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4 HONEE is controlled via command-line options.
7 :::{list-table} Common Runtime Options
8 :header-rows: 1
10 * - Option
11 - Description
12 - Default value
14 * - `-ceed`
15 - CEED resource specifier
16 - `/cpu/self/opt/blocked`
18 * - `-problem`
19 …- Problem to solve (`advection`, `density_current`, `euler_vortex`, `shocktube`, `blasius`, `chann…
20 - `density_current`
22 * - `-implicit`
23 - Use implicit time integrator formulation
24 -
26 * - `-degree`
27 - Polynomial degree of tensor product basis (must be >= 1)
28 - `1`
30 * - `-q_extra`
31 - Number of extra quadrature points
32 - `0`
34 * - `-ts_monitor_wall_force`
35 …- Viewer for the force on each no-slip wall, e.g., `ascii:force.csv:ascii_csv` to write a CSV file.
36 -
38 * - `-ts_monitor_total_kinetic_energy`
39 …- Viewer for the total kinetic energy in the domain and other terms, e.g., `ascii:total_ke.csv:asc…
40 -
42 * - `-ts_monitor_total_kinetic_energy_interval`
43 - Number of timesteps between calculating and printing the total kinetic energy
44 - `1`
46 * - `-ts_monitor_cfl`
47 - Viewer for the min/max CFL in the domain e.g., `ascii:cfl.csv:ascii_csv` to write a CSV file.
48 -
50 * - `-ts_monitor_cfl_interval`
51 - Number of timesteps between calculating and printing the min/max CFL
52 - `1`
54 * - `-honee_check_step_interval`
55 …- Number of time steps between checking the solution for Nans. Negative interval indicates it will…
56 - `-1`
58 * - `-honee_max_wall_time_duration`
59 …- Wall clock duration of simulation before it should be stopped. Acceptable formats are `hh`, `hh:…
60 - `'0'`
62 * - `-honee_max_wall_time_buffer`
63 - Approximate time required to exit simulation cleanly (write checkpoints, etc.)
64 - `'00:01'`
66 * - `-honee_max_wall_time_interval`
67 …- Number of time steps between checking whether simulation should stop based on `-honee_max_wall_t…
68 - `1`
70 * - `-mesh_transform`
71 - Transform the mesh, usually for an initial box mesh.
72 - `none`
74 * - `-help`
75 - View comprehensive information about run-time options
76 -
79 ### File I/O Options
81 :::{list-table} File I/O Options
82 :header-rows: 1
84 * - Option
85 - Description
86 - Default value
88 * - `-dm_plex_filename`
89 - Filename of mesh file to load in
90 -
92 * - `-ts_monitor_solution`
93 - PETSc output format, such as `cgns:output-%d.cgns` (requires PETSc `--download-cgns`)
94 -
96 * - `-ts_monitor_solution_interval`
97 - Number of time steps between visualization output frames.
98 - `1`
100 * - `-viewer_cgns_batch_size`
101 - Number of frames written per CGNS file if the CGNS file name includes a format specifier (`%d`).
102 - `20`
104 * - `-checkpoint_interval`
105 …- Number of steps between writing binary checkpoints. `0` has no output, `-1` outputs final state …
106 - `0`
108 * - `-checkpoint_vtk`
109 …- Checkpoints include VTK (`*.vtu`) files for visualization. Consider `-ts_monitor_solution`instea…
110 - `false`
112 * - `-viz_refine`
113 - Use regular refinement for VTK visualization
114 - `0`
116 * - `-output_dir`
117 - Output directory for binary checkpoints and VTK files (if enabled).
118 - `.`
120 * - `-output_add_stepnum2bin`
121 - Whether to add step numbers to output binary files
122 - `false`
124 * - `-continue_filename`
125 - Path to file from which to continue from. Either binary file or CGNS
126 -
128 * - `-ts_eval_times`
129 …- Sets intermediate time points to evaluate the solution at. See [PETSc documentation](https://pet…
130 -
132 * - `-ts_eval_solutions_view`
133 - PETSc output format for `-ts_eval_times` solutions to be written to
134 -
138 Note that to use `-continue_filename` with CGNS files, the same file must be used with `-dm_plex_fi…
142 :::{list-table} Testing Options
143 :header-rows: 1
145 * - Option
146 - Description
147 - Default value
149 * - `-test_type`
150 …- Run in test mode and specify whether solution (`solver`) or turbulent statistics (`turb_spanstat…
151 - `none`
153 * - `-compare_final_state_atol`
154 - Test absolute tolerance
155 - `1E-11`
157 * - `-compare_final_state_filename`
158 - Test filename
159 -
161 * - `-newtonian_unit_tests`
162 - Run unit tests of Newtonian state variable transformation functions
163 - `false`
165 * - `-riemann_solver_unit_tests`
166 - Run unit tests of Riemann problem solver and it's Jacobian
167 - `false`
174 :::{list-table} Logging Options
175 :header-rows: 1
177 * - Option
178 - Description
179 - Default value
181 * - `-ts_pre_view`
182 - View PETSc `TS` solver configuration before it begins it's solve
183 -
185 * - `-mass_ksp_view_pre_ts_solve`
186 - View mass KSP once before `TSSolve()` is called
187 -
189 * - `-ts_monitor`
190 - View log for every timestep taken by the `TS` solver
191 -
193 * - `-snes_monitor`
194 - View log for every iteration taken by the `SNES` solver
195 -
197 * - `-snes_converged_reason`
198 - View convergence reason for every iteration taken by the `SNES` solver
199 -
201 * - `-ksp_converged_reason`
202 - View convergence reason for every iteration taken by the `KSP` solver
203 -
205 * - `-log_view`
206 - View PETSc performance log
207 -
209 * - `-ksp_post_solve_residual`
210 - Print KSP residual summary information after each
211 -
222 :::{list-table} Nondimensionalization Options
223 :header-rows: 1
225 * - Option
226 - Description
227 - Default value
229 * - `-units_meter`
230 - 1 meter in scaled length units
231 - `1`
233 * - `-units_second`
234 - 1 second in scaled time units
235 - `1`
237 * - `-units_kilogram`
238 - 1 kilogram in scaled mass units
239 - `1`
241 * - `-units_Kelvin`
242 - 1 Kelvin in scaled temperature units
243 - `1`
246 (bc-flags)=
249 :::{list-table} Boundary Condition Options
250 :header-rows: 1
252 * - Option
253 - Description
255 * - `-bc_wall`
256 - Use wall boundary conditions on this list of faces
258 * - `-wall_comps`
259 - An array of constrained component numbers for wall BCs
261 * - `-bc_slip`
262 - Use weak slip boundary condition on this list of faces
264 * - `-bc_symmetry_x`
265 - Use symmetry boundary conditions, for the x component, on this list of faces
267 * - `-bc_symmetry_y`
268 - Use symmetry boundary conditions, for the y component, on this list of faces
270 * - `-bc_symmetry_z`
271 - Use symmetry boundary conditions, for the z component, on this list of faces
273 * - `-bc_inflow`
274 - Use inflow boundary conditions on this list of faces
276 * - `-bc_outflow`
277 - Use outflow boundary conditions on this list of faces
279 * - `-bc_freestream`
280 - Use freestream boundary conditions on this list of faces
283 …ndices to be used with `-bc_wall`, `bc_inflow`, `bc_outflow`, `bc_freestream` and/or `-bc_symmetr…
285 :::{list-table} 2D Face ID Labels
286 :header-rows: 1
287 * - PETSc Face Name
288 - Cartesian direction
289 - Face ID
291 * - faceMarkerBottom
292 - -z
293 - 1
295 * - faceMarkerRight
296 - +x
297 - 2
299 * - faceMarkerTop
300 - +z
301 - 3
303 * - faceMarkerLeft
304 - -x
305 - 4
308 :::{list-table} 3D Face ID Labels
309 :header-rows: 1
310 * - PETSc Face Name
311 - Cartesian direction
312 - Face ID
314 * - faceMarkerBottom
315 - -z
316 - 1
318 * - faceMarkerTop
319 - +z
320 - 2
322 * - faceMarkerFront
323 - -y
324 - 3
326 * - faceMarkerBack
327 - +y
328 - 4
330 * - faceMarkerRight
331 - +x
332 - 5
334 * - faceMarkerLeft
335 - -x
336 - 6
350 Use `bc_inflow` and see {ref}`example-blasius` and discussion of synthetic turbulence generation fo…
359 …ile the simpler HLL converts thermal structures exiting the domain into grid-scale reflecting acou…
363 …ure`, requires that the flow be a strict outflow (or the problem becomes ill-posed and the solver …
365 The `pressure` variant is retained to facilitate comparison with other codes, such as PHASTA-C, but…
380 The coordinates for such cases are stored as a new field with special cell-based indexing to enable…
394 The `zbox` method uses [Z-ordering](https://en.wikipedia.org/wiki/Z-order_curve) to construct the m…
398 For the Density Current, Channel, and Blasius problems, the following common command-line options a…
400 :::{list-table} Newtonian Ideal Gas problems Runtime Options
401 :header-rows: 1
403 * - Option
404 - Description
405 - Default value
406 - Unit
408 * - `-stab`
409 - Stabilization method (`none`, `su`, or `supg`)
410 - `none`
411 -
413 * - `-Ctau_t`
414 - Stabilization time constant, $C_t$
415 - `1.0`
416 -
418 * - `-Ctau_v`
419 - Stabilization viscous constant, $C_v$
420 - `36, 60, 128 for degree = 1, 2, 3`
421 -
423 * - `-Ctau_C`
424 - Stabilization continuity constant, $C_c$
425 - `1.0`
426 -
428 * - `-Ctau_M`
429 - Stabilization momentum constant, $C_m$
430 - `1.0`
431 -
433 * - `-Ctau_E`
434 - Stabilization energy constant, $C_E$
435 - `1.0`
436 -
438 * - `-div_diff_flux_projection_method`
439 …- Method used to calculate divergence of diffusive flux projection (`none`, `direct`, or `indirect…
440 - `none`
441 -
443 * - `-div_diff_flux_projection_ksp*`
444 - Control the KSP object for the projection of the divergence of diffusive flux
445 - N/A
446 -
448 * - `-cv`
449 - Heat capacity at constant volume
450 - `717`
451 - `J/(kg K)`
453 * - `-cp`
454 - Heat capacity at constant pressure
455 - `1004`
456 - `J/(kg K)`
458 * - `-gravity`
459 - Gravitational acceleration vector
460 - `0,0,0`
461 - `m/s^2`
463 * - `-lambda`
464 - Stokes hypothesis second viscosity coefficient
465 - `-2/3`
466 -
468 * - `-mu`
469 - Shear dynamic viscosity coefficient
470 - `1.8e-5`
471 - `Pa s`
473 * - `-k`
474 - Thermal conductivity
475 - `0.02638`
476 - `W/(m K)`
478 * - `-state_var`
479 …- State variables to solve solution with. `conservative` ($\rho, \rho \bm{u}, \rho e$), `primitive…
480 - `conservative`
481 - string