Merge pull request #428 from CEED/valeria/small-doc-fixes

Small doc fixes

NS: Now, "E= internal energy+kinetic energy" and "rho g z u[2]" is brought to body force (It's needed for SUPG)

NS: dXdxdXdxT deleted from densitycurrent

Squashed-by: Jed Brown <jed@jedbrown.org>

NS: *.vtu added to .gitignore

.gitignore: nsplex

Makefile cleans for nsplex output. Tested with
./nsplex -naturalz -ts_monitor -petscspace_degree 2 -dm_plex_box_faces 20,20,1 -ts_adapt_dt_max .1 -ts_max_time 2 -problem advection -dm_view -CtauS .3

Makefile cleans for nsplex output. Tested with
./nsplex -naturalz -ts_monitor -petscspace_degree 2 -dm_plex_box_faces 20,20,1 -ts_adapt_dt_max .1 -ts_max_time 2 -problem advection -dm_view -CtauS .3 -implicit -snes_mf -ksp_atol 1e-3 -snes_type ksponly -ts_view -stab supg

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NS: add SUPG and IFunction for to advection.h

Thanks-to: Leila Ghaffari <Leila.Ghaffari@colorado.edu>
Squashed-by: Jed Brown <jed@jedbrown.org>

nsplex: support natural BCs in z direction

Example quasi-2D run:

mpiexec -n 2 ./nsplex -ts_monitor -petscspace_degree 2 -dm_plex_box_faces 20,20,1 -ts_max_time 2 -problem advection -dm_view -Ctau

nsplex: support natural BCs in z direction

Example quasi-2D run:

mpiexec -n 2 ./nsplex -ts_monitor -petscspace_degree 2 -dm_plex_box_faces 20,20,1 -ts_max_time 2 -problem advection -dm_view -CtauS .3 -implicit -snes_mf -ksp_atol 1e-3 -snes_type ksponly -ts_adapt_atol 2e-2 -ts_view -stab supg

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NS: more permissive TS limits trust error controller

ns: add to tests (requires recent PETSc)

ns: fix corrupted comment about run configurations

nsplex: build RHS/IFunction only when available

Reported-by: Leila Ghaffari <Leila.Ghaffari@colorado.edu>
Reported-by: James Wright <James.WrightIii@colorado.edu>

Small doc improvements to make it more readable and consistent

nsplex: add IFunction formulation with SUPG using BDF2 by default

./nsplex -ts_monitor -petscspace_degree 2 -dm_plex_box_faces 50,50 -ts_adapt_dt_max .1 -ts_max_time 2 -problem advection2d -dm_view

nsplex: add IFunction formulation with SUPG using BDF2 by default

./nsplex -ts_monitor -petscspace_degree 2 -dm_plex_box_faces 50,50 -ts_adapt_dt_max .1 -ts_max_time 2 -problem advection2d -dm_view -CtauS .2 -implicit -snes_mf -ksp_atol 1e-5 -snes_type ksponly -ts_adapt_atol 2e-2 -ts_view -stab supg

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CeedQFunctionCreateInterior: error handling when f or source is NULL

nsplex: add SUPG stabilization and strong/weak option for advection term

DMPlex for Navier-Stokes/Advection in 2D and 3D

Currently uses synthetic "box" meshes, but is entirely unstructured
semantically so you can read any mesh that DMPlex supports.

Add -problem advectio

DMPlex for Navier-Stokes/Advection in 2D and 3D

Currently uses synthetic "box" meshes, but is entirely unstructured
semantically so you can read any mesh that DMPlex supports.

Add -problem advection2d with basic (for now) advection scheme. This
is intended to become a testbed for stabilization techniques.

./nsplex -ts_monitor -petscspace_degree 2 -dm_plex_box_faces 30,30 -ts_adapt_dt_max .1 -ts_max_time 6 -problem advection2d -dm_view

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Promote CeedElemRestrictionGet* to public interface

These were formerly backend-only, but their availability can help
users write reliable code without needing to pass around redundant
numeric value

Promote CeedElemRestrictionGet* to public interface

These were formerly backend-only, but their availability can help
users write reliable code without needing to pass around redundant
numeric values.

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advection: adjust velocity and extend to boundary

advection: fix bug introduced in refactor

1980ef9facf02dd7cbce4041c567716dc51f62e7 NS - Use vla for clarity

CeedElemRestrictionGetMultiplicity: move TransposeMode to an input arg

Enables support for interlaced (CEED_TRANSPOSE), as typically used in
PETSc examples/apps.

Merge pull request #372 from CEED/jeremy/element-fdm-inv

FDM Element Inverse

Merge pull request #399 from CEED/jeremy/rstr-opt

Restriction Optimizations

Ceed - Define CEED_EPSILON for interface use

make style