xref: /libCEED/examples/fluids/README.md (revision 9f84436874b0bedcb473aab1faa446b08959d274)
1ccaff030SJeremy L Thompson## libCEED: Navier-Stokes Example
2ccaff030SJeremy L Thompson
3ccaff030SJeremy L ThompsonThis page provides a description of the Navier-Stokes example for the libCEED library, based on PETSc.
4b8962995SJeremy L ThompsonPETSc v3.17 or a development version of PETSc at commit 0e95d842 or later is required.
5ccaff030SJeremy L Thompson
677841947SLeila GhaffariThe Navier-Stokes problem solves the compressible Navier-Stokes equations in three dimensions using an explicit time integration.
777841947SLeila GhaffariThe state variables are mass density, momentum density, and energy density.
8ccaff030SJeremy L Thompson
977841947SLeila GhaffariThe main Navier-Stokes solver for libCEED is defined in [`navierstokes.c`](navierstokes.c) with different problem definitions according to the application of interest.
10ccaff030SJeremy L Thompson
113b219b86SJames Wright## Build instructions
123b219b86SJames Wright
13bc7bbd5dSLeila GhaffariBuild by using:
14ccaff030SJeremy L Thompson
15ccaff030SJeremy L Thompson`make`
16ccaff030SJeremy L Thompson
17bc7bbd5dSLeila Ghaffariand run with:
18ccaff030SJeremy L Thompson
19bc7bbd5dSLeila Ghaffari```
20bc7bbd5dSLeila Ghaffari./navierstokes -ceed [ceed] -problem [problem type] -degree [degree]
21bc7bbd5dSLeila Ghaffari```
22ccaff030SJeremy L Thompson
233b219b86SJames WrightIf you want to do *in situ* machine-learning training, specify `SMARTREDIS_DIR` in the make command like:
243b219b86SJames Wright
253b219b86SJames Wright```
263b219b86SJames Wrightmake SMARTREDIS_DIR=~/software/smartredis/install
273b219b86SJames Wright```
283b219b86SJames Wright
29bc7bbd5dSLeila Ghaffari## Runtime options
30ccaff030SJeremy L Thompson
31bc7bbd5dSLeila Ghaffari% inclusion-fluids-marker
32ccaff030SJeremy L Thompson
33bc7bbd5dSLeila GhaffariThe Navier-Stokes mini-app is controlled via command-line options.
34bc7bbd5dSLeila GhaffariThe following options are common among all problem types:
35ccaff030SJeremy L Thompson
36bc7bbd5dSLeila Ghaffari:::{list-table} Common Runtime Options
37bc7bbd5dSLeila Ghaffari:header-rows: 1
38ccaff030SJeremy L Thompson
39bc7bbd5dSLeila Ghaffari* - Option
40bc7bbd5dSLeila Ghaffari  - Description
41bc7bbd5dSLeila Ghaffari  - Default value
42ccaff030SJeremy L Thompson
43bc7bbd5dSLeila Ghaffari* - `-ceed`
44bc7bbd5dSLeila Ghaffari  - CEED resource specifier
45bc7bbd5dSLeila Ghaffari  - `/cpu/self/opt/blocked`
46ccaff030SJeremy L Thompson
473866774cSJames Wright* - `-test_type`
483866774cSJames Wright  - Run in test mode and specify whether solution (`solver`) or turbulent statistics (`turb_spanstats`) output should be verified
493866774cSJames Wright  - `none`
50ccaff030SJeremy L Thompson
51bc7bbd5dSLeila Ghaffari* - `-compare_final_state_atol`
52bc7bbd5dSLeila Ghaffari  - Test absolute tolerance
53bc7bbd5dSLeila Ghaffari  - `1E-11`
54ccaff030SJeremy L Thompson
55bc7bbd5dSLeila Ghaffari* - `-compare_final_state_filename`
56bc7bbd5dSLeila Ghaffari  - Test filename
57bc7bbd5dSLeila Ghaffari  -
58ccaff030SJeremy L Thompson
59bc7bbd5dSLeila Ghaffari* - `-problem`
609e529eadSJames Wright  - Problem to solve (`advection`, `density_current`, `euler_vortex`, `shocktube`, `blasius`, `channel`, `gaussian_wave`, and `taylor_green`)
61bc7bbd5dSLeila Ghaffari  - `density_current`
62ccaff030SJeremy L Thompson
63bc7bbd5dSLeila Ghaffari* - `-implicit`
649e576805SJames Wright  - Use implicit time integrator formulation
65bc7bbd5dSLeila Ghaffari  -
66ccaff030SJeremy L Thompson
67bc7bbd5dSLeila Ghaffari* - `-degree`
68bc7bbd5dSLeila Ghaffari  - Polynomial degree of tensor product basis (must be >= 1)
69bc7bbd5dSLeila Ghaffari  - `1`
70ccaff030SJeremy L Thompson
712288fb52SJeremy L Thompson* - `-q_extra`
72bc7bbd5dSLeila Ghaffari  - Number of extra quadrature points
73fc14f3f6SLeila Ghaffari  - `0`
74ccaff030SJeremy L Thompson
7537cbb16aSJed Brown* - `-ts_monitor_solution`
7637cbb16aSJed Brown  - PETSc output format, such as `cgns:output-%d.cgns` (requires PETSc `--download-cgns`)
7737cbb16aSJed Brown  -
78ccaff030SJeremy L Thompson
7937cbb16aSJed Brown* - `-ts_monitor_solution_interval`
8037cbb16aSJed Brown  - Number of time steps between visualization output frames.
8137cbb16aSJed Brown  - `1`
8237cbb16aSJed Brown
8337cbb16aSJed Brown* - `-viewer_cgns_batch_size`
8437cbb16aSJed Brown  - Number of frames written per CGNS file if the CGNS file name includes a format specifier (`%d`).
8537cbb16aSJed Brown  - `20`
8637cbb16aSJed Brown
8737cbb16aSJed Brown* - `-checkpoint_interval`
8837cbb16aSJed Brown  - Number of steps between writing binary checkpoints. `0` has no output, `-1` outputs final state only
89bc7bbd5dSLeila Ghaffari  - `10`
90ccaff030SJeremy L Thompson
9137cbb16aSJed Brown* - `-checkpoint_vtk`
9237cbb16aSJed Brown  - Checkpoints include VTK (`*.vtu`) files for visualization. Consider `-ts_monitor_solution`instead.
9337cbb16aSJed Brown  - `false`
9437cbb16aSJed Brown
9537cbb16aSJed Brown* - `-viz_refine`
9637cbb16aSJed Brown  - Use regular refinement for VTK visualization
9737cbb16aSJed Brown  - `0`
9837cbb16aSJed Brown
99bc7bbd5dSLeila Ghaffari* - `-output_dir`
10037cbb16aSJed Brown  - Output directory for binary checkpoints and VTK files (if enabled).
101bc7bbd5dSLeila Ghaffari  - `.`
102ccaff030SJeremy L Thompson
10369293791SJames Wright* - `-output_add_stepnum2bin`
10469293791SJames Wright  - Whether to add step numbers to output binary files
10569293791SJames Wright  - `false`
10669293791SJames Wright
10769293791SJames Wright* - `-continue`
10869293791SJames Wright  - Continue from previous solution (input is step number of previous solution)
10969293791SJames Wright  - `0`
11069293791SJames Wright
11169293791SJames Wright* - `-continue_filename`
11269293791SJames Wright  - Path to solution binary file from which to continue from
11369293791SJames Wright  - `[output_dir]/ns-solution.bin`
11469293791SJames Wright
11569293791SJames Wright* - `-continue_time_filename`
1164de8550aSJed Brown  - Path to time stamp binary file (only for legacy checkpoints)
11769293791SJames Wright  - `[output_dir]/ns-time.bin`
11869293791SJames Wright
1194534a52eSLeila Ghaffari* - `-bc_wall`
1204534a52eSLeila Ghaffari  - Use wall boundary conditions on this list of faces
1214534a52eSLeila Ghaffari  -
1224534a52eSLeila Ghaffari
1234534a52eSLeila Ghaffari* - `-wall_comps`
1244534a52eSLeila Ghaffari  - An array of constrained component numbers for wall BCs
1254534a52eSLeila Ghaffari  -
1264534a52eSLeila Ghaffari
127*9f844368SJames Wright* - `-bc_slip`
128*9f844368SJames Wright  - Use weak slip boundary condition on this list of faces
129*9f844368SJames Wright  -
130*9f844368SJames Wright
1317c5bba50SJames Wright* - `-bc_symmetry_x`
1327c5bba50SJames Wright  - Use symmetry boundary conditions, for the x component, on this list of faces
1334534a52eSLeila Ghaffari  -
1344534a52eSLeila Ghaffari
1357c5bba50SJames Wright* - `-bc_symmetry_y`
1367c5bba50SJames Wright  - Use symmetry boundary conditions, for the y component, on this list of faces
1374534a52eSLeila Ghaffari  -
1384534a52eSLeila Ghaffari
1397c5bba50SJames Wright* - `-bc_symmetry_z`
1407c5bba50SJames Wright  - Use symmetry boundary conditions, for the z component, on this list of faces
1414534a52eSLeila Ghaffari  -
1424534a52eSLeila Ghaffari
1434534a52eSLeila Ghaffari* - `-bc_inflow`
1444534a52eSLeila Ghaffari  - Use inflow boundary conditions on this list of faces
1454534a52eSLeila Ghaffari  -
1464534a52eSLeila Ghaffari
1474534a52eSLeila Ghaffari* - `-bc_outflow`
1484534a52eSLeila Ghaffari  - Use outflow boundary conditions on this list of faces
1494534a52eSLeila Ghaffari  -
15089d0f5c0SLeila Ghaffari
1517ec884f8SJames Wright* - `-bc_freestream`
1527ec884f8SJames Wright  - Use freestream boundary conditions on this list of faces
1537ec884f8SJames Wright  -
1547ec884f8SJames Wright
155b7d66439SJames Wright* - `-ts_monitor_turbulence_spanstats_collect_interval`
156ee3de563SJames Wright  - Number of timesteps between statistics collection
157ee3de563SJames Wright  - `1`
158ee3de563SJames Wright
159b7d66439SJames Wright* - `-ts_monitor_turbulence_spanstats_viewer`
160b7d66439SJames Wright  - Sets the PetscViewer for the statistics file writing, such as `cgns:output-%d.cgns` (requires PETSc `--download-cgns`). Also turns the statistics collection on.
1618ed52730SJames Wright  -
1628ed52730SJames Wright
163b7d66439SJames Wright* - `-ts_monitor_turbulence_spanstats_viewer_interval`
164ee3de563SJames Wright  - Number of timesteps between statistics file writing (`-1` means only at end of run)
165ee3de563SJames Wright  - `-1`
166ee3de563SJames Wright
167b7d66439SJames Wright* - `-ts_monitor_turbulence_spanstats_viewer_cgns_batch_size`
1688ed52730SJames Wright  - Number of frames written per CGNS file if the CGNS file name includes a format specifier (`%d`).
1698ed52730SJames Wright  - `20`
1708ed52730SJames Wright
171ca69d878SAdeleke O. Bankole* - `-ts_monitor_wall_force`
172ca69d878SAdeleke O. Bankole  - Viewer for the force on each no-slip wall, e.g., `ascii:force.csv:ascii_csv` to write a CSV file.
173ca69d878SAdeleke O. Bankole  -
174ca69d878SAdeleke O. Bankole
1752526956eSJames Wright* - `-mesh_transform`
1762526956eSJames Wright  - Transform the mesh, usually for an initial box mesh.
1772526956eSJames Wright  - `none`
1782526956eSJames Wright
179bc7bbd5dSLeila Ghaffari* - `-snes_view`
180bc7bbd5dSLeila Ghaffari  - View PETSc `SNES` nonlinear solver configuration
181bc7bbd5dSLeila Ghaffari  -
18289d0f5c0SLeila Ghaffari
183bc7bbd5dSLeila Ghaffari* - `-log_view`
184bc7bbd5dSLeila Ghaffari  - View PETSc performance log
185bc7bbd5dSLeila Ghaffari  -
186ccaff030SJeremy L Thompson
187bc7bbd5dSLeila Ghaffari* - `-help`
188bc7bbd5dSLeila Ghaffari  - View comprehensive information about run-time options
189bc7bbd5dSLeila Ghaffari  -
190bc7bbd5dSLeila Ghaffari:::
191ccaff030SJeremy L Thompson
1927c5bba50SJames WrightFor the case of a square/cubic mesh, the list of face indices to be used with `-bc_wall`, `bc_inflow`, `bc_outflow`, `bc_freestream`  and/or `-bc_symmetry_x`, `-bc_symmetry_y`, and `-bc_symmetry_z` are:
1934534a52eSLeila Ghaffari
19488626eedSJames Wright:::{list-table} 2D Face ID Labels
19588626eedSJames Wright:header-rows: 1
19688626eedSJames Wright* - PETSc Face Name
19788626eedSJames Wright  - Cartesian direction
19888626eedSJames Wright  - Face ID
19988626eedSJames Wright
20088626eedSJames Wright* - faceMarkerBottom
20188626eedSJames Wright  - -z
20288626eedSJames Wright  - 1
20388626eedSJames Wright
20488626eedSJames Wright* - faceMarkerRight
20588626eedSJames Wright  - +x
20688626eedSJames Wright  - 2
20788626eedSJames Wright
20888626eedSJames Wright* - faceMarkerTop
20988626eedSJames Wright  - +z
21088626eedSJames Wright  - 3
21188626eedSJames Wright
21288626eedSJames Wright* - faceMarkerLeft
21388626eedSJames Wright  - -x
21488626eedSJames Wright  - 4
21588626eedSJames Wright:::
21688626eedSJames Wright
217b5e826a6SLeila Ghaffari:::{list-table} 3D Face ID Labels
21888626eedSJames Wright:header-rows: 1
21988626eedSJames Wright* - PETSc Face Name
22088626eedSJames Wright  - Cartesian direction
22188626eedSJames Wright  - Face ID
22288626eedSJames Wright
22388626eedSJames Wright* - faceMarkerBottom
22488626eedSJames Wright  - -z
22588626eedSJames Wright  - 1
22688626eedSJames Wright
22788626eedSJames Wright* - faceMarkerTop
22888626eedSJames Wright  - +z
22988626eedSJames Wright  - 2
23088626eedSJames Wright
23188626eedSJames Wright* - faceMarkerFront
23288626eedSJames Wright  - -y
23388626eedSJames Wright  - 3
23488626eedSJames Wright
23588626eedSJames Wright* - faceMarkerBack
23688626eedSJames Wright  - +y
23788626eedSJames Wright  - 4
23888626eedSJames Wright
23988626eedSJames Wright* - faceMarkerRight
24088626eedSJames Wright  - +x
24188626eedSJames Wright  - 5
24288626eedSJames Wright
24388626eedSJames Wright* - faceMarkerLeft
24488626eedSJames Wright  - -x
24588626eedSJames Wright  - 6
24688626eedSJames Wright:::
2474534a52eSLeila Ghaffari
2488a94a473SJed Brown### Boundary conditions
2498a94a473SJed Brown
2503b219b86SJames WrightBoundary conditions for compressible viscous flows are notoriously tricky.
2513b219b86SJames WrightHere we offer some recommendations.
2528a94a473SJed Brown
2538a94a473SJed Brown#### Inflow
2548a94a473SJed Brown
2558a94a473SJed BrownIf in a region where the flow velocity is known (e.g., away from viscous walls), use `bc_freestream`, which solves a Riemann problem and can handle inflow and outflow (simultaneously and dynamically).
2568a94a473SJed BrownIt is stable and the least reflective boundary condition for acoustics.
2578a94a473SJed Brown
2588a94a473SJed BrownIf near a viscous wall, you may want a specified inflow profile.
2598a94a473SJed BrownUse `bc_inflow` and see {ref}`example-blasius` and discussion of synthetic turbulence generation for ways to analytically generate developed inflow profiles.
2608a94a473SJed BrownThese conditions may be either weak or strong, with the latter specifying velocity and temperature as essential boundary conditions and evaluating a boundary integral for the mass flux.
2618a94a473SJed BrownThe strong approach gives sharper resolution of velocity structures.
2628a94a473SJed BrownWe have described the primitive variable formulation here; the conservative variants are similar, but not equivalent.
2638a94a473SJed Brown
264f3f66076SJames Wright#### Outflow
2658a94a473SJed Brown
2668a94a473SJed BrownIf you know the complete exterior state, `bc_freestream` is the least reflective boundary condition, but is disruptive to viscous flow structures.
2678a94a473SJed BrownIf thermal anomalies must exit the domain, the Riemann solver must resolve the contact wave to avoid reflections.
2688a94a473SJed BrownThe default Riemann solver, HLLC, is sufficient in this regard while the simpler HLL converts thermal structures exiting the domain into grid-scale reflecting acoustics.
2698a94a473SJed Brown
2708a94a473SJed BrownIf acoustic reflections are not a concern and/or the flow is impacted by walls or interior structures that you wish to resolve to near the boundary, choose `bc_outflow`. This condition (with default `outflow_type: riemann`) is stable for both inflow and outflow, so can be used in areas that have recirculation and lateral boundaries in which the flow fluctuates.
2718a94a473SJed Brown
2728a94a473SJed BrownThe simpler `bc_outflow` variant, `outflow_type: pressure`, requires that the flow be a strict outflow (or the problem becomes ill-posed and the solver will diverge).
2738a94a473SJed BrownIn our experience, `riemann` is slightly less reflective but produces similar flows in cases of strict outflow.
2748a94a473SJed BrownThe `pressure` variant is retained to facilitate comparison with other codes, such as PHASTA-C, but we recommend `riemann` for general use.
2758a94a473SJed Brown
276f3f66076SJames Wright#### Periodicity
2778a94a473SJed Brown
2788a94a473SJed BrownPETSc provides two ways to specify periodicity:
2798a94a473SJed Brown
2808a94a473SJed Brown1. Topological periodicity, in which the donor and receiver dofs are the same, obtained using:
2818a94a473SJed Brown
2828a94a473SJed Brown```yaml
2838a94a473SJed Browndm_plex:
2848a94a473SJed Brown  shape: box
2858a94a473SJed Brown  box_faces: 10,12,4
2868a94a473SJed Brown  box_bd: none,none,periodic
2878a94a473SJed Brown```
2888a94a473SJed Brown
289ca69d878SAdeleke O. BankoleThe coordinates for such cases are stored as a new field with special cell-based indexing to enable wrapping through the boundary.
290ca69d878SAdeleke O. BankoleThis choice of coordinates prevents evaluating boundary integrals that cross the periodicity, such as for the outflow Riemann problem in the presence of spanwise periodicity.
291ca69d878SAdeleke O. Bankole
292ca69d878SAdeleke O. Bankole2. Isoperiodicity, in which the donor and receiver dofs are distinct in local vectors. This is obtained using `zbox`, as in:
293ca69d878SAdeleke O. Bankole
294ca69d878SAdeleke O. Bankole```yaml
295ca69d878SAdeleke O. Bankoledm_plex:
296ca69d878SAdeleke O. Bankole  shape: zbox
297ca69d878SAdeleke O. Bankole  box_faces: 10,12,4
298ca69d878SAdeleke O. Bankole  box_bd: none,none,periodic
299ca69d878SAdeleke O. Bankole```
300ca69d878SAdeleke O. Bankole
301ca69d878SAdeleke O. BankoleIsoperiodicity enables standard boundary integrals, and is recommended for general use.
302ca69d878SAdeleke O. BankoleAt the time of this writing, it only supports one direction of periodicity.
303ca69d878SAdeleke O. BankoleThe `zbox` method uses [Z-ordering](https://en.wikipedia.org/wiki/Z-order_curve) to construct the mesh in parallel and provide an adequate initial partition, which makes it higher performance and avoids needing a partitioning package.
3048a94a473SJed Brown
305019b7682STimothy Aiken### Advection
306019b7682STimothy Aiken
30717be3a41SJeremy L ThompsonFor testing purposes, there is a reduced mode for pure advection, which holds density $\rho$ and momentum density $\rho \bm u$ constant while advecting "total energy density" $E$.
3089e529eadSJames WrightThe advection problems can be run in both 2D and 3D, based on the DM defined for the problem.
30994a05c6fSJames WrightThe following additional command-line options are available:
310019b7682STimothy Aiken
31194a05c6fSJames Wright:::{list-table} Advection Runtime Options
312bc7bbd5dSLeila Ghaffari:header-rows: 1
313e43605a5SLeila Ghaffari
314bc7bbd5dSLeila Ghaffari* - Option
315bc7bbd5dSLeila Ghaffari  - Description
316bc7bbd5dSLeila Ghaffari  - Default value
317bc7bbd5dSLeila Ghaffari  - Unit
318e43605a5SLeila Ghaffari
319bc7bbd5dSLeila Ghaffari* - `-rc`
320bc7bbd5dSLeila Ghaffari  - Characteristic radius of thermal bubble
321bc7bbd5dSLeila Ghaffari  - `1000`
322bc7bbd5dSLeila Ghaffari  - `m`
323e43605a5SLeila Ghaffari
324bc7bbd5dSLeila Ghaffari* - `-units_meter`
325bc7bbd5dSLeila Ghaffari  - 1 meter in scaled length units
326bc7bbd5dSLeila Ghaffari  - `1E-2`
327bc7bbd5dSLeila Ghaffari  -
328e43605a5SLeila Ghaffari
329bc7bbd5dSLeila Ghaffari* - `-units_second`
330bc7bbd5dSLeila Ghaffari  - 1 second in scaled time units
331bc7bbd5dSLeila Ghaffari  - `1E-2`
332bc7bbd5dSLeila Ghaffari  -
333e43605a5SLeila Ghaffari
334bc7bbd5dSLeila Ghaffari* - `-units_kilogram`
335bc7bbd5dSLeila Ghaffari  - 1 kilogram in scaled mass units
336bc7bbd5dSLeila Ghaffari  - `1E-6`
337bc7bbd5dSLeila Ghaffari  -
338e43605a5SLeila Ghaffari
339bc7bbd5dSLeila Ghaffari* - `-strong_form`
340bc7bbd5dSLeila Ghaffari  - Strong (1) or weak/integrated by parts (0) residual
341bc7bbd5dSLeila Ghaffari  - `0`
342bc7bbd5dSLeila Ghaffari  -
343e43605a5SLeila Ghaffari
344bc7bbd5dSLeila Ghaffari* - `-stab`
345bc7bbd5dSLeila Ghaffari  - Stabilization method (`none`, `su`, or `supg`)
346bc7bbd5dSLeila Ghaffari  - `none`
347bc7bbd5dSLeila Ghaffari  -
348e43605a5SLeila Ghaffari
349bc7bbd5dSLeila Ghaffari* - `-CtauS`
350bc7bbd5dSLeila Ghaffari  - Scale coefficient for stabilization tau (nondimensional)
351bc7bbd5dSLeila Ghaffari  - `0`
352bc7bbd5dSLeila Ghaffari  -
353e43605a5SLeila Ghaffari
354bc7bbd5dSLeila Ghaffari* - `-wind_type`
355bc7bbd5dSLeila Ghaffari  - Wind type in Advection (`rotation` or `translation`)
356bc7bbd5dSLeila Ghaffari  - `rotation`
357bc7bbd5dSLeila Ghaffari  -
358e43605a5SLeila Ghaffari
359bc7bbd5dSLeila Ghaffari* - `-wind_translation`
360bc7bbd5dSLeila Ghaffari  - Constant wind vector when `-wind_type translation`
361bc7bbd5dSLeila Ghaffari  - `1,0,0`
362bc7bbd5dSLeila Ghaffari  -
363e43605a5SLeila Ghaffari
364bc7bbd5dSLeila Ghaffari* - `-E_wind`
365bc7bbd5dSLeila Ghaffari  - Total energy of inflow wind when `-wind_type translation`
366bc7bbd5dSLeila Ghaffari  - `1E6`
367bc7bbd5dSLeila Ghaffari  - `J`
368e43605a5SLeila Ghaffari
3697b77ddfdSJames Wright* - `-advection_ic_type`
3707b77ddfdSJames Wright  - Initial condition type, from `sphere`, `cylinder`, `cosine_hill`, and `skew`
371f3f66076SJames Wright  - `sphere`
372bc7bbd5dSLeila Ghaffari  -
373e43605a5SLeila Ghaffari
374bc7bbd5dSLeila Ghaffari* - `-bubble_continuity`
3759e529eadSJames Wright  - Different shapes for `sphere` and `cylinder` initial conditions, from `smooth`, `back_sharp`, `thick`, or `cosine`
376bc7bbd5dSLeila Ghaffari  - `smooth`
377bc7bbd5dSLeila Ghaffari  -
378bc7bbd5dSLeila Ghaffari:::
379ccaff030SJeremy L Thompson
38094a05c6fSJames WrightFor 3D advection, an example of the `rotation` mode can be run with:
381ccaff030SJeremy L Thompson
382bc7bbd5dSLeila Ghaffari```
3834534a52eSLeila Ghaffari./navierstokes -problem advection -dm_plex_box_faces 10,10,10 -dm_plex_dim 3 -dm_plex_box_lower 0,0,0 -dm_plex_box_upper 8000,8000,8000 -bc_wall 1,2,3,4,5,6 -wall_comps 4 -wind_type rotation -implicit -stab su
384bc7bbd5dSLeila Ghaffari```
385ccaff030SJeremy L Thompson
386bc7bbd5dSLeila Ghaffariand the `translation` mode with:
387ccaff030SJeremy L Thompson
388bc7bbd5dSLeila Ghaffari```
3894534a52eSLeila Ghaffari./navierstokes -problem advection -dm_plex_box_faces 10,10,10 -dm_plex_dim 3 -dm_plex_box_lower 0,0,0 -dm_plex_box_upper 8000,8000,8000 -wind_type translation -wind_translation .5,-1,0 -bc_inflow 1,2,3,4,5,6
390bc7bbd5dSLeila Ghaffari```
391ccaff030SJeremy L Thompson
39294a05c6fSJames WrightFor 2D advection, an example of the `rotation` mode can be run with:
39394a05c6fSJames Wright
39494a05c6fSJames Wright```
3959e529eadSJames Wright./navierstokes -problem advection -dm_plex_box_faces 20,20 -dm_plex_box_lower 0,0 -dm_plex_box_upper 1000,1000 -bc_wall 1,2,3,4 -wall_comps 4 -wind_type rotation -implicit -stab supg
39694a05c6fSJames Wright```
39794a05c6fSJames Wright
39894a05c6fSJames Wrightand the `translation` mode with:
39994a05c6fSJames Wright
40094a05c6fSJames Wright```
4019e529eadSJames Wright./navierstokes -problem advection -dm_plex_box_faces 20,20 -dm_plex_box_lower 0,0 -dm_plex_box_upper 1000,1000 -units_meter 1e-4 -wind_type translation -wind_translation 1,-.5 -bc_inflow 1,2,3,4
40294a05c6fSJames Wright```
40394a05c6fSJames WrightNote the lengths in `-dm_plex_box_upper` are given in meters, and will be nondimensionalized according to `-units_meter`.
40494a05c6fSJames Wright
405019b7682STimothy Aiken### Inviscid Ideal Gas
406019b7682STimothy Aiken
407019b7682STimothy Aiken#### Isentropic Euler vortex
408019b7682STimothy Aiken
409bc7bbd5dSLeila GhaffariFor the Isentropic Vortex problem, the following additional command-line options are available:
410ccaff030SJeremy L Thompson
411bc7bbd5dSLeila Ghaffari:::{list-table} Isentropic Vortex Runtime Options
412bc7bbd5dSLeila Ghaffari:header-rows: 1
413ccaff030SJeremy L Thompson
414bc7bbd5dSLeila Ghaffari* - Option
415bc7bbd5dSLeila Ghaffari  - Description
416bc7bbd5dSLeila Ghaffari  - Default value
417bc7bbd5dSLeila Ghaffari  - Unit
418ccaff030SJeremy L Thompson
419bc7bbd5dSLeila Ghaffari* - `-center`
420bc7bbd5dSLeila Ghaffari  - Location of vortex center
421bc7bbd5dSLeila Ghaffari  - `(lx,ly,lz)/2`
422bc7bbd5dSLeila Ghaffari  - `(m,m,m)`
423ccaff030SJeremy L Thompson
424bc7bbd5dSLeila Ghaffari* - `-units_meter`
425bc7bbd5dSLeila Ghaffari  - 1 meter in scaled length units
426bc7bbd5dSLeila Ghaffari  - `1E-2`
427bc7bbd5dSLeila Ghaffari  -
428ccaff030SJeremy L Thompson
429bc7bbd5dSLeila Ghaffari* - `-units_second`
430bc7bbd5dSLeila Ghaffari  - 1 second in scaled time units
431bc7bbd5dSLeila Ghaffari  - `1E-2`
432bc7bbd5dSLeila Ghaffari  -
433ccaff030SJeremy L Thompson
434bc7bbd5dSLeila Ghaffari* - `-mean_velocity`
435bc7bbd5dSLeila Ghaffari  - Background velocity vector
436bc7bbd5dSLeila Ghaffari  - `(1,1,0)`
437bc7bbd5dSLeila Ghaffari  -
438ccaff030SJeremy L Thompson
439bc7bbd5dSLeila Ghaffari* - `-vortex_strength`
440bc7bbd5dSLeila Ghaffari  - Strength of vortex < 10
441bc7bbd5dSLeila Ghaffari  - `5`
442bc7bbd5dSLeila Ghaffari  -
443932417b3SJed Brown
444932417b3SJed Brown* - `-c_tau`
445932417b3SJed Brown  - Stabilization constant
446504dc8e0SLeila Ghaffari  - `0.5`
447932417b3SJed Brown  -
448bc7bbd5dSLeila Ghaffari:::
449ccaff030SJeremy L Thompson
450bc7bbd5dSLeila GhaffariThis problem can be run with:
451ccaff030SJeremy L Thompson
452bc7bbd5dSLeila Ghaffari```
4537c5bba50SJames Wright./navierstokes -problem euler_vortex -dm_plex_box_faces 20,20,1 -dm_plex_box_lower 0,0,0 -dm_plex_box_upper 1000,1000,50 -dm_plex_dim 3 -bc_inflow 4,6 -bc_outflow 3,5 -bc_symmetry_z 1,2 -mean_velocity .5,-.8,0.
454bc7bbd5dSLeila Ghaffari```
455ccaff030SJeremy L Thompson
456019b7682STimothy Aiken#### Sod shock tube
457019b7682STimothy Aiken
458019b7682STimothy AikenFor the Shock Tube problem, the following additional command-line options are available:
459019b7682STimothy Aiken
460019b7682STimothy Aiken:::{list-table} Shock Tube Runtime Options
461019b7682STimothy Aiken:header-rows: 1
462019b7682STimothy Aiken
463019b7682STimothy Aiken* - Option
464019b7682STimothy Aiken  - Description
465019b7682STimothy Aiken  - Default value
466019b7682STimothy Aiken  - Unit
467019b7682STimothy Aiken
468019b7682STimothy Aiken* - `-units_meter`
469019b7682STimothy Aiken  - 1 meter in scaled length units
470019b7682STimothy Aiken  - `1E-2`
471019b7682STimothy Aiken  -
472019b7682STimothy Aiken
473019b7682STimothy Aiken* - `-units_second`
474019b7682STimothy Aiken  - 1 second in scaled time units
475019b7682STimothy Aiken  - `1E-2`
476019b7682STimothy Aiken  -
477019b7682STimothy Aiken
478019b7682STimothy Aiken* - `-yzb`
479019b7682STimothy Aiken  - Use YZB discontinuity capturing
480019b7682STimothy Aiken  - `none`
481019b7682STimothy Aiken  -
482019b7682STimothy Aiken
483019b7682STimothy Aiken* - `-stab`
484019b7682STimothy Aiken  - Stabilization method (`none`, `su`, or `supg`)
485019b7682STimothy Aiken  - `none`
486019b7682STimothy Aiken  -
487019b7682STimothy Aiken:::
488019b7682STimothy Aiken
489019b7682STimothy AikenThis problem can be run with:
490019b7682STimothy Aiken
491019b7682STimothy Aiken```
4927c5bba50SJames Wright./navierstokes -problem shocktube -yzb -stab su -bc_symmetry_z 3,4 -bc_symmetry_y 1,2 -bc_wall 5,6 -dm_plex_dim 3 -dm_plex_box_lower 0,0,0 -dm_plex_box_upper 1000,100,100 -dm_plex_box_faces 200,1,1 -units_second 0.1
493019b7682STimothy Aiken```
494019b7682STimothy Aiken
495019b7682STimothy Aiken### Newtonian viscosity, Ideal Gas
496019b7682STimothy Aiken
49788626eedSJames WrightFor the Density Current, Channel, and Blasius problems, the following common command-line options are available:
498ccaff030SJeremy L Thompson
49988626eedSJames Wright:::{list-table} Newtonian Ideal Gas problems Runtime Options
500bc7bbd5dSLeila Ghaffari:header-rows: 1
501ccaff030SJeremy L Thompson
502bc7bbd5dSLeila Ghaffari* - Option
503bc7bbd5dSLeila Ghaffari  - Description
504bc7bbd5dSLeila Ghaffari  - Default value
505bc7bbd5dSLeila Ghaffari  - Unit
506ccaff030SJeremy L Thompson
507bc7bbd5dSLeila Ghaffari* - `-units_meter`
508bc7bbd5dSLeila Ghaffari  - 1 meter in scaled length units
50988626eedSJames Wright  - `1`
510bc7bbd5dSLeila Ghaffari  -
511ccaff030SJeremy L Thompson
512bc7bbd5dSLeila Ghaffari* - `-units_second`
513bc7bbd5dSLeila Ghaffari  - 1 second in scaled time units
51488626eedSJames Wright  - `1`
515bc7bbd5dSLeila Ghaffari  -
516ccaff030SJeremy L Thompson
517bc7bbd5dSLeila Ghaffari* - `-units_kilogram`
518bc7bbd5dSLeila Ghaffari  - 1 kilogram in scaled mass units
51988626eedSJames Wright  - `1`
520bc7bbd5dSLeila Ghaffari  -
521ccaff030SJeremy L Thompson
522bc7bbd5dSLeila Ghaffari* - `-units_Kelvin`
523bc7bbd5dSLeila Ghaffari  - 1 Kelvin in scaled temperature units
524bc7bbd5dSLeila Ghaffari  - `1`
525bc7bbd5dSLeila Ghaffari  -
526ccaff030SJeremy L Thompson
527bc7bbd5dSLeila Ghaffari* - `-stab`
528bc7bbd5dSLeila Ghaffari  - Stabilization method (`none`, `su`, or `supg`)
529bc7bbd5dSLeila Ghaffari  - `none`
530bc7bbd5dSLeila Ghaffari  -
531ccaff030SJeremy L Thompson
532932417b3SJed Brown* - `-c_tau`
53388626eedSJames Wright  - Stabilization constant, $c_\tau$
534504dc8e0SLeila Ghaffari  - `0.5`
535932417b3SJed Brown  -
536932417b3SJed Brown
53788626eedSJames Wright* - `-Ctau_t`
53888626eedSJames Wright  - Stabilization time constant, $C_t$
53988626eedSJames Wright  - `1.0`
54088626eedSJames Wright  -
541ccaff030SJeremy L Thompson
54288626eedSJames Wright* - `-Ctau_v`
54388626eedSJames Wright  - Stabilization viscous constant, $C_v$
54494c01735SLeila Ghaffari  - `36, 60, 128 for degree = 1, 2, 3`
54588626eedSJames Wright  -
546ccaff030SJeremy L Thompson
54788626eedSJames Wright* - `-Ctau_C`
54888626eedSJames Wright  - Stabilization continuity constant, $C_c$
54988626eedSJames Wright  - `1.0`
55088626eedSJames Wright  -
551ccaff030SJeremy L Thompson
55288626eedSJames Wright* - `-Ctau_M`
55388626eedSJames Wright  - Stabilization momentum constant, $C_m$
55488626eedSJames Wright  - `1.0`
55588626eedSJames Wright  -
55688626eedSJames Wright
55788626eedSJames Wright* - `-Ctau_E`
55888626eedSJames Wright  - Stabilization energy constant, $C_E$
55988626eedSJames Wright  - `1.0`
56088626eedSJames Wright  -
561ccaff030SJeremy L Thompson
562bc7bbd5dSLeila Ghaffari* - `-cv`
563bc7bbd5dSLeila Ghaffari  - Heat capacity at constant volume
564bc7bbd5dSLeila Ghaffari  - `717`
565bc7bbd5dSLeila Ghaffari  - `J/(kg K)`
566ccaff030SJeremy L Thompson
567bc7bbd5dSLeila Ghaffari* - `-cp`
568bc7bbd5dSLeila Ghaffari  - Heat capacity at constant pressure
569bc7bbd5dSLeila Ghaffari  - `1004`
570bc7bbd5dSLeila Ghaffari  - `J/(kg K)`
571ccaff030SJeremy L Thompson
572a2726bdbSJames Wright* - `-gravity`
573a2726bdbSJames Wright  - Gravitational acceleration vector
574a2726bdbSJames Wright  - `0,0,0`
575bc7bbd5dSLeila Ghaffari  - `m/s^2`
576ccaff030SJeremy L Thompson
577bc7bbd5dSLeila Ghaffari* - `-lambda`
578bc7bbd5dSLeila Ghaffari  - Stokes hypothesis second viscosity coefficient
579bc7bbd5dSLeila Ghaffari  - `-2/3`
580bc7bbd5dSLeila Ghaffari  -
581ccaff030SJeremy L Thompson
582bc7bbd5dSLeila Ghaffari* - `-mu`
583bc7bbd5dSLeila Ghaffari  - Shear dynamic viscosity coefficient
584a2726bdbSJames Wright  - `1.8e-5`
585bc7bbd5dSLeila Ghaffari  -  `Pa s`
58677841947SLeila Ghaffari
587bc7bbd5dSLeila Ghaffari* - `-k`
588bc7bbd5dSLeila Ghaffari  - Thermal conductivity
589bc7bbd5dSLeila Ghaffari  - `0.02638`
590bc7bbd5dSLeila Ghaffari  - `W/(m K)`
591a1df05f8SJed Brown
592a1df05f8SJed Brown* - `-newtonian_unit_tests`
593a1df05f8SJed Brown  - Developer option to test properties
594a1df05f8SJed Brown  - `false`
595a1df05f8SJed Brown  - boolean
596de2fdd78SJames Wright
5975c0afad3SJames Wright* - `-state_var`
5985c0afad3SJames Wright  - State variables to solve solution with. `conservative` ($\rho, \rho \bm{u}, \rho e$) or `primitive` ($P, \bm{u}, T$)
5995c0afad3SJames Wright  - `conservative`
6005c0afad3SJames Wright  - string
601530ad8c4SKenneth E. Jansen
602530ad8c4SKenneth E. Jansen* - `-idl_decay_time`
603530ad8c4SKenneth E. Jansen  - Characteristic timescale of the pressure deviance decay. The timestep is good starting point
604530ad8c4SKenneth E. Jansen  - `-1` (disabled)
605530ad8c4SKenneth E. Jansen  - `s`
606530ad8c4SKenneth E. Jansen
607530ad8c4SKenneth E. Jansen* - `-idl_start`
608530ad8c4SKenneth E. Jansen  - Start of IDL in the x direction
609530ad8c4SKenneth E. Jansen  - `0`
610530ad8c4SKenneth E. Jansen  - `m`
611530ad8c4SKenneth E. Jansen
612530ad8c4SKenneth E. Jansen* - `-idl_length`
613530ad8c4SKenneth E. Jansen  - Length of IDL in the positive x direction
614530ad8c4SKenneth E. Jansen  - `0`
615530ad8c4SKenneth E. Jansen  - `m`
616530ad8c4SKenneth E. Jansen
617c79d6dc9SJames Wright* - `-sgs_model_type`
618c79d6dc9SJames Wright  - Type of subgrid stress model to use. Currently only `data_driven` is available
619c79d6dc9SJames Wright  - `none`
620c79d6dc9SJames Wright  - string
621c79d6dc9SJames Wright
622c79d6dc9SJames Wright* - `-sgs_model_dd_leakyrelu_alpha`
623c79d6dc9SJames Wright  - Slope parameter for Leaky ReLU activation function. `0` corresponds to normal ReLU
624c79d6dc9SJames Wright  - 0
625c79d6dc9SJames Wright  -
626c79d6dc9SJames Wright
627c79d6dc9SJames Wright* - `-sgs_model_dd_parameter_dir`
628c79d6dc9SJames Wright  - Path to directory with data-driven model parameters (weights, biases, etc.)
629c79d6dc9SJames Wright  - `./dd_sgs_parameters`
630c79d6dc9SJames Wright  - string
631c79d6dc9SJames Wright
632cf90ec9bSJames Wright* - `-sgs_model_dd_use_fused`
633cf90ec9bSJames Wright  - Whether to use "fused" mode for data-driven model evaluation
634cf90ec9bSJames Wright  - `true`
635cf90ec9bSJames Wright  - boolean
636cf90ec9bSJames Wright
6373f89fbfdSJames Wright* - `-diff_filter_monitor`
6383f89fbfdSJames Wright  - Enable differential filter TSMonitor
6393f89fbfdSJames Wright  - `false`
6403f89fbfdSJames Wright  - boolean
6413f89fbfdSJames Wright
6423f89fbfdSJames Wright* - `-diff_filter_grid_based_width`
6433f89fbfdSJames Wright  - Use filter width based on the grid size
6443f89fbfdSJames Wright  - `false`
6453f89fbfdSJames Wright  - boolean
6463f89fbfdSJames Wright
6473f89fbfdSJames Wright* - `-diff_filter_width_scaling`
6483f89fbfdSJames Wright  - Anisotropic scaling for filter width in wall-aligned coordinates (snz)
6493f89fbfdSJames Wright  - `1,1,1`
6503f89fbfdSJames Wright  - `m`
6513f89fbfdSJames Wright
6523f89fbfdSJames Wright* - `-diff_filter_kernel_scaling`
6533f89fbfdSJames Wright  - Scaling to make differential kernel size equivalent to other filter kernels
6543f89fbfdSJames Wright  - `0.1`
6553f89fbfdSJames Wright  - `m^2`
6563f89fbfdSJames Wright
6573f89fbfdSJames Wright* - `-diff_filter_wall_damping_function`
6583f89fbfdSJames Wright  - Damping function to use at the wall for anisotropic filtering (`none`, `van_driest`)
6593f89fbfdSJames Wright  - `none`
6603f89fbfdSJames Wright  - string
6613f89fbfdSJames Wright
6623f89fbfdSJames Wright* - `-diff_filter_wall_damping_constant`
6639d9c52bbSJed Brown  - Constant for the wall-damping function. $A^+$ for `van_driest` damping function.
6643f89fbfdSJames Wright  - 25
6653f89fbfdSJames Wright  -
6663f89fbfdSJames Wright
6673f89fbfdSJames Wright* - `-diff_filter_friction_length`
6683f89fbfdSJames Wright  - Friction length associated with the flow, $\delta_\nu$. Used in wall-damping functions
6693f89fbfdSJames Wright  - 0
6703f89fbfdSJames Wright  - `m`
6713f89fbfdSJames Wright
6723b219b86SJames Wright* - `-sgs_train_enable`
6733b219b86SJames Wright  - Whether to enable *in situ* training of data-driven SGS model. Require building with SmartRedis.
6743b219b86SJames Wright  - `false`
6753b219b86SJames Wright  - boolean
6763b219b86SJames Wright
6773b219b86SJames Wright* - `-sgs_train_write_data_interval`
6783b219b86SJames Wright  - Number of timesteps between writing training data into SmartRedis database
6793b219b86SJames Wright  - `1`
6803b219b86SJames Wright  -
6813b219b86SJames Wright
6823b219b86SJames Wright* - `-sgs_train_overwrite_data`
6833b219b86SJames Wright  - Whether new training data should overwrite old data on database
6843b219b86SJames Wright  - `true`
6853b219b86SJames Wright  - boolean
6863b219b86SJames Wright
6873b219b86SJames Wright* - `-smartsim_collocated_num_ranks`
6883b219b86SJames Wright  - Number of MPI ranks associated with each collocated database (i.e. ranks per node)
6893b219b86SJames Wright  - `1`
6903b219b86SJames Wright  -
691bc7bbd5dSLeila Ghaffari:::
69277841947SLeila Ghaffari
693530ad8c4SKenneth E. Jansen#### Gaussian Wave
6947ec884f8SJames Wright
695530ad8c4SKenneth E. JansenThe Gaussian wave problem has the following command-line options in addition to the Newtonian Ideal Gas options:
6967ec884f8SJames Wright
697530ad8c4SKenneth E. Jansen:::{list-table} Gaussian Wave Runtime Options
6987ec884f8SJames Wright:header-rows: 1
6997ec884f8SJames Wright
7007ec884f8SJames Wright* - Option
7017ec884f8SJames Wright  - Description
7027ec884f8SJames Wright  - Default value
7037ec884f8SJames Wright  - Unit
7047ec884f8SJames Wright
705f1e435c9SJed Brown* - `-freestream_riemann`
706f1e435c9SJed Brown  - Riemann solver for boundaries (HLL or HLLC)
707f1e435c9SJed Brown  - `hllc`
708f1e435c9SJed Brown  -
709f1e435c9SJed Brown
710f1e435c9SJed Brown* - `-freestream_velocity`
7117ec884f8SJames Wright  - Freestream velocity vector
7127ec884f8SJames Wright  - `0,0,0`
7137ec884f8SJames Wright  - `m/s`
7147ec884f8SJames Wright
715f1e435c9SJed Brown* - `-freestream_temperature`
7167ec884f8SJames Wright  - Freestream temperature
7177ec884f8SJames Wright  - `288`
7187ec884f8SJames Wright  - `K`
7197ec884f8SJames Wright
720f1e435c9SJed Brown* - `-freestream_pressure`
72189e3cb53SJames Wright  - Freestream pressure
7227ec884f8SJames Wright  - `1.01e5`
7237ec884f8SJames Wright  - `Pa`
7247ec884f8SJames Wright
7257ec884f8SJames Wright* - `-epicenter`
7267ec884f8SJames Wright  - Coordinates of center of perturbation
7277ec884f8SJames Wright  - `0,0,0`
7287ec884f8SJames Wright  - `m`
7297ec884f8SJames Wright
7307ec884f8SJames Wright* - `-amplitude`
7317ec884f8SJames Wright  - Amplitude of the perturbation
7327ec884f8SJames Wright  - `0.1`
7337ec884f8SJames Wright  -
7347ec884f8SJames Wright
7357ec884f8SJames Wright* - `-width`
7367ec884f8SJames Wright  - Width parameter of the perturbation
7377ec884f8SJames Wright  - `0.002`
7387ec884f8SJames Wright  - `m`
7397ec884f8SJames Wright
7407ec884f8SJames Wright:::
7417ec884f8SJames Wright
742530ad8c4SKenneth E. JansenThis problem can be run with the `gaussianwave.yaml` file via:
7437ec884f8SJames Wright
7447ec884f8SJames Wright```
745530ad8c4SKenneth E. Jansen./navierstokes -options_file gaussianwave.yaml
7467ec884f8SJames Wright```
7477ec884f8SJames Wright
748530ad8c4SKenneth E. Jansen```{literalinclude} ../../../../../examples/fluids/gaussianwave.yaml
7497ec884f8SJames Wright:language: yaml
7507ec884f8SJames Wright```
751a1df05f8SJed Brown
752d310b3d3SAdeleke O. Bankole#### Vortex Shedding - Flow past Cylinder
753d310b3d3SAdeleke O. Bankole
754d310b3d3SAdeleke O. BankoleThe vortex shedding, flow past cylinder problem has the following command-line options in addition to the Newtonian Ideal Gas options:
755d310b3d3SAdeleke O. Bankole
756d310b3d3SAdeleke O. Bankole:::{list-table} Vortex Shedding Runtime Options
757d310b3d3SAdeleke O. Bankole:header-rows: 1
758d310b3d3SAdeleke O. Bankole
759d310b3d3SAdeleke O. Bankole* - Option
760d310b3d3SAdeleke O. Bankole  - Description
761d310b3d3SAdeleke O. Bankole  - Default value
762d310b3d3SAdeleke O. Bankole  - Unit
763d310b3d3SAdeleke O. Bankole
764d310b3d3SAdeleke O. Bankole* - `-freestream_velocity`
765d310b3d3SAdeleke O. Bankole  - Freestream velocity vector
766d310b3d3SAdeleke O. Bankole  - `0,0,0`
767d310b3d3SAdeleke O. Bankole  - `m/s`
768d310b3d3SAdeleke O. Bankole
769d310b3d3SAdeleke O. Bankole* - `-freestream_temperature`
770d310b3d3SAdeleke O. Bankole  - Freestream temperature
771d310b3d3SAdeleke O. Bankole  - `288`
772d310b3d3SAdeleke O. Bankole  - `K`
773d310b3d3SAdeleke O. Bankole
774d310b3d3SAdeleke O. Bankole* - `-freestream_pressure`
775d310b3d3SAdeleke O. Bankole  - Freestream pressure
776d310b3d3SAdeleke O. Bankole  - `1.01e5`
777d310b3d3SAdeleke O. Bankole  - `Pa`
778d310b3d3SAdeleke O. Bankole
779d310b3d3SAdeleke O. Bankole:::
780d310b3d3SAdeleke O. Bankole
781d310b3d3SAdeleke O. BankoleThe initial condition is taken from `-reference_temperature` and `-reference_pressure`.
782d310b3d3SAdeleke O. BankoleTo run this problem, first generate a mesh:
783d310b3d3SAdeleke O. Bankole
784d310b3d3SAdeleke O. Bankole```console
785d310b3d3SAdeleke O. Bankole$ make -C examples/fluids/meshes
786d310b3d3SAdeleke O. Bankole```
787d310b3d3SAdeleke O. Bankole
788d310b3d3SAdeleke O. BankoleThen run by building the executable and running:
789d310b3d3SAdeleke O. Bankole
790d310b3d3SAdeleke O. Bankole```console
791d310b3d3SAdeleke O. Bankole$ make build/fluids-navierstokes
792ca69d878SAdeleke O. Bankole$ mpiexec -n 6 build/fluids-navierstokes -options_file examples/fluids/vortexshedding.yaml -{ts,snes}_monitor_
793d310b3d3SAdeleke O. Bankole```
794d310b3d3SAdeleke O. Bankole
795ca69d878SAdeleke O. BankoleThe vortex shedding period is roughly 5.6 and this problem runs until time 100 (2000 time steps).
796ca69d878SAdeleke O. BankoleThe above run writes a file named `force.csv` (see `ts_monitor_wall_force` in `vortexshedding.yaml`), which can be postprocessed by running to create a figure showing lift and drag coefficients over time.
797ca69d878SAdeleke O. Bankole
798ca69d878SAdeleke O. Bankole```console
799d6734f85SAdeleke O. Bankole$ python examples/fluids/postprocess/vortexshedding.py
800ca69d878SAdeleke O. Bankole```
801d310b3d3SAdeleke O. Bankole
802d310b3d3SAdeleke O. Bankole```{literalinclude} ../../../../../examples/fluids/vortexshedding.yaml
803d310b3d3SAdeleke O. Bankole:language: yaml
804d310b3d3SAdeleke O. Bankole```
805d310b3d3SAdeleke O. Bankole
806019b7682STimothy Aiken#### Density current
807019b7682STimothy Aiken
808061ff11eSJames WrightThe Density Current problem has the following command-line options in addition to the Newtonian Ideal Gas options:
80988626eedSJames Wright
81088626eedSJames Wright:::{list-table} Density Current Runtime Options
81188626eedSJames Wright:header-rows: 1
81288626eedSJames Wright
81388626eedSJames Wright* - Option
81488626eedSJames Wright  - Description
81588626eedSJames Wright  - Default value
81688626eedSJames Wright  - Unit
81788626eedSJames Wright
81888626eedSJames Wright* - `-center`
81988626eedSJames Wright  - Location of bubble center
82088626eedSJames Wright  - `(lx,ly,lz)/2`
82188626eedSJames Wright  - `(m,m,m)`
82288626eedSJames Wright
82388626eedSJames Wright* - `-dc_axis`
82488626eedSJames Wright  - Axis of density current cylindrical anomaly, or `(0,0,0)` for spherically symmetric
82588626eedSJames Wright  - `(0,0,0)`
82688626eedSJames Wright  -
82788626eedSJames Wright
82888626eedSJames Wright* - `-rc`
82988626eedSJames Wright  - Characteristic radius of thermal bubble
83088626eedSJames Wright  - `1000`
83188626eedSJames Wright  - `m`
83288626eedSJames Wright
83388626eedSJames Wright* - `-theta0`
83488626eedSJames Wright  - Reference potential temperature
83588626eedSJames Wright  - `300`
83688626eedSJames Wright  - `K`
83788626eedSJames Wright
83888626eedSJames Wright* - `-thetaC`
83988626eedSJames Wright  - Perturbation of potential temperature
84088626eedSJames Wright  - `-15`
84188626eedSJames Wright  - `K`
84288626eedSJames Wright
84388626eedSJames Wright* - `-P0`
84488626eedSJames Wright  - Atmospheric pressure
84588626eedSJames Wright  - `1E5`
84688626eedSJames Wright  - `Pa`
84788626eedSJames Wright
84888626eedSJames Wright* - `-N`
84988626eedSJames Wright  - Brunt-Vaisala frequency
85088626eedSJames Wright  - `0.01`
85188626eedSJames Wright  - `1/s`
85288626eedSJames Wright:::
85388626eedSJames Wright
854bc7bbd5dSLeila GhaffariThis problem can be run with:
855ccaff030SJeremy L Thompson
856bc7bbd5dSLeila Ghaffari```
8577c5bba50SJames Wright./navierstokes -problem density_current -dm_plex_box_faces 16,1,8 -degree 1 -dm_plex_box_lower 0,0,0 -dm_plex_box_upper 2000,125,1000 -dm_plex_dim 3 -rc 400. -bc_wall 1,2,5,6 -wall_comps 1,2,3 -bc_symmetry_y 3,4 -mu 75
85888626eedSJames Wright```
85988626eedSJames Wright
860019b7682STimothy Aiken#### Channel flow
861019b7682STimothy Aiken
862061ff11eSJames WrightThe Channel problem has the following command-line options in addition to the Newtonian Ideal Gas options:
86388626eedSJames Wright
86488626eedSJames Wright:::{list-table} Channel Runtime Options
86588626eedSJames Wright:header-rows: 1
86688626eedSJames Wright
86788626eedSJames Wright* - Option
86888626eedSJames Wright  - Description
86988626eedSJames Wright  - Default value
87088626eedSJames Wright  - Unit
87188626eedSJames Wright
87288626eedSJames Wright* - `-umax`
87388626eedSJames Wright  - Maximum/centerline velocity of the flow
87488626eedSJames Wright  - `10`
87588626eedSJames Wright  - `m/s`
87688626eedSJames Wright
87788626eedSJames Wright* - `-theta0`
87888626eedSJames Wright  - Reference potential temperature
87988626eedSJames Wright  - `300`
88088626eedSJames Wright  - `K`
88188626eedSJames Wright
88288626eedSJames Wright* - `-P0`
88388626eedSJames Wright  - Atmospheric pressure
88488626eedSJames Wright  - `1E5`
88588626eedSJames Wright  - `Pa`
886a1df05f8SJed Brown
887a1df05f8SJed Brown* - `-body_force_scale`
888a1df05f8SJed Brown  - Multiplier for body force (`-1` for flow reversal)
889a1df05f8SJed Brown  - 1
890a1df05f8SJed Brown  -
89188626eedSJames Wright:::
89288626eedSJames Wright
89388626eedSJames WrightThis problem can be run with the `channel.yaml` file via:
89488626eedSJames Wright
89588626eedSJames Wright```
89688626eedSJames Wright./navierstokes -options_file channel.yaml
89788626eedSJames Wright```
89888626eedSJames Wright```{literalinclude} ../../../../../examples/fluids/channel.yaml
89988626eedSJames Wright:language: yaml
90088626eedSJames Wright```
90188626eedSJames Wright
9028a94a473SJed Brown(example-blasius)=
9038a94a473SJed Brown
904019b7682STimothy Aiken#### Blasius boundary layer
905019b7682STimothy Aiken
906061ff11eSJames WrightThe Blasius problem has the following command-line options in addition to the Newtonian Ideal Gas options:
90788626eedSJames Wright
90888626eedSJames Wright:::{list-table} Blasius Runtime Options
90988626eedSJames Wright:header-rows: 1
91088626eedSJames Wright
91188626eedSJames Wright* - Option
91288626eedSJames Wright  - Description
91388626eedSJames Wright  - Default value
91488626eedSJames Wright  - Unit
91588626eedSJames Wright
916fb455ff0SLeila Ghaffari* - `-velocity_infinity`
91788626eedSJames Wright  - Freestream velocity
91888626eedSJames Wright  - `40`
91988626eedSJames Wright  - `m/s`
92088626eedSJames Wright
921fb455ff0SLeila Ghaffari* - `-temperature_infinity`
922fb455ff0SLeila Ghaffari  - Freestream temperature
92388626eedSJames Wright  - `288`
92488626eedSJames Wright  - `K`
92588626eedSJames Wright
926fb455ff0SLeila Ghaffari* - `-temperature_wall`
927fb455ff0SLeila Ghaffari  - Wall temperature
92807d14e58SLeila Ghaffari  - `288`
929fb455ff0SLeila Ghaffari  - `K`
930fb455ff0SLeila Ghaffari
931fb455ff0SLeila Ghaffari* - `-delta0`
932fb455ff0SLeila Ghaffari  - Boundary layer height at the inflow
933fb455ff0SLeila Ghaffari  - `4.2e-3`
934fb455ff0SLeila Ghaffari  - `m`
935fb455ff0SLeila Ghaffari
93688626eedSJames Wright* - `-P0`
93788626eedSJames Wright  - Atmospheric pressure
93888626eedSJames Wright  - `1.01E5`
93988626eedSJames Wright  - `Pa`
94088626eedSJames Wright
9419309e21cSJames Wright* - `-platemesh_modify_mesh`
9429309e21cSJames Wright  - Whether to modify the mesh using the given options below.
9439309e21cSJames Wright  - `false`
9449309e21cSJames Wright  -
9459309e21cSJames Wright
94691eaef80SJames Wright* - `-platemesh_refine_height`
94791eaef80SJames Wright  - Height at which `-platemesh_Ndelta` number of elements should refined into
94888626eedSJames Wright  - `5.9E-4`
94988626eedSJames Wright  - `m`
95088626eedSJames Wright
95191eaef80SJames Wright* - `-platemesh_Ndelta`
95291eaef80SJames Wright  - Number of elements to keep below `-platemesh_refine_height`
95388626eedSJames Wright  - `45`
95488626eedSJames Wright  -
95588626eedSJames Wright
95691eaef80SJames Wright* - `-platemesh_growth`
95788626eedSJames Wright  - Growth rate of the elements in the refinement region
95888626eedSJames Wright  - `1.08`
95988626eedSJames Wright  -
96088626eedSJames Wright
96191eaef80SJames Wright* - `-platemesh_top_angle`
96288626eedSJames Wright  - Downward angle of the top face of the domain. This face serves as an outlet.
96388626eedSJames Wright  - `5`
96488626eedSJames Wright  - `degrees`
965ba6664aeSJames Wright
96691eaef80SJames Wright* - `-platemesh_y_node_locs_path`
96791eaef80SJames Wright  - Path to file with y node locations. If empty, will use mesh warping instead.
96891eaef80SJames Wright  - `""`
96991eaef80SJames Wright  -
970fb455ff0SLeila Ghaffari
9719309e21cSJames Wright* - `-stg_use`
9729309e21cSJames Wright  - Whether to use STG for the inflow conditions
9739309e21cSJames Wright  - `false`
9749309e21cSJames Wright  -
9759309e21cSJames Wright
97607d14e58SLeila Ghaffari* - `-n_chebyshev`
977fb455ff0SLeila Ghaffari  - Number of Chebyshev terms
978fb455ff0SLeila Ghaffari  - `20`
979fb455ff0SLeila Ghaffari  -
980fb455ff0SLeila Ghaffari
98107d14e58SLeila Ghaffari* - `-chebyshev_`
98207d14e58SLeila Ghaffari  - Prefix for Chebyshev snes solve
98307d14e58SLeila Ghaffari  -
98407d14e58SLeila Ghaffari  -
98507d14e58SLeila Ghaffari
98688626eedSJames Wright:::
98788626eedSJames Wright
98888626eedSJames WrightThis problem can be run with the `blasius.yaml` file via:
98988626eedSJames Wright
99088626eedSJames Wright```
99188626eedSJames Wright./navierstokes -options_file blasius.yaml
99288626eedSJames Wright```
99388626eedSJames Wright
99488626eedSJames Wright```{literalinclude} ../../../../../examples/fluids/blasius.yaml
99588626eedSJames Wright:language: yaml
996bc7bbd5dSLeila Ghaffari```
997ba6664aeSJames Wright
998ba6664aeSJames Wright#### STG Inflow for Flat Plate
999ba6664aeSJames Wright
100017be3a41SJeremy L ThompsonUsing the STG Inflow for the blasius problem adds the following command-line options:
1001ba6664aeSJames Wright
1002ba6664aeSJames Wright:::{list-table} Blasius Runtime Options
1003ba6664aeSJames Wright:header-rows: 1
1004ba6664aeSJames Wright
1005ba6664aeSJames Wright* - Option
1006ba6664aeSJames Wright  - Description
1007ba6664aeSJames Wright  - Default value
1008ba6664aeSJames Wright  - Unit
1009ba6664aeSJames Wright
1010ba6664aeSJames Wright* - `-stg_inflow_path`
1011ba6664aeSJames Wright  - Path to the STGInflow file
1012ba6664aeSJames Wright  - `./STGInflow.dat`
1013ba6664aeSJames Wright  -
1014ba6664aeSJames Wright
1015ba6664aeSJames Wright* - `-stg_rand_path`
1016ba6664aeSJames Wright  - Path to the STGRand file
1017ba6664aeSJames Wright  - `./STGRand.dat`
1018ba6664aeSJames Wright  -
1019ba6664aeSJames Wright
1020ba6664aeSJames Wright* - `-stg_alpha`
1021ba6664aeSJames Wright  - Growth rate of the wavemodes
1022ba6664aeSJames Wright  - `1.01`
1023ba6664aeSJames Wright  -
1024ba6664aeSJames Wright
1025ba6664aeSJames Wright* - `-stg_u0`
1026ba6664aeSJames Wright  - Convective velocity, $U_0$
1027ba6664aeSJames Wright  - `0.0`
1028ba6664aeSJames Wright  - `m/s`
1029ba6664aeSJames Wright
1030ba6664aeSJames Wright* - `-stg_mean_only`
1031ba6664aeSJames Wright  - Only impose the mean velocity (no fluctutations)
1032ba6664aeSJames Wright  - `false`
1033ba6664aeSJames Wright  -
1034ba6664aeSJames Wright
103530af3636SJames Wright* - `-stg_strong`
103630af3636SJames Wright  - Strongly enforce the STG inflow boundary condition
103730af3636SJames Wright  - `false`
103830af3636SJames Wright  -
103930af3636SJames Wright
104089060322SJames Wright* - `-stg_fluctuating_IC`
104189060322SJames Wright  - "Extrude" the fluctuations through the domain as an initial condition
104289060322SJames Wright  - `false`
104389060322SJames Wright  -
104489060322SJames Wright
1045ba6664aeSJames Wright:::
1046ba6664aeSJames Wright
1047ba6664aeSJames WrightThis problem can be run with the `blasius.yaml` file via:
1048ba6664aeSJames Wright
1049ba6664aeSJames Wright```
1050ba6664aeSJames Wright./navierstokes -options_file blasius.yaml -stg_use true
1051ba6664aeSJames Wright```
1052ba6664aeSJames Wright
105317be3a41SJeremy L ThompsonNote the added `-stg_use true` flag
105417be3a41SJeremy L ThompsonThis overrides the `stg: use: false` setting in the `blasius.yaml` file, enabling the use of the STG inflow.
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