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Reapply GK passive advection work (PR #1084) #1102

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Merged
Antoinehoff merged 20 commits into from
Sep 2, 2026
Merged

Reapply GK passive advection work (PR #1084) #1102

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c7a6260
Add a new GK equation object to do passive advection, with a velocity…
manauref Jul 3, 2026
93e5a40
Change field_id in rt_gk_passive so that the omega_H dt doesn't show …
manauref Jul 3, 2026
21b5951
Sync advection speeds so that parallel runs come out correctly. Add 2…
manauref Jul 4, 2026
a730b0d
I think the changes to rect_grid_find_cell in a recent PR might've br…
manauref Jul 6, 2026
59812b2
Add TS BC unit test corresponding to figure 14 of the paper. Seems to…
manauref Jul 6, 2026
fe7b669
Protect against integrating over zero-volume regions in some sub-cell…
manauref Jul 7, 2026
00e5450
Add passive advection CBC test. Works fine with constant q, but the q…
manauref Jul 7, 2026
cc92dbc
Add a TS BC unit test with the same setup as the CBC reg test. We may…
manauref Jul 7, 2026
057b35f
Add an assert in twistshift BC updater that errors out of the change …
manauref Jul 9, 2026
1854d08
Change the way we look for shifted cells in periodic copies along y i…
manauref Jul 9, 2026
34859d5
Fix y extents in CBC input files so the wedge number is indeed an int…
manauref Jul 9, 2026
d262b5e
Fix kernel selection in device code, and add some missing casts.
manauref Jul 10, 2026
b5afcd9
Add device CBC unit test. Add bc_twistshift_new method, instead of in…
manauref Jul 10, 2026
718cd63
Change signature of bc_twistshift_new so that structs are passed by a…
manauref Jul 10, 2026
f9ac3ff
Detected through compute sanitizer that delta_ts_x_dev was never rele…
Antoinehoff Aug 4, 2026
881ec87
Increase resolution in d3d_iwl and tcv_iwl tests so they run (they ca…
manauref Aug 4, 2026
d7d773c
Increase another tolerance to 1e-9 in TS BC unit test so it passes on…
manauref Aug 4, 2026
12e1f57
Fix mem leak in GK app where an array was not released at program's end.
manauref Aug 5, 2026
948ce2b
Update perlmutter CPU machine files to remove all possibility of GPU …
manauref Aug 5, 2026
3933c44
Reduce Nmu in TCV iwl test to reduce runtime.
manauref Aug 5, 2026
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1 change: 1 addition & 0 deletions core/zero/gkyl_eqn_type.h
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Original file line number Diff line number Diff line change
Expand Up @@ -186,4 +186,5 @@ enum gkyl_gk_collisionless_type {
GKYL_GK_COLLISIONLESS_EM_BPAR, // Electromagnetic with B_par fluctuations.
GKYL_GK_COLLISIONLESS_EM, // Electromagnetic with B_perp and B_par fluctuations.
GKYL_GK_COLLISIONLESS_NEUTRAL, // Neutral collisionless terms.
GKYL_GK_COLLISIONLESS_PASSIVE, // Passive advection (for dev/debug).
};
3 changes: 1 addition & 2 deletions core/zero/gkyl_rect_grid.h
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Expand Up @@ -50,7 +50,7 @@ struct gkyl_rect_grid* gkyl_rect_grid_new(int ndim,
* @param pick_lower If point is on a cell boundary, pick the lower cell if true (per direction).
* @param known_index Any known indices of where the point is (<0 if not known).
* @param cell_index Pointer to cell indices.
* Asserts: point lies within cell(s) specified by knownIdx (if specified).
* Asserts: point lies within cell(s) specified by known_index (if specified).
*/
GKYL_CU_DH
void gkyl_rect_grid_find_cell(const struct gkyl_rect_grid *grid, const double *point,
Expand Down Expand Up @@ -158,4 +158,3 @@ bool gkyl_rect_grid_read(struct gkyl_rect_grid *grid, FILE *fp);
* @param grid Grid object.
*/
void gkyl_rect_grid_release(struct gkyl_rect_grid *grid);

3 changes: 1 addition & 2 deletions core/zero/rect_grid.c
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ gkyl_rect_grid_find_cell(const struct gkyl_rect_grid *grid, const double *point,
}
for (int i=0; i<search_num; i++){
for (int j=0; j<2; j++){
new_index[i] = GKYL_MAX2(GKYL_MIN2(mid_index[i] + plusminus[j],cells[i]),0);
new_index[i] = GKYL_MAX2(GKYL_MIN2(mid_index[i] + plusminus[j],cells[search_dim[i]]),1);
if (is_in_cell(grid, point, new_index, dim_trans, known_index))
low_high_index[j*nDim+search_dim[i]] = new_index[i];
}
Expand Down Expand Up @@ -212,4 +212,3 @@ gkyl_rect_grid_release(struct gkyl_rect_grid *grid)
{
gkyl_free(grid);
}

24 changes: 12 additions & 12 deletions gyrokinetic/apps/gk_field_2x3x.c
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Expand Up @@ -259,10 +259,10 @@ gk_field_2x3x_add_TS_updaters(struct gkyl_gyrokinetic_app *app, struct gk_field
.shear_dir = 0, // shift varies with x.
.edge = GKYL_LOWER_EDGE,
.cdim = app->cdim,
.bcdir_ext_update_r = app->global_par_ext,
.bcdir_ext_update_r = &app->global_par_ext,
.num_ghost = ghost, // one ghost per config direction
.basis = app->basis,
.grid = app->grid,
.basis = &app->basis,
.grid = &app->grid,
.use_gpu = app->use_gpu,
};
if (app->gk_geom->geometry_id == GKYL_GEOMETRY_TOKAMAK)
Expand All @@ -271,7 +271,7 @@ gk_field_2x3x_add_TS_updaters(struct gkyl_gyrokinetic_app *app, struct gk_field
T_LU_lo.shift_func = app->gk_geom->parallel_lower_bc_shift_func;
T_LU_lo.shift_func_ctx = app->gk_geom->parallel_lower_bc_shift_ctx;
}
f->bc_ts_lo = gkyl_bc_twistshift_new(&T_LU_lo);
f->bc_ts_lo = gkyl_bc_twistshift_inew(&T_LU_lo);

// TS BC updater for upper edge.
struct gkyl_bc_twistshift_inp T_UL_up = {
Expand All @@ -280,10 +280,10 @@ gk_field_2x3x_add_TS_updaters(struct gkyl_gyrokinetic_app *app, struct gk_field
.shear_dir = 0, // shift varies with x.
.edge = GKYL_UPPER_EDGE,
.cdim = app->cdim,
.bcdir_ext_update_r = app->global_par_ext,
.bcdir_ext_update_r = &app->global_par_ext,
.num_ghost = ghost, // one ghost per config direction
.basis = app->basis,
.grid = app->grid,
.basis = &app->basis,
.grid = &app->grid,
.use_gpu = app->use_gpu,
};
if (app->gk_geom->geometry_id == GKYL_GEOMETRY_TOKAMAK)
Expand All @@ -292,7 +292,7 @@ gk_field_2x3x_add_TS_updaters(struct gkyl_gyrokinetic_app *app, struct gk_field
T_UL_up.shift_func = app->gk_geom->parallel_upper_bc_shift_func;
T_UL_up.shift_func_ctx = app->gk_geom->parallel_upper_bc_shift_ctx;
}
f->bc_ts_up = gkyl_bc_twistshift_new(&T_UL_up);
f->bc_ts_up = gkyl_bc_twistshift_inew(&T_UL_up);

long buff_sz = app->global_lower_ghost[par_dir].volume;
f->bc_buffer = mkarr(app->use_gpu, app->basis.num_basis, buff_sz);
Expand Down Expand Up @@ -356,10 +356,10 @@ gk_field_2x3x_add_IWL_updaters(struct gkyl_gyrokinetic_app *app, struct gk_field
.shear_dir = 0, // shift varies with x.
.edge = GKYL_LOWER_EDGE,
.cdim = app->cdim,
.bcdir_ext_update_r = app->global_par_ext_core,
.bcdir_ext_update_r = &app->global_par_ext_core,
.num_ghost = ghost, // one ghost per config direction
.basis = app->basis,
.grid = app->grid,
.basis = &app->basis,
.grid = &app->grid,
.use_gpu = app->use_gpu,
};
if (app->gk_geom->geometry_id == GKYL_GEOMETRY_TOKAMAK)
Expand All @@ -368,7 +368,7 @@ gk_field_2x3x_add_IWL_updaters(struct gkyl_gyrokinetic_app *app, struct gk_field
T_LU_lo.shift_func = app->gk_geom->parallel_lower_bc_shift_func;
T_LU_lo.shift_func_ctx = app->gk_geom->parallel_lower_bc_shift_ctx;
}
f->bc_ts_lo = gkyl_bc_twistshift_new(&T_LU_lo);
f->bc_ts_lo = gkyl_bc_twistshift_inew(&T_LU_lo);

long buff_sz = GKYL_MAX2(app->global_lower_ghost_par_sol.volume, app->global_lower_ghost_par_core.volume);
f->bc_buffer = mkarr(app->use_gpu, app->basis.num_basis, buff_sz);
Expand Down
32 changes: 16 additions & 16 deletions gyrokinetic/apps/gk_species.c
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Expand Up @@ -886,10 +886,10 @@ gk_species_init_dynamic(struct gkyl_gk *gk_app_inp, struct gkyl_gyrokinetic_app
.shear_dir = 0, // shift varies with x.
.edge = GKYL_LOWER_EDGE,
.cdim = cdim,
.bcdir_ext_update_r = gks->local_par_ext,
.bcdir_ext_update_r = &gks->local_par_ext,
.num_ghost = ghost,
.basis = gks->basis,
.grid = gks->grid,
.basis = &gks->basis,
.grid = &gks->grid,
.use_gpu = app->use_gpu,
};
if (app->gk_geom->geometry_id == GKYL_GEOMETRY_TOKAMAK)
Expand All @@ -899,7 +899,7 @@ gk_species_init_dynamic(struct gkyl_gk *gk_app_inp, struct gkyl_gyrokinetic_app
tsinp.shift_func_ctx = app->gk_geom->parallel_lower_bc_shift_ctx;
}

gks->bc_ts_lo = gkyl_bc_twistshift_new(&tsinp);
gks->bc_ts_lo = gkyl_bc_twistshift_inew(&tsinp);

}
else if ( (gks->lower_bc[d].type == GKYL_BC_GK_SPECIES_COPY) ||
Expand Down Expand Up @@ -946,10 +946,10 @@ gk_species_init_dynamic(struct gkyl_gk *gk_app_inp, struct gkyl_gyrokinetic_app
.shear_dir = 0, // shift varies with x.
.edge = GKYL_UPPER_EDGE,
.cdim = cdim,
.bcdir_ext_update_r = gks->local_par_ext,
.bcdir_ext_update_r = &gks->local_par_ext,
.num_ghost = ghost,
.basis = gks->basis,
.grid = gks->grid,
.basis = &gks->basis,
.grid = &gks->grid,
.use_gpu = app->use_gpu,
};
if (app->gk_geom->geometry_id == GKYL_GEOMETRY_TOKAMAK)
Expand All @@ -959,7 +959,7 @@ gk_species_init_dynamic(struct gkyl_gk *gk_app_inp, struct gkyl_gyrokinetic_app
tsinp.shift_func_ctx = app->gk_geom->parallel_upper_bc_shift_ctx;
}

gks->bc_ts_up = gkyl_bc_twistshift_new(&tsinp);
gks->bc_ts_up = gkyl_bc_twistshift_inew(&tsinp);
}
else if ( (gks->upper_bc[d].type == GKYL_BC_GK_SPECIES_COPY) ||
(gks->upper_bc[d].type == GKYL_BC_GK_SPECIES_ABSORB) ||
Expand Down Expand Up @@ -999,10 +999,10 @@ gk_species_init_dynamic(struct gkyl_gk *gk_app_inp, struct gkyl_gyrokinetic_app
.shear_dir = 0, // shift varies with x.
.edge = GKYL_LOWER_EDGE,
.cdim = cdim,
.bcdir_ext_update_r = gks->local_par_ext_core,
.bcdir_ext_update_r = &gks->local_par_ext_core,
.num_ghost = ghost,
.basis = gks->basis,
.grid = gks->grid,
.basis = &gks->basis,
.grid = &gks->grid,
.use_gpu = app->use_gpu,
};
if (app->gk_geom->geometry_id == GKYL_GEOMETRY_TOKAMAK)
Expand All @@ -1011,18 +1011,18 @@ gk_species_init_dynamic(struct gkyl_gk *gk_app_inp, struct gkyl_gyrokinetic_app
tsinp_lo.shift_func = app->gk_geom->parallel_lower_bc_shift_func;
tsinp_lo.shift_func_ctx = app->gk_geom->parallel_lower_bc_shift_ctx;
}
gks->bc_ts_lo = gkyl_bc_twistshift_new(&tsinp_lo);
gks->bc_ts_lo = gkyl_bc_twistshift_inew(&tsinp_lo);

struct gkyl_bc_twistshift_inp tsinp_up = {
.bc_dir = par_dir,
.shift_dir = 1, // y shift.
.shear_dir = 0, // shift varies with x.
.edge = GKYL_UPPER_EDGE,
.cdim = cdim,
.bcdir_ext_update_r = gks->local_par_ext_core,
.bcdir_ext_update_r = &gks->local_par_ext_core,
.num_ghost = ghost,
.basis = gks->basis,
.grid = gks->grid,
.basis = &gks->basis,
.grid = &gks->grid,
.use_gpu = app->use_gpu,
};
if (app->gk_geom->geometry_id == GKYL_GEOMETRY_TOKAMAK)
Expand All @@ -1031,7 +1031,7 @@ gk_species_init_dynamic(struct gkyl_gk *gk_app_inp, struct gkyl_gyrokinetic_app
tsinp_up.shift_func = app->gk_geom->parallel_upper_bc_shift_func;
tsinp_up.shift_func_ctx = app->gk_geom->parallel_upper_bc_shift_ctx;
}
gks->bc_ts_up = gkyl_bc_twistshift_new(&tsinp_up);
gks->bc_ts_up = gkyl_bc_twistshift_inew(&tsinp_up);
}

// Set function pointers.
Expand Down
5 changes: 4 additions & 1 deletion gyrokinetic/apps/gk_species_bflux.c
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Expand Up @@ -688,8 +688,11 @@ gk_species_bflux_init(struct gkyl_gyrokinetic_app *app, void *species,
bflux->eqns = gkyl_malloc(bflux->num_eqns*sizeof(struct gkyl_dg_eqn *));

int eqc = 0;
if (gk_s->collisionless.collisionless_id)
if (gk_s->collisionless.collisionless_id == GKYL_GK_COLLISIONLESS_PASSIVE)
bflux->eqns[eqc++] = gkyl_dg_updater_gyrokinetic_passive_acquire_eqn(gk_s->collisionless.passive_slvr);
else if (gk_s->collisionless.collisionless_id)
bflux->eqns[eqc++] = gkyl_dg_updater_gyrokinetic_acquire_eqn(gk_s->collisionless.slvr);

if (gk_s->anom_diff.anom_diff_id)
bflux->eqns[eqc++] = gkyl_dg_updater_gk_anomalous_diffusion_acquire_eqn(gk_s->anom_diff.slvr);

Expand Down
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