {
336: PetscCall(PetscDrawCreate(comm, NULL, "Max Electric Field", 0, 0, 400, 300, &draw));
337: PetscCall(PetscDrawSetSave(draw, "ex2_Efield"));
338: PetscCall(PetscDrawSetFromOptions(draw));
339: } else {
340: PetscCall(PetscDrawOpenNull(comm, &draw));
341: }
342: PetscCall(PetscDrawLGCreate(draw, 1, &user->drawlgE));
343: PetscCall(PetscDrawDestroy(&draw));
344: PetscCall(PetscDrawLGGetAxis(user->drawlgE, &axis));
345: PetscCall(PetscDrawAxisSetLabels(axis, "Max Electric Field", "time", "E_max"));
346: PetscCall(PetscDrawLGSetLimits(user->drawlgE, 0., user->steps * user->stepSize, user->drawlgEmin, 0.));
347: }
349: if (user->initial_monitor) {
350: PetscDraw drawic_x, drawic_v;
351: PetscDrawAxis axis1, axis2;
352: PetscReal dmboxlower[2], dmboxupper[2];
353: PetscInt dim, cStart, cEnd;
355: PetscCall(DMGetDimension(sw, &dim));
356: PetscCall(DMGetBoundingBox(dm, dmboxlower, dmboxupper));
357: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
359: PetscCall(PetscDrawCreate(comm, NULL, "monitor_initial_conditions_x", 0, 300, 400, 300, &drawic_x));
360: PetscCall(PetscDrawSetSave(drawic_x, "ex2_ic_x"));
361: PetscCall(PetscDrawSetFromOptions(drawic_x));
362: PetscCall(PetscDrawHGCreate(drawic_x, (int)dim, &user->drawhgic_x));
363: PetscCall(PetscDrawHGCalcStats(user->drawhgic_x, PETSC_TRUE));
364: PetscCall(PetscDrawHGGetAxis(user->drawhgic_x, &axis1));
365: PetscCall(PetscDrawHGSetNumberBins(user->drawhgic_x, (int)(cEnd - cStart)));
366: PetscCall(PetscDrawAxisSetLabels(axis1, "Initial X Distribution", "X", "weight"));
367: PetscCall(PetscDrawAxisSetLimits(axis1, dmboxlower[0], dmboxupper[0], 0, 0));
368: PetscCall(PetscDrawDestroy(&drawic_x));
370: PetscCall(PetscDrawCreate(comm, NULL, "monitor_initial_conditions_v", 400, 300, 400, 300, &drawic_v));
371: PetscCall(PetscDrawSetSave(drawic_v, "ex9_ic_v"));
372: PetscCall(PetscDrawSetFromOptions(drawic_v));
373: PetscCall(PetscDrawHGCreate(drawic_v, (int)dim, &user->drawhgic_v));
374: PetscCall(PetscDrawHGCalcStats(user->drawhgic_v, PETSC_TRUE));
375: PetscCall(PetscDrawHGGetAxis(user->drawhgic_v, &axis2));
376: PetscCall(PetscDrawHGSetNumberBins(user->drawhgic_v, 21));
377: PetscCall(PetscDrawAxisSetLabels(axis2, "Initial V_x Distribution", "V", "weight"));
378: PetscCall(PetscDrawAxisSetLimits(axis2, -6, 6, 0, 0));
379: PetscCall(PetscDrawDestroy(&drawic_v));
380: }
382: if (user->velocity_monitor >= 0) {
383: DM vdm;
384: DMSwarmCellDM celldm;
385: PetscDraw drawcell_v;
386: PetscDrawAxis axis;
387: PetscReal dmboxlower[2], dmboxupper[2];
388: PetscInt dim;
389: char title[PETSC_MAX_PATH_LEN];
391: PetscCall(DMSwarmGetCellDMByName(sw, "velocity", &celldm));
392: PetscCall(DMSwarmCellDMGetDM(celldm, &vdm));
393: PetscCall(DMGetDimension(vdm, &dim));
394: PetscCall(DMGetBoundingBox(vdm, dmboxlower, dmboxupper));
396: PetscCall(PetscSNPrintf(title, PETSC_MAX_PATH_LEN, "Cell %" PetscInt_FMT ": Velocity Distribution", user->velocity_monitor));
397: PetscCall(PetscDrawCreate(comm, NULL, title, 400, 300, 400, 300, &drawcell_v));
398: PetscCall(PetscDrawSetSave(drawcell_v, "ex2_cell_v"));
399: PetscCall(PetscDrawSetFromOptions(drawcell_v));
400: PetscCall(PetscDrawHGCreate(drawcell_v, (int)dim, &user->drawhgcell_v));
401: PetscCall(PetscDrawHGCalcStats(user->drawhgcell_v, PETSC_TRUE));
402: PetscCall(PetscDrawHGGetAxis(user->drawhgcell_v, &axis));
403: PetscCall(PetscDrawHGSetNumberBins(user->drawhgcell_v, 21));
404: PetscCall(PetscDrawAxisSetLabels(axis, "V_x Distribution", "V", "weight"));
405: PetscCall(PetscDrawAxisSetLimits(axis, dmboxlower[0], dmboxupper[0], 0, 0));
406: PetscCall(PetscDrawDestroy(&drawcell_v));
407: }
409: if (user->positions_monitor) {
410: PetscDraw draw;
411: PetscDrawAxis axis;
413: PetscCall(PetscDrawCreate(comm, NULL, "Particle Position", 0, 0, 400, 300, &draw));
414: PetscCall(PetscDrawSetSave(draw, "ex9_pos"));
415: PetscCall(PetscDrawSetFromOptions(draw));
416: PetscCall(PetscDrawSPCreate(draw, 10, &user->drawspX));
417: PetscCall(PetscDrawDestroy(&draw));
418: PetscCall(PetscDrawSPSetDimension(user->drawspX, 1));
419: PetscCall(PetscDrawSPGetAxis(user->drawspX, &axis));
420: PetscCall(PetscDrawAxisSetLabels(axis, "Particles", "x", "v"));
421: PetscCall(PetscDrawSPReset(user->drawspX));
422: }
423: if (user->poisson_monitor) {
424: Vec rho, rhohat, phi;
425: PetscDraw draw;
426: PetscDrawAxis axis;
428: PetscCall(PetscDrawCreate(comm, NULL, "Electric_Field", 0, 0, 400, 300, &draw));
429: PetscCall(PetscDrawSetFromOptions(draw));
430: PetscCall(PetscDrawSetSave(draw, "ex9_E_spatial"));
431: PetscCall(PetscDrawSPCreate(draw, 10, &user->drawspE));
432: PetscCall(PetscDrawDestroy(&draw));
433: PetscCall(PetscDrawSPSetDimension(user->drawspE, 1));
434: PetscCall(PetscDrawSPGetAxis(user->drawspE, &axis));
435: PetscCall(PetscDrawAxisSetLabels(axis, "Particles", "x", "E"));
436: PetscCall(PetscDrawSPReset(user->drawspE));
438: PetscCall(PetscViewerDrawOpen(comm, NULL, "Charge Density", 0, 0, 400, 300, &user->viewerRho));
439: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerRho, "rho_"));
440: PetscCall(PetscViewerDrawGetDraw(user->viewerRho, 0, &draw));
441: PetscCall(PetscDrawSetSave(draw, "ex9_rho_spatial"));
442: PetscCall(PetscViewerSetFromOptions(user->viewerRho));
443: PetscCall(DMGetNamedGlobalVector(user->dmPot, "rho", &rho));
444: PetscCall(PetscObjectSetName((PetscObject)rho, "charge_density"));
445: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "rho", &rho));
447: PetscInt dim, N;
449: PetscCall(DMGetDimension(user->dmPot, &dim));
450: if (dim == 1) {
451: PetscCall(DMGetNamedGlobalVector(user->dmPot, "rhohat", &rhohat));
452: PetscCall(VecGetSize(rhohat, &N));
453: PetscCall(MatCreateFFT(comm, dim, &N, MATFFTW, &user->fftPot));
454: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "rhohat", &rhohat));
455: PetscCall(MatCreateVecs(user->fftPot, &user->fftX, &user->fftY));
456: PetscCall(ISCreateStride(PETSC_COMM_SELF, N, 0, 1, &user->fftReal));
457: }
459: PetscCall(PetscViewerDrawOpen(comm, NULL, "rhohat: Charge Density FT", 0, 0, 400, 300, &user->viewerRhoHat));
460: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerRhoHat, "rhohat_"));
461: PetscCall(PetscViewerDrawGetDraw(user->viewerRhoHat, 0, &draw));
462: PetscCall(PetscDrawSetSave(draw, "ex9_rho_ft"));
463: PetscCall(PetscViewerSetFromOptions(user->viewerRhoHat));
464: PetscCall(DMGetNamedGlobalVector(user->dmPot, "rhohat", &rhohat));
465: PetscCall(PetscObjectSetName((PetscObject)rhohat, "charge_density_ft"));
466: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "rhohat", &rhohat));
468: PetscCall(PetscViewerDrawOpen(comm, NULL, "Potential", 400, 0, 400, 300, &user->viewerPhi));
469: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerPhi, "phi_"));
470: PetscCall(PetscViewerDrawGetDraw(user->viewerPhi, 0, &draw));
471: PetscCall(PetscDrawSetSave(draw, "ex9_phi_spatial"));
472: PetscCall(PetscViewerSetFromOptions(user->viewerPhi));
473: PetscCall(DMGetNamedGlobalVector(user->dmPot, "phi", &phi));
474: PetscCall(PetscObjectSetName((PetscObject)phi, "potential"));
475: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "phi", &phi));
476: }
477: if (user->moment_field_monitor) {
478: Vec n, p, e;
479: Vec nres, pres, eres;
480: PetscDraw draw;
482: PetscCall(PetscViewerDrawOpen(comm, NULL, "Number Density", 400, 0, 400, 300, &user->viewerN));
483: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerN, "n_"));
484: PetscCall(PetscViewerDrawGetDraw(user->viewerN, 0, &draw));
485: PetscCall(PetscDrawSetSave(draw, "ex4_n_spatial"));
486: PetscCall(PetscViewerSetFromOptions(user->viewerN));
487: PetscCall(DMGetNamedGlobalVector(user->dmN, "n", &n));
488: PetscCall(PetscObjectSetName((PetscObject)n, "Number Density"));
489: PetscCall(DMRestoreNamedGlobalVector(user->dmN, "n", &n));
491: PetscCall(PetscViewerDrawOpen(comm, NULL, "Momentum Density", 800, 0, 400, 300, &user->viewerP));
492: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerP, "p_"));
493: PetscCall(PetscViewerDrawGetDraw(user->viewerP, 0, &draw));
494: PetscCall(PetscDrawSetSave(draw, "ex4_p_spatial"));
495: PetscCall(PetscViewerSetFromOptions(user->viewerP));
496: PetscCall(DMGetNamedGlobalVector(user->dmP, "p", &p));
497: PetscCall(PetscObjectSetName((PetscObject)p, "Momentum Density"));
498: PetscCall(DMRestoreNamedGlobalVector(user->dmP, "p", &p));
500: PetscCall(PetscViewerDrawOpen(comm, NULL, "Emergy Density (Pressure)", 1200, 0, 400, 300, &user->viewerE));
501: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerE, "e_"));
502: PetscCall(PetscViewerDrawGetDraw(user->viewerE, 0, &draw));
503: PetscCall(PetscDrawSetSave(draw, "ex4_e_spatial"));
504: PetscCall(PetscViewerSetFromOptions(user->viewerE));
505: PetscCall(DMGetNamedGlobalVector(user->dmE, "e", &e));
506: PetscCall(PetscObjectSetName((PetscObject)e, "Energy Density (Pressure)"));
507: PetscCall(DMRestoreNamedGlobalVector(user->dmE, "e", &e));
509: PetscDrawAxis axis;
511: PetscCall(PetscDrawCreate(comm, NULL, "Moment Residual", 0, 320, 400, 300, &draw));
512: PetscCall(PetscDrawSetSave(draw, "ex4_moment_res"));
513: PetscCall(PetscDrawSetFromOptions(draw));
514: PetscCall(PetscDrawLGCreate(draw, 3, &user->drawlgMomRes));
515: PetscCall(PetscDrawDestroy(&draw));
516: PetscCall(PetscDrawLGGetAxis(user->drawlgMomRes, &axis));
517: PetscCall(PetscDrawAxisSetLabels(axis, "Moment Residial", "time", "Residual Norm"));
518: PetscCall(PetscDrawLGSetLimits(user->drawlgMomRes, 0., user->steps * user->stepSize, -8, 0));
520: PetscCall(PetscViewerDrawOpen(comm, NULL, "Number Density Residual", 400, 300, 400, 300, &user->viewerNRes));
521: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerNRes, "nres_"));
522: PetscCall(PetscViewerDrawGetDraw(user->viewerNRes, 0, &draw));
523: PetscCall(PetscDrawSetSave(draw, "ex4_nres_spatial"));
524: PetscCall(PetscViewerSetFromOptions(user->viewerNRes));
525: PetscCall(DMGetNamedGlobalVector(user->dmN, "nres", &nres));
526: PetscCall(PetscObjectSetName((PetscObject)nres, "Number Density Residual"));
527: PetscCall(DMRestoreNamedGlobalVector(user->dmN, "nres", &nres));
529: PetscCall(PetscViewerDrawOpen(comm, NULL, "Momentum Density Residual", 800, 300, 400, 300, &user->viewerPRes));
530: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerPRes, "pres_"));
531: PetscCall(PetscViewerDrawGetDraw(user->viewerPRes, 0, &draw));
532: PetscCall(PetscDrawSetSave(draw, "ex4_pres_spatial"));
533: PetscCall(PetscViewerSetFromOptions(user->viewerPRes));
534: PetscCall(DMGetNamedGlobalVector(user->dmP, "pres", &pres));
535: PetscCall(PetscObjectSetName((PetscObject)pres, "Momentum Density Residual"));
536: PetscCall(DMRestoreNamedGlobalVector(user->dmP, "pres", &pres));
538: PetscCall(PetscViewerDrawOpen(comm, NULL, "Energy Density Residual", 1200, 300, 400, 300, &user->viewerERes));
539: PetscCall(PetscObjectSetOptionsPrefix((PetscObject)user->viewerERes, "eres_"));
540: PetscCall(PetscViewerDrawGetDraw(user->viewerERes, 0, &draw));
541: PetscCall(PetscDrawSetSave(draw, "ex4_eres_spatial"));
542: PetscCall(PetscViewerSetFromOptions(user->viewerERes));
543: PetscCall(DMGetNamedGlobalVector(user->dmE, "eres", &eres));
544: PetscCall(PetscObjectSetName((PetscObject)eres, "Energy Density Residual"));
545: PetscCall(DMRestoreNamedGlobalVector(user->dmE, "eres", &eres));
546: }
547: PetscFunctionReturn(PETSC_SUCCESS);
548: }
550: static PetscErrorCode DestroyContext(AppCtx *user)
551: {
552: PetscFunctionBeginUser;
553: PetscCall(PetscDrawHGDestroy(&user->drawhgic_x));
554: PetscCall(PetscDrawHGDestroy(&user->drawhgic_v));
555: PetscCall(PetscDrawHGDestroy(&user->drawhgcell_v));
557: PetscCall(PetscDrawLGDestroy(&user->drawlgE));
558: PetscCall(PetscDrawSPDestroy(&user->drawspE));
559: PetscCall(PetscDrawSPDestroy(&user->drawspX));
560: PetscCall(PetscViewerDestroy(&user->viewerRho));
561: PetscCall(PetscViewerDestroy(&user->viewerRhoHat));
562: PetscCall(MatDestroy(&user->fftPot));
563: PetscCall(VecDestroy(&user->fftX));
564: PetscCall(VecDestroy(&user->fftY));
565: PetscCall(ISDestroy(&user->fftReal));
566: PetscCall(PetscViewerDestroy(&user->viewerPhi));
567: PetscCall(PetscViewerDestroy(&user->viewerN));
568: PetscCall(PetscViewerDestroy(&user->viewerP));
569: PetscCall(PetscViewerDestroy(&user->viewerE));
570: PetscCall(PetscViewerDestroy(&user->viewerNRes));
571: PetscCall(PetscViewerDestroy(&user->viewerPRes));
572: PetscCall(PetscViewerDestroy(&user->viewerERes));
573: PetscCall(PetscDrawLGDestroy(&user->drawlgMomRes));
575: PetscCall(PetscBagDestroy(&user->bag));
576: PetscFunctionReturn(PETSC_SUCCESS);
577: }
579: static PetscErrorCode CheckNonNegativeWeights(DM sw, AppCtx *user)
580: {
581: const PetscScalar *w;
582: PetscInt Np;
584: PetscFunctionBeginUser;
585: if (!user->checkweights) PetscFunctionReturn(PETSC_SUCCESS);
586: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&w));
587: PetscCall(DMSwarmGetLocalSize(sw, &Np));
588: for (PetscInt p = 0; p < Np; ++p) PetscCheck(w[p] >= 0.0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Particle %" PetscInt_FMT " has negative weight %g", p, w[p]);
589: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&w));
590: PetscFunctionReturn(PETSC_SUCCESS);
591: }
593: static void f0_Dirichlet(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[])
594: {
595: for (PetscInt d = 0; d < dim; ++d) f0[0] += 0.5 * PetscSqr(u_x[d]);
596: }
598: static PetscErrorCode computeFieldEnergy(DM dm, Vec u, PetscReal *En)
599: {
600: PetscDS ds;
601: const PetscInt field = 0;
602: PetscInt Nf;
603: void *ctx;
605: PetscFunctionBegin;
606: PetscCall(DMGetApplicationContext(dm, &ctx));
607: PetscCall(DMGetDS(dm, &ds));
608: PetscCall(PetscDSGetNumFields(ds, &Nf));
609: PetscCheck(Nf == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "We currently only support 1 field, not %" PetscInt_FMT, Nf);
610: PetscCall(PetscDSSetObjective(ds, field, &f0_Dirichlet));
611: PetscCall(DMPlexComputeIntegralFEM(dm, u, En, ctx));
612: PetscFunctionReturn(PETSC_SUCCESS);
613: }
615: static PetscErrorCode computeVelocityFEMMoments(DM sw, PetscReal moments[], AppCtx *user)
616: {
617: DMSwarmCellDM celldm;
618: DM vdm;
619: Vec u[1];
620: const char *fields[1] = {"w_q"};
622: PetscFunctionBegin;
623: PetscCall(DMSwarmSetCellDMActive(sw, "velocity"));
624: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
625: PetscCall(DMSwarmCellDMGetDM(celldm, &vdm));
626: PetscCall(DMGetGlobalVector(vdm, &u[0]));
627: PetscCall(DMSwarmProjectFields(sw, vdm, 1, fields, u, SCATTER_FORWARD));
628: PetscCall(DMPlexComputeMoments(vdm, u[0], moments));
629: PetscCall(DMRestoreGlobalVector(vdm, &u[0]));
630: PetscCall(DMSwarmSetCellDMActive(sw, "space"));
631: PetscFunctionReturn(PETSC_SUCCESS);
632: }
634: static void f0_grad_phi2(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[])
635: {
636: f0[0] = 0.;
637: for (PetscInt d = 0; d < dim; ++d) f0[0] += PetscSqr(u_x[uOff_x[0] + d * dim + d]);
638: }
640: // Our model is E_max(t) = C e^{-gamma t} |cos(omega t - phi)|
641: static PetscErrorCode ComputeEmaxResidual(Tao tao, Vec x, Vec res, void *user)
642: {
643: EmaxCtx *ctx = (EmaxCtx *)user;
644: const PetscScalar *a;
645: PetscScalar *F;
646: PetscReal C, gamma, omega, phi;
648: PetscFunctionBegin;
649: PetscCall(VecGetArrayRead(x, &a));
650: PetscCall(VecGetArray(res, &F));
651: C = PetscRealPart(a[0]);
652: gamma = PetscRealPart(a[1]);
653: omega = PetscRealPart(a[2]);
654: phi = PetscRealPart(a[3]);
655: PetscCall(VecRestoreArrayRead(x, &a));
656: for (PetscInt i = ctx->s; i < ctx->e; ++i) F[i - ctx->s] = PetscPowReal(10., ctx->Emax[i]) - C * PetscExpReal(-gamma * ctx->t[i]) * PetscAbsReal(PetscCosReal(omega * ctx->t[i] - phi));
657: PetscCall(VecRestoreArray(res, &F));
658: PetscFunctionReturn(PETSC_SUCCESS);
659: }
661: // The Jacobian of the residual J = dr(x)/dx
662: static PetscErrorCode ComputeEmaxJacobian(Tao tao, Vec x, Mat J, Mat Jpre, void *user)
663: {
664: EmaxCtx *ctx = (EmaxCtx *)user;
665: const PetscScalar *a;
666: PetscScalar *jac;
667: PetscReal C, gamma, omega, phi;
668: const PetscInt n = ctx->e - ctx->s;
670: PetscFunctionBegin;
671: PetscCall(VecGetArrayRead(x, &a));
672: C = PetscRealPart(a[0]);
673: gamma = PetscRealPart(a[1]);
674: omega = PetscRealPart(a[2]);
675: phi = PetscRealPart(a[3]);
676: PetscCall(VecRestoreArrayRead(x, &a));
677: PetscCall(MatDenseGetArray(J, &jac));
678: for (PetscInt i = 0; i < n; ++i) {
679: const PetscInt k = i + ctx->s;
681: jac[i * 4 + 0] = -PetscExpReal(-gamma * ctx->t[k]) * PetscAbsReal(PetscCosReal(omega * ctx->t[k] - phi));
682: jac[i * 4 + 1] = C * ctx->t[k] * PetscExpReal(-gamma * ctx->t[k]) * PetscAbsReal(PetscCosReal(omega * ctx->t[k] - phi));
683: jac[i * 4 + 2] = C * ctx->t[k] * PetscExpReal(-gamma * ctx->t[k]) * (PetscCosReal(omega * ctx->t[k] - phi) < 0. ? -1. : 1.) * PetscSinReal(omega * ctx->t[k] - phi);
684: jac[i * 4 + 3] = -C * PetscExpReal(-gamma * ctx->t[k]) * (PetscCosReal(omega * ctx->t[k] - phi) < 0. ? -1. : 1.) * PetscSinReal(omega * ctx->t[k] - phi);
685: }
686: PetscCall(MatDenseRestoreArray(J, &jac));
687: PetscFunctionReturn(PETSC_SUCCESS);
688: }
690: // Our model is log_10 E_max(t) = log_10 C - gamma t log_10 e + log_10 |cos(omega t - phi)|
691: static PetscErrorCode ComputeLogEmaxResidual(Tao tao, Vec x, Vec res, void *user)
692: {
693: EmaxCtx *ctx = (EmaxCtx *)user;
694: const PetscScalar *a;
695: PetscScalar *F;
696: PetscReal C, gamma, omega, phi;
698: PetscFunctionBegin;
699: PetscCall(VecGetArrayRead(x, &a));
700: PetscCall(VecGetArray(res, &F));
701: C = PetscRealPart(a[0]);
702: gamma = PetscRealPart(a[1]);
703: omega = PetscRealPart(a[2]);
704: phi = PetscRealPart(a[3]);
705: PetscCall(VecRestoreArrayRead(x, &a));
706: for (PetscInt i = ctx->s; i < ctx->e; ++i) {
707: if (C < 0) {
708: F[i - ctx->s] = 1e10;
709: continue;
710: }
711: F[i - ctx->s] = ctx->Emax[i] - (PetscLog10Real(C) - gamma * ctx->t[i] * PetscLog10Real(PETSC_E) + PetscLog10Real(PetscAbsReal(PetscCosReal(omega * ctx->t[i] - phi))));
712: }
713: PetscCall(VecRestoreArray(res, &F));
714: PetscFunctionReturn(PETSC_SUCCESS);
715: }
717: // The Jacobian of the residual J = dr(x)/dx
718: static PetscErrorCode ComputeLogEmaxJacobian(Tao tao, Vec x, Mat J, Mat Jpre, void *user)
719: {
720: EmaxCtx *ctx = (EmaxCtx *)user;
721: const PetscScalar *a;
722: PetscScalar *jac;
723: PetscReal C, omega, phi;
724: const PetscInt n = ctx->e - ctx->s;
726: PetscFunctionBegin;
727: PetscCall(VecGetArrayRead(x, &a));
728: C = PetscRealPart(a[0]);
729: omega = PetscRealPart(a[2]);
730: phi = PetscRealPart(a[3]);
731: PetscCall(VecRestoreArrayRead(x, &a));
732: PetscCall(MatDenseGetArray(J, &jac));
733: for (PetscInt i = 0; i < n; ++i) {
734: const PetscInt k = i + ctx->s;
736: jac[0 * n + i] = -1. / (PetscLog10Real(PETSC_E) * C);
737: jac[1 * n + i] = ctx->t[k] * PetscLog10Real(PETSC_E);
738: jac[2 * n + i] = (PetscCosReal(omega * ctx->t[k] - phi) < 0. ? -1. : 1.) * ctx->t[k] * PetscSinReal(omega * ctx->t[k] - phi) / (PetscLog10Real(PETSC_E) * PetscAbsReal(PetscCosReal(omega * ctx->t[k] - phi)));
739: jac[3 * n + i] = -(PetscCosReal(omega * ctx->t[k] - phi) < 0. ? -1. : 1.) * PetscSinReal(omega * ctx->t[k] - phi) / (PetscLog10Real(PETSC_E) * PetscAbsReal(PetscCosReal(omega * ctx->t[k] - phi)));
740: }
741: PetscCall(MatDenseRestoreArray(J, &jac));
742: PetscCall(MatViewFromOptions(J, NULL, "-emax_jac_view"));
743: PetscFunctionReturn(PETSC_SUCCESS);
744: }
746: static PetscErrorCode MonitorEField(TS ts, PetscInt step, PetscReal t, Vec U, void *ctx)
747: {
748: AppCtx *user = (AppCtx *)ctx;
749: DM sw;
750: PetscScalar intESq;
751: PetscReal *E, *x, *weight;
752: PetscReal Enorm = 0., lgEnorm, lgEmax, sum = 0., Emax = 0., chargesum = 0.;
753: PetscReal pmoments[4]; /* \int f, \int v f, \int v^2 f */
754: PetscInt *species, dim, Np, gNp;
755: MPI_Comm comm;
756: PetscMPIInt rank;
758: PetscFunctionBeginUser;
759: if (step < 0 || !user->validE) PetscFunctionReturn(PETSC_SUCCESS);
760: PetscCall(PetscObjectGetComm((PetscObject)ts, &comm));
761: PetscCallMPI(MPI_Comm_rank(comm, &rank));
762: PetscCall(TSGetDM(ts, &sw));
763: PetscCall(DMGetDimension(sw, &dim));
764: PetscCall(DMSwarmGetLocalSize(sw, &Np));
765: PetscCall(DMSwarmGetSize(sw, &gNp));
766: PetscCall(DMSwarmSortGetAccess(sw));
767: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
768: PetscCall(DMSwarmGetField(sw, "E_field", NULL, NULL, (void **)&E));
769: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
770: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&weight));
772: for (PetscInt p = 0; p < Np; ++p) {
773: for (PetscInt d = 0; d < 1; ++d) {
774: PetscReal temp = PetscAbsReal(E[p * dim + d]);
775: if (temp > Emax) Emax = temp;
776: }
777: Enorm += PetscSqrtReal(E[p * dim] * E[p * dim]);
778: sum += E[p * dim];
779: chargesum += user->charges[0] * weight[p];
780: }
781: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &Emax, 1, MPIU_REAL, MPIU_MAX, comm));
782: lgEnorm = Enorm != 0 ? PetscLog10Real(Enorm) : -16.;
783: lgEmax = Emax != 0 ? PetscLog10Real(Emax) : user->drawlgEmin;
785: PetscDS ds;
786: Vec phi;
788: PetscCall(DMGetNamedGlobalVector(user->dmPot, "phi", &phi));
789: PetscCall(DMGetDS(user->dmPot, &ds));
790: PetscCall(PetscDSSetObjective(ds, 0, &f0_grad_phi2));
791: PetscCall(DMPlexComputeIntegralFEM(user->dmPot, phi, &intESq, user));
792: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "phi", &phi));
794: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
795: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
796: PetscCall(DMSwarmRestoreField(sw, "E_field", NULL, NULL, (void **)&E));
797: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
798: PetscCall(PetscDrawLGAddPoint(user->drawlgE, &t, &lgEmax));
799: if (user->efield_monitor == E_MONITOR_FULL) {
800: PetscDraw draw;
802: PetscCall(PetscDrawLGDraw(user->drawlgE));
803: PetscCall(PetscDrawLGGetDraw(user->drawlgE, &draw));
804: PetscCall(PetscDrawSave(draw));
806: PetscCall(DMSwarmComputeMoments(sw, "velocity", "w_q", pmoments));
807: PetscCall(PetscPrintf(comm, "E: %f\t%+e\t%e\t%f\t%20.15e\t%f\t%f\t%f\t%20.15e\t%20.15e\t%20.15e\t%" PetscInt_FMT "\t(%" PetscInt_FMT ")\n", (double)t, (double)sum, (double)Enorm, (double)lgEnorm, (double)Emax, (double)lgEmax, (double)chargesum, (double)pmoments[0], (double)pmoments[1], (double)pmoments[1 + dim], (double)PetscSqrtReal(intESq), gNp, step));
808: PetscCall(DMViewFromOptions(sw, NULL, "-sw_efield_view"));
809: }
811: // Compute decay rate and frequency
812: PetscCall(PetscDrawLGGetData(user->drawlgE, NULL, &user->emaxCtx.e, &user->emaxCtx.t, &user->emaxCtx.Emax));
813: if (!rank && !(user->emaxCtx.e % user->emaxCtx.per)) {
814: Tao tao;
815: Mat J;
816: Vec x, r;
817: PetscScalar *a;
818: PetscBool fitLog = PETSC_TRUE, debug = PETSC_FALSE;
820: PetscCall(TaoCreate(PETSC_COMM_SELF, &tao));
821: PetscCall(TaoSetOptionsPrefix(tao, "emax_"));
822: PetscCall(VecCreateSeq(PETSC_COMM_SELF, 4, &x));
823: PetscCall(TaoSetSolution(tao, x));
824: PetscCall(VecCreateSeq(PETSC_COMM_SELF, user->emaxCtx.e - user->emaxCtx.s, &r));
825: if (fitLog) PetscCall(TaoSetResidualRoutine(tao, r, ComputeLogEmaxResidual, &user->emaxCtx));
826: else PetscCall(TaoSetResidualRoutine(tao, r, ComputeEmaxResidual, &user->emaxCtx));
827: PetscCall(VecDestroy(&r));
828: PetscCall(MatCreateSeqDense(PETSC_COMM_SELF, user->emaxCtx.e - user->emaxCtx.s, 4, NULL, &J));
829: if (fitLog) PetscCall(TaoSetJacobianResidualRoutine(tao, J, J, ComputeLogEmaxJacobian, &user->emaxCtx));
830: else PetscCall(TaoSetJacobianResidualRoutine(tao, J, J, ComputeEmaxJacobian, &user->emaxCtx));
831: PetscCall(MatDestroy(&J));
832: PetscCall(TaoSetFromOptions(tao));
833: PetscCall(VecGetArray(x, &a));
834: a[0] = 0.02;
835: a[1] = 0.15;
836: a[2] = 1.4;
837: a[3] = 0.45;
838: PetscCall(VecRestoreArray(x, &a));
839: PetscCall(TaoSolve(tao));
840: if (debug) {
841: PetscCall(PetscPrintf(PETSC_COMM_SELF, "t = ["));
842: for (PetscInt i = 0; i < user->emaxCtx.e; ++i) {
843: if (i > 0) PetscCall(PetscPrintf(PETSC_COMM_SELF, ", "));
844: PetscCall(PetscPrintf(PETSC_COMM_SELF, "%g", user->emaxCtx.t[i]));
845: }
846: PetscCall(PetscPrintf(PETSC_COMM_SELF, "]\n"));
847: PetscCall(PetscPrintf(PETSC_COMM_SELF, "Emax = ["));
848: for (PetscInt i = 0; i < user->emaxCtx.e; ++i) {
849: if (i > 0) PetscCall(PetscPrintf(PETSC_COMM_SELF, ", "));
850: PetscCall(PetscPrintf(PETSC_COMM_SELF, "%g", user->emaxCtx.Emax[i]));
851: }
852: PetscCall(PetscPrintf(PETSC_COMM_SELF, "]\n"));
853: }
854: PetscDraw draw;
855: PetscDrawAxis axis;
856: char title[PETSC_MAX_PATH_LEN];
858: PetscCall(VecGetArray(x, &a));
859: user->gamma = a[1];
860: user->omega = a[2];
861: if (user->efield_monitor == E_MONITOR_FULL) {
862: PetscCall(PetscPrintf(PETSC_COMM_SELF, "Emax Fit: gamma %g omega %g C %g phi %g\n", a[1], a[2], a[0], a[3]));
863: PetscCall(PetscDrawLGGetDraw(user->drawlgE, &draw));
864: PetscCall(PetscSNPrintf(title, PETSC_MAX_PATH_LEN, "Max Electric Field gamma %.4g omega %.4g", a[1], a[2]));
865: PetscCall(PetscDrawSetTitle(draw, title));
866: PetscCall(PetscDrawLGGetAxis(user->drawlgE, &axis));
867: PetscCall(PetscDrawAxisSetLabels(axis, title, "time", "E_max"));
868: }
869: PetscCall(VecRestoreArray(x, &a));
870: PetscCall(VecDestroy(&x));
871: PetscCall(TaoDestroy(&tao));
872: }
873: PetscFunctionReturn(PETSC_SUCCESS);
874: }
876: static PetscErrorCode MonitorMoments(TS ts, PetscInt step, PetscReal t, Vec U, void *ctx)
877: {
878: AppCtx *user = (AppCtx *)ctx;
879: DM sw;
880: PetscReal pmoments[4], fmoments[4]; /* \int f, \int v f, \int v^2 f */
882: PetscFunctionBeginUser;
883: if (step < 0) PetscFunctionReturn(PETSC_SUCCESS);
884: PetscCall(TSGetDM(ts, &sw));
886: PetscCall(DMSwarmComputeMoments(sw, "velocity", "w_q", pmoments));
887: PetscCall(computeVelocityFEMMoments(sw, fmoments, user));
889: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%f\t%f\t%f\t%f\t%f\t%f\t%f\n", (double)t, (double)pmoments[0], (double)pmoments[1], (double)pmoments[3], (double)fmoments[0], (double)fmoments[1], (double)fmoments[2]));
890: PetscFunctionReturn(PETSC_SUCCESS);
891: }
893: static PetscErrorCode zero(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nc, PetscScalar *u, void *ctx)
894: {
895: u[0] = 0.0;
896: return PETSC_SUCCESS;
897: }
899: /*
900: M_p w_p
901: - Make M_p with "moments"
902: - Get w_p from Swarm
903: M_p v_p w_p
904: - Get v_p from Swarm
905: - pointwise multiply v_p and w_p
906: M_p (v_p - (\sum_j p_F \phi_j(x_p)) / m (\sum_k n_F \phi_k(x_p)))^2 w_p
907: - ProjectField(sw, {n, p} U, {v_p} A, tmp_p)
908: - pointwise multiply tmp_p and w_p
910: Projection works fpr swarms
911: Fields are FE from the CellDM, and aux fields are the swarm fields
912: */
913: static PetscErrorCode ComputeMomentFields(TS ts)
914: {
915: AppCtx *user;
916: DM sw;
917: KSP ksp;
918: Mat M_p, D_p;
919: Vec f, v, E, tmpMom;
920: Vec m, mold, mfluxold, mres, n, nrhs, nflux, nres, p, prhs, pflux, pres, e, erhs, eflux, eres;
921: PetscReal dt, t;
922: PetscInt Nts;
924: PetscFunctionBegin;
925: PetscCall(TSGetStepNumber(ts, &Nts));
926: PetscCall(TSGetTimeStep(ts, &dt));
927: PetscCall(TSGetTime(ts, &t));
928: PetscCall(TSGetDM(ts, &sw));
929: PetscCall(DMGetApplicationContext(sw, (void *)&user));
930: PetscCall(DMSwarmSetCellDMActive(sw, "moment fields"));
931: PetscCall(DMSwarmMigrate(sw, PETSC_FALSE));
932: // TODO In higher dimensions, we will have to create different M_p and D_p for each field
933: PetscCall(DMCreateMassMatrix(sw, user->dmN, &M_p));
934: PetscCall(DMCreateGradientMatrix(sw, user->dmN, &D_p));
935: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "w_q", &f));
936: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "velocity", &v));
937: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "E_field", &E));
938: PetscCall(PetscObjectSetName((PetscObject)f, "particle weight"));
940: PetscCall(MatViewFromOptions(user->MN, NULL, "-mn_view"));
941: PetscCall(MatViewFromOptions(user->MP, NULL, "-mp_view"));
942: PetscCall(MatViewFromOptions(user->ME, NULL, "-me_view"));
943: PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
945: PetscCall(DMGetGlobalVector(user->dmN, &nrhs));
946: PetscCall(DMGetGlobalVector(user->dmN, &nflux));
947: PetscCall(PetscObjectSetName((PetscObject)nrhs, "Weak number density"));
948: PetscCall(DMGetNamedGlobalVector(user->dmN, "n", &n));
949: PetscCall(DMGetGlobalVector(user->dmP, &prhs));
950: PetscCall(DMGetGlobalVector(user->dmP, &pflux));
951: PetscCall(PetscObjectSetName((PetscObject)prhs, "Weak momentum density"));
952: PetscCall(DMGetNamedGlobalVector(user->dmP, "p", &p));
953: PetscCall(DMGetGlobalVector(user->dmE, &erhs));
954: PetscCall(DMGetGlobalVector(user->dmE, &eflux));
955: PetscCall(PetscObjectSetName((PetscObject)erhs, "Weak energy density (pressure)"));
956: PetscCall(DMGetNamedGlobalVector(user->dmE, "e", &e));
958: // Compute moments and fluxes
959: PetscCall(VecDuplicate(f, &tmpMom));
961: PetscCall(MatMultTranspose(M_p, f, nrhs));
963: PetscCall(VecPointwiseMult(tmpMom, f, v));
964: PetscCall(MatMultTranspose(M_p, tmpMom, prhs));
965: PetscCall(MatMultTranspose(D_p, tmpMom, nflux));
967: PetscCall(VecPointwiseMult(tmpMom, tmpMom, v));
968: PetscCall(MatMultTranspose(M_p, tmpMom, erhs));
969: PetscCall(MatMultTranspose(D_p, tmpMom, pflux));
971: PetscCall(VecPointwiseMult(tmpMom, tmpMom, v));
972: PetscCall(MatMultTranspose(D_p, tmpMom, eflux));
974: PetscCall(VecPointwiseMult(tmpMom, f, E));
975: PetscCall(MatMultTransposeAdd(M_p, tmpMom, pflux, pflux));
977: PetscCall(VecPointwiseMult(tmpMom, v, E));
978: PetscCall(VecScale(tmpMom, 2.));
979: PetscCall(MatMultTransposeAdd(M_p, tmpMom, eflux, eflux));
981: PetscCall(VecDestroy(&tmpMom));
982: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "velocity", &v));
983: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", &f));
984: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "E_field", &E));
986: PetscCall(MatDestroy(&M_p));
987: PetscCall(MatDestroy(&D_p));
989: PetscCall(KSPCreate(PetscObjectComm((PetscObject)sw), &ksp));
990: PetscCall(KSPSetOptionsPrefix(ksp, "mom_proj_"));
991: PetscCall(KSPSetOperators(ksp, user->MN, user->MN));
992: PetscCall(KSPSetFromOptions(ksp));
993: PetscCall(KSPSolve(ksp, nrhs, n));
994: PetscCall(KSPSetOperators(ksp, user->MP, user->MP));
995: PetscCall(KSPSetFromOptions(ksp));
996: PetscCall(KSPSolve(ksp, prhs, p));
997: PetscCall(KSPSetOperators(ksp, user->ME, user->ME));
998: PetscCall(KSPSetFromOptions(ksp));
999: PetscCall(KSPSolve(ksp, erhs, e));
1000: PetscCall(KSPDestroy(&ksp));
1001: PetscCall(DMRestoreGlobalVector(user->dmN, &nrhs));
1002: PetscCall(DMRestoreGlobalVector(user->dmP, &prhs));
1003: PetscCall(DMRestoreGlobalVector(user->dmE, &erhs));
1005: // Check moment residual
1006: // TODO Fix global2local here
1007: PetscReal res[3], logres[3];
1009: PetscCall(DMGetGlobalVector(user->dmMom, &m));
1010: PetscCall(VecISCopy(m, user->isN, SCATTER_FORWARD, n));
1011: PetscCall(VecISCopy(m, user->isP, SCATTER_FORWARD, p));
1012: PetscCall(VecISCopy(m, user->isE, SCATTER_FORWARD, e));
1013: PetscCall(DMGetNamedGlobalVector(user->dmMom, "mold", &mold));
1014: PetscCall(DMGetNamedGlobalVector(user->dmMom, "mfluxold", &mfluxold));
1015: if (!Nts) goto end;
1017: // e = \Tr{\tau}
1018: // M_p w^{k+1} - M_p w^k - \Delta t D_p (w^k \vb{v}^k) = 0
1019: // M_p \vb{p}^{k+1} - M_p \vb{p}^k - \Delta t D_p \tau - e \Delta t M_p \left( n \vb{E} \right) = 0
1020: // M_p e^{k+1} - M_p e^k - \Delta t D_p \vb{Q} - 2 e \Delta t M_p \left( \vb{p} \cdot \vb{E} \right) = 0
1021: PetscCall(DMGetGlobalVector(user->dmMom, &mres));
1022: PetscCall(VecCopy(mfluxold, mres));
1023: PetscCall(VecAXPBYPCZ(mres, 1. / dt, -1. / dt, -1., m, mold));
1025: PetscCall(DMGetNamedGlobalVector(user->dmN, "nres", &nres));
1026: PetscCall(DMGetNamedGlobalVector(user->dmP, "pres", &pres));
1027: PetscCall(DMGetNamedGlobalVector(user->dmE, "eres", &eres));
1028: PetscCall(VecISCopy(mres, user->isN, SCATTER_REVERSE, nres));
1029: PetscCall(VecISCopy(mres, user->isP, SCATTER_REVERSE, pres));
1030: PetscCall(VecISCopy(mres, user->isE, SCATTER_REVERSE, eres));
1031: PetscCall(VecNorm(nres, NORM_2, &res[0]));
1032: PetscCall(VecNorm(pres, NORM_2, &res[1]));
1033: PetscCall(VecNorm(eres, NORM_2, &res[2]));
1034: PetscCall(PetscPrintf(PetscObjectComm((PetscObject)sw), "Mass Residual: %g\n", (double)res[0]));
1035: PetscCall(PetscPrintf(PetscObjectComm((PetscObject)sw), "Momentum Residual: %g\n", (double)res[1]));
1036: PetscCall(PetscPrintf(PetscObjectComm((PetscObject)sw), "Energy Residual: %g\n", (double)res[2]));
1037: PetscCall(DMRestoreNamedGlobalVector(user->dmN, "nres", &nres));
1038: PetscCall(DMRestoreNamedGlobalVector(user->dmP, "pres", &pres));
1039: PetscCall(DMRestoreNamedGlobalVector(user->dmE, "eres", &eres));
1040: PetscCall(DMRestoreGlobalVector(user->dmMom, &mres));
1042: for (PetscInt i = 0; i < 3; ++i) logres[i] = PetscLog10Real(res[i]);
1043: PetscCall(PetscDrawLGAddCommonPoint(user->drawlgMomRes, t, logres));
1044: PetscCall(PetscDrawLGDraw(user->drawlgMomRes));
1045: {
1046: PetscDraw draw;
1048: PetscCall(PetscDrawLGGetDraw(user->drawlgMomRes, &draw));
1049: PetscCall(PetscDrawSave(draw));
1050: }
1052: end:
1053: PetscCall(VecCopy(m, mold));
1054: PetscCall(DMRestoreGlobalVector(user->dmMom, &m));
1055: PetscCall(DMRestoreNamedGlobalVector(user->dmMom, "mold", &mold));
1056: PetscCall(VecISCopy(mfluxold, user->isN, SCATTER_FORWARD, nflux));
1057: PetscCall(VecISCopy(mfluxold, user->isP, SCATTER_FORWARD, pflux));
1058: PetscCall(VecISCopy(mfluxold, user->isE, SCATTER_FORWARD, eflux));
1059: PetscCall(DMRestoreNamedGlobalVector(user->dmMom, "mfluxold", &mfluxold));
1061: PetscCall(DMRestoreGlobalVector(user->dmN, &nflux));
1062: PetscCall(DMRestoreGlobalVector(user->dmP, &pflux));
1063: PetscCall(DMRestoreGlobalVector(user->dmE, &eflux));
1064: PetscCall(DMRestoreNamedGlobalVector(user->dmN, "n", &n));
1065: PetscCall(DMRestoreNamedGlobalVector(user->dmP, "p", &p));
1066: PetscCall(DMRestoreNamedGlobalVector(user->dmE, "e", &e));
1067: PetscCall(DMSwarmSetCellDMActive(sw, "space"));
1068: PetscFunctionReturn(PETSC_SUCCESS);
1069: }
1071: static PetscErrorCode MonitorMomentFields(TS ts, PetscInt step, PetscReal t, Vec U, void *ctx)
1072: {
1073: AppCtx *user = (AppCtx *)ctx;
1074: Vec n, p, e;
1075: Vec nres, pres, eres;
1077: PetscFunctionBeginUser;
1078: if (step < 0) PetscFunctionReturn(PETSC_SUCCESS);
1079: PetscCall(ComputeMomentFields(ts));
1081: PetscCall(DMGetNamedGlobalVector(user->dmN, "n", &n));
1082: PetscCall(VecView(n, user->viewerN));
1083: PetscCall(DMRestoreNamedGlobalVector(user->dmN, "n", &n));
1085: PetscCall(DMGetNamedGlobalVector(user->dmP, "p", &p));
1086: PetscCall(VecView(p, user->viewerP));
1087: PetscCall(DMRestoreNamedGlobalVector(user->dmP, "p", &p));
1089: PetscCall(DMGetNamedGlobalVector(user->dmE, "e", &e));
1090: PetscCall(VecView(e, user->viewerE));
1091: PetscCall(DMRestoreNamedGlobalVector(user->dmE, "e", &e));
1093: PetscCall(DMGetNamedGlobalVector(user->dmN, "nres", &nres));
1094: PetscCall(VecView(nres, user->viewerNRes));
1095: PetscCall(DMRestoreNamedGlobalVector(user->dmN, "nres", &nres));
1097: PetscCall(DMGetNamedGlobalVector(user->dmP, "pres", &pres));
1098: PetscCall(VecView(pres, user->viewerPRes));
1099: PetscCall(DMRestoreNamedGlobalVector(user->dmP, "pres", &pres));
1101: PetscCall(DMGetNamedGlobalVector(user->dmE, "eres", &eres));
1102: PetscCall(VecView(eres, user->viewerERes));
1103: PetscCall(DMRestoreNamedGlobalVector(user->dmE, "eres", &eres));
1104: PetscFunctionReturn(PETSC_SUCCESS);
1105: }
1107: PetscErrorCode MonitorInitialConditions(TS ts, PetscInt step, PetscReal t, Vec U, void *ctx)
1108: {
1109: AppCtx *user = (AppCtx *)ctx;
1110: DM sw;
1111: PetscDraw drawic_x, drawic_v;
1112: PetscReal *weight, *pos, *vel;
1113: PetscInt dim, Np;
1115: PetscFunctionBegin;
1116: if (step < 0) PetscFunctionReturn(PETSC_SUCCESS); /* -1 indicates interpolated solution */
1117: if (step == 0) {
1118: PetscCall(TSGetDM(ts, &sw));
1119: PetscCall(DMGetDimension(sw, &dim));
1120: PetscCall(DMSwarmGetLocalSize(sw, &Np));
1122: PetscCall(PetscDrawHGReset(user->drawhgic_x));
1123: PetscCall(PetscDrawHGGetDraw(user->drawhgic_x, &drawic_x));
1124: PetscCall(PetscDrawClear(drawic_x));
1125: PetscCall(PetscDrawFlush(drawic_x));
1127: PetscCall(PetscDrawHGReset(user->drawhgic_v));
1128: PetscCall(PetscDrawHGGetDraw(user->drawhgic_v, &drawic_v));
1129: PetscCall(PetscDrawClear(drawic_v));
1130: PetscCall(PetscDrawFlush(drawic_v));
1132: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&pos));
1133: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&vel));
1134: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&weight));
1135: for (PetscInt p = 0; p < Np; ++p) {
1136: PetscCall(PetscDrawHGAddWeightedValue(user->drawhgic_x, pos[p * dim], weight[p]));
1137: PetscCall(PetscDrawHGAddWeightedValue(user->drawhgic_v, vel[p * dim], weight[p]));
1138: }
1139: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&pos));
1140: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&vel));
1141: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
1143: PetscCall(PetscDrawHGDraw(user->drawhgic_x));
1144: PetscCall(PetscDrawHGSave(user->drawhgic_x));
1145: PetscCall(PetscDrawHGDraw(user->drawhgic_v));
1146: PetscCall(PetscDrawHGSave(user->drawhgic_v));
1147: }
1148: PetscFunctionReturn(PETSC_SUCCESS);
1149: }
1151: // Right now, make the complete velocity histogram
1152: PetscErrorCode MonitorVelocity(TS ts, PetscInt step, PetscReal t, Vec U, void *ctx)
1153: {
1154: AppCtx *user = (AppCtx *)ctx;
1155: DM sw, dm;
1156: Vec ks;
1157: PetscProbFn *cdf;
1158: PetscDraw drawcell_v;
1159: PetscScalar *ksa;
1160: PetscReal *weight, *vel;
1161: PetscInt *pidx;
1162: PetscInt dim, Npc, cStart, cEnd, cell = user->velocity_monitor;
1164: PetscFunctionBegin;
1165: PetscCall(TSGetDM(ts, &sw));
1166: PetscCall(DMGetDimension(sw, &dim));
1168: PetscCall(DMSwarmGetCellDM(sw, &dm));
1169: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
1170: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &ks));
1171: PetscCall(PetscObjectSetName((PetscObject)ks, "KS Statistic by Cell"));
1172: PetscCall(VecSetSizes(ks, cEnd - cStart, PETSC_DETERMINE));
1173: PetscCall(VecSetFromOptions(ks));
1174: switch (dim) {
1175: case 1:
1176: //cdf = PetscCDFMaxwellBoltzmann1D;
1177: cdf = PetscCDFGaussian1D;
1178: break;
1179: case 2:
1180: cdf = PetscCDFMaxwellBoltzmann2D;
1181: break;
1182: case 3:
1183: cdf = PetscCDFMaxwellBoltzmann3D;
1184: break;
1185: default:
1186: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Dimension %" PetscInt_FMT " not supported", dim);
1187: }
1189: PetscCall(PetscDrawHGReset(user->drawhgcell_v));
1190: PetscCall(PetscDrawHGGetDraw(user->drawhgcell_v, &drawcell_v));
1191: PetscCall(PetscDrawClear(drawcell_v));
1192: PetscCall(PetscDrawFlush(drawcell_v));
1194: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&vel));
1195: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&weight));
1196: PetscCall(DMSwarmSortGetAccess(sw));
1197: PetscCall(VecGetArrayWrite(ks, &ksa));
1198: for (PetscInt c = cStart; c < cEnd; ++c) {
1199: Vec cellv, cellw;
1200: PetscScalar *cella, *cellaw;
1201: PetscReal totWgt = 0.;
1203: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
1204: PetscCall(VecCreate(PETSC_COMM_SELF, &cellv));
1205: PetscCall(VecSetBlockSize(cellv, dim));
1206: PetscCall(VecSetSizes(cellv, Npc * dim, Npc));
1207: PetscCall(VecSetFromOptions(cellv));
1208: PetscCall(VecCreate(PETSC_COMM_SELF, &cellw));
1209: PetscCall(VecSetSizes(cellw, Npc, Npc));
1210: PetscCall(VecSetFromOptions(cellw));
1211: PetscCall(VecGetArrayWrite(cellv, &cella));
1212: PetscCall(VecGetArrayWrite(cellw, &cellaw));
1213: for (PetscInt q = 0; q < Npc; ++q) {
1214: const PetscInt p = pidx[q];
1215: if (c == cell) PetscCall(PetscDrawHGAddWeightedValue(user->drawhgcell_v, vel[p * dim], weight[p]));
1216: for (PetscInt d = 0; d < dim; ++d) cella[q * dim + d] = vel[p * dim + d];
1217: cellaw[q] = weight[p];
1218: totWgt += weight[p];
1219: }
1220: PetscCall(VecRestoreArrayWrite(cellv, &cella));
1221: PetscCall(VecRestoreArrayWrite(cellw, &cellaw));
1222: PetscCall(VecScale(cellw, 1. / totWgt));
1223: PetscCall(PetscProbComputeKSStatisticWeighted(cellv, cellw, cdf, &ksa[c - cStart]));
1224: PetscCall(VecDestroy(&cellv));
1225: PetscCall(VecDestroy(&cellw));
1226: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Npc, &pidx));
1227: }
1228: PetscCall(VecRestoreArrayWrite(ks, &ksa));
1229: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&vel));
1230: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
1231: PetscCall(DMSwarmSortRestoreAccess(sw));
1233: PetscReal minalpha, maxalpha;
1234: PetscInt mincell, maxcell;
1236: PetscCall(VecFilter(ks, PETSC_SMALL));
1237: PetscCall(VecMin(ks, &mincell, &minalpha));
1238: PetscCall(VecMax(ks, &maxcell, &maxalpha));
1239: PetscCall(PetscPrintf(PetscObjectComm((PetscObject)dm), "Step %" PetscInt_FMT ": Min/Max KS statistic %g/%g in cell %" PetscInt_FMT "/%" PetscInt_FMT "\n", step, minalpha, maxalpha, mincell, maxcell));
1240: PetscCall(VecViewFromOptions(ks, NULL, "-ks_view"));
1241: PetscCall(VecDestroy(&ks));
1243: PetscCall(PetscDrawHGDraw(user->drawhgcell_v));
1244: PetscCall(PetscDrawHGSave(user->drawhgcell_v));
1245: PetscFunctionReturn(PETSC_SUCCESS);
1246: }
1248: static PetscErrorCode MonitorPositions_2D(TS ts, PetscInt step, PetscReal t, Vec U, void *ctx)
1249: {
1250: AppCtx *user = (AppCtx *)ctx;
1251: DM dm, sw;
1252: PetscDrawAxis axis;
1253: char title[1024];
1254: PetscScalar *x, *v, *weight;
1255: PetscReal lower[3], upper[3], speed;
1256: const PetscInt *s;
1257: PetscInt dim, cStart, cEnd, c;
1259: PetscFunctionBeginUser;
1260: if (step > 0 && step % user->ostep == 0) {
1261: PetscCall(TSGetDM(ts, &sw));
1262: PetscCall(DMSwarmGetCellDM(sw, &dm));
1263: PetscCall(DMGetDimension(dm, &dim));
1264: PetscCall(DMGetBoundingBox(dm, lower, upper));
1265: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
1266: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
1267: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&v));
1268: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&weight));
1269: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&s));
1270: PetscCall(DMSwarmSortGetAccess(sw));
1271: PetscCall(PetscDrawSPReset(user->drawspX));
1272: PetscCall(PetscDrawSPGetAxis(user->drawspX, &axis));
1273: PetscCall(PetscSNPrintf(title, 1024, "Step %" PetscInt_FMT " Time: %g", step, (double)t));
1274: PetscCall(PetscDrawAxisSetLabels(axis, title, "x", "v"));
1275: PetscCall(PetscDrawSPSetLimits(user->drawspX, lower[0], upper[0], lower[1], upper[1]));
1276: PetscCall(PetscDrawSPSetLimits(user->drawspX, lower[0], upper[0], -12, 12));
1277: for (c = 0; c < cEnd - cStart; ++c) {
1278: PetscInt *pidx, Npc, q;
1279: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
1280: for (q = 0; q < Npc; ++q) {
1281: const PetscInt p = pidx[q];
1282: if (s[p] == 0) {
1283: speed = 0.;
1284: for (PetscInt d = 0; d < dim; ++d) speed += PetscSqr(v[p * dim + d]);
1285: speed = PetscSqrtReal(speed);
1286: if (dim == 1) {
1287: PetscCall(PetscDrawSPAddPointColorized(user->drawspX, &x[p * dim], &v[p * dim], &speed));
1288: } else {
1289: PetscCall(PetscDrawSPAddPointColorized(user->drawspX, &x[p * dim], &x[p * dim + 1], &speed));
1290: }
1291: } else if (s[p] == 1) {
1292: PetscCall(PetscDrawSPAddPoint(user->drawspX, &x[p * dim], &v[p * dim]));
1293: }
1294: }
1295: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Npc, &pidx));
1296: }
1297: PetscCall(PetscDrawSPDraw(user->drawspX, PETSC_TRUE));
1298: PetscDraw draw;
1299: PetscCall(PetscDrawSPGetDraw(user->drawspX, &draw));
1300: PetscCall(PetscDrawSave(draw));
1301: PetscCall(DMSwarmSortRestoreAccess(sw));
1302: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
1303: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
1304: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&v));
1305: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&s));
1306: }
1307: PetscFunctionReturn(PETSC_SUCCESS);
1308: }
1310: static PetscErrorCode MonitorPoisson(TS ts, PetscInt step, PetscReal t, Vec U, void *ctx)
1311: {
1312: AppCtx *user = (AppCtx *)ctx;
1313: DM dm, sw;
1315: PetscFunctionBeginUser;
1316: if (step > 0 && step % user->ostep == 0) {
1317: PetscCall(TSGetDM(ts, &sw));
1318: PetscCall(DMSwarmGetCellDM(sw, &dm));
1320: if (user->validE) {
1321: PetscScalar *x, *E, *weight;
1322: PetscReal lower[3], upper[3], xval;
1323: PetscDraw draw;
1324: PetscInt dim, cStart, cEnd;
1326: PetscCall(DMGetDimension(dm, &dim));
1327: PetscCall(DMGetBoundingBox(dm, lower, upper));
1328: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
1330: PetscCall(PetscDrawSPReset(user->drawspE));
1331: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
1332: PetscCall(DMSwarmGetField(sw, "E_field", NULL, NULL, (void **)&E));
1333: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&weight));
1335: PetscCall(DMSwarmSortGetAccess(sw));
1336: for (PetscInt c = 0; c < cEnd - cStart; ++c) {
1337: PetscReal Eavg = 0.0;
1338: PetscInt *pidx, Npc;
1340: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
1341: for (PetscInt q = 0; q < Npc; ++q) {
1342: const PetscInt p = pidx[q];
1343: Eavg += E[p * dim];
1344: }
1345: Eavg /= Npc;
1346: xval = (c + 0.5) * ((upper[0] - lower[0]) / (cEnd - cStart));
1347: PetscCall(PetscDrawSPAddPoint(user->drawspE, &xval, &Eavg));
1348: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Npc, &pidx));
1349: }
1350: PetscCall(PetscDrawSPDraw(user->drawspE, PETSC_TRUE));
1351: PetscCall(PetscDrawSPGetDraw(user->drawspE, &draw));
1352: PetscCall(PetscDrawSave(draw));
1353: PetscCall(DMSwarmSortRestoreAccess(sw));
1354: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
1355: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
1356: PetscCall(DMSwarmRestoreField(sw, "E_field", NULL, NULL, (void **)&E));
1357: }
1359: Vec rho, rhohat, phi;
1361: PetscCall(DMGetNamedGlobalVector(user->dmPot, "rho", &rho));
1362: PetscCall(DMGetNamedGlobalVector(user->dmPot, "rhohat", &rhohat));
1363: PetscCall(VecView(rho, user->viewerRho));
1364: PetscCall(VecISCopy(user->fftX, user->fftReal, SCATTER_FORWARD, rho));
1365: PetscCall(MatMult(user->fftPot, user->fftX, user->fftY));
1366: PetscCall(VecFilter(user->fftY, PETSC_SMALL));
1367: PetscCall(VecViewFromOptions(user->fftX, NULL, "-real_view"));
1368: PetscCall(VecViewFromOptions(user->fftY, NULL, "-fft_view"));
1369: PetscCall(VecISCopy(user->fftY, user->fftReal, SCATTER_REVERSE, rhohat));
1370: PetscCall(VecSetValue(rhohat, 0, 0., INSERT_VALUES)); // Remove large DC component
1371: PetscCall(VecView(rhohat, user->viewerRhoHat));
1372: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "rho", &rho));
1373: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "rhohat", &rhohat));
1375: PetscCall(DMGetNamedGlobalVector(user->dmPot, "phi", &phi));
1376: PetscCall(VecView(phi, user->viewerPhi));
1377: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "phi", &phi));
1378: }
1379: PetscFunctionReturn(PETSC_SUCCESS);
1380: }
1382: static PetscErrorCode SetupParameters(MPI_Comm comm, AppCtx *ctx)
1383: {
1384: PetscBag bag;
1385: Parameter *p;
1387: PetscFunctionBeginUser;
1388: /* setup PETSc parameter bag */
1389: PetscCall(PetscBagGetData(ctx->bag, (void **)&p));
1390: PetscCall(PetscBagSetName(ctx->bag, "par", "Vlasov-Poisson Parameters"));
1391: bag = ctx->bag;
1392: PetscCall(PetscBagRegisterScalar(bag, &p->v0, 1.0, "v0", "Velocity scale, m/s"));
1393: PetscCall(PetscBagRegisterScalar(bag, &p->t0, 1.0, "t0", "Time scale, s"));
1394: PetscCall(PetscBagRegisterScalar(bag, &p->x0, 1.0, "x0", "Space scale, m"));
1395: PetscCall(PetscBagRegisterScalar(bag, &p->v0, 1.0, "phi0", "Potential scale, kg*m^2/A*s^3"));
1396: PetscCall(PetscBagRegisterScalar(bag, &p->q0, 1.0, "q0", "Charge Scale, A*s"));
1397: PetscCall(PetscBagRegisterScalar(bag, &p->m0, 1.0, "m0", "Mass Scale, kg"));
1398: PetscCall(PetscBagRegisterScalar(bag, &p->epsi0, 1.0, "epsi0", "Permittivity of Free Space, kg"));
1399: PetscCall(PetscBagRegisterScalar(bag, &p->kb, 1.0, "kb", "Boltzmann Constant, m^2 kg/s^2 K^1"));
1401: PetscCall(PetscBagRegisterScalar(bag, &p->sigma, 1.0, "sigma", "Charge per unit area, C/m^3"));
1402: PetscCall(PetscBagRegisterScalar(bag, &p->poissonNumber, 1.0, "poissonNumber", "Non-Dimensional Poisson Number"));
1403: PetscCall(PetscBagRegisterScalar(bag, &p->vlasovNumber, 1.0, "vlasovNumber", "Non-Dimensional Vlasov Number"));
1404: PetscCall(PetscBagSetFromOptions(bag));
1405: {
1406: PetscViewer viewer;
1407: PetscViewerFormat format;
1408: PetscBool flg;
1410: PetscCall(PetscOptionsCreateViewer(comm, NULL, NULL, "-param_view", &viewer, &format, &flg));
1411: if (flg) {
1412: PetscCall(PetscViewerPushFormat(viewer, format));
1413: PetscCall(PetscBagView(bag, viewer));
1414: PetscCall(PetscViewerFlush(viewer));
1415: PetscCall(PetscViewerPopFormat(viewer));
1416: PetscCall(PetscViewerDestroy(&viewer));
1417: }
1418: }
1419: PetscFunctionReturn(PETSC_SUCCESS);
1420: }
1422: static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
1423: {
1424: PetscFunctionBeginUser;
1425: PetscCall(DMCreate(comm, dm));
1426: PetscCall(DMSetType(*dm, DMPLEX));
1427: PetscCall(DMSetFromOptions(*dm));
1428: PetscCall(PetscObjectSetName((PetscObject)*dm, "space"));
1429: PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view"));
1431: // Cache the mesh geometry
1432: DMField coordField;
1433: IS cellIS;
1434: PetscQuadrature quad;
1435: PetscReal *wt, *pt;
1436: PetscInt cdim, cStart, cEnd;
1438: PetscCall(DMGetCoordinateField(*dm, &coordField));
1439: PetscCheck(coordField, comm, PETSC_ERR_USER, "DM must have a coordinate field");
1440: PetscCall(DMGetCoordinateDim(*dm, &cdim));
1441: PetscCall(DMPlexGetHeightStratum(*dm, 0, &cStart, &cEnd));
1442: PetscCall(ISCreateStride(PETSC_COMM_SELF, cEnd - cStart, cStart, 1, &cellIS));
1443: PetscCall(PetscQuadratureCreate(PETSC_COMM_SELF, &quad));
1444: PetscCall(PetscMalloc1(1, &wt));
1445: PetscCall(PetscMalloc1(2, &pt));
1446: wt[0] = 1.;
1447: pt[0] = -1.;
1448: pt[1] = -1.;
1449: PetscCall(PetscQuadratureSetData(quad, cdim, 1, 1, pt, wt));
1450: PetscCall(DMFieldCreateFEGeom(coordField, cellIS, quad, PETSC_FEGEOM_BASIC, &user->fegeom));
1451: PetscCall(PetscQuadratureDestroy(&quad));
1452: PetscCall(ISDestroy(&cellIS));
1453: PetscFunctionReturn(PETSC_SUCCESS);
1454: }
1456: static void ion_f0(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[])
1457: {
1458: f0[0] = -constants[SIGMA];
1459: }
1461: static void laplacian_f1(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 f1[])
1462: {
1463: PetscInt d;
1464: for (d = 0; d < dim; ++d) f1[d] = u_x[d];
1465: }
1467: static void laplacian_g3(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 g3[])
1468: {
1469: PetscInt d;
1470: for (d = 0; d < dim; ++d) g3[d * dim + d] = 1.0;
1471: }
1473: /*
1474: / I -grad\ / q \ = /0\
1475: \-div 0 / \phi/ \f/
1476: */
1477: static void f0_q(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[])
1478: {
1479: for (PetscInt d = 0; d < dim; ++d) f0[d] += u[uOff[0] + d];
1480: }
1482: static void f1_q(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 f1[])
1483: {
1484: for (PetscInt d = 0; d < dim; ++d) f1[d * dim + d] = u[uOff[1]];
1485: }
1487: static void f0_phi_backgroundCharge(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[])
1488: {
1489: f0[0] += constants[SIGMA];
1490: for (PetscInt d = 0; d < dim; ++d) f0[0] += u_x[uOff_x[0] + d * dim + d];
1491: }
1493: /* Boundary residual. Dirichlet boundary for u means u_bdy=p*n */
1494: static void g0_qq(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[])
1495: {
1496: for (PetscInt d = 0; d < dim; ++d) g0[d * dim + d] = 1.0;
1497: }
1499: static void g2_qphi(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 g2[])
1500: {
1501: for (PetscInt d = 0; d < dim; ++d) g2[d * dim + d] = 1.0;
1502: }
1504: static void g1_phiq(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 g1[])
1505: {
1506: for (PetscInt d = 0; d < dim; ++d) g1[d * dim + d] = 1.0;
1507: }
1509: static PetscErrorCode CreateFEM(DM dm, AppCtx *user)
1510: {
1511: PetscFE fephi, feq;
1512: PetscDS ds;
1513: PetscBool simplex;
1514: PetscInt dim;
1516: PetscFunctionBeginUser;
1517: PetscCall(DMGetDimension(dm, &dim));
1518: PetscCall(DMPlexIsSimplex(dm, &simplex));
1519: if (user->em == EM_MIXED) {
1520: DMLabel label;
1521: const PetscInt id = 1;
1523: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, dim, simplex, "field_", PETSC_DETERMINE, &feq));
1524: PetscCall(PetscObjectSetName((PetscObject)feq, "field"));
1525: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, simplex, "potential_", PETSC_DETERMINE, &fephi));
1526: PetscCall(PetscObjectSetName((PetscObject)fephi, "potential"));
1527: PetscCall(PetscFECopyQuadrature(feq, fephi));
1528: PetscCall(DMSetField(dm, 0, NULL, (PetscObject)feq));
1529: PetscCall(DMSetField(dm, 1, NULL, (PetscObject)fephi));
1530: PetscCall(DMCreateDS(dm));
1531: PetscCall(PetscFEDestroy(&fephi));
1532: PetscCall(PetscFEDestroy(&feq));
1534: PetscCall(DMGetLabel(dm, "marker", &label));
1535: PetscCall(DMGetDS(dm, &ds));
1537: PetscCall(PetscDSSetResidual(ds, 0, f0_q, f1_q));
1538: PetscCall(PetscDSSetResidual(ds, 1, f0_phi_backgroundCharge, NULL));
1539: PetscCall(PetscDSSetJacobian(ds, 0, 0, g0_qq, NULL, NULL, NULL));
1540: PetscCall(PetscDSSetJacobian(ds, 0, 1, NULL, NULL, g2_qphi, NULL));
1541: PetscCall(PetscDSSetJacobian(ds, 1, 0, NULL, g1_phiq, NULL, NULL));
1543: PetscCall(DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", label, 1, &id, 0, 0, NULL, (void (*)(void))zero, NULL, NULL, NULL));
1545: } else {
1546: MatNullSpace nullsp;
1547: PetscCall(PetscFECreateDefault(PETSC_COMM_SELF, dim, 1, simplex, NULL, PETSC_DETERMINE, &fephi));
1548: PetscCall(PetscObjectSetName((PetscObject)fephi, "potential"));
1549: PetscCall(DMSetField(dm, 0, NULL, (PetscObject)fephi));
1550: PetscCall(DMCreateDS(dm));
1551: PetscCall(DMGetDS(dm, &ds));
1552: PetscCall(PetscDSSetResidual(ds, 0, ion_f0, laplacian_f1));
1553: PetscCall(PetscDSSetJacobian(ds, 0, 0, NULL, NULL, NULL, laplacian_g3));
1554: PetscCall(MatNullSpaceCreate(PetscObjectComm((PetscObject)dm), PETSC_TRUE, 0, NULL, &nullsp));
1555: PetscCall(PetscObjectCompose((PetscObject)fephi, "nullspace", (PetscObject)nullsp));
1556: PetscCall(MatNullSpaceDestroy(&nullsp));
1557: PetscCall(PetscFEDestroy(&fephi));
1558: }
1559: PetscFunctionReturn(PETSC_SUCCESS);
1560: }
1562: static PetscErrorCode CreatePoisson(DM dm, AppCtx *user)
1563: {
1564: SNES snes;
1565: Mat J;
1566: MatNullSpace nullSpace;
1568: PetscFunctionBeginUser;
1569: PetscCall(CreateFEM(dm, user));
1570: PetscCall(SNESCreate(PetscObjectComm((PetscObject)dm), &snes));
1571: PetscCall(SNESSetOptionsPrefix(snes, "em_"));
1572: PetscCall(SNESSetDM(snes, dm));
1573: PetscCall(DMPlexSetSNESLocalFEM(dm, PETSC_FALSE, user));
1574: PetscCall(SNESSetFromOptions(snes));
1576: PetscCall(DMCreateMatrix(dm, &J));
1577: PetscCall(MatNullSpaceCreate(PetscObjectComm((PetscObject)dm), PETSC_TRUE, 0, NULL, &nullSpace));
1578: PetscCall(MatSetNullSpace(J, nullSpace));
1579: PetscCall(MatNullSpaceDestroy(&nullSpace));
1580: PetscCall(SNESSetJacobian(snes, J, J, NULL, NULL));
1581: PetscCall(MatDestroy(&J));
1582: if (user->em == EM_MIXED) {
1583: const PetscInt potential = 1;
1585: PetscCall(DMCreateSubDM(dm, 1, &potential, &user->isPot, &user->dmPot));
1586: } else {
1587: user->dmPot = dm;
1588: PetscCall(PetscObjectReference((PetscObject)user->dmPot));
1589: }
1590: PetscCall(DMCreateMassMatrix(user->dmPot, user->dmPot, &user->M));
1591: PetscCall(DMPlexCreateClosureIndex(dm, NULL));
1592: user->snes = snes;
1593: PetscFunctionReturn(PETSC_SUCCESS);
1594: }
1596: // Conservation of mass (m = 1.0)
1597: // n_t + 1/ m p_x = 0
1598: static void f0_mass(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[])
1599: {
1600: for (PetscInt d = 0; d < dim; ++d) f0[0] += u_t[uOff[0]] + u_x[uOff_x[1] + d * dim + d];
1601: }
1603: // Conservation of momentum (m = 1, e = 1)
1604: // p_t + (u p)_x = -pr_x + e n E
1605: // p_t + (div u) p + u . grad p = -pr_x + e n E
1606: // p_t + (div p) p / n - (p . grad n) p / n^2 + p / n . grad p = -pr_x + e n E
1607: static void f0_momentum(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[])
1608: {
1609: const PetscScalar n = u[uOff[0]];
1611: for (PetscInt d = 0; d < dim; ++d) {
1612: PetscReal divp = 0.;
1614: f0[d] += u_t[uOff[1] + d];
1615: for (PetscInt e = 0; e < dim; ++e) {
1616: f0[d] += u[uOff[1] + e] * u_x[uOff_x[1] + d * dim + e] / n; // p / n . grad p
1617: f0[d] -= (u[uOff[1] + e] * u_x[uOff_x[0] + e]) * u[uOff[1] + d] / PetscSqr(n); // -(p . grad n) p / n^2
1618: divp += u_x[uOff_x[1] + e * dim + e];
1619: }
1620: f0[d] += divp * u[uOff[1] + d] / n; // (div p) p / n
1621: f0[d] += u_x[uOff_x[2] + d]; // pr_x
1622: f0[d] -= n * a[d]; // -e n E
1623: }
1624: }
1626: // Conservation of energy
1627: // pr_t + (u pr)_x = -3 pr u_x - q_x
1628: // pr_t + (div u) pr + u . grad pr = -3 pr (div u) - q_x
1629: // pr_t + 4 (div u) pr + u . grad pr = -q_x
1630: // pr_t + 4 div p pr / n - 4 (p . grad n) pr / n^2 + p . grad pr / n = -q_x
1631: static void f0_energy(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[])
1632: {
1633: const PetscScalar n = u[uOff[0]];
1634: const PetscScalar pr = u[uOff[2]];
1635: PetscReal divp = 0.;
1637: f0[0] += u_t[uOff[2]];
1638: for (PetscInt d = 0; d < dim; ++d) {
1639: f0[0] += u[uOff[1] + d] * u_x[uOff_x[2] + d] / n; // p . grad pr / n
1640: f0[0] -= 4. * u[uOff[1] + d] * u_x[uOff_x[0] + d] * pr / PetscSqr(n); // -4 (p . grad n) pr / n^2
1641: divp += u_x[uOff_x[1] + d * dim + d];
1642: }
1643: f0[0] += 4. * divp * pr / n; // 4 div p pr / n
1644: }
1646: static PetscErrorCode SetupMomentProblem(DM dm, AppCtx *ctx)
1647: {
1648: PetscDS ds;
1650: PetscFunctionBegin;
1651: PetscCall(DMGetDS(dm, &ds));
1652: PetscCall(PetscDSSetResidual(ds, 0, f0_mass, NULL));
1653: PetscCall(PetscDSSetResidual(ds, 1, f0_momentum, NULL));
1654: PetscCall(PetscDSSetResidual(ds, 2, f0_energy, NULL));
1655: //PetscCall(PetscDSSetJacobian(ds, 0, 0, g0_mass_uu, NULL, NULL, NULL));
1656: PetscFunctionReturn(PETSC_SUCCESS);
1657: }
1659: static PetscErrorCode CreateMomentFields(DM odm, AppCtx *user)
1660: {
1661: DM dm;
1662: PetscFE fe;
1663: DMPolytopeType ct;
1664: PetscInt dim, cStart;
1666: PetscFunctionBeginUser;
1667: PetscCall(DMClone(odm, &dm));
1668: PetscCall(DMGetDimension(dm, &dim));
1669: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, NULL));
1670: PetscCall(DMPlexGetCellType(dm, cStart, &ct));
1671: PetscCall(PetscFECreateByCell(PETSC_COMM_SELF, dim, 1, ct, NULL, PETSC_DETERMINE, &fe));
1672: PetscCall(PetscObjectSetName((PetscObject)fe, "number density"));
1673: PetscCall(DMSetField(dm, 0, NULL, (PetscObject)fe));
1674: PetscCall(PetscFEDestroy(&fe));
1675: PetscCall(PetscFECreateByCell(PETSC_COMM_SELF, dim, dim, ct, NULL, PETSC_DETERMINE, &fe));
1676: PetscCall(PetscObjectSetName((PetscObject)fe, "momentum density"));
1677: PetscCall(DMSetField(dm, 1, NULL, (PetscObject)fe));
1678: PetscCall(PetscFEDestroy(&fe));
1679: PetscCall(PetscFECreateByCell(PETSC_COMM_SELF, dim, 1, ct, NULL, PETSC_DETERMINE, &fe));
1680: PetscCall(PetscObjectSetName((PetscObject)fe, "energy density"));
1681: PetscCall(DMSetField(dm, 2, NULL, (PetscObject)fe));
1682: PetscCall(PetscFEDestroy(&fe));
1683: PetscCall(DMCreateDS(dm));
1684: PetscCall(SetupMomentProblem(dm, user));
1685: user->dmMom = dm;
1686: PetscInt field;
1688: field = 0;
1689: PetscCall(DMCreateSubDM(user->dmMom, 1, &field, &user->isN, &user->dmN));
1690: PetscCall(DMCreateMassMatrix(user->dmN, user->dmN, &user->MN));
1691: field = 1;
1692: PetscCall(DMCreateSubDM(user->dmMom, 1, &field, &user->isP, &user->dmP));
1693: PetscCall(DMCreateMassMatrix(user->dmP, user->dmP, &user->MP));
1694: field = 2;
1695: PetscCall(DMCreateSubDM(user->dmMom, 1, &field, &user->isE, &user->dmE));
1696: PetscCall(DMCreateMassMatrix(user->dmE, user->dmE, &user->ME));
1697: PetscFunctionReturn(PETSC_SUCCESS);
1698: }
1700: PetscErrorCode PetscPDFPertubedConstant2D(const PetscReal x[], const PetscReal dummy[], PetscReal p[])
1701: {
1702: p[0] = (1 + 0.01 * PetscCosReal(0.5 * x[0])) / (2 * PETSC_PI);
1703: p[1] = (1 + 0.01 * PetscCosReal(0.5 * x[1])) / (2 * PETSC_PI);
1704: return PETSC_SUCCESS;
1705: }
1706: PetscErrorCode PetscPDFPertubedConstant1D(const PetscReal x[], const PetscReal dummy[], PetscReal p[])
1707: {
1708: p[0] = (1. + 0.01 * PetscCosReal(0.5 * x[0])) / (2 * PETSC_PI);
1709: return PETSC_SUCCESS;
1710: }
1712: PetscErrorCode PetscPDFCosine1D(const PetscReal x[], const PetscReal scale[], PetscReal p[])
1713: {
1714: const PetscReal alpha = scale ? scale[0] : 0.0;
1715: const PetscReal k = scale ? scale[1] : 1.;
1716: p[0] = (1 + alpha * PetscCosReal(k * x[0]));
1717: return PETSC_SUCCESS;
1718: }
1720: PetscErrorCode PetscPDFCosine2D(const PetscReal x[], const PetscReal scale[], PetscReal p[])
1721: {
1722: const PetscReal alpha = scale ? scale[0] : 0.;
1723: const PetscReal k = scale ? scale[0] : 1.;
1724: p[0] = (1 + alpha * PetscCosReal(k * (x[0] + x[1])));
1725: return PETSC_SUCCESS;
1726: }
1728: static PetscErrorCode CreateVelocityDM(DM sw, DM *vdm)
1729: {
1730: PetscFE fe;
1731: DMPolytopeType ct;
1732: PetscInt dim, cStart;
1733: const char *prefix = "v";
1735: PetscFunctionBegin;
1736: PetscCall(DMCreate(PETSC_COMM_SELF, vdm));
1737: PetscCall(DMSetType(*vdm, DMPLEX));
1738: PetscCall(DMPlexSetOptionsPrefix(*vdm, prefix));
1739: PetscCall(DMSetFromOptions(*vdm));
1740: PetscCall(PetscObjectSetName((PetscObject)*vdm, "velocity"));
1741: PetscCall(DMViewFromOptions(*vdm, NULL, "-dm_view"));
1743: PetscCall(DMGetDimension(*vdm, &dim));
1744: PetscCall(DMPlexGetHeightStratum(*vdm, 0, &cStart, NULL));
1745: PetscCall(DMPlexGetCellType(*vdm, cStart, &ct));
1746: PetscCall(PetscFECreateByCell(PETSC_COMM_SELF, dim, 1, ct, prefix, PETSC_DETERMINE, &fe));
1747: PetscCall(PetscObjectSetName((PetscObject)fe, "distribution"));
1748: PetscCall(DMSetField(*vdm, 0, NULL, (PetscObject)fe));
1749: PetscCall(DMCreateDS(*vdm));
1750: PetscCall(PetscFEDestroy(&fe));
1751: PetscFunctionReturn(PETSC_SUCCESS);
1752: }
1754: /*
1755: InitializeParticles_Centroid - Initialize a regular grid of particles.
1757: Input Parameters:
1758: + sw - The `DMSWARM`
1759: - force1D - Treat the spatial domain as 1D
1761: Notes:
1762: This functions sets the species, cellid, spatial coordinate, and velocity fields for all particles.
1764: It places one particle in the centroid of each cell in the implicit tensor product of the spatial
1765: and velocity meshes.
1766: */
1767: static PetscErrorCode InitializeParticles_Centroid(DM sw)
1768: {
1769: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1770: DMSwarmCellDM celldm;
1771: DM xdm, vdm;
1772: PetscReal vmin[3], vmax[3];
1773: PetscReal *x, *v;
1774: PetscInt *species, *cellid;
1775: PetscInt dim, xcStart, xcEnd, vcStart, vcEnd, Ns, Np, Npc, debug;
1776: PetscBool flg;
1777: MPI_Comm comm;
1778: const char *cellidname;
1780: PetscFunctionBegin;
1781: PetscCall(PetscObjectGetComm((PetscObject)sw, &comm));
1783: PetscOptionsBegin(comm, "", "DMSwarm Options", "DMSWARM");
1784: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
1785: PetscCall(PetscOptionsInt("-dm_swarm_num_species", "The number of species", "DMSwarmSetNumSpecies", Ns, &Ns, &flg));
1786: if (flg) PetscCall(DMSwarmSetNumSpecies(sw, Ns));
1787: PetscCall(PetscOptionsBoundedInt("-dm_swarm_print_coords", "Debug output level for particle coordinate computations", "InitializeParticles", 0, &swarm->printCoords, NULL, 0));
1788: PetscCall(PetscOptionsBoundedInt("-dm_swarm_print_weights", "Debug output level for particle weight computations", "InitializeWeights", 0, &swarm->printWeights, NULL, 0));
1789: PetscOptionsEnd();
1790: debug = swarm->printCoords;
1792: PetscCall(DMGetDimension(sw, &dim));
1793: PetscCall(DMSwarmGetCellDM(sw, &xdm));
1794: PetscCall(DMPlexGetHeightStratum(xdm, 0, &xcStart, &xcEnd));
1796: PetscCall(DMSwarmGetCellDMByName(sw, "velocity", &celldm));
1797: PetscCall(DMSwarmCellDMGetDM(celldm, &vdm));
1798: PetscCall(DMPlexGetHeightStratum(vdm, 0, &vcStart, &vcEnd));
1800: // One particle per centroid on the tensor product grid
1801: Npc = (vcEnd - vcStart) * Ns;
1802: Np = (xcEnd - xcStart) * Npc;
1803: PetscCall(DMSwarmSetLocalSizes(sw, Np, 0));
1804: if (debug) {
1805: PetscInt gNp, gNc, Nc = xcEnd - xcStart;
1806: PetscCallMPI(MPIU_Allreduce(&Np, &gNp, 1, MPIU_INT, MPIU_SUM, comm));
1807: PetscCall(PetscPrintf(comm, "Global Np = %" PetscInt_FMT "\n", gNp));
1808: PetscCallMPI(MPIU_Allreduce(&Nc, &gNc, 1, MPIU_INT, MPIU_SUM, comm));
1809: PetscCall(PetscPrintf(comm, "Global X-cells = %" PetscInt_FMT "\n", gNc));
1810: PetscCall(PetscPrintf(comm, "Global V-cells = %" PetscInt_FMT "\n", vcEnd - vcStart));
1811: }
1813: // Set species and cellid
1814: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
1815: PetscCall(DMSwarmCellDMGetCellID(celldm, &cellidname));
1816: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
1817: PetscCall(DMSwarmGetField(sw, cellidname, NULL, NULL, (void **)&cellid));
1818: for (PetscInt c = 0, p = 0; c < xcEnd - xcStart; ++c) {
1819: for (PetscInt s = 0; s < Ns; ++s) {
1820: for (PetscInt q = 0; q < Npc / Ns; ++q, ++p) {
1821: species[p] = s;
1822: cellid[p] = c;
1823: }
1824: }
1825: }
1826: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
1827: PetscCall(DMSwarmRestoreField(sw, cellidname, NULL, NULL, (void **)&cellid));
1829: // Set particle coordinates
1830: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
1831: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&v));
1832: PetscCall(DMSwarmSortGetAccess(sw));
1833: PetscCall(DMGetBoundingBox(vdm, vmin, vmax));
1834: PetscCall(DMGetCoordinatesLocalSetUp(xdm));
1835: for (PetscInt c = 0; c < xcEnd - xcStart; ++c) {
1836: const PetscInt cell = c + xcStart;
1837: PetscInt *pidx, Npc;
1838: PetscReal centroid[3], volume;
1840: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
1841: PetscCall(DMPlexComputeCellGeometryFVM(xdm, cell, &volume, centroid, NULL));
1842: for (PetscInt s = 0; s < Ns; ++s) {
1843: for (PetscInt q = 0; q < Npc / Ns; ++q) {
1844: const PetscInt p = pidx[q * Ns + s];
1846: for (PetscInt d = 0; d < dim; ++d) {
1847: x[p * dim + d] = centroid[d];
1848: v[p * dim + d] = vmin[0] + (q + 0.5) * ((vmax[0] - vmin[0]) / (Npc / Ns));
1849: }
1850: if (debug > 1) {
1851: PetscCall(PetscPrintf(PETSC_COMM_SELF, "Particle %4" PetscInt_FMT " ", p));
1852: PetscCall(PetscPrintf(PETSC_COMM_SELF, " x: ("));
1853: for (PetscInt d = 0; d < dim; ++d) {
1854: if (d > 0) PetscCall(PetscPrintf(PETSC_COMM_SELF, ", "));
1855: PetscCall(PetscPrintf(PETSC_COMM_SELF, "%g", x[p * dim + d]));
1856: }
1857: PetscCall(PetscPrintf(PETSC_COMM_SELF, ") v:("));
1858: for (PetscInt d = 0; d < dim; ++d) {
1859: if (d > 0) PetscCall(PetscPrintf(PETSC_COMM_SELF, ", "));
1860: PetscCall(PetscPrintf(PETSC_COMM_SELF, "%g", v[p * dim + d]));
1861: }
1862: PetscCall(PetscPrintf(PETSC_COMM_SELF, ")\n"));
1863: }
1864: }
1865: }
1866: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Npc, &pidx));
1867: }
1868: PetscCall(DMSwarmSortRestoreAccess(sw));
1869: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
1870: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&v));
1871: PetscFunctionReturn(PETSC_SUCCESS);
1872: }
1874: /*
1875: InitializeWeights - Compute weight for each local particle
1877: Input Parameters:
1878: + sw - The `DMSwarm`
1879: . totalWeight - The sum of all particle weights
1880: . func - The PDF for the particle spatial distribution
1881: - param - The PDF parameters
1883: Notes:
1884: The PDF for velocity is assumed to be a Gaussian
1886: The particle weights are returned in the `w_q` field of `sw`.
1887: */
1888: static PetscErrorCode InitializeWeights(DM sw, PetscReal totalWeight, PetscProbFn *func, const PetscReal param[])
1889: {
1890: DM xdm, vdm;
1891: DMSwarmCellDM celldm;
1892: PetscScalar *weight;
1893: PetscQuadrature xquad;
1894: const PetscReal *xq, *xwq;
1895: const PetscInt order = 5;
1896: PetscReal xi0[3];
1897: PetscReal xwtot = 0., pwtot = 0.;
1898: PetscInt xNq;
1899: PetscInt dim, Ns, xcStart, xcEnd, vcStart, vcEnd, debug = ((DM_Swarm *)sw->data)->printWeights;
1900: MPI_Comm comm;
1901: PetscMPIInt rank;
1903: PetscFunctionBegin;
1904: PetscCall(PetscObjectGetComm((PetscObject)sw, &comm));
1905: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1906: PetscCall(DMGetDimension(sw, &dim));
1907: PetscCall(DMSwarmGetCellDM(sw, &xdm));
1908: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
1909: PetscCall(DMPlexGetHeightStratum(xdm, 0, &xcStart, &xcEnd));
1910: PetscCall(DMSwarmGetCellDMByName(sw, "velocity", &celldm));
1911: PetscCall(DMSwarmCellDMGetDM(celldm, &vdm));
1912: PetscCall(DMPlexGetHeightStratum(vdm, 0, &vcStart, &vcEnd));
1914: // Setup Quadrature for spatial and velocity weight calculations
1915: PetscCall(PetscDTGaussTensorQuadrature(dim, 1, order, -1.0, 1.0, &xquad));
1916: PetscCall(PetscQuadratureGetData(xquad, NULL, NULL, &xNq, &xq, &xwq));
1917: for (PetscInt d = 0; d < dim; ++d) xi0[d] = -1.0;
1919: // Integrate the density function to get the weights of particles in each cell
1920: PetscCall(DMGetCoordinatesLocalSetUp(vdm));
1921: PetscCall(DMSwarmSortGetAccess(sw));
1922: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&weight));
1923: for (PetscInt c = xcStart; c < xcEnd; ++c) {
1924: PetscReal xv0[3], xJ[9], xinvJ[9], xdetJ, xqr[3], xden, xw = 0.;
1925: PetscInt *pidx, Npc;
1926: PetscInt xNc;
1927: const PetscScalar *xarray;
1928: PetscScalar *xcoords = NULL;
1929: PetscBool xisDG;
1931: PetscCall(DMPlexGetCellCoordinates(xdm, c, &xisDG, &xNc, &xarray, &xcoords));
1932: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
1933: PetscCheck(Npc == (vcEnd - vcStart) * Ns, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of particles %" PetscInt_FMT " in cell (rank %d) != %" PetscInt_FMT " number of velocity vertices", Npc, rank, (vcEnd - vcStart) * Ns);
1934: PetscCall(DMPlexComputeCellGeometryFEM(xdm, c, NULL, xv0, xJ, xinvJ, &xdetJ));
1935: for (PetscInt q = 0; q < xNq; ++q) {
1936: // Transform quadrature points from ref space to real space
1937: CoordinatesRefToReal(dim, dim, xi0, xv0, xJ, &xq[q * dim], xqr);
1938: // Get probability density at quad point
1939: // No need to scale xqr since PDF will be periodic
1940: PetscCall((*func)(xqr, param, &xden));
1941: xw += xden * (xwq[q] * xdetJ);
1942: }
1943: xwtot += xw;
1944: if (debug) {
1945: IS globalOrdering;
1946: const PetscInt *ordering;
1948: PetscCall(DMPlexGetCellNumbering(xdm, &globalOrdering));
1949: PetscCall(ISGetIndices(globalOrdering, &ordering));
1950: PetscCall(PetscSynchronizedPrintf(comm, "c:%" PetscInt_FMT " [x_a,x_b] = %1.15f,%1.15f -> cell weight = %1.15f\n", ordering[c], (double)PetscRealPart(xcoords[0]), (double)PetscRealPart(xcoords[0 + dim]), (double)xw));
1951: PetscCall(ISRestoreIndices(globalOrdering, &ordering));
1952: }
1953: // Set weights to be Gaussian in velocity cells
1954: for (PetscInt vc = vcStart; vc < vcEnd; ++vc) {
1955: const PetscInt p = pidx[vc * Ns + 0];
1956: PetscReal vw = 0.;
1957: PetscInt vNc;
1958: const PetscScalar *varray;
1959: PetscScalar *vcoords = NULL;
1960: PetscBool visDG;
1962: PetscCall(DMPlexGetCellCoordinates(vdm, vc, &visDG, &vNc, &varray, &vcoords));
1963: // TODO: Fix 2 stream Ask Joe
1964: // Two stream function from 1/2pi v^2 e^(-v^2/2)
1965: // vw = 1. / (PetscSqrtReal(2 * PETSC_PI)) * (((coords_v[0] * PetscExpReal(-PetscSqr(coords_v[0]) / 2.)) - (coords_v[1] * PetscExpReal(-PetscSqr(coords_v[1]) / 2.)))) - 0.5 * PetscErfReal(coords_v[0] / PetscSqrtReal(2.)) + 0.5 * (PetscErfReal(coords_v[1] / PetscSqrtReal(2.)));
1966: vw = 0.5 * (PetscErfReal(vcoords[1] / PetscSqrtReal(2.)) - PetscErfReal(vcoords[0] / PetscSqrtReal(2.)));
1968: weight[p] = totalWeight * vw * xw;
1969: pwtot += weight[p];
1970: PetscCheck(weight[p] <= 10., PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Particle %" PetscInt_FMT " weight exceeded 1: %g, %g, %g", p, xw, vw, totalWeight);
1971: PetscCall(DMPlexRestoreCellCoordinates(vdm, vc, &visDG, &vNc, &varray, &vcoords));
1972: if (debug > 1) PetscCall(PetscPrintf(comm, "particle %" PetscInt_FMT ": %g, vw: %g xw: %g\n", p, weight[p], vw, xw));
1973: }
1974: PetscCall(DMPlexRestoreCellCoordinates(xdm, c, &xisDG, &xNc, &xarray, &xcoords));
1975: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Npc, &pidx));
1976: }
1977: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
1978: PetscCall(DMSwarmSortRestoreAccess(sw));
1979: PetscCall(PetscQuadratureDestroy(&xquad));
1981: if (debug) {
1982: PetscReal wtot[2] = {pwtot, xwtot}, gwtot[2];
1984: PetscCall(PetscSynchronizedFlush(comm, NULL));
1985: PetscCallMPI(MPIU_Allreduce(wtot, gwtot, 2, MPIU_REAL, MPIU_SUM, PETSC_COMM_WORLD));
1986: PetscCall(PetscPrintf(comm, "particle weight sum = %1.10f cell weight sum = %1.10f\n", (double)gwtot[0], (double)gwtot[1]));
1987: }
1988: PetscFunctionReturn(PETSC_SUCCESS);
1989: }
1991: static PetscErrorCode InitializeParticles_PerturbedWeights(DM sw, AppCtx *user)
1992: {
1993: PetscReal scale[2] = {user->cosine_coefficients[0], user->cosine_coefficients[1]};
1994: PetscInt dim;
1996: PetscFunctionBegin;
1997: PetscCall(DMGetDimension(sw, &dim));
1998: PetscCall(InitializeParticles_Centroid(sw));
1999: PetscCall(InitializeWeights(sw, user->totalWeight, dim == 1 ? PetscPDFCosine1D : PetscPDFCosine2D, scale));
2000: PetscFunctionReturn(PETSC_SUCCESS);
2001: }
2003: static PetscErrorCode InitializeConstants(DM sw, AppCtx *user)
2004: {
2005: DM dm;
2006: PetscInt *species;
2007: PetscReal *weight, totalCharge = 0., totalWeight = 0., gmin[3], gmax[3], global_charge, global_weight;
2008: PetscInt Np, dim;
2010: PetscFunctionBegin;
2011: PetscCall(DMSwarmGetCellDM(sw, &dm));
2012: PetscCall(DMGetDimension(sw, &dim));
2013: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2014: PetscCall(DMGetBoundingBox(dm, gmin, gmax));
2015: PetscCall(DMSwarmGetField(sw, "w_q", NULL, NULL, (void **)&weight));
2016: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
2017: for (PetscInt p = 0; p < Np; ++p) {
2018: totalWeight += weight[p];
2019: totalCharge += user->charges[species[p]] * weight[p];
2020: }
2021: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
2022: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
2023: {
2024: Parameter *param;
2025: PetscReal Area;
2027: PetscCall(PetscBagGetData(user->bag, (void **)¶m));
2028: switch (dim) {
2029: case 1:
2030: Area = (gmax[0] - gmin[0]);
2031: break;
2032: case 2:
2033: Area = (gmax[0] - gmin[0]) * (gmax[1] - gmin[1]);
2034: break;
2035: case 3:
2036: Area = (gmax[0] - gmin[0]) * (gmax[1] - gmin[1]) * (gmax[2] - gmin[2]);
2037: break;
2038: default:
2039: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Dimension %" PetscInt_FMT " not supported", dim);
2040: }
2041: PetscCallMPI(MPIU_Allreduce(&totalWeight, &global_weight, 1, MPIU_REAL, MPIU_SUM, PETSC_COMM_WORLD));
2042: PetscCallMPI(MPIU_Allreduce(&totalCharge, &global_charge, 1, MPIU_REAL, MPIU_SUM, PETSC_COMM_WORLD));
2043: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "dim = %" PetscInt_FMT "\ttotalWeight = %f, user->charges[species[0]] = %f\ttotalCharge = %f, Total Area = %f\n", dim, (double)global_weight, (double)user->charges[0], (double)global_charge, (double)Area));
2044: param->sigma = PetscAbsReal(global_charge / (Area));
2046: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "sigma: %g\n", (double)param->sigma));
2047: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "(x0,v0,t0,m0,q0,phi0): (%e, %e, %e, %e, %e, %e) - (P, V) = (%e, %e)\n", (double)param->x0, (double)param->v0, (double)param->t0, (double)param->m0, (double)param->q0, (double)param->phi0, (double)param->poissonNumber,
2048: (double)param->vlasovNumber));
2049: }
2050: /* Setup Constants */
2051: {
2052: PetscDS ds;
2053: Parameter *param;
2054: PetscCall(PetscBagGetData(user->bag, (void **)¶m));
2055: PetscScalar constants[NUM_CONSTANTS];
2056: constants[SIGMA] = param->sigma;
2057: constants[V0] = param->v0;
2058: constants[T0] = param->t0;
2059: constants[X0] = param->x0;
2060: constants[M0] = param->m0;
2061: constants[Q0] = param->q0;
2062: constants[PHI0] = param->phi0;
2063: constants[POISSON] = param->poissonNumber;
2064: constants[VLASOV] = param->vlasovNumber;
2065: PetscCall(DMGetDS(dm, &ds));
2066: PetscCall(PetscDSSetConstants(ds, NUM_CONSTANTS, constants));
2067: }
2068: PetscFunctionReturn(PETSC_SUCCESS);
2069: }
2071: static PetscErrorCode CreateSwarm(DM dm, AppCtx *user, DM *sw)
2072: {
2073: DMSwarmCellDM celldm;
2074: DM vdm;
2075: PetscReal v0[2] = {1., 0.};
2076: PetscInt dim;
2078: PetscFunctionBeginUser;
2079: PetscCall(DMGetDimension(dm, &dim));
2080: PetscCall(DMCreate(PetscObjectComm((PetscObject)dm), sw));
2081: PetscCall(DMSetType(*sw, DMSWARM));
2082: PetscCall(DMSetDimension(*sw, dim));
2083: PetscCall(DMSwarmSetType(*sw, DMSWARM_PIC));
2084: PetscCall(DMSetApplicationContext(*sw, user));
2086: PetscCall(DMSwarmRegisterPetscDatatypeField(*sw, "w_q", 1, PETSC_SCALAR));
2087: PetscCall(DMSwarmRegisterPetscDatatypeField(*sw, "velocity", dim, PETSC_REAL));
2088: PetscCall(DMSwarmRegisterPetscDatatypeField(*sw, "species", 1, PETSC_INT));
2089: PetscCall(DMSwarmRegisterPetscDatatypeField(*sw, "E_field", dim, PETSC_REAL));
2091: const char *fieldnames[2] = {DMSwarmPICField_coor, "velocity"};
2093: PetscCall(DMSwarmCellDMCreate(dm, 2, fieldnames, 1, fieldnames, &celldm));
2094: PetscCall(DMSwarmAddCellDM(*sw, celldm));
2095: PetscCall(DMSwarmCellDMDestroy(&celldm));
2097: const char *vfieldnames[2] = {"w_q"};
2099: PetscCall(CreateVelocityDM(*sw, &vdm));
2100: PetscCall(DMSwarmCellDMCreate(vdm, 1, vfieldnames, 1, &fieldnames[1], &celldm));
2101: PetscCall(DMSwarmAddCellDM(*sw, celldm));
2102: PetscCall(DMSwarmCellDMDestroy(&celldm));
2103: PetscCall(DMDestroy(&vdm));
2105: DM mdm;
2107: PetscCall(DMClone(dm, &mdm));
2108: PetscCall(PetscObjectSetName((PetscObject)mdm, "moments"));
2109: PetscCall(DMCopyDisc(dm, mdm));
2110: PetscCall(DMSwarmCellDMCreate(mdm, 1, vfieldnames, 1, fieldnames, &celldm));
2111: PetscCall(DMDestroy(&mdm));
2112: PetscCall(DMSwarmAddCellDM(*sw, celldm));
2113: PetscCall(DMSwarmCellDMDestroy(&celldm));
2115: DM mfdm;
2117: PetscCall(DMClone(dm, &mfdm));
2118: PetscCall(PetscObjectSetName((PetscObject)mfdm, "moment fields"));
2119: PetscCall(DMCopyDisc(dm, mfdm));
2120: PetscCall(DMSwarmCellDMCreate(mfdm, 1, &fieldnames[1], 1, fieldnames, &celldm));
2121: PetscCall(DMDestroy(&mfdm));
2122: PetscCall(DMSwarmAddCellDM(*sw, celldm));
2123: PetscCall(DMSwarmCellDMDestroy(&celldm));
2125: PetscCall(DMSetFromOptions(*sw));
2126: PetscCall(DMSetUp(*sw));
2128: PetscCall(DMSwarmSetCellDMActive(*sw, "space"));
2129: user->swarm = *sw;
2130: // TODO: This is redundant init since it is done in InitializeSolveAndSwarm, however DMSetUp() requires the local size be set
2131: if (user->perturbed_weights) {
2132: PetscCall(InitializeParticles_PerturbedWeights(*sw, user));
2133: } else {
2134: PetscCall(DMSwarmComputeLocalSizeFromOptions(*sw));
2135: PetscCall(DMSwarmInitializeCoordinates(*sw));
2136: PetscCall(DMSwarmInitializeVelocitiesFromOptions(*sw, v0));
2137: }
2138: PetscCall(PetscObjectSetName((PetscObject)*sw, "Particles"));
2139: PetscCall(DMViewFromOptions(*sw, NULL, "-sw_view"));
2140: PetscFunctionReturn(PETSC_SUCCESS);
2141: }
2143: static PetscErrorCode ComputeFieldAtParticles_Coulomb(SNES snes, DM sw, PetscReal E[])
2144: {
2145: AppCtx *user;
2146: PetscReal *coords;
2147: PetscInt *species, dim, Np, Ns;
2148: PetscMPIInt size;
2150: PetscFunctionBegin;
2151: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)snes), &size));
2152: PetscCheck(size == 1, PetscObjectComm((PetscObject)snes), PETSC_ERR_SUP, "Coulomb code only works in serial");
2153: PetscCall(DMGetDimension(sw, &dim));
2154: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2155: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
2156: PetscCall(DMGetApplicationContext(sw, (void *)&user));
2158: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2159: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
2160: for (PetscInt p = 0; p < Np; ++p) {
2161: PetscReal *pcoord = &coords[p * dim];
2162: PetscReal pE[3] = {0., 0., 0.};
2164: /* Calculate field at particle p due to particle q */
2165: for (PetscInt q = 0; q < Np; ++q) {
2166: PetscReal *qcoord = &coords[q * dim];
2167: PetscReal rpq[3], r, r3, q_q;
2169: if (p == q) continue;
2170: q_q = user->charges[species[q]] * 1.;
2171: for (PetscInt d = 0; d < dim; ++d) rpq[d] = pcoord[d] - qcoord[d];
2172: r = DMPlex_NormD_Internal(dim, rpq);
2173: if (r < PETSC_SQRT_MACHINE_EPSILON) continue;
2174: r3 = PetscPowRealInt(r, 3);
2175: for (PetscInt d = 0; d < dim; ++d) pE[d] += q_q * rpq[d] / r3;
2176: }
2177: for (PetscInt d = 0; d < dim; ++d) E[p * dim + d] = pE[d];
2178: }
2179: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
2180: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2181: PetscFunctionReturn(PETSC_SUCCESS);
2182: }
2184: static PetscErrorCode ComputeFieldAtParticles_Primal(SNES snes, DM sw, Mat M_p, PetscReal E[])
2185: {
2186: DM dm;
2187: AppCtx *user;
2188: PetscDS ds;
2189: PetscFE fe;
2190: KSP ksp;
2191: Vec rhoRhs; // Weak charge density, \int phi_i rho
2192: Vec rho; // Charge density, M^{-1} rhoRhs
2193: Vec phi, locPhi; // Potential
2194: Vec f; // Particle weights
2195: PetscReal *coords;
2196: PetscInt dim, cStart, cEnd, Np;
2198: PetscFunctionBegin;
2199: PetscCall(DMGetApplicationContext(sw, (void *)&user));
2200: PetscCall(PetscLogEventBegin(user->ESolveEvent, snes, sw, 0, 0));
2201: PetscCall(DMGetDimension(sw, &dim));
2202: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2204: PetscCall(SNESGetDM(snes, &dm));
2205: PetscCall(DMGetGlobalVector(dm, &rhoRhs));
2206: PetscCall(PetscObjectSetName((PetscObject)rhoRhs, "Weak charge density"));
2207: PetscCall(DMGetNamedGlobalVector(user->dmPot, "rho", &rho));
2208: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "w_q", &f));
2209: PetscCall(PetscObjectSetName((PetscObject)f, "particle weight"));
2211: PetscCall(MatViewFromOptions(M_p, NULL, "-mp_view"));
2212: PetscCall(MatViewFromOptions(user->M, NULL, "-m_view"));
2213: PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
2215: PetscCall(MatMultTranspose(M_p, f, rhoRhs));
2216: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", &f));
2218: PetscCall(KSPCreate(PetscObjectComm((PetscObject)dm), &ksp));
2219: PetscCall(KSPSetOptionsPrefix(ksp, "em_proj_"));
2220: PetscCall(KSPSetOperators(ksp, user->M, user->M));
2221: PetscCall(KSPSetFromOptions(ksp));
2222: PetscCall(KSPSolve(ksp, rhoRhs, rho));
2224: PetscCall(VecScale(rhoRhs, -1.0));
2226: PetscCall(VecViewFromOptions(rhoRhs, NULL, "-rho_view"));
2227: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "rho", &rho));
2228: PetscCall(KSPDestroy(&ksp));
2230: PetscCall(DMGetNamedGlobalVector(user->dmPot, "phi", &phi));
2231: PetscCall(VecSet(phi, 0.0));
2232: PetscCall(SNESSolve(snes, rhoRhs, phi));
2233: PetscCall(DMRestoreGlobalVector(dm, &rhoRhs));
2234: PetscCall(VecViewFromOptions(phi, NULL, "-phi_view"));
2236: PetscCall(DMGetLocalVector(dm, &locPhi));
2237: PetscCall(DMGlobalToLocalBegin(dm, phi, INSERT_VALUES, locPhi));
2238: PetscCall(DMGlobalToLocalEnd(dm, phi, INSERT_VALUES, locPhi));
2239: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "phi", &phi));
2240: PetscCall(PetscLogEventEnd(user->ESolveEvent, snes, sw, 0, 0));
2242: PetscCall(DMGetDS(dm, &ds));
2243: PetscCall(PetscDSGetDiscretization(ds, 0, (PetscObject *)&fe));
2244: PetscCall(DMSwarmSortGetAccess(sw));
2245: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
2246: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2248: PetscCall(PetscLogEventBegin(user->ETabEvent, snes, sw, 0, 0));
2249: PetscTabulation tab;
2250: PetscReal *pcoord, *refcoord;
2251: PetscFEGeom *chunkgeom = NULL;
2252: PetscInt maxNcp = 0;
2254: for (PetscInt c = cStart; c < cEnd; ++c) {
2255: PetscInt Ncp;
2257: PetscCall(DMSwarmSortGetNumberOfPointsPerCell(sw, c, &Ncp));
2258: maxNcp = PetscMax(maxNcp, Ncp);
2259: }
2260: PetscCall(DMGetWorkArray(dm, maxNcp * dim, MPIU_REAL, &refcoord));
2261: PetscCall(DMGetWorkArray(dm, maxNcp * dim, MPIU_REAL, &pcoord));
2262: // This can raise an FP_INEXACT in the dgemm inside
2263: PetscCall(PetscFPTrapPush(PETSC_FP_TRAP_OFF));
2264: PetscCall(PetscFECreateTabulation(fe, 1, maxNcp, refcoord, 1, &tab));
2265: PetscCall(PetscFPTrapPop());
2266: for (PetscInt c = cStart; c < cEnd; ++c) {
2267: PetscScalar *clPhi = NULL;
2268: PetscInt *points;
2269: PetscInt Ncp;
2271: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Ncp, &points));
2272: for (PetscInt cp = 0; cp < Ncp; ++cp)
2273: for (PetscInt d = 0; d < dim; ++d) pcoord[cp * dim + d] = coords[points[cp] * dim + d];
2274: {
2275: PetscCall(PetscFEGeomGetChunk(user->fegeom, c - cStart, c - cStart + 1, &chunkgeom));
2276: for (PetscInt i = 0; i < Ncp; ++i) {
2277: const PetscReal x0[3] = {-1., -1., -1.};
2278: CoordinatesRealToRef(dim, dim, x0, chunkgeom->v, chunkgeom->invJ, &pcoord[dim * i], &refcoord[dim * i]);
2279: }
2280: }
2281: PetscCall(PetscFEComputeTabulation(fe, Ncp, refcoord, 1, tab));
2282: PetscCall(DMPlexVecGetClosure(dm, NULL, locPhi, c, NULL, &clPhi));
2283: for (PetscInt cp = 0; cp < Ncp; ++cp) {
2284: const PetscReal *basisDer = tab->T[1];
2285: const PetscInt p = points[cp];
2287: for (PetscInt d = 0; d < dim; ++d) E[p * dim + d] = 0.;
2288: PetscCall(PetscFEFreeInterpolateGradient_Static(fe, basisDer, clPhi, dim, chunkgeom->invJ, NULL, cp, &E[p * dim]));
2289: for (PetscInt d = 0; d < dim; ++d) E[p * dim + d] *= -1.0;
2290: }
2291: PetscCall(DMPlexVecRestoreClosure(dm, NULL, locPhi, c, NULL, &clPhi));
2292: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Ncp, &points));
2293: }
2294: PetscCall(DMRestoreWorkArray(dm, maxNcp * dim, MPIU_REAL, &pcoord));
2295: PetscCall(DMRestoreWorkArray(dm, maxNcp * dim, MPIU_REAL, &refcoord));
2296: PetscCall(PetscTabulationDestroy(&tab));
2297: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2298: PetscCall(DMSwarmSortRestoreAccess(sw));
2299: PetscCall(DMRestoreLocalVector(dm, &locPhi));
2300: PetscCall(PetscFEGeomRestoreChunk(user->fegeom, 0, 1, &chunkgeom));
2301: PetscCall(PetscLogEventEnd(user->ETabEvent, snes, sw, 0, 0));
2302: PetscFunctionReturn(PETSC_SUCCESS);
2303: }
2305: static PetscErrorCode ComputeFieldAtParticles_Mixed(SNES snes, DM sw, Mat M_p, PetscReal E[])
2306: {
2307: DM dm;
2308: AppCtx *user;
2309: PetscDS ds;
2310: PetscFE fe;
2311: KSP ksp;
2312: Vec rhoRhs, rhoRhsFull; // Weak charge density, \int phi_i rho, and embedding in mixed problem
2313: Vec rho; // Charge density, M^{-1} rhoRhs
2314: Vec phi, locPhi, phiFull; // Potential and embedding in mixed problem
2315: Vec f; // Particle weights
2316: PetscReal *coords;
2317: PetscInt dim, cStart, cEnd, Np;
2319: PetscFunctionBegin;
2320: PetscCall(DMGetApplicationContext(sw, &user));
2321: PetscCall(PetscLogEventBegin(user->ESolveEvent, snes, sw, 0, 0));
2322: PetscCall(DMGetDimension(sw, &dim));
2323: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2325: PetscCall(SNESGetDM(snes, &dm));
2326: PetscCall(DMGetGlobalVector(user->dmPot, &rhoRhs));
2327: PetscCall(PetscObjectSetName((PetscObject)rhoRhs, "Weak charge density"));
2328: PetscCall(DMGetGlobalVector(dm, &rhoRhsFull));
2329: PetscCall(PetscObjectSetName((PetscObject)rhoRhsFull, "Weak charge density"));
2330: PetscCall(DMGetNamedGlobalVector(user->dmPot, "rho", &rho));
2331: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "w_q", &f));
2332: PetscCall(PetscObjectSetName((PetscObject)f, "particle weight"));
2334: PetscCall(MatViewFromOptions(M_p, NULL, "-mp_view"));
2335: PetscCall(MatViewFromOptions(user->M, NULL, "-m_view"));
2336: PetscCall(VecViewFromOptions(f, NULL, "-weights_view"));
2338: PetscCall(MatMultTranspose(M_p, f, rhoRhs));
2339: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "w_q", &f));
2341: PetscCall(KSPCreate(PetscObjectComm((PetscObject)dm), &ksp));
2342: PetscCall(KSPSetOptionsPrefix(ksp, "em_proj"));
2343: PetscCall(KSPSetOperators(ksp, user->M, user->M));
2344: PetscCall(KSPSetFromOptions(ksp));
2345: PetscCall(KSPSolve(ksp, rhoRhs, rho));
2347: PetscCall(VecISCopy(rhoRhsFull, user->isPot, SCATTER_FORWARD, rhoRhs));
2348: //PetscCall(VecScale(rhoRhsFull, -1.0));
2350: PetscCall(VecViewFromOptions(rhoRhs, NULL, "-rho_view"));
2351: PetscCall(VecViewFromOptions(rhoRhsFull, NULL, "-rho_full_view"));
2352: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "rho", &rho));
2353: PetscCall(DMRestoreGlobalVector(user->dmPot, &rhoRhs));
2354: PetscCall(KSPDestroy(&ksp));
2356: PetscCall(DMGetGlobalVector(dm, &phiFull));
2357: PetscCall(DMGetNamedGlobalVector(user->dmPot, "phi", &phi));
2358: PetscCall(VecSet(phiFull, 0.0));
2359: PetscCall(SNESSolve(snes, rhoRhsFull, phiFull));
2360: PetscCall(DMRestoreGlobalVector(dm, &rhoRhsFull));
2361: PetscCall(VecViewFromOptions(phi, NULL, "-phi_view"));
2363: PetscCall(VecISCopy(phiFull, user->isPot, SCATTER_REVERSE, phi));
2364: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "phi", &phi));
2366: PetscCall(DMGetLocalVector(dm, &locPhi));
2367: PetscCall(DMGlobalToLocalBegin(dm, phiFull, INSERT_VALUES, locPhi));
2368: PetscCall(DMGlobalToLocalEnd(dm, phiFull, INSERT_VALUES, locPhi));
2369: PetscCall(DMRestoreGlobalVector(dm, &phiFull));
2370: PetscCall(PetscLogEventEnd(user->ESolveEvent, snes, sw, 0, 0));
2372: PetscCall(DMGetDS(dm, &ds));
2373: PetscCall(PetscDSGetDiscretization(ds, 0, (PetscObject *)&fe));
2374: PetscCall(DMSwarmSortGetAccess(sw));
2375: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
2376: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2378: PetscCall(PetscLogEventBegin(user->ETabEvent, snes, sw, 0, 0));
2379: PetscTabulation tab;
2380: PetscReal *pcoord, *refcoord;
2381: PetscFEGeom *chunkgeom = NULL;
2382: PetscInt maxNcp = 0;
2384: for (PetscInt c = cStart; c < cEnd; ++c) {
2385: PetscInt Ncp;
2387: PetscCall(DMSwarmSortGetNumberOfPointsPerCell(sw, c, &Ncp));
2388: maxNcp = PetscMax(maxNcp, Ncp);
2389: }
2390: PetscCall(DMGetWorkArray(dm, maxNcp * dim, MPIU_REAL, &refcoord));
2391: PetscCall(DMGetWorkArray(dm, maxNcp * dim, MPIU_REAL, &pcoord));
2392: PetscCall(PetscFECreateTabulation(fe, 1, maxNcp, refcoord, 1, &tab));
2393: for (PetscInt c = cStart; c < cEnd; ++c) {
2394: PetscScalar *clPhi = NULL;
2395: PetscInt *points;
2396: PetscInt Ncp;
2398: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Ncp, &points));
2399: for (PetscInt cp = 0; cp < Ncp; ++cp)
2400: for (PetscInt d = 0; d < dim; ++d) pcoord[cp * dim + d] = coords[points[cp] * dim + d];
2401: {
2402: PetscCall(PetscFEGeomGetChunk(user->fegeom, c - cStart, c - cStart + 1, &chunkgeom));
2403: for (PetscInt i = 0; i < Ncp; ++i) {
2404: const PetscReal x0[3] = {-1., -1., -1.};
2405: CoordinatesRealToRef(dim, dim, x0, chunkgeom->v, chunkgeom->invJ, &pcoord[dim * i], &refcoord[dim * i]);
2406: }
2407: }
2408: PetscCall(PetscFEComputeTabulation(fe, Ncp, refcoord, 1, tab));
2409: PetscCall(DMPlexVecGetClosure(dm, NULL, locPhi, c, NULL, &clPhi));
2410: for (PetscInt cp = 0; cp < Ncp; ++cp) {
2411: const PetscInt p = points[cp];
2413: for (PetscInt d = 0; d < dim; ++d) E[p * dim + d] = 0.;
2414: PetscCall(PetscFEInterpolateAtPoints_Static(fe, tab, clPhi, chunkgeom, cp, &E[p * dim]));
2415: PetscCall(PetscFEPushforward(fe, chunkgeom, 1, &E[p * dim]));
2416: for (PetscInt d = 0; d < dim; ++d) E[p * dim + d] *= -1.0;
2417: }
2418: PetscCall(DMPlexVecRestoreClosure(dm, NULL, locPhi, c, NULL, &clPhi));
2419: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Ncp, &points));
2420: }
2421: PetscCall(DMRestoreWorkArray(dm, maxNcp * dim, MPIU_REAL, &pcoord));
2422: PetscCall(DMRestoreWorkArray(dm, maxNcp * dim, MPIU_REAL, &refcoord));
2423: PetscCall(PetscTabulationDestroy(&tab));
2424: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2425: PetscCall(DMSwarmSortRestoreAccess(sw));
2426: PetscCall(DMRestoreLocalVector(dm, &locPhi));
2427: PetscCall(PetscFEGeomRestoreChunk(user->fegeom, 0, 1, &chunkgeom));
2428: PetscCall(PetscLogEventEnd(user->ETabEvent, snes, sw, 0, 0));
2429: PetscFunctionReturn(PETSC_SUCCESS);
2430: }
2432: static PetscErrorCode ComputeFieldAtParticles(SNES snes, DM sw)
2433: {
2434: AppCtx *user;
2435: Mat M_p;
2436: PetscReal *E;
2437: PetscInt dim, Np;
2439: PetscFunctionBegin;
2442: PetscCall(DMGetDimension(sw, &dim));
2443: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2444: PetscCall(DMGetApplicationContext(sw, &user));
2446: PetscCall(DMSwarmSetCellDMActive(sw, "moments"));
2447: // TODO: Could share sort context with space cellDM
2448: PetscCall(DMSwarmMigrate(sw, PETSC_FALSE));
2449: PetscCall(DMCreateMassMatrix(sw, user->dmPot, &M_p));
2450: PetscCall(DMSwarmSetCellDMActive(sw, "space"));
2452: PetscCall(DMSwarmGetField(sw, "E_field", NULL, NULL, (void **)&E));
2453: PetscCall(PetscArrayzero(E, Np * dim));
2454: user->validE = PETSC_TRUE;
2456: switch (user->em) {
2457: case EM_COULOMB:
2458: PetscCall(ComputeFieldAtParticles_Coulomb(snes, sw, E));
2459: break;
2460: case EM_PRIMAL:
2461: PetscCall(ComputeFieldAtParticles_Primal(snes, sw, M_p, E));
2462: break;
2463: case EM_MIXED:
2464: PetscCall(ComputeFieldAtParticles_Mixed(snes, sw, M_p, E));
2465: break;
2466: case EM_NONE:
2467: break;
2468: default:
2469: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No solver for electrostatic model %s", EMTypes[user->em]);
2470: }
2471: PetscCall(DMSwarmRestoreField(sw, "E_field", NULL, NULL, (void **)&E));
2472: PetscCall(MatDestroy(&M_p));
2473: PetscFunctionReturn(PETSC_SUCCESS);
2474: }
2476: static PetscErrorCode RHSFunction(TS ts, PetscReal t, Vec U, Vec G, void *ctx)
2477: {
2478: DM sw;
2479: SNES snes = ((AppCtx *)ctx)->snes;
2480: const PetscScalar *u;
2481: PetscScalar *g;
2482: PetscReal *E, m_p = 1., q_p = -1.;
2483: PetscInt dim, d, Np, p;
2485: PetscFunctionBeginUser;
2486: PetscCall(TSGetDM(ts, &sw));
2487: PetscCall(ComputeFieldAtParticles(snes, sw));
2489: PetscCall(DMGetDimension(sw, &dim));
2490: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2491: PetscCall(DMSwarmGetField(sw, "E_field", NULL, NULL, (void **)&E));
2492: PetscCall(VecGetArrayRead(U, &u));
2493: PetscCall(VecGetArray(G, &g));
2494: Np /= 2 * dim;
2495: for (p = 0; p < Np; ++p) {
2496: for (d = 0; d < dim; ++d) {
2497: g[(p * 2 + 0) * dim + d] = u[(p * 2 + 1) * dim + d];
2498: g[(p * 2 + 1) * dim + d] = q_p * E[p * dim + d] / m_p;
2499: }
2500: }
2501: PetscCall(DMSwarmRestoreField(sw, "E_field", NULL, NULL, (void **)&E));
2502: PetscCall(VecRestoreArrayRead(U, &u));
2503: PetscCall(VecRestoreArray(G, &g));
2504: PetscFunctionReturn(PETSC_SUCCESS);
2505: }
2507: /* J_{ij} = dF_i/dx_j
2508: J_p = ( 0 1)
2509: (-w^2 0)
2510: TODO Now there is another term with w^2 from the electric field. I think we will need to invert the operator.
2511: Perhaps we can approximate the Jacobian using only the cellwise P-P gradient from Coulomb
2512: */
2513: static PetscErrorCode RHSJacobian(TS ts, PetscReal t, Vec U, Mat J, Mat P, void *ctx)
2514: {
2515: DM sw;
2516: const PetscReal *coords, *vel;
2517: PetscInt dim, d, Np, p, rStart;
2519: PetscFunctionBeginUser;
2520: PetscCall(TSGetDM(ts, &sw));
2521: PetscCall(DMGetDimension(sw, &dim));
2522: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2523: PetscCall(MatGetOwnershipRange(J, &rStart, NULL));
2524: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2525: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&vel));
2526: Np /= 2 * dim;
2527: for (p = 0; p < Np; ++p) {
2528: // TODO This is not right because dv/dx has the electric field in it
2529: PetscScalar vals[4] = {0., 1., -1., 0.};
2531: for (d = 0; d < dim; ++d) {
2532: const PetscInt rows[2] = {(p * 2 + 0) * dim + d + rStart, (p * 2 + 1) * dim + d + rStart};
2533: PetscCall(MatSetValues(J, 2, rows, 2, rows, vals, INSERT_VALUES));
2534: }
2535: }
2536: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2537: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&vel));
2538: PetscCall(MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY));
2539: PetscCall(MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY));
2540: PetscFunctionReturn(PETSC_SUCCESS);
2541: }
2543: static PetscErrorCode RHSFunctionX(TS ts, PetscReal t, Vec V, Vec Xres, void *ctx)
2544: {
2545: AppCtx *user = (AppCtx *)ctx;
2546: DM sw;
2547: const PetscScalar *v;
2548: PetscScalar *xres;
2549: PetscInt Np, p, d, dim;
2551: PetscFunctionBeginUser;
2552: PetscCall(PetscLogEventBegin(user->RhsXEvent, ts, 0, 0, 0));
2553: PetscCall(TSGetDM(ts, &sw));
2554: PetscCall(DMGetDimension(sw, &dim));
2555: PetscCall(VecGetLocalSize(Xres, &Np));
2556: PetscCall(VecGetArrayRead(V, &v));
2557: PetscCall(VecGetArray(Xres, &xres));
2558: Np /= dim;
2559: for (p = 0; p < Np; ++p) {
2560: for (d = 0; d < dim; ++d) xres[p * dim + d] = v[p * dim + d];
2561: }
2562: PetscCall(VecRestoreArrayRead(V, &v));
2563: PetscCall(VecRestoreArray(Xres, &xres));
2564: PetscCall(PetscLogEventEnd(user->RhsXEvent, ts, 0, 0, 0));
2565: PetscFunctionReturn(PETSC_SUCCESS);
2566: }
2568: static PetscErrorCode RHSFunctionV(TS ts, PetscReal t, Vec X, Vec Vres, void *ctx)
2569: {
2570: DM sw;
2571: AppCtx *user = (AppCtx *)ctx;
2572: SNES snes = ((AppCtx *)ctx)->snes;
2573: const PetscScalar *x;
2574: PetscScalar *vres;
2575: PetscReal *E, m_p, q_p;
2576: PetscInt Np, p, dim, d;
2577: Parameter *param;
2579: PetscFunctionBeginUser;
2580: PetscCall(PetscLogEventBegin(user->RhsVEvent, ts, 0, 0, 0));
2581: PetscCall(TSGetDM(ts, &sw));
2582: PetscCall(ComputeFieldAtParticles(snes, sw));
2584: PetscCall(DMGetDimension(sw, &dim));
2585: PetscCall(DMSwarmGetField(sw, "E_field", NULL, NULL, (void **)&E));
2586: PetscCall(PetscBagGetData(user->bag, (void **)¶m));
2587: m_p = user->masses[0] * param->m0;
2588: q_p = user->charges[0] * param->q0;
2589: PetscCall(VecGetLocalSize(Vres, &Np));
2590: PetscCall(VecGetArrayRead(X, &x));
2591: PetscCall(VecGetArray(Vres, &vres));
2592: Np /= dim;
2593: for (p = 0; p < Np; ++p) {
2594: for (d = 0; d < dim; ++d) vres[p * dim + d] = q_p * E[p * dim + d] / m_p;
2595: }
2596: PetscCall(VecRestoreArrayRead(X, &x));
2597: /*
2598: Synchronized, ordered output for parallel/sequential test cases.
2599: In the 1D (on the 2D mesh) case, every y component should be zero.
2600: */
2601: if (user->checkVRes) {
2602: PetscBool pr = user->checkVRes > 1 ? PETSC_TRUE : PETSC_FALSE;
2603: PetscInt step;
2605: PetscCall(TSGetStepNumber(ts, &step));
2606: if (pr) PetscCall(PetscPrintf(PETSC_COMM_WORLD, "step: %" PetscInt_FMT "\n", step));
2607: for (PetscInt p = 0; p < Np; ++p) {
2608: if (pr) PetscCall(PetscSynchronizedPrintf(PETSC_COMM_WORLD, "Residual: %.12g %.12g\n", (double)PetscRealPart(vres[p * dim + 0]), (double)PetscRealPart(vres[p * dim + 1])));
2609: PetscCheck(PetscAbsScalar(vres[p * dim + 1]) < PETSC_SMALL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Y velocity should be 0., not %g", (double)PetscRealPart(vres[p * dim + 1]));
2610: }
2611: if (pr) PetscCall(PetscSynchronizedFlush(PETSC_COMM_WORLD, PETSC_STDOUT));
2612: }
2613: PetscCall(VecRestoreArray(Vres, &vres));
2614: PetscCall(DMSwarmRestoreField(sw, "E_field", NULL, NULL, (void **)&E));
2615: PetscCall(PetscLogEventEnd(user->RhsVEvent, ts, 0, 0, 0));
2616: PetscFunctionReturn(PETSC_SUCCESS);
2617: }
2619: /* Discrete Gradients Formulation: S, F, gradF (G) */
2620: PetscErrorCode RHSJacobianS(TS ts, PetscReal t, Vec U, Mat S, void *ctx)
2621: {
2622: PetscScalar vals[4] = {0., 1., -1., 0.};
2623: DM sw;
2624: PetscInt dim, d, Np, p, rStart;
2626: PetscFunctionBeginUser;
2627: PetscCall(TSGetDM(ts, &sw));
2628: PetscCall(DMGetDimension(sw, &dim));
2629: PetscCall(VecGetLocalSize(U, &Np));
2630: PetscCall(MatGetOwnershipRange(S, &rStart, NULL));
2631: Np /= 2 * dim;
2632: for (p = 0; p < Np; ++p) {
2633: for (d = 0; d < dim; ++d) {
2634: const PetscInt rows[2] = {(p * 2 + 0) * dim + d + rStart, (p * 2 + 1) * dim + d + rStart};
2635: PetscCall(MatSetValues(S, 2, rows, 2, rows, vals, INSERT_VALUES));
2636: }
2637: }
2638: PetscCall(MatAssemblyBegin(S, MAT_FINAL_ASSEMBLY));
2639: PetscCall(MatAssemblyEnd(S, MAT_FINAL_ASSEMBLY));
2640: PetscFunctionReturn(PETSC_SUCCESS);
2641: }
2643: PetscErrorCode RHSObjectiveF(TS ts, PetscReal t, Vec U, PetscScalar *F, void *ctx)
2644: {
2645: AppCtx *user = (AppCtx *)ctx;
2646: DM sw;
2647: Vec phi;
2648: const PetscScalar *u;
2649: PetscInt dim, Np, cStart, cEnd;
2650: PetscReal *vel, *coords, m_p = 1.;
2652: PetscFunctionBeginUser;
2653: PetscCall(TSGetDM(ts, &sw));
2654: PetscCall(DMGetDimension(sw, &dim));
2655: PetscCall(DMPlexGetHeightStratum(user->dmPot, 0, &cStart, &cEnd));
2657: PetscCall(DMGetNamedGlobalVector(user->dmPot, "phi", &phi));
2658: PetscCall(VecViewFromOptions(phi, NULL, "-phi_view_dg"));
2659: PetscCall(computeFieldEnergy(user->dmPot, phi, F));
2660: PetscCall(DMRestoreNamedGlobalVector(user->dmPot, "phi", &phi));
2662: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2663: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&vel));
2664: PetscCall(DMSwarmSortGetAccess(sw));
2665: PetscCall(VecGetArrayRead(U, &u));
2666: PetscCall(VecGetLocalSize(U, &Np));
2667: Np /= 2 * dim;
2668: for (PetscInt c = cStart; c < cEnd; ++c) {
2669: PetscInt *points;
2670: PetscInt Ncp;
2672: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Ncp, &points));
2673: for (PetscInt cp = 0; cp < Ncp; ++cp) {
2674: const PetscInt p = points[cp];
2675: const PetscReal v2 = DMPlex_DotRealD_Internal(dim, &u[(p * 2 + 1) * dim], &u[(p * 2 + 1) * dim]);
2677: *F += 0.5 * m_p * v2;
2678: }
2679: PetscCall(DMSwarmSortRestorePointsPerCell(sw, c, &Ncp, &points));
2680: }
2681: PetscCall(VecRestoreArrayRead(U, &u));
2682: PetscCall(DMSwarmSortRestoreAccess(sw));
2683: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2684: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&vel));
2685: PetscFunctionReturn(PETSC_SUCCESS);
2686: }
2688: /* dF/dx = q E dF/dv = v */
2689: PetscErrorCode RHSFunctionG(TS ts, PetscReal t, Vec U, Vec G, void *ctx)
2690: {
2691: DM sw;
2692: SNES snes = ((AppCtx *)ctx)->snes;
2693: const PetscReal *coords, *vel, *E;
2694: const PetscScalar *u;
2695: PetscScalar *g;
2696: PetscReal m_p = 1., q_p = -1.;
2697: PetscInt dim, d, Np, p;
2699: PetscFunctionBeginUser;
2700: PetscCall(TSGetDM(ts, &sw));
2701: PetscCall(DMGetDimension(sw, &dim));
2702: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2703: PetscCall(VecGetArrayRead(U, &u));
2704: PetscCall(VecGetArray(G, &g));
2706: PetscLogEvent COMPUTEFIELD;
2707: PetscCall(PetscLogEventRegister("COMPFIELDATPART", TS_CLASSID, &COMPUTEFIELD));
2708: PetscCall(PetscLogEventBegin(COMPUTEFIELD, 0, 0, 0, 0));
2709: PetscCall(ComputeFieldAtParticles(snes, sw));
2710: PetscCall(PetscLogEventEnd(COMPUTEFIELD, 0, 0, 0, 0));
2711: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2712: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&vel));
2713: PetscCall(DMSwarmGetField(sw, "E_field", NULL, NULL, (void **)&E));
2714: for (p = 0; p < Np; ++p) {
2715: for (d = 0; d < dim; ++d) {
2716: g[(p * 2 + 0) * dim + d] = -(q_p / m_p) * E[p * dim + d];
2717: g[(p * 2 + 1) * dim + d] = m_p * u[(p * 2 + 1) * dim + d];
2718: }
2719: }
2720: PetscCall(DMSwarmRestoreField(sw, "E_field", NULL, NULL, (void **)&E));
2721: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&coords));
2722: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&vel));
2723: PetscCall(VecRestoreArrayRead(U, &u));
2724: PetscCall(VecRestoreArray(G, &g));
2725: PetscFunctionReturn(PETSC_SUCCESS);
2726: }
2728: static PetscErrorCode CreateSolution(TS ts)
2729: {
2730: DM sw;
2731: Vec u;
2732: PetscInt dim, Np;
2734: PetscFunctionBegin;
2735: PetscCall(TSGetDM(ts, &sw));
2736: PetscCall(DMGetDimension(sw, &dim));
2737: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2738: PetscCall(VecCreate(PETSC_COMM_WORLD, &u));
2739: PetscCall(VecSetBlockSize(u, dim));
2740: PetscCall(VecSetSizes(u, 2 * Np * dim, PETSC_DECIDE));
2741: PetscCall(VecSetUp(u));
2742: PetscCall(TSSetSolution(ts, u));
2743: PetscCall(VecDestroy(&u));
2744: PetscFunctionReturn(PETSC_SUCCESS);
2745: }
2747: static PetscErrorCode SetProblem(TS ts)
2748: {
2749: AppCtx *user;
2750: DM sw;
2752: PetscFunctionBegin;
2753: PetscCall(TSGetDM(ts, &sw));
2754: PetscCall(DMGetApplicationContext(sw, (void **)&user));
2755: // Define unified system for (X, V)
2756: {
2757: Mat J;
2758: PetscInt dim, Np;
2760: PetscCall(DMGetDimension(sw, &dim));
2761: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2762: PetscCall(MatCreate(PETSC_COMM_WORLD, &J));
2763: PetscCall(MatSetSizes(J, 2 * Np * dim, 2 * Np * dim, PETSC_DECIDE, PETSC_DECIDE));
2764: PetscCall(MatSetBlockSize(J, 2 * dim));
2765: PetscCall(MatSetFromOptions(J));
2766: PetscCall(MatSetUp(J));
2767: PetscCall(TSSetRHSFunction(ts, NULL, RHSFunction, user));
2768: PetscCall(TSSetRHSJacobian(ts, J, J, RHSJacobian, user));
2769: PetscCall(MatDestroy(&J));
2770: }
2771: /* Define split system for X and V */
2772: {
2773: Vec u;
2774: IS isx, isv, istmp;
2775: const PetscInt *idx;
2776: PetscInt dim, Np, rstart;
2778: PetscCall(TSGetSolution(ts, &u));
2779: PetscCall(DMGetDimension(sw, &dim));
2780: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2781: PetscCall(VecGetOwnershipRange(u, &rstart, NULL));
2782: PetscCall(ISCreateStride(PETSC_COMM_WORLD, Np, (rstart / dim) + 0, 2, &istmp));
2783: PetscCall(ISGetIndices(istmp, &idx));
2784: PetscCall(ISCreateBlock(PETSC_COMM_WORLD, dim, Np, idx, PETSC_COPY_VALUES, &isx));
2785: PetscCall(ISRestoreIndices(istmp, &idx));
2786: PetscCall(ISDestroy(&istmp));
2787: PetscCall(ISCreateStride(PETSC_COMM_WORLD, Np, (rstart / dim) + 1, 2, &istmp));
2788: PetscCall(ISGetIndices(istmp, &idx));
2789: PetscCall(ISCreateBlock(PETSC_COMM_WORLD, dim, Np, idx, PETSC_COPY_VALUES, &isv));
2790: PetscCall(ISRestoreIndices(istmp, &idx));
2791: PetscCall(ISDestroy(&istmp));
2792: PetscCall(TSRHSSplitSetIS(ts, "position", isx));
2793: PetscCall(TSRHSSplitSetIS(ts, "momentum", isv));
2794: PetscCall(ISDestroy(&isx));
2795: PetscCall(ISDestroy(&isv));
2796: PetscCall(TSRHSSplitSetRHSFunction(ts, "position", NULL, RHSFunctionX, user));
2797: PetscCall(TSRHSSplitSetRHSFunction(ts, "momentum", NULL, RHSFunctionV, user));
2798: }
2799: // Define symplectic formulation U_t = S . G, where G = grad F
2800: {
2801: PetscCall(TSDiscGradSetFormulation(ts, RHSJacobianS, RHSObjectiveF, RHSFunctionG, user));
2802: }
2803: PetscFunctionReturn(PETSC_SUCCESS);
2804: }
2806: static PetscErrorCode DMSwarmTSRedistribute(TS ts)
2807: {
2808: DM sw;
2809: Vec u;
2810: PetscReal t, maxt, dt;
2811: PetscInt n, maxn;
2813: PetscFunctionBegin;
2814: PetscCall(TSGetDM(ts, &sw));
2815: PetscCall(TSGetTime(ts, &t));
2816: PetscCall(TSGetMaxTime(ts, &maxt));
2817: PetscCall(TSGetTimeStep(ts, &dt));
2818: PetscCall(TSGetStepNumber(ts, &n));
2819: PetscCall(TSGetMaxSteps(ts, &maxn));
2821: PetscCall(TSReset(ts));
2822: PetscCall(TSSetDM(ts, sw));
2823: PetscCall(TSSetFromOptions(ts));
2824: PetscCall(TSSetTime(ts, t));
2825: PetscCall(TSSetMaxTime(ts, maxt));
2826: PetscCall(TSSetTimeStep(ts, dt));
2827: PetscCall(TSSetStepNumber(ts, n));
2828: PetscCall(TSSetMaxSteps(ts, maxn));
2830: PetscCall(CreateSolution(ts));
2831: PetscCall(SetProblem(ts));
2832: PetscCall(TSGetSolution(ts, &u));
2833: PetscFunctionReturn(PETSC_SUCCESS);
2834: }
2836: PetscErrorCode line(PetscInt dim, PetscReal time, const PetscReal dummy[], PetscInt p, PetscScalar x[], void *ctx)
2837: {
2838: DM sw, cdm;
2839: PetscInt Np;
2840: PetscReal low[2], high[2];
2841: AppCtx *user = (AppCtx *)ctx;
2843: sw = user->swarm;
2844: PetscCall(DMSwarmGetCellDM(sw, &cdm));
2845: // Get the bounding box so we can equally space the particles
2846: PetscCall(DMGetLocalBoundingBox(cdm, low, high));
2847: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2848: // shift it by h/2 so nothing is initialized directly on a boundary
2849: x[0] = ((high[0] - low[0]) / Np) * (p + 0.5);
2850: x[1] = 0.;
2851: return PETSC_SUCCESS;
2852: }
2854: /*
2855: InitializeSolveAndSwarm - Set the solution values to the swarm coordinates and velocities, and also possibly set the initial values.
2857: Input Parameters:
2858: + ts - The TS
2859: - useInitial - Flag to also set the initial conditions to the current coordinates and velocities and setup the problem
2861: Output Parameters:
2862: . u - The initialized solution vector
2864: Level: advanced
2866: .seealso: InitializeSolve()
2867: */
2868: static PetscErrorCode InitializeSolveAndSwarm(TS ts, PetscBool useInitial)
2869: {
2870: DM sw;
2871: Vec u, gc, gv;
2872: IS isx, isv;
2873: PetscInt dim;
2874: AppCtx *user;
2876: PetscFunctionBeginUser;
2877: PetscCall(TSGetDM(ts, &sw));
2878: PetscCall(DMGetApplicationContext(sw, &user));
2879: PetscCall(DMGetDimension(sw, &dim));
2880: if (useInitial) {
2881: PetscReal v0[2] = {1., 0.};
2882: if (user->perturbed_weights) {
2883: PetscCall(InitializeParticles_PerturbedWeights(sw, user));
2884: } else {
2885: PetscCall(DMSwarmComputeLocalSizeFromOptions(sw));
2886: PetscCall(DMSwarmInitializeCoordinates(sw));
2887: PetscCall(DMSwarmInitializeVelocitiesFromOptions(sw, v0));
2888: }
2889: PetscCall(DMSwarmMigrate(sw, PETSC_TRUE));
2890: PetscCall(DMSwarmTSRedistribute(ts));
2891: }
2892: PetscCall(DMSetUp(sw));
2893: PetscCall(TSGetSolution(ts, &u));
2894: PetscCall(TSRHSSplitGetIS(ts, "position", &isx));
2895: PetscCall(TSRHSSplitGetIS(ts, "momentum", &isv));
2896: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, DMSwarmPICField_coor, &gc));
2897: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "velocity", &gv));
2898: PetscCall(VecISCopy(u, isx, SCATTER_FORWARD, gc));
2899: PetscCall(VecISCopy(u, isv, SCATTER_FORWARD, gv));
2900: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, DMSwarmPICField_coor, &gc));
2901: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "velocity", &gv));
2902: PetscFunctionReturn(PETSC_SUCCESS);
2903: }
2905: static PetscErrorCode InitializeSolve(TS ts, Vec u)
2906: {
2907: PetscFunctionBegin;
2908: PetscCall(TSSetSolution(ts, u));
2909: PetscCall(InitializeSolveAndSwarm(ts, PETSC_TRUE));
2910: PetscFunctionReturn(PETSC_SUCCESS);
2911: }
2913: static PetscErrorCode MigrateParticles(TS ts)
2914: {
2915: DM sw, cdm;
2916: const PetscReal *L;
2917: AppCtx *ctx;
2919: PetscFunctionBeginUser;
2920: PetscCall(TSGetDM(ts, &sw));
2921: PetscCall(DMGetApplicationContext(sw, &ctx));
2922: PetscCall(DMViewFromOptions(sw, NULL, "-migrate_view_pre"));
2923: {
2924: Vec u, gc, gv, position, momentum;
2925: IS isx, isv;
2926: PetscReal *pos, *mom;
2928: PetscCall(TSGetSolution(ts, &u));
2929: PetscCall(TSRHSSplitGetIS(ts, "position", &isx));
2930: PetscCall(TSRHSSplitGetIS(ts, "momentum", &isv));
2931: PetscCall(VecGetSubVector(u, isx, &position));
2932: PetscCall(VecGetSubVector(u, isv, &momentum));
2933: PetscCall(VecGetArray(position, &pos));
2934: PetscCall(VecGetArray(momentum, &mom));
2935: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, DMSwarmPICField_coor, &gc));
2936: PetscCall(DMSwarmCreateGlobalVectorFromField(sw, "velocity", &gv));
2937: PetscCall(VecISCopy(u, isx, SCATTER_REVERSE, gc));
2938: PetscCall(VecISCopy(u, isv, SCATTER_REVERSE, gv));
2940: PetscCall(DMSwarmGetCellDM(sw, &cdm));
2941: PetscCall(DMGetPeriodicity(cdm, NULL, NULL, &L));
2942: PetscCheck(L, PetscObjectComm((PetscObject)cdm), PETSC_ERR_ARG_WRONG, "Mesh must be periodic");
2943: if ((L[0] || L[1]) >= 0.) {
2944: PetscReal *x, *v, upper[3], lower[3];
2945: PetscInt Np, dim;
2947: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2948: PetscCall(DMGetDimension(cdm, &dim));
2949: PetscCall(DMGetBoundingBox(cdm, lower, upper));
2950: PetscCall(VecGetArray(gc, &x));
2951: PetscCall(VecGetArray(gv, &v));
2952: for (PetscInt p = 0; p < Np; ++p) {
2953: for (PetscInt d = 0; d < dim; ++d) {
2954: if (pos[p * dim + d] < lower[d]) {
2955: x[p * dim + d] = pos[p * dim + d] + (upper[d] - lower[d]);
2956: } else if (pos[p * dim + d] > upper[d]) {
2957: x[p * dim + d] = pos[p * dim + d] - (upper[d] - lower[d]);
2958: } else {
2959: x[p * dim + d] = pos[p * dim + d];
2960: }
2961: PetscCheck(x[p * dim + d] >= lower[d] && x[p * dim + d] <= upper[d], PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "p: %" PetscInt_FMT "x[%" PetscInt_FMT "] %g", p, d, (double)x[p * dim + d]);
2962: v[p * dim + d] = mom[p * dim + d];
2963: }
2964: }
2965: PetscCall(VecRestoreArray(gc, &x));
2966: PetscCall(VecRestoreArray(gv, &v));
2967: }
2968: PetscCall(VecRestoreArray(position, &pos));
2969: PetscCall(VecRestoreArray(momentum, &mom));
2970: PetscCall(VecRestoreSubVector(u, isx, &position));
2971: PetscCall(VecRestoreSubVector(u, isv, &momentum));
2972: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, "velocity", &gv));
2973: PetscCall(DMSwarmDestroyGlobalVectorFromField(sw, DMSwarmPICField_coor, &gc));
2974: }
2975: PetscCall(DMSwarmMigrate(sw, PETSC_TRUE));
2976: PetscInt step;
2978: PetscCall(TSGetStepNumber(ts, &step));
2979: if (!(step % ctx->remapFreq)) {
2980: // Monitor electric field before we destroy it
2981: PetscReal ptime;
2982: PetscInt step;
2984: PetscCall(TSGetStepNumber(ts, &step));
2985: PetscCall(TSGetTime(ts, &ptime));
2986: if (ctx->efield_monitor) PetscCall(MonitorEField(ts, step, ptime, NULL, ctx));
2987: if (ctx->poisson_monitor) PetscCall(MonitorPoisson(ts, step, ptime, NULL, ctx));
2988: PetscCall(DMSwarmRemap(sw));
2989: ctx->validE = PETSC_FALSE;
2990: }
2991: // This MUST come last, since it recreates the subswarms and they must DMClone() the new swarm
2992: PetscCall(DMSwarmTSRedistribute(ts));
2993: PetscCall(InitializeSolveAndSwarm(ts, PETSC_FALSE));
2994: PetscFunctionReturn(PETSC_SUCCESS);
2995: }
2997: int main(int argc, char **argv)
2998: {
2999: DM dm, sw;
3000: TS ts;
3001: Vec u;
3002: PetscReal dt;
3003: PetscInt maxn;
3004: AppCtx user;
3006: PetscCall(PetscInitialize(&argc, &argv, NULL, help));
3007: PetscCall(ProcessOptions(PETSC_COMM_WORLD, &user));
3008: PetscCall(PetscBagCreate(PETSC_COMM_SELF, sizeof(Parameter), &user.bag));
3009: PetscCall(CreateMesh(PETSC_COMM_WORLD, &user, &dm));
3010: PetscCall(CreatePoisson(dm, &user));
3011: PetscCall(CreateMomentFields(dm, &user));
3012: PetscCall(CreateSwarm(dm, &user, &sw));
3013: PetscCall(SetupParameters(PETSC_COMM_WORLD, &user));
3014: PetscCall(InitializeConstants(sw, &user));
3015: PetscCall(DMSetApplicationContext(sw, &user));
3017: PetscCall(TSCreate(PETSC_COMM_WORLD, &ts));
3018: PetscCall(TSSetProblemType(ts, TS_NONLINEAR));
3019: PetscCall(TSSetDM(ts, sw));
3020: PetscCall(TSSetMaxTime(ts, 0.1));
3021: PetscCall(TSSetTimeStep(ts, 0.00001));
3022: PetscCall(TSSetMaxSteps(ts, 100));
3023: PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP));
3025: if (user.efield_monitor) PetscCall(TSMonitorSet(ts, MonitorEField, &user, NULL));
3026: if (user.moment_monitor) PetscCall(TSMonitorSet(ts, MonitorMoments, &user, NULL));
3027: if (user.moment_field_monitor) PetscCall(TSMonitorSet(ts, MonitorMomentFields, &user, NULL));
3028: if (user.initial_monitor) PetscCall(TSMonitorSet(ts, MonitorInitialConditions, &user, NULL));
3029: if (user.positions_monitor) PetscCall(TSMonitorSet(ts, MonitorPositions_2D, &user, NULL));
3030: if (user.poisson_monitor) PetscCall(TSMonitorSet(ts, MonitorPoisson, &user, NULL));
3031: if (user.velocity_monitor >= 0) PetscCall(TSMonitorSet(ts, MonitorVelocity, &user, NULL));
3033: PetscCall(TSSetFromOptions(ts));
3034: PetscCall(TSGetTimeStep(ts, &dt));
3035: PetscCall(TSGetMaxSteps(ts, &maxn));
3036: user.steps = maxn;
3037: user.stepSize = dt;
3038: PetscCall(SetupContext(dm, sw, &user));
3039: PetscCall(TSSetComputeInitialCondition(ts, InitializeSolve));
3040: PetscCall(TSSetPostStep(ts, MigrateParticles));
3041: PetscCall(CreateSolution(ts));
3042: PetscCall(TSGetSolution(ts, &u));
3043: PetscCall(TSComputeInitialCondition(ts, u));
3044: PetscCall(CheckNonNegativeWeights(sw, &user));
3045: PetscCall(TSSolve(ts, NULL));
3047: if (user.checkLandau) {
3048: // We should get a lookup table based on charge density and \hat k
3049: const PetscReal gammaEx = -0.15336;
3050: const PetscReal omegaEx = 1.4156;
3051: const PetscReal tol = 1e-2;
3053: PetscCheck(PetscAbsReal((user.gamma - gammaEx) / gammaEx) < tol, PETSC_COMM_WORLD, PETSC_ERR_LIB, "Invalid Landau gamma %g != %g", user.gamma, gammaEx);
3054: PetscCheck(PetscAbsReal((user.omega - omegaEx) / omegaEx) < tol, PETSC_COMM_WORLD, PETSC_ERR_LIB, "Invalid Landau omega %g != %g", user.omega, omegaEx);
3055: }
3057: PetscCall(SNESDestroy(&user.snes));
3058: PetscCall(DMDestroy(&user.dmN));
3059: PetscCall(ISDestroy(&user.isN));
3060: PetscCall(MatDestroy(&user.MN));
3061: PetscCall(DMDestroy(&user.dmP));
3062: PetscCall(ISDestroy(&user.isP));
3063: PetscCall(MatDestroy(&user.MP));
3064: PetscCall(DMDestroy(&user.dmE));
3065: PetscCall(ISDestroy(&user.isE));
3066: PetscCall(MatDestroy(&user.ME));
3067: PetscCall(DMDestroy(&user.dmMom));
3068: PetscCall(DMDestroy(&user.dmPot));
3069: PetscCall(ISDestroy(&user.isPot));
3070: PetscCall(MatDestroy(&user.M));
3071: PetscCall(PetscFEGeomDestroy(&user.fegeom));
3072: PetscCall(TSDestroy(&ts));
3073: PetscCall(DMDestroy(&sw));
3074: PetscCall(DMDestroy(&dm));
3075: PetscCall(DestroyContext(&user));
3076: PetscCall(PetscFinalize());
3077: return 0;
3078: }
3080: /*TEST
3082: build:
3083: requires: !complex double
3085: # This tests that we can compute the correct decay rate and frequency
3086: # For gold runs, use -dm_plex_box_faces 160 -vdm_plex_box_faces 450 -remap_dm_plex_box_faces 80,150 -ts_max_steps 1000
3087: # -remap_freq 100 -emax_start_step 50 -emax_solve_step 100
3088: testset:
3089: args: -cosine_coefficients 0.01 -charges -1. -perturbed_weights -total_weight 1. \
3090: -dm_plex_dim 1 -dm_plex_box_faces 80 -dm_plex_box_lower 0. -dm_plex_box_upper 12.5664 \
3091: -dm_plex_box_bd periodic -dm_plex_hash_location \
3092: -vdm_plex_dim 1 -vdm_plex_box_faces 220 -vdm_plex_box_lower -6 -vdm_plex_box_upper 6 \
3093: -vpetscspace_degree 2 -vdm_plex_hash_location \
3094: -remap_freq 1 -dm_swarm_remap_type pfak -remap_dm_plex_dim 2 -remap_dm_plex_simplex 0 \
3095: -remap_dm_plex_box_faces 40,110 -remap_dm_plex_box_bd periodic,none \
3096: -remap_dm_plex_box_lower 0.,-6. -remap_dm_plex_box_upper 12.5664,6. \
3097: -remap_petscspace_degree 1 -remap_dm_plex_hash_location \
3098: -ftop_ksp_type lsqr -ftop_pc_type none -ftop_ksp_rtol 1.e-14 -ptof_pc_type lu \
3099: -em_type primal -petscspace_degree 1 -em_snes_atol 1.e-12 -em_snes_error_if_not_converged \
3100: -em_ksp_error_if_not_converged -em_pc_type svd -em_proj_pc_type lu \
3101: -ts_dt 0.03 -ts_max_steps 2 -ts_max_time 100 \
3102: -emax_tao_type brgn -emax_tao_max_it 100 -emax_tao_brgn_regularization_type l2pure \
3103: -emax_tao_brgn_regularizer_weight 1e-5 -tao_brgn_subsolver_tao_bnk_ksp_rtol 1e-12 \
3104: -emax_start_step 1 -emax_solve_step 1 \
3105: -output_step 1 -efield_monitor quiet
3107: test:
3108: suffix: landau_damping_1d_bs
3109: args: -ts_type basicsymplectic -ts_basicsymplectic_type 1
3111: test:
3112: suffix: landau_damping_1d_dg
3113: args: -ts_type discgrad -ts_discgrad_type average -snes_type qn
3115: TEST*/