Remove a bunch of unused variables and update doc

Update README: remove density_current_primitive problem option for now

Use const in VLA declaration casts to suppress icc warning also in densitycurrent_primitive

Just for consistency with the other usages. Even if this case does not work right now. In case someone wan

Use const in VLA declaration casts to suppress icc warning also in densitycurrent_primitive

Just for consistency with the other usages. Even if this case does not work right now. In case someone wants to pick it up in the future.

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Remove a bunch of unused or double-declared variables

Update README

NS: use const in VLA casts to suppress icc warning

Reported-by: Valeria Barra <valeriabarra21@gmail.com>

NS: add command-line support for specifying DC center/axis

This runs slip boundary conditions on all the vertical walls, and
places the initial (cylindrical) density anomaly on the symmetry plane
wi

NS: add command-line support for specifying DC center/axis

This runs slip boundary conditions on all the vertical walls, and
places the initial (cylindrical) density anomaly on the symmetry plane
with axis pointing in the y direction. The Jacobian (computed using
coloring) and preconditioner are rebuilt once every 100 SNES solves.

./navierstokes -petscspace_degree 2 -qextra 2 -problem density_current -dm_plex_box_faces 20,1,20 -lx 4000 -ly 200 -lz 4000 -bc_wall 1,2 -bc_slip_x 5,6 -bc_slip_y 3,4 -center 0,0,2000 -dc_axis 0,1,0 -ts_adapt_monitor -ts_adapt_safety 0.8 -implicit -pc_type ilu -stab supg -snes_atol 1e-3 -ksp_atol 1e-4 -ksp_rtol 1e-3 -ts_type alpha -ts_dt 5e-3 -ksp_type bcgs -snes_lag_jacobian 100 -snes_lag_jacobian_persists -snes_mf_operator

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NS: return to insulated no-slip walls instead of full-Dirichlet

NS: remove dead code for scaling VTK output back to dimensional units

Reported-by: Valeria Barra <valeriabarra21@gmail.com>

NS: add support for free slip wall boundary conditions

* -naturalz is removed since it's too specific to cartesian meshes.

* The new interface is -bc_slip_x, -bc_slip_y, and -bc_slip_z. These
ta

NS: add support for free slip wall boundary conditions

* -naturalz is removed since it's too specific to cartesian meshes.

* The new interface is -bc_slip_x, -bc_slip_y, and -bc_slip_z. These
take a list of face sets. For the standard box mesh, these are:
cf. DMPlexCreateCubeMesh_Internal:

switch (dim) {
case 2:
faceMarkerTop = 3;
faceMarkerBottom = 1;
faceMarkerRight = 2;
faceMarkerLeft = 4;
break;
case 3:
faceMarkerBottom = 1;
faceMarkerTop = 2;
faceMarkerFront = 3;
faceMarkerBack = 4;
faceMarkerRight = 5;
faceMarkerLeft = 6;

One can run a quasi-2D density current model by setting slip
conditions on the ±y faces and making the domain only one element
thick in that dimension.

./navierstokes -petscspace_degree 3 -problem density_current -dm_plex_box_faces 32,1,16 -ly 250 -bc_wall 1,2,5,6 -bc_slip_y 3,4 -ts_adapt_monitor -ts_adapt_safety 0.7

Physically, this is like running the experiment sandwiched in a tank
with free-slip walls in the ±y dimensions.

Note: this feature currently depends on a PETSc bug-fix branch that
has not yet been merged to master.

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NS density_current: remove redundant initial/boundary condition and trailing whitespace

Some changes in documentation

Update examples/README

Update examples/navier-stokes/README

Update .gitignore

Update documentation

Initialize *problem pointer as NULL

This avoids -Wmaybe-uninitialized compiler warning

NS: move nsplex.c to navierstokes.c

NS: remove legacy navierstokes.c

fix(navierstokes): Remove Units redefinition

- Fix compiler warning on Xcode

fix(nsplex): Add nsplex macro, ifdefs to functions

- To remove 'unused-function' warnings during navierstokes compilation

test(navierstokes): Remove stdout output for testing

test(nsplex): Remove stdout output during test

navierstokes: Rename User struct to UserNS

nsplex: Update stdoutParsing.py for new nsplex outputs

- Add entries for FEM space degree and for dm_plex_box_faces
- Example for-loop for building DataFrame no longer dictates column
headers
- In

nsplex: Update stdoutParsing.py for new nsplex outputs

- Add entries for FEM space degree and for dm_plex_box_faces
- Example for-loop for building DataFrame no longer dictates column
headers
- Individual box_face columns are now added
- (style) Expand regex flags

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