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 top-level README

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

Merge branch 'jrwrigh/ns-dmplex' into jed/ns-dmplex [PR #430]

* jrwrigh/ns-dmplex:
fix(navierstokes): Remove Units redefinition
fix(nsplex): Add nsplex macro, ifdefs to functions
test(navierst

Merge branch 'jrwrigh/ns-dmplex' into jed/ns-dmplex [PR #430]

* jrwrigh/ns-dmplex:
fix(navierstokes): Remove Units redefinition
fix(nsplex): Add nsplex macro, ifdefs to functions
test(navierstokes): Remove stdout output for testing
test(nsplex): Remove stdout output during test
nsplex: Update nsplex /tests/output file
navierstokes: Rename User struct to UserNS
nsplex: Update stdoutParsing.py for new nsplex outputs
nsplex: Print dm_plex_box_faces value
nsplex: Print FEM space degree
nsplex: Move python parsing function to stdoutParsing.py
nsplex: Calculate computation time
nsplex advection2d: choose only the smooth initial condition
nsplex advection2d: make solution time-dependent
nsplex: Calculate exact solution at final time
nsplex: Implement ICs_PetscMultiplicity function
nsplex: Add non_zero_time flag to problemData
nsplex: Create SetupContext struct, add to ICs* qfuncs
nsplex: Move User_ and Units_ to common.h
Update .gitignore with misc editor dirs

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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

nsplex: Update nsplex /tests/output file

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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nsplex: Print dm_plex_box_faces value

nsplex: Print FEM space degree

nsplex: Move python parsing function to stdoutParsing.py

- Contains function for parsing STDOUT of nsplex function
- Python function outputs dictionary, which can be easily turned into
pandas Data

nsplex: Move python parsing function to stdoutParsing.py

- Contains function for parsing STDOUT of nsplex function
- Python function outputs dictionary, which can be easily turned into
pandas DataFrame

nsplex: remove FLAG ARGS from stdoutParsing.py regex

- "FLAG ARGUMENTS" was a feature from a script I ran, not from the
nsplex executable itself.

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nsplex: Calculate computation time

nsplex advection2d: choose only the smooth initial condition